From c3ce694e8bd2e32b3e974cf1e9dc806178b267e8 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 26 Jan 2022 18:52:53 +0100 Subject: [PATCH 0001/1454] first check for validation schema --- relecov-tools/validation_jsons.py | 34 + schema/phage_V0.json | 2693 +++++++++++++++++++++++++++++ schema/phage_plus_V0.json | 344 ++-- 3 files changed, 2897 insertions(+), 174 deletions(-) create mode 100644 relecov-tools/validation_jsons.py create mode 100644 schema/phage_V0.json diff --git a/relecov-tools/validation_jsons.py b/relecov-tools/validation_jsons.py new file mode 100644 index 00000000..ddbdd5de --- /dev/null +++ b/relecov-tools/validation_jsons.py @@ -0,0 +1,34 @@ +#!/usr/bin/env python +from jsonschema import validate +from jsonschema import Draft202012Validator +import json + +data = {"sample_name":'s1', "collecting_institution" :'inst2', + "submitting_institution":'sub', + "sample_collection_date": '12/02/2022', + "geo_loc_country":'Afghanistan', + "geo_loc_state":'Western', + "organism":'Coronaviridae', + "isolate":'SARS-CoV-2/', + "host_scientific_name":'Bos taurus', + "host_disease":'Homo sapiens', + "sequencing_instrument_model" :'COVID-19', + "sequencing_instrument_platform": 'Illumina sequencing instrument', + "consensus_sequence_software_name":'MinIon', + "consensus_sequence_software_version":'Ivar' +} + +schema_file = open('/home/lchapado/Projects/Proyecto_ERA/relecov-tools/schema/phage_plus_V0.json') + +fage_plus_schema = json.load(schema_file) +try: + Draft202012Validator.check_schema(fage_plus_schema) +except: + print('Invalid schema') + exit(1) +try: + validate(instance=data,schema=fage_plus_schema) +except: + print('Invalid input data') + exit() +print('Completed') diff --git a/schema/phage_V0.json b/schema/phage_V0.json new file mode 100644 index 00000000..bf7c2597 --- /dev/null +++ b/schema/phage_V0.json @@ -0,0 +1,2693 @@ +{ + "$schema": "http://json-schema.org/draft/2019-09/schema#", + "required": [ + "sequence_submitted_by", + "sample_collected_by", + "sequencing_instrument", + "host_scientific_name", + "isolate", + "sample_collection_date", + "host_disease", + "consensus_sequence_software_name", + "geo_loc_name_state_province_territory", + "specimen_collector_sample_id", + "consensus_sequence_software_version", + "organism", + "geo_loc_name_country" + ], + "type": "object", + "properties": { + "sample_collector_contact_email": { + "examples": ["johnnyblogs@lab.ca"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "format": "email" + }, + "depth_of_coverage_value": { + "ontology": "GENEPIO:0001474", + "type": "number", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "examples": [400.0] + }, + "exposure_details": { + "ontology": "GENEPIO:0001431", + "type": "string", + "description": "Additional host exposure information.", + "examples": ["Host role - Other: Bus Driver"] + }, + "breadth_of_coverage_value": { + "ontology": "GENEPIO:0001472", + "type": "number", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "examples": [0.95] + }, + "most_recent_travel_departure_date": { + "examples": ["16/03/2020"], + "ontology": "GENEPIO:0001414", + "type": "string", + "description": "The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.", + "format": "date" + }, + "sequencing_protocol": { + "ontology": "GENEPIO:0001454", + "type": "string", + "description": "The protocol used to generate the sequence.", + "examples": [ + "Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits." + ] + }, + "host_age_bin": { + "Enums": [ + "0 - 9 [GENEPIO:0100049]", + "10 - 19 [GENEPIO:0100050]", + "20 - 29 [GENEPIO:0100051]", + "30 - 39 [GENEPIO:0100052]", + "40 - 49 [GENEPIO:0100053]", + "50 - 59 [GENEPIO:0100054]", + "60 - 69 [GENEPIO:0100055]", + "70 - 79 [GENEPIO:0100056]", + "80 - 89 [GENEPIO:0100057]", + "90 - 99 [GENEPIO:0100058]", + "100+ [GENEPIO:0100059]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001394", + "type": "string", + "description": "The age category of the host at the time of sampling.", + "examples": ["50 - 59 [GENEPIO:0100054]"] + }, + "anatomical_material": { + "Enums": [ + "Blood [UBERON:0000178]", + "Fluid [UBERON:0006314]", + "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", + "Fluid (Pericardial) [UBERON:0002409]", + "Fluid (Pleural) [UBERON:0001087]", + "Fluid (Vaginal) [UBERON:0036243]", + "Fluid (Amniotic) [UBERON:0000173]", + "Saliva [UBERON:0001836]", + "Tissue [UBERON:0000479]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001211", + "type": "string", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "examples": ["Blood [UBERON:0000178]"] + }, + "sample_collection_date": { + "examples": ["19/03/2020"], + "ontology": "GENEPIO:0001174", + "type": "string", + "description": "The date on which the sample was collected. ", + "format": "date" + }, + "diagnostic_pcr_ct_value_2": { + "ontology": "GENEPIO:0001512", + "type": "integer", + "description": "The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "examples": [36] + }, + "number_of_vaccine_doses_received": { + "ontology": "GENEPIO:0001406", + "type": "integer", + "description": "The number of doses of the vaccine recived by the host.", + "examples": [2] + }, + "lab_host": { + "Enums": [ + "293/ACE2 Cell Line [GENEPIO:0100041]", + "Caco2 Cell Line [BTO:0000195]", + "Calu3 Cell Line [BTO:0002750]", + "EFK3B Cell Line [GENEPIO:0100042]", + "HEK293T Cell Line [BTO:0002181]", + "HRCE Cell Line [GENEPIO:0100043]", + "Huh7 Cell Line [BTO:0001950]", + "LLCMk2 Cell Line [CLO:0007330]", + "MDBK Cell Line [BTO:0000836]", + "NHBE Cell Line [BTO:0002924]", + "PK-15 Cell Line [BTO:0001865]", + "RK-13 Cell Line [BTO:0002909]", + "U251 Cell Line [BTO:0002035]", + "Vero Cell Line [BTO:0001444]", + "Vero E6 Cell Line [BTO:0004755]", + "Vero E6/TMPRSS2 Cell Line [GENEPIO:0100044]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001255", + "type": "string", + "description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.", + "examples": ["Vero E6 Cell Line [BTO:0004755]"] + }, + "anatomical_part": { + "Enums": [ + "Anus [UBERON:0001245]", + "Duodenum [UBERON:0002114]", + "Eye [UBERON:0000970]", + "Intestine [UBERON:0000160]", + "Lower respiratory tract [UBERON:0001558]", + "Bronchus [UBERON:0002185]", + "Lung [UBERON:0002048]", + "Bronchiole [UBERON:0002186]", + "Alveolar sac [UBERON:0002169]", + "Pleural sac [UBERON:0009778]", + "Pleural cavity [UBERON:0002402]", + "Trachea [UBERON:0003126]", + "Rectum [UBERON:0001052]", + "Skin [UBERON:0001003]", + "Stomach [UBERON:0000945]", + "Upper respiratory tract [UBERON:0001557]", + "Anterior Nares [UBERON:2001427]", + "Esophagus [UBERON:0001043]", + "Ethmoid sinus [UBERON:0002453]", + "Nasal Cavity [UBERON:0001707]", + "Middle Nasal Turbinate [UBERON:0005921]", + "Inferior Nasal Turbinate [UBERON:0005922]", + "Nasopharynx (NP) [UBERON:0001728]", + "Oropharynx (OP) [UBERON:0001729]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001214", + "type": "string", + "description": "An anatomical part of an organism e.g. oropharynx. ", + "examples": ["Nasopharynx (NP) [UBERON:0001728]"] + }, + "host_health_outcome": { + "Enums": [ + "Deceased [NCIT:C28554]", + "Deteriorating [NCIT:C25254]", + "Recovered [NCIT:C49498]", + "Stable [NCIT:C30103]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001390", + "type": "string", + "description": "Disease outcome in the host.", + "examples": ["Recovered [NCIT:C49498]"] + }, + "sequencing_date": { + "examples": ["22/06/2020"], + "ontology": "GENEPIO:0001447", + "type": "string", + "description": "The date the sample was sequenced.", + "format": "date" + }, + "passage_number": { + "ontology": "GENEPIO:0001261", + "type": "integer", + "description": "Number of passages.", + "examples": [3] + }, + "ns_per_100_kbp": { + "ontology": "GENEPIO:0001484", + "type": "integer", + "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", + "examples": [300] + }, + "case_id": { + "ontology": "GENEPIO:0100281", + "type": "string", + "description": "The identifier used to specify an epidemiologically detected case of disease.", + "examples": ["ABCD1234"] + }, + "biosample_accession": { + "pattern": "^SAM(D|N|E([AG]?))[0-9]+", + "ontology": "GENEPIO:0001139", + "type": "string", + "description": "The identifier assigned to a BioSample in INSDC archives.", + "examples": ["SAMN14180202"] + }, + "last_dose_vacicnation_date": { + "examples": ["09/04/2021"], + "ontology": "GENEPIO:0001408", + "type": "string", + "description": "The date the host received their last dose of vaccine.", + "format": "date" + }, + "bioinformatics_protocol": { + "ontology": "GENEPIO:0001489", + "type": "string", + "description": "The name and version number of the bioinformatics protocol used.", + "examples": [ + "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" + ] + }, + "prior_sars_cov_2_antiviral_treatment": { + "Enums": [ + "Prior antiviral treatment [GENEPIO:0100037]", + "No prior antiviral treatment [GENEPIO:0100233]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001438", + "type": "string", + "description": "Whether there was prior SARS-CoV-2 treatment with an antiviral agent.", + "examples": ["Prior antiviral treatment [GENEPIO:0100037]"] + }, + "gene_name_2": { + "Enums": [ + "E gene (orf4) [GENEPIO:0100151]", + "M gene (orf5) [GENEPIO:0100152]", + "N gene (orf9) [GENEPIO:0100153]", + "Spike gene (orf2) [GENEPIO:0100154]", + "orf1ab (rep) [GENEPIO:0100155]", + "orf1a (pp1a) [GENEPIO:0100156]", + "nsp11 [GENEPIO:0100157]", + "nsp1 [GENEPIO:0100158]", + "nsp2 [GENEPIO:0100159]", + "nsp3 [GENEPIO:0100160]", + "nsp4 [GENEPIO:0100161]", + "nsp5 [GENEPIO:0100162]", + "nsp6 [GENEPIO:0100163]", + "nsp7 [GENEPIO:0100164]", + "nsp8 [GENEPIO:0100165]", + "nsp9 [GENEPIO:0100166]", + "nsp10 [GENEPIO:0100167]", + "RdRp gene (nsp12) [GENEPIO:0100168]", + "hel gene (nsp13) [GENEPIO:0100169]", + "exoN gene (nsp14) [GENEPIO:0100170]", + "nsp15 [GENEPIO:0100171]", + "nsp16 [GENEPIO:0100172]", + "orf3a [GENEPIO:0100173]", + "orf3b [GENEPIO:0100174]", + "orf6 (ns6) [GENEPIO:0100175]", + "orf7a [GENEPIO:0100176]", + "orf7b (ns7b) [GENEPIO:0100177]", + "orf8 (ns8) [GENEPIO:0100178]", + "orf9b [GENEPIO:0100179]", + "orf9c [GENEPIO:0100180]", + "orf10 [GENEPIO:0100181]", + "orf14 [GENEPIO:0100182]", + "SARS-COV-2 5' UTR [GENEPIO:0100183]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001510", + "type": "string", + "description": "The name of the gene used in the diagnostic RT-PCR test.", + "examples": ["RdRp gene (nsp12) [GENEPIO:0100168]"] + }, + "body_product": { + "Enums": [ + "Breast Milk [UBERON:0001913]", + "Feces [UBERON:0001988]", + "Mucus [UBERON:0000912]", + "Semen [UBERON:0006530]", + "Sputum [UBERON:0007311]", + "Sweat [UBERON:0001089]", + "Tear [UBERON:0001827]", + "Urine [UBERON:0001088]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001216", + "type": "string", + "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", + "examples": ["Feces [UBERON:0001988]"] + }, + "host_age": { + "ontology": "GENEPIO:0001392", + "anyOf": [ + { "type": "integer" }, + { "pattern": "\\d+-\\d+", "type": "string" } + ], + "description": "Age of host at the time of sampling.", + "examples": [79] + }, + "host_ethnicity": { + "ontology": "GECKO:0000061", + "type": "string", + "description": "The self-identified ethnicity(ies) of the host.", + "examples": ["Indigenous, European"] + }, + "collection_device": { + "Enums": [ + "Air filter [ENVO:00003968]", + "Blood Collection Tube [OBI:0002859]", + "Bronchoscope [OBI:0002826]", + "Collection Container [OBI:0002088]", + "Collection Cup [GENEPIO:0100026]", + "Fibrobronchoscope Brush [OBI:0002825]", + "Filter [GENEPIO:0100103]", + "Fine Needle [OBI:0002827]", + "Microcapillary tube [OBI:0002858]", + "Micropipette [OBI:0001128]", + "Needle [OBI:0000436]", + "Serum Collection Tube [OBI:0002860]", + "Sputum Collection Tube [OBI:0002861]", + "Suction Catheter [OBI:0002831]", + "Swab [GENEPIO:0100027]", + "Urine Collection Tube [OBI:0002862]", + "Virus Transport Medium [OBI:0002866]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001234", + "type": "string", + "description": "The instrument or container used to collect the sample e.g. swab.", + "examples": ["Swab [GENEPIO:0100027]"] + }, + "purpose_of_sequencing": { + "Enums": [ + "Baseline surveillance (random sampling) [GENEPIO:0100005]", + "Targeted surveillance (non-random sampling) [GENEPIO:0100006]", + "Priority surveillance projects [GENEPIO:0100007]", + "Screening for Variants of Concern (VOC) [GENEPIO:0100008]", + "Sample has epidemiological link to Variant of Concern (VoC) [GENEPIO:0100273]", + "Sample has epidemiological link to Omicron Variant [GENEPIO:0100274]", + "Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]", + "Re-infection surveillance [GENEPIO:0100010]", + "Vaccine escape surveillance [GENEPIO:0100011]", + "Travel-associated surveillance [GENEPIO:0100012]", + "Domestic travel surveillance [GENEPIO:0100013]", + "Interstate/ interprovincial travel surveillance [GENEPIO:0100275]", + "Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276]", + "International travel surveillance [GENEPIO:0100014]", + "Surveillance of international border crossing by air travel or ground transport [GENEPIO:0100015]", + "Surveillance of international border crossing by air travel [GENEPIO:0100016]", + "Surveillance of international border crossing by ground transport [GENEPIO:0100017]", + "Surveillance from international worker testing [GENEPIO:0100018]", + "Cluster/Outbreak investigation [GENEPIO:0100019]", + "Multi-jurisdictional outbreak investigation [GENEPIO:0100020]", + "Intra-jurisdictional outbreak investigation [GENEPIO:0100021]", + "Research [GENEPIO:0100022]", + "Viral passage experiment [GENEPIO:0100023]", + "Protocol testing [GENEPIO:0100024]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001445", + "type": "string", + "description": "The reason that the sample was sequenced.", + "examples": ["Baseline surveillance (random sampling) [GENEPIO:0100005]"] + }, + "raw_sequence_data_processing_method": { + "ontology": "GENEPIO:0001458", + "type": "string", + "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "examples": ["Porechop 0.2.3,Porechop 0.2.3"] + }, + "sequence_submitter_contact_address": { + "ontology": "GENEPIO:0001167", + "type": "string", + "description": "The mailing address of the agency submitting the sequence.", + "examples": ["123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"] + }, + "depth_of_coverage_threshold": { + "ontology": "GENEPIO:0001475", + "type": "number", + "description": "The threshold used as a cut-off for the depth of coverage.", + "examples": [100.0] + }, + "specimen_processing": { + "Enums": [ + "Virus Passage [GENEPIO:0100039]", + "RNA Re-Extraction (Post RT-PCR) [GENEPIO:0100040]", + "Specimens Pooled [OBI:0600016]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001253", + "type": "string", + "description": "Any processing applied to the sample during or after receiving the sample. ", + "examples": ["Virus Passage [GENEPIO:0100039]"] + }, + "flow_cell_barcode": { + "ontology": "GENEPIO:0001451", + "type": "string", + "description": "The barcode of the flow cell used for sequencing.", + "examples": ["FAB06069"] + }, + "r1_fastq_filename": { + "ontology": "GENEPIO:0001476", + "type": "string", + "description": "The user-specified filename of the r1 FASTQ file.", + "examples": ["ABC123_S1_L001_R1_001.fastq.gz"] + }, + "destination_of_most_recent_travel_city": { + "ontology": "GENEPIO:0001411", + "type": "string", + "description": "The name of the city that was the destination of most recent travel.", + "examples": ["New York City"] + }, + "r1_fastq_filepath": { + "ontology": "GENEPIO:0001478", + "type": "string", + "description": "The filepath of the r1 FASTQ file.", + "examples": [ + "/User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz" + ] + }, + "library_id": { + "ontology": "GENEPIO:0001448", + "type": "string", + "description": "The user-specified identifier for the library prepared for sequencing.", + "examples": ["XYZ_123345"] + }, + "host_vaccination_status": { + "Enums": [ + "Fully Vaccinated [GENEPIO:0100100]", + "Partially Vaccinated [GENEPIO:0100101]", + "Not Vaccinated [GENEPIO:0100102]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001404", + "type": "string", + "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", + "examples": ["Fully Vaccinated [GENEPIO:0100100]"] + }, + "geo_loc_longitude": { + "ontology": "OBI:0001621", + "type": "string", + "description": "The longitude coordinates of the geographical location of sample collection.", + "examples": ["77.11 W"] + }, + "genbank_ena_ddbj_accession": { + "pattern": "^([a-zA-Z]{2})\\d*.\\d{1}", + "ontology": "GENEPIO:0001145", + "type": "string", + "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", + "examples": ["MN908947.3"] + }, + "bioproject_accession": { + "pattern": "^PRJ(N|E|D)([a-zA-Z]?)[0-9]+*", + "ontology": "GENEPIO:0001136", + "type": "string", + "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs. ", + "examples": ["PRJNA12345"] + }, + "lineage_clade_analysis_software_name": { + "ontology": "GENEPIO:0001501", + "type": "string", + "description": "The name of the software used to determine the lineage/clade.", + "examples": ["Pangolin"] + }, + "location_of_exposure_geo_loc_name_country": { + "Enums": [ + "Afghanistan [GAZ:00006882]", + "Albania [GAZ:00002953]", + "Algeria [GAZ:00000563]", + "American Samoa [GAZ:00003957]", + "Andorra [GAZ:00002948]", + "Angola [GAZ:00001095]", + "Anguilla [GAZ:00009159]", + "Antarctica [GAZ:00000462]", + "Antigua and Barbuda [GAZ:00006883]", + "Argentina [GAZ:00002928]", + "Armenia [GAZ:00004094]", + "Aruba [GAZ:00004025]", + "Ashmore and Cartier Islands [GAZ:00005901]", + "Australia [GAZ:00000463]", + "Austria [GAZ:00002942]", + "Azerbaijan [GAZ:00004941]", + "Bahamas [GAZ:00002733]", + "Bahrain [GAZ:00005281]", + "Baker Island [GAZ:00007117]", + "Bangladesh [GAZ:00003750]", + "Barbados [GAZ:00001251]", + "Bassas da India [GAZ:00005810]", + "Belarus [GAZ:00006886]", + "Belgium [GAZ:00002938]", + "Belize [GAZ:00002934]", + "Benin [GAZ:00000904]", + "Bermuda [GAZ:00001264]", + "Bhutan [GAZ:00003920]", + "Bolivia [GAZ:00002511]", + "Borneo [GAZ:00025355]", + "Bosnia and Herzegovina [GAZ:00006887]", + "Botswana [GAZ:00001097]", + "Bouvet Island [GAZ:00001453]", + "Brazil [GAZ:00002828]", + "British Virgin Islands [GAZ:00003961]", + "Brunei [GAZ:00003901]", + "Bulgaria [GAZ:00002950]", + "Burkina Faso [GAZ:00000905]", + "Burundi [GAZ:00001090]", + "Cambodia [GAZ:00006888]", + "Cameroon [GAZ:00001093]", + "Canada [GAZ:00002560]", + "Cape Verde [GAZ:00001227]", + "Cayman Islands [GAZ:00003986]", + "Central African Republic [GAZ:00001089]", + "Chad [GAZ:00000586]", + "Chile [GAZ:00002825]", + "China [GAZ:00002845]", + "Christmas Island [GAZ:00005915]", + "Clipperton Island [GAZ:00005838]", + "Cocos Islands [GAZ:00009721]", + "Colombia [GAZ:00002929]", + "Comoros [GAZ:00005820]", + "Cook Islands [GAZ:00053798]", + "Coral Sea Islands [GAZ:00005917]", + "Costa Rica [GAZ:00002901]", + "Cote d'Ivoire [GAZ:00000906]", + "Croatia [GAZ:00002719]", + "Cuba [GAZ:00003762]", + "Curacao [GAZ:00012582]", + "Cyprus [GAZ:00004006]", + "Czech Republic [GAZ:00002954]", + "Democratic Republic of the Congo [GAZ:00001086]", + "Denmark [GAZ:00005852]", + "Djibouti [GAZ:00000582]", + "Dominica [GAZ:00006890]", + "Dominican Republic [GAZ:00003952]", + "Ecuador [GAZ:00002912]", + "Egypt [GAZ:00003934]", + "El Salvador [GAZ:00002935]", + "Equatorial Guinea [GAZ:00001091]", + "Eritrea [GAZ:00000581]", + "Estonia [GAZ:00002959]", + "Eswatini [GAZ:00001099]", + "Ethiopia [GAZ:00000567]", + "Europa Island [GAZ:00005811]", + "Falkland Islands (Islas Malvinas) [GAZ:00001412]", + "Faroe Islands [GAZ:00059206]", + "Fiji [GAZ:00006891]", + "Finland [GAZ:00002937]", + "France [GAZ:00003940]", + "French Guiana [GAZ:00002516]", + "French Polynesia [GAZ:00002918]", + "French Southern and Antarctic Lands [GAZ:00003753]", + "Gabon [GAZ:00001092]", + "Gambia [GAZ:00000907]", + "Gaza Strip [GAZ:00009571]", + "Georgia [GAZ:00004942]", + "Germany [GAZ:00002646]", + "Ghana [GAZ:00000908]", + "Gibraltar [GAZ:00003987]", + "Glorioso Islands [GAZ:00005808]", + "Greece [GAZ:00002945]", + "Greenland [GAZ:00001507]", + "Grenada [GAZ:02000573]", + "Guadeloupe [GAZ:00067142]", + "Guam [GAZ:00003706]", + "Guatemala [GAZ:00002936]", + "Guernsey [GAZ:00001550]", + "Guinea [GAZ:00000909]", + "Guinea-Bissau [GAZ:00000910]", + "Guyana [GAZ:00002522]", + "Haiti [GAZ:00003953]", + "Heard Island and McDonald Islands [GAZ:00009718]", + "Honduras [GAZ:00002894]", + "Hong Kong [GAZ:00003203]", + "Howland Island [GAZ:00007120]", + "Hungary [GAZ:00002952]", + "Iceland [GAZ:00000843]", + "India [GAZ:00002839]", + "Indonesia [GAZ:00003727]", + "Iran [GAZ:00004474]", + "Iraq [GAZ:00004483]", + "Ireland [GAZ:00002943]", + "Isle of Man [GAZ:00052477]", + "Israel [GAZ:00002476]", + "Italy [GAZ:00002650]", + "Jamaica [GAZ:00003781]", + "Jan Mayen [GAZ:00005853]", + "Japan [GAZ:00002747]", + "Jarvis Island [GAZ:00007118]", + "Jersey [GAZ:00001551]", + "Johnston Atoll [GAZ:00007114]", + "Jordan [GAZ:00002473]", + "Juan de Nova Island [GAZ:00005809]", + "Kazakhstan [GAZ:00004999]", + "Kenya [GAZ:00001101]", + "Kerguelen Archipelago [GAZ:00005682]", + "Kingman Reef [GAZ:00007116]", + "Kiribati [GAZ:00006894]", + "Kosovo [GAZ:00011337]", + "Kuwait [GAZ:00005285]", + "Kyrgyzstan [GAZ:00006893]", + "Laos [GAZ:00006889]", + "Latvia [GAZ:00002958]", + "Lebanon [GAZ:00002478]", + "Lesotho [GAZ:00001098]", + "Liberia [GAZ:00000911]", + "Libya [GAZ:00000566]", + "Liechtenstein [GAZ:00003858]", + "Line Islands [GAZ:00007144]", + "Lithuania [GAZ:00002960]", + "Luxembourg [GAZ:00002947]", + "Macau [GAZ:00003202]", + "Madagascar [GAZ:00001108]", + "Malawi [GAZ:00001105]", + "Malaysia [GAZ:00003902]", + "Maldives [GAZ:00006924]", + "Mali [GAZ:00000584]", + "Malta [GAZ:00004017]", + "Marshall Islands [GAZ:00007161]", + "Martinique [GAZ:00067143]", + "Mauritania [GAZ:00000583]", + "Mauritius [GAZ:00003745]", + "Mayotte [GAZ:00003943]", + "Mexico [GAZ:00002852]", + "Micronesia [GAZ:00005862]", + "Midway Islands [GAZ:00007112]", + "Moldova [GAZ:00003897]", + "Monaco [GAZ:00003857]", + "Mongolia [GAZ:00008744]", + "Montenegro [GAZ:00006898]", + "Montserrat [GAZ:00003988]", + "Morocco [GAZ:00000565]", + "Mozambique [GAZ:00001100]", + "Myanmar [GAZ:00006899]", + "Namibia [GAZ:00001096]", + "Nauru [GAZ:00006900]", + "Navassa Island [GAZ:00007119]", + "Nepal [GAZ:00004399]", + "Netherlands [GAZ:00002946]", + "New Caledonia [GAZ:00005206]", + "New Zealand [GAZ:00000469]", + "Nicaragua [GAZ:00002978]", + "Niger [GAZ:00000585]", + "Nigeria [GAZ:00000912]", + "Niue [GAZ:00006902]", + "Norfolk Island [GAZ:00005908]", + "North Korea [GAZ:00002801]", + "North Macedonia [GAZ:00006895]", + "North Sea [GAZ:00002284]", + "Northern Mariana Islands [GAZ:00003958]", + "Norway [GAZ:00002699]", + "Oman [GAZ:00005283]", + "Pakistan [GAZ:00005246]", + "Palau [GAZ:00006905]", + "Panama [GAZ:00002892]", + "Papua New Guinea [GAZ:00003922]", + "Paracel Islands [GAZ:00010832]", + "Paraguay [GAZ:00002933]", + "Peru [GAZ:00002932]", + "Philippines [GAZ:00004525]", + "Pitcairn Islands [GAZ:00005867]", + "Poland [GAZ:00002939]", + "Portugal [GAZ:00004126]", + "Puerto Rico [GAZ:00006935]", + "Qatar [GAZ:00005286]", + "Republic of the Congo [GAZ:00001088]", + "Reunion [GAZ:00003945]", + "Romania [GAZ:00002951]", + "Ross Sea [GAZ:00023304]", + "Russia [GAZ:00002721]", + "Rwanda [GAZ:00001087]", + "Saint Helena [GAZ:00000849]", + "Saint Kitts and Nevis [GAZ:00006906]", + "Saint Lucia [GAZ:00006909]", + "Saint Pierre and Miquelon [GAZ:00003942]", + "Saint Martin [GAZ:00005841]", + "Saint Vincent and the Grenadines [GAZ:02000565]", + "Samoa [GAZ:00006910]", + "San Marino [GAZ:00003102]", + "Sao Tome and Principe [GAZ:00006927]", + "Saudi Arabia [GAZ:00005279]", + "Senegal [GAZ:00000913]", + "Serbia [GAZ:00002957]", + "Seychelles [GAZ:00006922]", + "Sierra Leone [GAZ:00000914]", + "Singapore [GAZ:00003923]", + "Sint Maarten [GAZ:00012579]", + "Slovakia [GAZ:00002956]", + "Slovenia [GAZ:00002955]", + "Solomon Islands [GAZ:00005275]", + "Somalia [GAZ:00001104]", + "South Africa [GAZ:00001094]", + "South Georgia and the South Sandwich Islands [GAZ:00003990]", + "South Korea [GAZ:00002802]", + "South Sudan [GAZ:00233439]", + "Spain [GAZ:00003936]", + "Spratly Islands [GAZ:00010831]", + "Sri Lanka [GAZ:00003924]", + "State of Palestine [GAZ:00002475]", + "Sudan [GAZ:00000560]", + "Suriname [GAZ:00002525]", + "Svalbard [GAZ:00005396]", + "Swaziland [GAZ:00001099]", + "Sweden [GAZ:00002729]", + "Switzerland [GAZ:00002941]", + "Syria [GAZ:00002474]", + "Taiwan [GAZ:00005341]", + "Tajikistan [GAZ:00006912]", + "Tanzania [GAZ:00001103]", + "Thailand [GAZ:00003744]", + "Timor-Leste [GAZ:00006913]", + "Togo [GAZ:00000915]", + "Tokelau [GAZ:00260188]", + "Tonga [GAZ:00006916]", + "Trinidad and Tobago [GAZ:00003767]", + "Tromelin Island [GAZ:00005812]", + "Tunisia [GAZ:00000562]", + "Turkey [GAZ:00000558]", + "Turkmenistan [GAZ:00005018]", + "Turks and Caicos Islands [GAZ:00003955]", + "Tuvalu [GAZ:00009715]", + "USA [GAZ:00002459]", + "Uganda [GAZ:00001102]", + "Ukraine [GAZ:00002724]", + "United Arab Emirates [GAZ:00005282]", + "United Kingdom [GAZ:00002637]", + "Uruguay [GAZ:00002930]", + "Uzbekistan [GAZ:00004979]", + "Vanuatu [GAZ:00006918]", + "Venezuela [GAZ:00002931]", + "Viet Nam [GAZ:00003756]", + "Virgin Islands [GAZ:00003959]", + "Wake Island [GAZ:00007111]", + "Wallis and Futuna [GAZ:00007191]", + "West Bank [GAZ:00009572]", + "Western Sahara [GAZ:00000564]", + "Yemen [GAZ:00005284]", + "Zambia [GAZ:00001107]", + "Zimbabwe [GAZ:00001106]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001410", + "type": "string", + "description": "The country where the host was likely exposed to the causative agent of the illness.", + "examples": ["South Africa [GAZ:00001094]"] + }, + "sample_plan_name": { + "ontology": "GENEPIO:0100285", + "type": "string", + "description": "The name of the sample plan implemented for sample collection.", + "examples": ["CanCOGeN Sampling Strategy 1.0"] + }, + "prior_sars_cov_2_antiviral_treatment_date": { + "examples": ["28/01/2021"], + "ontology": "GENEPIO:0001440", + "type": "string", + "description": "The date treatment was first administered during the prior SARS-CoV-2 infection.", + "format": "date" + }, + "library_preparation_kit": { + "ontology": "GENEPIO:0001450", + "type": "string", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "examples": ["Nextera XT"] + }, + "fast5_filename": { + "ontology": "GENEPIO:0001480", + "type": "string", + "description": "The user-specified filename of the FAST5 file.", + "examples": ["batch1a_sequences.fast5"] + }, + "diagnostic_pcr_ct_value_1": { + "ontology": "GENEPIO:0001509", + "type": "integer", + "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "examples": [21] + }, + "collection_method": { + "Enums": [ + "Amniocentesis [NCIT:C52009]", + "Aspiration [NCIT:C15631]", + "Suprapubic Aspiration [GENEPIO:0100028]", + "Tracheal Aspiration [GENEPIO:0100029]", + "Vacuum Aspiration [GENEPIO:0100030]", + "Biopsy [OBI:0002650]", + "Needle Biopsy [OBI:0002651]", + "Filtration [OBI:0302885]", + "Air Filtration [GENEPIO:0100031]", + "Lavage [OBI:0600044]", + "Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]", + "Gastric Lavage [GENEPIO:0100033]", + "Lumbar Puncture [NCIT:C15327]", + "Necropsy [MMO:0000344]", + "Phlebotomy [NCIT:C28221]", + "Rinsing [GENEPIO:0002116]", + "Saline gargle (mouth rinse and gargle) [GENEPIO:0100034]", + "Scraping [GENEPIO:0100035]", + "Swabbing [GENEPIO:0002117]", + "Finger Prick [GENEPIO:0100036]", + "Washout Tear Collection [GENEPIO:0100038]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001241", + "type": "string", + "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", + "examples": ["Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]"] + }, + "geo_loc_name_county_region": { + "ontology": "GENEPIO:0100280", + "type": "string", + "description": "The county/region of origin of the sample.", + "examples": ["Derbyshire"] + }, + "consensus_genome_length": { + "ontology": "GENEPIO:0001483", + "type": "integer", + "description": "Size of the assembled genome described as the number of base pairs.", + "examples": [38677] + }, + "r2_fastq_filepath": { + "ontology": "GENEPIO:0001479", + "type": "string", + "description": "The filepath of the r2 FASTQ file.", + "examples": [ + "/User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz" + ] + }, + "destination_of_most_recent_travel_state_province_territory": { + "ontology": "GENEPIO:0001412", + "type": "string", + "description": "The name of the province that was the destination of most recent travel.", + "examples": ["California"] + }, + "sample_received_date": { + "examples": ["20/03/2020"], + "ontology": "GENEPIO:0001179", + "type": "string", + "description": "The date on which the sample was received.", + "format": "date" + }, + "host_common_name": { + "Enums": [ + "Human [NCBITaxon:9606]", + "Bat [NCBITaxon:9397]", + "Cat [NCBITaxon:9685]", + "Chicken [NCBITaxon:9031]", + "Civet [NCBITaxon:9673]", + "Cow [NCBITaxon:9913]", + "Dog [NCBITaxon:9615]", + "Lion [NCBITaxon:9689]", + "Mink [NCBITaxon:452646]", + "Pangolin [NCBITaxon:9973]", + "Pig [NCBITaxon:9825]", + "Pigeon [NCBITaxon:8930]", + "Tiger [NCBITaxon:9694]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001386", + "type": "string", + "description": "The commonly used name of the host.", + "examples": ["Human [NCBITaxon:9606]"] + }, + "geo_loc_name_state_province_territory": { + "ontology": "GENEPIO:0001185", + "type": "string", + "description": "The state/province/territory of origin of the sample.", + "examples": ["Western Cape"] + }, + "lineage_clade_analysis_software_version": { + "ontology": "GENEPIO:0001502", + "type": "string", + "description": "The version of the software used to determine the lineage/clade.", + "examples": ["2.1.10"] + }, + "host_subject_id": { + "ontology": "GENEPIO:0001398", + "type": "string", + "description": "A unique identifier by which each host can be referred to e.g. #131", + "examples": ["BCxy123"] + }, + "sra_accession": { + "pattern": "^(SRR|ERR|DRR)[0-9]+", + "ontology": "GENEPIO:0001142", + "type": "string", + "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", + "examples": ["SRR11177792"] + }, + "authors": { + "ontology": "GENEPIO:0001517", + "type": "string", + "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", + "examples": ["Tejinder Singh, Fei Hu, Johnny Blogs"] + }, + "host_role": { + "Enums": [ + "Attendee [GENEPIO:0100249]", + "Student [OMRSE:00000058]", + "Patient [OMRSE:00000030]", + "Inpatient [NCIT:C25182]", + "Outpatient [NCIT:C28293]", + "Passenger [GENEPIO:0100250]", + "Resident [GENEPIO:0100251]", + "Visitor [GENEPIO:0100252]", + "Volunteer [GENEPIO:0100253]", + "Work [GENEPIO:0100254]", + "Administrator [GENEPIO:0100255]", + "First Responder [GENEPIO:0100256]", + "Firefighter [GENEPIO:0100257]", + "Paramedic [GENEPIO:0100258]", + "Police Officer [GENEPIO:0100259]", + "Housekeeper [GENEPIO:0100260]", + "Kitchen Worker [GENEPIO:0100261]", + "Laboratory Worker [GENEPIO:0100262]", + "Nurse [OMRSE:00000014]", + "Personal Care Aid [GENEPIO:0100263]", + "Pharmacist [GENEPIO:0100264]", + "Physician [OMRSE:00000013]", + "Vet [GENEPIO:0100265]", + "Social role [OMRSE:00000001]", + "Acquaintance of case [GENEPIO:0100266]", + "Relative of case [GENEPIO:0100267]", + "Child of case [GENEPIO:0100268]", + "Parent of case [GENEPIO:0100269]", + "Father of case [GENEPIO:0100270]", + "Mother of case [GENEPIO:0100271]", + "Spouse of case [GENEPIO:0100272]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001419", + "type": "string", + "description": "The role of the host in relation to the exposure setting.", + "examples": ["Patient [OMRSE:00000030]"] + }, + "consensus_sequence_name": { + "ontology": "GENEPIO:0001460", + "type": "string", + "description": "The name of the consensus sequence.", + "examples": ["ncov123assembly3"] + }, + "gisaid_accession": { + "pattern": "^EPI_ISL_\\d*", + "ontology": "GENEPIO:0001147", + "type": "string", + "description": "The GISAID accession number assigned to the sequence.", + "examples": ["EPI_ISL_123456"] + }, + "geo_loc_name_country": { + "Enums": [ + "Afghanistan [GAZ:00006882]", + "Albania [GAZ:00002953]", + "Algeria [GAZ:00000563]", + "American Samoa [GAZ:00003957]", + "Andorra [GAZ:00002948]", + "Angola [GAZ:00001095]", + "Anguilla [GAZ:00009159]", + "Antarctica [GAZ:00000462]", + "Antigua and Barbuda [GAZ:00006883]", + "Argentina [GAZ:00002928]", + "Armenia [GAZ:00004094]", + "Aruba [GAZ:00004025]", + "Ashmore and Cartier Islands [GAZ:00005901]", + "Australia [GAZ:00000463]", + "Austria [GAZ:00002942]", + "Azerbaijan [GAZ:00004941]", + "Bahamas [GAZ:00002733]", + "Bahrain [GAZ:00005281]", + "Baker Island [GAZ:00007117]", + "Bangladesh [GAZ:00003750]", + "Barbados [GAZ:00001251]", + "Bassas da India [GAZ:00005810]", + "Belarus [GAZ:00006886]", + "Belgium [GAZ:00002938]", + "Belize [GAZ:00002934]", + "Benin [GAZ:00000904]", + "Bermuda [GAZ:00001264]", + "Bhutan [GAZ:00003920]", + "Bolivia [GAZ:00002511]", + "Borneo [GAZ:00025355]", + "Bosnia and Herzegovina [GAZ:00006887]", + "Botswana [GAZ:00001097]", + "Bouvet Island [GAZ:00001453]", + "Brazil [GAZ:00002828]", + "British Virgin Islands [GAZ:00003961]", + "Brunei [GAZ:00003901]", + "Bulgaria [GAZ:00002950]", + "Burkina Faso [GAZ:00000905]", + "Burundi [GAZ:00001090]", + "Cambodia [GAZ:00006888]", + "Cameroon [GAZ:00001093]", + "Canada [GAZ:00002560]", + "Cape Verde [GAZ:00001227]", + "Cayman Islands [GAZ:00003986]", + "Central African Republic [GAZ:00001089]", + "Chad [GAZ:00000586]", + "Chile [GAZ:00002825]", + "China [GAZ:00002845]", + "Christmas Island [GAZ:00005915]", + "Clipperton Island [GAZ:00005838]", + "Cocos Islands [GAZ:00009721]", + "Colombia [GAZ:00002929]", + "Comoros [GAZ:00005820]", + "Cook Islands [GAZ:00053798]", + "Coral Sea Islands [GAZ:00005917]", + "Costa Rica [GAZ:00002901]", + "Cote d'Ivoire [GAZ:00000906]", + "Croatia [GAZ:00002719]", + "Cuba [GAZ:00003762]", + "Curacao [GAZ:00012582]", + "Cyprus [GAZ:00004006]", + "Czech Republic [GAZ:00002954]", + "Democratic Republic of the Congo [GAZ:00001086]", + "Denmark [GAZ:00005852]", + "Djibouti [GAZ:00000582]", + "Dominica [GAZ:00006890]", + "Dominican Republic [GAZ:00003952]", + "Ecuador [GAZ:00002912]", + "Egypt [GAZ:00003934]", + "El Salvador [GAZ:00002935]", + "Equatorial Guinea [GAZ:00001091]", + "Eritrea [GAZ:00000581]", + "Estonia [GAZ:00002959]", + "Eswatini [GAZ:00001099]", + "Ethiopia [GAZ:00000567]", + "Europa Island [GAZ:00005811]", + "Falkland Islands (Islas Malvinas) [GAZ:00001412]", + "Faroe Islands [GAZ:00059206]", + "Fiji [GAZ:00006891]", + "Finland [GAZ:00002937]", + "France [GAZ:00003940]", + "French Guiana [GAZ:00002516]", + "French Polynesia [GAZ:00002918]", + "French Southern and Antarctic Lands [GAZ:00003753]", + "Gabon [GAZ:00001092]", + "Gambia [GAZ:00000907]", + "Gaza Strip [GAZ:00009571]", + "Georgia [GAZ:00004942]", + "Germany [GAZ:00002646]", + "Ghana [GAZ:00000908]", + "Gibraltar [GAZ:00003987]", + "Glorioso Islands [GAZ:00005808]", + "Greece [GAZ:00002945]", + "Greenland [GAZ:00001507]", + "Grenada [GAZ:02000573]", + "Guadeloupe [GAZ:00067142]", + "Guam [GAZ:00003706]", + "Guatemala [GAZ:00002936]", + "Guernsey [GAZ:00001550]", + "Guinea [GAZ:00000909]", + "Guinea-Bissau [GAZ:00000910]", + "Guyana [GAZ:00002522]", + "Haiti [GAZ:00003953]", + "Heard Island and McDonald Islands [GAZ:00009718]", + "Honduras [GAZ:00002894]", + "Hong Kong [GAZ:00003203]", + "Howland Island [GAZ:00007120]", + "Hungary [GAZ:00002952]", + "Iceland [GAZ:00000843]", + "India [GAZ:00002839]", + "Indonesia [GAZ:00003727]", + "Iran [GAZ:00004474]", + "Iraq [GAZ:00004483]", + "Ireland [GAZ:00002943]", + "Isle of Man [GAZ:00052477]", + "Israel [GAZ:00002476]", + "Italy [GAZ:00002650]", + "Jamaica [GAZ:00003781]", + "Jan Mayen [GAZ:00005853]", + "Japan [GAZ:00002747]", + "Jarvis Island [GAZ:00007118]", + "Jersey [GAZ:00001551]", + "Johnston Atoll [GAZ:00007114]", + "Jordan [GAZ:00002473]", + "Juan de Nova Island [GAZ:00005809]", + "Kazakhstan [GAZ:00004999]", + "Kenya [GAZ:00001101]", + "Kerguelen Archipelago [GAZ:00005682]", + "Kingman Reef [GAZ:00007116]", + "Kiribati [GAZ:00006894]", + "Kosovo [GAZ:00011337]", + "Kuwait [GAZ:00005285]", + "Kyrgyzstan [GAZ:00006893]", + "Laos [GAZ:00006889]", + "Latvia [GAZ:00002958]", + "Lebanon [GAZ:00002478]", + "Lesotho [GAZ:00001098]", + "Liberia [GAZ:00000911]", + "Libya [GAZ:00000566]", + "Liechtenstein [GAZ:00003858]", + "Line Islands [GAZ:00007144]", + "Lithuania [GAZ:00002960]", + "Luxembourg [GAZ:00002947]", + "Macau [GAZ:00003202]", + "Madagascar [GAZ:00001108]", + "Malawi [GAZ:00001105]", + "Malaysia [GAZ:00003902]", + "Maldives [GAZ:00006924]", + "Mali [GAZ:00000584]", + "Malta [GAZ:00004017]", + "Marshall Islands [GAZ:00007161]", + "Martinique [GAZ:00067143]", + "Mauritania [GAZ:00000583]", + "Mauritius [GAZ:00003745]", + "Mayotte [GAZ:00003943]", + "Mexico [GAZ:00002852]", + "Micronesia [GAZ:00005862]", + "Midway Islands [GAZ:00007112]", + "Moldova [GAZ:00003897]", + "Monaco [GAZ:00003857]", + "Mongolia [GAZ:00008744]", + "Montenegro [GAZ:00006898]", + "Montserrat [GAZ:00003988]", + "Morocco [GAZ:00000565]", + "Mozambique [GAZ:00001100]", + "Myanmar [GAZ:00006899]", + "Namibia [GAZ:00001096]", + "Nauru [GAZ:00006900]", + "Navassa Island [GAZ:00007119]", + "Nepal [GAZ:00004399]", + "Netherlands [GAZ:00002946]", + "New Caledonia [GAZ:00005206]", + "New Zealand [GAZ:00000469]", + "Nicaragua [GAZ:00002978]", + "Niger [GAZ:00000585]", + "Nigeria [GAZ:00000912]", + "Niue [GAZ:00006902]", + "Norfolk Island [GAZ:00005908]", + "North Korea [GAZ:00002801]", + "North Macedonia [GAZ:00006895]", + "North Sea [GAZ:00002284]", + "Northern Mariana Islands [GAZ:00003958]", + "Norway [GAZ:00002699]", + "Oman [GAZ:00005283]", + "Pakistan [GAZ:00005246]", + "Palau [GAZ:00006905]", + "Panama [GAZ:00002892]", + "Papua New Guinea [GAZ:00003922]", + "Paracel Islands [GAZ:00010832]", + "Paraguay [GAZ:00002933]", + "Peru [GAZ:00002932]", + "Philippines [GAZ:00004525]", + "Pitcairn Islands [GAZ:00005867]", + "Poland [GAZ:00002939]", + "Portugal [GAZ:00004126]", + "Puerto Rico [GAZ:00006935]", + "Qatar [GAZ:00005286]", + "Republic of the Congo [GAZ:00001088]", + "Reunion [GAZ:00003945]", + "Romania [GAZ:00002951]", + "Ross Sea [GAZ:00023304]", + "Russia [GAZ:00002721]", + "Rwanda [GAZ:00001087]", + "Saint Helena [GAZ:00000849]", + "Saint Kitts and Nevis [GAZ:00006906]", + "Saint Lucia [GAZ:00006909]", + "Saint Pierre and Miquelon [GAZ:00003942]", + "Saint Martin [GAZ:00005841]", + "Saint Vincent and the Grenadines [GAZ:02000565]", + "Samoa [GAZ:00006910]", + "San Marino [GAZ:00003102]", + "Sao Tome and Principe [GAZ:00006927]", + "Saudi Arabia [GAZ:00005279]", + "Senegal [GAZ:00000913]", + "Serbia [GAZ:00002957]", + "Seychelles [GAZ:00006922]", + "Sierra Leone [GAZ:00000914]", + "Singapore [GAZ:00003923]", + "Sint Maarten [GAZ:00012579]", + "Slovakia [GAZ:00002956]", + "Slovenia [GAZ:00002955]", + "Solomon Islands [GAZ:00005275]", + "Somalia [GAZ:00001104]", + "South Africa [GAZ:00001094]", + "South Georgia and the South Sandwich Islands [GAZ:00003990]", + "South Korea [GAZ:00002802]", + "South Sudan [GAZ:00233439]", + "Spain [GAZ:00003936]", + "Spratly Islands [GAZ:00010831]", + "Sri Lanka [GAZ:00003924]", + "State of Palestine [GAZ:00002475]", + "Sudan [GAZ:00000560]", + "Suriname [GAZ:00002525]", + "Svalbard [GAZ:00005396]", + "Swaziland [GAZ:00001099]", + "Sweden [GAZ:00002729]", + "Switzerland [GAZ:00002941]", + "Syria [GAZ:00002474]", + "Taiwan [GAZ:00005341]", + "Tajikistan [GAZ:00006912]", + "Tanzania [GAZ:00001103]", + "Thailand [GAZ:00003744]", + "Timor-Leste [GAZ:00006913]", + "Togo [GAZ:00000915]", + "Tokelau [GAZ:00260188]", + "Tonga [GAZ:00006916]", + "Trinidad and Tobago [GAZ:00003767]", + "Tromelin Island [GAZ:00005812]", + "Tunisia [GAZ:00000562]", + "Turkey [GAZ:00000558]", + "Turkmenistan [GAZ:00005018]", + "Turks and Caicos Islands [GAZ:00003955]", + "Tuvalu [GAZ:00009715]", + "USA [GAZ:00002459]", + "Uganda [GAZ:00001102]", + "Ukraine [GAZ:00002724]", + "United Arab Emirates [GAZ:00005282]", + "United Kingdom [GAZ:00002637]", + "Uruguay [GAZ:00002930]", + "Uzbekistan [GAZ:00004979]", + "Vanuatu [GAZ:00006918]", + "Venezuela [GAZ:00002931]", + "Viet Nam [GAZ:00003756]", + "Virgin Islands [GAZ:00003959]", + "Wake Island [GAZ:00007111]", + "Wallis and Futuna [GAZ:00007191]", + "West Bank [GAZ:00009572]", + "Western Sahara [GAZ:00000564]", + "Yemen [GAZ:00005284]", + "Zambia [GAZ:00001107]", + "Zimbabwe [GAZ:00001106]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001181", + "type": "string", + "description": "The country of origin of the sample.", + "examples": ["South Africa [GAZ:00001094]"] + }, + "consensus_sequence_filepath": { + "ontology": "GENEPIO:0001462", + "type": "string", + "description": "The filepath of the consesnsus sequence file.", + "examples": ["/User/Documents/RespLab/Data/ncov123assembly.fasta"] + }, + "number_of_base_pairs_sequenced": { + "ontology": "GENEPIO:0001482", + "type": "integer", + "description": "The number of total base pairs generated by the sequencing process.", + "examples": [387566] + }, + "destination_of_most_recent_travel_country": { + "ontology": "GENEPIO:0001413", + "type": "string", + "description": "The name of the country that was the destination of most recent travel.", + "examples": ["United Kingdom"] + }, + "fast5_filepath": { + "ontology": "GENEPIO:0001481", + "type": "string", + "description": "The filepath of the FAST5 file.", + "examples": ["/User/Documents/RespLab/Data/rona123assembly.fast5"] + }, + "culture_collection": { + "ontology": "GENEPIO:0100284", + "type": "string", + "description": "The name of the source collection and unique culture identifier. ", + "examples": ["/culture_collection=\"ATCC:26370\""] + }, + "amplicon_size": { + "ontology": "GENEPIO:0001449", + "type": "string", + "description": "The length of the amplicon generated by PCR amplification.", + "examples": ["300bp"] + }, + "sample_collector_contact_address": { + "ontology": "GENEPIO:0001158", + "type": "string", + "description": "The mailing address of the agency submitting the sample.", + "examples": ["655 Lab St,Vancouver, British Columbia, V5N 2A2, Canada"] + }, + "collection_protocol": { + "ontology": "GENEPIO:0001243", + "type": "string", + "description": "The name and version of a particular protocol used for sampling.", + "examples": ["SC2SamplingProtocol 1.2"] + }, + "variant_evidence": { + "ontology": "GENEPIO:0001504", + "type": "string", + "description": "The evidence used to make the variant determination.", + "examples": [ + "lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)" + ] + }, + "most_recent_travel_return_date": { + "examples": ["26/04/2020"], + "ontology": "GENEPIO:0001415", + "type": "string", + "description": "The date of a person's most recent return to some residence from a journey originating at that residence.", + "format": "date" + }, + "exposure_contact_level": { + "Enums": [ + "Direct (human-to-human contact) [TRANS:0000001]", + "Indirect contact [GENEPIO:0100246]", + "Close contact (face-to-face contact) [GENEPIO:0100247]", + "Casual contact [GENEPIO:0100248]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001418", + "type": "string", + "description": "The exposure transmission contact type.", + "examples": ["Direct (human-to-human contact) [TRANS:0000001]"] + }, + "prior_sars_cov_2_infection": { + "Enums": [ + "Prior infection [GENEPIO:0100234]", + "No prior infection [GENEPIO:0100236]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001435", + "type": "string", + "description": "Whether there was prior SARS-CoV-2 infection.", + "examples": ["Prior infection [GENEPIO:0100234]"] + }, + "gisaid_virus_name": { + "ontology": "GENEPIO:0100282", + "type": "string", + "description": "The user-defined GISAID virus name assigned to the sequence.", + "examples": ["hCoV-19/Canada/prov_rona_99/2020"] + }, + "specimen_collector_sample_id": { + "ontology": "GENEPIO:0001123", + "type": "string", + "description": "The user-defined name for the sample. ", + "examples": ["prov_rona_99"] + }, + "host_scientific_name": { + "Enums": [ + "Bos taurus [NCBITaxon:9913]", + "Canis lupus familiaris [NCBITaxon:9615]", + "Chiroptera [NCBITaxon:9397]", + "Columbidae [NCBITaxon:8930]", + "Felis catus [NCBITaxon:9685]", + "Gallus gallus [NCBITaxon:9031]", + "Homo sapiens [NCBITaxon:9606]", + "Manis [NCBITaxon:9973]", + "Manis javanica [NCBITaxon:9974]", + "Neovison vison [NCBITaxon:452646]", + "Panthera leo [NCBITaxon:9689]", + "Panthera tigris [NCBITaxon:9694]", + "Rhinolophidae [NCBITaxon:58055]", + "Rhinolophus affinis [NCBITaxon:59477]", + "Sus scrofa domesticus [NCBITaxon:9825]", + "Viverridae [NCBITaxon:9673]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001387", + "type": "string", + "description": "The taxonomic, or scientific name of the host.", + "examples": ["Homo sapiens [NCBITaxon:9606]"] + }, + "host_disease": { + "Enums": [ + "COVID-19 [MONDO:0100096]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001391", + "type": "string", + "description": "The name of the disease experienced by the host.", + "examples": ["COVID-19 [MONDO:0100096]"] + }, + "passage_method": { + "ontology": "GENEPIO:0001264", + "type": "string", + "description": "Description of how organism was passaged.", + "examples": [ + "AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain." + ] + }, + "symptom_onset_date": { + "examples": ["16/03/2020"], + "ontology": "GENEPIO:0001399", + "type": "string", + "description": "The date on which the symptoms began or were first noted.", + "format": "date" + }, + "r2_fastq_filename": { + "ontology": "GENEPIO:0001477", + "type": "string", + "description": "The user-specified filename of the r2 FASTQ file.", + "examples": ["ABC123_S1_L001_R2_001.fastq.gz"] + }, + "prior_sars_cov_2_infection_date": { + "examples": ["23/01/2021"], + "ontology": "GENEPIO:0001437", + "type": "string", + "description": "The date of diagnosis of the prior SARS-CoV-2 infection.", + "format": "date" + }, + "exposure_event": { + "Enums": [ + "Mass Gathering [GENEPIO:0100237]", + "Convention [GENEPIO:0100238]", + "Convocation [GENEPIO:0100239]", + "Agricultural Event [GENEPIO:0100240]", + "Religious Gathering [GENEPIO:0100241]", + "Mass [GENEPIO:0100242]", + "Social Gathering [PCO:0000033]", + "Baby Shower [PCO:0000039]", + "Community Event [PCO:0000034]", + "Family Gathering [GENEPIO:0100243]", + "Family Reunion [GENEPIO:0100244]", + "Funeral [GENEPIO:0100245]", + "Party [PCO:0000035]", + "Potluck [PCO:0000037]", + "Wedding [PCO:0000038]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001417", + "type": "string", + "description": "Event leading to exposure.", + "examples": ["Mass Gathering [GENEPIO:0100237]"] + }, + "sequencing_kit_number": { + "ontology": "GENEPIO:0001455", + "type": "string", + "description": "The manufacturer's kit number.", + "examples": ["AB456XYZ789"] + }, + "purpose_of_sampling_details": { + "ontology": "GENEPIO:0001200", + "type": "string", + "description": "Further details pertaining to the reason the sample was collected.", + "examples": ["Screening of bat specimens in museum collections."] + }, + "host_gender": { + "Enums": [ + "Female [NCIT:C46110]", + "Male [NCIT:C46109]", + "Non-binary Gender [GSSO:000132]", + "Transgender (assigned male at birth) [GSSO:004004]", + "Transgender (assigned female at birth) [GSSO:004005]", + "Undeclared [NCIT:C110959]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001395", + "type": "string", + "description": "The gender of the host at the time of sample collection.", + "examples": ["Male [NCIT:C46109]"] + }, + "prior_sars_cov_2_antiviral_treatment_agent": { + "ontology": "GENEPIO:0001439", + "type": "string", + "description": "The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection.", + "examples": ["Remdesivir"] + }, + "diagnostic_pcr_protocol_2": { + "ontology": "GENEPIO:0001511", + "type": "string", + "description": "The name and version number of the protocol used for diagnostic marker amplification.", + "examples": ["PCRRdRpGene 3.0"] + }, + "diagnostic_pcr_protocol_1": { + "ontology": "GENEPIO:0001508", + "type": "string", + "description": "The name and version number of the protocol used for diagnostic marker amplification.", + "examples": ["PCREGene 2.0"] + }, + "host_specimen_voucher": { + "ontology": "GENEPIO:0100283", + "type": "string", + "description": "Identifier for the physical specimen.", + "examples": [ + "URI: http://portal.vertnet.org/o/fmnh/mammals?id=33e55cfe-330b-40d9-aaae-8d042cba7542 INSDC triplet: UAM:Mamm:52179" + ] + }, + "exposure_setting": { + "Enums": [ + "Human Exposure [ECTO:3000005]", + "Contact with Known COVID-19 Case [GENEPIO:0100184]", + "Contact with Patient [GENEPIO:0100185]", + "Contact with Probable COVID-19 Case [GENEPIO:0100186]", + "Contact with Person with Acute Respiratory Illness [GENEPIO:0100187]", + "Contact with Person with Fever and/or Cough [GENEPIO:0100188]", + "Contact with Person who Recently Travelled [GENEPIO:0100189]", + "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]", + "Abbatoir [ECTO:1000033]", + "Animal Rescue [GENEPIO:0100191]", + "Childcare [GENEPIO:0100192]", + "Daycare [GENEPIO:0100193]", + "Nursery [GENEPIO:0100194]", + "Community Service Centre [GENEPIO:0100195]", + "Correctional Facility [GENEPIO:0100196]", + "Dormitory [GENEPIO:0100197]", + "Farm [ECTO:1000034]", + "First Nations Reserve [GENEPIO:0100198]", + "Funeral Home [GENEPIO:0100199]", + "Group Home [GENEPIO:0100200]", + "Healthcare Setting [GENEPIO:0100201]", + "Ambulance [GENEPIO:0100202]", + "Acute Care Facility [GENEPIO:0100203]", + "Clinic [GENEPIO:0100204]", + "Community Health Centre [GENEPIO:0100205]", + "Hospital [ECTO:1000035]", + "Emergency Department [GENEPIO:0100206]", + "ICU [GENEPIO:0100207]", + "Ward [GENEPIO:0100208]", + "Laboratory [ECTO:1000036]", + "Long-Term Care Facility [GENEPIO:0100209]", + "Pharmacy [GENEPIO:0100210]", + "Physician's Office [GENEPIO:0100211]", + "Household [GENEPIO:0100212]", + "Insecure Housing (Homeless) [GENEPIO:0100213]", + "Occupational Exposure [GENEPIO:0100214]", + "Worksite [GENEPIO:0100215]", + "Office [ECTO:1000037]", + "Outdoors [GENEPIO:0100216]", + "Camp/camping [ECTO:5000009]", + "Hiking Trail [GENEPIO:0100217]", + "Hunting Ground [ECTO:6000030]", + "Ski Resort [GENEPIO:0100218]", + "Petting zoo [ECTO:5000008]", + "Place of Worship [GENEPIO:0100220]", + "Church [GENEPIO:0100221]", + "Mosque [GENEPIO:0100222]", + "Temple [GENEPIO:0100223]", + "Restaurant [ECTO:1000040]", + "Retail Store [ECTO:1000041]", + "School [GENEPIO:0100224]", + "Temporary Residence [GENEPIO:0100225]", + "Homeless Shelter [GENEPIO:0100226]", + "Hotel [GENEPIO:0100227]", + "Veterinary Care Clinic [GENEPIO:0100228]", + "Travel Exposure [GENEPIO:0100229]", + "Travelled on a Cruise Ship [GENEPIO:0100230]", + "Travelled on a Plane [GENEPIO:0100231]", + "Travelled on Ground Transport [GENEPIO:0100232]", + "Travelled outside Province/Territory [GENEPIO:0001118]", + "Travelled outside Canada [GENEPIO:0001119]", + "Other Exposure Setting [GENEPIO:0100235]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001428", + "type": "string", + "description": "The setting leading to exposure.", + "examples": ["Healthcare Setting [GENEPIO:0100201]"] + }, + "lineage_clade_name": { + "ontology": "GENEPIO:0001500", + "type": "string", + "description": "The name of the lineage or clade.", + "examples": ["B.1.1.7"] + }, + "gene_name_1": { + "Enums": [ + "E gene (orf4) [GENEPIO:0100151]", + "M gene (orf5) [GENEPIO:0100152]", + "N gene (orf9) [GENEPIO:0100153]", + "Spike gene (orf2) [GENEPIO:0100154]", + "orf1ab (rep) [GENEPIO:0100155]", + "orf1a (pp1a) [GENEPIO:0100156]", + "nsp11 [GENEPIO:0100157]", + "nsp1 [GENEPIO:0100158]", + "nsp2 [GENEPIO:0100159]", + "nsp3 [GENEPIO:0100160]", + "nsp4 [GENEPIO:0100161]", + "nsp5 [GENEPIO:0100162]", + "nsp6 [GENEPIO:0100163]", + "nsp7 [GENEPIO:0100164]", + "nsp8 [GENEPIO:0100165]", + "nsp9 [GENEPIO:0100166]", + "nsp10 [GENEPIO:0100167]", + "RdRp gene (nsp12) [GENEPIO:0100168]", + "hel gene (nsp13) [GENEPIO:0100169]", + "exoN gene (nsp14) [GENEPIO:0100170]", + "nsp15 [GENEPIO:0100171]", + "nsp16 [GENEPIO:0100172]", + "orf3a [GENEPIO:0100173]", + "orf3b [GENEPIO:0100174]", + "orf6 (ns6) [GENEPIO:0100175]", + "orf7a [GENEPIO:0100176]", + "orf7b (ns7b) [GENEPIO:0100177]", + "orf8 (ns8) [GENEPIO:0100178]", + "orf9b [GENEPIO:0100179]", + "orf9c [GENEPIO:0100180]", + "orf10 [GENEPIO:0100181]", + "orf14 [GENEPIO:0100182]", + "SARS-COV-2 5' UTR [GENEPIO:0100183]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001507", + "type": "string", + "description": "The name of the gene used in the diagnostic RT-PCR test.", + "examples": ["E gene (orf4) [GENEPIO:0100151]"] + }, + "consensus_sequence_software_name": { + "ontology": "GENEPIO:0001463", + "type": "string", + "description": "The name of software used to generate the consensus sequence.", + "examples": ["Ivar"] + }, + "reference_genome_accession": { + "ontology": "GENEPIO:0001485", + "type": "string", + "description": "A persistent, unique identifier of a genome database entry.", + "examples": ["NC_045512.2"] + }, + "host_residence_geo_loc_name_country": { + "Enums": [ + "Afghanistan [GAZ:00006882]", + "Albania [GAZ:00002953]", + "Algeria [GAZ:00000563]", + "American Samoa [GAZ:00003957]", + "Andorra [GAZ:00002948]", + "Angola [GAZ:00001095]", + "Anguilla [GAZ:00009159]", + "Antarctica [GAZ:00000462]", + "Antigua and Barbuda [GAZ:00006883]", + "Argentina [GAZ:00002928]", + "Armenia [GAZ:00004094]", + "Aruba [GAZ:00004025]", + "Ashmore and Cartier Islands [GAZ:00005901]", + "Australia [GAZ:00000463]", + "Austria [GAZ:00002942]", + "Azerbaijan [GAZ:00004941]", + "Bahamas [GAZ:00002733]", + "Bahrain [GAZ:00005281]", + "Baker Island [GAZ:00007117]", + "Bangladesh [GAZ:00003750]", + "Barbados [GAZ:00001251]", + "Bassas da India [GAZ:00005810]", + "Belarus [GAZ:00006886]", + "Belgium [GAZ:00002938]", + "Belize [GAZ:00002934]", + "Benin [GAZ:00000904]", + "Bermuda [GAZ:00001264]", + "Bhutan [GAZ:00003920]", + "Bolivia [GAZ:00002511]", + "Borneo [GAZ:00025355]", + "Bosnia and Herzegovina [GAZ:00006887]", + "Botswana [GAZ:00001097]", + "Bouvet Island [GAZ:00001453]", + "Brazil [GAZ:00002828]", + "British Virgin Islands [GAZ:00003961]", + "Brunei [GAZ:00003901]", + "Bulgaria [GAZ:00002950]", + "Burkina Faso [GAZ:00000905]", + "Burundi [GAZ:00001090]", + "Cambodia [GAZ:00006888]", + "Cameroon [GAZ:00001093]", + "Canada [GAZ:00002560]", + "Cape Verde [GAZ:00001227]", + "Cayman Islands [GAZ:00003986]", + "Central African Republic [GAZ:00001089]", + "Chad [GAZ:00000586]", + "Chile [GAZ:00002825]", + "China [GAZ:00002845]", + "Christmas Island [GAZ:00005915]", + "Clipperton Island [GAZ:00005838]", + "Cocos Islands [GAZ:00009721]", + "Colombia [GAZ:00002929]", + "Comoros [GAZ:00005820]", + "Cook Islands [GAZ:00053798]", + "Coral Sea Islands [GAZ:00005917]", + "Costa Rica [GAZ:00002901]", + "Cote d'Ivoire [GAZ:00000906]", + "Croatia [GAZ:00002719]", + "Cuba [GAZ:00003762]", + "Curacao [GAZ:00012582]", + "Cyprus [GAZ:00004006]", + "Czech Republic [GAZ:00002954]", + "Democratic Republic of the Congo [GAZ:00001086]", + "Denmark [GAZ:00005852]", + "Djibouti [GAZ:00000582]", + "Dominica [GAZ:00006890]", + "Dominican Republic [GAZ:00003952]", + "Ecuador [GAZ:00002912]", + "Egypt [GAZ:00003934]", + "El Salvador [GAZ:00002935]", + "Equatorial Guinea [GAZ:00001091]", + "Eritrea [GAZ:00000581]", + "Estonia [GAZ:00002959]", + "Eswatini [GAZ:00001099]", + "Ethiopia [GAZ:00000567]", + "Europa Island [GAZ:00005811]", + "Falkland Islands (Islas Malvinas) [GAZ:00001412]", + "Faroe Islands [GAZ:00059206]", + "Fiji [GAZ:00006891]", + "Finland [GAZ:00002937]", + "France [GAZ:00003940]", + "French Guiana [GAZ:00002516]", + "French Polynesia [GAZ:00002918]", + "French Southern and Antarctic Lands [GAZ:00003753]", + "Gabon [GAZ:00001092]", + "Gambia [GAZ:00000907]", + "Gaza Strip [GAZ:00009571]", + "Georgia [GAZ:00004942]", + "Germany [GAZ:00002646]", + "Ghana [GAZ:00000908]", + "Gibraltar [GAZ:00003987]", + "Glorioso Islands [GAZ:00005808]", + "Greece [GAZ:00002945]", + "Greenland [GAZ:00001507]", + "Grenada [GAZ:02000573]", + "Guadeloupe [GAZ:00067142]", + "Guam [GAZ:00003706]", + "Guatemala [GAZ:00002936]", + "Guernsey [GAZ:00001550]", + "Guinea [GAZ:00000909]", + "Guinea-Bissau [GAZ:00000910]", + "Guyana [GAZ:00002522]", + "Haiti [GAZ:00003953]", + "Heard Island and McDonald Islands [GAZ:00009718]", + "Honduras [GAZ:00002894]", + "Hong Kong [GAZ:00003203]", + "Howland Island [GAZ:00007120]", + "Hungary [GAZ:00002952]", + "Iceland [GAZ:00000843]", + "India [GAZ:00002839]", + "Indonesia [GAZ:00003727]", + "Iran [GAZ:00004474]", + "Iraq [GAZ:00004483]", + "Ireland [GAZ:00002943]", + "Isle of Man [GAZ:00052477]", + "Israel [GAZ:00002476]", + "Italy [GAZ:00002650]", + "Jamaica [GAZ:00003781]", + "Jan Mayen [GAZ:00005853]", + "Japan [GAZ:00002747]", + "Jarvis Island [GAZ:00007118]", + "Jersey [GAZ:00001551]", + "Johnston Atoll [GAZ:00007114]", + "Jordan [GAZ:00002473]", + "Juan de Nova Island [GAZ:00005809]", + "Kazakhstan [GAZ:00004999]", + "Kenya [GAZ:00001101]", + "Kerguelen Archipelago [GAZ:00005682]", + "Kingman Reef [GAZ:00007116]", + "Kiribati [GAZ:00006894]", + "Kosovo [GAZ:00011337]", + "Kuwait [GAZ:00005285]", + "Kyrgyzstan [GAZ:00006893]", + "Laos [GAZ:00006889]", + "Latvia [GAZ:00002958]", + "Lebanon [GAZ:00002478]", + "Lesotho [GAZ:00001098]", + "Liberia [GAZ:00000911]", + "Libya [GAZ:00000566]", + "Liechtenstein [GAZ:00003858]", + "Line Islands [GAZ:00007144]", + "Lithuania [GAZ:00002960]", + "Luxembourg [GAZ:00002947]", + "Macau [GAZ:00003202]", + "Madagascar [GAZ:00001108]", + "Malawi [GAZ:00001105]", + "Malaysia [GAZ:00003902]", + "Maldives [GAZ:00006924]", + "Mali [GAZ:00000584]", + "Malta [GAZ:00004017]", + "Marshall Islands [GAZ:00007161]", + "Martinique [GAZ:00067143]", + "Mauritania [GAZ:00000583]", + "Mauritius [GAZ:00003745]", + "Mayotte [GAZ:00003943]", + "Mexico [GAZ:00002852]", + "Micronesia [GAZ:00005862]", + "Midway Islands [GAZ:00007112]", + "Moldova [GAZ:00003897]", + "Monaco [GAZ:00003857]", + "Mongolia [GAZ:00008744]", + "Montenegro [GAZ:00006898]", + "Montserrat [GAZ:00003988]", + "Morocco [GAZ:00000565]", + "Mozambique [GAZ:00001100]", + "Myanmar [GAZ:00006899]", + "Namibia [GAZ:00001096]", + "Nauru [GAZ:00006900]", + "Navassa Island [GAZ:00007119]", + "Nepal [GAZ:00004399]", + "Netherlands [GAZ:00002946]", + "New Caledonia [GAZ:00005206]", + "New Zealand [GAZ:00000469]", + "Nicaragua [GAZ:00002978]", + "Niger [GAZ:00000585]", + "Nigeria [GAZ:00000912]", + "Niue [GAZ:00006902]", + "Norfolk Island [GAZ:00005908]", + "North Korea [GAZ:00002801]", + "North Macedonia [GAZ:00006895]", + "North Sea [GAZ:00002284]", + "Northern Mariana Islands [GAZ:00003958]", + "Norway [GAZ:00002699]", + "Oman [GAZ:00005283]", + "Pakistan [GAZ:00005246]", + "Palau [GAZ:00006905]", + "Panama [GAZ:00002892]", + "Papua New Guinea [GAZ:00003922]", + "Paracel Islands [GAZ:00010832]", + "Paraguay [GAZ:00002933]", + "Peru [GAZ:00002932]", + "Philippines [GAZ:00004525]", + "Pitcairn Islands [GAZ:00005867]", + "Poland [GAZ:00002939]", + "Portugal [GAZ:00004126]", + "Puerto Rico [GAZ:00006935]", + "Qatar [GAZ:00005286]", + "Republic of the Congo [GAZ:00001088]", + "Reunion [GAZ:00003945]", + "Romania [GAZ:00002951]", + "Ross Sea [GAZ:00023304]", + "Russia [GAZ:00002721]", + "Rwanda [GAZ:00001087]", + "Saint Helena [GAZ:00000849]", + "Saint Kitts and Nevis [GAZ:00006906]", + "Saint Lucia [GAZ:00006909]", + "Saint Pierre and Miquelon [GAZ:00003942]", + "Saint Martin [GAZ:00005841]", + "Saint Vincent and the Grenadines [GAZ:02000565]", + "Samoa [GAZ:00006910]", + "San Marino [GAZ:00003102]", + "Sao Tome and Principe [GAZ:00006927]", + "Saudi Arabia [GAZ:00005279]", + "Senegal [GAZ:00000913]", + "Serbia [GAZ:00002957]", + "Seychelles [GAZ:00006922]", + "Sierra Leone [GAZ:00000914]", + "Singapore [GAZ:00003923]", + "Sint Maarten [GAZ:00012579]", + "Slovakia [GAZ:00002956]", + "Slovenia [GAZ:00002955]", + "Solomon Islands [GAZ:00005275]", + "Somalia [GAZ:00001104]", + "South Africa [GAZ:00001094]", + "South Georgia and the South Sandwich Islands [GAZ:00003990]", + "South Korea [GAZ:00002802]", + "South Sudan [GAZ:00233439]", + "Spain [GAZ:00003936]", + "Spratly Islands [GAZ:00010831]", + "Sri Lanka [GAZ:00003924]", + "State of Palestine [GAZ:00002475]", + "Sudan [GAZ:00000560]", + "Suriname [GAZ:00002525]", + "Svalbard [GAZ:00005396]", + "Swaziland [GAZ:00001099]", + "Sweden [GAZ:00002729]", + "Switzerland [GAZ:00002941]", + "Syria [GAZ:00002474]", + "Taiwan [GAZ:00005341]", + "Tajikistan [GAZ:00006912]", + "Tanzania [GAZ:00001103]", + "Thailand [GAZ:00003744]", + "Timor-Leste [GAZ:00006913]", + "Togo [GAZ:00000915]", + "Tokelau [GAZ:00260188]", + "Tonga [GAZ:00006916]", + "Trinidad and Tobago [GAZ:00003767]", + "Tromelin Island [GAZ:00005812]", + "Tunisia [GAZ:00000562]", + "Turkey [GAZ:00000558]", + "Turkmenistan [GAZ:00005018]", + "Turks and Caicos Islands [GAZ:00003955]", + "Tuvalu [GAZ:00009715]", + "USA [GAZ:00002459]", + "Uganda [GAZ:00001102]", + "Ukraine [GAZ:00002724]", + "United Arab Emirates [GAZ:00005282]", + "United Kingdom [GAZ:00002637]", + "Uruguay [GAZ:00002930]", + "Uzbekistan [GAZ:00004979]", + "Vanuatu [GAZ:00006918]", + "Venezuela [GAZ:00002931]", + "Viet Nam [GAZ:00003756]", + "Virgin Islands [GAZ:00003959]", + "Wake Island [GAZ:00007111]", + "Wallis and Futuna [GAZ:00007191]", + "West Bank [GAZ:00009572]", + "Western Sahara [GAZ:00000564]", + "Yemen [GAZ:00005284]", + "Zambia [GAZ:00001107]", + "Zimbabwe [GAZ:00001106]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001396", + "type": "string", + "description": "The country where the host resides.", + "examples": ["South Africa [GAZ:00001094]"] + }, + "travel_history": { + "ontology": "GENEPIO:0001416", + "type": "string", + "description": "Travel history in last six months.", + "examples": ["Canada, Vancouver, USA, Seattle, Italy, Milan"] + }, + "consensus_sequence_software_version": { + "ontology": "GENEPIO:0001469", + "type": "string", + "description": "The version of the software used to generate the consensus sequence.", + "examples": ["1.3"] + }, + "complications": { + "Enums": [ + "Abnormal blood oxygen level [HP:0500165]", + "Acute kidney injury [HP:0001919]", + "Acute lung injury [MONDO:0015796]", + "Ventilation induced lung injury (VILI) [GENEPIO:0100092]", + "Acute respiratory failure [MONDO:0001208]", + "Arrhythmia (complication) [HP:0011675]", + "Tachycardia [HP:0001649]", + "Polymorphic ventricular tachycardia (VT) [HP:0031677]", + "Tachyarrhythmia [GENEPIO:0100084]", + "Noncardiogenic pulmonary edema [GENEPIO:0100085]", + "Acute respiratory distress syndrome (ARDS) [HP:0033677]", + "COVID-19 associated ARDS (CARDS) [NCIT:C171551]", + "Neurogenic pulmonary edema (NPE) [GENEPIO:0100086]", + "Cardiac injury [GENEPIO:0100087]", + "Cardiac arrest [HP:0001695]", + "Cardiogenic shock [HP:0030149]", + "Blood clot [HP:0001977]", + "Arterial clot [HP:0004420]", + "Deep vein thrombosis (DVT) [HP:0002625]", + "Pulmonary embolism (PE) [HP:0002204]", + "Cardiomyopathy [HP:0001638]", + "Central nervous system invasion [MONDO:0024619]", + "Stroke (complication) [HP:0001297]", + "Central Nervous System Vasculitis [MONDO:0003346]", + "Acute ischemic stroke [HP:0002140]", + "Coma [HP:0001259]", + "Convulsions [HP:0011097]", + "COVID-19 associated coagulopathy (CAC) [NCIT:C171562]", + "Cystic fibrosis [MONDO:0009061]", + "Cytokine release syndrome [MONDO:0600008]", + "Disseminated intravascular coagulation (DIC) [MPATH:108]", + "Encephalopathy [HP:0001298]", + "Fulminant myocarditis [GENEPIO:0100088]", + "Guillain-Barr\u00e9 syndrome [MONDO:0016218]", + "Internal hemorrhage (complication; internal bleeding) [HP:0011029]", + "Intracerebral haemorrhage [MONDO:0013792]", + "Kawasaki disease [MONDO:0012727]", + "Complete Kawasaki disease [GENEPIO:0100089]", + "Incomplete Kawasaki disease [GENEPIO:0100090]", + "Liver dysfunction [HP:0001410]", + "Acute liver injury [GENEPIO:0100091]", + "Long COVID-19 [MONDO:0100233]", + "Meningitis [HP:0001287]", + "Migraine [HP:0002076]", + "Miscarriage [HP:0005268]", + "Multisystem inflammatory syndrome in children (MIS-C) [MONDO:0100163]", + "Muscle injury [GENEPIO:0100093]", + "Myalgic encephalomyelitis (chronic fatigue syndrome) [MONDO:0005404]", + "Myocardial infarction (heart attack) [MONDO:0005068]", + "Acute myocardial infarction [MONDO:0004781]", + "ST-segment elevation myocardial infarction [MONDO:0041656]", + "Myocardial injury [HP:0001700]", + "Neonatal complications [NCIT:C168498]", + "Organ failure [GENEPIO:0100094]", + "Heart failure [HP:0001635]", + "Liver failure [MONDO:0100192]", + "Paralysis [HP:0003470]", + "Pneumothorax (collapsed lung) [HP:0002107]", + "Spontaneous pneumothorax [HP:0002108]", + "Spontaneous tension pneymothorax [MONDO:0002075]", + "Pneumonia (complication) [HP:0002090]", + "COVID-19 pneumonia [NCIT:C171550]", + "Pregancy complications [HP:0001197]", + "Rhabdomyolysis [HP:0003201]", + "Secondary infection [IDO:0000567]", + "Secondary staph infection [GENEPIO:0100095]", + "Secondary strep infection [GENEPIO:0100096]", + "Seizure (complication) [HP:0001250]", + "Motor seizure [HP:0020219]", + "Sepsis/Septicemia [HP:0100806]", + "Sepsis (systemic inflammatory response to infection) [IDO:0000636]", + "Septicemia (bloodstream infection) [NCIT:C3364]", + "Shock [HP:0031273]", + "Hyperinflammatory shock [GENEPIO:0100097]", + "Refractory cardiogenic shock [GENEPIO:0100098]", + "Refractory cardiogenic plus vasoplegic shock [GENEPIO:0100099]", + "Septic shock [NCIT:C35018]", + "Vasculitis [HP:0002633]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001402", + "type": "string", + "description": "Patient medical complications that are believed to have occurred as a result of host disease.", + "examples": ["Acute respiratory failure [MONDO:0001208]"] + }, + "geo_loc_name_city": { + "ontology": "GENEPIO:0001189", + "type": "string", + "description": "The city of origin of the sample.", + "examples": ["Vancouver"] + }, + "umbrella_bioproject_accession": { + "pattern": "^PRJ(N|E|D)([a-zA-Z]?)[0-9]+*", + "ontology": "GENEPIO:0001133", + "type": "string", + "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs. ", + "examples": ["PRJNA623807"] + }, + "biomaterial_extracted": { + "Enums": [ + "mRNA (cDNA) [OBI:0002754]", + "RNA (Total) [OBI:0000895]", + "RNA (Poly-A) [OBI:0000869]", + "RNA (Ribo-Depleted) [OBI:0002627]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001266", + "type": "string", + "description": "The biomaterial extracted from samples for the purpose of sequencing.", + "examples": ["RNA (Total) [OBI:0000895]"] + }, + "host_age_unit": { + "Enums": [ + "months [UO:0000035]", + "years [UO:0000036]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001393", + "type": "string", + "description": "The units used to measure the host's age.", + "examples": ["years [UO:0000036]"] + }, + "geo_loc_latitude": { + "ontology": "OBI:0001620", + "type": "string", + "description": "The latitude coordinates of the geographical location of sample collection.", + "examples": ["38.98 N"] + }, + "environmental_material": { + "Enums": [ + "Air vent [ENVO:03501208]", + "Banknote [ENVO:00003896]", + "Bed rail [ENVO:03501209]", + "Building Floor [ENVO:01000486]", + "Cloth [ENVO:02000058]", + "Control Panel [ENVO:03501210]", + "Door [ENVO:03501220]", + "Door Handle [ENVO:03501211]", + "Face Mask [OBI:0002787]", + "Face Shield [OBI:0002791]", + "Food [FOODON:00002403]", + "Food Packaging [FOODON:03490100]", + "Glass [ENVO:01000481]", + "Handrail [ENVO:03501212]", + "Hospital Gown [OBI:0002796]", + "Light Switch [ENVO:03501213]", + "Locker [ENVO:03501214]", + "N95 Mask [OBI:0002790]", + "Nurse Call Button [ENVO:03501215]", + "Paper [ENVO:03501256]", + "Particulate Matter [ENVO:01000060]", + "Plastic [ENVO:01000404]", + "PPE Gown [GENEPIO:0100025]", + "Sewage [ENVO:00002018]", + "Sink [ENVO:01000990]", + "Soil [ENVO:00001998]", + "Stainless Steel [ENVO:03501216]", + "Tissue Paper [ENVO:03501217]", + "Toilet Bowl [ENVO:03501218]", + "Water [ENVO:00002006]", + "Wastewater [ENVO:00002001]", + "Window [ENVO:03501219]", + "Wood [ENVO:00002040]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001223", + "type": "string", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "examples": ["Face Mask [OBI:0002787]"] + }, + "sequence_submitter_contact_email": { + "examples": ["RespLab@lab.ca"], + "ontology": "GENEPIO:0001165", + "type": "string", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "format": "email" + }, + "environmental_site": { + "Enums": [ + "Acute care facility [ENVO:03501135]", + "Animal house [ENVO:00003040]", + "Bathroom [ENVO:01000422]", + "Clinical assessment centre [ENVO:03501136]", + "Conference venue [ENVO:03501127]", + "Corridor [ENVO:03501121]", + "Daycare [ENVO:01000927]", + "Emergency room (ER) [ENVO:03501145]", + "Family practice clinic [ENVO:03501186]", + "Group home [ENVO:03501196]", + "Homeless shelter [ENVO:03501133]", + "Hospital [ENVO:00002173]", + "Intensive Care Unit (ICU) [ENVO:03501152]", + "Long Term Care Facility [ENVO:03501194]", + "Patient room [ENVO:03501180]", + "Prison [ENVO:03501204]", + "Production Facility [ENVO:01000536]", + "School [ENVO:03501130]", + "Sewage Plant [ENVO:00003043]", + "Subway train [ENVO:03501109]", + "Wet market [ENVO:03501198]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001232", + "type": "string", + "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", + "examples": ["Hospital [ENVO:00002173]"] + }, + "pre_existing_conditions_and_risk_factors": { + "Enums": [ + "Age 60+ [VO:0004925]", + "Anemia [HP:0001903]", + "Anorexia [HP:0002039]", + "Birthing labor [NCIT:C92743]", + "Bone marrow failure [NCIT:C80693]", + "Cancer [MONDO:0004992]", + "Breast cancer [MONDO:0007254]", + "Colorectal cancer [MONDO:0005575]", + "Hematologic malignancy [DOID:2531]", + "Lung cancer [MONDO:0008903]", + "Metastatic disease [MONDO:0024880]", + "Cancer treatment [NCIT:C16212]", + "Cancer surgery [NCIT:C157740]", + "Chemotherapy [NCIT:C15632]", + "Adjuvant chemotherapy [NCIT:C15360]", + "Cardiac disorder [NCIT:C3079]", + "Arrhythmia [HP:0011675]", + "Cardiac disease [MONDO:0005267]", + "Cardiomyopathy [HP:0001638]", + "Cardiac injury [GENEPIO:0100074]", + "Hypertension (high blood pressure) [HP:0000822]", + "Hypotension (low blood pressure) [HP:0002615]", + "Cesarean section [HP:0011410]", + "Chronic cough [GENEPIO:0100075]", + "Chronic gastrointestinal disease [GENEPIO:0100076]", + "Chronic lung disease [HP:0006528]", + "Corticosteroids [NCIT:C211]", + "Diabetes mellitus (diabetes) [HP:0000819]", + "Type I diabetes mellitus (T1D) [HP:0100651]", + "Type II diabetes mellitus (T2D) [HP:0005978]", + "Eczema [HP:0000964]", + "Electrolyte disturbance [HP:0003111]", + "Hypocalcemia [HP:0002901]", + "Hypokalemia [HP:0002900]", + "Hypomagnesemia [HP:0002917]", + "Encephalitis (brain inflammation) [HP:0002383]", + "Epilepsy [MONDO:0005027]", + "Hemodialysis [NCIT:C15248]", + "Hemoglobinopathy [MONDO:0044348]", + "Human immunodeficiency virus (HIV) [MONDO:0005109]", + "Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268]", + "HIV and antiretroviral therapy (ART) [NCIT:C16118]", + "Immunocompromised [NCIT:C14139]", + "Lupus [MONDO:0004670]", + "Inflammatory bowel disease (IBD) [MONDO:0005265]", + "Colitis [HP:0002583]", + "Ulcerative colitis [HP:0100279]", + "Crohn's disease [HP:0100280]", + "Renal disorder [NCIT:C3149]", + "Renal disease [MONDO:0005240]", + "Chronic renal disease [HP:0012622]", + "Renal failure [HP:0000083]", + "Liver disease [MONDO:0005154]", + "Chronic liver disease [NCIT:C113609]", + "Fatty liver disease (FLD) [HP:0001397]", + "Myalgia (muscle pain) [HP:0003326]", + "Myalgic encephalomyelitis (chronic fatigue syndrome) [MONDO:0005404]", + "Neurological disorder [MONDO:0005071]", + "Neuromuscular disorder [MONDO:0019056]", + "Obesity [HP:0001513]", + "Severe obesity [MONDO:0005139]", + "Respiratory disorder [MONDO:0005087]", + "Asthma [HP:0002099]", + "Chronic bronchitis [HP:0004469]", + "Chronic pulmonary disease [HP:0006528]", + "Chronic obstructive pulmonary disease [HP:0006510]", + "Emphysema [HP:0002097]", + "Lung disease [MONDO:0005275]", + "Chronic lung disease [HP:0006528]", + "Pulmonary fibrosis [HP:0002206]", + "Pneumonia [HP:0002090]", + "Respiratory failure [HP:0002878]", + "Adult respiratory distress syndrome [HP:0033677]", + "Newborn respiratory distress syndrome [MONDO:0009971]", + "Tuberculosis [MONDO:0018076]", + "Postpartum (\u22646 weeks) [GENEPIO:0100077]", + "Pregnancy [NCIT:C25742]", + "Rheumatic disease [MONDO:0005554]", + "Sickle cell disease [MONDO:0011382]", + "Substance use [NBO:0001845]", + "Alcohol abuse [MONDO:0002046]", + "Drug abuse [GENEPIO:0100078]", + "Injection drug abuse [GENEPIO:0100079]", + "Smoking [NBO:0015005]", + "Vaping [NCIT:C173621]", + "Tachypnea (accelerated respiratory rate) [HP:0002789]", + "Transplant [NCIT:C159659]", + "Cardiac transplant [GENEPIO:0100080]", + "Hematopoietic stem cell transplant (bone marrow transplant) [NCIT:C131759]", + "Kidney transplant [NCIT:C157332]", + "Liver transplant [GENEPIO:0100081]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001401", + "type": "string", + "description": "Patient pre-existing conditions and risk factors.\nPre-existing condition: A medical condition that existed prior to the current infection.\nRisk Factor: A variable associated with an increased risk of disease or infection.", + "examples": ["Asthma [HP:0002099]"] + }, + "first_dose_vaccination_date": { + "examples": ["26/02/2021"], + "ontology": "GENEPIO:0001407", + "type": "string", + "description": "The date the host was first vaccinated.", + "format": "date" + }, + "variant_designation": { + "Enums": [ + "Variant of Interest (VOI) [GENEPIO:0100082]", + "Variant of Concern (VOC) [GENEPIO:0100083]", + "Variant Under Monitoring (VUM) [GENEPIO:0100279]" + ], + "ontology": "GENEPIO:0001503", + "type": "string", + "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", + "examples": ["Variant of Concern (VOC) [GENEPIO:0100083]"] + }, + "sample_collected_in_quarantine": { + "Enums": [ + "Yes [NCIT:C49488]", + "No [NCIT:C49487]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0100277", + "type": "string", + "description": "Whether the sample was collected from an individual in quarantine.", + "examples": ["Yes [NCIT:C49488]"] + }, + "sample_collected_by": { + "ontology": "GENEPIO:0001153", + "type": "string", + "description": "The name of the agency that collected the original sample.", + "examples": ["Public Health Agency of Canada"] + }, + "sequencing_instrument": { + "Enums": [ + "Illumina sequencing instrument [GENEPIO:0100105]", + "Illumina Genome Analyzer [GENEPIO:0100106]", + "Illumina Genome Analyzer II [GENEPIO:0100107]", + "Illumina Genome Analyzer IIx [GENEPIO:0100108]", + "Illumina HiScanSQ [GENEPIO:0100109]", + "Illumina HiSeq [GENEPIO:0100110]", + "Illumina HiSeq X [GENEPIO:0100111]", + "Illumina HiSeq X Five [GENEPIO:0100112]", + "Illumina HiSeq X Ten [GENEPIO:0100113]", + "Illumina HiSeq 1000 [GENEPIO:0100114]", + "Illumina HiSeq 1500 [GENEPIO:0100115]", + "Illumina HiSeq 2000 [GENEPIO:0100116]", + "Illumina HiSeq 2500 [GENEPIO:0100117]", + "Illumina HiSeq 3000 [GENEPIO:0100118]", + "Illumina HiSeq 4000 [GENEPIO:0100119]", + "Illumina iSeq [GENEPIO:0100120]", + "Illumina iSeq 100 [GENEPIO:0100121]", + "Illumina NovaSeq [GENEPIO:0100122]", + "Illumina NovaSeq 6000 [GENEPIO:0100123]", + "Illumina MiniSeq [GENEPIO:0100124]", + "Illumina MiSeq [GENEPIO:0100125]", + "Illumina NextSeq [GENEPIO:0100126]", + "Illumina NextSeq 500 [GENEPIO:0100127]", + "Illumina NextSeq 550 [GENEPIO:0100128]", + "Illumina NextSeq 2000 [GENEPIO:0100129]", + "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", + "PacBio RS [GENEPIO:0100131]", + "PacBio RS II [GENEPIO:0100132]", + "PacBio Sequel [GENEPIO:0100133]", + "PacBio Sequel II [GENEPIO:0100134]", + "Ion Torrent sequencing instrument [GENEPIO:0100135]", + "Ion Torrent PGM [GENEPIO:0100136]", + "Ion Torrent Proton [GENEPIO:0100137]", + "Ion Torrent S5 XL [GENEPIO:0100138]", + "Ion Torrent S5 [GENEPIO:0100139]", + "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", + "Oxford Nanopore GridION [GENEPIO:0100141]", + "Oxford Nanopore MinION [GENEPIO:0100142]", + "Oxford Nanopore PromethION [GENEPIO:0100143]", + "BGI Genomics sequencing instrument [GENEPIO:0100144]", + "BGI SEQ-500 [GENEPIO:0100145]", + "MGI sequencing instrument [GENEPIO:0100146]", + "MGI DNBSEQ-T7 [GENEPIO:0100147]", + "MGI DNBSEQ-G400 [GENEPIO:0100148]", + "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", + "MGI DNBSEQ-G50 [GENEPIO:0100150]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001452", + "type": "string", + "description": "The model of the sequencing instrument used.", + "examples": ["Oxford Nanopore MinION [GENEPIO:0100142]"] + }, + "host_health_status_details": { + "Enums": [ + "Hospitalized [NCIT:C25179]", + "Hospitalized (Non-ICU) [GENEPIO:0100045]", + "Hospitalized (ICU) [GENEPIO:0100046]", + "Mechanical Ventilation [NCIT:C70909]", + "Medically Isolated [GENEPIO:0100047]", + "Medically Isolated (Negative Pressure) [GENEPIO:0100048]", + "Self-quarantining [NCIT:C173768]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001389", + "type": "string", + "description": "Further details pertaining to the health or disease status of the host at time of collection.", + "examples": ["Hospitalized (ICU) [GENEPIO:0100046]"] + }, + "isolate": { + "ontology": "GENEPIO:0001644", + "type": "string", + "description": "Identifier of the specific isolate.", + "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"] + }, + "host_health_state": { + "Enums": [ + "Asymptomatic [NCIT:C3833]", + "Deceased [NCIT:C28554]", + "Healthy [NCIT:C115935]", + "Recovered [NCIT:C49498]", + "Symptomatic [NCIT:C25269]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001388", + "type": "string", + "description": "Health status of the host at the time of sample collection.", + "examples": ["Asymptomatic [NCIT:C3833]"] + }, + "signs_and_symptoms": { + "Enums": [ + "Abnormal lung auscultation [HP:0030829]", + "Ageusia (complete loss of taste) [HP:0041051]", + "Parageusia (distorted sense of taste) [HP:0031249]", + "Hypogeusia (reduced sense of taste) [HP:0000224]", + "Abnormality of the sense of smell [HP:0004408]", + "Anosmia (lost sense of smell) [HP:0000458]", + "Hyposmia (reduced sense of smell) [HP:0004409]", + "Acute Respiratory Distress Syndrome [HP:0033677]", + "Altered mental status [HP:0011446]", + "Arrhythmia [HP:0011675]", + "Cognitive impairment [HP:0100543]", + "Coma [HP:0001259]", + "Confusion [HP:0001289]", + "Delirium (sudden severe confusion) [HP:0031258]", + "Inability to arouse (inability to stay awake) [GENEPIO:0100061]", + "Irritability [HP:0000737]", + "Loss of speech [HP:0002371]", + "Asthenia (generalized weakness) [HP:0025406]", + "Chest tightness or pressure [HP:0031352]", + "Rigors (fever shakes) [HP:0025145]", + "Chills (sudden cold sensation) [HP:0025143]", + "Conjunctival injection [HP:0030953]", + "Conjunctivitis (pink eye) [HP:0000509]", + "Coryza [MP:0001867]", + "Cough [HP:0012735]", + "Nonproductive cough (dry cough) [HP:0031246]", + "Productive cough (wet cough) [HP:0031245]", + "Cyanosis (blueish skin discolouration) [HP:0000961]", + "Acrocyanosis [HP:0001063]", + "Circumoral cyanosis (bluish around mouth) [HP:0032556]", + "Cyanotic face (bluish face) [GENEPIO:0100062]", + "Central Cyanosis [GENEPIO:0100063]", + "Cyanotic lips (bluish lips) [GENEPIO:0100064]", + "Peripheral Cyanosis [GENEPIO:0100065]", + "Dyspnea (breathing difficulty) [HP:0002094]", + "Diarrhea (watery stool) [HP:0002014]", + "Dry gangrene [MP:0031127]", + "Encephalitis (brain inflammation) [HP:0002383]", + "Encephalopathy [HP:0001298]", + "Fatigue (tiredness) [HP:0012378]", + "Fever [HP:0001945]", + "Fever (>=38\u00baC) [GENEPIO:0100066]", + "Glossitis (inflammation of the tongue) [HP:0000206]", + "Ground Glass Opacities (GGO) [GENEPIO:0100067]", + "Headache [HP:0002315]", + "Hemoptysis (coughing up blood) [HP:0002105]", + "Hypocapnia [HP:0012417]", + "Hypotension (low blood pressure) [HP:0002615]", + "Hypoxemia (low blood oxygen) [HP:0012418]", + "Silent hypoxemia [GENEPIO:0100068]", + "Internal hemorrhage (internal bleeding) [HP:0011029]", + "Loss of Fine Movements [NCIT:C121416]", + "Low appetite [HP:0004396]", + "Malaise (general discomfort/unease) [HP:0033834]", + "Meningismus/nuchal rigidity [HP:0031179]", + "Muscle weakness [HP:0001324]", + "Nasal obstruction (stuffy nose) [HP:0001742]", + "Nausea [HP:0002018]", + "Nose bleed [HP:0000421]", + "Otitis [GENEPIO:0100069]", + "Pain [HP:0012531]", + "Abdominal pain [HP:0002027]", + "Arthralgia (painful joints) [HP:0002829]", + "Chest pain [HP:0100749]", + "Pleuritic chest pain [HP:0033771]", + "Myalgia (muscle pain) [HP:0003326]", + "Pharyngitis (sore throat) [HP:0025439]", + "Pharyngeal exudate [GENEPIO:0100070]", + "Pleural effusion [HP:0002202]", + "Pneumonia [HP:0002090]", + "Prostration [GENEPIO:0100071]", + "Pseudo-chilblains [HP:0033696]", + "Pseudo-chilblains on fingers (covid fingers) [GENEPIO:0100072]", + "Pseudo-chilblains on toes (covid toes) [GENEPIO:0100073]", + "Rash [HP:0000988]", + "Rhinorrhea (runny nose) [HP:0031417]", + "Seizure [HP:0001250]", + "Motor seizure [HP:0020219]", + "Shivering (involuntary muscle twitching) [HP:0025144]", + "Slurred speech [HP:0001350]", + "Sneezing [HP:0025095]", + "Sputum Production [HP:0033709]", + "Stroke [HP:0001297]", + "Swollen Lymph Nodes [HP:0002716]", + "Tachypnea (accelerated respiratory rate) [HP:0002789]", + "Vertigo (dizziness) [HP:0002321]", + "Vomiting (throwing up) [HP:0002013]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001400", + "type": "string", + "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.", + "examples": [ + "Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145]" + ] + }, + "dehosting_method": { + "ontology": "GENEPIO:0001459", + "type": "string", + "description": "The method used to remove host reads from the pathogen sequence.", + "examples": ["Nanostripper"] + }, + "amplicon_pcr_primer_scheme": { + "ontology": "GENEPIO:0001456", + "type": "string", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "examples": [ + "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv" + ] + }, + "vaccine_name": { + "ontology": "GENEPIO:0001405", + "type": "string", + "description": "The name of the vaccine(s) administered.", + "examples": ["BNT162b2, Pfizer-BioNTech"] + }, + "data_abstraction_details": { + "ontology": "GENEPIO:0100278", + "type": "string", + "description": "A description of how any data elements were altered to preserve patient privacy.", + "examples": [ + "Jitter added to publicly shared collection dates to prevent re-identifiability." + ] + }, + "consensus_sequence_filename": { + "ontology": "GENEPIO:0001461", + "type": "string", + "description": "The name of the consensus sequence file.", + "examples": ["ncov123assembly.fasta"] + }, + "purpose_of_sequencing_details": { + "Enums": [ + "Screened for S gene target failure (S dropout)", + "Screened for mink variants", + "Screened for B.1.1.7 variant", + "Screened for B.1.135 variant", + "Screened for P.1 variant", + "Screened due to travel history", + "Screened due to close contact with infected individual", + "Assessing public health control measures", + "Determining early introductions and spread", + "Investigating airline-related exposures", + "Investigating temporary foreign worker", + "Investigating remote regions", + "Investigating health care workers", + "Investigating schools/universities", + "Investigating reinfection" + ], + "ontology": "GENEPIO:0001446", + "type": "string", + "description": "The description of why the sample was sequenced providing specific details.", + "examples": ["Screened for S gene target failure (S dropout)"] + }, + "sequence_submitted_by": { + "ontology": "GENEPIO:0001159", + "type": "string", + "description": "The name of the agency that generated the sequence.", + "examples": ["Centers for Disease Control and Prevention"] + }, + "sequencing_protocol_name": { + "ontology": "GENEPIO:0001453", + "type": "string", + "description": "The name and version number of the sequencing protocol used.", + "examples": ["1D_DNA_MinION, ARTIC Network Protocol V3"] + }, + "prior_sars_cov_2_infection_isolate": { + "ontology": "GENEPIO:0001436", + "type": "string", + "description": "The identifier of the isolate found in the prior SARS-CoV-2 infection.", + "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"] + }, + "organism": { + "Enums": [ + "Coronaviridae [NCBITaxon:11118]", + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001191", + "type": "string", + "description": "Taxonomic name of the organism.", + "examples": [ + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]" + ] + }, + "purpose_of_sampling": { + "Enums": [ + "Cluster/Outbreak Investigation [GENEPIO:0100001]", + "Diagnostic Testing [GENEPIO:0100002]", + "Research [GENEPIO:0100003]", + "Protocol Testing [GENEPIO:0100024]", + "Surveillance [GENEPIO:0100004]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001198", + "type": "string", + "description": "The reason that the sample was collected.", + "examples": ["Diagnostic Testing [GENEPIO:0100002]"] + } + } +} diff --git a/schema/phage_plus_V0.json b/schema/phage_plus_V0.json index f81543d2..8e6b5528 100644 --- a/schema/phage_plus_V0.json +++ b/schema/phage_plus_V0.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft/2019-09/schema#", + "$schema": "http://json-schema.org/draft/2020-12/schema", "required": [ "sample_name", "collecting_institution", @@ -23,19 +23,19 @@ "ontology": "GENEPIO:0001156", "type": "string", "description": "The user-defined name for the sample.", - "clasification":"Database Identifiers", + "clasification":"Database Identifiers" }, "collecting_institution": { "examples": ["Public Health Agency of Canada"], "ontology": "GENEPIO:0001156", "type": "string", - "description": "The name of the agency that collected the original sample.", + "description": "The name of the agency that collected the original sample." }, "submitting_institution": { "examples": ["Centers for Disease Control and Prevention"], "ontology": "GENEPIO:0001159", "type": "string", - "description": "The name of the agency that generated the sequence.", + "description": "The name of the agency that generated the sequence." }, "sample_collection_date": { "examples": ["3/19/2020"], @@ -332,7 +332,7 @@ "examples": ["Western Cape"], "ontology": "GENEPIO:0001185", "type": "string", - "description": "The state/province/territory of origin of the sample.", + "description": "The state/province/territory of origin of the sample." }, "organism": { "Enums": [ @@ -356,7 +356,7 @@ "ontology": "GENEPIO:0001644", "type": "string", "description": "Identifier of the specific isolate.", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "host_scientific_name": { "Enums": [ @@ -464,102 +464,102 @@ "examples": ["MinIon"], "ontology": "GENEPIO:0001156", "type": "string", - "description": "The model of the sequencing instrument used.", + "description": "The model of the sequencing instrument used." }, "consensus_sequence_software_name": { "examples": ["Ivar"], "ontology": "GENEPIO:0001463", "type": "string", - "description": "The name of software used to generate the consensus sequence.", + "description": "The name of software used to generate the consensus sequence." }, "consensus_sequence_software_version": { "examples": ["1.3"], "ontology": "GENEPIO:0001469", "type": "string", - "description": "The version of the software used to generate the consensus sequence.", + "description": "The version of the software used to generate the consensus sequence." }, "submitting_lab_sequence_id": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", - "description": "Sample ID given by the submitting laboratory", + "description": "Sample ID given by the submitting laboratory" }, "bioproject_umbrella_accession_ENA": { "examples": ["PRJNA623807"], "ontology": "GENEPIO:0001133", "type": "string", "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", - "clasification":"Database Identifiers", + "clasification":"Database Identifiers" }, "bioproject_accession_ENA": { "examples": ["PRJNA12345"], "ontology": "GENEPIO:0001156", "type": "string", "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", - "clasification":"Database Identifiers", + "clasification":"Database Identifiers" }, "biosample_accession_ENA": { "examples": ["SAMN14180202"], "ontology": "GENEPIO:0001139", "type": "string", "description": "The identifier assigned to a BioSample in INSDC archives.", - "clasification":"Database Identifiers", + "clasification":"Database Identifiers" }, "sra_accession": { "examples": ["SRR11177792"], "ontology": "GENEPIO:0001142", "type": "string", "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "clasification":"Database Identifiers", + "clasification":"Database Identifiers" }, "genBank/ENA/DDBJ_accession": { "examples": ["MN908947.3"], "ontology": "GENEPIO:0001156", "type": "string", "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", - "clasification":"Database Identifiers", + "clasification":"Database Identifiers" }, "gisaid_accession": { "examples": ["EPI_ISL_123456"], "ontology": "GENEPIO:0001147", "type": "string", "description": "The GISAID accession number assigned to the sequence.", - "clasification":"Database Identifiers", + "clasification":"Database Identifiers" }, "virus_name": { "examples": ["hCoV-19/Canada/prov_rona_99/2020"], "ontology": "GENEPIO:0001156", "type": "string", "description": "The user-defined GISAID virus name assigned to the sequence.", - "clasification":"Database Identifiers", + "clasification":"Database Identifiers" }, "collecting_institution_email": { "examples": ["johnnyblogs@lab.ca"], "ontology": "GENEPIO:0001156", "type": "string", "description": "The email address of the contact responsible for follow-up regarding the sample.", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "collecting_institution_address": { "examples": ["655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada"], "ontology": "GENEPIO:0001158", "type": "string", "description": "The mailing address of the agency submitting the sample.", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "submitting_institution_email": { "examples": ["RespLab@lab.ca"], "ontology": "GENEPIO:0001165", "type": "string", "description": "The email address of the contact responsible for follow-up regarding the sequence.", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "submitting_institution_address": { "examples": ["123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"], "ontology": "GENEPIO:0001156", "type": "string", "description": "The mailing address of the agency submitting the sequence.", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "sample_received_date": { "examples": ["3/21/2020"], @@ -567,7 +567,7 @@ "type": "string", "description": "The date on which the sample was received.", "format":"date", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "shipping_date": { "examples": ["3/20/2020"], @@ -575,7 +575,7 @@ "type": "string", "description": "The date on which the sample was sent.", "format":"date", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "results_emission_date": { "examples": ["3/23/2020"], @@ -583,35 +583,35 @@ "type": "string", "description": "The date on which the results were emitted.", "format":"date", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "geo_loc_region": { "examples": ["Derbyshire"], "ontology": "GENEPIO:0100280", "type": "string", "description": "The county/region of origin of the sample.", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "geo_loc_city": { "examples": ["Vancouver"], "ontology": "GENEPIO:0001189", "type": "string", "description": "The city of origin of the sample.", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "geo_loc_latitude": { "examples": ["38.98 N"], "ontology": "GENEPIO:0001156", "type": "string", "description": "The latitude coordinates of the geographical location of sample collection.", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "geo_loc_longitude": { "examples": ["77.11 W"], "ontology": "OBI:0001621", "type": "string", "description": "The longitude coordinates of the geographical location of sample collection.", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "anatomical_material": { "Enums": [ @@ -842,7 +842,7 @@ "ontology": "GENEPIO:0001243", "type": "string", "description": "The name and version of a particular protocol used for sampling.", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "specimen_processing": { "Enums": [ @@ -894,14 +894,14 @@ "ontology": "GENEPIO:0001261", "type": "string", "description": "Number of passages.", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "passage_method": { "examples": ["AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain."], "ontology": "GENEPIO:0001264", "type": "string", "description": "Description of how organism was passaged.", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "biomaterial_extracted": { "Enums": [ @@ -925,28 +925,28 @@ "ontology": "GENEPIO:0001156", "type": "string", "description": "The NCBITaxon identifier for the organism being sequenced.", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "scientific_name": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "The taxonomic name of the organism.", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "common_name": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "The common name of the organism.", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "center_name": { "examples": [" KAROLINSKA INSITUTET"], "ontology": "GENEPIO:0001156", "type": "string", "description": "The name of the institution", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "virus_id": { @@ -954,7 +954,7 @@ "ontology": "GENEPIO:0001156", "type": "string", "description": "The user-defined name for the sample.", - "clasification":"Database Identifiers", + "clasification":"Database Identifiers" }, "host_common_name": { "Enums": [ @@ -987,14 +987,14 @@ "ontology": "GENEPIO:0001156", "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", + "clasification":"Host information" }, "additional_host_information": { "examples": ["e.g. Patient infected while traveling in …."], "ontology": "GENEPIO:0001156", "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", + "clasification":"Host information" }, "purpose_of_sequencing": { "Enums": [ @@ -1062,56 +1062,56 @@ "type": "string", "description": "The date the sample was sequenced.", "format":"date", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "rna_extraction_Protocol": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "library_kit": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "library_id": { "examples": ["XYZ_123345"], "ontology": "GENEPIO:0001448", "type": "string", "description": "The user-specified identifier for the library prepared for sequencing.", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "enrichment_protocol": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "if_enrichment_protocol_is_other_specify": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "amplicon protocol": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "if_amplicon_protocol_if_other_especify": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "amplicon_version": { @@ -1119,14 +1119,14 @@ "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "amplicon_size": { "examples": ["300bp"], "ontology": "GENEPIO:0001449", "type": "string", "description": "The length of the amplicon generated by PCR amplification.", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "was_phix_used?": { @@ -1134,7 +1134,7 @@ "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "number_of_samples_in_run": { @@ -1142,7 +1142,7 @@ "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "flowcell_kit": { @@ -1150,7 +1150,7 @@ "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "runID": { @@ -1158,7 +1158,7 @@ "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "sequencing_platforms": { @@ -1166,7 +1166,7 @@ "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "library_preparation_kit": { @@ -1174,7 +1174,7 @@ "ontology": "GENEPIO:0001450", "type": "string", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "flow_cell_barcode": { @@ -1182,77 +1182,77 @@ "ontology": "GENEPIO:0001451", "type": "string", "description": "The barcode of the flow cell used for sequencing.", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "sequencing_protocol_name": { "examples": ["1D_DNA_MinION, ARTIC Network Protocol V3"], "ontology": "GENEPIO:0001453", "type": "string", "description": "The name and version number of the sequencing protocol used.", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "sequencing_protocol": { "examples": ["Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits."], "ontology": "GENEPIO:0001454", "type": "string", "description": "The protocol used to generate the sequence.", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "sequencing_kit_number": { "examples": ["AB456XYZ789"], "ontology": "GENEPIO:0001455", "type": "string", "description": "The manufacturer's kit number.", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "amplicon_pcr_primer_scheme": { "examples": ["https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv"], "ontology": "GENEPIO:0001456", "type": "string", "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "library_source": { "examples": ["METAGENOMIC"], "ontology": "GENEPIO:0001156", "type": "string", "description": "Molecule type used to make the library.", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "library_selection": { "examples": ["RANDOM PCR"], "ontology": "GENEPIO:0001156", "type": "string", "description": "Library capture method.", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "library_strategy": { "examples": ["WGS"], "ontology": "GENEPIO:0001156", "type": "string", "description": "Overall sequencing strategy or approach.", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "library_layout": { "examples": ["PAIRED"], "ontology": "GENEPIO:0001156", "type": "string", "description": "Single or paired.", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "library_name": { "examples": ["P17157_1007"], "ontology": "GENEPIO:0001156", "type": "string", "description": "Name of the used library", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "nominal_length ": { "examples": ["350"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "raw_sequence_data_processing_method": { @@ -1260,287 +1260,287 @@ "ontology": "GENEPIO:0001458", "type": "string", "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "dehosting_method": { "examples": ["Nanostripper"], "ontology": "GENEPIO:0001459", "type": "string", "description": "The method used to remove host reads from the pathogen sequence.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "assembly": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "if_assembly_other": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "assembly_params": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "variant_Calling": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "if_variant_Calling_other": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "variant_Calling_params": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "consensus_sequence_filepath": { "examples": ["/User/Documents/RespLab/Data/ncov123assembly.fasta"], "ontology": "GENEPIO:0001462", "type": "string", "description": "The filepath of the consesnsus sequence file.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "consensus_sequence_software_name": { "examples": ["Ivar"], "ontology": "GENEPIO:0001156", "type": "string", "description": "The name of software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "if_consensus_other": { "examples": ["1.3"], "ontology": "GENEPIO:0001156", "type": "string", "description": "The version of the software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "consensus_sequence_software_version": { "examples": ["1.3"], "ontology": "GENEPIO:0001156", "type": "string", "description": "The version of the software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "consensus_criteria": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "quality_control_metrics": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "breadth_of_coverage_value": { "examples": ["95%"], "ontology": "GENEPIO:0001472", "type": "string", "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "depth_of_coverage_value": { "examples": ["400x"], "ontology": "GENEPIO:0001474", "type": "string", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "depth_of_coverage_threshold": { "examples": ["100x"], "ontology": "GENEPIO:0001475", "type": "string", "description": "The threshold used as a cut-off for the depth of coverage.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "sequence_file_R1_fastq": { "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], "ontology": "GENEPIO:0001476", "type": "string", "description": "The user-specified filename of the r1 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "sequence_file_R2_fastq": { "examples": ["ABC123_S1_L001_R2_001.fastq.gz"], "ontology": "GENEPIO:0001156", "type": "string", "description": "The user-specified filename of the r2 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "r1_fastq_filepath": { "examples": ["/User/Documents/RespLab/Data/"], "ontology": "GENEPIO:0001478", "type": "string", "description": "The filepath of the r1 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "r2_fastq_filepath": { "examples": ["/User/Documents/RespLab/Data/"], "ontology": "GENEPIO:0001479", "type": "string", "description": "The filepath of the r2 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "fast5_filename": { "examples": ["batch1a_sequences.fast5"], "ontology": "GENEPIO:0001480", "type": "string", "description": "The user-specified filename of the FAST5 file.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "fast5_filepath": { "examples": ["/User/Documents/RespLab/Data/"], "ontology": "GENEPIO:0001481", "type": "string", "description": "The filepath of the FAST5 file.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "number_of_base_pairs_sequenced": { "examples": ["387566"], "ontology": "GENEPIO:0001482", "type": "string", "description": "The number of total base pairs generated by the sequencing process.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "consensus_genome_length": { "examples": ["38677"], "ontology": "GENEPIO:0001483", "type": "string", "description": "Size of the assembled genome described as the number of base pairs.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "ns_per_100_kbp": { "examples": ["300"], "ontology": "GENEPIO:0001484", "type": "string", "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "reference_genome_accession": { "examples": ["NC_045512.2"], "ontology": "GENEPIO:0001485", "type": "string", "description": "A persistent, unique identifier of a genome database entry.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "bioinformatics_protocol": { "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], "ontology": "GENEPIO:0001489", "type": "string", "description": "The name of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "if_bioinformatic_protocol_is_other_specify": { "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], "ontology": "GENEPIO:0001156", "type": "string", "description": "The name of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "bioinformatic_protocol_version": { "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], "ontology": "GENEPIO:0001156", "type": "string", "description": "The version number of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "commercial/open-source/both": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "preprocessing": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "if_preprocessing_other": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "preprocessing_params": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", + "clasification":"Bioinformatics and QC metrics" }, "mapping": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Lineage and Variant information", + "clasification":"Lineage and Variant information" }, "if_mapping_other": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Lineage and Variant information", + "clasification":"Lineage and Variant information" }, "Mapping_params": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Lineage and Variant information", + "clasification":"Lineage and Variant information" }, "lineage/clade_name": { "examples": ["B.1.1.7"], "ontology": "GENEPIO:0001500", "type": "string", "description": "The name of the lineage or clade.", - "clasification":"Lineage and Variant information", + "clasification":"Lineage and Variant information" }, "lineage/clade_analysis_software_name": { "examples": ["Pangolin"], "ontology": "GENEPIO:0001156", "type": "string", "description": "The name of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information", + "clasification":"Lineage and Variant information" }, "if_lineage_identification_other": { "examples": ["Other than Pangolin"], "ontology": "GENEPIO:0001156", "type": "string", "description": "The name of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information", + "clasification":"Lineage and Variant information" }, "lineage/clade_analysis_software_version": { "examples": ["2.1.10"], "ontology":"GENEPIO:0001502", "type": "string", "description": "The version of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information", + "clasification":"Lineage and Variant information" }, "variant_designation": { "Enums": [ @@ -1558,7 +1558,7 @@ "ontology": "GENEPIO:0001504", "type": "string", "description": "The evidence used to make the variant determination.", - "clasification":"Lineage and Variant information", + "clasification":"Lineage and Variant information" }, "gene_name_1": { "Enums": [ @@ -1611,91 +1611,91 @@ "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", + "clasification":"Pathogen diagnostic testing" }, "%qc_filtered": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", + "clasification":"Pathogen diagnostic testing" }, "%reads_host": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", + "clasification":"Pathogen diagnostic testing" }, "%reads_virus": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", + "clasification":"Pathogen diagnostic testing" }, "%unmapped": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", + "clasification":"Pathogen diagnostic testing" }, "% genome _greater_10x": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", + "clasification":"Pathogen diagnostic testing" }, "mean_depth_of_coverage_value": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", + "clasification":"Pathogen diagnostic testing" }, "%Ns": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", + "clasification":"Pathogen diagnostic testing" }, "Number_of_variants_(AF_greater_75%)": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", + "clasification":"Pathogen diagnostic testing" }, "Numer_of_variants_with_effect": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", + "clasification":"Pathogen diagnostic testing" }, "reference_genome_accession": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", + "clasification":"Pathogen diagnostic testing" }, "diagnostic_pcr_protocol_1": { "examples": ["PCREGene 2.0"], "ontology": "GENEPIO:0001508", "type": "string", "description": "The name and version number of the protocol used for diagnostic marker amplification.", - "clasification":"Pathogen diagnostic testing", + "clasification":"Pathogen diagnostic testing" }, "diagnostic_pcr_Ct_value_1": { "examples": ["21"], "ontology": "GENEPIO:0001509", "type": "string", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "clasification":"Pathogen diagnostic testing", + "clasification":"Pathogen diagnostic testing" }, "gene_name_2": { "Enums": [ @@ -1748,105 +1748,105 @@ "ontology": "GENEPIO:0001511", "type": "string", "description": "The name and version number of the protocol used for diagnostic marker amplification.", - "clasification":"Pathogen diagnostic testing", + "clasification":"Pathogen diagnostic testing" }, "diagnostic_pcr_Ct_value_2": { "examples": ["36"], "ontology": "GENEPIO:0001512", "type": "string", "description": "The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "clasification":"Pathogen diagnostic testing", + "clasification":"Pathogen diagnostic testing" }, "analysis_author": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Contributor Acknowledgement", + "clasification":"Contributor Acknowledgement" }, "author_submitter": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Contributor Acknowledgement", + "clasification":"Contributor Acknowledgement" }, "submitter": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"enter your GISAID-Username", + "clasification":"enter your GISAID-Username" }, "authors": { "examples": [""], "ontology": "GENEPIO:0001517", "type": "string", "description": "", - "clasification":"Contributor Acknowledgement", + "clasification":"Contributor Acknowledgement" }, "tax_id": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "scientific_name": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "common_name": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sample collection and processing", + "clasification":"Sample collection and processing" }, "library_source": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "library_selection": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "library_strategy": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "library_layout": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "library_name": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "nominal_length": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Sequencing", + "clasification":"Sequencing" }, "analysis_accession": { "examples": [""], @@ -1874,63 +1874,63 @@ "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "secondary_sample_accession": { "examples": ["e.g ERS4858671"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "experiment_accession": { "examples": ["e.g ERX4331406"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "run_accession": { "examples": ["e.g ERX4331406"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "submission_accession": { "examples": ["e.g ERA2794974"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "read_count": { "examples": ["e.g 837055"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "read_length": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "base_count": { "examples": ["e.g 503907110"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "first_public": { "examples": ["e.g 2020-08-07"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "last_updated": { "examples": ["e.g 2020-07-29"], @@ -1938,175 +1938,175 @@ "type": "string", "description": "", "clasification":"Submission ENA", - "format":"date", + "format":"date" }, "experiment_title": { "examples": ["e.g Illumina MiSeq paired end sequencing"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "study_title": { "examples": ["e.g SARS-CoV-2 genomes from late April in Stockholm"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "study_alias": { "examples": ["e.g Sweden"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "experiment_alias": { "examples": ["e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "run_alias": { "examples": ["e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "fastq_bytes": { "examples": ["e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "fastq_md5": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "fastq_ftp": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "fastq_aspera": { "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "fastq_galaxy": { "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "submitted_bytes": { "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "submitted_md5": { "examples": ["e.g 139853010;166270048"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "submitted_ftp": { "examples": ["e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "submitted_aspera": { "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "submitted_galaxy": { "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "submitted_format": { "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "sra_bytes": { "examples": ["e.g FASTQ;FASTQ"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "sra_md5": { "examples": ["e.g 260236789"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "sra_ftp": { "examples": ["e.g 2cf0d467d6dc4ae0a5473774d54c059c"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "sra_aspera": { "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "sra_galaxy": { "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "broker_name": { "examples": ["P17157_1007"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "nominal_sdev": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "first_created": { "examples": ["e.g 2020-08-07"], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Submission ENA", + "clasification":"Submission ENA" }, "type": { "examples": ["betacoronavirus"], @@ -2114,10 +2114,6 @@ "type": "string", "description": "default must remain 'betacoronavirus'", "clasification":"Database Identifiers" - }, - - - - + } } } From 0aca41b30bad2fc7c69b7b735aa09e11a41b1bc0 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 27 Jan 2022 23:14:08 +0100 Subject: [PATCH 0002/1454] Pre-defining classes to use --- relecov-tools/validation_jsons.py | 35 +++++++++++++++++++++++++++---- 1 file changed, 31 insertions(+), 4 deletions(-) diff --git a/relecov-tools/validation_jsons.py b/relecov-tools/validation_jsons.py index ddbdd5de..32e3a2a1 100644 --- a/relecov-tools/validation_jsons.py +++ b/relecov-tools/validation_jsons.py @@ -2,6 +2,25 @@ from jsonschema import validate from jsonschema import Draft202012Validator import json +import pandas as pd + +class RelecovSchema : + def __init__ (self, schema): + self.schema = schema + + + +class PhagePlus : + def __init__ (self,data, json_schema): + self.data = data + self.schema = json_schema + + + def convert_json(schema): + pass + + def get_data(self, field): + return self.data[field]) data = {"sample_name":'s1', "collecting_institution" :'inst2', "submitting_institution":'sub', @@ -20,15 +39,23 @@ schema_file = open('/home/lchapado/Projects/Proyecto_ERA/relecov-tools/schema/phage_plus_V0.json') -fage_plus_schema = json.load(schema_file) +json_phage_plus_schema = json.load(schema_file) try: - Draft202012Validator.check_schema(fage_plus_schema) + Draft202012Validator.check_schema(json_phage_plus_schema) except: print('Invalid schema') exit(1) +phage_plus_schema = RelecovSchema(json_phage_plus_schema) try: - validate(instance=data,schema=fage_plus_schema) + validate(instance=data,schema=json_phage_plus_schema) except: print('Invalid input data') - exit() + exit(1) + +sample_list = [] +df = pd.read_excel('sample.xlsx') +for idx, row in df.iterrows(): + sample_list.append(PhagePlus(row.to_dict(),phage_plus_schema)) + + print('Completed') From de985f1cf65d1b4756b70099d649404465fe8fd0 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 28 Jan 2022 13:14:43 +0100 Subject: [PATCH 0003/1454] update with dummy methods --- relecov-tools/validation_jsons.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/relecov-tools/validation_jsons.py b/relecov-tools/validation_jsons.py index 32e3a2a1..e84cbe53 100644 --- a/relecov-tools/validation_jsons.py +++ b/relecov-tools/validation_jsons.py @@ -6,8 +6,13 @@ class RelecovSchema : def __init__ (self, schema): - self.schema = schema + self.schema = json.load(schema) + def get_gontology(self,geontology): + for key, value in schema['properties'].items(): + if value['ontology'] == geontology : + return value + return None class PhagePlus : From f40d441e34fa9c038480ba25568a93296ce455ee Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 31 Jan 2022 17:42:56 +0100 Subject: [PATCH 0004/1454] test validation --- docs/Metadata LAB.xlsx | Bin 0 -> 49945 bytes relecov-tools/validation_jsons.py | 49 ++++++++++++++++++++++++------ 2 files changed, 39 insertions(+), 10 deletions(-) create mode 100644 docs/Metadata LAB.xlsx diff --git a/docs/Metadata LAB.xlsx b/docs/Metadata LAB.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..4bf546658af57b0d6e77effecd7f064fec68c0cb GIT binary patch literal 49945 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zyL`YEjyjP?r|ptCaPd<}bsRO{GXz}x{Dt}>*1&yUExX&jUK9AR5I${jICHdTdTjJj zN>$aVbAQq@s=B;0#oj>p_+%%Qz;l$wLfpsQWHWT_BTex5!UxqRseK$!icjCoW$R64 zPx6J4pd{C=lLDcxgT_o7;FtZmg)Pq0R8La_X9vEcxSZDlwc=fEa8u!!$5CcTBVL3! z#khs#m`AMpBybN&DbpmRV^MT0Ql1Iw(>p%C*={=TT^$Xx;&GlT_45%I0Hy4dPYWY< zN?dkdxC@vQt=VC2!v?H3XHX~mU~WXM-w~uF%Z{*prLA7C`kFaqT$Eo+9LQ~~>@a-qoXsI<-(yD2-dw((A)fd22`HS7IJ@)3vk*1+2xP%{x~Wq= zm>e0k)ik%z*0#A|Yg=s-qYy`>z*PHwJ&sDA|DgbMt7+)SLR4s6L@b;sbY!S^7v!SU z74=96p&DviV|P5axdb{gqY+TpIn*ft3BlSG2g6i&mhTVC6$x*l_l6qV`#RMbsEe=hTFItVZ*aIuw++Qnw?hv z+I0#BiCQgMZhU%o`oqYaW1N81QR$Z+Bve!Plsl3yg1E_VLBWbQ7Bq+BQ#Mb78W}qj zjqLbF%obSWQZZ>MVCmPHIcU<5j(RKrVP7)V5(aLep`o14ZVf}nAVDKRyKvzG z+WJe7it(41rBlGWB1C|xA5+GJt6k8x4*4cU;$j*Bbz@ zQvK}LKpMR&$CRRT0LpC@Q& zXLqyx`Uk=LIj^0mk&(R}@HSWAi~H=}w!f7!^1pVw;#L^Y<<3AOP)(5$$7+fRHd6|( zA7{G*bjxRNbW?W7U^T@Qn<*cje|)nM=oTs9eZHt}xuuEK6f Date: Tue, 1 Feb 2022 11:45:16 +0100 Subject: [PATCH 0005/1454] added ena schema and test script --- schema/ena_v01.json | 1070 +++++++++++++++++++++++++++++++++++++++++++ test/mapping.py | 26 ++ 2 files changed, 1096 insertions(+) create mode 100644 schema/ena_v01.json create mode 100644 test/mapping.py diff --git a/schema/ena_v01.json b/schema/ena_v01.json new file mode 100644 index 00000000..3696df41 --- /dev/null +++ b/schema/ena_v01.json @@ -0,0 +1,1070 @@ +{ + "$schema": "http://json-schema.org/draft/2019-09/schema#", + "required": [ + "sample_name", + "collecting_institution", + "geographic_location_(country_and/or_sea)", + "isolate", + "host_scientific_name", + "host_common_name", + "host_health_state", + "host_sex", + "host_subject_id", + "instrument_model", + "file_name", + "sample_name", + "tax_id", + "scientific_name", + "common_name", + "sample_description", + "library_source", + "library_selection", + "library_strategy", + "library_layout" + ], + "type": "object", + "properties": { + "sample_name": { + "examples": ["prov_rona_99"], + "ontology": "GENEPIO_0000079", + "type": "string", + "description": "The user-defined name for the sample.", + "clasification":"Database Identifiers", + "genepio_label":"sequencing run sample identifier", + + }, + "collecting_institution": { + "examples": ["Public Health Agency of Canada"], + "ontology": "GENEPIO_0001651", + "type": "string", + "description": "The name of the agency that collected the original sample.", + "genepio_label":"INSDC institution code", + + }, + "collection_date": { + "examples": ["19/03/2020"], + "ontology": "GENEPIO:0001174", + "type": "string", + "description": "The date on which the sample was collected. ", + "format": "date", + "genepio_label":"", + + }, + "receipt_date": { + "examples": ["20/03/2020"], + "ontology": "GENEPIO:0001179", + "type": "string", + "description": "The date on which the sample was received.", + "format": "date", + "genepio_label":"", + + }, + "geographic_location_(country_and/or_sea)": { + "Enums": [ + "Afghanistan [GAZ:00006882]", + "Albania [GAZ:00002953]", + "Algeria [GAZ:00000563]", + "American Samoa [GAZ:00003957]", + "Andorra [GAZ:00002948]", + "Angola [GAZ:00001095]", + "Anguilla [GAZ:00009159]", + "Antarctica [GAZ:00000462]", + "Antigua and Barbuda [GAZ:00006883]", + "Argentina [GAZ:00002928]", + "Armenia [GAZ:00004094]", + "Aruba [GAZ:00004025]", + "Ashmore and Cartier Islands [GAZ:00005901]", + "Australia [GAZ:00000463]", + "Austria [GAZ:00002942]", + "Azerbaijan [GAZ:00004941]", + "Bahamas [GAZ:00002733]", + "Bahrain [GAZ:00005281]", + "Baker Island [GAZ:00007117]", + "Bangladesh [GAZ:00003750]", + "Barbados [GAZ:00001251]", + "Bassas da India [GAZ:00005810]", + "Belarus [GAZ:00006886]", + "Belgium [GAZ:00002938]", + "Belize [GAZ:00002934]", + "Benin [GAZ:00000904]", + "Bermuda [GAZ:00001264]", + "Bhutan [GAZ:00003920]", + "Bolivia [GAZ:00002511]", + "Borneo [GAZ:00025355]", + "Bosnia and Herzegovina [GAZ:00006887]", + "Botswana [GAZ:00001097]", + "Bouvet Island [GAZ:00001453]", + "Brazil [GAZ:00002828]", + "British Virgin Islands [GAZ:00003961]", + "Brunei [GAZ:00003901]", + "Bulgaria [GAZ:00002950]", + "Burkina Faso [GAZ:00000905]", + "Burundi [GAZ:00001090]", + "Cambodia [GAZ:00006888]", + "Cameroon [GAZ:00001093]", + "Canada [GAZ:00002560]", + "Cape Verde [GAZ:00001227]", + "Cayman Islands [GAZ:00003986]", + "Central African Republic [GAZ:00001089]", + "Chad [GAZ:00000586]", + "Chile [GAZ:00002825]", + "China [GAZ:00002845]", + "Christmas Island [GAZ:00005915]", + "Clipperton Island [GAZ:00005838]", + "Cocos Islands [GAZ:00009721]", + "Colombia [GAZ:00002929]", + "Comoros [GAZ:00005820]", + "Cook Islands [GAZ:00053798]", + "Coral Sea Islands [GAZ:00005917]", + "Costa Rica [GAZ:00002901]", + "Cote d'Ivoire [GAZ:00000906]", + "Croatia [GAZ:00002719]", + "Cuba [GAZ:00003762]", + "Curacao [GAZ:00012582]", + "Cyprus [GAZ:00004006]", + "Czech Republic [GAZ:00002954]", + "Democratic Republic of the Congo [GAZ:00001086]", + "Denmark [GAZ:00005852]", + "Djibouti [GAZ:00000582]", + "Dominica [GAZ:00006890]", + "Dominican Republic [GAZ:00003952]", + "Ecuador [GAZ:00002912]", + "Egypt [GAZ:00003934]", + "El Salvador [GAZ:00002935]", + "Equatorial Guinea [GAZ:00001091]", + "Eritrea [GAZ:00000581]", + "Estonia [GAZ:00002959]", + "Eswatini [GAZ:00001099]", + "Ethiopia [GAZ:00000567]", + "Europa Island [GAZ:00005811]", + "Falkland Islands (Islas Malvinas) [GAZ:00001412]", + "Faroe Islands [GAZ:00059206]", + "Fiji [GAZ:00006891]", + "Finland [GAZ:00002937]", + "France [GAZ:00003940]", + "French Guiana [GAZ:00002516]", + "French Polynesia [GAZ:00002918]", + "French Southern and Antarctic Lands [GAZ:00003753]", + "Gabon [GAZ:00001092]", + "Gambia [GAZ:00000907]", + "Gaza Strip [GAZ:00009571]", + "Georgia [GAZ:00004942]", + "Germany [GAZ:00002646]", + "Ghana [GAZ:00000908]", + "Gibraltar [GAZ:00003987]", + "Glorioso Islands [GAZ:00005808]", + "Greece [GAZ:00002945]", + "Greenland [GAZ:00001507]", + "Grenada [GAZ:02000573]", + "Guadeloupe [GAZ:00067142]", + "Guam [GAZ:00003706]", + "Guatemala [GAZ:00002936]", + "Guernsey [GAZ:00001550]", + "Guinea [GAZ:00000909]", + "Guinea-Bissau [GAZ:00000910]", + "Guyana [GAZ:00002522]", + "Haiti [GAZ:00003953]", + "Heard Island and McDonald Islands [GAZ:00009718]", + "Honduras [GAZ:00002894]", + "Hong Kong [GAZ:00003203]", + "Howland Island [GAZ:00007120]", + "Hungary [GAZ:00002952]", + "Iceland [GAZ:00000843]", + "India [GAZ:00002839]", + "Indonesia [GAZ:00003727]", + "Iran [GAZ:00004474]", + "Iraq [GAZ:00004483]", + "Ireland [GAZ:00002943]", + "Isle of Man [GAZ:00052477]", + "Israel [GAZ:00002476]", + "Italy [GAZ:00002650]", + "Jamaica [GAZ:00003781]", + "Jan Mayen [GAZ:00005853]", + "Japan [GAZ:00002747]", + "Jarvis Island [GAZ:00007118]", + "Jersey [GAZ:00001551]", + "Johnston Atoll [GAZ:00007114]", + "Jordan [GAZ:00002473]", + "Juan de Nova Island [GAZ:00005809]", + "Kazakhstan [GAZ:00004999]", + "Kenya [GAZ:00001101]", + "Kerguelen Archipelago [GAZ:00005682]", + "Kingman Reef [GAZ:00007116]", + "Kiribati [GAZ:00006894]", + "Kosovo [GAZ:00011337]", + "Kuwait [GAZ:00005285]", + "Kyrgyzstan [GAZ:00006893]", + "Laos [GAZ:00006889]", + "Latvia [GAZ:00002958]", + "Lebanon [GAZ:00002478]", + "Lesotho [GAZ:00001098]", + "Liberia [GAZ:00000911]", + "Libya [GAZ:00000566]", + "Liechtenstein [GAZ:00003858]", + "Line Islands [GAZ:00007144]", + "Lithuania [GAZ:00002960]", + "Luxembourg [GAZ:00002947]", + "Macau [GAZ:00003202]", + "Madagascar [GAZ:00001108]", + "Malawi [GAZ:00001105]", + "Malaysia [GAZ:00003902]", + "Maldives [GAZ:00006924]", + "Mali [GAZ:00000584]", + "Malta [GAZ:00004017]", + "Marshall Islands [GAZ:00007161]", + "Martinique [GAZ:00067143]", + "Mauritania [GAZ:00000583]", + "Mauritius [GAZ:00003745]", + "Mayotte [GAZ:00003943]", + "Mexico [GAZ:00002852]", + "Micronesia [GAZ:00005862]", + "Midway Islands [GAZ:00007112]", + "Moldova [GAZ:00003897]", + "Monaco [GAZ:00003857]", + "Mongolia [GAZ:00008744]", + "Montenegro [GAZ:00006898]", + "Montserrat [GAZ:00003988]", + "Morocco [GAZ:00000565]", + "Mozambique [GAZ:00001100]", + "Myanmar [GAZ:00006899]", + "Namibia [GAZ:00001096]", + "Nauru [GAZ:00006900]", + "Navassa Island [GAZ:00007119]", + "Nepal [GAZ:00004399]", + "Netherlands [GAZ:00002946]", + "New Caledonia [GAZ:00005206]", + "New Zealand [GAZ:00000469]", + "Nicaragua [GAZ:00002978]", + "Niger [GAZ:00000585]", + "Nigeria [GAZ:00000912]", + "Niue [GAZ:00006902]", + "Norfolk Island [GAZ:00005908]", + "North Korea [GAZ:00002801]", + "North Macedonia [GAZ:00006895]", + "North Sea [GAZ:00002284]", + "Northern Mariana Islands [GAZ:00003958]", + "Norway [GAZ:00002699]", + "Oman [GAZ:00005283]", + "Pakistan [GAZ:00005246]", + "Palau [GAZ:00006905]", + "Panama [GAZ:00002892]", + "Papua New Guinea [GAZ:00003922]", + "Paracel Islands [GAZ:00010832]", + "Paraguay [GAZ:00002933]", + "Peru [GAZ:00002932]", + "Philippines [GAZ:00004525]", + "Pitcairn Islands [GAZ:00005867]", + "Poland [GAZ:00002939]", + "Portugal [GAZ:00004126]", + "Puerto Rico [GAZ:00006935]", + "Qatar [GAZ:00005286]", + "Republic of the Congo [GAZ:00001088]", + "Reunion [GAZ:00003945]", + "Romania [GAZ:00002951]", + "Ross Sea [GAZ:00023304]", + "Russia [GAZ:00002721]", + "Rwanda [GAZ:00001087]", + "Saint Helena [GAZ:00000849]", + "Saint Kitts and Nevis [GAZ:00006906]", + "Saint Lucia [GAZ:00006909]", + "Saint Pierre and Miquelon [GAZ:00003942]", + "Saint Martin [GAZ:00005841]", + "Saint Vincent and the Grenadines [GAZ:02000565]", + "Samoa [GAZ:00006910]", + "San Marino [GAZ:00003102]", + "Sao Tome and Principe [GAZ:00006927]", + "Saudi Arabia [GAZ:00005279]", + "Senegal [GAZ:00000913]", + "Serbia [GAZ:00002957]", + "Seychelles [GAZ:00006922]", + "Sierra Leone [GAZ:00000914]", + "Singapore [GAZ:00003923]", + "Sint Maarten [GAZ:00012579]", + "Slovakia [GAZ:00002956]", + "Slovenia [GAZ:00002955]", + "Solomon Islands [GAZ:00005275]", + "Somalia [GAZ:00001104]", + "South Africa [GAZ:00001094]", + "South Georgia and the South Sandwich Islands [GAZ:00003990]", + "South Korea [GAZ:00002802]", + "South Sudan [GAZ:00233439]", + "Spain [GAZ:00003936]", + "Spratly Islands [GAZ:00010831]", + "Sri Lanka [GAZ:00003924]", + "State of Palestine [GAZ:00002475]", + "Sudan [GAZ:00000560]", + "Suriname [GAZ:00002525]", + "Svalbard [GAZ:00005396]", + "Swaziland [GAZ:00001099]", + "Sweden [GAZ:00002729]", + "Switzerland [GAZ:00002941]", + "Syria [GAZ:00002474]", + "Taiwan [GAZ:00005341]", + "Tajikistan [GAZ:00006912]", + "Tanzania [GAZ:00001103]", + "Thailand [GAZ:00003744]", + "Timor-Leste [GAZ:00006913]", + "Togo [GAZ:00000915]", + "Tokelau [GAZ:00260188]", + "Tonga [GAZ:00006916]", + "Trinidad and Tobago [GAZ:00003767]", + "Tromelin Island [GAZ:00005812]", + "Tunisia [GAZ:00000562]", + "Turkey [GAZ:00000558]", + "Turkmenistan [GAZ:00005018]", + "Turks and Caicos Islands [GAZ:00003955]", + "Tuvalu [GAZ:00009715]", + "USA [GAZ:00002459]", + "Uganda [GAZ:00001102]", + "Ukraine [GAZ:00002724]", + "United Arab Emirates [GAZ:00005282]", + "United Kingdom [GAZ:00002637]", + "Uruguay [GAZ:00002930]", + "Uzbekistan [GAZ:00004979]", + "Vanuatu [GAZ:00006918]", + "Venezuela [GAZ:00002931]", + "Viet Nam [GAZ:00003756]", + "Virgin Islands [GAZ:00003959]", + "Wake Island [GAZ:00007111]", + "Wallis and Futuna [GAZ:00007191]", + "West Bank [GAZ:00009572]", + "Western Sahara [GAZ:00000564]", + "Yemen [GAZ:00005284]", + "Zambia [GAZ:00001107]", + "Zimbabwe [GAZ:00001106]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO_0000118", + "type": "string", + "description": "The country of origin of the sample.", + "examples": ["South Africa [GAZ:00001094]"], + "genepio_label":"specimen collection location - country", + + }, + "geographic location (region and locality)": { + "ontology": "GENEPIO:0100280", + "type": "string", + "description": "The county/region of origin of the sample.", + "examples": ["Derbyshire"], + "genepio_label":"", + + }, + "geographic location (latitude)": { + "ontology": "OBI:0001620", + "type": "string", + "description": "The latitude coordinates of the geographical location of sample collection.", + "examples": ["38.98 N"], + "genepio_label":"", + + }, + "geographic location (longitude)": { + "ontology": "OBI:0001621", + "type": "string", + "description": "The longitude coordinates of the geographical location of sample collection.", + "examples": ["77.11 W"], + "genepio_label":"", + + }, + "scientific_name": { + "Enums": [ + "Coronaviridae [NCBITaxon:11118]", + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001191", + "type": "string", + "description": "Taxonomic name of the organism.", + "examples": ["Severe acute respiratory syndrome coronavirus 2 "], + "genepio_label":"", + + }, + "isolate": { + "ontology": "GENEPIO:0001644", + "type": "string", + "description": "Identifier of the specific isolate.", + "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"], + "genepio_label":"isolate identifier", + + }, + "purpose_sampling": { + "examples": ["Diagnostic testing"], + "ontology": "NCIT_C146997", + "type": "string", + "description": "The reason that the sample was collected.", + "clasification":"Sample collection and processing" + }, + "isolation source host-associated": { + "Enums": [ + "Blood [UBERON:0000178]", + "Fluid [UBERON:0006314]", + "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", + "Fluid (Pericardial) [UBERON:0002409]", + "Fluid (Pleural) [UBERON:0001087]", + "Fluid (Vaginal) [UBERON:0036243]", + "Fluid (Amniotic) [UBERON:0000173]", + "Saliva [UBERON:0001836]", + "Tissue [UBERON:0000479]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001211", + "type": "string", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "examples": ["Blood [UBERON:0000178]"], + "genepio_label":"", + + }, + "host common name": { + "Enums": [ + "Human [NCBITaxon:9606]", + "Bat [NCBITaxon:9397]", + "Cat [NCBITaxon:9685]", + "Chicken [NCBITaxon:9031]", + "Civet [NCBITaxon:9673]", + "Cow [NCBITaxon:9913]", + "Dog [NCBITaxon:9615]", + "Lion [NCBITaxon:9689]", + "Mink [NCBITaxon:452646]", + "Pangolin [NCBITaxon:9973]", + "Pig [NCBITaxon:9825]", + "Pigeon [NCBITaxon:8930]", + "Tiger [NCBITaxon:9694]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO_0001724", + "type": "string", + "description": "The commonly used name of the host.", + "examples": ["Human [NCBITaxon:9606]"], + "genepio_label":"subject organism common name", + + }, + "host scientific name": { + "Enums": [ + "Bos taurus [NCBITaxon:9913]", + "Canis lupus familiaris [NCBITaxon:9615]", + "Chiroptera [NCBITaxon:9397]", + "Columbidae [NCBITaxon:8930]", + "Felis catus [NCBITaxon:9685]", + "Gallus gallus [NCBITaxon:9031]", + "Homo sapiens [NCBITaxon:9606]", + "Manis [NCBITaxon:9973]", + "Manis javanica [NCBITaxon:9974]", + "Neovison vison [NCBITaxon:452646]", + "Panthera leo [NCBITaxon:9689]", + "Panthera tigris [NCBITaxon:9694]", + "Rhinolophidae [NCBITaxon:58055]", + "Rhinolophus affinis [NCBITaxon:59477]", + "Sus scrofa domesticus [NCBITaxon:9825]", + "Viverridae [NCBITaxon:9673]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO_0001567", + "type": "string", + "description": "The taxonomic, or scientific name of the host.", + "examples": ["Homo sapiens [NCBITaxon:9606]"], + "genepio_label":"subject organism (host) taxonomic species", + + }, + "host_health_state": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Health status of the host at the time of sample collection.", + "clasification":"Host information", + "genepio_label":"", + + }, + "host_age": { + "examples": ["e.g. 65 or 7 months, or unknown. Caution: the host age may be considered public health identifiable information. Consult the data steward before sharing. If the information is unknown or can not be shared, put unknown"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Patient age", + "clasification":"Host information" + }, + + "host_sex": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Gender or sex of the host.", + "clasification":"Host information", + "genepio_label":"", + + }, + "host_subject_id": { + "examples": ["e.g. #131"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "a unique identifier by which each subject can be referred to, de-identified.", + "clasification":"Host information", + "genepio_label":"", + + }, + "type exposure": { + "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification":"Host information", + "genepio_label":"", + + }, + "subject exposure duration": { + "examples": ["e.g. Patient infected while traveling in …."], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification":"Host information", + "genepio_label":"", + + }, + "instrument_model": { + "Enums": ["454 Genome Sequencer [GENEPIO:0001937]", + "454 Genome Sequence 20 [OBI:0000689]", + "454 Genome Sequencer FLX [OBI:0000702]", + "454 Genome Sequencer FLX Titanium [GENEPIO:0001936]", + "454 Genome Sequencer Junior [GENEPIO:0001938]", + "AB SOLiD System [OBI:0000696]", + "SOLiD 3 Plus System [OBI:0002007]", + "SOLiD 4 [OBI:0002024]", + "SOLiD 4hq System [GENPIO:0001928]", + "SOLiD 5500 [GENPIO:0001929]", + "SOLiD 5500xl [GENPIO:0001930]", + "SOLiD PI System [GENPIO:0001931]", + "SOLiD System 2.0 [GENPIO:0001932]", + "SOLiD System 3.0 [GENPIO:0001933]", + "HeliScope Single Molecule Sequencer [OBI:0000717]", + "Illumina Genome Analyzer II [OBI:0000703]", + "Genome Analyzer IIe [OBI:0002027]", + "Genome Analyzer IIx [OBI:0002000]", + "Illumina HiSeq Sequencer [GENPIO:0001939]", + "Illumina HiSeq 1000 [OBI:0002022]", + "Illumina HiSeq 2000 [OBI:0002001]", + "Illumina HiSeq 2500 [OBI:0002002]", + "Illumina HiSeq 3000 [OBI:0002048]", + "Illumina HiSeq 4000 [OBI:0002049]", + "Ion Torrent PGM [GENPIO:0001935]", + "MiSeq [OBI:0002003]", + "NextSeq 500 [OBI:0002021]", + "PacBio RS II [OBI:0002012]", + ], + "ontology": "GENEPIO_0001921", + "type": "string", + "description": "The model of the sequencing instrument used.", + "examples": ["Oxford Nanopore MinION "], + "genepio_label":"sequencing instrument model", + + }, + "instrument_platform ": { + "examples": ["MinIon"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The model of the sequencing instrument used.", + "genepio_label":"", + + }, + "file_name": { + "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], + "ontology": "GENEPIO:0001476", + "type": "string", + "description": "The user-specified filename of the r1 FASTQ file.", + "clasification":"Bioinformatics and QC metrics", + "genepio_label":"", + + }, + "tax_id": { + "examples": ["probably 2697049 in all cases"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The NCBITaxon identifier for the organism being sequenced.", + "clasification":"Sample collection and processing", + "genepio_label":"", + + }, + "scientific_name": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The taxonomic name of the organism.", + "clasification":"Sample collection and processing", + "genepio_label":"", + + }, + "common_name": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The common name of the organism.", + "clasification":"Sample collection and processing", + "genepio_label":"", + + }, + "sample_description": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Free text description of the sample.", + "clasification":"Sample collection and processing", + "genepio_label":"", + + }, + "sample_storage_conditions": { + "examples": ["24 degrees celsius"], + "ontology": "NCIT_C115535", + "type": "string", + "description": "The name and version of a particular protocol used for sampling.", + "clasification":"Sample collection and processing" + }, + "library_source": { + "Enums": ["5-methycytidine antibody method [GENPIO:0001941]", + "CAGE method [GENPIO:0001942]", + "CF-H method [GENPIO:0001943]", + "CF-M method ]GENPIO:0001944]", + "CF-S method [GENPIO:0001945]", + "CF-T method [GENPIO:0001946]", + "ChIP method ]GENPIO:0001947]", + "DNAse method [GENPIO:0001948]", + "HMPR method [GENPIO:0001949]", + "Hybrid Selection Method [GENPIO:0001950]", + "MBD2 protein methyl-CpG binding domain method [GENPIO:0001951]", + "MF method [GENPIO:0001952]", + "MNase method [GENPIO:0001953]", + "MSLL method [GENPIO:0001954]", + "PCR method [GENPIO:0001955]", + "RACE method [GENPIO:0001956]", + "RANDOM PCR method [GENPIO:0001957]", + "RANDOM method [GENPIO:0001958]", + "RT-PCR method [GENPIO:0001959]", + "Reduced Representation method [GENPIO:0001960]", + "Resctriction Digest method [GENPIO:0001961]", + "cDNA method [GENPIO:0001962]", + "other library method [GENPIO:0001964]", + "size fractionation method [GENPIO:0001963]", + ], + "examples": ["METAGENOMIC"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Molecule type used to make the library.", + "clasification":"Sequencing", + }, + "library_selection": { + "examples": ["RANDOM PCR"], + "ontology": "GENPIO_0001940", + "type": "string", + "description": "Library capture method.", + "clasification":"Sequencing", + "genepio_label":"library selection", + + }, + "library_strategy": { + "Enums": ["Bisultife-Seq strategy [GENPIO:0001975]", + "CTS strategy [GENPIO:0001978]", + "ChIP-Seq strategy [GENPIO:0001979]", + "DNase-Hypersensitivity strategy [GENPIO:0001980]", + "EST strategy [GENPIO:0001981]", + "FL-cDNA strategy [GENPIO:0001983]", + "MB-Seq strategy [GENPIO:0001984]", + "MNase-Seq strategy [GENPIO:0001985]", + "MRE-Seq strategy [GENPIO:0001986]", + "MeDIP-Seq strategy [GENPIO:0001987]", + "RNA-Seq strategy [GENPIO:0001990]", + "WCS strategy [GENPIO:0001991]", + "WGS strategy [GENPIO:0001992]", + "WXS strategy [GENPIO:0001993]", + "amplicon strategy [GENPIO:0001974]", + "clone end strategy [GENPIO:0001976]", + "clone strategy [GENPIO:0001977]", + "finishing strategy [GENPIO:0001982]", + "other library strategy [GENPIO:0001988]", + "pool clone strategy [GENPIO:0001989]", + ], + "examples": ["WGS"], + "ontology": "GENPIO_0001973", + "type": "string", + "description": "Overall sequencing strategy or approach.", + "clasification":"Sequencing", + "genepio_label":"library strategy", + + }, + "library_layout": { + "examples": ["PAIRED"], + "ontology":"GENPIO_0000001", + "type": "string", + "description": "Single or paired.", + "clasification":"Sequencing", + "genepio_label":"library library_layout", + + }, + "library_name": { + "examples": ["e.g P17157_1007"], + "ontology": "GENEPIO_0001995", + "type": "string", + "description": "The submitter's name for this library.", + "clasification":"Sequencing", + "genepio_label":"Library Name", + }, + "nominal_length ": { + "examples": ["350"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing", + "genepio_label":"", + + }, + "analysis_accession": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "study_accession": { + "examples": ["e.g PRJEB39632"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "secondary_study_accession": { + "examples": ["e.g ERP123173"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "sample_accession": { + "examples": ["e.g SAMEA7098096"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "secondary_sample_accession": { + "examples": ["e.g ERS4858671"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "experiment_accession": { + "examples": ["e.g ERX4331406"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "run_accession": { + "examples": ["e.g ERX4331406"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "submission_accession": { + "examples": ["e.g ERA2794974"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "read_count": { + "examples": ["e.g 837055"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "base_count": { + "examples": ["e.g 503907110"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "center_name": { + "examples": [" KAROLINSKA INSITUTET"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The name of the institution", + "clasification":"Sample collection and processing", + "genepio_label":"", + + }, + "first_public": { + "examples": ["e.g 2020-08-07"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "last_updated": { + "examples": ["e.g 2020-07-29"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "format":"date", + "genepio_label":"", + + }, + "experiment_title": { + "examples": ["e.g Illumina MiSeq paired end sequencing"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "study_title": { + "examples": ["e.g SARS-CoV-2 genomes from late April in Stockholm"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "study_alias": { + "examples": ["e.g Sweden"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "experiment_alias": { + "examples": ["e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "run_alias": { + "examples": ["e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "fastq_bytes": { + "examples": ["e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "fastq_md5": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "fastq_ftp": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "fastq_aspera": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "fastq_galaxy": { + "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "submitted_bytes": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "submitted_md5": { + "examples": ["e.g 139853010;166270048"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "submitted_ftp": { + "examples": ["e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "submitted_aspera": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "submitted_galaxy": { + "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "submitted_format": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "sra_bytes": { + "examples": ["e.g FASTQ;FASTQ"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "sra_md5": { + "examples": ["e.g 260236789"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "sra_ftp": { + "examples": ["e.g 2cf0d467d6dc4ae0a5473774d54c059c"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "sra_aspera": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "sra_galaxy": { + "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "broker_name": { + "examples": ["P17157_1007"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "nominal_sdev": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "first_created": { + "examples": ["e.g 2020-08-07"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + + } +} diff --git a/test/mapping.py b/test/mapping.py new file mode 100644 index 00000000..da74569d --- /dev/null +++ b/test/mapping.py @@ -0,0 +1,26 @@ +import json +from types import SimpleNamespace + +# data = '{"name": "John Smith", "hometown": {"name": "New York", "id": 123}}' + +schema_file = open('/Users/erika/Desktop/BU-ISCIII/Relecov/ECDC-HERA/JSON SCHEMA/26_ENERO/ena_v01.json') + +# + +import json + +# Opening JSON file +f = open('ena_v01.json') + +# returns JSON object as +# a dictionary +data = json.load(f) + + + +# Closing file +f.close() +# - + +# Parse JSON into an object with attributes corresponding to dict keys. +x = json.loads(fage_plus_schema, object_hook=lambda d: SimpleNamespace(**d)) +#print(x.name, x.hometown.name, x.hometown.id) From d09b2e3f43c1046c19c58768c353adaa3e837bbe Mon Sep 17 00:00:00 2001 From: ErikaKvalem Date: Tue, 1 Feb 2022 16:42:19 +0100 Subject: [PATCH 0006/1454] update mapping --- test/{mapping.py => mapping_V0.py} | 23 +- test/mapping_V2.py | 3302 ++++++++++++++++++++++++++++ 2 files changed, 3324 insertions(+), 1 deletion(-) rename test/{mapping.py => mapping_V0.py} (55%) create mode 100644 test/mapping_V2.py diff --git a/test/mapping.py b/test/mapping_V0.py similarity index 55% rename from test/mapping.py rename to test/mapping_V0.py index da74569d..fbaed99c 100644 --- a/test/mapping.py +++ b/test/mapping_V0.py @@ -1,7 +1,28 @@ import json from types import SimpleNamespace -# data = '{"name": "John Smith", "hometown": {"name": "New York", "id": 123}}' +module_path = str(Path.cwd().parents[0]) +module_path + +# %cd .. + +# + +import sys +from pathlib import Path + +# in jupyter (lab / notebook), based on notebook path +module_path = str(Path.cwd().parents[0]) +# in standard python +#module_path = str(Path.cwd(__file__).parents[0] / "py") + +#if module_path not in sys.path: +# sys.path.append(module_path) + +#from modules import preparations +#import tools +# - + +module_path schema_file = open('/Users/erika/Desktop/BU-ISCIII/Relecov/ECDC-HERA/JSON SCHEMA/26_ENERO/ena_v01.json') diff --git a/test/mapping_V2.py b/test/mapping_V2.py new file mode 100644 index 00000000..5de020cc --- /dev/null +++ b/test/mapping_V2.py @@ -0,0 +1,3302 @@ +# -*- coding: utf-8 -*- +import pandas as pd + +import json +from types import SimpleNamespace +import sys +from pathlib import Path +import json + +pd.set_option('display.max_columns', None) +pd.set_option('display.max_rows', None) + +ENA_schema = { + "$schema": "http://json-schema.org/draft/2019-09/schema#", + "required": [ + "sample_name", + "collecting_institution", + "geographic_location_(country_and/or_sea)", + "isolate", + "host_scientific_name", + "host_common_name", + "host_health_state", + "host_sex", + "host_subject_id", + "instrument_model", + "file_name", + "sample_name", + "tax_id", + "scientific_name", + "common_name", + "sample_description", + "library_source", + "library_selection", + "library_strategy", + "library_layout" + ], + "type": "object", + "properties": { + "sample_name": { + "examples": ["prov_rona_99"], + "ontology": "GENEPIO_0000079", + "type": "string", + "description": "The user-defined name for the sample.", + "clasification":"Database Identifiers", + "genepio_label":"sequencing run sample identifier", + + }, + "collecting_institution": { + "examples": ["Public Health Agency of Canada"], + "ontology": "GENEPIO_0001651", + "type": "string", + "description": "The name of the agency that collected the original sample.", + "genepio_label":"INSDC institution code", + + }, + "collection_date": { + "examples": ["19/03/2020"], + "ontology": "GENEPIO:0001174", + "type": "string", + "description": "The date on which the sample was collected. ", + "format": "date", + "genepio_label":"", + + }, + "receipt_date": { + "examples": ["20/03/2020"], + "ontology": "GENEPIO:0001179", + "type": "string", + "description": "The date on which the sample was received.", + "format": "date", + "genepio_label":"", + + }, + "geographic_location_(country_and/or_sea)": { + "Enums": [ + "Afghanistan [GAZ:00006882]", + "Albania [GAZ:00002953]", + "Algeria [GAZ:00000563]", + "American Samoa [GAZ:00003957]", + "Andorra [GAZ:00002948]", + "Angola [GAZ:00001095]", + "Anguilla [GAZ:00009159]", + "Antarctica [GAZ:00000462]", + "Antigua and Barbuda [GAZ:00006883]", + "Argentina [GAZ:00002928]", + "Armenia [GAZ:00004094]", + "Aruba [GAZ:00004025]", + "Ashmore and Cartier Islands [GAZ:00005901]", + "Australia [GAZ:00000463]", + "Austria [GAZ:00002942]", + "Azerbaijan [GAZ:00004941]", + "Bahamas [GAZ:00002733]", + "Bahrain [GAZ:00005281]", + "Baker Island [GAZ:00007117]", + "Bangladesh [GAZ:00003750]", + "Barbados [GAZ:00001251]", + "Bassas da India [GAZ:00005810]", + "Belarus [GAZ:00006886]", + "Belgium [GAZ:00002938]", + "Belize [GAZ:00002934]", + "Benin [GAZ:00000904]", + "Bermuda [GAZ:00001264]", + "Bhutan [GAZ:00003920]", + "Bolivia [GAZ:00002511]", + "Borneo [GAZ:00025355]", + "Bosnia and Herzegovina [GAZ:00006887]", + "Botswana [GAZ:00001097]", + "Bouvet Island [GAZ:00001453]", + "Brazil [GAZ:00002828]", + "British Virgin Islands [GAZ:00003961]", + "Brunei [GAZ:00003901]", + "Bulgaria [GAZ:00002950]", + "Burkina Faso [GAZ:00000905]", + "Burundi [GAZ:00001090]", + "Cambodia [GAZ:00006888]", + "Cameroon [GAZ:00001093]", + "Canada [GAZ:00002560]", + "Cape Verde [GAZ:00001227]", + "Cayman Islands [GAZ:00003986]", + "Central African Republic [GAZ:00001089]", + "Chad [GAZ:00000586]", + "Chile [GAZ:00002825]", + "China [GAZ:00002845]", + "Christmas Island [GAZ:00005915]", + "Clipperton Island [GAZ:00005838]", + "Cocos Islands [GAZ:00009721]", + "Colombia [GAZ:00002929]", + "Comoros [GAZ:00005820]", + "Cook Islands [GAZ:00053798]", + "Coral Sea Islands [GAZ:00005917]", + "Costa Rica [GAZ:00002901]", + "Cote d'Ivoire [GAZ:00000906]", + "Croatia [GAZ:00002719]", + "Cuba [GAZ:00003762]", + "Curacao [GAZ:00012582]", + "Cyprus [GAZ:00004006]", + "Czech Republic [GAZ:00002954]", + "Democratic Republic of the Congo [GAZ:00001086]", + "Denmark [GAZ:00005852]", + "Djibouti [GAZ:00000582]", + "Dominica [GAZ:00006890]", + "Dominican Republic [GAZ:00003952]", + "Ecuador [GAZ:00002912]", + "Egypt [GAZ:00003934]", + "El Salvador [GAZ:00002935]", + "Equatorial Guinea [GAZ:00001091]", + "Eritrea [GAZ:00000581]", + "Estonia [GAZ:00002959]", + "Eswatini [GAZ:00001099]", + "Ethiopia [GAZ:00000567]", + "Europa Island [GAZ:00005811]", + "Falkland Islands (Islas Malvinas) [GAZ:00001412]", + "Faroe Islands [GAZ:00059206]", + "Fiji [GAZ:00006891]", + "Finland [GAZ:00002937]", + "France [GAZ:00003940]", + "French Guiana [GAZ:00002516]", + "French Polynesia [GAZ:00002918]", + "French Southern and Antarctic Lands [GAZ:00003753]", + "Gabon [GAZ:00001092]", + "Gambia [GAZ:00000907]", + "Gaza Strip [GAZ:00009571]", + "Georgia [GAZ:00004942]", + "Germany [GAZ:00002646]", + "Ghana [GAZ:00000908]", + "Gibraltar [GAZ:00003987]", + "Glorioso Islands [GAZ:00005808]", + "Greece [GAZ:00002945]", + "Greenland [GAZ:00001507]", + "Grenada [GAZ:02000573]", + "Guadeloupe [GAZ:00067142]", + "Guam [GAZ:00003706]", + "Guatemala [GAZ:00002936]", + "Guernsey [GAZ:00001550]", + "Guinea [GAZ:00000909]", + "Guinea-Bissau [GAZ:00000910]", + "Guyana [GAZ:00002522]", + "Haiti [GAZ:00003953]", + "Heard Island and McDonald Islands [GAZ:00009718]", + "Honduras [GAZ:00002894]", + "Hong Kong [GAZ:00003203]", + "Howland Island [GAZ:00007120]", + "Hungary [GAZ:00002952]", + "Iceland [GAZ:00000843]", + "India [GAZ:00002839]", + "Indonesia [GAZ:00003727]", + "Iran [GAZ:00004474]", + "Iraq [GAZ:00004483]", + "Ireland [GAZ:00002943]", + "Isle of Man [GAZ:00052477]", + "Israel [GAZ:00002476]", + "Italy [GAZ:00002650]", + "Jamaica [GAZ:00003781]", + "Jan Mayen [GAZ:00005853]", + "Japan [GAZ:00002747]", + "Jarvis Island [GAZ:00007118]", + "Jersey [GAZ:00001551]", + "Johnston Atoll [GAZ:00007114]", + "Jordan [GAZ:00002473]", + "Juan de Nova Island [GAZ:00005809]", + "Kazakhstan [GAZ:00004999]", + "Kenya [GAZ:00001101]", + "Kerguelen Archipelago [GAZ:00005682]", + "Kingman Reef [GAZ:00007116]", + "Kiribati [GAZ:00006894]", + "Kosovo [GAZ:00011337]", + "Kuwait [GAZ:00005285]", + "Kyrgyzstan [GAZ:00006893]", + "Laos [GAZ:00006889]", + "Latvia [GAZ:00002958]", + "Lebanon [GAZ:00002478]", + "Lesotho [GAZ:00001098]", + "Liberia [GAZ:00000911]", + "Libya [GAZ:00000566]", + "Liechtenstein [GAZ:00003858]", + "Line Islands [GAZ:00007144]", + "Lithuania [GAZ:00002960]", + "Luxembourg [GAZ:00002947]", + "Macau [GAZ:00003202]", + "Madagascar [GAZ:00001108]", + "Malawi [GAZ:00001105]", + "Malaysia [GAZ:00003902]", + "Maldives [GAZ:00006924]", + "Mali [GAZ:00000584]", + "Malta [GAZ:00004017]", + "Marshall Islands [GAZ:00007161]", + "Martinique [GAZ:00067143]", + "Mauritania [GAZ:00000583]", + "Mauritius [GAZ:00003745]", + "Mayotte [GAZ:00003943]", + "Mexico [GAZ:00002852]", + "Micronesia [GAZ:00005862]", + "Midway Islands [GAZ:00007112]", + "Moldova [GAZ:00003897]", + "Monaco [GAZ:00003857]", + "Mongolia [GAZ:00008744]", + "Montenegro [GAZ:00006898]", + "Montserrat [GAZ:00003988]", + "Morocco [GAZ:00000565]", + "Mozambique [GAZ:00001100]", + "Myanmar [GAZ:00006899]", + "Namibia [GAZ:00001096]", + "Nauru [GAZ:00006900]", + "Navassa Island [GAZ:00007119]", + "Nepal [GAZ:00004399]", + "Netherlands [GAZ:00002946]", + "New Caledonia [GAZ:00005206]", + "New Zealand [GAZ:00000469]", + "Nicaragua [GAZ:00002978]", + "Niger [GAZ:00000585]", + "Nigeria [GAZ:00000912]", + "Niue [GAZ:00006902]", + "Norfolk Island [GAZ:00005908]", + "North Korea [GAZ:00002801]", + "North Macedonia [GAZ:00006895]", + "North Sea [GAZ:00002284]", + "Northern Mariana Islands [GAZ:00003958]", + "Norway [GAZ:00002699]", + "Oman [GAZ:00005283]", + "Pakistan [GAZ:00005246]", + "Palau [GAZ:00006905]", + "Panama [GAZ:00002892]", + "Papua New Guinea [GAZ:00003922]", + "Paracel Islands [GAZ:00010832]", + "Paraguay [GAZ:00002933]", + "Peru [GAZ:00002932]", + "Philippines [GAZ:00004525]", + "Pitcairn Islands [GAZ:00005867]", + "Poland [GAZ:00002939]", + "Portugal [GAZ:00004126]", + "Puerto Rico [GAZ:00006935]", + "Qatar [GAZ:00005286]", + "Republic of the Congo [GAZ:00001088]", + "Reunion [GAZ:00003945]", + "Romania [GAZ:00002951]", + "Ross Sea [GAZ:00023304]", + "Russia [GAZ:00002721]", + "Rwanda [GAZ:00001087]", + "Saint Helena [GAZ:00000849]", + "Saint Kitts and Nevis [GAZ:00006906]", + "Saint Lucia [GAZ:00006909]", + "Saint Pierre and Miquelon [GAZ:00003942]", + "Saint Martin [GAZ:00005841]", + "Saint Vincent and the Grenadines [GAZ:02000565]", + "Samoa [GAZ:00006910]", + "San Marino [GAZ:00003102]", + "Sao Tome and Principe [GAZ:00006927]", + "Saudi Arabia [GAZ:00005279]", + "Senegal [GAZ:00000913]", + "Serbia [GAZ:00002957]", + "Seychelles [GAZ:00006922]", + "Sierra Leone [GAZ:00000914]", + "Singapore [GAZ:00003923]", + "Sint Maarten [GAZ:00012579]", + "Slovakia [GAZ:00002956]", + "Slovenia [GAZ:00002955]", + "Solomon Islands [GAZ:00005275]", + "Somalia [GAZ:00001104]", + "South Africa [GAZ:00001094]", + "South Georgia and the South Sandwich Islands [GAZ:00003990]", + "South Korea [GAZ:00002802]", + "South Sudan [GAZ:00233439]", + "Spain [GAZ:00003936]", + "Spratly Islands [GAZ:00010831]", + "Sri Lanka [GAZ:00003924]", + "State of Palestine [GAZ:00002475]", + "Sudan [GAZ:00000560]", + "Suriname [GAZ:00002525]", + "Svalbard [GAZ:00005396]", + "Swaziland [GAZ:00001099]", + "Sweden [GAZ:00002729]", + "Switzerland [GAZ:00002941]", + "Syria [GAZ:00002474]", + "Taiwan [GAZ:00005341]", + "Tajikistan [GAZ:00006912]", + "Tanzania [GAZ:00001103]", + "Thailand [GAZ:00003744]", + "Timor-Leste [GAZ:00006913]", + "Togo [GAZ:00000915]", + "Tokelau [GAZ:00260188]", + "Tonga [GAZ:00006916]", + "Trinidad and Tobago [GAZ:00003767]", + "Tromelin Island [GAZ:00005812]", + "Tunisia [GAZ:00000562]", + "Turkey [GAZ:00000558]", + "Turkmenistan [GAZ:00005018]", + "Turks and Caicos Islands [GAZ:00003955]", + "Tuvalu [GAZ:00009715]", + "USA [GAZ:00002459]", + "Uganda [GAZ:00001102]", + "Ukraine [GAZ:00002724]", + "United Arab Emirates [GAZ:00005282]", + "United Kingdom [GAZ:00002637]", + "Uruguay [GAZ:00002930]", + "Uzbekistan [GAZ:00004979]", + "Vanuatu [GAZ:00006918]", + "Venezuela [GAZ:00002931]", + "Viet Nam [GAZ:00003756]", + "Virgin Islands [GAZ:00003959]", + "Wake Island [GAZ:00007111]", + "Wallis and Futuna [GAZ:00007191]", + "West Bank [GAZ:00009572]", + "Western Sahara [GAZ:00000564]", + "Yemen [GAZ:00005284]", + "Zambia [GAZ:00001107]", + "Zimbabwe [GAZ:00001106]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO_0000118", + "type": "string", + "description": "The country of origin of the sample.", + "examples": ["South Africa [GAZ:00001094]"], + "genepio_label":"specimen collection location - country", + + }, + "geographic location (region and locality)": { + "ontology": "GENEPIO:0100280", + "type": "string", + "description": "The county/region of origin of the sample.", + "examples": ["Derbyshire"], + "genepio_label":"", + + }, + "geographic location (latitude)": { + "ontology": "OBI:0001620", + "type": "string", + "description": "The latitude coordinates of the geographical location of sample collection.", + "examples": ["38.98 N"], + "genepio_label":"", + + }, + "geographic location (longitude)": { + "ontology": "OBI:0001621", + "type": "string", + "description": "The longitude coordinates of the geographical location of sample collection.", + "examples": ["77.11 W"], + "genepio_label":"", + + }, + "scientific_name": { + "Enums": [ + "Coronaviridae [NCBITaxon:11118]", + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001191", + "type": "string", + "description": "Taxonomic name of the organism.", + "examples": ["Severe acute respiratory syndrome coronavirus 2 "], + "genepio_label":"", + + }, + "isolate": { + "ontology": "GENEPIO:0001644", + "type": "string", + "description": "Identifier of the specific isolate.", + "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"], + "genepio_label":"isolate identifier", + + }, + "purpose_sampling": { + "examples": ["Diagnostic testing"], + "ontology": "NCIT_C146997", + "type": "string", + "description": "The reason that the sample was collected.", + "clasification":"Sample collection and processing" + }, + "isolation source host-associated": { + "Enums": [ + "Blood [UBERON:0000178]", + "Fluid [UBERON:0006314]", + "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", + "Fluid (Pericardial) [UBERON:0002409]", + "Fluid (Pleural) [UBERON:0001087]", + "Fluid (Vaginal) [UBERON:0036243]", + "Fluid (Amniotic) [UBERON:0000173]", + "Saliva [UBERON:0001836]", + "Tissue [UBERON:0000479]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001211", + "type": "string", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "examples": ["Blood [UBERON:0000178]"], + "genepio_label":"", + + }, + "host common name": { + "Enums": [ + "Human [NCBITaxon:9606]", + "Bat [NCBITaxon:9397]", + "Cat [NCBITaxon:9685]", + "Chicken [NCBITaxon:9031]", + "Civet [NCBITaxon:9673]", + "Cow [NCBITaxon:9913]", + "Dog [NCBITaxon:9615]", + "Lion [NCBITaxon:9689]", + "Mink [NCBITaxon:452646]", + "Pangolin [NCBITaxon:9973]", + "Pig [NCBITaxon:9825]", + "Pigeon [NCBITaxon:8930]", + "Tiger [NCBITaxon:9694]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO_0001724", + "type": "string", + "description": "The commonly used name of the host.", + "examples": ["Human [NCBITaxon:9606]"], + "genepio_label":"subject organism common name", + + }, + "host scientific name": { + "Enums": [ + "Bos taurus [NCBITaxon:9913]", + "Canis lupus familiaris [NCBITaxon:9615]", + "Chiroptera [NCBITaxon:9397]", + "Columbidae [NCBITaxon:8930]", + "Felis catus [NCBITaxon:9685]", + "Gallus gallus [NCBITaxon:9031]", + "Homo sapiens [NCBITaxon:9606]", + "Manis [NCBITaxon:9973]", + "Manis javanica [NCBITaxon:9974]", + "Neovison vison [NCBITaxon:452646]", + "Panthera leo [NCBITaxon:9689]", + "Panthera tigris [NCBITaxon:9694]", + "Rhinolophidae [NCBITaxon:58055]", + "Rhinolophus affinis [NCBITaxon:59477]", + "Sus scrofa domesticus [NCBITaxon:9825]", + "Viverridae [NCBITaxon:9673]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO_0001567", + "type": "string", + "description": "The taxonomic, or scientific name of the host.", + "examples": ["Homo sapiens [NCBITaxon:9606]"], + "genepio_label":"subject organism (host) taxonomic species", + + }, + "host_health_state": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Health status of the host at the time of sample collection.", + "clasification":"Host information", + "genepio_label":"", + + }, + "host_age": { + "examples": ["e.g. 65 or 7 months, or unknown. Caution: the host age may be considered public health identifiable information. Consult the data steward before sharing. If the information is unknown or can not be shared, put unknown"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Patient age", + "clasification":"Host information" + }, + + "host_sex": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Gender or sex of the host.", + "clasification":"Host information", + "genepio_label":"", + + }, + "host_subject_id": { + "examples": ["e.g. #131"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "a unique identifier by which each subject can be referred to, de-identified.", + "clasification":"Host information", + "genepio_label":"", + + }, + "type exposure": { + "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification":"Host information", + "genepio_label":"", + + }, + "subject exposure duration": { + "examples": ["e.g. Patient infected while traveling in …."], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification":"Host information", + "genepio_label":"", + + }, + "instrument_model": { + "Enums": ["454 Genome Sequencer [GENEPIO:0001937]", + "454 Genome Sequence 20 [OBI:0000689]", + "454 Genome Sequencer FLX [OBI:0000702]", + "454 Genome Sequencer FLX Titanium [GENEPIO:0001936]", + "454 Genome Sequencer Junior [GENEPIO:0001938]", + "AB SOLiD System [OBI:0000696]", + "SOLiD 3 Plus System [OBI:0002007]", + "SOLiD 4 [OBI:0002024]", + "SOLiD 4hq System [GENPIO:0001928]", + "SOLiD 5500 [GENPIO:0001929]", + "SOLiD 5500xl [GENPIO:0001930]", + "SOLiD PI System [GENPIO:0001931]", + "SOLiD System 2.0 [GENPIO:0001932]", + "SOLiD System 3.0 [GENPIO:0001933]", + "HeliScope Single Molecule Sequencer [OBI:0000717]", + "Illumina Genome Analyzer II [OBI:0000703]", + "Genome Analyzer IIe [OBI:0002027]", + "Genome Analyzer IIx [OBI:0002000]", + "Illumina HiSeq Sequencer [GENPIO:0001939]", + "Illumina HiSeq 1000 [OBI:0002022]", + "Illumina HiSeq 2000 [OBI:0002001]", + "Illumina HiSeq 2500 [OBI:0002002]", + "Illumina HiSeq 3000 [OBI:0002048]", + "Illumina HiSeq 4000 [OBI:0002049]", + "Ion Torrent PGM [GENPIO:0001935]", + "MiSeq [OBI:0002003]", + "NextSeq 500 [OBI:0002021]", + "PacBio RS II [OBI:0002012]", + ], + "ontology": "GENEPIO_0001921", + "type": "string", + "description": "The model of the sequencing instrument used.", + "examples": ["Oxford Nanopore MinION "], + "genepio_label":"sequencing instrument model", + + }, + "instrument_platform ": { + "examples": ["MinIon"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The model of the sequencing instrument used.", + "genepio_label":"", + + }, + "file_name": { + "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], + "ontology": "GENEPIO:0001476", + "type": "string", + "description": "The user-specified filename of the r1 FASTQ file.", + "clasification":"Bioinformatics and QC metrics", + "genepio_label":"", + + }, + "tax_id": { + "examples": ["probably 2697049 in all cases"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The NCBITaxon identifier for the organism being sequenced.", + "clasification":"Sample collection and processing", + "genepio_label":"", + + }, + "scientific_name": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The taxonomic name of the organism.", + "clasification":"Sample collection and processing", + "genepio_label":"", + + }, + "common_name": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The common name of the organism.", + "clasification":"Sample collection and processing", + "genepio_label":"", + + }, + "sample_description": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Free text description of the sample.", + "clasification":"Sample collection and processing", + "genepio_label":"", + + }, + "sample_storage_conditions": { + "examples": ["24 degrees celsius"], + "ontology": "NCIT_C115535", + "type": "string", + "description": "The name and version of a particular protocol used for sampling.", + "clasification":"Sample collection and processing" + }, + "library_source": { + "Enums": ["5-methycytidine antibody method [GENPIO:0001941]", + "CAGE method [GENPIO:0001942]", + "CF-H method [GENPIO:0001943]", + "CF-M method ]GENPIO:0001944]", + "CF-S method [GENPIO:0001945]", + "CF-T method [GENPIO:0001946]", + "ChIP method ]GENPIO:0001947]", + "DNAse method [GENPIO:0001948]", + "HMPR method [GENPIO:0001949]", + "Hybrid Selection Method [GENPIO:0001950]", + "MBD2 protein methyl-CpG binding domain method [GENPIO:0001951]", + "MF method [GENPIO:0001952]", + "MNase method [GENPIO:0001953]", + "MSLL method [GENPIO:0001954]", + "PCR method [GENPIO:0001955]", + "RACE method [GENPIO:0001956]", + "RANDOM PCR method [GENPIO:0001957]", + "RANDOM method [GENPIO:0001958]", + "RT-PCR method [GENPIO:0001959]", + "Reduced Representation method [GENPIO:0001960]", + "Resctriction Digest method [GENPIO:0001961]", + "cDNA method [GENPIO:0001962]", + "other library method [GENPIO:0001964]", + "size fractionation method [GENPIO:0001963]", + ], + "examples": ["METAGENOMIC"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Molecule type used to make the library.", + "clasification":"Sequencing", + }, + "library_selection": { + "examples": ["RANDOM PCR"], + "ontology": "GENPIO_0001940", + "type": "string", + "description": "Library capture method.", + "clasification":"Sequencing", + "genepio_label":"library selection", + + }, + "library_strategy": { + "Enums": ["Bisultife-Seq strategy [GENPIO:0001975]", + "CTS strategy [GENPIO:0001978]", + "ChIP-Seq strategy [GENPIO:0001979]", + "DNase-Hypersensitivity strategy [GENPIO:0001980]", + "EST strategy [GENPIO:0001981]", + "FL-cDNA strategy [GENPIO:0001983]", + "MB-Seq strategy [GENPIO:0001984]", + "MNase-Seq strategy [GENPIO:0001985]", + "MRE-Seq strategy [GENPIO:0001986]", + "MeDIP-Seq strategy [GENPIO:0001987]", + "RNA-Seq strategy [GENPIO:0001990]", + "WCS strategy [GENPIO:0001991]", + "WGS strategy [GENPIO:0001992]", + "WXS strategy [GENPIO:0001993]", + "amplicon strategy [GENPIO:0001974]", + "clone end strategy [GENPIO:0001976]", + "clone strategy [GENPIO:0001977]", + "finishing strategy [GENPIO:0001982]", + "other library strategy [GENPIO:0001988]", + "pool clone strategy [GENPIO:0001989]", + ], + "examples": ["WGS"], + "ontology": "GENPIO_0001973", + "type": "string", + "description": "Overall sequencing strategy or approach.", + "clasification":"Sequencing", + "genepio_label":"library strategy", + + }, + "library_layout": { + "examples": ["PAIRED"], + "ontology":"GENPIO_0000001", + "type": "string", + "description": "Single or paired.", + "clasification":"Sequencing", + "genepio_label":"library library_layout", + + }, + "library_name": { + "examples": ["e.g P17157_1007"], + "ontology": "GENEPIO_0001995", + "type": "string", + "description": "The submitter's name for this library.", + "clasification":"Sequencing", + "genepio_label":"Library Name", + }, + "nominal_length ": { + "examples": ["350"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing", + "genepio_label":"", + + }, + "analysis_accession": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "study_accession": { + "examples": ["e.g PRJEB39632"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "secondary_study_accession": { + "examples": ["e.g ERP123173"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "sample_accession": { + "examples": ["e.g SAMEA7098096"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "secondary_sample_accession": { + "examples": ["e.g ERS4858671"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "experiment_accession": { + "examples": ["e.g ERX4331406"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "run_accession": { + "examples": ["e.g ERX4331406"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "submission_accession": { + "examples": ["e.g ERA2794974"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "read_count": { + "examples": ["e.g 837055"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "base_count": { + "examples": ["e.g 503907110"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "center_name": { + "examples": [" KAROLINSKA INSITUTET"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The name of the institution", + "clasification":"Sample collection and processing", + "genepio_label":"", + + }, + "first_public": { + "examples": ["e.g 2020-08-07"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "last_updated": { + "examples": ["e.g 2020-07-29"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "format":"date", + "genepio_label":"", + + }, + "experiment_title": { + "examples": ["e.g Illumina MiSeq paired end sequencing"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "study_title": { + "examples": ["e.g SARS-CoV-2 genomes from late April in Stockholm"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "study_alias": { + "examples": ["e.g Sweden"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "experiment_alias": { + "examples": ["e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + 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"clasification":"Submission ENA", + "genepio_label":"", + + }, + "sra_aspera": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "sra_galaxy": { + "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "broker_name": { + "examples": ["P17157_1007"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "nominal_sdev": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + "first_created": { + "examples": ["e.g 2020-08-07"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "genepio_label":"", + + }, + + } +} + + +phage_schema= { + "$schema": "http://json-schema.org/draft/2020-12/schema", + "required": [ + "sample_name", + "collecting_institution", + "submitting_institution", + "sample_collection_date", + "geo_loc_country", + "geo_loc_state", + "organism", + "isolate", + "host_scientific_name", + "host_disease", + "sequencing_instrument_model", + "sequencing_instrument_platform", + "consensus_sequence_software_name", + "consensus_sequence_software_version" + ], + "type": "object", + "properties": { + "sample_name": { + "examples": ["prov_rona_99"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The user-defined name for the sample.", + "clasification":"Database Identifiers" + }, + "collecting_institution": { + "examples": ["Public Health Agency of Canada"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The name of the agency that collected the original sample." + }, + "submitting_institution": { + "examples": ["Centers for Disease Control and Prevention"], + "ontology": "GENEPIO:0001159", + "type": "string", + "description": "The name of the agency that generated the sequence." + }, + "sample_collection_date": { + "examples": ["3/19/2020"], + "ontology": "GENEPIO:0001174", + "type": "string", + "description": "The date on which the sample was collected.", + "format":"date" + }, + "geo_loc_country": { + "Enums": [ + "Afghanistan [GAZ:00006882]", + "Albania [GAZ:00002953]", + "Algeria [GAZ:00000563]", + "American Samoa [GAZ:00003957]", + "Andorra [GAZ:00002948]", + "Angola [GAZ:00001095]", + "Anguilla [GAZ:00009159]", + "Antarctica [GAZ:00000462]", + "Antigua and Barbuda [GAZ:00006883]", + "Argentina [GAZ:00002928]", + "Armenia [GAZ:00004094]", + "Aruba [GAZ:00004025]", + "Ashmore and Cartier Islands [GAZ:00005901]", + "Australia [GAZ:00000463]", + "Austria [GAZ:00002942]", + "Azerbaijan [GAZ:00004941]", + "Bahamas [GAZ:00002733]", + "Bahrain [GAZ:00005281]", + "Baker Island [GAZ:00007117]", + "Bangladesh [GAZ:00003750]", + "Barbados [GAZ:00001251]", + "Bassas da India [GAZ:00005810]", + "Belarus [GAZ:00006886]", + "Belgium [GAZ:00002938]", + "Belize [GAZ:00002934]", + "Benin [GAZ:00000904]", + "Bermuda [GAZ:00001264]", + "Bhutan [GAZ:00003920]", + "Bolivia [GAZ:00002511]", + "Borneo [GAZ:00025355]", + "Bosnia and Herzegovina [GAZ:00006887]", + "Botswana [GAZ:00001097]", + "Bouvet Island [GAZ:00001453]", + "Brazil [GAZ:00002828]", + "British Virgin Islands [GAZ:00003961]", + "Brunei [GAZ:00003901]", + "Bulgaria [GAZ:00002950]", + "Burkina Faso [GAZ:00000905]", + "Burundi [GAZ:00001090]", + "Cambodia [GAZ:00006888]", + "Cameroon [GAZ:00001093]", + "Canada [GAZ:00002560]", + "Cape Verde [GAZ:00001227]", + "Cayman Islands [GAZ:00003986]", + "Central African Republic [GAZ:00001089]", + "Chad [GAZ:00000586]", + "Chile [GAZ:00002825]", + "China [GAZ:00002845]", + "Christmas Island [GAZ:00005915]", + "Clipperton Island [GAZ:00005838]", + "Cocos Islands [GAZ:00009721]", + "Colombia [GAZ:00002929]", + "Comoros [GAZ:00005820]", + "Cook Islands [GAZ:00053798]", + "Coral Sea Islands [GAZ:00005917]", + "Costa Rica [GAZ:00002901]", + "Cote d'Ivoire [GAZ:00000906]", + "Croatia [GAZ:00002719]", + "Cuba [GAZ:00003762]", + "Curacao [GAZ:00012582]", + "Cyprus [GAZ:00004006]", + "Czech Republic [GAZ:00002954]", + "Democratic Republic of the Congo [GAZ:00001086]", + "Denmark [GAZ:00005852]", + "Djibouti [GAZ:00000582]", + "Dominica [GAZ:00006890]", + "Dominican Republic [GAZ:00003952]", + "Ecuador [GAZ:00002912]", + "Egypt [GAZ:00003934]", + "El Salvador [GAZ:00002935]", + "Equatorial Guinea [GAZ:00001091]", + "Eritrea [GAZ:00000581]", + "Estonia [GAZ:00002959]", + "Eswatini [GAZ:00001099]", + "Ethiopia [GAZ:00000567]", + "Europa Island [GAZ:00005811]", + "Falkland Islands (Islas Malvinas) [GAZ:00001412]", + "Faroe Islands [GAZ:00059206]", + "Fiji [GAZ:00006891]", + "Finland [GAZ:00002937]", + "France [GAZ:00003940]", + "French Guiana [GAZ:00002516]", + "French Polynesia [GAZ:00002918]", + "French Southern and Antarctic Lands [GAZ:00003753]", + "Gabon [GAZ:00001092]", + "Gambia [GAZ:00000907]", + "Gaza Strip [GAZ:00009571]", + "Georgia [GAZ:00004942]", + "Germany [GAZ:00002646]", + "Ghana [GAZ:00000908]", + "Gibraltar [GAZ:00003987]", + "Glorioso Islands [GAZ:00005808]", + "Greece [GAZ:00002945]", + "Greenland [GAZ:00001507]", + "Grenada [GAZ:02000573]", + "Guadeloupe [GAZ:00067142]", + "Guam [GAZ:00003706]", + "Guatemala [GAZ:00002936]", + "Guernsey [GAZ:00001550]", + "Guinea [GAZ:00000909]", + "Guinea-Bissau [GAZ:00000910]", + "Guyana [GAZ:00002522]", + "Haiti [GAZ:00003953]", + "Heard Island and McDonald Islands [GAZ:00009718]", + "Honduras [GAZ:00002894]", + "Hong Kong [GAZ:00003203]", + "Howland Island [GAZ:00007120]", + "Hungary [GAZ:00002952]", + "Iceland [GAZ:00000843]", + "India [GAZ:00002839]", + "Indonesia [GAZ:00003727]", + "Iran [GAZ:00004474]", + "Iraq [GAZ:00004483]", + "Ireland [GAZ:00002943]", + "Isle of Man [GAZ:00052477]", + "Israel [GAZ:00002476]", + "Italy [GAZ:00002650]", + "Jamaica [GAZ:00003781]", + "Jan Mayen [GAZ:00005853]", + "Japan [GAZ:00002747]", + "Jarvis Island [GAZ:00007118]", + "Jersey [GAZ:00001551]", + "Johnston Atoll [GAZ:00007114]", + "Jordan [GAZ:00002473]", + "Juan de Nova Island [GAZ:00005809]", + "Kazakhstan [GAZ:00004999]", + "Kenya [GAZ:00001101]", + "Kerguelen Archipelago [GAZ:00005682]", + "Kingman Reef [GAZ:00007116]", + "Kiribati [GAZ:00006894]", + "Kosovo [GAZ:00011337]", + "Kuwait [GAZ:00005285]", + "Kyrgyzstan [GAZ:00006893]", + "Laos [GAZ:00006889]", + "Latvia [GAZ:00002958]", + "Lebanon [GAZ:00002478]", + "Lesotho [GAZ:00001098]", + "Liberia [GAZ:00000911]", + "Libya [GAZ:00000566]", + "Liechtenstein [GAZ:00003858]", + "Line Islands [GAZ:00007144]", + "Lithuania [GAZ:00002960]", + "Luxembourg [GAZ:00002947]", + "Macau [GAZ:00003202]", + "Madagascar [GAZ:00001108]", + "Malawi [GAZ:00001105]", + "Malaysia [GAZ:00003902]", + "Maldives [GAZ:00006924]", + "Mali [GAZ:00000584]", + "Malta [GAZ:00004017]", + "Marshall Islands [GAZ:00007161]", + "Martinique [GAZ:00067143]", + "Mauritania [GAZ:00000583]", + "Mauritius [GAZ:00003745]", + "Mayotte [GAZ:00003943]", + "Mexico [GAZ:00002852]", + "Micronesia [GAZ:00005862]", + "Midway Islands [GAZ:00007112]", + "Moldova [GAZ:00003897]", + "Monaco [GAZ:00003857]", + "Mongolia [GAZ:00008744]", + "Montenegro [GAZ:00006898]", + "Montserrat [GAZ:00003988]", + "Morocco [GAZ:00000565]", + "Mozambique [GAZ:00001100]", + "Myanmar [GAZ:00006899]", + "Namibia [GAZ:00001096]", + "Nauru [GAZ:00006900]", + "Navassa Island [GAZ:00007119]", + "Nepal [GAZ:00004399]", + "Netherlands [GAZ:00002946]", + "New Caledonia [GAZ:00005206]", + "New Zealand [GAZ:00000469]", + "Nicaragua [GAZ:00002978]", + "Niger [GAZ:00000585]", + "Nigeria [GAZ:00000912]", + "Niue [GAZ:00006902]", + "Norfolk Island [GAZ:00005908]", + "North Korea [GAZ:00002801]", + "North Macedonia [GAZ:00006895]", + "North Sea [GAZ:00002284]", + "Northern Mariana Islands [GAZ:00003958]", + "Norway [GAZ:00002699]", + "Oman [GAZ:00005283]", + "Pakistan [GAZ:00005246]", + "Palau [GAZ:00006905]", + "Panama [GAZ:00002892]", + "Papua New Guinea [GAZ:00003922]", + "Paracel Islands [GAZ:00010832]", + "Paraguay [GAZ:00002933]", + "Peru [GAZ:00002932]", + "Philippines [GAZ:00004525]", + "Pitcairn Islands [GAZ:00005867]", + "Poland [GAZ:00002939]", + "Portugal [GAZ:00004126]", + "Puerto Rico [GAZ:00006935]", + "Qatar [GAZ:00005286]", + "Republic of the Congo [GAZ:00001088]", + "Reunion [GAZ:00003945]", + "Romania [GAZ:00002951]", + "Ross Sea [GAZ:00023304]", + "Russia [GAZ:00002721]", + "Rwanda [GAZ:00001087]", + "Saint Helena [GAZ:00000849]", + "Saint Kitts and Nevis [GAZ:00006906]", + "Saint Lucia [GAZ:00006909]", + "Saint Pierre and Miquelon [GAZ:00003942]", + "Saint Martin [GAZ:00005841]", + "Saint Vincent and the Grenadines [GAZ:02000565]", + "Samoa [GAZ:00006910]", + "San Marino [GAZ:00003102]", + "Sao Tome and Principe [GAZ:00006927]", + "Saudi Arabia [GAZ:00005279]", + "Senegal [GAZ:00000913]", + "Serbia [GAZ:00002957]", + "Seychelles [GAZ:00006922]", + "Sierra Leone [GAZ:00000914]", + "Singapore [GAZ:00003923]", + "Sint Maarten [GAZ:00012579]", + "Slovakia [GAZ:00002956]", + "Slovenia [GAZ:00002955]", + "Solomon Islands [GAZ:00005275]", + "Somalia [GAZ:00001104]", + "South Africa [GAZ:00001094]", + "South Georgia and the South Sandwich Islands [GAZ:00003990]", + "South Korea [GAZ:00002802]", + "South Sudan [GAZ:00233439]", + "Spain [GAZ:00003936]", + "Spratly Islands [GAZ:00010831]", + "Sri Lanka [GAZ:00003924]", + "State of Palestine [GAZ:00002475]", + "Sudan [GAZ:00000560]", + "Suriname [GAZ:00002525]", + "Svalbard [GAZ:00005396]", + "Swaziland [GAZ:00001099]", + "Sweden [GAZ:00002729]", + "Switzerland [GAZ:00002941]", + "Syria [GAZ:00002474]", + "Taiwan [GAZ:00005341]", + "Tajikistan [GAZ:00006912]", + "Tanzania [GAZ:00001103]", + "Thailand [GAZ:00003744]", + "Timor-Leste [GAZ:00006913]", + "Togo [GAZ:00000915]", + "Tokelau [GAZ:00260188]", + "Tonga [GAZ:00006916]", + "Trinidad and Tobago [GAZ:00003767]", + "Tromelin Island [GAZ:00005812]", + "Tunisia [GAZ:00000562]", + "Turkey [GAZ:00000558]", + "Turkmenistan [GAZ:00005018]", + "Turks and Caicos Islands [GAZ:00003955]", + "Tuvalu [GAZ:00009715]", + "USA [GAZ:00002459]", + "Uganda [GAZ:00001102]", + "Ukraine [GAZ:00002724]", + "United Arab Emirates [GAZ:00005282]", + "United Kingdom [GAZ:00002637]", + "Uruguay [GAZ:00002930]", + "Uzbekistan [GAZ:00004979]", + "Vanuatu [GAZ:00006918]", + "Venezuela [GAZ:00002931]", + "Viet Nam [GAZ:00003756]", + "Virgin Islands [GAZ:00003959]", + "Wake Island [GAZ:00007111]", + "Wallis and Futuna [GAZ:00007191]", + "West Bank [GAZ:00009572]", + "Western Sahara [GAZ:00000564]", + "Yemen [GAZ:00005284]", + "Zambia [GAZ:00001107]", + "Zimbabwe [GAZ:00001106]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001181", + "type": "string", + "description": "The country of origin of the sample.", + "examples": ["South Africa [GAZ:00001094]"] + }, + "geo_loc_state": { + "examples": ["Western Cape"], + "ontology": "GENEPIO:0001185", + "type": "string", + "description": "The state/province/territory of origin of the sample." + }, + "organism": { + "Enums": [ + "Coronaviridae [NCBITaxon:11118]", + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001191", + "type": "string", + "description": "Taxonomic name of the organism.", + "examples": [ + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]" + ] + }, + "isolate": { + "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"], + "ontology": "GENEPIO:0001644", + "type": "string", + "description": "Identifier of the specific isolate.", + "clasification":"Sample collection and processing" + }, + "purpose_sampling": { + "examples": ["Diagnostic testing"], + "ontology": "NCIT_C146997", + "type": "string", + "description": "The reason that the sample was collected.", + "clasification":"Sample collection and processing" + }, + "host_scientific_name": { + "Enums": [ + "Bos taurus [NCBITaxon:9913]", + "Canis lupus familiaris [NCBITaxon:9615]", + "Chiroptera [NCBITaxon:9397]", + "Columbidae [NCBITaxon:8930]", + "Felis catus [NCBITaxon:9685]", + "Gallus gallus [NCBITaxon:9031]", + "Homo sapiens [NCBITaxon:9606]", + "Manis [NCBITaxon:9973]", + "Manis javanica [NCBITaxon:9974]", + "Neovison vison [NCBITaxon:452646]", + "Panthera leo [NCBITaxon:9689]", + "Panthera tigris [NCBITaxon:9694]", + "Rhinolophidae [NCBITaxon:58055]", + "Rhinolophus affinis [NCBITaxon:59477]", + "Sus scrofa domesticus [NCBITaxon:9825]", + "Viverridae [NCBITaxon:9673]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001387", + "type": "string", + "description": "The taxonomic, or scientific name of the host.", + "examples": ["Homo sapiens [NCBITaxon:9606]"] + }, + "host_health_state": { + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Health status of the host at the time of sample collection.", + }, + "host_gender": { + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Gender or sex of the host.", + }, + "host_subject_id": { + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "a unique identifier by which each subject can be referred to, de-identified, e.g. #131", + }, + + "host_disease": { + "Enums": [ + "COVID-19 [MONDO:0100096]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001391", + "type": "string", + "description": "The name of the disease experienced by the host.", + "examples": ["COVID-19 [MONDO:0100096]"] + }, + "sequencing_instrument_model": { + "Enums": [ + "Illumina sequencing instrument [GENEPIO:0100105]", + "Illumina Genome Analyzer [GENEPIO:0100106]", + "Illumina Genome Analyzer II [GENEPIO:0100107]", + "Illumina Genome Analyzer IIx [GENEPIO:0100108]", + "Illumina HiScanSQ [GENEPIO:0100109]", + "Illumina HiSeq [GENEPIO:0100110]", + "Illumina HiSeq X [GENEPIO:0100111]", + "Illumina HiSeq X Five [GENEPIO:0100112]", + "Illumina HiSeq X Ten [GENEPIO:0100113]", + "Illumina HiSeq 1000 [GENEPIO:0100114]", + "Illumina HiSeq 1500 [GENEPIO:0100115]", + "Illumina HiSeq 2000 [GENEPIO:0100116]", + "Illumina HiSeq 2500 [GENEPIO:0100117]", + "Illumina HiSeq 3000 [GENEPIO:0100118]", + "Illumina HiSeq 4000 [GENEPIO:0100119]", + "Illumina iSeq [GENEPIO:0100120]", + "Illumina iSeq 100 [GENEPIO:0100121]", + "Illumina NovaSeq [GENEPIO:0100122]", + "Illumina NovaSeq 6000 [GENEPIO:0100123]", + "Illumina MiniSeq [GENEPIO:0100124]", + "Illumina MiSeq [GENEPIO:0100125]", + "Illumina NextSeq [GENEPIO:0100126]", + "Illumina NextSeq 500 [GENEPIO:0100127]", + "Illumina NextSeq 550 [GENEPIO:0100128]", + "Illumina NextSeq 2000 [GENEPIO:0100129]", + "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", + "PacBio RS [GENEPIO:0100131]", + "PacBio RS II [GENEPIO:0100132]", + "PacBio Sequel [GENEPIO:0100133]", + "PacBio Sequel II [GENEPIO:0100134]", + "Ion Torrent sequencing instrument [GENEPIO:0100135]", + "Ion Torrent PGM [GENEPIO:0100136]", + "Ion Torrent Proton [GENEPIO:0100137]", + "Ion Torrent S5 XL [GENEPIO:0100138]", + "Ion Torrent S5 [GENEPIO:0100139]", + "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", + "Oxford Nanopore GridION [GENEPIO:0100141]", + "Oxford Nanopore MinION [GENEPIO:0100142]", + "Oxford Nanopore PromethION [GENEPIO:0100143]", + "BGI Genomics sequencing instrument [GENEPIO:0100144]", + "BGI SEQ-500 [GENEPIO:0100145]", + "MGI sequencing instrument [GENEPIO:0100146]", + "MGI DNBSEQ-T7 [GENEPIO:0100147]", + "MGI DNBSEQ-G400 [GENEPIO:0100148]", + "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", + "MGI DNBSEQ-G50 [GENEPIO:0100150]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001452", + "type": "string", + "description": "The model of the sequencing instrument used.", + "examples": ["Oxford Nanopore MinION [GENEPIO:0100142]"] + }, + "sequencing_instrument_platform": { + "examples": ["MinIon"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The model of the sequencing instrument used." + }, + "consensus_sequence_software_name": { + "examples": ["Ivar"], + "ontology": "GENEPIO:0001463", + "type": "string", + "description": "The name of software used to generate the consensus sequence." + }, + "consensus_sequence_software_version": { + "examples": ["1.3"], + "ontology": "GENEPIO:0001469", + "type": "string", + "description": "The version of the software used to generate the consensus sequence." + }, + "submitting_lab_sequence_id": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Sample ID given by the submitting laboratory" + }, + "bioproject_umbrella_accession_ENA": { + "examples": ["PRJNA623807"], + "ontology": "GENEPIO:0001133", + "type": "string", + "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", + "clasification":"Database Identifiers" + }, + "bioproject_accession_ENA": { + "examples": ["PRJNA12345"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", + "clasification":"Database Identifiers" + }, + "biosample_accession_ENA": { + "examples": ["SAMN14180202"], + "ontology": "GENEPIO:0001139", + "type": "string", + "description": "The identifier assigned to a BioSample in INSDC archives.", + "clasification":"Database Identifiers" + }, + "sra_accession": { + "examples": ["SRR11177792"], + "ontology": "GENEPIO:0001142", + "type": "string", + "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", + "clasification":"Database Identifiers" + }, + "genBank/ENA/DDBJ_accession": { + "examples": ["MN908947.3"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", + "clasification":"Database Identifiers" + }, + "gisaid_accession": { + "examples": ["EPI_ISL_123456"], + "ontology": "GENEPIO:0001147", + "type": "string", + "description": "The GISAID accession number assigned to the sequence.", + "clasification":"Database Identifiers" + }, + "virus_name": { + "examples": ["hCoV-19/Canada/prov_rona_99/2020"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The user-defined GISAID virus name assigned to the sequence.", + "clasification":"Database Identifiers" + }, + "collecting_institution_email": { + "examples": ["johnnyblogs@lab.ca"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "clasification":"Sample collection and processing" + }, + "collecting_institution_address": { + "examples": ["655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada"], + "ontology": "GENEPIO:0001158", + "type": "string", + "description": "The mailing address of the agency submitting the sample.", + "clasification":"Sample collection and processing" + }, + "submitting_institution_email": { + "examples": ["RespLab@lab.ca"], + "ontology": "GENEPIO:0001165", + "type": "string", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "clasification":"Sample collection and processing" + }, + "submitting_institution_address": { + "examples": ["123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The mailing address of the agency submitting the sequence.", + "clasification":"Sample collection and processing" + }, + "sample_received_date": { + "examples": ["3/21/2020"], + "ontology": "GENEPIO:0001179", + "type": "string", + "description": "The date on which the sample was received.", + "format":"date", + "clasification":"Sample collection and processing" + }, + "results_emission_date": { + "examples": ["3/23/2020"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The date on which the results were emitted.", + "format":"date", + "clasification":"Sample collection and processing" + }, + "geo_loc_region": { + "examples": ["Derbyshire"], + "ontology": "GENEPIO:0100280", + "type": "string", + "description": "The county/region of origin of the sample.", + "clasification":"Sample collection and processing" + }, + "geo_loc_city": { + "examples": ["Vancouver"], + "ontology": "GENEPIO:0001189", + "type": "string", + "description": "The city of origin of the sample.", + "clasification":"Sample collection and processing" + }, + "geo_loc_latitude": { + "examples": ["38.98 N"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The latitude coordinates of the geographical location of sample collection.", + "clasification":"Sample collection and processing" + }, + "geo_loc_longitude": { + "examples": ["77.11 W"], + "ontology": "OBI:0001621", + "type": "string", + "description": "The longitude coordinates of the geographical location of sample collection.", + "clasification":"Sample collection and processing" + }, + "anatomical_material": { + "Enums": [ + "Blood [UBERON:0000178]", + "Fluid [UBERON:0006314]", + "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", + "Fluid (Pericardial) [UBERON:0002409]", + "Fluid (Pleural) [UBERON:0001087]", + "Fluid (Vaginal) [UBERON:0036243]", + "Fluid (Amniotic) [UBERON:0000173]", + "Saliva [UBERON:0001836]", + "Tissue [UBERON:0000479]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001211", + "type": "string", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "examples": ["Blood [UBERON:0000178]"] + }, + "anatomical_part": { + "Enums": [ + "Anus [UBERON:0001245]", + "Duodenum [UBERON:0002114]", + "Eye [UBERON:0000970]", + "Intestine [UBERON:0000160]", + "Lower respiratory tract [UBERON:0001558]", + "Bronchus [UBERON:0002185]", + "Lung [UBERON:0002048]", + "Bronchiole [UBERON:0002186]", + "Alveolar sac [UBERON:0002169]", + "Pleural sac [UBERON:0009778]", + "Pleural cavity [UBERON:0002402]", + "Trachea [UBERON:0003126]", + "Rectum [UBERON:0001052]", + "Skin [UBERON:0001003]", + "Stomach [UBERON:0000945]", + "Upper respiratory tract [UBERON:0001557]", + "Anterior Nares [UBERON:2001427]", + "Esophagus [UBERON:0001043]", + "Ethmoid sinus [UBERON:0002453]", + "Nasal Cavity [UBERON:0001707]", + "Middle Nasal Turbinate [UBERON:0005921]", + "Inferior Nasal Turbinate [UBERON:0005922]", + "Nasopharynx (NP) [UBERON:0001728]", + "Oropharynx (OP) [UBERON:0001729]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001214", + "type": "string", + "description": "An anatomical part of an organism e.g. oropharynx. ", + "examples": ["Nasopharynx (NP) [UBERON:0001728]"] + }, + "body_product": { + "Enums": [ + "Breast Milk [UBERON:0001913]", + "Feces [UBERON:0001988]", + "Mucus [UBERON:0000912]", + "Semen [UBERON:0006530]", + "Sputum [UBERON:0007311]", + "Sweat [UBERON:0001089]", + "Tear [UBERON:0001827]", + "Urine [UBERON:0001088]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001216", + "type": "string", + "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", + "examples": ["Feces [UBERON:0001988]"] + }, + "environmental_material": { + "Enums": [ + "Air vent [ENVO:03501208]", + "Banknote [ENVO:00003896]", + "Bed rail [ENVO:03501209]", + "Building Floor [ENVO:01000486]", + "Cloth [ENVO:02000058]", + "Control Panel [ENVO:03501210]", + "Door [ENVO:03501220]", + "Door Handle [ENVO:03501211]", + "Face Mask [OBI:0002787]", + "Face Shield [OBI:0002791]", + "Food [FOODON:00002403]", + "Food Packaging [FOODON:03490100]", + "Glass [ENVO:01000481]", + "Handrail [ENVO:03501212]", + "Hospital Gown [OBI:0002796]", + "Light Switch [ENVO:03501213]", + "Locker [ENVO:03501214]", + "N95 Mask [OBI:0002790]", + "Nurse Call Button [ENVO:03501215]", + "Paper [ENVO:03501256]", + "Particulate Matter [ENVO:01000060]", + "Plastic [ENVO:01000404]", + "PPE Gown [GENEPIO:0100025]", + "Sewage [ENVO:00002018]", + "Sink [ENVO:01000990]", + "Soil [ENVO:00001998]", + "Stainless Steel [ENVO:03501216]", + "Tissue Paper [ENVO:03501217]", + "Toilet Bowl [ENVO:03501218]", + "Water [ENVO:00002006]", + "Wastewater [ENVO:00002001]", + "Window [ENVO:03501219]", + "Wood [ENVO:00002040]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001223", + "type": "string", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "examples": ["Face Mask [OBI:0002787]"] + }, + "environmental_site": { + "Enums": [ + "Acute care facility [ENVO:03501135]", + "Animal house [ENVO:00003040]", + "Bathroom [ENVO:01000422]", + "Clinical assessment centre [ENVO:03501136]", + "Conference venue [ENVO:03501127]", + "Corridor [ENVO:03501121]", + "Daycare [ENVO:01000927]", + "Emergency room (ER) [ENVO:03501145]", + "Family practice clinic [ENVO:03501186]", + "Group home [ENVO:03501196]", + "Homeless shelter [ENVO:03501133]", + "Hospital [ENVO:00002173]", + "Intensive Care Unit (ICU) [ENVO:03501152]", + "Long Term Care Facility [ENVO:03501194]", + "Patient room [ENVO:03501180]", + "Prison [ENVO:03501204]", + "Production Facility [ENVO:01000536]", + "School [ENVO:03501130]", + "Sewage Plant [ENVO:00003043]", + "Subway train [ENVO:03501109]", + "Wet market [ENVO:03501198]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001232", + "type": "string", + "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", + "examples": ["Hospital [ENVO:00002173]"] + }, + "collection_device": { + "Enums": [ + "Air filter [ENVO:00003968]", + "Blood Collection Tube [OBI:0002859]", + "Bronchoscope [OBI:0002826]", + "Collection Container [OBI:0002088]", + "Collection Cup [GENEPIO:0100026]", + "Fibrobronchoscope Brush [OBI:0002825]", + "Filter [GENEPIO:0100103]", + "Fine Needle [OBI:0002827]", + "Microcapillary tube [OBI:0002858]", + "Micropipette [OBI:0001128]", + "Needle [OBI:0000436]", + "Serum Collection Tube [OBI:0002860]", + "Sputum Collection Tube [OBI:0002861]", + "Suction Catheter [OBI:0002831]", + "Swab [GENEPIO:0100027]", + "Urine Collection Tube [OBI:0002862]", + "Virus Transport Medium [OBI:0002866]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001234", + "type": "string", + "description": "The instrument or container used to collect the sample e.g. swab.", + "examples": ["Swab [GENEPIO:0100027]"] + }, + "collection_method": { + "Enums": [ + "Amniocentesis [NCIT:C52009]", + "Aspiration [NCIT:C15631]", + "Suprapubic Aspiration [GENEPIO:0100028]", + "Tracheal Aspiration [GENEPIO:0100029]", + "Vacuum Aspiration [GENEPIO:0100030]", + "Biopsy [OBI:0002650]", + "Needle Biopsy [OBI:0002651]", + "Filtration [OBI:0302885]", + "Air Filtration [GENEPIO:0100031]", + "Lavage [OBI:0600044]", + "Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]", + "Gastric Lavage [GENEPIO:0100033]", + "Lumbar Puncture [NCIT:C15327]", + "Necropsy [MMO:0000344]", + "Phlebotomy [NCIT:C28221]", + "Rinsing [GENEPIO:0002116]", + "Saline gargle (mouth rinse and gargle) [GENEPIO:0100034]", + "Scraping [GENEPIO:0100035]", + "Swabbing [GENEPIO:0002117]", + "Finger Prick [GENEPIO:0100036]", + "Washout Tear Collection [GENEPIO:0100038]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001241", + "type": "string", + "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", + "examples": ["Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]"] + }, + "collection_protocol": { + "examples": ["SC2SamplingProtocol 1.2"], + "ontology": "GENEPIO:0001243", + "type": "string", + "description": "Conditions at which sample was stored, usually storage temperature, duration and location", + "clasification":"Sample collection and processing" + }, + "sample_storage_conditions": { + "examples": ["24 degrees celsius"], + "ontology": "NCIT_C115535", + "type": "string", + "description": "The name and version of a particular protocol used for sampling.", + "clasification":"Sample collection and processing" + }, + "specimen_processing": { + "Enums": [ + "Virus Passage [GENEPIO:0100039]", + "RNA Re-Extraction (Post RT-PCR) [GENEPIO:0100040]", + "Specimens Pooled [OBI:0600016]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001253", + "type": "string", + "description": "Any processing applied to the sample during or after receiving the sample. ", + "examples": ["Virus Passage [GENEPIO:0100039]"] + }, + "lab_host": { + "Enums": [ + "293/ACE2 Cell Line [GENEPIO:0100041]", + "Caco2 Cell Line [BTO:0000195]", + "Calu3 Cell Line [BTO:0002750]", + "EFK3B Cell Line [GENEPIO:0100042]", + "HEK293T Cell Line [BTO:0002181]", + "HRCE Cell Line [GENEPIO:0100043]", + "Huh7 Cell Line [BTO:0001950]", + "LLCMk2 Cell Line [CLO:0007330]", + "MDBK Cell Line [BTO:0000836]", + "NHBE Cell Line [BTO:0002924]", + "PK-15 Cell Line [BTO:0001865]", + "RK-13 Cell Line [BTO:0002909]", + "U251 Cell Line [BTO:0002035]", + "Vero Cell Line [BTO:0001444]", + "Vero E6 Cell Line [BTO:0004755]", + "Vero E6/TMPRSS2 Cell Line [GENEPIO:0100044]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001255", + "type": "string", + "description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.", + "examples": ["Vero E6 Cell Line [BTO:0004755]"] + }, + "passage_number": { + "examples": ["3"], + "ontology": "GENEPIO:0001261", + "type": "string", + "description": "Number of passages.", + "clasification":"Sample collection and processing" + }, + "passage_method": { + "examples": ["AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain."], + "ontology": "GENEPIO:0001264", + "type": "string", + "description": "Description of how organism was passaged.", + "clasification":"Sample collection and processing" + }, + "biomaterial_extracted": { + "Enums": [ + "mRNA (cDNA) [OBI:0002754]", + "RNA (Total) [OBI:0000895]", + "RNA (Poly-A) [OBI:0000869]", + "RNA (Ribo-Depleted) [OBI:0002627]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001266", + "type": "string", + "description": "The biomaterial extracted from samples for the purpose of sequencing.", + "examples": ["RNA (Total) [OBI:0000895]"] + }, + "tax_id": { + "examples": ["probably 2697049 in all cases"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The NCBITaxon identifier for the organism being sequenced.", + "clasification":"Sample collection and processing" + }, + "scientific_name": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The taxonomic name of the organism.", + "clasification":"Sample collection and processing" + }, + "common_name": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The common name of the organism.", + "clasification":"Sample collection and processing" + }, + "sample_description": { + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Free text description of the sample.", + "clasification":"Sample collection and processing" + }, + + "center_name": { + "examples": [" KAROLINSKA INSITUTET"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The name of the institution", + "clasification":"Sample collection and processing" + }, + + "virus_id": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The user-defined name for the sample.", + "clasification":"Database Identifiers" + }, + "host_common_name": { + "Enums": [ + "Human [NCBITaxon:9606]", + "Bat [NCBITaxon:9397]", + "Cat [NCBITaxon:9685]", + "Chicken [NCBITaxon:9031]", + "Civet [NCBITaxon:9673]", + "Cow [NCBITaxon:9913]", + "Dog [NCBITaxon:9615]", + "Lion [NCBITaxon:9689]", + "Mink [NCBITaxon:452646]", + "Pangolin [NCBITaxon:9973]", + "Pig [NCBITaxon:9825]", + "Pigeon [NCBITaxon:8930]", + "Tiger [NCBITaxon:9694]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001386", + "type": "string", + "description": "The commonly used name of the host.", + "examples": ["Human [NCBITaxon:9606]"] + }, + "outbreak": { + "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification":"Host information" + }, + "additional_host_information": { + "examples": ["e.g. Patient infected while traveling in …."], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification":"Host information" + }, + "host_age": { + "examples": ["e.g. 65 or 7 months, or unknown. Caution: the host age may be considered public health identifiable information. Consult the data steward before sharing. If the information is unknown or can not be shared, put unknown"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Patient age", + "clasification":"Host information" + }, + "host_age_unit": { + "examples": ["years"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The units used to measure the host's age.", + "clasification":"Host information" + }, + "host_age_bin": { + "examples": ["20-30"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The age category of the host at the time of sampling.", + "clasification":"Host information" + }, + "host_gender": { + "examples": ["Male, Female, or unknown.Caution: the host gender may be considered public health identifiable information. Consult the data steward before sharing. If the information is unknown or can not be shared, put unknown"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Gender", + "clasification":"Host information" + }, + "purpose_of_sequencing": { + "Enums": [ + "Baseline surveillance (random sampling) [GENEPIO:0100005]", + "Targeted surveillance (non-random sampling) [GENEPIO:0100006]", + "Priority surveillance projects [GENEPIO:0100007]", + "Screening for Variants of Concern (VOC) [GENEPIO:0100008]", + "Sample has epidemiological link to Variant of Concern (VoC) [GENEPIO:0100273]", + "Sample has epidemiological link to Omicron Variant [GENEPIO:0100274]", + "Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]", + "Re-infection surveillance [GENEPIO:0100010]", + "Vaccine escape surveillance [GENEPIO:0100011]", + "Travel-associated surveillance [GENEPIO:0100012]", + "Domestic travel surveillance [GENEPIO:0100013]", + "Interstate/ interprovincial travel surveillance [GENEPIO:0100275]", + "Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276]", + "International travel surveillance [GENEPIO:0100014]", + "Surveillance of international border crossing by air travel or ground transport [GENEPIO:0100015]", + "Surveillance of international border crossing by air travel [GENEPIO:0100016]", + "Surveillance of international border crossing by ground transport [GENEPIO:0100017]", + "Surveillance from international worker testing [GENEPIO:0100018]", + "Cluster/Outbreak investigation [GENEPIO:0100019]", + "Multi-jurisdictional outbreak investigation [GENEPIO:0100020]", + "Intra-jurisdictional outbreak investigation [GENEPIO:0100021]", + "Research [GENEPIO:0100022]", + "Viral passage experiment [GENEPIO:0100023]", + "Protocol testing [GENEPIO:0100024]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001445", + "type": "string", + "description": "The reason that the sample was sequenced.", + "examples": ["Baseline surveillance (random sampling) [GENEPIO:0100005]"] + }, + "purpose_of_sequencing_details": { + "Enums": [ + "Screened for S gene target failure (S dropout)", + "Screened for mink variants", + "Screened for B.1.1.7 variant", + "Screened for B.1.135 variant", + "Screened for P.1 variant", + "Screened due to travel history", + "Screened due to close contact with infected individual", + "Assessing public health control measures", + "Determining early introductions and spread", + "Investigating airline-related exposures", + "Investigating temporary foreign worker", + "Investigating remote regions", + "Investigating health care workers", + "Investigating schools/universities", + "Investigating reinfection" + ], + "ontology": "GENEPIO:0001446", + "type": "string", + "description": "The description of why the sample was sequenced providing specific details.", + "examples": ["Screened for S gene target failure (S dropout)"] + }, + "sequencing_date": { + "examples": ["4/26/2021"], + "ontology": "GENEPIO:0001447", + "type": "string", + "description": "The date the sample was sequenced.", + "format":"date", + "clasification":"Sequencing" + }, + "rna_extraction_Protocol": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + "library_kit": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + "library_name": { + "examples": ["e.g P17157_1007"], + "ontology": "GENEPIO_0001995", + "type": "string", + "description": "The submitter's name for this library.", + "clasification":"Sequencing", + "genepio_label":"Library Name", + }, + "enrichment_protocol": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + "if_enrichment_protocol_is_other_specify": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + "amplicon protocol": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + "if_amplicon_protocol_if_other_especify": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + + "amplicon_version": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + "amplicon_size": { + "examples": ["300bp"], + "ontology": "GENEPIO:0001449", + "type": "string", + "description": "The length of the amplicon generated by PCR amplification.", + "clasification":"Sequencing" + }, + + "was_phix_used?": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + + "number_of_samples_in_run": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + + "flowcell_kit": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + + "runID": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + + "sequencing_platforms": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + + "library_preparation_kit": { + "examples": ["Nextera XT"], + "ontology": "GENEPIO:0001450", + "type": "string", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "clasification":"Sequencing" + }, + + "flow_cell_barcode": { + "examples": ["FAB06069"], + "ontology": "GENEPIO:0001451", + "type": "string", + "description": "The barcode of the flow cell used for sequencing.", + "clasification":"Sequencing" + }, + "sequencing_protocol_name": { + "examples": ["1D_DNA_MinION, ARTIC Network Protocol V3"], + "ontology": "GENEPIO:0001453", + "type": "string", + "description": "The name and version number of the sequencing protocol used.", + "clasification":"Sequencing" + }, + "sequencing_protocol": { + "examples": ["Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits."], + "ontology": "GENEPIO:0001454", + "type": "string", + "description": "The protocol used to generate the sequence.", + "clasification":"Sequencing" + }, + "sequencing_kit_number": { + "examples": ["AB456XYZ789"], + "ontology": "GENEPIO:0001455", + "type": "string", + "description": "The manufacturer's kit number.", + "clasification":"Sequencing" + }, + "amplicon_pcr_primer_scheme": { + "examples": ["https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv"], + "ontology": "GENEPIO:0001456", + "type": "string", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "clasification":"Sequencing" + }, + "library_source": { + "examples": ["METAGENOMIC"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Molecule type used to make the library.", + "clasification":"Sequencing" + }, + "library_selection": { + "examples": ["RANDOM PCR"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Library capture method.", + "clasification":"Sequencing" + }, + "library_strategy": { + "examples": ["WGS"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Overall sequencing strategy or approach.", + "clasification":"Sequencing" + }, + "library_layout": { + "examples": ["PAIRED"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Single or paired.", + "clasification":"Sequencing" + }, + "library_name": { + "examples": ["P17157_1007"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Name of the used library", + "clasification":"Sequencing" + }, + "nominal_length ": { + "examples": ["350"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + + "raw_sequence_data_processing_method": { + "examples": ["Porechop 0.2.3"], + "ontology": "GENEPIO:0001458", + "type": "string", + "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "clasification":"Bioinformatics and QC metrics" + }, + "dehosting_method": { + "examples": ["Nanostripper"], + "ontology": "GENEPIO:0001459", + "type": "string", + "description": "The method used to remove host reads from the pathogen sequence.", + "clasification":"Bioinformatics and QC metrics" + }, + "assembly": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics" + }, + "if_assembly_other": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics" + }, + "assembly_params": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics" + }, + "variant_Calling": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics" + }, + "if_variant_Calling_other": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics" + }, + "variant_Calling_params": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics" + }, + "consensus_sequence_filepath": { + "examples": ["/User/Documents/RespLab/Data/ncov123assembly.fasta"], + "ontology": "GENEPIO:0001462", + "type": "string", + "description": "The filepath of the consesnsus sequence file.", + "clasification":"Bioinformatics and QC metrics" + }, + "consensus_sequence_software_name": { + "examples": ["Ivar"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The name of software used to generate the consensus sequence.", + "clasification":"Bioinformatics and QC metrics" + }, + "if_consensus_other": { + "examples": ["1.3"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The version of the software used to generate the consensus sequence.", + "clasification":"Bioinformatics and QC metrics" + }, + "consensus_sequence_software_version": { + "examples": ["1.3"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The version of the software used to generate the consensus sequence.", + "clasification":"Bioinformatics and QC metrics" + }, + "consensus_criteria": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics" + }, + "quality_control_metrics": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics" + }, + "breadth_of_coverage_value": { + "examples": ["95%"], + "ontology": "GENEPIO:0001472", + "type": "string", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "clasification":"Bioinformatics and QC metrics" + }, + "depth_of_coverage_value": { + "examples": ["400x"], + "ontology": "GENEPIO:0001474", + "type": "string", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "clasification":"Bioinformatics and QC metrics" + }, + "depth_of_coverage_threshold": { + "examples": ["100x"], + "ontology": "GENEPIO:0001475", + "type": "string", + "description": "The threshold used as a cut-off for the depth of coverage.", + "clasification":"Bioinformatics and QC metrics" + }, + "sequence_file_R1_fastq": { + "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], + "ontology": "GENEPIO:0001476", + "type": "string", + "description": "The user-specified filename of the r1 FASTQ file.", + "clasification":"Bioinformatics and QC metrics" + }, + "sequence_file_R2_fastq": { + "examples": ["ABC123_S1_L001_R2_001.fastq.gz"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The user-specified filename of the r2 FASTQ file.", + "clasification":"Bioinformatics and QC metrics" + }, + "r1_fastq_filepath": { + "examples": ["/User/Documents/RespLab/Data/"], + "ontology": "GENEPIO:0001478", + "type": "string", + "description": "The filepath of the r1 FASTQ file.", + "clasification":"Bioinformatics and QC metrics" + }, + "r2_fastq_filepath": { + "examples": ["/User/Documents/RespLab/Data/"], + "ontology": "GENEPIO:0001479", + "type": "string", + "description": "The filepath of the r2 FASTQ file.", + "clasification":"Bioinformatics and QC metrics" + }, + "fast5_filename": { + "examples": ["batch1a_sequences.fast5"], + "ontology": "GENEPIO:0001480", + "type": "string", + "description": "The user-specified filename of the FAST5 file.", + "clasification":"Bioinformatics and QC metrics" + }, + "fast5_filepath": { + "examples": ["/User/Documents/RespLab/Data/"], + "ontology": "GENEPIO:0001481", + "type": "string", + "description": "The filepath of the FAST5 file.", + "clasification":"Bioinformatics and QC metrics" + }, + "number_of_base_pairs_sequenced": { + "examples": ["387566"], + "ontology": "GENEPIO:0001482", + "type": "string", + "description": "The number of total base pairs generated by the sequencing process.", + "clasification":"Bioinformatics and QC metrics" + }, + "consensus_genome_length": { + "examples": ["38677"], + "ontology": "GENEPIO:0001483", + "type": "string", + "description": "Size of the assembled genome described as the number of base pairs.", + "clasification":"Bioinformatics and QC metrics" + }, + "ns_per_100_kbp": { + "examples": ["300"], + "ontology": "GENEPIO:0001484", + "type": "string", + "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", + "clasification":"Bioinformatics and QC metrics" + }, + "reference_genome_accession": { + "examples": ["NC_045512.2"], + "ontology": "GENEPIO:0001485", + "type": "string", + "description": "A persistent, unique identifier of a genome database entry.", + "clasification":"Bioinformatics and QC metrics" + }, + "bioinformatics_protocol": { + "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], + "ontology": "GENEPIO:0001489", + "type": "string", + "description": "The name of the bioinformatics protocol used.", + "clasification":"Bioinformatics and QC metrics" + }, + "if_bioinformatic_protocol_is_other_specify": { + "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The name of the bioinformatics protocol used.", + "clasification":"Bioinformatics and QC metrics" + }, + "bioinformatic_protocol_version": { + "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The version number of the bioinformatics protocol used.", + "clasification":"Bioinformatics and QC metrics" + }, + "commercial/open-source/both": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics" + }, + "preprocessing": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics" + }, + "if_preprocessing_other": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics" + }, + "preprocessing_params": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics" + }, + "mapping": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Lineage and Variant information" + }, + "if_mapping_other": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Lineage and Variant information" + }, + "Mapping_params": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Lineage and Variant information" + }, + "lineage/clade_name": { + "examples": ["B.1.1.7"], + "ontology": "GENEPIO:0001500", + "type": "string", + "description": "The name of the lineage or clade.", + "clasification":"Lineage and Variant information" + }, + "lineage/clade_analysis_software_name": { + "examples": ["Pangolin"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The name of the software used to determine the lineage/clade.", + "clasification":"Lineage and Variant information" + }, + "if_lineage_identification_other": { + "examples": ["Other than Pangolin"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The name of the software used to determine the lineage/clade.", + "clasification":"Lineage and Variant information" + }, + "lineage/clade_analysis_software_version": { + "examples": ["2.1.10"], + "ontology":"GENEPIO:0001502", + "type": "string", + "description": "The version of the software used to determine the lineage/clade.", + "clasification":"Lineage and Variant information" + }, + "variant_designation": { + "Enums": [ + "Variant of Interest (VOI) [GENEPIO:0100082]", + "Variant of Concern (VOC) [GENEPIO:0100083]", + "Variant Under Monitoring (VUM) [GENEPIO:0100279]" + ], + "ontology": "GENEPIO:0001503", + "type": "string", + "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", + "examples": ["Variant of Concern (VOC) [GENEPIO:0100083]"] + }, + "variant_evidence": { + "examples": ["lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)"], + "ontology": "GENEPIO:0001504", + "type": "string", + "description": "The evidence used to make the variant determination.", + "clasification":"Lineage and Variant information" + }, + "gene_name_1": { + "Enums": [ + "E gene (orf4) [GENEPIO:0100151]", + "M gene (orf5) [GENEPIO:0100152]", + "N gene (orf9) [GENEPIO:0100153]", + "Spike gene (orf2) [GENEPIO:0100154]", + "orf1ab (rep) [GENEPIO:0100155]", + "orf1a (pp1a) [GENEPIO:0100156]", + "nsp11 [GENEPIO:0100157]", + "nsp1 [GENEPIO:0100158]", + "nsp2 [GENEPIO:0100159]", + "nsp3 [GENEPIO:0100160]", + "nsp4 [GENEPIO:0100161]", + "nsp5 [GENEPIO:0100162]", + "nsp6 [GENEPIO:0100163]", + "nsp7 [GENEPIO:0100164]", + "nsp8 [GENEPIO:0100165]", + "nsp9 [GENEPIO:0100166]", + "nsp10 [GENEPIO:0100167]", + "RdRp gene (nsp12) [GENEPIO:0100168]", + "hel gene (nsp13) [GENEPIO:0100169]", + "exoN gene (nsp14) [GENEPIO:0100170]", + "nsp15 [GENEPIO:0100171]", + "nsp16 [GENEPIO:0100172]", + "orf3a [GENEPIO:0100173]", + "orf3b [GENEPIO:0100174]", + "orf6 (ns6) [GENEPIO:0100175]", + "orf7a [GENEPIO:0100176]", + "orf7b (ns7b) [GENEPIO:0100177]", + "orf8 (ns8) [GENEPIO:0100178]", + "orf9b [GENEPIO:0100179]", + "orf9c [GENEPIO:0100180]", + "orf10 [GENEPIO:0100181]", + "orf14 [GENEPIO:0100182]", + "SARS-COV-2 5' UTR [GENEPIO:0100183]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001507", + "type": "string", + "description": "The name of the gene used in the diagnostic RT-PCR test.", + "examples": ["E gene (orf4) [GENEPIO:0100151]"] + }, + "Protocol_SARS-CoV-2_detection": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing" + }, + "%qc_filtered": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing" + }, + "%reads_host": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing" + }, + "%reads_virus": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing" + }, + "%unmapped": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing" + }, + "% genome _greater_10x": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing" + }, + "mean_depth_of_coverage_value": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing" + }, + "%Ns": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing" + }, + "Number_of_variants_(AF_greater_75%)": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing" + }, + "Numer_of_variants_with_effect": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing" + }, + "reference_genome_accession": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing" + }, + "diagnostic_pcr_protocol_1": { + "examples": ["PCREGene 2.0"], + "ontology": "GENEPIO:0001508", + "type": "string", + "description": "The name and version number of the protocol used for diagnostic marker amplification.", + "clasification":"Pathogen diagnostic testing" + }, + "diagnostic_pcr_Ct_value_1": { + "examples": ["21"], + "ontology": "GENEPIO:0001509", + "type": "string", + "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "clasification":"Pathogen diagnostic testing" + }, + "gene_name_2": { + "Enums": [ + "E gene (orf4) [GENEPIO:0100151]", + "M gene (orf5) [GENEPIO:0100152]", + "N gene (orf9) [GENEPIO:0100153]", + "Spike gene (orf2) [GENEPIO:0100154]", + "orf1ab (rep) [GENEPIO:0100155]", + "orf1a (pp1a) [GENEPIO:0100156]", + "nsp11 [GENEPIO:0100157]", + "nsp1 [GENEPIO:0100158]", + "nsp2 [GENEPIO:0100159]", + "nsp3 [GENEPIO:0100160]", + "nsp4 [GENEPIO:0100161]", + "nsp5 [GENEPIO:0100162]", + "nsp6 [GENEPIO:0100163]", + "nsp7 [GENEPIO:0100164]", + "nsp8 [GENEPIO:0100165]", + "nsp9 [GENEPIO:0100166]", + "nsp10 [GENEPIO:0100167]", + "RdRp gene (nsp12) [GENEPIO:0100168]", + "hel gene (nsp13) [GENEPIO:0100169]", + "exoN gene (nsp14) [GENEPIO:0100170]", + "nsp15 [GENEPIO:0100171]", + "nsp16 [GENEPIO:0100172]", + "orf3a [GENEPIO:0100173]", + "orf3b [GENEPIO:0100174]", + "orf6 (ns6) [GENEPIO:0100175]", + "orf7a [GENEPIO:0100176]", + "orf7b (ns7b) [GENEPIO:0100177]", + "orf8 (ns8) [GENEPIO:0100178]", + "orf9b [GENEPIO:0100179]", + "orf9c [GENEPIO:0100180]", + "orf10 [GENEPIO:0100181]", + "orf14 [GENEPIO:0100182]", + "SARS-COV-2 5' UTR [GENEPIO:0100183]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001510", + "type": "string", + "description": "The name of the gene used in the diagnostic RT-PCR test.", + "examples": ["RdRp gene (nsp12) [GENEPIO:0100168]"] + }, + "diagnostic_pcr_protocol_2": { + "examples": ["PCRRdRpGene 3.0"], + "ontology": "GENEPIO:0001511", + "type": "string", + "description": "The name and version number of the protocol used for diagnostic marker amplification.", + "clasification":"Pathogen diagnostic testing" + }, + "diagnostic_pcr_Ct_value_2": { + "examples": ["36"], + "ontology": "GENEPIO:0001512", + "type": "string", + "description": "The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "clasification":"Pathogen diagnostic testing" + }, + "analysis_author": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Contributor Acknowledgement" + }, + "author_submitter": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Contributor Acknowledgement" + }, + "submitter": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"enter your GISAID-Username" + }, + "authors": { + "examples": [""], + "ontology": "GENEPIO:0001517", + "type": "string", + "description": "", + "clasification":"Contributor Acknowledgement" + }, + "tax_id": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sample collection and processing" + }, + "scientific_name": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sample collection and processing" + }, + "common_name": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sample collection and processing" + }, + "library_source": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + "library_selection": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + "library_strategy": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + "library_layout": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + "library_name": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + "nominal_length": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + "analysis_accession": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "study_accession": { + "examples": ["e.g PRJEB39632"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "secondary_study_accession": { + "examples": ["e.g ERP123173"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "sample_accession": { + "examples": ["e.g SAMEA7098096"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "secondary_sample_accession": { + "examples": ["e.g ERS4858671"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "experiment_accession": { + "examples": ["e.g ERX4331406"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "run_accession": { + "examples": ["e.g ERX4331406"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "submission_accession": { + "examples": ["e.g ERA2794974"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "read_count": { + "examples": ["e.g 837055"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "read_length": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "base_count": { + "examples": ["e.g 503907110"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "first_public": { + "examples": ["e.g 2020-08-07"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "last_updated": { + "examples": ["e.g 2020-07-29"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "format":"date" + }, + "experiment_title": { + "examples": ["e.g Illumina MiSeq paired end sequencing"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "study_title": { + "examples": ["e.g SARS-CoV-2 genomes from late April in Stockholm"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "study_alias": { + "examples": ["e.g Sweden"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "experiment_alias": { + "examples": ["e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "run_alias": { + "examples": ["e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "fastq_bytes": { + "examples": ["e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "fastq_md5": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "fastq_ftp": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "fastq_aspera": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "fastq_galaxy": { + "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "submitted_bytes": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "submitted_md5": { + "examples": ["e.g 139853010;166270048"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "submitted_ftp": { + "examples": ["e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "submitted_aspera": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "submitted_galaxy": { + "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "submitted_format": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "sra_bytes": { + "examples": ["e.g FASTQ;FASTQ"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "sra_md5": { + "examples": ["e.g 260236789"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "sra_ftp": { + "examples": ["e.g 2cf0d467d6dc4ae0a5473774d54c059c"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "sra_aspera": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "sra_galaxy": { + "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "broker_name": { + "examples": ["P17157_1007"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "nominal_sdev": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "first_created": { + "examples": ["e.g 2020-08-07"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Submission ENA" + }, + "type": { + "examples": ["betacoronavirus"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "default must remain 'betacoronavirus'", + "clasification":"Database Identifiers" + } + } +} + + +ENA_schema.keys() + +properties = ENA_schema['properties'] + +properties_phage = phage_schema['properties'] + +phage_df = pd.DataFrame.from_dict(properties_phage) + +ENA_df = pd.DataFrame.from_dict(properties) + +ENA_df.columns + +ENA_df['geographic_location_(country_and/or_sea)']['Enums']; + +p_col = phage_df.columns +lista_phage = p_col.tolist() + +ENA_col = ENA_df.columns +lista_ENA = ENA_col.tolist() + +# + + +df = pd.DataFrame(lista_phage, columns = ['PHA4GE']) + +# + + +df_2 = pd.DataFrame(lista_ENA, columns = ['ENA']) +# - + +#result = pd.concat([df, df_2], axis=1) +#result = df.merge(df_2, left_on ='PHA4GE', right_on = "ENA") +#result = df.merge(df_2, left_on=None) +result = df.join(df_2) + +result + +phage_df + + From 486363145f7e0914097bb34694e04156970482bb Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 2 Feb 2022 12:37:03 +0100 Subject: [PATCH 0007/1454] testing alternatives --- relecov-tools/validation_jsons.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/relecov-tools/validation_jsons.py b/relecov-tools/validation_jsons.py index 1e44124c..79ec06e0 100644 --- a/relecov-tools/validation_jsons.py +++ b/relecov-tools/validation_jsons.py @@ -90,6 +90,18 @@ def get_data(self, field): df = pd.read_excel('sample.xlsx') for idx, row in df.iterrows(): sample_list.append(PhagePlus(row.to_dict(),phage_plus_schema)) +from openpyxl import Workbook +wbFile = openpyxl.load_workbook('my_test_file.xlsx', data_only=True) +wsFile = wbFile['METADATA_LAB'] +heading = [] +for cell in wsFile[1]: + heading.append(cell.value) + +for row in islice(wsFile.values,1,wsFile.max_row): + samples = OrderedDict() + for idx in range(len(heading)): + samples[heading[idx]] = row[idx].value + print('Completed') From c3a31c897302487112722a4c9543a8abaef1f1c5 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 2 Feb 2022 17:01:36 +0100 Subject: [PATCH 0008/1454] testing the excel validation --- relecov-tools/validation_jsons.py | 80 ++++++++++++++++++++----------- 1 file changed, 53 insertions(+), 27 deletions(-) diff --git a/relecov-tools/validation_jsons.py b/relecov-tools/validation_jsons.py index 79ec06e0..fafa60b7 100644 --- a/relecov-tools/validation_jsons.py +++ b/relecov-tools/validation_jsons.py @@ -3,20 +3,34 @@ from jsonschema import Draft202012Validator import json #import pandas as pd -import excel2json-3 +#import excel2json-3 -class RelecovSchema : +class PhagePlusSchema : def __init__ (self, schema): - self.schema = json.load(schema) + self.schema = schema - def get_gontology(self,geontology): - for key, value in schema['properties'].items(): - if value['ontology'] == geontology : - return value - return None + def get_gontology(self,property_item): + ''' + Description: + The function return the geontology value for a property in the schema + Input: + property_item # property name to fetch its geontology + Return: + Return ontology value or None + ''' + try: + return self.schema['properties'][property_item]['ontology'] + except: + return None + def maping_schemas_based_on_geontology(mappep_to_schema): + ''' -class PhagePlus : + ''' + return + + +class PhagePlusData : def __init__ (self,data, json_schema): self.data = data self.schema = json_schema @@ -71,7 +85,9 @@ def get_data(self, field): "consensus_sequence_software_version":'Ivar' }] -schema_file = open('/home/lchapado/Projects/Proyecto_ERA/relecov-tools/schema/phage_plus_V0.json') +# schema_file = open('/home/lchapado/Projects/Proyecto_ERA/relecov-tools/schema/phage_plus_V0.json') +schema_file = open('/home/bioinfo/Projects/relecov-tools/schema/phage_plus_V0.json') + json_phage_plus_schema = json.load(schema_file) try: @@ -79,29 +95,39 @@ def get_data(self, field): except: print('Invalid schema') exit(1) -phage_plus_schema = RelecovSchema(json_phage_plus_schema) -try: - validate(instance=data,schema=json_phage_plus_schema) -except: - print('Invalid input data') - exit(1) -import pdb; pdb.set_trace() +phage_plus_schema = PhagePlusSchema(json_phage_plus_schema) +#try: +# validate(instance=data,schema=json_phage_plus_schema) +#except: +# print('Invalid input data') +# exit(1) + sample_list = [] -df = pd.read_excel('sample.xlsx') -for idx, row in df.iterrows(): - sample_list.append(PhagePlus(row.to_dict(),phage_plus_schema)) +#df = pd.read_excel('sample.xlsx') +#for idx, row in df.iterrows(): +# sample_list.append(PhagePlus(row.to_dict(),phage_plus_schema)) from openpyxl import Workbook -wbFile = openpyxl.load_workbook('my_test_file.xlsx', data_only=True) -wsFile = wbFile['METADATA_LAB'] +import openpyxl +from itertools import islice +excel_input_file = '/home/bioinfo/Projects/relecov-tools/test/my_test_file.xlsx' +wb_file = openpyxl.load_workbook(excel_input_file, data_only=True) +ws_metadata_lab = wb_file['METADATA_LAB'] heading = [] -for cell in wsFile[1]: +for cell in ws_metadata_lab[1]: heading.append(cell.value) -for row in islice(wsFile.values,1,wsFile.max_row): - samples = OrderedDict() +for row in islice(ws_metadata_lab.values,1,ws_metadata_lab.max_row): + sample_data_row = {} for idx in range(len(heading)): - samples[heading[idx]] = row[idx].value - + sample_data_row[heading[idx]] = row[idx] + try: + import pdb; pdb.set_trace() + validate(instance=json.dumps(sample_data_row),schema=json_phage_plus_schema) + except: + print('Unsuccessful validation for sample ' , sample_data_row['sample_name']) + continue + sample_list.append(PhagePlusData(sample_data_row,phage_plus_schema)) +import pdb; pdb.set_trace() print('Completed') From a338950173b2e7e6755f672be90bf7055647527a Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 3 Feb 2022 16:47:05 +0100 Subject: [PATCH 0009/1454] successful validatation of excel for phage-plus mandatory fields --- relecov-tools/validation_jsons.py | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/relecov-tools/validation_jsons.py b/relecov-tools/validation_jsons.py index fafa60b7..bae32887 100644 --- a/relecov-tools/validation_jsons.py +++ b/relecov-tools/validation_jsons.py @@ -119,15 +119,16 @@ def get_data(self, field): for row in islice(ws_metadata_lab.values,1,ws_metadata_lab.max_row): sample_data_row = {} for idx in range(len(heading)): - sample_data_row[heading[idx]] = row[idx] - + if 'date' in heading[idx]: + sample_data_row[heading[idx]] = row[idx].strftime('%d/%m/%Y') + else: + sample_data_row[heading[idx]] = row[idx] try: - import pdb; pdb.set_trace() - validate(instance=json.dumps(sample_data_row),schema=json_phage_plus_schema) + validate(instance=sample_data_row,schema=json_phage_plus_schema) except: print('Unsuccessful validation for sample ' , sample_data_row['sample_name']) + continue + sample_list.append(PhagePlusData(sample_data_row,phage_plus_schema)) - sample_list.append(PhagePlusData(sample_data_row,phage_plus_schema)) -import pdb; pdb.set_trace() print('Completed') From 617ff03f8ef0591e275fa32d4cc7b95fd75085cf Mon Sep 17 00:00:00 2001 From: Albertolema Date: Thu, 3 Feb 2022 17:41:34 +0100 Subject: [PATCH 0010/1454] Add files via upload bash script to download sFTp directories --- sftp_download.sh | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 sftp_download.sh diff --git a/sftp_download.sh b/sftp_download.sh new file mode 100644 index 00000000..a2bf5d2c --- /dev/null +++ b/sftp_download.sh @@ -0,0 +1,14 @@ +#!/bin/bash + +echo -n Password: + +read -s password + +usuario=bioinfoadm +host=sftprelecov.isciii.es + +SSHPASS=$password sshpass -e sftp $usuario@$host < Date: Thu, 3 Feb 2022 23:50:51 +0100 Subject: [PATCH 0011/1454] Including conversion mapping method --- relecov-tools/utils/common_functions.py | 12 ++ relecov-tools/validation_jsons.py | 189 ++++++++++++++---------- 2 files changed, 124 insertions(+), 77 deletions(-) create mode 100644 relecov-tools/utils/common_functions.py diff --git a/relecov-tools/utils/common_functions.py b/relecov-tools/utils/common_functions.py new file mode 100644 index 00000000..0bc334b4 --- /dev/null +++ b/relecov-tools/utils/common_functions.py @@ -0,0 +1,12 @@ +import os + +def file_exists(file_to_check): + ''' + Input: + file_to_check # file name to check if exists + Return: + True if exists + ''' + if os.path.isfile(file_to_check): + return True + return False diff --git a/relecov-tools/validation_jsons.py b/relecov-tools/validation_jsons.py index bae32887..1167ef92 100644 --- a/relecov-tools/validation_jsons.py +++ b/relecov-tools/validation_jsons.py @@ -1,13 +1,19 @@ #!/usr/bin/env python from jsonschema import validate from jsonschema import Draft202012Validator -import json -#import pandas as pd -#import excel2json-3 +import json ,sys +from openpyxl import Workbook +import openpyxl +from itertools import islice +from utils import * class PhagePlusSchema : def __init__ (self, schema): self.schema = schema + self.ontology = {} + for key , values in schema['properties'].items(): + self.ontology[values['onotlogy']] = key + def get_gontology(self,property_item): ''' @@ -23,11 +29,25 @@ def get_gontology(self,property_item): except: return None - def maping_schemas_based_on_geontology(mappep_to_schema): + def maping_schemas_based_on_geontology(mapped_to_schema): ''' + Description: + The function return a dictionnary with + Input: + mapped_to_schema # json schema to be mapped + Return: + mapped_dict contains as key the property in the mapped_to_schema and value de property in the self.schema ''' - return + mapped_dict = OrderedDict() + for key, values in mapped_to_schema.items(): + try: + mapped_dict[key] = self.ontology[values['onotology']] + except: + # There is no exact match on ontology. Search for the parent + # to be implemented later + pass + return mapped_dict class PhagePlusData : @@ -42,6 +62,39 @@ def convert_json(schema): def get_data(self, field): return self.data[field] + def map_sample_to_schema(mapped_structure): + map_sample_dict = OrderedDict() + for item, value in mapped_structure.items: + mapped_sample_list[item] = self.data[value] + return map_sample_dict + + + +def check_arg (args=None) : + ''' + The function is used for parsing the input parameters form the command line + using the standard python package argparse. The package itself is handling + the validation and the return errors messages + Input: + args # Contains the arguments from the command line + Return: + parser.parse_args() # The variable contains the valid parameters + ''' + parser = argparse.ArgumentParser(prog = 'validation_jsons.py', + formatter_class=argparse.RawDescriptionHelpFormatter, + description= 'Read the excel input user files and store them in the LIMS') + + parser.add_argument('-v', '--version', action='version', version='%(prog)s 0.0.1') + parser.add_argument('-p', '--phagePlusSchema' , required = True, + help='file where the phage plus schema is located') + parser.add_argument('-i', '--inputFile', required =True, + help='Execl file with the user collected data') + parser.add_argument('-c', '--convertedSchema', required = True, + help='schema where the user input must be mapped to') + return parser.parse_args() + + + data ={"sample_name":'s1', "collecting_institution" :'inst2', "submitting_institution":'sub', "sample_collection_date": '12/02/2022', @@ -56,79 +109,61 @@ def get_data(self, field): "consensus_sequence_software_name":'MinIon', "consensus_sequence_software_version":'Ivar' } -data2 = [{"sample_name":'s1', "collecting_institution" :'inst2', - "submitting_institution":'sub', - "sample_collection_date": '12/02/2022', - "geo_loc_country":'Afghanistan', - "geo_loc_state":'Western', - "organism":'Coronaviridae', - "isolate":'SARS-CoV-2/', - "host_scientific_name":'Bos taurus', - "host_disease":'Homo sapiens', - "sequencing_instrument_model" :'COVID-19', - "sequencing_instrument_platform": 'Illumina sequencing instrument', - "consensus_sequence_software_name":'MinIon', - "consensus_sequence_software_version":'Ivar' -}, -{"sample_name":'s1', "collecting_institution" :'inst3', - "submitting_institution":'sub', - "sample_collection_date": '12/02/2022', - "geo_loc_country":'Afghanistan', - "geo_loc_state":'Western', - "organism":'Coronaviridae', - "isolate":'SARS-CoV-2/', - "host_scientific_name":'Bos taurus', - "host_disease":'Homo sapiens', - "sequencing_instrument_model" :'COVID-19', - "sequencing_instrument_platform": 'Illumina sequencing instrument', - "consensus_sequence_software_name":'MinIon', - "consensus_sequence_software_version":'Ivar' -}] - -# schema_file = open('/home/lchapado/Projects/Proyecto_ERA/relecov-tools/schema/phage_plus_V0.json') -schema_file = open('/home/bioinfo/Projects/relecov-tools/schema/phage_plus_V0.json') - - -json_phage_plus_schema = json.load(schema_file) -try: - Draft202012Validator.check_schema(json_phage_plus_schema) -except: - print('Invalid schema') - exit(1) -phage_plus_schema = PhagePlusSchema(json_phage_plus_schema) -#try: -# validate(instance=data,schema=json_phage_plus_schema) -#except: -# print('Invalid input data') -# exit(1) - -sample_list = [] -#df = pd.read_excel('sample.xlsx') -#for idx, row in df.iterrows(): -# sample_list.append(PhagePlus(row.to_dict(),phage_plus_schema)) -from openpyxl import Workbook -import openpyxl -from itertools import islice -excel_input_file = '/home/bioinfo/Projects/relecov-tools/test/my_test_file.xlsx' -wb_file = openpyxl.load_workbook(excel_input_file, data_only=True) -ws_metadata_lab = wb_file['METADATA_LAB'] -heading = [] -for cell in ws_metadata_lab[1]: - heading.append(cell.value) - -for row in islice(ws_metadata_lab.values,1,ws_metadata_lab.max_row): - sample_data_row = {} - for idx in range(len(heading)): - if 'date' in heading[idx]: - sample_data_row[heading[idx]] = row[idx].strftime('%d/%m/%Y') - else: - sample_data_row[heading[idx]] = row[idx] + + +if __name__ == '__main__': + if len (sys.argv) == 1 : + print('Usage: validation_jsons.py [ARGUMENTS] ') + print('Try validation_jsons.py --help for more information.') + exit(2) + arguments = check_arg(sys.argv[1:]) + if not check_if_file_exists(arguments.phagePlusSchema): + print('phage plus schema file does not exist\n') + exit(2) + if not check_if_file_exists(arguments.inputFile): + print('excel file does not exist\n') + exit(2) + if not check_if_file_exists(arguments.convertedSchema): + print('file for converting schema does not exist\n') + exit(2) + # schema_file = open('/home/lchapado/Projects/Proyecto_ERA/relecov-tools/schema/phage_plus_V0.json') + schema_file = open(arguments.phagePlusSchema) + + + json_phage_plus_schema = json.load(schema_file) try: - validate(instance=sample_data_row,schema=json_phage_plus_schema) + Draft202012Validator.check_schema(json_phage_plus_schema) except: - print('Unsuccessful validation for sample ' , sample_data_row['sample_name']) + print('Invalid schema') + exit(1) + phage_plus_schema = PhagePlusSchema(json_phage_plus_schema) + + sample_list = [] + wb_file = openpyxl.load_workbook(arguments.inputFile, data_only=True) + ws_metadata_lab = wb_file['METADATA_LAB'] + heading = [] + for cell in ws_metadata_lab[1]: + heading.append(cell.value) + + for row in islice(ws_metadata_lab.values,1,ws_metadata_lab.max_row): + sample_data_row = {} + for idx in range(len(heading)): + if 'date' in heading[idx]: + sample_data_row[heading[idx]] = row[idx].strftime('%d/%m/%Y') + else: + sample_data_row[heading[idx]] = row[idx] + try: + validate(instance=sample_data_row,schema=json_phage_plus_schema) + except: + print('Unsuccessful validation for sample ' , sample_data_row['sample_name']) + + continue + sample_list.append(PhagePlusData(sample_data_row,phage_plus_schema)) + # create the information mapped to the new schema + mapped_structure = maping_schemas_based_on_geontology(arguments.convertedSchema) + mapped_sample_list = [] + for sample in sample_list: + mapped_sample_list.append(map_sample_to_schema(mapped_structure)) - continue - sample_list.append(PhagePlusData(sample_data_row,phage_plus_schema)) -print('Completed') + print('Completed') From 13b0d8c0ed34918563fa8e88234e38ff69dc4c93 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 3 Feb 2022 23:52:12 +0100 Subject: [PATCH 0012/1454] adding testing excel file --- test/my_test_file.xlsx 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zOAUk=yQn*h({$^@HtVFf0U}7$FLb1dGt&wW&2!YBpTwm5;H0k>YMh2^Fb}O4eEX{V zB~@92W)-1Hsm`HBipOXu z<)SD@7ZE{CG+qX5>-X_mh@xL#JcL~`0x(&ym+KlRvlhQtWT*A=pE$iPumIz z1lwSHUttjoL=c(ao_@7z`e1Y$YzJ*&VcGI-B{su$^68EA^^k!A)*XyS4($Z zk#Cv5yyv5FQl5TRP)GD;%VBB5@J=6GkRNyYK=Z`1jh4&ndC{B?KnVIROrCG#F413t z4h_Qs$>{z(H2K%9{_Fh@Bb2HN{{;Bw@YY|3Ki``n(c*8TT#pU^IneTV!(~Wu`F|g8 zd5rUToZ&YTJ)|@BXt?3A@#9AHZ{rH&U&g=N(vM9a_xOIBMx*`D_x}Gnevbhkx6FP6 z#zG>;zc=!4z~2qD$0(1h^S@CnA;o$K%Hvx7V}Qq{k>3E!kb?gomhr1l@)+gu^TTfx zC9+>A|M4{O7~!AE=5Ko_C}RpJsK=@2W9!HA{@b3F`q%gWL+l@0KNh^-*19ymtRKnU qALZ{c=syGfZ%8PpCfdJk=&!J^ssIo111Kmo$j@7dD{(RWJo|sVtmqd2 literal 0 HcmV?d00001 From 7a42205623f54cb6eb3acc70657b2675ff30b046 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 4 Feb 2022 09:00:20 +0100 Subject: [PATCH 0013/1454] fixing typos --- relecov-tools/validation_jsons.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/relecov-tools/validation_jsons.py b/relecov-tools/validation_jsons.py index 1167ef92..12ff3fc5 100644 --- a/relecov-tools/validation_jsons.py +++ b/relecov-tools/validation_jsons.py @@ -12,7 +12,7 @@ def __init__ (self, schema): self.schema = schema self.ontology = {} for key , values in schema['properties'].items(): - self.ontology[values['onotlogy']] = key + self.ontology[values['ontology']] = key def get_gontology(self,property_item): @@ -32,17 +32,17 @@ def get_gontology(self,property_item): def maping_schemas_based_on_geontology(mapped_to_schema): ''' Description: - The function return a dictionnary with + The function return a dictionnary with the properties of the mapped_to_schema as key and + properties of phagePlusSchema as value Input: mapped_to_schema # json schema to be mapped - Return: mapped_dict contains as key the property in the mapped_to_schema and value de property in the self.schema ''' mapped_dict = OrderedDict() for key, values in mapped_to_schema.items(): try: - mapped_dict[key] = self.ontology[values['onotology']] + mapped_dict[key] = self.ontology[values['ontology']] except: # There is no exact match on ontology. Search for the parent # to be implemented later @@ -90,7 +90,7 @@ def check_arg (args=None) : parser.add_argument('-i', '--inputFile', required =True, help='Execl file with the user collected data') parser.add_argument('-c', '--convertedSchema', required = True, - help='schema where the user input must be mapped to') + help='schema to be mapped') return parser.parse_args() From 77f5ed824b070213776368a0902361d3266c9747 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 5 Feb 2022 17:30:58 +0100 Subject: [PATCH 0014/1454] small changes --- relecov-tools/validation_jsons.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov-tools/validation_jsons.py b/relecov-tools/validation_jsons.py index 12ff3fc5..0d9fff53 100644 --- a/relecov-tools/validation_jsons.py +++ b/relecov-tools/validation_jsons.py @@ -40,7 +40,7 @@ def maping_schemas_based_on_geontology(mapped_to_schema): mapped_dict contains as key the property in the mapped_to_schema and value de property in the self.schema ''' mapped_dict = OrderedDict() - for key, values in mapped_to_schema.items(): + for key, values in mapped_to_schema['properties'].items(): try: mapped_dict[key] = self.ontology[values['ontology']] except: @@ -160,7 +160,7 @@ def check_arg (args=None) : continue sample_list.append(PhagePlusData(sample_data_row,phage_plus_schema)) # create the information mapped to the new schema - mapped_structure = maping_schemas_based_on_geontology(arguments.convertedSchema) + mapped_structure = phage_plus_schema.maping_schemas_based_on_geontology(arguments.convertedSchema) mapped_sample_list = [] for sample in sample_list: mapped_sample_list.append(map_sample_to_schema(mapped_structure)) From bc9d1b452179e581a81a5b090fd1b703662230fb Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 7 Feb 2022 15:12:30 +0100 Subject: [PATCH 0015/1454] Add genpio.owl file to test owlready2.py --- relecov-tools/owl_parsing.py | 41 + relecov-tools/validation_jsons.py | 7 + schema/genepio.owl | 22876 ++++++++++++++++++++++++++++ 3 files changed, 22924 insertions(+) create mode 100644 relecov-tools/owl_parsing.py create mode 100644 schema/genepio.owl diff --git a/relecov-tools/owl_parsing.py b/relecov-tools/owl_parsing.py new file mode 100644 index 00000000..66eb9a4d --- /dev/null +++ b/relecov-tools/owl_parsing.py @@ -0,0 +1,41 @@ +from owlready2 import * + + +class SparqlQueries: +def __init__(self): + my_world = World() + my_world.get_ontology("file://ExampleOntolohy.owl").load() #path to the owl file is given here + sync_reasoner(my_world) #reasoner is started and synchronized here + self.graph = my_world.as_rdflib_graph() + +def search(self): + #Search query is given here + #Base URL of your ontology has to be given here + query = "base " \ + "SELECT ?s ?p ?o " \ + "WHERE { " \ + "?s ?p ?o . " \ + "}" + + #query is being run + resultsList = self.graph.query(query) + + #creating json object + response = [] + for item in resultsList: + s = str(item['s'].toPython()) + s = re.sub(r'.*#',"",s) + + p = str(item['p'].toPython()) + p = re.sub(r'.*#', "", p) + + o = str(item['o'].toPython()) + o = re.sub(r'.*#', "", o) + response.append({'s' : s, 'p' : p, "o" : o}) + + print(response) #just to show the output + return response + + +runQuery = SparqlQueries() +runQuery.search() diff --git a/relecov-tools/validation_jsons.py b/relecov-tools/validation_jsons.py index 0d9fff53..bd9e2172 100644 --- a/relecov-tools/validation_jsons.py +++ b/relecov-tools/validation_jsons.py @@ -7,6 +7,13 @@ from itertools import islice from utils import * +''' +References: + genepio.owl https://github.com/GenEpiO/genepio/blob/master/genepio.owl + + +''' + class PhagePlusSchema : def __init__ (self, schema): self.schema = schema diff --git a/schema/genepio.owl b/schema/genepio.owl new file mode 100644 index 00000000..bde12348 --- /dev/null +++ b/schema/genepio.owl @@ -0,0 +1,22876 @@ + + + + + + + + + + + + + + + +]> + + + + + + + + + + + + + + + + + + + + + + + 2022-02-06 + The Genomic Epidemiology Ontology aims to provide a comprehensive controlled vocabulary for infectious disease surveillance and outbreak investigations. It is an application ontology that draws on many other ontologies including anatomy, taxonomy, disease, symptoms, environment and food types for foodborn pathogen metadata. + + Genomic Epidemiology Ontology + GENEPIO + + + + + + + + + + + + + metadata section + + + + + + + + term as in existing standard + + + + + + + + term source + + + + + + + + The user interface label is the label that should be placed on a datum when presented on a form or report + Damion Dooley + user interface label + + + + + + + + user interface definition + + + + + + + + A user interface help annotation is a textual phrase to display with an entity on a form or report that provides some detail about what the entity is or how it is being used. + Damion Dooley + user interface help + true + + + + + + + + Damion Dooley + + user interface hidden + true + + + + + + + + A user interface feature is a pre-set list of features and their acceptable values that a user interface rendering system should use to display an entity on a form or report + Damion Dooley + user interface feature + + + + + + + + This annotation can be used to select the value specification that a referenced entity or specification component has for data entry. Can be scalar value specification / categorical tree specification etc. + Damion Dooley + obsolete: user interface value specification + true + + + + + + + + UI regex normalize + + Damion Dooley + user interface regular epression normalize + + + + + + + + UI regex validate + + Damion Dooley + user interface regular expression validate + + + + + + + + UI regex format + + Damion Dooley + user interface regular expression display format + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + label + + + + + + + + see also + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + part of + + + + + + + + Damion comments: In GenEpiO, If an entity has more than one value specification (in a conjunction), then it means the entitiy is a complex entity that can have a value for each specification. Minimum data requirements can be spelled out using some, min 1, max 10 etc. restrictions. + + + + + + + + realized in + + + + + + + + + + + + + + obsolete has string specification of + true + + + + + + + + + + + T1 after t2 iff:= t2 before_or_simulataneous_with t1 and not (t1 simultaeous_with t2) + Damion Dooley + Damion Dooley's note: Intention is to have it be the inverse of "before". This allows axioms like "B after A" to be placed in class B, rather than having to phrase them as "A before B" in class A. + +I believe time dependency relations (conditions) don't imply existence by themselves. If B after A, and B exists, this doesn't necessarily mean that A exists, only that if A does exist, it must be before B. To add that extra existence implication probably requires the "causally downstream of" and "immediately causally downstream of" RO relations, in a closed system where B cannot exist any other way. + after + + + + + + + + + + obsolete: has string value specification + true + + + + + + + + obsolete: has categorical specification of + true + + + + + + + + + + obsolete: has categorical value specification + true + + + + + + + + has unit + + + + + + + + + is about + + + + + + + + specifies + + + + + + + + inheres in + + + + + + + + has participant + + + + + + + + + + + + + + location of + + + + + + + + located in + + + + + + + + aligned with + + + + + + + + T1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + + + + + + + + + + has component + + + + + + + + + adjacent to + + + + + + + + + has input + has input + + + + + + + + + has output + has output + + + + + + + + + + member of + + + + + + + + has member + + + + + + + + output of + + + + + + + + + link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch. + + exactMatch + + + + + + + + + + + + + + + + An object relation between a LinkML SlotDefinition to a LocalName. + + + + + + + + + + + + + + + + + + + + + + + An abstract class is a high level class or slot that is typically used to group common slots together and cannot be directly instantiated. + + + + + + + + + Notes and comments about an element intended for external consumption. + + + + + + + + + + + + + + + + + + Date/time at which the element was created. + + + + + + + + + Not Applicable; Missing; Not Collected; Not Provided; Restricted Access + A value (string or URI) indicating the data collection state an instance of a slot has. + + + + + + + + + A description of the element's purpose and use + + + + + + + + + A list of terms from different schemas or terminology systems that have identical meaning. + + + + + + + + + Id of the schema that defined the element. + + + + + + + + + + + + + + + + + + The imports entry that this element was derived from. Empty means primary source + + + + + + + + + + + The ncname of the source of the name. + + 2021-04-26T22:15:07Z + 2021-04-26T22:15:07Z + local_name_source + + + + + + + + + + + A name assigned to an element in a given ontology. + + + + + + + + + + For slots with ranges of type number, the value must be equal to or lowe than this + + + + + + + + + + + + + + + + + + For slots with ranges of type number, the value must be equal to or higher than this + + + + + + + + + + true means that slot can have more than one value + + + + + + + + + + The unique name of the element within the context of the schema. Name is combined with the default prefix to form the globally unique subject of the target class. + + + + + + + + + + The string value of the slot must conform to this regular expression + + + + + + + + + A list of possible values for a slot range. + + + + + + + + + + true if this slot is not required, but is recommended. + + + + + + + + + + true means that the slot must be present in the loaded definition. + + + + + + + + + + A reference. + + + + + + + + + + IAO:0000122 ('ready for release') + status of the element. + + + + + + + + + The uri that defines the possible values for the type definition + URI is typically drawn from the set of URI's defined in OWL (https://www.w3.org/TR/2012/REC-owl2-syntax-20121211/#Datatype_Maps) + + + + + + + + + + + + + + + + + + + + Description of what the value is doing. + + + + + + + + + + + + + + + + + + + + + + + + A persistent, unique identifier of a molecular sequence database entry. + Damion Dooley + EDAM + sequence accession + + + + + + + + + The name of a field in a database. + database field name + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + Damion Dooley + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CLSI + NCCLS + National Committee on Clinical Laboratory Standards (NCCLS) + On January 1, 2005 the National Committee on Clinical Laboratory Standards (NCCLS) changed its name to CLSI + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + depth:1 + + + + + + + + + + + + + + + + + order: +ARO:3004303 # nonsensitive +ARO:3004300 # intermediate +ARO:3004302 # sensitive +ARO:3004304 # sensitive - dose dependant +ARO:3004301 # resistant + + + + + + + + http://purl.obolibrary.org/obo/PATO_0000001 + + + + + + + + http://purl.obolibrary.org/obo/CHEBI_50906 + + + + + + + + Note that this can refer to a material entity like an organ or muscle, or an immaterial entity (a site or fiat boundary) like skin, stomach cavity or lung surface. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Trd + + + + + + + + + deoxyribonucleic acid + + + + + + + + + + STR + Sm + Stm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://purl.obolibrary.org/obo/CHEBI_33281 + obsolete: antibiotic + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Am + Amk + + + + + + + + + + + + + + + + + Amx + + + + + + + + + PAS + + + + + + + + + + + + + + + + + + + + + + + + + Rif + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Pto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CAP + Cm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Clr + + + + + + + + + Cfz + + + + + + + + + + + + + + + + + + + + + + + + + CYC + Cs + + + + + + + + + pyrazinamide + Pza + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + E + ETB + Emb + + + + + + + + + + + + + + + + + + ETH + Eto + + + + + + + + + + + + + + + + + + + + + + + + Currently "K antigen" is a CHEBI_73772 chemical entity rather than a role. + K antigen + + + + + + + + + + + + + + + + + Inh + isoniazid + + + + + + + + + + + + + + + + + Kan + + + + + + + + + Lfx + + + + + + + + + + Lzd + + + + + + + + + + MXF + Mfx + + + + + Mfx + https://www.ncbi.nlm.nih.gov/books/NBK247415/bin/part3-m17.pdf + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Bdq + + + + + + + + + + + + + + Damion Dooley's note: 'K antigen' can't be a subclass of antigen as chemical entity is disjoint from role. + Snomed: Concept 260824002 + + + + + + + + + + + + + + + + + + + Ofx + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + specimen extraction matrix + "This observable is important where process of capturing sample can affect dna extraction." + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://purl.obolibrary.org/obo/OGMS_0000031 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + state / province / territory / region + lookup:http://purl.obolibrary.org/obo/GAZ_00000448 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Transmission of a disease agent (infectious pathogen, toxic chemical, etc.) from a source that is common to those who acquire the disease. Common vehicles include air, water, food, injected substances. Legionellosis is an example of common vehicle spread in air that has passed through air conditioning equipment contaminated by the causal organism. HIV disease and hepatitis B and C can be spread among illicit drug users by the common vehicle of contaminated needles and syringes. Cholera and many other waterborne diseases are spread by the common vehicle of contaminated water. + common vehicle transmission + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A role that inheres in a material that is input as the subject of interest in a scientific technique - either as an entity about which data is generated in an assay or study, or an entity that is transformed or modified in a material processing technique (e.g. the source from which a biological sample is taken) + experimental subject role + + + + + + + + + + + + + + + + + + + + + depth:1 + + https://en.wikipedia.org/wiki/Medical_state + condition + medical condition + medical state + Damion Dooley note: GenEpiO includes various health status descriptors here; many are annotated as included in the American AHA HIPPA or United Kingdom NHS terminologies. The challenge is to map them or order them in such a way that merged data can be analyzed. + http://semanticscience.org/resource/SIO_010057 + + + + + + + + + + + Condition + + + + + + + + + + + Condition + + + + + + + + + The process of drawing in by breathing. + http://purl.obolibrary.org/obo/ExO_0000057 + inhalation + + + + + + + + + Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + MIxS + + + + + + + + + + A symptom onset date is a date-time entity that marks the start of one or more reported symptoms pertaining to an episode of human or animal illness + Damion Dooley + symptom onset date + + + + + + + + + + A substance, usually composed primarily of carbohydrates, fats, water and/or proteins, that can be eaten or drunk by an animal or human being for nutrition or pleasure. + Damion Dooley + + foodon product type + + + + + + + + lookup + + + + + + + + + + + + + + + + lookup + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + lookup + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + food packing medium + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + [Oceans and Seas] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Census Regions and Divisions are groupings of States that subdivide the United States. + Damion Dooley + United States Census Bureau + http://www.census.gov/econ/census/help/geography/regions_and_divisions.html + + + + + + + + + A census region in the United States of America + Damion Dooley + + + + + + + + + A census region in the United States of America + Damion Dooley + + + + + + + + + A census region in the United States of America + Damion Dooley + + + + + + + + + A census region in the United States of America + Damion Dooley + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + directly governed city (North Korea) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GSCID-BRC standard + + The GSCID-BRC Project and Sample Application Standard captures standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases. + The NIAID page for specifications has a broken link for Core Project. This is the existing page: + +https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project + +Link page is: + +https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards + Damion Dooley + This standard was developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs), and NIAID and informed by discussions and input with numerous collaborating scientists. + GSCID-BRC Project and Sample Application Standard + + + + + + + + + MIxS standard + + MixS is a unified standard for describing sequence data provided by the Genomic Standards Consortium (GSC) + Damion Dooley + Minimum Information about any (x) Sequence (MIxS) + + + + + + + + + MIMARKS standard + The "minimum information about a marker gene sequence" (MIMARKS) is a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences. + http://www.nature.com/nbt/journal/v29/n5/full/nbt.1823.html + Minimum information about a marker gene sequence + + + + + + + + + + "other (metadata choice)" indicates that for the given categorical variable, a respondent has chosen an other or additional response not listed. + This class cannot be referred to directly as a subclass of more than one class without involving inference from the respective classes. Instances of it may exist as a kind of metadata. Usually a reference to a parent categorical class, but not a subordinate, carries the same information. + Damion Dooley + other (metadata value) + + + + + + + + + other relevance + + + + + + + + + other + + Other: specify the sample scope that was used. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + other specimen scope + + + + + + + + + other material + + Other: specify the material that was used. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + other material derived from specimen + + + + + + + + + + "other capture type" is a free text description provided to indicate a target capture specification not covered by the other types. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + other capture type + + + + + + + + + + Specify the project method + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + other project method + + + + + + + + This is an organizational category for grouping parameters relevant to a biomedical sample. + Damion Dooley + + obsolete: draft GenEpiO BioSample standard + true + + + + + + + + An NCBI antibiogram data item is an antimicrobial susceptibility and resistance datum related to drug resistant pathogens. This information is provided within an antibiogram table on BioSample records. + Damion Dooley + + + obsolete: NCBI antibiogram data item + true + + + + + + + + + HIPPA PHI guideline + The American HIPPA Protected Health Information (PHI) guidelines cover information, including demographic information, which relates to: + +- the individual’s past, present, or future physical or mental health or condition, +- the provision of health care to the individual, or +- the past, present, or future payment for the provision of health care to the individual, and that identifies the individual or for which there is a reasonable basis to believe can be used to identify the individual. Protected health information includes many common identifiers (e.g., name, address, birth date, Social Security Number) when they can be associated with the health information listed above." + https://en.wikipedia.org/wiki/Health_Insurance_Portability_and_Accountability_Act + American HIPPA Protected Health Information (PHI) guidelines + + + + + + + + The natural (as opposed to laboratory) full scientific taxonomic name of a subject related to a given investigation, study and/or specimen. + Damion Dooley + + http://purl.obolibrary.org/obo/GENEPIO_0001567 + obsolete: subject species + true + + + + + + + + http://purl.obolibrary.org/obo/NCIT_C45908 + NCBI BioSample: intersex + obsolete: intersex + true + + + + + + + + Isolation date + inferred from BCCDC interviews + date the strain was isolated + Damion Dooley + http://purl.obolibrary.org/obo/GENEPIO_0000021 + obsolete: isolation date + true + + + + + + + + + Collection + Culture isolation date + suggested in metadata feedback + year/month/day + A culture isolation date is a date-time entity marking the end of a process in which a sample is isolated as a single colony or non-mixture culture + Damion Dooley + GROUP: IRIDA Ontology (Morag) + GENEPIO + culture isolation date + + + + + + + + + Collection + Frozen date + NML Labware LIMS + year/month/day + A culture frozen date is a date-time entity marking the beginning of a process in which a sample culture is frozen for preservation. + Damion Dooley + GROUP: IRIDA Ontology (Emma) + GENEPIO + culture frozen date + + + + + + + + + Collection + Received date + NML Labware LIMS + year/month/day + date lab received isolate + NML LIMS + GENEPIO + isolate received date + + + + + + + + + Collection + Upload date + NML Labware LIMS + month/day/year + date the isolate was entered into the database + NML LIMS + PulseNet: UploadDate + GENEPIO + isolate upload date + + + + + + + + + + + + + + + Pathogen Isolate + inferred from BCCDC interviews + gut, spine, tongue, lung + Name of body site where the specimen was obtained from, such as a specific organ or tissue. + Damion Dooley's note: Although term mentions "site" in label, this cannot be placed under "site" as it is intended to refer to organism material, and leads to unsatisfiable terms otherwise. + GROUP: MIxS + GENEPIO + subject anatomical site + http://gensc.org/ns/mixs/host_body_site + + + + + + + + + depth:1 + order: +NCIT:C115935 # healthy +NCIT:C25610 # pathologic +NCIT:C28554 # deceased + diseased + + Health or disease status of a given subject at time of specimen collection. + Currently this does not differ from the 'subject health status (GSCID-BRC)' item. It may be revised to have more options in the future. + Damion Dooley + subject health status at time of specimen collection + + + + + + + + + + + + 1 + + + + + + + 1 + + + + + + + + + + + + + + Environmental Isolate + sediment, chicken feces, cheese + + Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. + Damion Dooley + NCBI Biosample + specimen source context + + + + + + + + + + + + + + + Pathogen Isolate + feces, cerebral spinal fluid (CSF) + + Substance produced by the body, e.g. stool, mucus, where the specimen was obtained from. + Damion Dooley + subject body product + + + + + + + + + Environmental Isolate + Geographic location depth + GROUP: MIxS + value (5m) + Please refer to the definitions of depth in the environmental packages + GROUP: MIxS + GENEPIO + collection depth datum + + + + + + + + The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO + http://purl.obolibrary.org/obo/ENVO_00010483 + obsolete: specimen source environmental material + true + + + + + + + + + + + + + + + + A subject sex is the phenotypic sex of given subject (human or animal) related to a given investigation, study, and/or specimen. + Damion Dooley + Gender is not used because it is a term referencing human social and cultural convention. + subject sex specification + + + + + + + + + Environmental Isolate + Land use where sample was taken + Environment Canada Metadata + descriptive; type of human use (park, farm, urban) + Human use of land involving the management and modification of natural environment or wilderness into built environment. + URI: http://en.wikipedia.org/wiki/Land_use + GENEPIO + specimen collection site land use + + + + + + + + + + + + + + + + + + + + + + + + + + + + Environmental Isolate + Fecal Indicator Bacteria Number + Environment Canada Metadata + 12,456 cfu + Number of indicator micro-organisms (colony forming units) present in a sample that have been used to suggest the presence of pathogens. + URI: http://www.who.int/water_sanitation_health/dwq/iwachap13.pdf + GENEPIO + fecal indicator bacteria count + + + + + + + + + Environmental Isolate + Conductivity + GROUP: MIxS + milliSiemens per centimeter + electrical conductivity of water + GROUP: MIxS enviro package + GENEPIO + conductivity measurement datum + + + + + + + + + Environmental Isolate + Dissolved oxygen + GROUP: MIxS + micromole per kilogram + concentration of dissolved oxygen + GROUP: MIxS enviro package + GENEPIO + dissolved oxygen concentration + + + + + + + + + GMI MDM standard + + The Global Microbial Identifier "Minimum data for Matching" (MDM) standard is a standard that defines essential contextual data fields to be included in genomic sequence repository records. + Damion Dooley + the Global Microbial Identifier Minimum Data for Matching (MDM) Standard + http://www.globalmicrobialidentifier.org/-/media/Sites/gmi/News-and-events/2013/6th-meeting-2013-report.ashx?la=da + + + + + + + + + Environmental Isolate + Soluble inorganic material + GROUP: MIxS + soluble organic material name;measurement value + concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + GROUP: MIxS enviro package + GENEPIO + soluble inorganic material + + + + + + + + + Environmental Isolate + Soluble inorganic material + GROUP: MIxS + GENEPIO + soluble inorganic material concentration + + + + + + + + + Environmental Isolate + Nitrite + GROUP: MIxS + micromole per liter + concentration of nitrite + GROUP: MIxS enviro package + GENEPIO + nitrite concentration + + + + + + + + + Environmental Isolate + Nitrate + GROUP: MIxS + micromole per liter + concentration of nitrate + GROUP: MIxS enviro package + GENEPIO + nitrate concentration + + + + + + + + + Environmental Isolate + Total phosphorous + GROUP: MIxS + micromole per liter + total phosphorus concentration, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus. Can also be measured without filtering, reported as phosphorus + GROUP: MIxS enviro package + GENEPIO + total phosphorous concentration + + + + + + + + + + + + + + + + + 12 + + + + + + + Environmental Isolate + Stream order + Environment Canada Metadata + value, 1-12 + Stream order is a measure of the relative size of streams (The smallest tributaries are referred to as first-order streams, while the largest river in the world, the Amazon, is a twelfth-order waterway). + GROUP: Environment Canada Metadata + GENEPIO + stream order categorical measurement datum + + + + + + + + + Environmental Isolate + Density of bacteria in sample + Environment Canada Metadata + OD reading or cfu's or cells per millilitre + number of bacteria in sample + GROUP: Environment Canada Metadata + GENEPIO + bacteria density + + + + + + + + + Lab Analytic + Host Primary Enzyme + PulseNet Data Capture + pick list (XbaI, BlnI) + Restriction enzyme for first characterization + GROUP: IRIDA Ontology (Emma) + primary enzyme (LMAAI) + + + + + + + + + + + + 1 + + + + + + + 1 + + + + + GENEPIO + PFGE test specification + + + + + + + + + Lab Analytic + Host Primary PFGE Pattern + NML LIMS + + First PFGE pattern from given diagnostic restriction enzyme + GROUP: IRIDA Ontology (Emma) + GENEPIO + PFGE primary test + + + + + + + + + Lab Analytic + Host Secondary Enzyme + PulseNet Data Capture + pick list (XbaI, BlnI) + Restriction enzyme for second characterization + GROUP: IRIDA Ontology (Emma) + GENEPIO + secondary enzyme (LMACI) + + + + + + + + + Lab Analytic + Host Secondary PFGE Pattern + NML LIMS + + Second PFGE pattern from given diagnostic restriction enzyme + GROUP: IRIDA Ontology (Emma) + GENEPIO + PFGE secondary test + + + + + + + + + Lab Analytic + MLST Clonal Complex + inferred from BCCDC interviews and Bionumerics + pick list? + Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. Sequence types are grouped into clonal complexes by their similarity to a central allelic profile (genotype). As such, clonal complexes represent sequence types that share a number of identical alleles e.g. 5/7 + URI: http://en.wikipedia.org/wiki/Multilocus_sequence_typing ; http://eburst.mlst.net/3.asp + GENEPIO + MLST clonal complex + + + + + + + + + Lab Analytic + MLST Sequence Type + inferred from BCCDC interviews and Bionumerics + pick list? + Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. For each housekeeping gene, the different sequences present within a bacterial species are assigned as distinct alleles and, for each isolate, the alleles at each of the loci define the allelic profile or sequence type (ST). + + GENEPIO + MLST sequence typing + + + + + + + + + + The process of fingerprinting the core genome of a bacteria. + Add under upcomming OBI "DNA fingerprinting assay". + Damion Dooley + Some bacteria like E coli have a highly variable genome, and so to type them methods must focus on typing the core genome that is common to all strains. + GENEPIO + core genome fingerprinting assay + + + + + + + + + Lab Analytic + CGF type + inferred from BCCDC interviews + pick list + + output of CGF + GROUP: IRIDA Ontology (Emma) + GENEPIO + CGF type + + + + + + + + + Lab Analytic + 16S rRNA sequencing + inferred from BCCDC interviews + 16S ribosomal RNA sequencing is a sequencing method used to identify and compare bacteria present within a given sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study. + URI: http://www.illumina.com/applications/microbiology/microbial-sequencing-methods/16S-rrna-sequencing.html + GENEPIO + 16S rRNA sequencing + + + + + + + + + + + + + + + Lab Analytic + Stx toxin type + metadata feedback + Stx1 or Stx2 + pathogenic shiga toxin produced by STEC E. coli + GROUP: IRIDA Ontology (Emma) + GENEPIO + Stx toxin type datum + + + + + + + + + + + + + + + Lab Analytic + Stx toxin subtype + metadata feedback + stx1a, stx1c + shiga toxin variant + GROUP: IRIDA Ontology (Emma) + GENEPIO + Stx toxin subtype datum + + + + + + + + + + + + + + + Lab Analytic + Stx1 Toxin PCR result + NML Labware LIMS + CT value? + qPCR result of Stx1 gene amplification + GROUP: IRIDA Ontology (Emma) + GENEPIO + Stx1 Toxin PCR result + + + + + + + + + + + + + + + Lab Analytic + Stx1 Cell Culture + NML Labware LIMS + level of Stx1 toxin derived tissue culture toxicity + GROUP: IRIDA Ontology (Emma) + GENEPIO + Stx1 cell culture level + + + + + + + + + + + + + + + Lab Analytic + Stx2 Toxin PCR result + NML Labware LIMS + CT value? + qPCR result of Stx2 gene amplification + GROUP: IRIDA Ontology (Emma) + GENEPIO + Stx2 Toxin PCR result + + + + + + + + + + + + + + + Lab Analytic + Stx2 Cell Culture + NML Labware LIMS + value? + level of Stx2 toxin derived tissue culture toxicity + GROUP: IRIDA Ontology (Emma) + GENEPIO + Stx2 cell culture level + + + + + + + + + + + + + + + + An AccuProbe assay that uses a luminometer and DNA probe designed to identify a specific bacteria or fungus species within a culture. + Damion Dooley + Nucleic acid hybridization tests are based on the ability of complementary nucleic acid strands to specifically align and associate to form stable double-stranded complexes (6). The ACCUPROBE method uses a single-stranded DNA probe with a chemiluminescent label that is complementary to the ribosomal RNA of the target organism. After the ribosomal RNA is released from the target organism, the labeled DNA probe combines with the target organism’s ribosomal RNA to form a stable DNA:RNA hybrid. The Selection Reagent allows for the differentiation of non-hybridized and hybridized probes.The light signal emitted by the DNA:RNA hybrids is measured by a GEN-PROBE luminometer. A positive result is a luminometer reading equal to or greater than the cut-off. A value below this cut-off is the negative result. + GENEPIO + AccuProbe culture identification assay + + + + + + + + + + An AccuProbe reagent kit for identifying Listeria monocytogenes. + Damion Dooley + URI: http://www.hologic.com/sites/default/files/package%20inserts/103051F-EN-RevC.pdf + GENEPIO + AccuProbe Listeria monocytogenes culture identification reagent kit + + + + + + + + + + + + + + + Lab Analytic + NML Labware LIMS + positive, negative, not done + A categorical diagnostic result of an AccuProbe test. + NML LIMS + GENEPIO + AccuProbe test result + + + + + + + + + Ribotyping involves the fingerprinting of genomic DNA restriction fragments that contain all or part of the genes coding for the 16S and 23S rRNA. By digesting the genes with a specific restriction enzyme, fragments of different lengths are generated. By performing a Gel electrophoresis with the digested samples, the fragments can be visualised as lines on the gel, where larger fragments are close to the start of the gel, and smaller fragments further down. After blotting onto a matrix and probing, these lines form a unique pattern for each species and can be used to identify the origin of the DNA, almost like a barcode can identify a product. + + GENEPIO + ribotyping + + + + + + + + + This method is based on restriction endonuclease digestion of bacterial chromosomal DNA, followed by Southern hybridization to probes for sequences in the regions of bacterial DNA coding for the 5S-16S-23S (the Escherichia coli rrnB rRNA operon) rRNA operon. The probes have been developed that are directed to highly conserved regions of the rRNA operon present in all eubacteria and can therefore be used for ribotyping most bacteria + + GENEPIO + riboprinting + + + + + + + + + an automated system that takes a purified bacterial suspension, lyses the cells, extracts the DNA, restriction endonuclease digests the DNA, separates the digest on a gel, transfers the DNA bands to a membrane, probes the bands with non-radioisotope-labeled, 5S-16S-23S rRNA-specific probes (Southern hybridization), photographs the membrane, and finally compares the bar code-like pattern to databases in order to identify the genus and species. + + GENEPIO + Qualicon (DuPont) RiboPrinter Microbial Characterization System + + + + + + + + + a library of RiboPrinter recognised patterns + GENEPIO + DuPont identification pattern library + + + + + + + + + Lab Analytic + Riboprinter DUP Number + NML Labware LIMS + DUP-PST1-1211 + DuPont identification number from the DuPont identification library + NML LIMS + GENEPIO + RiboPrinter DUP Number + + + + + + + + + Lab Analytic + Riboprinter DUP similarity + NML Labware LIMS + The identification of an isolate was determined when the corresponding patterns matched one of the patterns of the DuPont Identification library of the RiboPrinter1 with a similarity of >0.85. The similarity threshold for an isolate joining a ribogroup is an adaptive value between 0.90 and 0.96, depending on the size of the ribogroup. + Similarity of pattern to one of the patterns of the DuPont Identification library of the RiboPrinter + + GENEPIO + RiboPrinter DUP similarity + + + + + + + + + + + + + + + + Sequencing + Sequencing Run Date + NML NGS Archive + yyyy/mm/dd + Date the sequencing run was performed + GROUP: IRIDA Ontology (Emma) + GENEPIO + sequencing run date + + + + + + + + + Sequencing + Sequencing Location + inferred from BCCDC interviews + location the sequencing run was performed + GROUP: IRIDA Ontology (Emma) + GENEPIO + sequencing location + + + + + + + + + Sequencing + Platform + https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._platform_descriptor_t/ + Illumina (MiSeq, HiSeq), PacBio, Ion Torrent, (Roche 454), SOLiD ABI + + A sequencing plaform (brand) is a name of a company that produces sequencer equipment. + GROUP: IRIDA Ontology (Emma) + GENEPIO + sequencing platform (brand) + + + + + + + + + Sequencing + Workflow + Derived from Sample Sheet + Resequencing, FastQ only + the workflow is the pre-defined sequence of steps to run the automated sequencing pipeline. + GROUP: IRIDA Ontology (Emma) + GENEPIO + sequencing workflow + + + + + + + + + Sequencing + Application + Derived from Illumina Sample Sheet + amplicon sequencing, WGS + the sequencing application is the use or purpose of the sequencing + GROUP: IRIDA Ontology (Emma) + GENEPIO + sequencing application + + + + + + + + Derived from Illumina Sample Sheet + the sequencing conditions and the analyte being measured + GROUP: IRIDA Ontology (Emma) + + obsolete: sequencing assay + true + + + + + + + + + Sequencing + Chemistry + Derived from Illumina Sample Sheet + amplicon, resequencing (WGS) + lab method to determine the order of nucleotides in a DNA molecule + GROUP: IRIDA Ontology (Emma) + GENEPIO + sequencing chemistry + + + + + + + + + Sequencing + Read Length + Derived from Illumina Sample Sheet + 151, 251 + number of base pairs per read + GROUP: IRIDA Ontology (Emma) + GENEPIO + read length + + + + + + + + A GSCID/BRC data item is a field in one of the GSCID/BRC Project and Sample Application Standard subsets. + Damion Dooley + + obsolete: GSCID-BRC data item + true + + + + + + + + + Sequencing + Multiplex identifiers + Derived from Illumina Sample Sheet + S017 + Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters + GROUP: MIxS + GENEPIO + sequencing run multiplex identifiers + + + + + + + + + Sequencing + Sample Name + Derived from Illumina Sample Sheet specification: http://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/miseq/miseq-sample-sheet-quick-ref-guide-15028392-j.pdf + 1,2,3, AX234, etc. + Control1, Tank1, Froglet1 + A sequencing run sample identifier is an alphanumeric identifier for a sample. In bioinformatics processing this identifier is assigned to a sample in order to track it through the process of sequencing and analysis. + GROUP: IRIDA Ontology (Emma) + Illumina SampleSheet: Sample_ID + PulseNet: SubmittedNumber + sample name + sample title + GENEPIO + sequencing run sample identifier + + + + + + + + + Sequencing + Number of cycles + Derived from Illumina Sample Sheet + 500 + Number of sequencing chemistry cycles + GROUP: IRIDA Ontology (Emma) + GENEPIO + sequencing count of chemistry cycles + + + + + + + + + Sequencing + Sequencing Kit + Derived from Illumina Sample Sheet + MiSeq reagent kit + Pre-filled, ready-to-use reagent cartridges. Used to produce improved chemistry, cluster density and read length as well as improve quality (Q) scores. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications. + GROUP: IRIDA Ontology (Emma) + GENEPIO + sequencing kit + + + + + + + + + Sequencing + Sequencing Kit version + Derived from Illumina Sample Sheet + v2, v3 + A string datum which is the version/configuration of the reagent cartidge. + GROUP: IRIDA Ontology (Emma) + GENEPIO + sequencing kit version + + + + + + + + + Sequencing + Adapters + Derived from Illumina Sample Sheet + adapter A and B sequence + Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters + GROUP: MIxS + GENEPIO + adapter sequence + + + + + + + + + Sequencing + Adapter Trimming + Derived from Illumina Sample Sheet + The removal of adapter sequences from demultiplexed data reads + GROUP: IRIDA Ontology (Emma) + GENEPIO + read adapter trimming + + + + + + + + + Sequencing + inferred from BCCDC interviews + Illumina metagenomic protocol (part 15044223), with Nextera + Packaged kits (containing adapters, indexes, enzymes, buffers etc), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids. + GROUP: IRIDA Ontology (Emma) and http://applications.illumina.com/applications/sequencing/ngs-library-prep.html + library preparation kit + + + + + + + + + Sequencing + Number of base pairs + inferred from BCCDC interviews + 300 000 + The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. + GROUP: MIxS + GENEPIO + number of expected base pairs per genome + + + + + + + + + Run QC + Number of Reads Passing Filter + Output from MiSeq + 0.92 + Raw data are filtered to remove any reads that do not meet the overall quality as measured by a chastity filter. The chastity of a base call is calculated as the ratio of the brightest intensity divided by the sum of the brightest and second brightest intensities. +Clusters passing filter are represented by PF in analysis reports. Clusters pass filter if no more than one base call in the first 25 cycles has a chastity of < 0.6. + URI: http://support.illumina.com/sequencing/sequencing_instruments/miseq/questions.html + GENEPIO + number of reads passing filter + + + + + + + + + Run QC + Cluster density + Output from MiSeq + 800 k/mm^2 + Cluster Generation is a process by which libraries amplified into clonal clusters on a flow cell. The density of those clusters in the lane, is the cluster density. + URI: https://www.broadinstitute.org/files/shared/illuminavids/clusterGenSlides.pdf + sequencer flow cell cluster density + + + + + + + + + Run QC + above 30 Qscore + Output from MiSeq + >75% + percentage of reads with a Phred quality score over 30, which indicates less than a 1/1000 chance that the base was called incorrectly + URI: http://en.wikipedia.org/wiki/Phred_quality_score + GENEPIO + phred quality score + + + + + + + + + + + + + + + + + Assembly QC + Assembly + Standard Term + the GROUP: MIxS term encompasses assembly method; estimated error rate; method of calculation + Assembly method refers to how the reads were assembled into contigs for which either a de novo or mapping (reference based) strategy is used. + GROUP: MIxS + GENEPIO + assembly method + + + + + + + + + Assembly QC + Assembly status + from within "Finishing strategy" in GROUP: MIxS + standard draft or finished + + "Attempting to convey the relative integrity and reliability of the data, six levels or terms have been proposed and applied to describe genome sequences." See subclass choices. + Damion Dooley + CITATION: Chain, P.S., Grafham, D.V., Fulton, R.S., Fitzgerald, M.G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D.C., Buhay, C., et al. (2009). Genomics. Genome project standards in a new era of sequencing. Science 326, 236-237. + GENEPIO + assembly status + + + + + + + + + Assembly QC + Coverage + from within "Finishing strategy" in GROUP: MIxS + 30 + + Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence. + URI: http://en.wikipedia.org/wiki/Shotgun_sequencing + GENEPIO + Damion Dooley's note: Wikipedia defines calculation with: "the length of the original genome (G), the number of reads(N), and the average read length(L) as N * L/G" + read coverage + + + + + + + + + + + + + + + + Assembly QC + Number of Contigs + 20 + http://purl.obolibrary.org/obo/IAO_0000428 + A contig count is the count of contigs that belong to a sequence assembly. + Damion Dooley + GENEPIO + contig count + + + + + + + + + + + + + + + Assembly QC + Assembly name + Standard Term + name and version of assemby + Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community + GROUP: MIxS + GENEPIO + assembly name (identifier) + + + + + + + + + Assembly QC + Annotation Algorithm + Standard Term + Prokka + Program used for annotation + GROUP: IRIDA Ontology (Emma) + GENEPIO + genome annotation algorithm + + + + + + + + + Assembly QC + Annotation Source + Standard Term + annotation source description + For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter + GROUP: MIxS + GENEPIO + genome annotation source + + + + + + + + Damion Dooley + + + obsolete: NCBI BioSample data item + true + + + + + + + + + CDC ID + + + + + + + + + + + + + + + + + Damion Dooley + + + + + + + + + Damion Dooley + + + + + + + + An NCBI BioProject data item is a datum within the NCBI BioProject standard collection + Damion Dooley + + + obsolete: NCBI BioProject data item + true + + + + + + + + The INDISC consortium "Minimum data for Matching" standard aims to define a format to capture reads and minimum metadata. It is developed by the "Repository and storage of sequence and meta-data" workgroup 2. It is used in the Global Microbial Identifier platform. + Damion Dooley + http://purl.obolibrary.org/obo/GENEPIO_0000036 + obsolete: INSDC MDM standard + true + + + + + + + + A MixS data item is a term or field defined in the Genomic Standards Consortium MIxS standard. + Damion Dooley + + obsolete: MIxS data item + true + + + + + + + + + + The 'draft data standard' class contains draft representations of formal or defacto third party standards and related components. These representations may have been crafted without any involvement of related standards issuers and so no guarantee can be provided about their currency, accuracy or veracity. + Damion Dooley + draft data standard + + + + + + + + + + obsolete: HIPPA PHI data item + true + + + + + + + + + + obsolete: PulseNet data item + true + + + + + + + + + + The I2B2 Workbench Data Protection role standard is a standard which names and lists data protection roles between a user and a given dataset that define the level of detail a user has access to. + Damion Dooley + Derived from the Data Protection Track of the I2B2 Workbench software specification: https://www.i2b2.org/software/files/PDF/current/IM_Architecture.pdf + I2B2 Data Protection role standard + + + + + + + + + depth:1 + order: +NCIT:C115935 # healthy +NCIT:C25610 # pathologic / diseased +NCIT:C28554 # deceased + + A description of whether a given subject organism appeared healthy, sick or deceased at the time of specimen extraction. If sick or deceased, additional details should be provided in project-specific fields. + Damion Dooley + CS8 + subject health status (GSCID-BRC) + + + + + + + + + + + + + + + + The GSCID-BRC Core Sample Standard is an extension of the GMI MDM data standard + Damion Dooley + https://www.niaid.nih.gov/research/dmid-metadata-standards-core-sample + GSCID-BRC Core Sample standard + + + + + + + + + + A Core Project item is a field in the GSCID/BRC Project and Sample Application Core Project Standard. + Damion Dooley + https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project + GSCID-BRC Core Project standard + + + + + + + + + + Specimen category is a categorical variable that broadly indicates the source of a specimen in order for data processing systems like NCBI's biosample submission portal to anticipate other fields related to the source. Currently this distinguishes between "clinical or host associated" specimens and "environmental/food or other pathogen" specimens. + Damion Dooley + specimen category + + + + + + + + + day, week, month, year + + Age unit of the age measurement of a subject (individual organism). + Damion Dooley Feb 20, 2017: GSCID-BRC calls for an explicit field here whereas NCBI Biosample and MIxS don't. + Damion Dooley + NIAID GSCID-BRC metadata working group + subject age - unit + + + + + + + + + The National Center for Biotechnology Information offers standards for submitting genomic project data to their BioProject and BioSample databases. + Damion Dooley + National Center for Biotechnology Information standard + NCBI standard + + + + + + + + + + + + + + + + + + + + + + + A datum containing the city or region or more precise geographical location identifier for the site of a specimen collection event. + Damion Dooley + Adapted from NIAID GSCID-BRC metadata working group + Note that this is expressed in a particular format in some standards. + specimen collection location - city or region + + + + + + + + + + + + + + + + + + lookup + + + + + + + + + + + + + + + + The country of the site of a given specimen collection event. + Damion Dooley + NIAID GSCID-BRC metadata working group + specimen collection location - country + + + + + + + + + + The Darwin Core is body of standards. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing reference definitions, examples, and commentaries. + Damion Dooley + http://tdwg.github.io/dwc/terms/index.htm + Darwin Core Terms + + + + + + + + + + A datetime measurement related to a person's travel with respect to potential epidemilogical implications. + Damion Dooley + travel history item + + + + + + + + + + The date of a person's departure from their primary residence (at that time) on a journey to one or more other locations. + Damion Dooley + travel start date + + + + + + + + + + + + + + + + The date of a person's return to some residence from a journey originating at that residence. + Damion Dooley + travel end date + + + + + + + + + + Infection aquired during travel is a boolean datum indicating a diagnosis of a traveller's infection during a given trip. + Damion Dooley + infection aquired during travel + + + + + + + + + + This is a model of the datums involved in an epidemiology investigation. + Damion Dooley + draft pathogenic epidemiology case investigation record + + + + + + + + + + The draft epi case exposure model describes datums related to the possible transmission of a pathogen between a case person and other people, places, animals etc. + Damion Dooley + draft pathogenic epi case exposure record + + + + + + + + + + A description of a food item that a case patient has come in contact with. + Damion Dooley + draft pathogenic epi case food record + + + + + + + + + food brought back from travel + + + + + + + + + An epidemiology contact network model is a definition of the information necessary to connect pathogen transmission patterns between individuals or animals in connection with an outbreak investigation. + Damion Dooley + epidemiology contact network model + + + + + + + + + + An epi contact network - human is contact information about a person who may be involved in transmitting a pathogen. + Damion Dooley + epi contact network model - human + + + + + + + + + + This is a model that provides location and transportation information about an animal that may be involved in transmitting a pathogen to a human or other animal. + Damion Dooley + epi contact network model - animal + + + + + + + + + A note is text that provides human-readable information on one or more subjects. + Damion Dooley + note + + + + + + + + + + An epi case general info model contains datum specifications about an epidemiology investigation case including the person involved, contact information and their demographics. + Damion Dooley + draft pathogenic epi case general information record + + + + + + + + + + A record of the details around how, when, and from what an isolate was extracted. + Damion Dooley + draft pathogenic epi case isolate detail record + + + + + + + + + + + + + + + + + + + + + + + + + A specimen source substance is an organism substance or food product or environmental substance from which the specimen was extracted. + Damion Dooley + specimen source substance + + + + + + + + + + An isolate sequence filename is the file name (http://edamontology.org/data_1050) of the contig assembly file created by a bioinformatics assembly process. + Damion Dooley + isolate sequence filename + + + + + + + + + + A cluster identifier is an identifier that locates a genomic variant of an organism within a community of past or present genetically related organisms. + Damion Dooley + cluster identifier + + + + + + + + + + A laboratory test performed on a specimen from a patient with regard to potential pathogenic disease. + Damion Dooley + draft pathogenic epi case test record + + + + + + + + + + A lab test requestor is the individual or agency requesting that one or more tests be performed on a specimen. + Damion Dooley + contact specification - lab test requester + + + + + + + + + + A food cultural origin datum indicates the cultural origin of a food product. + Damion Dooley + food cultural origin + + + + + + + + + + A record of a patient's recent travel - departure and return, mode of travel and locations visited - as it may pertain to an outbreak pathogen transmission event. + Damion Dooley + draft pathogenic epi case travel record + + + + + + + + + Region (England) (entry subject to GAZ replacement) + + + + + + + + + + An epi network contact is a person who may have recieved or transmitted an infectious disease related to an outbreak investigation. + Damion Dooley + contact specification - epi network contact + + + + + + + + + + This model contains data type specifications for whole genome sequencing and epidemiology investigation contextual data. + Damion Dooley + public health lab epidemiology contextual data standard + + + + + + + + + This is a set of datums involved in laboratory processing of whole-genome-sequenced isolates. + Damion Dooley + draft whole genome sequencing lab test record + + + + + + + + + + + Damion Dooley + draft WGS lab bioinformatics process record + + + + + + + + + + + Damion Dooley + draft WGS lab sequencing record + + + + + + + + + + An NCBI SRA meta information item is a field specification for a NCBI Sequence Read Archive record. + Damion Dooley + NCBI SRA meta information standard + https://www.ncbi.nlm.nih.gov/books/NBK47529/#_SRA_Quick_Sub_BK_Experiment_ + + + + + + + + + An isolate raw read filename is the file name (http://edamontology.org/data_1050) of the raw read file created by a genomic sequencing assay. + isolate raw read filename + + + + + + + + + Sequencing + + The version identifier of a packaged kit tailored for specific sequencing workflows. + Damion Dooley + library preparation kit version + + + + + + + + + + The name and version of software used in a bioinformatics workflow to improve the quality of sequencing reads. + Damion Dooley + read trimming and filtering software + + + + + + + + + + + Damion Dooley + bioinformatics pipeline name + + + + + + + + + + + Damion Dooley + bioinformatics pipeline version + + + + + + + + + + + Damion Dooley + bioinformatics pipeline protocol + + + + + + + + + + + Damion Dooley + draft WGS lab sequencing quality metrics record + + + + + + + + + + + Damion Dooley + draft WGS lab assembly quality metrics record + + + + + + + + + + A general label indicating the primary study goal. These are only relevant for Primary submission projects (not Umbrella projects). + Damion Dooley + Damion Dooley's note: According to http://trace.ddbj.nig.ac.jp/news/2014-11-12_e.html, "A BioProject record can have multiple project data types" + project data type + + + + + + + + + + Genome assembly project utilizing already existing sequence data including data that was submitted by a different group + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + assembly project + + + + + + + + + + A sequencing project involving clone-ends + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + clone ends project + + + + + + + + + + A sequencing project involving DNA methylation, histone modification, and/or chromatin accessibility datasets + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + epigenomics project + + + + + + + + + + Exome resequencing project + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + exome resequencing project + + + + + + + + + + A whole, or partial, genome sequencing project (with or without a genome assembly) + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + genome sequencing project + + + + + + + + + The Relational Sequencing TB Data Platform (ReSeqTB) catalogs a vast amount of genotypic, phenotypic and related metadata from Mycobacterium tuberculosis (Mtb) strains to enable the development of clinically useful, WHO-endorsed in vitro diagnostic assays for rapid drug susceptibility testing of Mtb. + Damion Dooley + https://platform.reseqtb.org/ + draft ReSeq Tuberculosis data platform standard + + + + + + + + + In expressions like: "<= 8mg/L" + + The measurement comparator is a sign indicating that a measurement is above, equal to, or below a given threshold. + Damion Dooley + test threshold measurement comparator + + + + + + + + + < + + The "less than" comparator indicates that a given substance was present at less than a given quantity or concentration. + Damion Dooley + < + less than + + + + + + + + + <= + + The "less than or equal to" comparator indicates that a given substance was present at less than or equal to a given quantity or concentration. + Damion Dooley + <= + less than or equal to + + + + + + + + + == + + The "equal to" comparator indicates that a given substance was present at the given quantity or concentration. + Damion Dooley + == + equal to + + + + + + + + + >= + + The "greater than or equal to" comparator indicates that a given substance was present at greater than or equal to a given quantity or concentration. + Damion Dooley + >= + greater than or equal to + + + + + + + + + > + + The "greater than" comparator indicates that a given substance was present at greater than a given quantity or concentration. + Damion Dooley + > + greater than + + + + + + + + + order: +OBI:0001616 # specimen identifier +OBI:0001614 # GenBank ID +GENEPIO:0001100 # antibiogram drug test model +GENEPIO:0002062 # amr testing reference standard +GENEPIO:0002045 # amr resistance testing method +GENEPIO:0002047 # ... version or reagent +GENEPIO:0002049 # amr testing platform +GENEPIO:0002056 # ... vendor + + The NCBI antibiogram standard details the reporting specifications for antimicrobial susceptibility and resistance data derived from drug resistant pathogens. This information is submitted as an antibiogram table on BioSample records. + Damion Dooley + NCBI Antibiogram standard + https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/ + + + + + + + + http://purl.obolibrary.org/obo/GENEPIO_0001007 + obsolete: NCBI isolate AMR testing model + true + + + + + + + + A restaurant or an eatery, is a business which prepares and serves food and drinks to customers in exchange for money. + Damion Dooley + https://en.wikipedia.org/wiki/Restaurant + http://purl.obolibrary.org/obo/ENVO_01000934 + obsolete: restaurant + true + + + + + + + + + iPHIS standard + + The Canadian Integrated Public Health Information System (iPHIS) System provides a standard for holding reportable disease cases from participating jurisdictions. + Damion Dooley + Canadian Integrated Public Health Information System (iPHIS) Standard + + + + + + + + + 254532233433235152213423 + + The MIRU24 - international standard is a mycobacterial interspersed repetitive units (MIRU) typing method that classifies Mycobacterium tuberculosis complex (MBTC) bacteria according to a multiple locus VNTR [variable number of tandem repeats] analysis (MLVA) typing scheme of counts of repeats at 24 sequence loci. + The ordering of loci is as follows: MIRU 04, MIRU 26, MIRU 40, MIRU 10, MIRU 16, MIRU 31, 424 577, 2165, 401, 3690, 4156, 2163, 1955, 4052, MIRU 02, MIRU 23, MIRU 39, MIRU 20, MIRU 24, MIRU 27, 2347, 2461, 3171 + MIRU24 - international standard + + + + + + + + + + The MIRU24 - Canadian standard is a Mycobacterium tuberculosis typing method exactly like MIRU24 - international standard except that the report of the ordering of the matching loci is different. + Damion Dooley + The ordering of loci is as follows: MIRU 02, MIRU 04, MIRU 10, MIRU 16, MIRU 20, MIRU 23, MIRU 24, MIRU 26, MIRU 27, MIRU 31, MIRU 39, MIRU 40, 424, 577, 1955, 2163, 2165, 2347, 2401, 2461, 3171, 3690, 4052, 4156 + MIRU24 - Canadian standard + + + + + + + + + spray-wading water + + + + + + + + + pool water + + + + + + + + + obsolete: hot tub + true + + + + + + + + A cafeteria is a type of food service location in which there is little or no waiting staff table service, whether a restaurant or within an institution such as a large office building or school. + Damion Dooley + https://en.wikipedia.org/wiki/Cafeteria + http://purl.obolibrary.org/obo/ENVO_01000969 + obsolete: cafeteria + true + + + + + + + + http://purl.obolibrary.org/obo/ENVO_00003864 + obsolete: bakery + true + + + + + + + + A delicatessen or deli is a retail establishment that sells a selection of unusual or foreign prepared foods. + Damion Dooley + https://en.wikipedia.org/wiki/Delicatessen + http://purl.obolibrary.org/obo/ENVO_01000970 + obsolete: delicatessen + true + + + + + + + + A food kiosk is a kiosk (a booth with an open window on one side) that sells food. + Damion Dooley + http://purl.obolibrary.org/obo/ENVO_01000974 + obsolete: food kiosk + true + + + + + + + + A grocery store is a retail store that primarily sells food. + Damion Dooley + http://purl.obolibrary.org/obo/ENVO_01000984 + obsolete: grocery store + true + + + + + + + + A specialty/ethnic food store is a store specializing in a particular variety of food or food of cultural / regional origin. + Damion Dooley + http://purl.obolibrary.org/obo/ENVO_01000988 + obsolete: specialty/ethnic store + true + + + + + + + + A market, or marketplace, is a location where people regularly gather for the purchase and sale of provisions, livestock, and other goods + Damion Dooley + http://purl.obolibrary.org/obo/ENVO_01000987 + obsolete: market + true + + + + + + + + + + A time measurement datum that pertains to a patient's medical treatment. + Damion Dooley + treatment history datum + + + + + + + + A restaurant providing prepared meals or other food items that the purchaser intends to eat elsewhere + Damion Dooley + https://en.wikipedia.org/wiki/Take-out + http://purl.obolibrary.org/obo/ENVO_01000972 + obsolete: take out restaurant + true + + + + + + + + + + A treatment start date is a date/time datum which indicates the start of a particular medical treatment for a patient. + Damion Dooley + treatment start date + + + + + + + + + canoeing / kayaking / boating + + + + + + + + + hiking + + + + + + + + + camping + + + + + + + + Damion Dooley + http://purl.obolibrary.org/obo/PCO_0000033 + obsolete: social gathering + true + + + + + + + + http://purl.obolibrary.org/obo/PCO_0000035 + obsolete: party + true + + + + + + + + http://purl.obolibrary.org/obo/PCO_0000038 + obsolete: wedding + true + + + + + + + + http://purl.obolibrary.org/obo/PCO_0000039 + obsolete: baby shower + true + + + + + + + + http://purl.obolibrary.org/obo/PCO_0000037 + obsolete: potluck + true + + + + + + + + http://purl.obolibrary.org/obo/PCO_0000034 + obsolete: community event + true + + + + + + + + A long term care facility provides a type of residential care. It is a place of residence for people who require continual nursing care and have significant difficulty coping with the required activities of daily living. + Damion Dooley + https://en.wikipedia.org/wiki/Nursing_home_care + http://purl.obolibrary.org/obo/ENVO_01000932 + obsolete: long term care facility + true + + + + + + + + + + + + + + + + A treatment end date is a date/time datum which indicates the end of a particular medical treatment for a patient. + Damion Dooley + treatment end date + + + + + + + + + Damion Dooley + food related exposure event + + + + + + + + + + Some bacteria are associated with particular foods. Need relationship + Damion Dooley + infection-specific food detail + + + + + + + + + + A tuberculosis treatment antibiotic is an antibiotic used in the treatment of tuberculosis. + Damion Dooley + tuberculosis treatment drug + “Treatment of Tuberculosis Guidelines”, WHO, Geneva, 2010, 30 www.who.int/tb/ - See more at: http://www.tbfacts.org/tb-drugs/#sthash.nibuzCLV.dpuf + + + + + + + + + vegetarian + + + + + + + + + + A time measurement datum that pertains to an organism's physical location. + Damion Dooley + organism location history datum + + + + + + + + + This will take on a sub-herarchy of food types. + food avoidance + + + + + + + + + special diet + + + + + + + + + water related exposure event + + + + + + + + + municipal water + + + + + + + + + + A time measurement datum indicating the year a person immigrated to a given country. + Damion Dooley + immigration year of arrival + + + + + + + + + bottled water + + + + + + + + + An event (occuring at some location and for some duration of time) where + Damion Dooley + infectious disease exposure event + + + + + + + + + Damion Dooley + human related exposure event + + + + + + + + + Damion Dooley + animal related exposure event + + + + + + + + + + Identification or description of the specific individual from which this sample was obtained + Damion Dooley + https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ + NCBI BioSample isolate (human name or description) + + + + + + + + Damion Dooley + http://purl.obolibrary.org/obo/ENVO_01000923 + obsolete: petting zoo + true + + + + + + + + + Damion Dooley + agricultural fair + + + + + + + + + An isolate passage history is a record of the cyclic growth process that led to it, including number of times its was put through the process, and the method used. + Damion Dooley + http://purl.obolibrary.org/obo/GENEPIO_0001835 + isolate passage history datum + + + + + + + + + For Eschericia coli: STEC, UPEC + A pathotype is a common name for a group of organisms (of the same species) that have the same pathogenicity on a specified host + https://en.wiktionary.org/wiki/pathotype + NCBI pathotype + + + + + + + + + Damion Dooley + + pet treat + + + + + + + + + Damion Dooley + + pet food (raw) + + + + + + + + + + An epidemiology travel datum is a datum regarding a particular human's travel trip destination, mode, and motivation, with respect to an epidemiology investigation. + Damion Dooley + human exposure event - travel datum + + + + + + + + + boat / cruise travel + + + + + + + + + train travel + + + + + + + + + bus travel + + + + + + + + + car travel + + + + + + + + + airline travel + + + + + + + + + + A travel mode is a type of transportation which a given human has used while travelling on a particular trip. + Damion Dooley + travel mode + + + + + + + + + + A travel reason is a motivation for traveling on a particular trip expressed by the traveller. + Damion Dooley + travel reason + + + + + + + + + travel for pleasure + + + + + + + + + business activity + + + + + + + + + religious missionairy activity + + + + + + + + + rural backpacking activity + + + + + + + + + visiting relative/friends + + + + + + + + + travel tour + + + + + + + + + unsure of travel reason + + + + + + + + + The tuberculosis draft standard is a GenEpiO set of draft genomic and clinical data items related to Mycobacterium tuberculosis that various agencies are using in their own reporting. + draft tuberculosis - specimen contextual data standard + + + + + + + + + + + Damion Dooley + + behavioural risk factor + + + + + + + + http://purl.obolibrary.org/obo/GENEPIO_0001686 + obsolete: E. coli serotype part + true + + + + + + + + + Snomed: Concept 260827009 + O antigen + + + + + + + + + Snomed: Concept 260823008 + H antigen + + + + + + + + + + + Damion Dooley + + homeless status + + + + + + + + + + A serotype or serovar is a distinct variation within a species of bacteria or virus or among immune cells of different individuals. These microorganisms, viruses, or cells are classified together based on their cell surface antigens, allowing the epidemiologic classification of organisms to the sub-species level + Damion Dooley + https://en.wikipedia.org/wiki/Serotype + serovar/serotype common name + + + + + + + + + + + + + + + Salmonella serovar + + + + + + + + + Salmonella serovar name + + + + + + + + + + + + + + + Salmonella antigenic formula + + + + + + + + + + + Damion Dooley + + drug use status + + + + + + + + + + + Damion Dooley + + incarceration status + + + + + + + + + + + Damion Dooley + + HIV status + + + + + + + + + + + Damion Dooley + + HIV risk status + + + + + + + + + + + Damion Dooley + + A.I.D.S status + + + + + + + + + + + Damion Dooley + + drug abuse status + + + + + + + + + + + Damion Dooley + + injection drug use status + + + + + + + + + + + Damion Dooley + + recreational drug use status + + + + + + + + + + + Damion Dooley + + methadone use status + + + + + + + + + + + Damion Dooley + + substantial alcohol use/abuse status + + + + + + + + + + + Damion Dooley + smoking status + + + + + + + + + + + + + + + + + + + + + + A country of birth is the country that a given person (or animal) was born in. + Damion Dooley + country of birth + + + + + + + + + Tb_1 (with respect to an Illumina SampleSheet.csv spreadsheet) +13 (with respect to a ReSeqTB SNP pipeline sample report) + + A sequence number is a numeric identifier of a sequence with respect to a particular data table or dataset. + sequence number + + + + + + + + + + Damion Dooley + The 'date last seen alive' is the date that a subject (patient) was last known (seen, heard, messaged) to be alive. + date last seen alive + + + + + + + + + second line or reserve tuberculosis drug + + + + + + + + + tuberculosis infection anatomical site + + + + + + + + http://purl.obolibrary.org/obo/GENEPIO_0001007 + obsolete: NCBI Antibiogram model + true + + + + + + + + + order: +GENEPIO:0001187 # antimicrobial resistance test drug +GENEPIO:0002112 # drug MIC +GENEPIO:0002080 # drug minimum inhibitory concentration unit +GENEPIO:0001001 # measurement comparator +NCIT:C85539 # antimicrobial resistance phenotype +GENEPIO:0002181 # antimicrobial resistance phenotype - ECOFF + + This is the minimal set of parameters for drug test results for a particular antimicrobial agent. + Damion Dooley + draft antibiogram drug test model + http://the-vet.net/DVMWiz/Vetlibrary/Lab-%20Microbiology%20Guide%20to%20Interpreting%20MIC.htm + https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/ + + + + + + + + + A date-time datum that marks the predicted start of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time. + Damion Dooley + predicted exposure start + + + + + + + + + A date-time datum that marks the predicted end of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time. + Damion Dooley + predicted exposure end + + + + + + + + + + Map: - project that results in non-sequence map data such as genetic map, radiation hybrid map, cytogenetic map, optical map, and etc. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + map project + + + + + + + + + + Metagenome: sequence analysis of environmental samples + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + metagenome project + + + + + + + + + + Metagenome assembly: a genome assembly generated from sequenced environmental samples + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + metagenome assembly project + + + + + + + + + + Other: a free text description is provided to indicate Other data type + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + other project data type + + + + + + + + + + Phenotype or Genotype: project correlating phenotype and genotype + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + phenotype or genotype project + + + + + + + + + + Proteome: large scale proteomics experiment including mass spec. analysis + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + proteome project + + + + + + + + + + Random Survey: sequence generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + random survey project + + + + + + + + + + Targeted locus (loci): project to sequence specific loci, such as a 16S rRNA sequencing + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + targeted locus (loci) project + + + + + + + + + + Transcriptome or Gene expression: large scale RNA sequencing or expression analysis. Includes cDNA, EST, RNA_seq, and microarray. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + transcriptome or gene expression + + + + + + + + + + A sequencing project with a primary goal of identifying large or small sequence variation across populations. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + variation project + + + + + + + + + + + + + + + + + + + + + + + + (Afghanistan|Albania|Algeria|American Samoa|Andorra|Angola|Anguilla|Antarctica|Antigua and Barbuda|Arctic Ocean|Argentina|Armenia|Aruba|Ashmore and Cartier Islands|Atlantic Ocean|Australia|Austria|Azerbaijan|Bahamas|Bahrain|Baltic Sea|Baker Island|Bangladesh|Barbados|Bassas da India|Belarus|Belgium|Belize|Benin|Bermuda|Bhutan|Bolivia|Borneo|Bosnia and Herzegovina|Botswana|Bouvet Island|Brazil|British Virgin Islands|Brunei|Bulgaria|Burkina Faso|Burundi|Cambodia|Cameroon|Canada|Cape Verde|Cayman Islands|Central African Republic|Chad|Chile|China|Christmas Island|Clipperton Island|Cocos Islands|Colombia|Comoros|Cook Islands|Coral Sea Islands|Costa Rica|Cote d'Ivoire|Croatia|Cuba|Curacao|Cyprus|Czech Republic|Democratic Republic of the Congo|Denmark|Djibouti|Dominica|Dominican Republic|East Timor|Ecuador|Egypt|El Salvador|Equatorial Guinea|Eritrea|Estonia|Ethiopia|Europa Island|Falkland Islands (Islas Malvinas)|Faroe Islands|Fiji|Finland|France|French Guiana|French Polynesia|French Southern and Antarctic Lands|Gabon|Gambia|Gaza Strip|Georgia|Germany|Ghana|Gibraltar|Glorioso Islands|Greece|Greenland|Grenada|Guadeloupe|Guam|Guatemala|Guernsey|Guinea|Guinea-Bissau|Guyana|Haiti|Heard Island and McDonald Islands|Honduras|Hong Kong|Howland Island|Hungary|Iceland|India|Indian Ocean|Indonesia|Iran|Iraq|Ireland|Isle of Man|Israel|Italy|Jamaica|Jan Mayen|Japan|Jarvis Island|Jersey|Johnston Atoll|Jordan|Juan de Nova Island|Kazakhstan|Kenya|Kerguelen Archipelago|Kingman Reef|Kiribati|Kosovo|Kuwait|Kyrgyzstan|Laos|Latvia|Lebanon|Lesotho|Liberia|Libya|Liechtenstein|Line Islands|Lithuania|Luxembourg|Macau|Macedonia|Madagascar|Malawi|Malaysia|Maldives|Mali|Malta|Marshall Islands|Martinique|Mauritania|Mauritius|Mayotte|Mediterranean Sea|Mexico|Micronesia|Midway Islands|Moldova|Monaco|Mongolia|Montenegro|Montserrat|Morocco|Mozambique|Myanmar|Namibia|Nauru|Navassa Island|Nepal|Netherlands|New Caledonia|New Zealand|Nicaragua|Niger|Nigeria|Niue|Norfolk Island|North Korea|North Sea|Northern Mariana Islands|Norway|Oman|Pacific Ocean|Pakistan|Palau|Palmyra Atoll|Panama|Papua New Guinea|Paracel Islands|Paraguay|Peru|Philippines|Pitcairn Islands|Poland|Portugal|Puerto Rico|Qatar|Republic of the Congo|Reunion|Romania|Ross Sea|Russia|Rwanda|Saint Helena|Saint Kitts and Nevis|Saint Lucia|Saint Pierre and Miquelon|Saint Vincent and the Grenadines|Samoa|San Marino|Sao Tome and Principe|Saudi Arabia|Senegal|Serbia|Seychelles|Sierra Leone|Singapore|Sint Maarten|Slovakia|Slovenia|Solomon Islands|Somalia|South Africa|South Georgia and the South Sandwich Islands|South Korea|South Sudan|Southern Ocean|Spain|Spratly Islands|Sri Lanka|State of Palestine|Sudan|Suriname|Svalbard|Swaziland|Sweden|Switzerland|Syria|Taiwan|Tajikistan|Tanzania|Tasman Sea|Thailand|Togo|Tokelau|Tonga|Trinidad and Tobago|Tromelin Island|Tunisia|Turkey|Turkmenistan|Turks and Caicos Islands|Tuvalu|USA|Uganda|Ukraine|United Arab Emirates|United Kingdom|Uruguay|Uzbekistan|Vanuatu|Venezuela|Viet Nam|Virgin Islands|Wake Island|Wallis and Futuna|West Bank|Western Sahara|Yemen|Zambia|Zimbabwe|Historical Country Names|Belgian Congo|British Guiana|Burma|Czechoslovakia|Former Yugoslav Republic of Macedonia|Korea|Netherlands Antilles|Serbia and Montenegro|Siam|USSR|Yugoslavia|Zaire)(:[a-zA-Z0-9 ]+)? + + + + + + + help: Consult the http://www.insdc.org/country.html country list for valid options. + The INSDC country qualifier is a textual controlled vocabulary used to indicate the country of origin of a DNA sample. It can also have the following format: country:sub_region, such as: "Canada:Vancouver". + Damion Dooley + INSDC country qualifier + + + + + + + + + phenotype + + Phenotype: phenotypic measurements for submission to dbGaP + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + phenotype project objective + + + + + + + + + + + + + + + genome material + + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + genome material from specimen + + + + + + + + + TB lineage 7 - Ethiopia + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An object aggregate which has as members whole organs or parts of organs, possibly from different organisms. + + 2021-04-19T23:36:25Z + organs or organ parts + + + + + + + + + A travel destination which a given human has travelled to on a particular trip and is outside Canada. + + 2021-05-27T04:35:17Z + travel outside Canada + + + + + + + + + A travel destination which a given human has travelled to on a particular trip and is outside a given province/territory of interest. + + 2021-05-27T04:36:13Z + travel outside province/territory + + + + + + + + + requires discussion + A data specification established for use by The Canadian COVID-19 Genomics Network (CanCOGeN) project DataHarmonizer application, for contextual data (metadata) harmonization and curation across data providers. + https://orcid.org/0000-0002-9578-0788 + https://github.com/Public-Health-Bioinformatics/DataHarmonizer/blob/master/template/canada_covid19/SOP.pdf + 2021-04-24T00:18:57Z + draft CanCOGeN DataHarmonizer specification + + + + + + + + + + A livespan history item is a date-associated event pertaining to the life of a subject. + Damion Dooley + lifespan history item + + + + + + + + + untreated water + + + + + + + + + treated water - ambient temperature + + + + + + + + + epidemiology investigation data item + + + + + + + + Unclear semantics and origin + obsolete distribution event + true + + + + + + + + obsolete supply point / event + true + + + + + + + + + + well water - treated + + + + + + + + + + Well water - untreated + + + + + + + + + + + + + + + organism datum + + + + + + + + + + http://purl.obolibrary.org/obo/GENEPIO_0001171 + http://purl.obolibrary.org/obo/OBI_0100026 + http://purl.obolibrary.org/obo/PATO_0000047 + + + + + + + + + + + + + + + a role which inheres in an organism and is realized by the process of being alive + organism role + + + + + + + + + isolate organism role + + + + + + + + + + + + + + + + + + + + animal role + + + + + + + + + + + + + + + + + + + + plant role + + + + + + + + + + Damion Dooley + taxonomic datum + + + + + + + + + + A course of treatment designed to resolve an infectious disease + Damion Dooley + infectious disease treatment + + + + + + + + + + + + + + + + + + + + + This is a collection of drugs used to test antimicrobial resistance. + This is a class of chemicals by use. They are organized more indirectly in CHEBI via 'has role' some 'antimicrobial agent'. + +Note: NCBI provides special requirements for antibiotic test-selection for BETA-LACTAMASE, see https://www.ncbi.nlm.nih.gov/biosample/docs/beta-lactamase/ + +Damion Dooley note: Used http://cts.fiehnlab.ucdavis.edu/conversion/batchConvert to convert antibiotic name to CHEBI entries. 60% match, some matches off, had to curate hits manually. + +Note that this is a longer list of antibiotics that we will need to incorporate, perhaps through ARO: +https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/?format=txt + Damion Dooley + antimicrobial resistance test drug + + + + + + + + + + Damion Dooley + Judgements here are marked down after an agent's (doctor/veterenary) analysis of symptoms. + analytic datum + + + + + + + + Damion Dooley + http://purl.obolibrary.org/obo/DOID_4 + obsolete: type of illness + true + + + + + + + + + + A specimen which has been confirmed by laboratory test(s) to contain a disease-causing agent such as a pathogen + Damion Dooley + specimen with confirmed presence of disease agent + + + + + + + + + dietary restriction + + + + + + + + + + A person which has a patient care role. + Damion Dooley + patient type + + + + + + + + + obsolete: mother + true + + + + + + + + + NCBI BioSample + depth:1 + lookup + + A subject disease outcome is an assessment of the persistence of a given disease course in a subject (patient) + Damion Dooley + Note that this is closely related to OGMS_0000063 "disease course" that lists chronic, progressive, transient and accute processes. + subject disease outcome + + + + + + + + + treated water - warm/hot + + + + + + + + + jacuzzi water + + + + + + + + + spa water + + + + + + + + + whirlpool water + + + + + + + + + + + + + + + + A host datum is a datum that pertains to infection-related information about an organism (animal or human) who is likely bearing a pathogen + Damion Dooley + patient as host datum + + + + + + + + + pregnancy history item + + + + + + + + + date of conception + + + + + + + + + + Damion Dooley + lifespan history record + + + + + + + + http://purl.obolibrary.org/obo/FOODON_03450002 + obsolete: food cooking method + true + + + + + + + + http://purl.obolibrary.org/obo/FOODON_03470107 + obsolete: food preservation method + true + + + + + + + + + infectious disease case datum + + + + + + + + + laboratory data + + + + + + + + + + Damion Dooley + specimen record + + + + + + + + + + The type of material from which the specimen was obtained. Specimens are usually categorized as food, body products or tissues, or environmental material. + Damion Dooley + specimen type (host or environmental context) + specimen source material category + + + + + + + + + Organism has a symbiotic relationship with host + symbiotic role + + + + + + + + http://purl.obolibrary.org/obo/GENEPIO_0000113 + obsolete: NCBI BioSample attribute package + true + + + + + + + + Damion Dooley + http://purl.obolibrary.org/obo/GENEPIO_0000025 + http://purl.obolibrary.org/obo/GENEPIO_0000028 + obsolete: host sample material + true + + + + + + + + + + Damion Dooley + food specimen detail + + + + + + + + + patient specimen + + + + + + + + + environmental + NCBI Biosample: environmental (swab or sampling) + environmental specimen + + + + + + + + + + A specimen extracted from an animal + Damion Dooley + animal specimen + + + + + + + + + built environment specimen + + + + + + + + + food specimen + + + + + + + + + natural environment specimen + + + + + + + + + + The type of person a patient had epidemiological (i.e. close proximity) contact with. + Damion Dooley + exposure event person + + + + + + + + + + Damion Dooley + An exposure group statistics record is a sumary of disease outbreak statistics on a certain date of a group of humans or animals potentially exposed to a pathogen. + exposure group statistics record + + + + + + + + + + symptom history item + + + + + + + + + + Damion Dooley + health state record + + + + + + + + http://purl.obolibrary.org/obo/NCIT_C17627 + obsolete: swab + true + + + + + + + + [WHICH DEFINITION?] See http://medical-dictionary.thefreedictionary.com/aspirate + Damion Dooley + + obsolete: fluid - aspirate + true + + + + + + + + + + + + + + + + + + Plant rinse is a rinse derived from plant material from one or more plants. + Damion Dooley + plant rinse + + + + + + + + + Damion Dooley + outbreak animal exposure event location + + + + + + + + + Damion Dooley + animal exposure process + + + + + + + + + Damion Dooley + animal exposure event by material + + + + + + + + + Damion Dooley + exposure by human contact + + + + + + + + Damion Dooley + unnecessary distinction + + obsolete: human exposure activity type + true + + + + + + + + + Damion Dooley + outbreak human exposure event location + + + + + + + + + + A process in which one or more humans may be exposed to one or more contagious human infectious disease carriers. + Damion Dooley + human to human exposure process + + + + + + + + + water exposure by source + + + + + + + + + human water activity + + + + + + + + + This list would be customized to include organizations local to an application's software installation. It is an example of a set of ontology terms that would best be organized by a central authority if federated installations need to share investigator contact info for example. + health authority + + + + + + + + + order: +HP:0000118 # symptom +FLU:0000976 # onset +GENEPIO:0001789 # cessation +GENEPIO:0001784 # duration + + Damion Dooley + symptom record + + + + + + + + + + + + + + + A visual pattern caused by DNA fragments concentrated in stratefied bands in a Pulsed-field gel electrophoresis (PFGE) gel plate. + PFGE pattern + + + + + + + + + + phage type salmonella (DT) + + + + + + + + + + phage type e-coli 0157 (PT) + + + + + + + + + + Damion Dooley + sequence record + + + + + + + + + + A type of built structure that is suspected to be related to an outbreak investigation. + Damion Dooley + outbreak exposure event location + http://purl.obolibrary.org/obo/ENVO_00000070 + + + + + + + + + + Damion Dooley + lab test history record + + + + + + + + + obsolete: earth surface + true + + + + + + + + + + A data specification is a specification of a data structure that can hold a categorical, textual or numeric variable, or that has such variables or other data structures as component parts. + A data standard, may be defined as a data specification, but a data specification isn't necessarily a formal or de-facto data standard - it would have to be sanctioned by a community of users and developers to take on that status. + Damion Dooley + data specification + + + + + + + + + + + + A specimen history item is a time-related datum about a particular specimen + Damion Dooley + specimen history item + + + + + + + + + + Damion Dooley + diagnostic test + + + + + + + + Damion Dooley + obsolete: sample datum + true + + + + + + + + A laboratory sequencing datum is a datum related to the sequencing assay process applied to an isolate. + Damion Dooley + http://purl.obolibrary.org/obo/GENEPIO_0001681 + obsolete: laboratory sequencing datum + true + + + + + + + + + genomic sequencing annotation datum + + + + + + + + + + Damion Dooley + ISSUE: lab test results are appropriate to lab test types. Logic around that? + lab test record + + + + + + + + + + + + + + + sequencing assembly datum + + + + + + + + + + A container id is an identifier that refers to a container object about a patient specimen. Container ids are referenced in clinical patient records reported to be suspect, or lab test results. + Damion Dooley + container record + + + + + + + + + Damion Dooley + identifier of a person with the context of a health care system + health care personal identifier + + + + + + + + + + + + + + + + A strain identifier is the unique microbial or eukaryotic strain name from a reference database that a sample has been matched to. + Damion Dooley + strain identifier + + + + + + + + + + A line list is a collection of suspected or known disease outbreak cases. It may also include details about healthy patients associated with an exposure event (picnic, concert etc.) who have been interviewed in order to compare food intake, assess risk factors, etc. + +Note that the health status of people associated with an exposure event can change from healthy or unknown status, to ill patient. + Damion Dooley + line list object + + + + + + + + + This class is a temporary holding bin for items that need a class hierarchy home, definition, and/or subclass items. Some classes have subclasses that are currently disjoint in other ontologies like ENVO, so awaiting resolution on such issues. + Damion Dooley + awaiting ontology review + + + + + + + + + The IRIDA user ID is a user account identifier provided by the IRIDA.ca system. + Damion Dooley + + + + + + + + + The count of healthy individuals or animals on a certain date/time from a group that was likely exposed to a pathogen + Damion Dooley + exposure group healthy count + + + + + + + + + The count of ill individuals or animals on a certain date/time from a group that was likely exposed to a pathogen + Damion Dooley + exposure group ill count + + + + + + + + + human general activity + + + + + + + + + + Damion Dooley + An exposure can be narrowed down to a single date, or can be reasoned to exist with a lower and/or upper bound date. A single date exposure has lower and upper bound dates set as the same value. + exposure history record + + + + + + + + + + Damion Dooley + isolate history record + + + + + + + + + + Damion Dooley + An outbreak date may have an official start, but because it might be ongoing, it may not have an end (yet). + outbreak history record + + + + + + + + + + Damion Dooley + Needs to cover the various pregnancy events + pregnancy history record + + + + + + + + + + Damion Dooley + Issue: a diagnosis is a set of diseases, each of which can be marked primary or secondary "Illness causality" with respect to a particular case? Requires a relation annotation. + diagnosis record + + + + + + + + + + Damion Dooley + exposure event record + + + + + + + + + + Damion Dooley + hospitalization event record + + + + + + + + + An exposure can be narrowed down to a single date, or can be reasoned to exist with a lower and/or upper bound date. A single date exposure has lower and upper bound dates set as the same value. + exposure history item + + + + + + + + + hospital admission date + + + + + + + + + A date-time datum that marks the end of possible human or animal exposure to a pathogen agent, directly or indirectly. + Damion Dooley + exposure event end + + + + + + + + + A date-time datum that marks the start of a human or animal exposure event to a suspected pathogen agent, directly or indirectly. + Damion Dooley + This datum is NOT predicted as a function of pathogen and first symptom date. + exposure event start + + + + + + + + + hospitalization history item + + + + + + + + + isolate history item + + + + + + + + + An outbreak date may have an official start, but because it might be ongoing, it may not have an end (yet). + outbreak history item + + + + + + + + + + + + + + + hospital discharge date + + + + + + + + + + A notification date is the date that an outbreak is suspected by a laboratory or other agency and is reported per outbreak detection guidelines. + Damion Dooley + notification date + + + + + + + + + + An outbreak date is on which disease onset appears to have occured + Damion Dooley + outbreak date + + + + + + + + + + + + + + + + An outbreak over date is the date on which a disease outbreak appears to have abated + Damion Dooley + outbreak over + + + + + + + + + + test history item + + + + + + + + + + lab test result date + + + + + + + + + requires discussion + A data item that is a set of entities, referenced by mention, that don't necessarily have something in common. + 0000-0002-8844-9165 + 0000-0002-9578-0788 + 2022-01-31T03:45:04Z + While "enumeration" is a "data item" not everything referenced within an enumeration qualifies as a "data item". Not to be confused with "data set" which describes "data item"s of the same type that have something in common. + enumeration + + + + + + + + + An analytic datum which describes the observed or detectable signs, and experienced symptomps of an illness, injury, or condition. + 0000-0002-9578-0788 + https://en.wikipedia.org/wiki/Signs_and_symptoms + 2022-01-31T23:08:50Z + signs & symptoms + signs and symptoms + + + + + + + + + + A particular attribute (feature, quality or process history) of a food sample. + Damion Dooley + The underlying facets will be supplied from the FoodOn food ontology. + food specimen datum + + + + + + + + + order: +FOODON:03411564 # food source +FOODON:00002381 # food product by organism +FOODON:03311737 # processed food product +NCIT:C71898 # brand name + + A food specimen type is a categorization of a food specimen, by the organism it is or came from, or by a class of food products. + Damion Dooley + food specimen specification + + + + + + + + + + An agency that has reported a disease cluster. + Damion Dooley + disease cluster notification agency + + + + + + + + This is a subset of OBI investigation identifier. It pertains only to NCBI Biosample projects + Damion Dooley + http://purl.obolibrary.org/obo/OBI_0001628 + obsolete: NCBI BioProject ID + true + + + + + + + + + The count of individuals or animals for which no health status is available on a certain date/time from a group that was likely exposed to a pathogen. + Damion Dooley + exposure group unknown health status count + + + + + + + + + + + + + + + + + + + + + A role which inheres in a person and is realized by the process of being in the context of civilization + Damion Dooley + person role + + + + + + + + + An exposed person role is the role a person takes on who has been exposed to a pathogen. In serious situations this may call for special treatment, e.g. quarantine. + Damion Dooley + exposed person role + + + + + + + + + parent-guardian role + + + + + + + + + + Damion Dooley + illness causality + + + + + + + + + pre-existing condition + + + + + + + + + + + + + + + + To restore to the normal state after some pathologic process. + Damion Dooley + Dorland's Illustrated Medical Dictionary, 30th ed. + improving + recovering + resolving health trend + + + + + + + + + Damion Dooley + close interpersonal relationship exposure + + + + + + + + + Damion Dooley + household exposure + + + + + + + + + Damion Dooley + exposure to individual with diarrhea + + + + + + + + + Damion Dooley + other human exposure + + + + + + + + + Damion Dooley + sexual contact exposure + + + + + + + + + Damion Dooley + exposure via diaper changing (human fecal) + + + + + + + + + container identifier + + + + + + + + + PulseNet: Outbreak + outbreak identifier + + + + + + + + + + + + + + + + + + + + + + GENEPIO + reference genome size + + + + + + + + + + + + + + + + The assembly genome size is the sum of all lengths of a sequence assembly's contigs. + Damion Dooley + GENEPIO + As noted in Quast documentation: " The total assembly size may increase (and in some cases exceeds the genome size) due to contaminants (see Chitsaz et al. (2011)), misassembled contigs, repeats, and hubs that contribute to multiple contigs. " + assembly genome size + + + + + + + + + + + + + + + + Identifier for a reference genome (used to build or compare an assembly) that is used in the genome browsers and in the community + Damion Dooley + GENEPIO + reference genome identifier + + + + + + + + + Assembly QC + + The 'genome size delta ratio' is a ratio of the difference between a sample's genome assembly size and the size of a given reference genome, over the reference genome size. + +The formula: + +| (reference_genome_size - assembly_genome_size) | / reference_genome_size + +This yeilds a decimal / percentage ranging from 0 = exact length, to say .1 which is equivalent to a 10% variance. If the ratio is too far from a quality control ratio that depends on the species in question, this indicates a bad assembly or a mis-identified sample. + Damion Dooley + GENEPIO + genome size delta ratio + + + + + + + + + Assembly QC + + This is the upper acceptable limit of the 'genome size delta ratio' with respect to a particular species. + +For Salmonella a 0.10 variance in length between an assembly size and a reference genome size may be acceptable. For E-coli a more generous 0.30 or .40 variance should be allowed, given the pathogenic subspecies’ highly dynamic genome. + GENEPIO + genome size delta ratio QC threshold + + + + + + + + + Assembly QC + http://purl.obolibrary.org/obo/IAO_0000428 + The contig N50 length QC threshold is a minimum length threshold that a contig N50 length datum should be above for good QC. A lower length is indicative of assembly problems (insufficient read depth) or a mismatched reference genome. + Damion Dooley + GENEPIO + contig N50 length QC threshold + + + + + + + + + Assembly QC + 2000 + + The contig N99 length QC threshold is the minimum length that a contig N99 or NG99 length datum can be for satisfactory QC. This threshold avoids having too many gene coding regions prematurely clipped inside short contigs. An assembly having 1% or more of its content in less than 2Kbp chunks is cause for concern. Bacterial genes are generally about 1Kbp in length. + Damion Dooley + GENEPIO + contig N99 length QC threshold + + + + + + + + + + + + + + + + + + + + + + + lookup + Homo sapiens + + The species of the host organism from which a specimen (pathogen) organism was obtained. Use the full taxonomic name, eg, "Homo sapiens". + Damion Dooley + + subject organism (host) taxonomic species + + + + + + + + + + + + + + + + + + + lookup + + + + + + + + + + + + + + + Assembly QC + + A single datum having to do with a metric for genomic sequence assembly quality control. + +A "quality control measurement" can be defined as a measurement that has some norm within a definable context, e.g. for a certain subspecies. It may be a calculated quantity. + +A "quality control metric" is an upper or lower bound threshold that a measurement is compared to. Surpassing the threshold may indicate an error situation. + +A "measure" can indicate an amount of activity, consumption, transformation, etc. but doesn't itself convey an over-stepping of bounds in the way that a metric does. + Damion Dooley + GENEPIO + assembly quality control datum + + + + + + + + + + + + + + + + + + + + + Damion Dooley + GSCID-BRC:Clinical/host-associated pathogen + NCBI:Pathogen.cl + clinical or host-associated pathogen + + + + + + + + + + + Clinical/host-associated pathogen + + + + + + + + + + + Pathogen.cl + + + + + + + + + Assembly QC + http://purl.obolibrary.org/obo/IAO_0000428 + The N99 length definition is identical to the N50 definition except that the threshold for determining the contigs is 1% of the nucleotides. This contig basepair length can be compared to a minimum threshold to determine if gene annotation (where contigs greater than say 2000bp are necessary) would generally succeed. + Damion Dooley + GENEPIO + contig N99 + + + + + + + + + Assembly QC + http://purl.obolibrary.org/obo/IAO_0000428 + The upper threshold of contig counts that are acceptable in a genome assembly. This may vary based on the overall genome length and depth of coverage. + +A large contig count may indicate insufficient read coverage. + Damion Dooley + contig count QC threshold + + + + + + + + + + Indicates how the knowledge derived from the project can be applied, and to what field(s). + Damion Dooley's note: NAIAD GRCID-BRC has Project Relevance map to OBO Foundry Study Design (http://purl.obolibrary.org/obo/OBI_0500000) but this is a bit of a stretch. + Damion Dooley + https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project + project relevance + + + + + + + + + agricultural project relevance + + + + + + + + + medical knowledge relevance + + + + + + + + + industrial processing relevance + + + + + + + + + evolution modelling relevance + + + + + + + + + environmental project relevance + + + + + + + + + model organism relevance + + + + + + + + The NCBI BioProject model includes all datums associated with the current NCBI BioProject specification. + Damion Dooley + + obsolete: NCBI BioProject model + true + + + + + + + + http://purl.obolibrary.org/obo/GENEPIO_0000147 + obsolete: NCBI SRA model + true + + + + + + + + + http://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ + http://www.ncbi.nlm.nih.gov/biosample/docs/packages/Pathogen.cl.1.0/ + + Damion Dooley notes: NCBI doesn't quite make the distinction but it may be helpful to distinguish sample submission facilitator vs submitter/repository organization contact? So should we have a +BioSample_submission_facilitator field and a BioSample_contact_information field? + Damion Dooley + Damion's note: There are a few different kinds of biosample, and required fields depend on the type selected. + draft NCBI BioSample model - mixed clinical and environmental/food/other + + + + + + + + + monoisolate + + A monoisolate sample scope involves specimens from a single animal, cultured cell-line, inbred population, or possibly a heterogeneous population when a single genome assembly is generated from a pooled sample because multiple individuals are needed to collect enough material and an inbred line is not available; however, this situation is not preferred. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + monoisolate + monoisolate sample scope + + + + + + + + + multiisolate + + A multiisolate sample scope contains multiple individuals that represent distinct specimen collections, a population (representative of a species). + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + This is often used for variation or phenotype and genotype studies. This should not be used when multiple genomes will be annotated. Eventually, multiple locus_tag prefixes will be able to be assigned to a single multiisolate genome sequencing project, but currently only a single prefix can be registered per project. Therefore, individual monoisolate projects need to be registered when more than one genome will be annotated. + multiisolate sample scope + + + + + + + + + multispecies + + A multi-species sample scope involves a sample representing multiple species. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + multispecies sample scope + + + + + + + + + environment + + An environment sample scope indicates that the species content of the sample is not known. Generally, nucleic acid is directly isolated from an environmental sample for analysis. This is used for metagenome studies. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + environment sample scope + + + + + + + + + + A synthetic sample scope involves a sample synthesized in a laboratory. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + synthetic sample scope + + + + + + + + + + Damion Dooley + single cell + + + + + + + + + other + + Other project objective: specify an objective not listed above + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + other project objective + + + + + + + + + + + + + + + + + + + + + Damion Dooley + GSCID-BRC:environmental/food/other + NCBI:Pathogen.env + environmental, food or other pathogen + + + + + + + + + + + environmental/food/other + + + + + + + + + + + Pathogen.env + + + + + + + + + whole + + Whole: the project makes use of the whole sample material (most common case). Use this for whole genome sequencing studies, transcriptome studies that are not targeting specific loci, epigenetic studies of a genome, and metagenomes or unbiased transcriptome studies of metagenomes. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + whole genomic data capture + + + + + + + + + raw sequence reads + + A raw sequence reads project objective has the goal of submission of raw reads to SRA or Trace repositories + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + raw sequence read objective + + + + + + + + + sequence + + A sequence project objective has a goal of submission of sequence data to standard archival sequence databases (yielding accession.version identifiers; e.g., whole genome shotgun, cDNA sequences, transcript shotgun assemblies) + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + sequence project objective + + + + + + + + + analysis + + An "analysis project objective" indicates there was an other analysis not otherwise indicated, includes submission of BAM files. + This defn. could be a negation of the "not otherwise indicated". + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + analysis objective + + + + + + + + + assembly + + Submission of genome assembly (AGP data) + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + assembly objective + + + + + + + + + annotation + + Sequence annotation data + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + sequence annotation objective + + + + + + + + + sequence variation + + Variation: identification of sequence variation data for submission to dbSNP or dbVAR + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + sequence variation project objective + + + + + + + + + epigenetic markers + + DNA methylation, histone modification, chromatin accessibility datasets + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + epigenetic markers objective + + + + + + + + + expression + + Expression: assays of transcript or protein existence or abundance + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + transcript or protein expression objective + + + + + + + + + maps + + Maps: non-sequence based map data; e.g., genetic, radiation hybrid, cytogenetic, etc. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + mapping objective + + + + + + + + + + Phenotypic descriptive data. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + phenotypic observation data from specimen + + + + + + + + + select sequence if any sequence data is generated from this project. + sequencing + + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + sequencing project method + + + + + + + + + array + + Select Array if that is the primary method and no sequence data is submitted + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + array project method + + + + + + + + + mass spectrometry + + Select Mass Spectrometry if that is the primary method + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + mass spectrometry project method + + + + + + + + + order: +NCIT:C40974 # first name +NCIT:C40975 # last name +NCIT:C42775 # email address +GENEPIO:0001756 # phone + contact specification - person + + + + + + + + + A categorical investigation datum is a datum pertaining to some entity examined for scientific research or diagnostic purposes and which has a scope that is broader than one of the clinical, environmental or epidemiological domains. + Damion Dooley + investigation datum + + + + + + + + + An organism and its host share physical space but no evidence exists to determine if one benefits from this arrangement. + commensal role + + + + + + + + + draft isolate details model + + + + + + + + + + A subject age is the age since birth of a given organism that is involved in an investigation or study at a given time. + Damion Dooley + subject age + + + + + + + + + + draft NCBI component model + + + + + + + + + draft IRIDA BioSample model + + + + + + + + + + + + + + + draft GenEpiO epidemiology case record + + + + + + + + + + + + + + + A subject description is a field containing additional information about an organism (related to an investigation, study and/or specimen) that is not included in other defined vocabulary fields. + Damion Dooley + http://purl.obolibrary.org/obo/GENEPIO_0001835 + subject description + + + + + + + + + + + host description + + + + + + + + + NCBI BioSample + The host profile or identifiers text is the "identification or description of the specific individual from which this sample was obtained". + Damion Dooley + NCBI BioSample: isolate + host profile or identifers + + + + + + + + + + A subject identifier is an identifier of a subject organism within the context of a particular investigation, study, or specimen extraction event. + Damion Dooley + This varies in its type (numeric or string) and its central repository depending on its context (use in a particular application/instance). + +Note: GSCID-BRC specification states " 'Host' is not the preferred term since some specimens may lack any detectable pathogen". In other words, a person would technically (logically) only have a host identifier AFTER they have been diagnosed as having a pathogen. A health care personal identifier, or a case identifier would be better than a more ephemeral "host id" + subject identifier + + + + + + + + + + + + + + + + Name of disease in a subject that is related to a given investigation, study and/or specimen. + Damion Dooley + NIAID GSCID-BRC metadata working group + Controlled vocabulary. Human specimen source: https://bioportal.bioontology.org/ontologies/DOID +or https://www.ncbi.nlm.nih.gov/mesh/1000067 + subject disease + + + + + + + + + INSDC term (top level) + A categorical choice recorded when a measurement value was known to be recorded in the past but the observed value cannot be located or retrieved for some reason. + + + NCBI Biosample: missing + missing + + + + + + + + + INSDC term (top level) + 'not applicable' is an appropriate value for the measure of femur length for a patient with a missing limb + + A categorical choice recorded when a measurable datum does not apply to a given context. + Damion Dooley + + + + not applicable + + + + + + + + + INSDC term (lower level) + A categorical choice recorded when a datum was not measured with respect to some entity during some process. + + + NCBI Biosample: not collected + not collected + + + + + + + + + draft isolate identifier model + + + + + + + + + + draft GenEpiO isolate testing model + + + + + + + + + + draft NCBI isolate source location model + + + + + + + + + draft GenEpiO isolate environment model + + + + + + + + + A subject disease stage is a measure of the acuteness of a subject organism's diagnosed disease, if any, at a given time in an investigation, study or specimen extraction event. + Damion Dooley + http://purl.obolibrary.org/obo/GENEPIO_0001835 + subject disease stage + + + + + + + + + environmental datum + + + + + + + + + + + + + + + temperature of sample + + + + + + + + + + de-novo assembly + + + + + + + + + http://purl.obolibrary.org/obo/GENEPIO_0000025 + obsolete: sample body source + true + + + + + + + + + contig pre-analysis minimum length QC threshold + + A 'contig length QC threshold' is an integer setting which can be applied by an algorithm to an array of assembly and annotation contig lengths to remove (filter out) all items less than the threshold value. The reduced array is used for calculation of statistics. + Damion Dooley + http://quast.bioinf.spbau.ru/manual.html + QUAST specifies which of its report stats are affected by the "--min-contig" minimum contig length parameter. + contig length QC threshold + + + + + + + + + + The NG50 length is the same as the N50 length except that the length of the reference genome is used in the calculation rather than the assembly genome size. + Damion Dooley + "Note that N50 is calculated in the context of the assembly size rather than the genome size. Therefore, comparisons of N50 values derived from assemblies of significantly different lengths are usually not informative, even if for the same genome. To address this, the authors of the Assemblathon competition derived a new measure called NG50. The NG50 statistic is the same as N50 except that it is 50% of the known or estimated genome size that must be of the NG50 length or longer. This allows for meaningful comparisons between different assemblies. In the typical case that the assembly size is not more than the genome size, the NG50 statistic will not be more than the N50 statistic." - wikipedia + contig NG50 + + + + + + + + + + + + + + + + A contig length is the count of base pairs in a given sequence assembly contig. + Damion Dooley + contig length + + + + + + + + + Assembly QC + http://purl.obolibrary.org/obo/IAO_0000428 + Contig L50 is the number of contigs equal to or longer than contig N50. The length of the assembly itself is used in the calculation. + Damion Dooley + QUAST manual + contig L50 + + + + + + + + + Assembly QC + http://purl.obolibrary.org/obo/IAO_0000428 + The LG99 count is like the L99 count except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths. + Damion Dooley + contig LG99 + + + + + + + + + An organism isolate datum is any datum pertaining to an isolate organism + Damion Dooley + obsolete: specimen from subject datum + true + + + + + + + + + + + + + + + + A product of an animal, as in blood, feces, sputum, etc. that has no particular anatomical site + Damion Dooley + animal body product + + + + + + + + This is the scientific role or category that the subject organism or material has with respect to an investigation. + Damion Dooley + http://purl.obolibrary.org/obo/GENEPIO_0001237 + obsolete: specimen source material category + true + + + + + + + + + draft GenEpiO general information record + + + + + + + + + + + + + + + + + + + + + An antigenic formula is a string composed of codes representing categorized results of tests performed on various viral, bacterial or immune cell surface antigens. + Damion Dooley + antigenic formula + http://medical-dictionary.thefreedictionary.com/antigen + + + + + + + + + + + + + + + + + + + + + + + + lookup + + This is the taxonomic species descriptor of a specimen isolate (an organism found within a specimen.) + Damion Dooley + specimen organism taxonomy (species) + + + + + + + + + + An identifier moe3l indicates an identifier, the organization it has been issued by, and the status of the identifier - whether it is a primary one, active or archaic. + Damion Dooley + identifier model + + + + + + + + + help:This should be populated with a selection from INSDC.org controlled vocabulary for providers: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/coll_dump.txt + + The curator organization name is the name of an organization that manages a given repository of entities (samples, isolates, sequences ...) + Damion Dooley + curator organization name + + + + + + + + + INSDC:institution_code:BRS + IRIDA:ACK + Agriculture and Agri-Food Canada + + + + + + + + + + An isolate identifier is an identifier assigned to a given isolate by a particular agency that is handling or storing it. + Damion Dooley + isolate identifier + + + + + + + + + + An identifier status describes the principle role of an identifier assigned to an entity by its curator or handler. An entity may have a number of identifiers assigned to it over time. An identifier may be phased-out as can happen when its content is transferred to another curator. + Damion Dooley + identifier status + + + + + + + + + GenEpiO + + A data protection role is a role (or user permission) that a user has with respect to particular data. + A data server may be able to provide a protected(modified) dataset with metadata indicating what parts have a protection role with respect to the user requesting this information. A data protection role would be inherited from a user's relation to an entitiy to the entity's components or subclasses. + Damion Dooley + data protection role + + + + + + + + + + + An identifier used in the initial submission of content to a repository. + original submission + + + + + + + + + + This was created to help define a contributing organization to a repository. However this still needs organizing. The "collected_by" field is free text but contact name AND organization could be associated with this in controlled vocabulary. + NCBI Contributing organization / project + + + + + + + + + food - liquid + + + + + + + + + + draft NCBI BioSample identifier model + + + + + + + + + + An INSDC institution code is an identifier of an organization from a list of sequence repository organizations managed by INSDC. + Damion Dooley + http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier + INSDC institution code + + + + + + + + + draft IRIDA epidemiological case model + + + + + + + + + + An identifier that had been used previously but is no longer promoted. + Damion Dooley + previous (archaic) identifier + + + + + + + + + + A geographical location datum is a datum that refers to a real, hypothesized or fanciful spatial location + Damion Dooley + geographic location datum + + + + + + + + A categorical tree specification datum is a categorical value specification which takes its value from the ontology URI identifier of any one of its subclass items; these may be organized in a hierarchy. + Damion Dooley + http://purl.obolibrary.org/obo/OBI_0001930 + A categorical tree specification datum may have its own URI identifier as its value. This could be interpreted to mean that the datum was recorded but that no particular categorical subclass distinction was observed. This in effect makes the datum act as a boolean variable. + obsolete: categorical tree specification + true + + + + + + + + + + Damion Dooley + A geographic coordinate entity composed of both latitude and longitude components. + latitude and longitude coordinate (ISO 6709) + + + + + + + + + + + + + + + order: +NCIT:C25464 # country +ENVO:00000005 # state / province etc. + + Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps" + Damion Dooley + draft NCBI BioSample geo_loc_name model + + + + + + + + + draft GenEpiO isolate sequencing model + + + + + + + + + A case ID is a unique identifier associated with a particular episode of care for an individual or animal. + Damion Dooley + case identifier + + + + + + + + + + + An animal that has had a substantial part of its reproductive organs removed surgically. + Damion Dooley + NCBI BioSample: neuter + Not a PATO phenotypic sex catigorical value. + neuter + + + + + + + + + + + + + + + + + NCBI BioSample + 'pooled male and female' is a categorical value used when the male and female categories or levels of a factor are combined. If used to describe a single organism, then the organism will be one or the other. + Not a PATO phenotypic sex catigorical value. + Damion Dooley + NCBI BioSample: 'pooled male and female' + pooled male and female + + + + + + + + + + A categorical choice recorded while the data for a given measurable datum has not finished being collected, is awaiting a conclusion, or has not yet been communicated. + Damion Dooley + undetermined + in process + + + + + + + + + swimming / wading + + + + + + + + + + Damion Dooley + NECESSARY? : What details are categorical and what are freehand? This item was originally too broad; moved sub-items to Treatment. + infection detail datum + + + + + + + + + + This is problematic - its not clear if this is reporting that antibiotics were administered, or whether they are recommended as a result of diagnosis. + Damion Dooley + antibiotics required + + + + + + + + + + The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. INSDC covers the spectrum of data raw reads, though alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations. + Damion Dooley + International Nucleotide Database Collaboration standard + INSDC + INSDC standard + + + + + + + + + + Damion Dooley + outcome of pregnancy associated with illness + + + + + + + + + INSDC term (lower level) + a categorical choice indicating that information of an expected format was not given; a value may be given at the later stage. + + + not provided + + + + + + + + + + + + + + + + + + + + + + Damion Dooley + stable health status + http://purl.obolibrary.org/obo/GENEPIO_0002026 + + + + + + + + + induced abortion + + + + + + + + + + live birth + + + + + + + + Damion Dooley + http://purl.obolibrary.org/obo/VT_0002292 + obsolete: gestation duration (weeks) + true + + + + + + + + + + + + + + + date of pregnancy outcome + + + + + + + + + + + + + + + + + + + + + + contact specification - physician + + + + + + + + obsolete: matrix - solid + true + + + + + + + + + + + + + + + + contact specification - parent/guardian + + + + + + + + + + + + + + + + + + + + + + contact specification - patient + + + + + + + + + draft GenEpiO case epidemiology record + + + + + + + + + order: +NCIT:C25464 # Country +ENVO:00000005 # major administrative subdivision aka state/province/territory/region (via GenEpiO -> GAZ ) +NCIT:C80234 # Municipality (via GenEpiO -> GAZ cities) +NCIT:C25690 # Street Address +NCIT:C25621 # postal code + + The address component of a contact specification. + contact specification - address + + + + + + + + + GENEPIO_0001829 + obsolete: draft IRIDA model + true + + + + + + + + + + A datum related to the sequencing assay process applied to an isolate. + Damion Dooley + laboratory sequencing datum + http://purl.obolibrary.org/obo/OBI_0001901 + http://purl.obolibrary.org/obo/OBI_0400103 + + + + + + + + + + Damion Dooley + host illness associated with + + + + + + + + + draft subject demographic specification + + + + + + + + + + + + + + + + + + + + + + + K(1|2a|2ac|3|4|5|6|7|8|9|10|11|12|13|14|15|16|18a|18ab|19|20|22|23|24|26|27|28|29|30|31|34|37|39|40|41|42|43|44|45|46|47|49|50|51|52|53|54|56|96|55|74|82|84|85ab|85ac|87|92|93|95|97|98|100|101|102|103|X104|X105|X106) + + + + + + + E. coli K antigen specification + + + + + + + + + + + + + + + + + + 1 + + + + + + 6 + + + + + + + other antigen specification + + + + + + + + + + E. coli serotype specification + + + + + + + + + + Damion's note: This will be converted to a categorical tree specification list of serovars by name or id asap. + Salmonella serovar specification + + + + + + + + + + A lab test specification indicates the inputs and outputs (results / conclusions) of a test. + Damion Dooley + test specification + + + + + + + + + + + + + + + + + + + + + + + (1/2|1/2a|1/2b|1/2c|3a|3b|3c|4a|4ab|4b|4c|4d|4e|1|7) + + + + + + + listeria antigen + + + + + + + + obsolete: matrix - fluid + true + + + + + + + + + listeria serotype 1/2a + + + + + + + + + listeria serotype 1/2b + + + + + + + + + listeria serotype 1/2c + + + + + + + + + listeria serotype 1/2 + + + + + + + + + listeria serotype 3a + + + + + + + + + listeria serotype 3b + + + + + + + + + listeria serotype 4a + + + + + + + + + listeria serotype 4b + + + + + + + + + listeria serotype 4c + + + + + + + + + listeria serotype 4d + + + + + + + + + listeria serotype 4e + + + + + + + + + non-monocytogenes listeria antigen + + + + + + + + + listeria serotype 3c + + + + + + + + + textual test result + + + + + + + + This is an organizational category for grouping parameters relevant to biomedical research projects. + Damion Dooley + + obsolete: draft GenEpiO BioProject standard + true + + + + + + + + + Damion Dooley + NCBI BioSample: collection_code + NCBI BioSample collection code + + + + + + + + + + + + + + + + draft NCBI BioSample host model + + + + + + + + + food - solid + + + + + + + + + lab test datum + + + + + + + + + Xbal + + + + + + + + + Ascl + + + + + + + + + Smal + + + + + + + + + Blnl + + + + + + + + + Apal + + + + + + + + + Kpnl + + + + + + + + + + Taxonomy below subspecies; sometimes used in viruses to denote subgroups taken from a single isolate. + Damion Dooley + NCBI Biosample + subgroup + + + + + + + + + help:This is an optional additional subtype classification as per organism convention + + A viral subtype is a classification name for a virus according to some protocol. + Damion Dooley + NCBI BioSample + viral subtype + + + + + + + + + + + + 1 + + + + + + + 1 + + + + + serotype specification + + + + + + + + + IRIDA + + An integer and character referring to a pattern of opaque or confluent lysis caused by a panel of bacteriophage infections e.g. 14a. + Damion Dooley + SNOMED: http://www.snomedbrowser.com/Codes/Details/272405002 + phage type specification + + + + + + + + + obsolete: swab - food contact surface + true + + + + + + + + + ATCC:26370 + An NCBI culture collection is a composite identifier containing “institution code:collection code”. + Annotation with a culture_collection qualifier implies that the sequence was obtained from a sample retrieved (by the submitter or a collaborator) from the indicated culture collection, or that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in the indicated culture collection. See the description for the proper format and list of allowed institutes, http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier. + NCBI culture collection + + + + + + + + + UAM:Mamm:52179 + The NCBI specimen voucher is an identifier composed of “institution code:collection code:specimen id” parts. In addition to a specimen identifier, it includes an institution-code (and optional collection-code) taken from a controlled vocabulary maintained by the INSDC that denotes the museum or herbarium collection where the specimen resides. + INSDC:specimen_voucher + NCBI specimen voucher + http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier. + + + + + + + + + culture identifier + + + + + + + + + + + + + + + human; dog; horse + The natural language (non-taxonomic) name of the type of organism (human or animal) that is the subject of a given investigation, study and/or specimen. + Damion Dooley's note: as of 2017 this is a problematic field for NCBI Biosample because it is slotted into "host" field, yet field is listed as "host common name" which does not fit with requirement that scientific name be provided. + Person: Damion Dooley + subject organism common name + + + + + + + + + + + + + + + + + + + + + temperature of air - average daily + + + + + + + + + obsolete: swab - inanimate object surface + true + + + + + + + + + obsolete: swab - meat + true + + + + + + + + + obsolete: swab - rectal swab + true + + + + + + + + + obsolete: swab - tissue + true + + + + + + + + + unknown source + + + + + + + + + + patient sample + human clinical specimen + + + + + + + + "environment (swab or sampling)" is a specific response for NCBI BioSample that could be mapped or unified with "environment sample" used elsewhere in GenEpiO + Damion Dooley + http://purl.obolibrary.org/obo/GENEPIO_0001246 + obsolete: environmental (swab or sampling) + true + + + + + + + + + avian - wild + + + + + + + + + avian - domesticated + + + + + + + + + human clinical specimen - invasive + + + + + + + + + In chemistry, pH is a numeric scale used to specify the acidity or basicity(alkalinity) of an aqueous solution + Damion Dooley + Wikipedia + Normally falls within the bounds of 0 - 14 + pH measurement + + + + + + + + + precipitation + + + + + + + + + + The assembly and annotation objective is the set of objectives that assembly and annotation techniques (including instruments and software platforms) applied to a sample are meant to satisfy. This impacts on the quality control thresholds applied to the sequencing project. + Damion Dooley + assembly and annotation project objective + + + + + + + + + + Damion Dooley + line list row record + + + + + + + + + + This class contains components under development for fulfilling GenEpiO and other standard data specifications. Components are relevant to epidemiological, laboratory, clinical or environmental pathogen sample data collection and analysis. + Damion Dooley + draft GenEpiO component record + + + + + + + + + + + + region + lookup:http://purl.obolibrary.org/obo/GAZ_00000448 + + A subnational region is a type of subnational entity similar to a nation's state, province, or territory. + Damion Dooley + subnational region + + + + + + + + + + A data standard related to public health research and service delivery. + Damion Dooley + public health data standard + + + + + + + + + Damion Dooley + + + + + + + + + + Reagent: material studied was obtained by chemical reaction, precipitation. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + reagent derived material from specimen + + + + + + + + + transcriptome + + Transcriptome: transcript and/or expression data. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + transcriptome data from specimen + + + + + + + + + proteome + + Proteome material is protein or peptide sequences. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + proteome data derived from specimen + + + + + + + + + purified chromosome + + Purified chromosome: one or more chromosomes or replicons were experimentally purified. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + purified chromosome from specimen + + + + + + + + + targeted locus/loci + + TargetedLocusLoci: capturing specific loci (gene, genomic region, bar code standard). + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + Targeted Locus Loci data capture + + + + + + + + + clone ends + + CloneEnds: capturing clone end data. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + clone end data capture + + + + + + + + + exome + + Exome: capturing exon-specific data. + Damion Dooley + NCBI BioSample + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + exome specific data capture + + + + + + + + + random survey + + Sequences generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material + Is this with respect to an isolate or a specimen derived culture? + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54364/ + random survey data capture + + + + + + + + + + This is a collection of various human (and animal contact location) contact information specifications used in data standards. + Damion Dooley + contact specification + + + + + + + + + order: +NCIT:C40978 # phone +GENEPIO:0001896 # phone type + + contact specification - phone + + + + + + + + + + Damion Dooley + millimetres per day + + + + + + + + + obsolete: millisiemens + true + + + + + + + + + + Damion Dooley + millisiemens per centimetre + + + + + + + + + + Damion Dooley + cubic metre per second + + + + + + + + + umol/kg + + Damion Dooley + micromole per kilogram + + + + + + + + + + Damion Dooley + micromole per litre + + + + + + + + + + Damion Dooley + quality control record + + + + + + + + + Standard draft: describing the minimum information needed for submission to a public database. + Damion Dooley + 1 - standard draft + + + + + + + + + High quality draft: describing sequences with little to no manual review. + Damion Dooley + 2 - high quality draft + + + + + + + + + Improved high quality draft: in which data is either reviewed by people or machines to some extent to indicate that most of the genetic data is assembled correctly, but some errors may still be present. + Damion Dooley + 3 - improved high quality draft + + + + + + + + + Annotation-directed improvement: in which genetic information in various gene regions is represented as accurately as possible. + Damion Dooley + 4 - annotation-directed improvement + + + + + + + + + Non-contiguous finished: which includes sequences that have been reviewed by both people and machines and would be considered complete except for “recalcitrant regions” that are proving problematic for genome closure. + Damion Dooley + 5 - non-contiguous finished + + + + + + + + + Finished: which describes un-gapped complete sequences that have minimal errors, if any. The biology of the microbe will determine whether this finished genome consists of more than one chromosome. + Damion Dooley + 6 - finished + + + + + + + + + Assembly QC + http://purl.obolibrary.org/obo/IAO_0000428 + The NG99 length is the same as the N99 length except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths. + Damion Dooley + GENEPIO + contig NG99 + + + + + + + + + Assembly QC + http://purl.obolibrary.org/obo/IAO_0000428 + Contig L50 is the number of contigs equal to or longer than contig N50. The length of the assembly itself is used in the calculation. + Damion Dooley + contig LG50 + + + + + + + + + Assembly QC + http://purl.obolibrary.org/obo/IAO_0000428 + Contig L99 is the number of contigs equal to or longer than contig N99. The length of the assembly itself is used in the calculation. + Damion Dooley + contig L99 + + + + + + + + + + A subject age at time of specimen extraction is the age (since birth) of the organism at the time a given specimen was extracted. + Damion Dooley + subject age at time of specimen collection + + + + + + + + + + A public health related data standard involving a particular species of pathogen. + Damion Dooley + pathogen specific data standard + + + + + + + + + + The draft tuberculosis contextual data standard is a data standard for the collection of contextual information of a given tuberculosis case that pertain to typing, clinical treatment, and potential research questions. + Damion Dooley + draft tuberculosis contextual data standard + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + PulseNet:Outbreak + + + + + + + + The PulseNet Canada Salmonella submission standard details the fields required in a PuseNet Canada pathogen submission report for Salmonella in spreadsheet format + Damion Dooley + draft PulseNet Canada Salmonella submission standard + http://www.pulsenetinternational.org/assets/PulseNet/uploads/wgs/PND18-NCBI-Biosample-Submission.pdf + + + + + + + + + + + + + + + A PFGE pattern resulting from DNA fragmentation induced by the Xbal enzyme. + + PFGE Xbal pattern + + + + + + + + + + + + + + + A PFGE pattern resulting from DNA fragmentation induced by the Blnl enzyme. + + PFGE Blnl pattern + + + + + + + + + NLEP ID + An NLEP ID is a unique identifier code for a sample registered with the Canadian "National Laboratory for Enteric Pathogens" (NLEP) + Damion Dooley + Pulsenet Canada spreadsheet. + National Laboratory for Enteric Pathogens Identifier + + + + + + + + + + + + + + + PulseNet spreadsheet + Date an uploaded sample was re-uploaded or had its metadata modified. + Damion Dooley + PulseNet: UploadModifiedDate + upload modified date + + + + + + + + + + A travel destination is a destination city (or populated place of some scale) which a given human has travelled to on a particular trip. + Damion Dooley + travel destination + + + + + + + + + + + A symptom duration is a date-time entity which is the duration (in hours or days or weeks etc.) that one or more symptoms persist for in a particular human or animal + Damion Dooley + This may be a calculated field if symptoms are reported to cease on a particular date. Often however symptom duration is reported more generally as a date or time range since cesation date is less certain. + symptom duration + + + + + + + + + + + + + + + + The city where a specimen was collected (taken) from a subject or environment + Damion Dooley + specimen collection location - city + + + + + + + + + + + lookup + + + + + + + + Damion Dooley + + + obsolete: sample city + true + + + + + + + + + + + + + + + + This is the genus-level taxonomic name of an organism playing a pathogen role + Damion Dooley + genus of pathogen + + + + + + + + + + + + + + + + This is the species-level taxonomic name of an organism playing a pathogen role + Damion Dooley + species of pathogen + + + + + + + + + + A symptom cessation date is a date-time entity that marks the end of one or more reported symptoms pertaining to an episode of human or animal illness + Damion Dooley + symptom cessation date + + + + + + + + + + + + + + + This is a catch-all category for listing specimen related terms + Damion Dooley + specimen datum + + + + + + + + + + + + + http://purl.obolibrary.org/obo/GENEPIO_0002105 + http://purl.obolibrary.org/obo/OBI_0001616 + + + + + + + + + + + + + + + + isolate identifier specification + + + + + + + + + + The 'data obfuscated' role between a user and given data entails that the user is authorized to see particular fields that have been transformed consistently such that statistics performed on those fields would yeild the same results as statistics applied to the un-obfuscated data. The purpose of obfuscation is to prevent related individuals or organizations from being identified. + Damion Dooley + data obfuscated + https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/ + + + + + + + + + + The 'data aggregated' role between a user and given data entails that the user is authorized to see aggregated results (like the patient count) via preset reports, queries or views. The results are not obfuscated. + Damion Dooley + data aggregated + + + + + + + + + + A 'limited data set' role between a user and given data entails that a user is authorized to see some of the fields but the remainder are withheld (or encrypted). + Damion Dooley + limited data set + + + + + + + + + help:In this dataset, selected data have been de-identified (anonymized) for access by dataset users. + + A 'de-identified data' role between a user and given data entails that the user is authorized to see only those fields (including those that are encrypted) which do not contain information that could be use to identify particular individuals (whether patients or medical practitioners) or potentially organizations in the case where an investigation may implicate them. + Damion Dooley's note: There is a case in the "draft tuberculosis contextual data standard" that has this be a boolean selection. If a categorical field is linked directly, and it has no underlings, this indicates that it is being treated as a boolean feature. + Damion Dooley + Generally de-identified data should include HIPAA patient privacy fields as indicated in https://www.hipaa.com/hipaa-protected-health-information-what-does-phi-include/ + de-identified data + + + + + + + + + + A 'data protected' role between a user and given data entails that a user must be authorized in order to view that data. + Damion Dooley + data protected + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + A datum containing the name of persons or institute who collected a given specimen. + Damion Dooley + https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ + specimen collector + + + + + + + + + + Damion Dooley + NCBI BioSample culture identifier + + + + + + + + + A user identifier is an identifier provided as part of an authentication process of a client (user) to a service (server). User identifiers normally persist over time, in contrast to session identifiers which are temporary. + Damion Dooley + user identifier + + + + + + + + + sequence identifier + + + + + + + + + metagenomic species identification + + + + + + + + + Note: REPLACE WITH Citation: SIO_000174 ???? + document citation identifier + + + + + + + + + organization identifier + + + + + + + + + collection identifier + + + + + + + + + variant calling / pathogen identification and clustering + + + + + + + + + isolate (pathogen) identification + + + + + + + + http://purl.obolibrary.org/obo/OBI_0001616 + obsolete: NCBI BioSample ID - + true + + + + + + + + + 1) Escherichia coli O104:H4 str. C227-11 clinical isolate 2010_333_NC-6 +2) CD8+ T cells from female TSG6-knockout BALB/c mouse +3) Human metagenome isolated from urine of healthy female + + A specimen (or sample) title should be short and informative. Each specimen title must be unique in a submission. + NCBI BioSample record documentation refers to a "BioSample title", stating that it is "auto-generated if one is not supplied by the submitter." This is distinct from any assigned BioSession accession, or other "external sample identifier" that may have been issued by the source database or repository. + Damion Dooley + specimen title + + + + + + + + + draft GenEpiO isolate source context + + + + + + + + + INSDC term (lower level) + + A categorical choice recorded when the data for a given measurable datum is available but not shared publicly because of information privacy concerns. + + + restricted access + + + + + + + + + State (United States of America) + + + + + + + + + + + + + + + + + + + + + + + + + + A health status trend is a short-term prognosis about whether health is improving, worsening or unchanging + Damion Dooley + health status trend datum + + + + + + + + + http://www.itis.gov + + The Integrated Taxonomic Information System (ITIS) contains authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world. + Damion Dooley + Integrated Taxonomic Information System + ITIS + ITIS + + + + + + + + + https://www.nlm.nih.gov/mesh/meshhome.html + + MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. + Damion Dooley + Medical Subject Headings + MSH + MESH + + + + + + + + + https://ncit.nci.nih.gov/ncitbrowser/ + + The National Cancer Institute Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities. + Damion Dooley + National Cancer Institude Thesaurus + NCI_Thesaurus + NCIt + NCIT + + + + + + + + + + The NIFSTD ontology of the Neuroscience Information Framework is composed of a collection of OWL modules with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, organism, function and dysfunction. + Damion Dooley + https://wiki.nci.nih.gov/display/VKC/NIFSTD+Ontology + NIFSTD + + + + + + + + + + SNOMED CT is a large clinical health terminology product owned and distributed by SNOMED International. + Damion Dooley + http://www.snomed.org/snomed-ct + SNOMEDCT + SNOMEDCT + + + + + + + + + http://www.fao.org/fishery/collection/asfis/en + + ASFIS is a database curated by the United Nations Food And Agriculture Organization (FAO) Fisheries and Aquaculture Statistics and Information Branch (FIPS). It contains over 12,700 species items selected according to their interest or relation to fisheries and aquaculture. + Damion Dooley + UN FAO Fisheries and Aquaculture Statistics and Information Branch database + FAO ASFIS + ASFIS + + + + + + + + + + FTT + + + + + + + + + + TGN + + + + + + + + + + Wikipedia is a free online encyclopedia that aims to allow anyone to edit articles. + Damion Dooley + https://en.wikipedia.org/wiki/Wikipedia + Wikipedia + + + + + + + + + + SWEETRealm + + + + + + + + + + The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge. + Damion Dooley + http://www.geonames.org/ + Geonames + + + + + + + + + http://ecolexicon.ugr.es/en/index.htm + + EcoLexicon is a terminological resource developed by the LexiCon Research Group at the University of Granada. + Damion Dooley + EcoLexicon + + + + + + + + + + A standard established for use by the Integrated Rapid Infectious Disease Analysis (IRIDA) project, which is a Canadian-led initiative to build an open source, end-to-end platform for infectious disease genomic epidemiology. + Damion Dooley + http://www.irida.ca/ + draft IRIDA standard + + + + + + + + + + ISO 3166-1 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for the names of countries, dependent territories, and special areas of geographical interest. + Damion Dooley + https://en.wikipedia.org/wiki/ISO_3166-2 + ISO3166-1 + + + + + + + + + + ISO 3166-2 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for identifying the principal subdivisions (e.g., provinces or states) of all countries coded in ISO 3166-1. + Damion Dooley + https://en.wikipedia.org/wiki/ISO_3166-1 + ISO3166-2 + + + + + + + + + + Information Technology – Codes For The Identification Of The States And Equivalent Areas Within The United States, Puerto Rico, And The Insular Areas + Damion Dooley + American National Standards Institute + ANSI INCITS 38 + + + + + + + + + + Damion Dooley + The Geographic Names Information System (GNIS), developed by the U.S. Geological Survey in cooperation with the U.S. Board on Geographic Names, contains information about physical and cultural geographic features in the United States and associated areas, both current and historical. + https://nhd.usgs.gov/gnis.html + GNISID + + + + + + + + + + LTER + + + + + + + + + + + + + + + order: +OBI:0001628 # investigation identifier +OBI:0001616 # specimen identifier +GENEPIO:0001808 # specimen title +GENEPIO:0000113 # specimen category +sep:00196 # specimen description +OBI:0001479 # specimen from organism +GENEPIO:0001640 # specimen organism taxonomy (species) +GENEPIO:0000027 # specimen source context +GENEPIO:0001722 # NCBI specimen voucher +GENEPIO:0001429 # strain identifier +GENEPIO:0001798 # NCBI BioSample culture identifier +GENEPIO:0001717 # viral subtype +OMP:0000207 # serotype phenotype +SO:0001027 # genotype +GENEPIO:0001079 # serovar +GENEPIO:0001716 # subgroup +GENEPIO:0001055 # NCBI pathotype +GENEPIO:0001054 # isolate passage history +GENEPIO:0001656 # latitude and longitude coordinate +GENEPIO:0001657 # NCBI BioSample geo_loc_name model +GENEPIO:0001051 # NCBI BioSample isolate (human name or description) +GENEPIO:0001648 # NCBI Contributing organization / project +GENEPIO:0001797 # specimen collector +OBI:0001619 # specimen collection date +OBI:0001888 # sequencing facility contact person +GENEPIO:0001651 # INSDC institution code +GENEPIO:0001721 # NCBI culture collection +GENEPIO:0001567 # subject (host) taxonomic species +GENEPIO:0001724 # subject organism common name +GENEPIO:0001775 # subject age at time of specimen collection +GENEPIO:0000026 # subject health status at time of specimen extraction +GENEPIO:0000031 # subject sex +GENEPIO:0001614 # subject description +GENEPIO:0001617 # subject disease +GENEPIO:0001625 # subject disease stage +GENEPIO:0001212 # subject disease outcome + + A National Center for Biotechnology Information BioSample specification defines fields and terms that provide "descriptions of biological source materials used in experimental assays". + Damion Dooley + http://www.ncbi.nlm.nih.gov/biosample/ + NCBI BioSample Pathogen.cl standard + https://www.ncbi.nlm.nih.gov/biosample/docs/packages/Pathogen.cl.1.0/ + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + 1 + + + + + + + 1 + + + + + + + 1 + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + The National Center for Biotechnology Information BioProject standard is a collection of datums that describe biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. + Damion Dooley + http://www.ncbi.nlm.nih.gov/bioproject/ + NCBI lists project data type and other controlled vocabulary fields at : https://www.ncbi.nlm.nih.gov/books/NBK54364/ + NCBI BioProject standard + + + + + + + + 1 + + + + + + + + + + + + + + Objective + + + + + + + + 1 + + + + The format of the BioProject Accession is five alpha-letters followed by one to six numbers. For example PRJNA43021 + Project Accession + + + + + + + + 1 + + + + + + + + + + + + + + Methodology + + + + + + + + + http://www.aha.org/content/00-10/overview0302.pdf + http://www.webcitation.org/5VBWPbFgY + + The American Hospital Association has issued HIPAA Updated Guidelines for Releasing Information on the Condition of Patients + Damion Dooley + American Hospital Association HIPAA Standard + AHA HIPPA + AHA HIPPA standard + + + + + + + + + http://www.ncbi.nlm.nih.gov/pubmed/ + + PubMed comprises more than 26 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. + NCBI PubMed + PMID + PubMed + + + + + + + + + http://www.pulsenetinternational.org/ + + PulseNet, a national and international surveillance system used to identify and respond to foodborne disease outbreaks, has a standardized laboratory method and data submission standard for pathogen isolate typing test results and related isolate contextual data. From this information clusters of disease can be identified that might represent unrecognized outbreaks. + Pulse Net International BioSample Metadata + PulseNet + PulseNet submission standard + https://www.cdc.gov/pulsenet/pathogens/index.html + https://www.nml-lnm.gc.ca/Pulsenet/index-eng.htm + + + + + + + + + + + + + + + + + + + + + + AHA HIPPA: http://www.aha.org/content/00-10/overview0302.pdf + + Good - Vital signs are stable and within normal limits. Patient is conscious and comfortable. Indicators are excellent. + Damion Dooley + + + AHA Hippa: Good + good health status + + + + + + Good + + + + + + satisfactory + + + + + + + + + + + + + + + + + + + + + + + Fair - Vital signs are stable and within normal limits. Patient is conscious, but may be uncomfortable. Indicators are favorable. + Damion Dooley + + fair health status + + + + + + fair + + + + + + Stable + + + + + + + + + + + + + + + + + + + + + + + Serious - Vital signs may be unstable and not within normal limits. Patient is acutely ill. Indicators are questionable. + Damion Dooley + + serious health status + + + + + + Serious + + + + + + + + + + + + + + + + + + + + + + + + + + A health status history datum is a record of the longer-term pattern or presence of a given patient's health status. + Damion Dooley + health status history datum + + + + + + + + + (0,0) is the origin of the cartesian coordinate system. + "In mathematics, the origin of a Euclidean space is a special point, usually denoted by the letter O, used as a fixed point of reference for the geometry of the surrounding space. + +In physical problems, the choice of origin is often arbitrary, meaning any choice of origin will ultimately give the same answer. This allows one to pick an origin point that makes the mathematics as simple as possible, often by taking advantage of some kind of geometric symmetry." + Damion Dooley + https://en.wikipedia.org/wiki/Origin_(mathematics) + origin + + + + + + + + + https://en.wikipedia.org/wiki/Medical_state + United Kingdom National Health Service trusts, boards, etc. have some terminology in common for public disclosure of patient health conditions. + Damion Dooley + National Health Service terminology + NHS standard + + + + + + + + + + + + + + + + + + + + + + + Damion Dooley + Damion Dooley's note: This is a contentious term. AHA calls for it never to be used, since the common phrase "critical but stable" is misleading by the very nature of "critical". The NHS however has it as one of its central terms. The use of "stable" also points to a health trend, rather than a state. A separate "health status trend datum" has been set up to capture this. + critical but stable health status + + + + + + critical but stable + + + + + + + + + + + + + + + + + + + + + + NHS Terms: https://en.wikipedia.org/wiki/Medical_state + + Damion Dooley + comfortable health status + + + + + + Comfortable + + + + + + + + + + + + + + + + + + + + + + + Damion Dooley + progressing well health status + + + + + + progressing well + + + + + + + + + + + Damion Dooley + Damion Dooley note: This term (weakly) implies that the patient is recovered enough to be released from hospital. Technically this isn't a health status though, it is a patient medical service state. + discharged from hospital + + + + + + discharged + + + + + + + + + + A data item which is about the collection state of a datum at some point in time. + Damion Dooley note: We'll need to incorporate NIAID GSCID-BRC Sample data standards mention: +Unknown/Not Applicable/Censored Allowed +Unknown/not applicable/not available/ available upon request + Damion Dooley + A given datum's datum status value is metadata, i.e. a statement about a particular datum, often when no actual data entry or categorical choice for that datum has been made. + datum status + INSDC missing value reporting terms: +http://www.ebi.ac.uk/ena/about/missing-values-reporting + + + + + + + + + + A categorical choice indicating that a datum is available for retrieval. + Damion Dooley + In theory any datum that has a recorded value has 'recorded' for its datum status. + recorded + + + + + + + + + + + Patient is awaiting physician and/or assessment. + Very similar to 'datum status' 'in process' status. + Damion Dooley + + undetermined health status - awaiting assessment + + + + + + + + + + + + + + + + Damion Dooley + deteriorating + worsening health trend + + + + + + + + + + This covers the description of data and abstract structure in n-dimensional space. Within space there are coordinate systems, coordinates, and entities made up of coordinates. + Damion Dooley + + + + + + + + + + + + + + + /^[N+](:<lat>\d(\.\d+)?)$/, $lat +/^S(:<lat>\d(\.\d+)?)$/, '-' + $lat + /^(:<lat>[-S+N])?(:<degree>[1-8]?[0-9](:<decimal>\.\d{1,6})?)$/, $lat$degree.$decimal +/^(:<lat>[-S+N])?(:<degree>90(:<decimal>\.0{1,6})?))$/, $lat$degree.$decimal + /^(\d(\.\d+)?)$/, '+\1' + + A decimal latitude measurement in degrees in conformance with the ISO 6709 standard. + This is failing Hermit reasoner since it rejects totalDigits, and fractionDigits: +'has primitive data type' exactly 1 xsd:decimal[>= -90.0 , <= 90.0 , totalDigits 8 , fractionDigits 6]' + Damion Dooley + + + + + + + + + + + + + + + /^(:<long>[-W+E])?(:<degree>(1[0-7]|[1-9])?[0-9])(:<decimal>\.\d{1,6})?)$/, $long$degree.$decimal +/^(:<long>[-W+E])?(:<degree>180(:<decimal>\.0{1,6})?)$,$long$degree.$decimal + + A decimal longitude measurement in degrees in conformance with the ISO 6709 standard. + Damion Dooley + + + + + + + + + Damion Dooley + + + + + + + + + A 2D coordinate system is a coordinate system in 2 dimensional space. Each coordinate is composed of an offset from the origin of each dimension + Damion Dooley + + + + + + + + + Damion Dooley + + + + + + + + + Damion Dooley + + + + + + + + + + + + + + + + + + + + + A datetime range intermediate datum is a datetime item grouped under a process, and occuring after some process start and before some process end. + Damion Dooley + datetime range intermediate + + + + + + + + + Damion Dooley + datetime range item + + + + + + + + + + + + + + + The ending date of a process + datetime range end + + + + + + + + + + + + + + + Damion Dooley + The starting date of a process + datetime range start + + + + + + + + + Damion Dooley + + + + + + + + + + + + + + + Damion Dooley + + + + + + + + + + A designated area on earth is one or more areas defined by one or more boundaries. A boundary can be defined by a polygon perimeter, a lat/long and radius, or a fiat-boundary geographic featureset like a named river channel or mountain ridge; it may have one or more names associated with it. Note that areas associated with a name may change their boundary definitions over time. + Damion Dooley + + + + + + + + + + A Canadian postal code is a postal code that pertains to a geographic region of Canada. + Note that a Canadian postal code can cover multiple communities. Secondly, postal codes can be retired, and then reintroduced elsewhere. Historical data associations may need to take the date of postal code mapping into account. + + + + + + + + A "USA zip code" is a five digit (Zone Improvement Plan) or 9 digit postal code pertaining to a region of the United States of America. The optional trailing 4 digits of a 9 digit zip code provide greater granularity of delivery target. + Damion Dooley + http://purl.obolibrary.org/obo/NCIT_C25720 + obsolete: US postal code + true + + + + + + + + + + Damion Dooley + entity history record + + + + + + + + + + Damion Dooley + generic range history record + + + + + + + + + + + + + + + + + + Damion Dooley + A set does not have a direct distance metric between its members. + + + + + + + + + + Damion Dooley + + + + + + + + + Damion Dooley + + + + + + + + + + Damion Dooley + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Damion Dooley + + + + + + + + + + A product name and model number of a manufacturer's genomic (dna) sequencer. + Damion Dooley + sequencing instrument model + + + + + + + + + + + + + + 1 + + + + + + + 1 + + + + + A circle is a simple closed shape in Euclidean geometry. It is the set of all points in a plane that are at a given distance from a given point, the centre; equivalently it is the curve traced out by a point that moves so that its distance from a given point is constant. + Damion Dooley + https://en.wikipedia.org/wiki/Circle + circle + + + + + + + + + NCBI SRA: ILLUMINA + Illumina platform + + + + + + + + + NCBI SRA: COMPLETE_GENOMICS + Damion Dooley's note: This platform is in-house and not a product per se. Complete Genomics states: "Complete Genomics’ sequencing platform employs high-density DNA nanoarrays that are populated with DNA nanoballs (DNBs™). Base identification is performed using an unchained ligation-based read technology known as combinatorial probe-anchor ligation (cPAL™). The sequencing instrumentation is custom-developed to support this process. Details are described in our Science publication (Drmanac et al., 2010)." + Complete Genomics platform + + + + + + + + + + + + 0 + + + + + + + 1 + + + + + Damion Dooley + earth area boundary census + + + + + + + + + NCBI SRA: LS454 + Roche LS454 platform + + + + + + + + + NCBI SRA: PACBIO_SMRT + PacBio platform + + + + + + + + + NCBI SRA: AB SOLiD 4hq + SOLiD 4hq System + + + + + + + + + NCBI SRA: AB SOLiD 5500 + SOLiD 5500 + + + + + + + + + NCBI SRA: AB SOLiD 5500xl + SOLiD 5500xl + + + + + + + + + NCBI SRA: AB SOLiD PI System + SOLiD PI System + + + + + + + + + NCBI SRA: AB SOLiD System 2.0 + SOLiD System 2.0 + + + + + + + + + NCBI SRA: AB SOLiD System 3.0 + SOLiD System 3.0 + + + + + + + + + + A two dimensional entity is an entity composed of one or more points on a two dimensional surface. + Damion Dooley + 2D entity + + + + + + + + NCBI SRA: Ion Torrent PGM + + + + + + + + + NCBI SRA: 454 GS FLX Titanium + 454 Genome Sequencer FLX Titanium + + + + + + + + + + NCBI SRA: 454 GS + 454 Genome Sequencer + + + + + + + + + NCBI SRA: 454 GS Junior + 454 Genome Sequencer Junior + + + + + + + + + + + + + + + https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly + Whether any method was used to select for or against, enrich, or screen the material being sequenced. + Damion Dooley + NCBI SRA: LIBRARY_SELECTION + library selection + + + + + + + + + Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C). + NCBI SRA: 5-methylcytidine antibody + 5-methylcytidine antibody method + + + + + + + + + Cap-analysis gene expression. + NCBI SRA: CAGE + CAGE method + + + + + + + + + Cot-filtered highly repetitive genomic DNA + NCBI SRA: CF-H + CF-H method + + + + + + + + + Cot-filtered moderately repetitive genomic DNA + NCBI SRA: CF-M + CF-M method + + + + + + + + + Cot-filtered single/low-copy genomic DNA + NCBI SRA: CF-S + CF-S method + + + + + + + + + Cot-filtered theoretical single-copy genomic DNA + NCBI SRA: CF-T + CF-T method + + + + + + + + + Chromatin immunoprecipitation + NCBI SRA: ChIP + ChIP method + + + + + + + + + Deoxyribonuclease (MNase) digestion + NCBI SRA: DNAse + DNAse method + + + + + + + + + Hypo-methylated partial restriction digest + NCBI SRA: HMPR + HMPR method + + + + + + + + + Selection by hybridization in array or solution. + NCBI SRA: Hybrid Selection + Hybrid Selection method + + + + + + + + + Enrichment by methyl-CpG binding domain. + NCBI SRA: MBD2 protein methyl-CpG binding domain + MBD2 protein methyl-CpG binding domain method + + + + + + + + + Methyl Filtrated + NCBI SRA: MF + MF method + + + + + + + + + Micrococcal Nuclease (MNase) digestion + NCBI SRA: MNase + MNase method + + + + + + + + + Methylation Spanning Linking Library + NCBI SRA: MSLL + MSLL method + + + + + + + + + Source material was selected by designed primers. + NCBI SRA: PCR + PCR method + + + + + + + + + Rapid Amplification of cDNA Ends. + NCBI SRA: RACE + RACE method + + + + + + + + + Source material was selected by randomly generated primers. + NCBI SRA: RANDOM PCR + RANDOM PCR method + + + + + + + + + Random selection by shearing or other method. + NCBI SRA: RANDOM + RANDOM method + + + + + + + + + Source material was selected by reverse transcription PCR + NCBI SRA: RT-PCR + RT-PCR method + + + + + + + + + Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling. + NCBI SRA: Reduced Representation + Reduced Representation method + + + + + + + + + DNA fractionation using restriction enzymes. + NCBI SRA: Restriction Digest + Restriction Digest method + + + + + + + + + PolyA selection or enrichment for messenger RNA (mRNA). complementary DNA. + NCBI SRA: cDNA + cDNA method + + + + + + + + + Physical selection of size appropriate targets. + NCBI SRA: size fractionation + size fractionation method + + + + + + + + + Other library enrichment, screening, or selection process. + NCBI SRA: other + other library method + + + + + + + + + https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly + The library source specifies the type of source material that is being sequenced. + Damion Dooley + library source + + + + + + + + + Genomic DNA (includes PCR products from genomic DNA). + Damion Dooley + NCBI SRA: GENOMIC + genomic source + + + + + + + + + Mixed material from metagenome. + Damion Dooley + NCBI SRA: METAGENOMIC + metagenomic source + + + + + + + + + Transcription products from community targets + Damion Dooley + NCBI SRA: METATRANSCRIPTOMIC + metatranscriptomic source + + + + + + + + + Other, unspecified, or unknown library source material. + Damion Dooley + NCBI SRA: OTHER + other library source + + + + + + + + + Synthetic DNA. + Damion Dooley + NCBI SRA: SYNTHETIC + synthetic source + + + + + + + + + Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries). + Damion Dooley + NCBI SRA: TRANSCRIPTOMIC + transcriptomic source + + + + + + + + + Viral RNA. + Damion Dooley + NCBI SRA: VIRAL RNA + viral RNA source + + + + + + + + + Sequencing technique intended for this library. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly + library strategy + + + + + + + + + Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling using SSU rRNA + NCBI SRA: AMPLICON + amplicon strategy + + + + + + + + + MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status. + NCBI SRA: Bisulfite-Seq + Bisulfite-Seq strategy + + + + + + + + + Clone end (5', 3', or both) sequencing. + NCBI SRA: CLONEEND + clone end strategy + + + + + + + + + Genomic clone based (hierarchical) sequencing. + NCBI SRA: CLONE + clone strategy + + + + + + + + + Concatenated Tag Sequencing + NCBI SRA: CTS + CTS strategy + + + + + + + + + Direct sequencing of chromatin immunoprecipitates. + NCBI SRA: ChIP-Seq + ChIP-Seq strategy + + + + + + + + + Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI. + NCBI SRA: DNase-Hypersensitivity + DNase-Hypersensitivity strategy + + + + + + + + + Single pass sequencing of cDNA templates + NCBI SRA: EST + EST strategy + + + + + + + + + Sequencing intended to finish (close) gaps in existing coverage. + NCBI SRA: FINISHING + finishing strategy + + + + + + + + + Full-length sequencing of cDNA templates + NCBI SRA: FL-cDNA + FL-cDNA strategy + + + + + + + + + Direct sequencing of methylated fractions sequencing strategy. + NCBI SRA: MBD-Seq + MBD-Seq strategy + + + + + + + + + Direct sequencing following MNase digestion. + NCBI SRA: MNase-Seq + MNase-Seq strategy + + + + + + + + + Methylation-Sensitive Restriction Enzyme Sequencing strategy. + NCBI SRA: MRE-Seq + MRE-Seq strategy + + + + + + + + + Methylated DNA Immunoprecipitation Sequencing strategy. + NCBI SRA: MeDIP-Seq + MeDIP-Seq strategy + + + + + + + + + Library strategy not listed. + NCBI SRA: OTHER + other library strategy + + + + + + + + + Shotgun of pooled clones (usually BACs and Fosmids). + NCBI SRA: POOLCLONE + pool clone strategy + + + + + + + + + Random sequencing of whole transcriptome. + NCBI SRA: RNA-Seq + RNA-Seq strategy + + + + + + + + + Random sequencing of a whole chromosome or other replicon isolated from a genome. + NCBI SRA: WCS + WCS strategy + + + + + + + + + Random sequencing of the whole genome. + NCBI SRA: WGS + WGS strategy + + + + + + + + + Random sequencing of exonic regions selected from the genome. + NCBI SRA: WXS + WXS strategy + + + + + + + + + Free form text describing the protocol by which the sequencing library was constructed. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly + library construction protocol + + + + + + + + + + The submitter's name for this library. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly + NCBI SRA: LIBRARY_NAME + library name + + + + + + + + + + A two dimensional boundary is a continuous path (loop) defined on a two dimensional surface. + Damion Dooley + 2D boundary + + + + + + + + + cfu/100mL + + A colony forming unit count which is a count of viable bacterial numbers in 100 milliliters of liquid. + Should this be deprecated? Need to find working examples that actually use / 100mL. + Damion Dooley + colony forming unit per 100 milliliter + + + + + + + + + + A multiplier in the decimal number system that has been applied to an accompanying number or set of numbers often to simplfy their appearance. Numbers described by multipliers may have lost significant digits through rounding or trimming. + Damion Dooley + decimal quantity unit + + + + + + + + + + draft tuberculosis - dataset features and provenance + + + + + + + + + + draft tuberculosis - case specimen characteristics + + + + + + + + + + draft tuberculosis - case subject characteristics + + + + + + + + + + draft tuberculosis - case risk factors + + + + + + + + + + draft tuberculosis - case clinical presentation + + + + + + + + + + draft tuberculosis - case laboratory testing + + + + + + + + + + draft tuberculosis - case medication + + + + + + + + + + draft isolate whole genome sequencing model + + + + + + + + + + draft tuberculosis - case model + + + + + + + + + + A Mycobacterium tuberculosis lineage is a named family of strains of tuberculosis, named usually with reference to their shared geographic origin. + Damion Dooley + Mycobacterium tuberculosis lineage + A TB-Lineage identification tool using spoligotypes and MIRU data: +http://tbinsight.cs.rpi.edu/run_tb_lineage.html + Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans +http://www.nature.com/ng/journal/v45/n10/full/ng.2744.html + + + + + + + + + TB lineage 2 - East-Asian, includes Bejing + + + + + + + + + TB lineage 3 - East-African Indian, includes CAS/Delhi + + + + + + + + + TB lineage 4 - Euro-American, includes Haarlem, LAM3, X, T, F11, H37Rv + + + + + + + + + TB lineage 1 - Indo-Oceanic + + + + + + + + + TB lineage 5 - West African 1 + + + + + + + + + TB lineage 6 - West African 2 + + + + + + + + + + Damion Dooley + An isolate preparation facility is a type of organization that provides the service of isolating organisms of interest from provided specimens. + isolate preparation facility + + + + + + + + + plant product + + + + + + + + + + + + + + + geospatial name + + + + + + + + + + A personal health datum is a datum that pertains to the health situation or history of an individual. + Personal health datum covers the following information + +'has member' some 'analytic datum' +'has member' some 'behavioural risk factor' +'has member' some 'country of birth' +'has member' some 'dietary restrictions' +'has member' some 'Disease Attributes' +'has member' some 'health status history datum' +'has member' some 'health status trend datum' +'has member' some 'host hospital service status' +'has member' some 'subject disease stage' +'has member' some 'subject health status' +'has member' some 'subject health status (AHA)' +'has member' some 'subject health status (GSCID-BRC)' +'has member' some 'subject health status (NCIT)' +'has member' some 'subject health status (UK NHS)' +'has member' some 'subject health status at time of specimen extraction' +'has member' some 'tuberculosis disease anatomical site' +'has member' some comorbidity +'has member' some disease +'has member' some symptom + Damion Dooley + personal health datum + + + + + + + + + A host hospital service status indicates the state of a host's interaction with hospital medical services. + Damion Dooley + host hospital service status + + + + + + + + + + Damion Dooley + admitted to hospital + + + + + + + + + + Received treatment but not admitted. + + treated and released (not admitted to hospital) + + + + + + Treated and Released + + + + + + + + + + Received treatment. Transferred to a different facility. + + treated and transferred + + + + + + Treated and Transferred + + + + + + + + + + + + + + + + + + + + + + + Damion Dooley + satisfactory health status + + + + + + satisfactory + + + + + + + + + depth:1 + subject health status (UK NHS) + + + + + + + + + depth:1 + subject health status (AHA) + http://purl.obolibrary.org/obo/GENEPIO_0002019 + + + + + + + + + + + + + + + + + + + + + stable health trend + http://purl.obolibrary.org/obo/GENEPIO_0001669 + + + + + + + + An ordinal variable is a categorical variable whose values have sequential order, but no distance metric between them. + Damion Dooley + http://purl.obolibrary.org/obo/STATO_0000228 + obsolete: ordinal variable + true + + + + + + + + + mapping (reference based) + + + + + + + + + data protection item + + + + + + + + + subject provided consent + + + + + + + + + + Damion Dooley + An ordinal tree specification is a value specification entity whose subclasses each represent a possible value selection, and which have a linear order with respect to their siblings. + ordinal value specification + + + + + + + + + consent datum + + + + + + + + + agency provided consent + + + + + + + + + + 2019-11-17T00:43:00Z + draft ISO sequence repository field + + + + + + + + + Centre of circle, ellipse or parabola; centre of mass. + + A centre point is a point used in the description of an n-dimentional entity from which other (given) aspects of the entity are most efficienty described. A point of symmetry. The entity must have only one such point. + Probably a better formal math defn? + Damion Dooley + centre point + + + + + + + + + + This covers the following entities: + +'has member' some 'antimicrobial phenotype' +'has member' some 'antimicrobial resistance test drug' +'has member' some 'antimicrobial resistance test platform' +'has member' some 'antimicrobial resistance testing method' +'has member' some 'antimicrobial resistance testing method version or reagent' +'has member' some 'antimicrobial resistance testing reference standard' +'has member' some 'antimicrobial resistance testing reference standard version' +'has member' some 'antimicrobial resistance tissue specificity' +'has member' some 'antimicrobial resistant plasmid type' +'has member' some 'automated testing platform vendor' +'has member' some 'draft antibiogram drug test model' +'has member' some 'in-vitro microbial susceptibility test' +'has member' some 'measurement comparator' +'has member' some 'MIC unit' +'has member' some 'MIC value' +'has member' some 'Minimum Inhibitory Concentration Test' +'has member' some 'test drug maximum concentration' +'has member' some 'test drug minimum concentration' +'has member' some 'tuberculosis treatment drug' + Damion Dooley + This is a collection of antibiotic resistance process parameters and outputs + phenotypic antimicrobial drug susceptibility test datum + + + + + + + + The resistance phenotype of an isolate represents the interpretation of an MIC value with regard to some breakpoint threshold e.g. resistant (R), sensitive (S), intermediate (I), wild type (WT), or non-wild type (NWT) + Damion Dooley + http://purl.obolibrary.org/obo/NCIT_C85539 + obsolete: antimicrobial resistance phenotype + true + + + + + + + + Intermediate resistance indicates that an isolate is observed to offer an intermediate level of resistance to a given antibiotic. + Damion Dooley + http://purl.obolibrary.org/obo/NCIT_C85560 + obsolete: antibiotic intermediate resistance (I) + true + + + + + + + + Non-susceptible indicates that an isolate is observed to offer complete resistance to a given antibiotic. + Damion Dooley + http://purl.obolibrary.org/obo/NCIT_C85561 + obsolete: antibiotic nonsensitive (high resistance) + true + + + + + + + + + + A not defined resistance indicates that an isolate was not tested against a given antibiotic, or the result of the test was inconclusive. + Damion Dooley note: Is this the same as "indeterminate"? + Damion Dooley + N + ND + antibiotic resistance not defined + + + + + + + + Resistant indicates that an isolate is observed to offer a greater than intermediate level of resistance to a given antibiotic. + Damion Dooley + http://purl.obolibrary.org/obo/NCIT_C85562 + obsolete: antibiotic resistant (R) + true + + + + + + + + Susceptible indicates that an isolate is observed to offer a detectable but less than intermediate level of resistance to a given antibiotic. + Damion Dooley + http://purl.obolibrary.org/obo/NCIT_C85563 + obsolete: antibiotic sensitive (S) + true + + + + + + + + Susceptible - dose dependent indicates that an isolate is observed to offer resistance to a given antibiotic when a sufficient dose is given. + Damion Dooley + http://purl.obolibrary.org/obo/NCIT_C85559 + obsolete: sensitive - dose dependent + true + + + + + + + + + + + + + + + + A MIC test measurement resulting from a laboratory dilution method. + Damion Dooley's note: is this still useful? Currently "MIC dilution measurement specification' refers directly via 'is about' to "broth dilution method" but that may be too specific. + Damion Dooley + MIC dilution measurement datum + + + + + + + + The type of assay used to determine the minimum inhibitory concentration. + Damion Dooley + http://purl.obolibrary.org/obo/NCIT_C85540 + obsolete: antimicrobial resistance testing method + true + + + + + + + + + http://purl.obolibrary.org/obo/NCIT_C85555 + obsolete: agar dilution evidence + true + + + + + + + + + + The commercial kit or product used to determine the MIC e.g. E-Test. If a commercial product was not used, include the type of media used. + Damion Dooley + antimicrobial resistance testing method device or reagent + + + + + + + + + + + antimicrobial resistant plasmid type + + + + + + + + The instrumentation used to determine minimum inhibitory concentration values. + Damion Dooley + http://purl.obolibrary.org/obo/ARO_3004390 + obsolete: antimicrobial resistance testing platform + true + + + + + + + + http://purl.obolibrary.org/obo/ARO_3004400 + obsolete: Microscan + true + + + + + + + + http://purl.obolibrary.org/obo/ARO_3004401 + obsolete: Phoenix + true + + + + + + + + http://purl.obolibrary.org/obo/ARO_3004402 + obsolete: Sensititre + true + + + + + + + + http://purl.obolibrary.org/obo/ARO_3004403 + obsolete: Vitek + true + + + + + + + + http://purl.obolibrary.org/obo/ARO_3004409 + obsolete: Trek + true + + + + + + + + + obsolete: manual - noncommercial + true + + + + + + + + The manufacturer of an antibiotic resistance lab typing platform + Damion Dooley + http://purl.obolibrary.org/obo/ARO_3004404 + obsolete: antimicrobial resistance testing platform vendor + true + + + + + + + + http://purl.obolibrary.org/obo/ARO_3004407 + obsolete: Siemens + true + + + + + + + + http://purl.obolibrary.org/obo/ARO_3004406 + obsolete: Biomérieux + true + + + + + + + + http://purl.obolibrary.org/obo/ARO_3004405 + obsolete: Becton Dickinson + true + + + + + + + + + + A manual in vitro diagnostic device used by laboratories to determine the MIC (Minimum Inhibitory Concentration) and whether or not a specific strain of bacterium or fungus is susceptible to the action of a specific antimicrobial. + Damion Dooley + + E-Test + Epsilometer test + Etest (device) + + + + + + + + + + GM-NEG + + + + + + + + The clinical and laboratory guidelines or standards that prescribe the threshold values for determining resistance phenotypes. + Damion Dooley + http://purl.obolibrary.org/obo/ARO_3004360 + obsolete: antimicrobial resistance testing reference standard + true + + + + + + + + BSAC is a British inter-professional organisation involved in antibiotic education, research and leadership + Damion Dooley + + BSAC + obsolete: British Society for Antimicrobial Chemotherapy (BSAC) + true + + + + + + + + The Clinical and Laboratory Standards Institute develops and implements clinical laboratory testing standards + Damion Dooley + NCCLS + http://clsi.org + + CLSI + On January 1, 2005 the National Committee on Clinical Laboratory Standards (NCCLS) changed its name to CLSI + obsolete: Clinical and Laboratory Standards Institute (CLSI) + true + + + + + + + + DIN is recognized by the Federal Government of Germany as the competent standards organization for Germany and as the national standards body representing Germany in non-governmental international standards organizations. + Damion Dooley + http://www.din.de/en/din-and-our-partners/din-e-v + + DIN + Deutsches Institut für Normung + obsolete: German Institute for Standardization (DIN) + true + + + + + + + + EUCAST is a standing committee jointly organized by ESCMID, ECDC and European national breakpoint committees; it deals with breakpoints and technical aspects of phenotypic in vitro antimicrobial susceptibility testing. + Damion Dooley + http://www.eucast.org/ + + EUCAST + obsolete: European Committe on Antimicrobial Susceptibility Testing (EUCAST) + true + + + + + + + + Damion Dooley + + NCCLS + obsolete: National Committee on Clinical Laboratory Standards (NCCLS) + true + + + + + + + + La SFM a vocation à rassembler les microbiologistes de France et des pays francophones, travaillant dans les différents domaines de la microbiologie médicale, industrielle, et environnementale, en physiologie, génétique, taxonomie, hygiène, agents antimicrobiens, ...concernant les bactéries, virus, champignons et parasites. + The French Society of Microbiology (SFM) is a non-profit association which aims to bring together microbiologists from French-speaking countries, working in the domains of bacteria, viruses, Fungi and parasites, and related medical, industrial and environmental microbiology, physiology, genetics, taxonomy, hygiene, and antimicrobial agents. + This isn't at moment considered a valid EBI antibiogram choice? + Damion Dooley + http://www.sfm-microbiologie.org/ + + SFM + obsolete: Société Française de Microbiologie (SFM) + true + + + + + + + + + + Damion Dooley + SIR + SIR + + + + + + + + + + Damion Dooley + WRG + WRG + + + + + + + + + first line tuberculosis drug + + + + + + + + + last resort antibiotic + + + + + + + + + NIAID standard + + NIAID provides The GSCID/BRC Project and Sample Application Standard. It is designed to capture standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases. + Damion Dooley + https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards + National Institute of Allergy and Infectious Disease standard + + + + + + + + + A RefSeq accession identifier is an accession identifier for selected NCBI-curated genomic, transcript and protein sequences. These identifiers are distinct from DDBJ/EMBL/GenBank identifiers. + Damion Dooley + RefSeq accession identifier + http://www.ncbi.nlm.nih.gov/refseq/about/ + + + + + + + + + A Genomic Standards Consortium standard is an international, community-driven standard to facilitate genomic data integration, discovery and comparison. + Damion Dooley + Genomic Standards Consortium (GSC) standard + http://gensc.org/ + + + + + + + + + + A landform, biome or built environment at site that a given specimen was collected from. + Damion Dooley + specimen collection site - geographic feature + + + + + + + + + + + + + + + A particular human patient, or a given animal or plant. + + An investigative subject which is an organism. + Damion Dooley + subject organism + + + + + + + + + + help=The number of passages should be expressed as a numerical value. + + The number of serial iterations that an isolate is grown in one environment. + Damion Dooley + number of passages + + + + + + + + + + help:The passage protocol should include, when applicable, inoculum size, media type, temperature and duration of incubation. + A passage protocol should detail the number of serial iterations that an isolate is grown in one environment, and the conditions of that environment. + Damion Dooley + passage protocol + + + + + + + + The unit provided for an antibiotic drug test dosage. + Damion Dooley + http://purl.obolibrary.org/obo/ARO_3004372 + obsolete: drug minimum inhibitory concentration unit + true + + + + + + + + + order: +GENEPIO:0001237 # specimen type (host or environmental context) +OBI:0001619 # specimen collection date +OBI:0000659 # specimen collection process +GENEPIO:0002094 # specimen collection device +GENEPIO:00001600 # draft sequence repository data - geographic location +ENVO:00010483 # environmental material +ENVO:00002297 # environmental feature +GENEPIO:0001567 # subject (host) taxonomic species +GENEPIO:0000110 # subject health status +GENEPIO:0001617 # subject disease +GENEPIO:0000028 # subject body product +GENEPIO:0000025 # specimen source anatomical site +FOODON:03411564 # draft sequence repository data - food processing + + draft sequence repository data - specimen collection + + + + + + + + + order: +GENEPIO:0002105 # Specimen processing organization role +NCIT:C93874 # organization name +NCIT:C40974 # first name +NCIT:C40975 # last name +NCIT:C93582 # job title +NCIT:C42775 # email address +GENEPIO:0001756 # phone +NCIT:C25464 # Country +ENVO:00000005 # major administrative subdivision -> GAZ state/province/territory/region) +NCIT:C80234 # Municipality” (via GenEpiO -> GAZ cities) +NCIT:C25690 # Street Address + + Contact information for an organization related to specimen collection, processing or storage. + Damion Dooley + contact specification - specimen related organization + + + + + + + + + dateFormat:ISO 8601 + order: +GENEPIO:0002082 # specimen related organization +GENEPIO:0002081 # specimen collection +GENEPIO:0002086 # geographic location +GENEPIO:0002084 # isolate +GENEPIO:0002087 # isolate history +GENEPIO:0002106 # food specimen +GENEPIO:0002088 # antibiogram +GENEPIO:0002085 # sequencing +GENEPIO:0002090 # sequencing QC +GENEPIO:0002089 # virulence +GENEPIO:0002092 # submission to EBI +GENEPIO:0002091 # submission to NCBI/DDBJ + + This draft specification provides a collection of fields related to the contextual data of a specimen, its genomic sequencing, and its pathogenic epidemiology. + Damion Dooley + draft sequence repository contextual data standard + + + + + + + + + order: +GENEPIO:0001640 # specimen taxonomy +GENEPIO:0001429 # strain identifier +GENEPIO:0001644 # isolate identifier +OBI:0000079 # culture medium +GENEPIO:0002107 # isolation medium + + draft sequence repository data - isolate + + + + + + + + + order: + +GENEPIO:0000069 # sequencing date +OBI:0000079 # culture medium” (via MicrO, yields a list of formulas). +GENEPIO:0002093 # sequencing dna extraction method +EFO:0000683 # replicate +GENEPIO:0000085 # library preparation kit +GENEPIO:0000149 # library preparation kit version +GENEPIO:0000075 # sequencing chemistry +GENEPIO:0001921 # sequencing instrument model +GENEPIO:0000150 # read trimming and filtering software +GENEPIO:0000084 # read adapter trimming software +GENEPIO:0002095 # read paired-end merging software +GENEPIO:0000090 # assembly method +GENEPIO:0000151 # bioinformatics pipeline name +GENEPIO:0000153 # bioinformatics pipeline protocol +GENEPIO:0000152 # bioinformatics pipeline version +GENEPIO:0000095 # genome annotation algorithm + + draft sequence repository data - sequencing + + + + + + + + + order: +GENEPIO_0001656 # latitude and longitude ISO 6709 +GENEPIO:0000118 # specimen collection country +GENEPIO:0002097 # specimen collection state/prov/ter/region +GENEPIO:0001785 # specimen collection city + + The geographical origin of the sample by city, region, country or latitude and logitude. + Damion Dooley + draft sequence repository data - geographic location + + + + + + + + + order: +GENEPIO:0002078 # number of passages +GENEPIO:0002079 # passage protocol + + draft sequence repository data - isolate passage history + + + + + + + + + order: +GENEPIO:0001100 # antimicrobial drug tests +GENEPIO:0002101 # test drug minimum concentration +GENEPIO:0002100 # test drug maximum concentration +GENEPIO:0002045 # antimicrobial resistance testing method +GENEPIO:0002047 # antimicrobial testing method version or reagent +GENEPIO:0002062 # antimicrobial resistance testing reference standard +GENEPIO:0002049 # antimicrobial resistance testing platform + + A dataset of the minimal inhibitory concentrations (value, unit, sign (<,>, =)) and resistance phenotypes (resistant, sensitive or undetermined) of the sequenced isolate against different antibiotics tested. + Damion Dooley + draft sequence repository data - antibiogram + + + + + + + + + order: +GENEPIO:0002130 # Virulence factor name +GENEPIO:0002131 # Virulence testing protocol +GENEPIO:0002132 # detection limit + + The virulence factors determined to be present in the sequenced isolate by phenotypic or target amplification methods e.g. Shiga toxins, hemolysins. + Damion Dooley + draft sequence repository data - virulence + + + + + + + + + order: +OBI:0001941 # N50 +GENEPIO_0000092 # sequencing depth / read coverage + + Measurements or calculated quantities used to assess the extent and success of the sequence assembly process. Metric thresholds are species-specific. + Damion Dooley + draft sequence repository data - sequencing quality control + + + + + + + + + order: +OBI:0001616 # specimen identifier +GENEPIO:0001644 # isolate identifier +GENEPIO:0001429 # strain identifier +GENEPIO:0001640 # specimen organism taxonomy +GENEPIO:0000113 # specimen category +OBI:0001619 # specimen collection date +GENEPIO:0001797 # specimen collector +GENEPIO:0001657 # geo_loc_name +GENEPIO:0001656 # latitude and longitude coord +GENEPIO:0000027 # specimen source context +GENEPIO:0001567 # subject organism taxonomy +GENEPIO:0001724 # subject organism common name +GENEPIO:0001617 # subject disease + + + Damion Dooley + draft sequence repository data - submission to NCBI/DDBJ + + + + + + + + + order: +GENEPIO:0001644 # isolate identifier +GENEPIO:0001429 # strain identifier +GENEPIO:0001640 # specimen organism taxonomy +GENEPIO:0001079 # serovar +GENEPIO:0002135 # EBI environmental feature +GENEPIO:0000113 # specimen category +OBI:0001619 # specimen collection date +GENEPIO:0001797 # specimen collector +GENEPIO:0002086 # geographic location +GENEPIO:0000027 # specimen source context +GENEPIO:0002076 # geographic feature +GENEPIO:0001567 # subject taxonomy +GENEPIO:0000110 # subject health status + + + Damion Dooley + draft sequence repository data - submission to EBI + https://www.ebi.ac.uk/ena/submit/pathogen-data + + + + + + + + + + The procedure used to obtain genomic DNA from a sample through chemical, physical or mechanical means. + Damion Dooley + sequencing dna extraction method datum + + + + + + + + + The tool or device used to extract a specimen. + Damion Dooley + specimen collection device + + + + + + + + + The name and version of the software used to merge paired-end reads before assembly. + read paired-end merging software + + + + + + + + + Sequencing + The name and version of the software product used for removal of adapter sequences from demultiplexed data reads + GROUP: IRIDA Ontology (Emma) + GENEPIO + read adapter trimming software + + + + + + + + + + + + + + + + + + + + + + + + + An ontology identifier or textual name of the most precise geographical location available for the site of a specimen collection event. + Damion Dooley + Adapted from NIAID GSCID-BRC metadata working group + Note that this is expressed in a particular format in some standards. + specimen collection location - state/province/territory/region + + + + + + + + + + + + + + + + + + + + lookup + + + + + + + + A wild type (WT) resistance phenotype indicates a bacterial pathogen belongs to a "Naïve", susceptible wild-type population with respect to a given antimicrobial. No acquired or mutational resistance mechanisms are +present to the antimicrobial in question. + Damion Dooley + https://sisu.ut.ee/sites/default/files/amr/files/pab_new_legislation_on_amr.pdf + http://purl.obolibrary.org/obo/ARO_3004432 + obsolete: wild type (WT) + true + + + + + + + + A non-wild type (WT) resistance phenotype indicates a bacterial pathogen has an acquired or mutational resistance mechanism present with respect to the antimicrobial in question. The bacteria has a reduced susceptibility to this agent. + Damion Dooley + https://sisu.ut.ee/sites/default/files/amr/files/pab_new_legislation_on_amr.pdf + http://purl.obolibrary.org/obo/ARO_3004433 + obsolete: non-wild type (NWT) + true + + + + + + + + + + This is the maximum concentration of a drug applied during an an assay. + Damion Dooley + test drug maximum concentration + + + + + + + + + + This is the minimum concentration of a drug applied during an an assay. + Damion Dooley + test drug minimum concentration + + + + + + + + The tissue type used to select breakpoints from a particular standard, for the interpretation of MIC results. + Damion Dooley + http://purl.obolibrary.org/obo/ARO_3004430 + obsolete: antimicrobial resistance tissue specificity + true + + + + + + + + + depth:1 + order: +NCIT:C115935 # healthy +NCIT:C126054 # non-pathalogical +NCIT:C25610 # pathologic +NCIT:C82508 # life threatening +NCIT:C28554 # deceased + subject health status (NCIT) + + + + + + + + + order: +NCIT:C40974 # first name +NCIT:C40975 # last name +NCIT:C93582 # job title +NCIT:C42775 # email address +GENEPIO:0001756 # phone + contact specification - professional role + + + + + + + + + + An organization related to the collection, isolate production, sequencing or storage of specimen material or data. + Damion Dooley + specimen processing organization type + + + + + + + + + order: +GENEPIO:0001533 # food specimen type +FOODON:03450002 # food cooking method +FOODON:03440011 # extent of heat treatment +FOODON:03430113 # physical state, shape or form +FOODON:03470107 # food preservation method +FOODON:03490100 # container or wrapping +FOODON:03480020 # food packing medium +FOODON:03500010 # food contact surface +GENEPIO:0000139 # food cultural origin +FOODON:03460111 # treatment applied to food + This specification offers food source, product type, packaging and processing attributes relevant to describing a food specimen. + draft sequence repository data - food specimen + + + + + + + + + + An isolation medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the same growth environment. + Chris has proposed this term for OBI as "enrichment culture medium" + Damion Dooley + isolation medium + + + + + + + + + order: +GENEPIO:0000121 # start date +GENEPIO:0000122 # end date +GENEPIO:0001783 # travel destination +GENEPIO:0001064 # travel mode +GENEPIO:0001065 # travel reason + + This record details a person's travel movement and duration for epidemiological analysis. + Damion Dooley + draft travel log specification + + + + + + + + + order: +OBI:0001616 # BioSample_ID +GENEPIO:0001640 # Species +GENEPIO:0001187 # Antibiotic_Name +GENEPIO:0002062 # AST_Standard +GENEPIO:0002111 # Breakpoint_version +NCIT:C85540 # Laboratory_typing_method +GENEPIO:0002112 # Measurement +GENEPIO:0002080 # Measurement_units +GENEPIO:0001001 # Measurement_sign +NCIT:C85539 # Resistance_phenotype +GENEPIO:0002181 # Resistance_phenotype - ECOFF +GENEPIO:0002049 # Platform + + A standard for European Bioinformatics Institute (EBI) antibiogram data submission + Damion Dooley + draft EBI antimicrobial susceptibility test V. 2017-08-30 + https://github.com/EBI-COMMUNITY/compare-amr/blob/master/Antimicrobial-susceptibility-testing-data-submission_V_2017-08-30.pdf + + + + + + + + + + + + + + + + A MIC test measurement resulting from a laboratory diffusion method. + Damion Dooley's note: is this still useful? Currently "MIC diffusion measurement specification' refers directly via 'is about' to "Disk Diffusion Method". + Damion Dooley + MIC diffusion measurement datum + + + + + + + + + + The version of the antimicrobial reistance testing reference standard protocol used in assessing an isolate. + Damion Dooley + antimicrobial resistance testing reference standard version + + + + + + + + + This is a component of an antibiogram that enables a choice of MIC measurements based on either the diffusion or dilution method. These methods call for different numeric input ranges and units. + draft sequence repository data - antibiogram MIC measurement + + + + + + + + + + + + 1 + + + + + + + + + + time value specification + + + + + + + + + + The process of collecting a portion of feces from an organism. + Emma Griffiths + stool collection + feces collection + + + + + + + + + + The process of collecting a portion of urine from an organism. + Emma Griffiths + sputum collection + + + + + + + + + + The process of removal and collection of specimen material from the surface of an entity by washing, or a similar application of fluids. + Emma Griffiths + rinsing for specimen collection + + + + + + + + + + The process of collecting specimen material using a swab collection device. + Emma Griffiths + swabbing for specimen collection + + + + + + + + + + The process of collecting bodily fluids that have been discharged from blood vessels usually arising from inflammation or injury. + Emma Griffiths + exudate collection + + + + + + + + + + The removal or collection of specimen material through the use of suction. + Emma Griffiths + vacuuming for specimen collection + + + + + + + + + + Emma Griffiths + NOTE: there are different types of tubes with coloured caps indicating different preservatives etc. + tube containing media or preservative + + + + + + + + + Emma Griffiths + NOTE: there are different types of tubes with coloured caps indicating different preservatives etc. + tube containing antimicrobial + + + + + + + + + + Emma Griffiths + Whirlpak sampling bag + + + + + + + + + + Emma Griffiths + spoon + + + + + + + + + + Emma Griffiths + fork + + + + + + + + + + Emma Griffiths + hand scoop + + + + + + + + + Emma Griffiths + trier + + + + + + + + + + Emma Griffiths + vaccum device + + + + + + + + + + + + + + + investigation identifier specification + + + + + + + + + order: +GENEPIO:0001640 # taxonomy +GENEPIO:0002086 # geographic location +GENEPIO:0002076 # geographic feature +GENEPIO:0002106 # food +FOODON:03510136 # food consumer +GENEPIO:0002094 # specimen collection device +GENEPIO:0000025 # anatomical site +GENEPIO:0000028 # body product +GENEPIO:0001724 # host organism common name +GENEPIO:0001567 # host taxonomy +UBERON:0000105 # life cycle +GENEPIO:0001639 # antigenic formula +GENEPIO:0001718 # serotype specification +GENEPIO:0000045 # PFGE test specification + + This is a draft (under development) collection of fields for capturing the contextual data for Enterobase (https://enterobase.warwick.ac.uk/) records. + Damion Dooley + draft Enterobase contextual data standard + + + + + + + + + + + + + + + + The name of the virulence factor molecule produced by a pathogen that specifically causes disease, or that influences the host's function to allow the pathogen to thrive. + Emma Griffiths + virulence factor name + + + + + + + + + + + + + + + help:The protocol for determining virulence should include, when applicable, inoculum preparation, platforms and instrumentation, conditions, cell lines and animal models. + + The laboratory protocol used to determine virulence phenotypes and markers. + Emma Griffiths + virulence testing protocol name + + + + + + + + + + + + + + + help:Detection limits should include the numerical cut-off (threshold) value and units for determining positive results e.g. qPCR value, CFUs. + The detection limit denotes the smallest measure that can be detected with reasonable certainty for a given analytical procedure. + Emma Griffiths + detection limit + + + + + + + + + + A disease cluster is an unusually high incidence of a particular disease or disorder occurring in close proximity in terms of both time and geography. + Damion Dooley + https://en.wikipedia.org/wiki/Disease_cluster + disease cluster + + + + + + + + + + + A disease cluster in which two or more cases have been linked by an infectious disease transmission process. + Damion Dooley + infectious disease cluster + + + + + + + + + help:used only with the source feature key; source feature keys containing the /environmental_sample qualifier should also contain the /isolation_source qualifier. entries including /environmental_sample must not include the /strain qualifier + Identifies sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism. Environmental samples include clinical samples, gut contents, and other sequences from anonymous organisms that may be associated with a particular host. They do not include endosymbionts that can be reliably recovered from a particular host, organisms from a readily identifiable but uncultured field sample (e.g., many cyanobacteria), or phytoplasmas that can be reliably recovered from diseased plants (even though these cannot be grown in axenic culture). + ENA Webin:environmental_feature + EBI ENA Webin environmental feature + + + + + + + + + + The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. Webin is an ENA interface and standard for sequence submissions. + https://www.ebi.ac.uk/ena + EBI European Nucleotide Archive Webin + https://www.ebi.ac.uk/ena/WebFeat/ + + + + + + + + + help:Breadth of coverage should be reported as a percentage value (e.g. 95%) to a fold of coverage (e.g. 10X). + + The breadth of coverage is the percentage of the genome that was sequenced to a prescribed depth of coverage. + Emma Griffiths + breadth of coverage + + + + + + + + + + The mean contig length is the count of base pairs in the average size contig of the sequence assembly. + Emma Griffiths + mean contig length + + + + + + + + + order: +GENEPIO:0000084 # read adapter trimming (y/n) +GENEPIO:0002096 # read adapter trimming software +GENEPIO:0002095 # read paired-end merging software +GENEPIO:0000150 # read trimming and filtering software + + The procedures used to remove adapters from raw sequence reads, trim low quality bases and where applicable, merge paired-end reads. + Emma Griffiths + raw sequence data processing datum + + + + + + + + + + Name of strain from which sample was obtained OR name of isolate from which sample was obtained. + Damion Dooley + specimen strain or isolate identifier + + + + + + + + + + + + + + + + + \s*(\d(.\d{1,4})?|[1-8]\d(.\d{1,4})?|90(.0{1,4})?)\s*[WEwe]\s*(\d(.\d{1,4})?|[1-9]\d(.\d{1,4})?|1[0-7]\d(.\d{1,4})?|180(.0{1,4})?)\s*[NSns]\s* + + + + + + + + The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W + Damion Dooley + https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ + latitude and longitude coordinate (NCBI BioSample format) + + + + + + + + + + + + + + + decimal value specification + + + + + + + + + + + + + + + floating point value specification + + + + + + + + + + + + + + + unsigned integer + A 32 bit number having a range 0 - 4294967295. + unsigned integer value specification + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + 1 + + + + + + + + + + date value specification + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + A specification for the size of an assembled genome as measured in base pairs. + This is a decimal because the megabasepair unit may involve a fractional component. + assembly genome size specification + + + + + + + + + + + + + + + sequencing facility name specification + + + + + + + + + date (ISO 8601) + A date should be recorded as YYYY-MM-DD according to ISO 8601. HOWEVER ... OWL 2.0 does not include xsd:date as a permitted data type, so this value specification only accepts xsd:dateTime + date value specification (ISO 8601) + + + + + + + + + + + + + + + strain identifier specification + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + 5 + + + 100 + + + + + + + A MIC test measurement resulting from a laboratory diffusion method. + Damion Dooley + MIC diffusion measurement specification + + + + + + + + + + + + + + + unsigned short + A 16 bit integer ranging from 0 - 65535 + unsigned short integer value specification + + + + + + + + + + + + 1 + + + + + + + + + + + genomic sequence length specification + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + 0.01 + + + 2048.0 + + + + + + + A MIC test measurement resulting from a laboratory dilution method. + Damion Dooley + MIC dilution measurement specification + + + + + + + + + + + + + + + The date on which a specimen was collected, in ISO 8601 format. + specimen collection date (ISO 8601) + + + + + + + + + + + + + + + date of diagnosis (ISO 8601) + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + 0 + + + + + + + A subject age is the age since birth of a given organism that is involved in an investigation or study at a given time. + Damion Dooley + subject age specification + + + + + + + + + + + + + + + subject age at time of specimen collection specification + + + + + + + + + + + + + + + + + + 1 + + + + boolean + + A boolean value specification indicates a presence (true value) or absence (false value) of a given feature. + Damion Dooley + boolean value specification + + + + + + + + + + + + + + + specimen identifier specification + + + + + + + + + + + + + + + + + + + + + + + [A-Za-z0-9]+([_.\-][A-Za-z0-9]+)*\@[A-Za-z0-9]+([.\-][A-Za-z0-9]+){1,3} + + + + + + + email address specification + + + + + + + + + + + + + + + + + + + + + + + + region, province, state or territory specification + + + + + + + + + + + + + + + A specification for a geographic location that a specimen was collected at. + specimen collection site specification + + + + + + + + + + + + + + + subject organism common name specification + + + + + + + + + + + + + + + A subject identifier specification is a specification including datatype pertaining to a given standard's subject identifier field. + Damion Dooley + subject identifier specification + + + + + + + + + + + + + + + + + + + + + Name of disease in a subject that is related to a given investigation, study and/or specimen. + Damion Dooley + NIAID GSCID-BRC metadata working group + Controlled vocabulary. Human specimen source: https://bioportal.bioontology.org/ontologies/DOID +or https://www.ncbi.nlm.nih.gov/mesh/1000067 + subject disease specification + + + + + + + + + + + + + + + unsigned long integer + A 64 bit integer ranging from 0 - 18446744073709551615 + unsigned long integer value specification + + + + + + + + + + + + + + + + + + + The physical location that a specimen was collected at. The location may be described by geographic coordinates, city or other geopolitical entity, biome, etc. + Damion Dooley + specimen collection site + + + + + + + + + + + + + + + + The unit provided for an antibiotic drug test dosage. + Damion Dooley + drug MIC unit specification + + + + + + + + + + + + + + + + + + + + + + + + + + + + Damion Dooley + A datum specification for the maximum concentration of a drug applied during an an assay. + test drug maximum concentration specification + + + + + + + + + + + + + + + + + + + + + + + + + + + + This is the minimum concentration of a drug applied during an an assay. + Damion Dooley + test drug minimum concentration specification + + + + + + + + + + + + + + + + + + + + + + + (1/2|1/2a|1/2b|1/2c|3a|3b|3c|4a|4ab|4b|4c|4d|4e|1|7) + + + + + + + listeria antigen specification + + + + + + + + + + + + + + + + + + 1 + + + + + + url + + + + + + + URL specification + + + + + + + + + + + + + + + + + + + + + + + + + + + + A travel destination is a destination city (or populated place of some scale) which a given human has travelled to on a particular trip. + Damion Dooley + travel destination specification + + + + + + + + + + + + + + + A specimen source substance is an organism substance or food product or environmental substance from which the specimen was extracted. + Damion Dooley + specimen source substance specification + + + + + + + + + + + + + + + Damion Dooley note: OBI has a variety of subclasses like "blood specimen" and "colon specimen" etc. which we have not added here. The are mapped to UBERON terms indirectly through the logic "derives from some [uberon term]". GenEpiO takes a different approach in describing this class with lists for "subject anatomical site", "subject body product", and "plant anatomy". + specimen from organism specification + + + + + + + + + + + + 1 + + + + + + + + + + + + 0 + + + + + + + duration specification + + + + + + + + + A field specification is the specification of a data field used in a data standard or database table. This includes at least a database field name, and optionally display name, description, and data type (binary blob, numeric, categorical, textual or cross-reference). + Damion Dooley + + 2019-04-17T23:04:53Z + obsolete: field specification + true + + + + + + + + Damion Dooley + http://purl.obolibrary.org/obo/ARO_3004431 + obsolete: antimicrobial resistance phenotype - epidemiological cut-off values + true + + + + + + + + + Damion Dooley + 2019-04-17T23:41:35Z + PulseNet Canada field + + + + + + + + + Damion Dooley + 2019-04-17T23:41:56Z + PulseNet Canada Salmonella field + + + + + + + + + Damion Dooley + 2019-05-03T02:44:38Z + specimen collection service + + + + + + + + + Damion Dooley + 2019-05-03T02:49:24Z + bioinformatics analysis service + + + + + + + + + An isolate preparation service prepares isolates for molecular sequencing. + Damion Dooley + 2019-05-03T02:51:51Z + + isolate preparation service + + + + + + + + + order: +GENEPIO:0002222 # specimen collection service +GENEPIO:0002226 # specimen repository/biobank service +GENEPIO:0002224 # isolate preparation service +OBI:0001904 # sequencing service +OBI:0000992 # DNA sequencing service +GENEPIO:0002223 # bioinformatics analysis service + Damion Dooley + 2019-05-03T02:52:19Z + specimen related service + + + + + + + + + Damion Dooley + 2019-05-03T03:24:33Z + specimen repository/biobank service + + + + + + + + + + + + + + + + + + Vital signs are unstable and not within normal limits. Patient may be unconscious. Indicators are unfavorable. + + 2019-11-19T22:17:43Z + grave + critical health status + + + + + + critical + + + + + + critical + + + + + + + + + A datum indicating one of six defined subspecies of Salmonella. + + + 2019-11-25T08:45:41Z + Salmonella subspecies + + + + + + + + + + A PFGE pattern resulting from DNA fragmentation induced by the Spel enzyme. + + 2019-11-25T09:07:26Z + PFGE Spel pattern + + + + + + + + + + A collection of organisms that is indicative of faecal +contamination. + + + 2020-02-08T20:15:43Z + Fecal indicator organism collections include bacterial groups such as thermotolerant coliforms or E. coli. Hence, they only infer that pathogens may be present + fecal indicator + + + + + + + + + + + + + + + + + + An isolate derived from a food sample. + Damion Dooley + 2019-06-28T23:41:26Z + food isolate + + + + + + + + + + A method for typing The RNA component of the small (30S) subunit of prokaryotic ribosomes. + + 2020-04-24T19:06:05Z + microbial 16S RNA typing + + + + + + + + + + + + + + + + + + + + + + + h(1|2|3|4|5|6|7|8|9|10|11|12|14|15|16|17|18|19|21|23|24|26|27|28|29|30|31|32|33|34|35|36|37|38|39|40|41|42|43|44|45|46|47|48|49|51|52|53|54|55|56) + + + + + + + E. coli H antigen specification + + + + + + + + + + + + + + + + + + + + + + + O([1-9][0-9][0-9]) + + + + + + + E. coli O antigen specification + + + + + + + + + + + + 1 + + + + string + string value specification + + + + + + + + + A sequencing platform brand provided by Helicos corporation (now defunct). + + 2020-04-24T22:50:49Z + Helicos platform + + + + + + + + + A sequencing platform provided by the Ion Torrent company. + + 2020-04-24T22:54:06Z + Ion Torrent platform + + + + + + + + + A sequencing platform provided by Life Technologies Corporation + + Sequencing by Oligonucleotide Ligation and Detection + 2020-04-24T22:55:31Z + SOLiD sequening platform + + + + + + + + + obsolete: drag swab + true + + + + + + + + + + + + + + + + Rinse is the liquid output of rinsing plant, animal or other material with liquid with the objective of extracting specimen material from that liquid. + Damion Dooley + 2019-06-28T20:07:25Z + rinse + + + + + + + + + + + + + + + + + Animal rinse is a rinse derived from animal material of one or more animals. + Damion Dooley + 2019-06-28T20:11:45Z + animal rinse + + + + + + + + + obsolete: surface wipe + true + + + + + + + + + + + + + + + + + + + + + requires discussion + A personal health datum which specifies host health complications at time of specimen collection. + 0000-0002-9578-0788 + 2022-01-31T23:52:14Z + host health complications at time of specimen collection + + + + + + + + + + + + + + + + + + + + + requires discussion + A personal health datum which specifies host pre-existing conditions and risk factors at time of specimen collection. + 0000-0002-9578-0788 + 2022-01-31T23:52:41Z + pre-existing conditions and risk factors at time of specimen collection + + + + + + + + + + + + + + + + + + + + + requires discussion + A personal health datum which specifies host signs and symptoms at time of specimen collection. + 0000-0002-9578-0788 + 2022-01-31T23:53:13Z + signs and symptoms at time of specimen collection + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + + + + + + symptom + http://purl.obolibrary.org/obo/SYMP_0000462 + + + + + + + + + position of phenotype abnormality + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.ebi.ac.uk/efo/EFO_0001444 + + + + + + + + Damion Dooley's note: See https://www.w3.org/TR/NOTE-datetime for ISO 8601 time standards + + + + + + + + Damion notes: Subclasses can actually have two components - the identifier, and the agency it is associated with. + +Under the general concept of "postal code" one can place particular national postal code systems like the US Postal code. + + + + + + + + + + 2020-04-24T22:38:17Z + pregnant woman + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.ontobee.org/ontology/MI + data source + + Database that originally provided the interaction record for exchange purposes. + PMID:14755292 + Damion Dooley's note: GenEpiO is using members of this class for the first part of the hasDbXref relation. This is where we are keeping the mapping between a code and its source database. + +Depending on its context, hasDbXref annotations may point directly to metadata field names in the target database, and may be annotated with additional information that guides any additional specifications that impact on data conversion of these fields. + source database + + + + + + + + + tissue collection (necropsy) + A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease. [database_cross_reference: Merriam-Webster:Merriam-Websters_Online_Dictionary--11th_Ed] + necropsy + + + + + + + + + + + + + + + + + The Archaea constitute a domain and kingdom of single-celled microorganisms + Damion Dooley + https://en.wikipedia.org/wiki/Archaea + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + subspecies + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Damion Dooley's note: this term was mistakenly placed in a list of GenEpiO diagnostic tests; in fact it references a material entity + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + healthy + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + NCIT offers this alternate definition which GenEpiO intends: +"A measurement that specifies the minimum concentration of the agent at which organism growth was inhibited." + MIC + Clinical and Laboratory Standards Institute MIC antimicrobial testing standards at http://em100.edaptivedocs.info/GetDoc.aspx?doc=CLSI%20M100%20S27:2017&scope=user + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of an absorbent material attached to one end of a small stick for the purpose of applying or collecting material. + + Emma Griffiths + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://purl.obolibrary.org/obo/GEO_000000396 + + + + + + + + + + + diseased + sick + + + + + + + + + + + + + + + + + + + lookup:http://purl.obolibrary.org/obo/GAZ_00000448 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + [A-Za-z0-9]+([_.\-][A-Za-z0-9]+)*\@[A-Za-z0-9]+([.\-][A-Za-z0-9]+){1,3} + + + + + + + /^(:<zip>\d{5}(-\d{4})?)/, $zip + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + deceased + + + + + + deceased + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + phone + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A hollow cylinder, especially one for holding or conveying liquids. + Damion Dooley + + + + + + + + + + + + + + + + + + + + + + + + + Damion Dooley's note: It can also be used as an authorization token in some identification processes. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Damion Dooley's note: here "sample" means more than one specimen merged together. + pooled + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Damion Dooley + + + + + + + + + + Damion Dooley + + + + + + + + + + + + + + + + + brand name + + + + + + + + + + + + + + + + + + + + + + + + + An entity, either biologic or otherwise, of interest in an investigation. [def-source: NCI] + Damion Dooley + NCIT Thesaurus + investigative subject + + + + + + + + + + lookup:http://purl.obolibrary.org/obo/GAZ_00000448 + http://semanticscience.org/resource/SIO_000665 + + + + + + + + + + + + + + + + + antimicrobial resistance testing method + + + + + + + + + + + + + + + + + E-test (Epsilometry) + + + + + + + + + + + + + + + + + + lookup:http://purl.obolibrary.org/obo/GAZ_00000448 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + lookup:http://purl.obolibrary.org/obo/GAZ_00000448 + + + + + + + + + + + + + + + + + + + http://purl.obolibrary.org/obo/ncit.owl + + + + + + + + + organization name + + Damion Dooley + NCI Thesaurus + + + + + + + + + + + + + + + + + antibiotic treatment + + + + + + + + + fetal death (miscarriage/still birth) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + NCBI SRA: 454 GS 20 + + + + + + + + + NCBI SRA: AB SOLiD System + + + + + + + + + NCBI SRA: 454 GS FLX + + + + + + + + + NCBI SRA: Illumina Genome Analyzer II + + + + + + + + + NCBI SRA: Helicos HeliScope + + + + + + + + + pathogen role + + + + + + + + + + + + + + + + + + + Note: testing use of 'transmitted by' relation; issue to be resolved is whether appropriate domain and range are involved. This use would place 'transmitted by' as a subclass of 'participates in' + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Damion Dooley note: OBI has a variety of subclasses like "blood specimen" and "colon specimen" etc. which we have not added here. The are mapped to UBERON terms indirectly through the logic "derives from some [uberon term]". GenEpiO takes a different approach in describing this class with lists for "subject anatomical site", "subject body product", and "plant anatomy". + + + + + + + + + ^SAM[NED](\w)?\d+$ + http://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000350 + http://www.ncbi.nlm.nih.gov/Sequin/acc.html + https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_accession_numbers_and_mole/ + + + + + + + + + + + + + + + + + + + + + + + + + + + NCBI BioProject + + + + + + + + + + + Project Description + + + + + + + + + + + Description* + + + + + + + + sample identifier + + + + + + + + + specimen collection date + + + + + + + + + help:Latitude should not be abstracted to the centre of a city, province/state or country as this may falsely implicate an existing location. + Damion Dooley's note: IAO lat/long can't be made a subclass of "angular coordinate" or disjoint contradiction arises. + See http://www.csgnetwork.com/gpscoordconv.html + +See http://www.geomidpoint.com/latlon.html +See http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org/obo/OBI_0001621 +See http://www.w3.org/2003/01/geo/wgs84_pos + + + + + + + + + + + + + + + + + + + + + + + NCBI BioProject + NIAID GSCID-BRC + + + + + + + + + + + + + + + Damion Dooley's note: A 'sovereign state' entity should have attribute or relationships to measurables - population, size, name, etc. So e.g. " 'country name' inheres in some 'sovereign state/country'". + +Also note historical name issue (Myanmar vs Burma) and diplomatic name issue (Taiwan vs "Republic of China"). Both point to needing a single entity with multiple names. + + + + + + + + http://purl.obolibrary.org/obo/OMIABIS_0000006 + + + + + + + + target material + NCBI BioProject: Material + Used in NCBI BioProject specifcation + + + + + + + + specimen sample scope + + + + + + + + + + + + + + + + + + + + + + + + sequencing facility + + + + + + + + project objective + NCBI BioProject: Objective + + + + + + + + + + + + + + + + + + + + + + project method + + + + + + + + + specimen provider PI email + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + categorical + + + + + + + + scalar + + + + + + + + Damion Dooley's note: +Often a value specification may need to allow for a "data item state" that indicates that a given datum doesn't have a recorded or observed or retrievable value, and the general reason for this state. + + + + + + + + + Assembly QC + Damion Dooley + http://www.nature.com/nature/journal.../409860a0.html + GENEPIO + + + + + + + + + + + + + + + + + + + + + + + + + NCBI SRA: Illumina MiSeq + + + + + + + + + NCBI SRA: PacBio RS + + + + + + + + + NCBI SRA: Illumina NextSeq + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + sample + + + + + + + + + + + + + + + + 2019-09-08T23:41:09Z + diagnosis + + + + + + + + + An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. + extended organism + + + + + + + + + + Damion Dooley + + NIAID: Comorbidity + complications + + + + + + Comorbidity + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://purl.obolibrary.org/obo/omit + + + + + + + + + + + + + + + + + + + + + + + + + + + Vital signs are unstable and not within normal limits. Patient may be unconscious. Indicators are unfavorable. + Damion Dooley + grave + + + + + + + + + + + + + + + + + + + + + + + + + + A type of Shiga toxin found in E. coli + Damion Dooley + Stx1 + + + + Shiga toxin 1 + + + + + + + + + + A type of Shiga toxin found in E. coli which is antigenically distinct from Shiga toxin 1 + Damion Dooley + Stx2 + + + + Shiga toxin 2 + + + + + + + + + + + + + + + + + MLST typing + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments. + physician role + + + + + + + + + + + + + + Damion's Note: Future use might prefer: CMO_0000015 body temperature. + + + + + + + + NCBI BioSample: female + + + + + + + + NCBI BioSample: male + + + + + + + + + + + + + + Phenotypic sex refers to an individual's sex as determined by their internal and external genitalia, expression of secondary sex characteristics, and behavior. + Note that NCBI Biosample has these values allowed: +male | female | pooled male and female | neuter | hermaphrodite | intersex | not determined | missing | not applicable | not collected + NCBI: http://www.ncbi.nlm.nih.gov/books/NBK10943/ + + + + + + + + + Damion Dooley's note: We can't say radius is a subclass of "linear coordinate" because length is considered a quality/specifically dependent continuant, which is disjoint with immaterial entity/independent continuant . I.e. "length" as quality unfortunately can't pertain to abstract entities, only "real" ones. + + + + + + + + + + + + + + + + + + + + + + + + + social gathering + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Damion Dooley + + + + + + + + + + + + + + + + + + 1 + + + + sequence assembly + http://edamontology.org/data_0925 + http://purl.obolibrary.org/obo/OBI_0000973 - 'sequence data' + + + + + + + + + + Damion Dooley + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://purl.obolibrary.org/obo/ERO_0002173 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Damion Dooley's note: Unfortunately an IAO "count" cannot be a subclass of immaterial entity "linear coordinate" as this leads to disjoint conflict. + Damion Dooley's note: A count datum often implicity carries a date range for which the count is ascertained, or estimated, or simulated for. + Damion Dooley's note: The result of the act of counting is a scalar number whose unit is a description of the thing being counted. One can count 10 oranges and compare that to a count of 5 oranges. One can generalize that a count of 5 oranges is a count of pieces of fruit. One can then compare 5 oranges and 5 apples, fruitfully! + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + variable type + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host. + https://www.ebi.ac.uk/ols/ontologies/trans + TRANS follows the CDC Epidemiology model of transmission between two hosts, a reservoir and host or other non-host, non-reservoir entities (e.g), a needle and a host. + transmission of infection + + + + + + + + + Direct and essentially immediate transfer of infectious agents to a receptive portal of entry through which human or animal infection may take place. This may be by direct contact such as touching, kissing, biting, or sexual intercourse or by the direct projection (droplet spread) of droplet spray onto the conjunctiva or the mucous membranes of the eyes, nose, or mouth. It may also be by direct exposure of susceptible tissue to an agent in soil, compost, or decaying vegetable matter or by the bite of a rabid animal. Transplacental transmission is another form of direct transmission. + https://www.ebi.ac.uk/ols/ontologies/trans + direct transmission + + + + + + + + + Indirect transmission is a transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by intermediary vehicles, vectors or as airborne dust particles. + https://www.ebi.ac.uk/ols/ontologies/trans + indirect transmission + + + + + + + + + Congenital transmission is a direct transmission process during which the pathogen is transmitted directly from mother to child at or around the time of birth. + https://www.ebi.ac.uk/ols/ontologies/trans + congenital + + + + + + + + + contact transmission + Contact transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by kissing, skin-to-skin contact, sexual intercourse, or by contact with soil or vegetation containing the pathogen. + https://www.ebi.ac.uk/ols/ontologies/trans + contact + + + + + + + + + Droplet spread transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by spray of aerosols over a short distance, spray from sneezing, coughing or talking. + https://www.ebi.ac.uk/ols/ontologies/trans + droplet spread + + + + + + + + + Vehicle-borne ingestion transmission is an indirect vehicle-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by ingestion of fluids or foods or food products including: food, water, milk, or meat products. + https://www.ebi.ac.uk/ols/ontologies/trans + vehicle-born ingestion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism body product + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + poultry fluff + Damion Dooley's note: Poultry fluff is both an 'anatomical structure' and a body product when it is shed. + + + + + + + + + + + + + + + + + + + + + + + + + Damion Dooley's note: Need to build this out further with reference to http://unitsofmeasure.org/trac and other unit ontologies: + +[1] R. Hodgson and P. J. Keller, "QUDT-quantities, units, dimensions and data types in OWL and XML." Online (September 2011) http://www. qudt.org +[2] M. van Assem, H. Rijgersberg, and J. Top, "Ontology of units of measure and related concepts." Semantic Web 4, no. 1 (2013): 3-13. +[3] G. V. Gkoutos, P. N. Schofield, and R. Hoehndorf, "The Units Ontology: a tool for integrating units of measurement in science." Database2012 (2012): bas033. + + + + + + + + + + + + + + mm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + µg/ml + + + + + + + + + + + + + + + + + + + + + + + + + ongoing pregnancy + + + + + + + + + ancestral group + + + + + + + + + + Damion Dooley + + + + + + + + + + + + + + + + + + + + + requires discussion + A personal health datum which specifies host role at time of specimen collection. + 0000-0002-9578-0788 + 2022-01-31T23:53:59Z + host role at time of specimen collection + + + + + + + + + + + + + + + + + MLVA typing + + + + + + + + + + + + + + + + + + + + + + + Damion Dooley's comment: On spheroids a polygon can be minimally defined by latitude and longitude coordinates, however technically this is ambiguous whether the larger or smaller area is being referred to. Unambiguously, such a polygon could be defined by an epicenter, and a latitude width and longitude height. + + + + + + + + + + In elementary geometry, a polygon is a plane figure that is bounded by a finite chain of straight line segments closing in a loop to form a closed chain or circuit. + Damion Dooley + https://en.wikipedia.org/wiki/Polygon + + + + + + + + + + + + + + + + + + + + + + + + + + PulseNet: Key + + + + + + + + + + + + + + + + + + + + + + + + + + Damion Dooley + medical health record (history / timeline) + + + + + + + + + + + + + + + + + + + + + + + + + depth:1 + lookup + + + + + + + + + + Bacterial bacteriophage typing + http://phinvads.cdc.gov/vads/http:/phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.6.96&code=22642004 + + + + + + + + + + + + + + + + + http://purl.obolibrary.org/obo/hancestro_0004 + obsolete: ancestral group + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI); The concept of ethnic origin is an attempt to classify people, not according to their current ethnicity, but according to where their ancestors came from. Ethnic origin has become a popular classification in statistics, where the concept of race has been largely discarded. (from Wikipedia) (NCI); a group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (CSP) + + + + + + + + + + + + + + + + + + + + + + + + Welcome to the GenEpiO ontology! The "information content entity" class has many GenEpiO terms. "data item > measurement data item" has many datum terms; see "data representational model" for collections of terms set up for compatibility with 3rd party sources. + +Note that this file contains examples of cities, provinces, states, territories, and soverign nations from around the world; customization of this geographical content would be expected for particular regional use. + + + + + + + + + + + + + + + + + + + + + + + + + + Base class for definitions. + + + + + + + + + A named element in the model. + + + + + + + + + Usage example and description. + + + + + + + + + An attributed label. + + + + + + + + + A permissible value, accompanied by intended text and an optional mapping to a concept URI. + + + + + + + + + A collection of subset, type, slot and class definitions. + + + + + + + + + The definition of a property or a slot. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Damion Dooley + Damion Dooley's note: Here we are exploring the use of individuals/instances to describe local picklists for GenEpiO driven software. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + United Nations + + + + + + + + MSH + + + + + + + + NCI_Thesaurus + + + + + + + + NIFSTD + + + + + + + + home + + + + + + + + _test_individual + + + + + + + + + LabID assigned by NLEP + Damion Dooley + 2019-04-17T23:31:44Z + PulseNet:LabID + + + + + + + + Country where isolate was collected + Damion Dooley + 2019-04-17T23:32:45Z + SourceCountry + + + + + + + + + Country where isolate was collected + Currently not used for PulseNet Canada + Damion Dooley + 2019-04-17T23:37:19Z + PulseNet:SourceCountry + + + + + + + + + (Province for PNC) where isolate was collected. + Damion Dooley + 2019-04-17T23:38:09Z + PulseNet:SourceState + + + + + + + + + Damion Dooley + 2019-04-17T23:40:57Z + PulseNet:SourceCity + + + + + + + + + Site of the source type where isolate was collected, e.g. blood, CSF, etc. + Damion Dooley + 2019-04-17T23:47:10Z + PulseNet:SourceSite + + + + + + + + + The source type of the isolate, e.g. human, environmental, etc. + Damion Dooley + 2019-04-17T23:48:49Z + PulseNet:SourceType + + + + + + + + + Other countries where the patient traveled + Damion Dooley + 2019-04-17T23:49:47Z + PulseNet:Traveled_To + + + + + + + + + Further description of the source type, e.g. bovine, chicken + Damion Dooley + 2019-04-17T23:51:02Z + PulseNet:TypeDetails + + + + + + + + + Submitted isolate # (if diff. From Key #), NLEP will enter Prov. Submitted # if sample was sent to NLEP for PFGE + Damion Dooley + 2019-04-17T23:52:01Z + PulseNet:SubmittedNumber + + + + + + + + + (Province for PNC) additional number used to identify the isolate + Damion Dooley + 2019-04-17T23:53:47Z + PulseNet:OtherStateIsolate + + + + + + + + + Age of patient when isolate was collected + Damion Dooley + 2019-04-17T23:54:24Z + PulseNet:PatientAge + + + + + + + + + Sex of patient when isolate was collected + Damion Dooley + 2019-04-17T23:55:04Z + PulseNet:PatientSex + + + + + + + + + + Date of collection + Damion Dooley + 2019-04-17T23:56:33Z + PulseNet:IsolatDate + + + + + + + + + Date the isolate is uploaded to the national database after initial upload + Damion Dooley + 2019-04-18T00:21:46Z + PulseNet:UploadModifiedDate + + + + + + + + + Antigenic Formula + Damion Dooley + 2019-04-18T00:23:18Z + PulseNet:AntigenForm + + + + + + + + + Subspecies, I - VI (roman numerals) + Damion Dooley + 2019-04-18T00:24:11Z + PulseNet:Subspecies + + + + + + + + + O polysaccharide (LPS) Group + Damion Dooley + 2019-04-18T00:24:53Z + PulseNet:OGroup + + + + + + + + + Serotype of isolate + Damion Dooley + 2019-04-18T00:25:22Z + PulseNet:Serotype + + + + + + + + + Code issued by CDC; see: 'Naming of outbreaks…' on WebBoard. (format YYMMLabIDLITScode-#) + Currently not used for PulseNet Canada + Damion Dooley + 2019-04-18T00:27:08Z + PulseNet:Outbreak + + + + + + + + + Number issued by CDC if isolate is run at CDC (Key will be # issued by NLEP if isolate run at NLEP) + Damion Dooley + 2019-04-18T00:28:01Z + PulseNet:cdc_id + + + + + + + + + Enzyme name present if part of that national list. + Damion Dooley + 2019-04-18T00:28:35Z + PulseNet:ListMember + + + + + + + + + Phage type + Damion Dooley + 2019-04-18T00:29:20Z + PulseNet:Phagetype + + + + + + + + + Provides LabID, gel and lane information + Damion Dooley + 2019-04-18T00:29:58Z + PulseNet:TEMP + + + + + + + + + Status of the isolate; this is only confirmed once CDC runs it. + Currently not used for PulseNet Canada + Damion Dooley + 2019-04-18T00:30:44Z + PulseNet:Status + + + + + + + + + Currently not used for PulseNet Canada + checked if the isolate is part of NARMS. + Damion Dooley + 2019-04-18T00:35:55Z + PulseNet:NARMS-EB + + + + + + + + + Checked if the isolate is part of FoodNet. + Currently not used for PulseNet Canada + Damion Dooley + 2019-04-18T00:36:39Z + PulseNet:FoodNet + + + + + + + + + XbaI gel where the isolate is located, lane of gel + Damion Dooley + 2019-04-18T00:38:57Z + PulseNet:PFGE-XbaI-file + + + + + + + + + XbaI pattern assigned by CDC (format XXXXXX.####) + Damion Dooley + 2019-04-18T00:39:23Z + PulseNet:PFGE-XbaI-pattern + + + + + + + + + The date the XbaI gel is run + Damion Dooley + 2019-04-18T00:40:05Z + PulseNet:PFGE-XbaI-rundate + + + + + + + + + Once the XbaI pattern is named, the status is confirmed by CDC + Damion Dooley + 2019-04-18T00:41:39Z + PulseNet:PFGE-XbaI-status + + + + + + + + + BlnI gel where the isolate is located, lane of gel + Damion Dooley + 2019-04-18T00:42:11Z + PulseNet:PFGE-BlnI-file + + + + + + + + + BlnI pattern assigned by CDC (format XXXXXX.####). + Damion Dooley + 2019-04-18T00:42:42Z + PulseNet:PFGE-BlnI-pattern + + + + + + + + + The date the BlnI gel is run + Damion Dooley + 2019-04-18T00:43:50Z + PulseNet:PFGE-BlnI-rundate + + + + + + + + + Once the BlnI pattern is named, the status is confirmed by CDC + Damion Dooley + 2019-04-18T00:44:44Z + PulseNet:PFGE-BlnI-status + + + + + + + + + SpeI gel where the isolate is located, lane of gel. + Damion Dooley + 2019-04-18T00:45:15Z + PulseNet:PFGE-SpeI-file + + + + + + + + + SpeI pattern assigned by CDC (format XXXXXX.####). + Damion Dooley + 2019-04-18T00:45:41Z + PulseNet:PFGE-SpeI-pattern + + + + + + + + + The date the SpeI gel is run. + Damion Dooley + 2019-04-18T00:46:21Z + PulseNet:PFGE-SpeI-rundate + + + + + + + + + Once the SpeI pattern is named, the status is confirmed by CDC. + Damion Dooley + 2019-04-18T00:47:00Z + PulseNet:PFGE-SpeI-status + + + + + + + + + Date WHICH (PH?) lab received isolate. + Damion Dooley + 2019-04-18T00:57:28Z + PulseNet:ReceivedDate + + + + + + + + + + 2019-11-17T00:54:44Z + ISO_23418.organization_contact.service + + + + + + + + + Date the isolate uploaded to the national database. + Damion Dooley + 2019-04-17T22:47:51Z + PulseNet:UploadDate + + + 2 + + + 2 + + + + + + + + I + intermediate + + + R + resistant + + + S + sensitive + susceptible + + + NS + nonsensitive + nonsusceptible + + + sensitive - dose dependent + susceptible - dose dependent + SSD + + + BSAC + + + DIN + + + EUCAST + + + SFM + + + Damion Dooley's note: this BFO class is incompatible with "immaterial entity" "n-dimensional concept". + + + food role + + + constructed feature + + + http://purl.obolibrary.org/obo/NCIT_C25464 + + + irrigation pond + + + http://purl.obolibrary.org/obo/NCIT_C80234 + + + stool + + + http://opendata.inra.fr/EOL/EOL_0001601#bedding + straw bedding + + + true + + + chicken cage + + + NCBI SRA: ION_TORRENT + + + asian tiger shrimp + black tiger shrimp + + + wild + gathered + + + Damion Dooley + + + + This is a catch-all category for Gazetteer items that have "located in" relations but not an imported GAZETTEER class parent in GenEpiO. + Damion Dooley + + + true + + Damion Dooley + obsolete: has primitive data type + + + + Damion Dooley + + + + Damion Dooley + + + + Damion Dooley + + + Damion Dooley + + + + Damion Dooley + + + + + Damion Dooley + + + + Damion Dooley + + + Damion Dooley's note: IAO lat/long can't be made a subclass of "angular coordinate" or disjoint contradiction arises with "immaterial entity" + Damion Dooley + + + + + Damion Dooley + + + + Damion Dooley + + + Damion Dooley + + + + + Damion Dooley + + + Damion Dooley + + + + Damion Dooley + This seems to be covered by 'datetime range intermediate' + + + + Damion Dooley + + + + Damion Dooley + + + + Damion Dooley + A datetime set item is a datetime that has been grouped semantically under a given type of process + + + Damion Dooley + + + + Damion Dooley + + + + Damion Dooley + + + + Damion Dooley + + + + Damion Dooley + + + + Damion Dooley + + + + mobile + + + work + + + + Damion Dooley + + + + An unordered set is a set of elements which have no intrinsic (semantic) order with respect to each other. The set of all living people is not intrinsically ordered; an ordering can only be provided by looking at some partiular feature of the given set elements. + Damion Dooley + + + + Damion Dooley + + + Damion Dooley + + + + + Damion Dooley + + + Damion Dooley + + https://en.wikipedia.org/wiki/Plane_(geometry) + + + Damion Dooley + + + + clam, squid, octopus + + + NCBI SRA: HELICOS + + + NCBI SRA: ABI_SOLID + + + A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. + + + specimen provider PI organization + + + NCBI SRA: Illumina Genome Analyzer IIx + + + NCBI SRA: AB SOLiD 3 Plus System + + + NCBI SRA: AB SOLiD 4 System + + + NCBI SRA: Illumina Genome Analyzer IIe + + + disease (OGMS) + + + + + + NCBI BioSample: hermaphrodite + + + This value is not present in NCBI BioSample host sex. + + + derives into + + + starts during + + + happens during + + + starts with + + + ends with + + + input of + + + Damion Dooley's note:Damion Dooley's note: Outstanding issue: How to attach units to each dimension? This depends on the instance of the problem involving a dimension? + +Linear offset can be decimal or integer or complex, or a count. + - Can have a unit: meter, kilometer, foot, light-year, oranges, apples, fruit + +Angular offset can be radians or degrees. + n-dimensional coordinate system + + + rectal + + + http://purl.obolibrary.org/obo/BTO_0000818 + + + cerebrospinal fluid (CSF) + + + Damion Dooley + + cfu/mL + + + Damion Dooley + + + + http://purl.obolibrary.org/obo/PATO_0000011 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From bf007b6d8448e16bb060bfd55b84b9889212ff24 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 7 Feb 2022 16:20:49 +0100 Subject: [PATCH 0016/1454] organize repo and add sscripts to do --- relecov_tools/__main__.py | 0 relecov_tools/download.py | 0 relecov_tools/read_excel.py | 0 relecov_tools/utils.py | 12 ++++++++++++ relecov_tools/validate_data.py | 0 5 files changed, 12 insertions(+) create mode 100644 relecov_tools/__main__.py create mode 100644 relecov_tools/download.py create mode 100644 relecov_tools/read_excel.py create mode 100644 relecov_tools/utils.py create mode 100644 relecov_tools/validate_data.py diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py new file mode 100644 index 00000000..e69de29b diff --git a/relecov_tools/download.py b/relecov_tools/download.py new file mode 100644 index 00000000..e69de29b diff --git a/relecov_tools/read_excel.py b/relecov_tools/read_excel.py new file mode 100644 index 00000000..e69de29b diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py new file mode 100644 index 00000000..0bc334b4 --- /dev/null +++ b/relecov_tools/utils.py @@ -0,0 +1,12 @@ +import os + +def file_exists(file_to_check): + ''' + Input: + file_to_check # file name to check if exists + Return: + True if exists + ''' + if os.path.isfile(file_to_check): + return True + return False diff --git a/relecov_tools/validate_data.py b/relecov_tools/validate_data.py new file mode 100644 index 00000000..e69de29b From 3c7e597ec6d09be73c487699dba9bb19edf3de5e Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 7 Feb 2022 18:56:57 +0100 Subject: [PATCH 0017/1454] Update new structure --- __main__.py | 0 relecov-tools/utils/common_functions.py | 12 ------------ {relecov-tools => test}/owl_parsing.py | 0 {relecov-tools => test}/validation_jsons.py | 0 4 files changed, 12 deletions(-) create mode 100644 __main__.py delete mode 100644 relecov-tools/utils/common_functions.py rename {relecov-tools => test}/owl_parsing.py (100%) rename {relecov-tools => test}/validation_jsons.py (100%) diff --git a/__main__.py b/__main__.py new file mode 100644 index 00000000..e69de29b diff --git a/relecov-tools/utils/common_functions.py b/relecov-tools/utils/common_functions.py deleted file mode 100644 index 0bc334b4..00000000 --- a/relecov-tools/utils/common_functions.py +++ /dev/null @@ -1,12 +0,0 @@ -import os - -def file_exists(file_to_check): - ''' - Input: - file_to_check # file name to check if exists - Return: - True if exists - ''' - if os.path.isfile(file_to_check): - return True - return False diff --git a/relecov-tools/owl_parsing.py b/test/owl_parsing.py similarity index 100% rename from relecov-tools/owl_parsing.py rename to test/owl_parsing.py diff --git a/relecov-tools/validation_jsons.py b/test/validation_jsons.py similarity index 100% rename from relecov-tools/validation_jsons.py rename to test/validation_jsons.py From e15e0d1aa4c1492f3a14ba01b9c6e01da21cbc1d Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Fri, 11 Feb 2022 12:12:55 +0100 Subject: [PATCH 0018/1454] started SFTP object --- relecov_tools/SFTP_connection_class.py | 64 ++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 relecov_tools/SFTP_connection_class.py diff --git a/relecov_tools/SFTP_connection_class.py b/relecov_tools/SFTP_connection_class.py new file mode 100644 index 00000000..0eb9c8b0 --- /dev/null +++ b/relecov_tools/SFTP_connection_class.py @@ -0,0 +1,64 @@ +''' +============================================================= +HEADER +============================================================= +INSTITUTION: BU-ISCIII +AUTHOR: Guillermo J. Gorines Cordero +MAIL: guillermo.gorines@urjc.es +VERSION: 0 +CREATED: 11-2-2022 +REVISED: 11-2-2022 +REVISED BY: guillermo.gorines@urjc.es +DESCRIPTION: + + Includes the SFTP connection class, and its methods. + +REQUIREMENTS: + -Python + -Paramiko + +TO DO: + +-Check minimal required Python version + +================================================================ +END_OF_HEADER +================================================================ +''' + +# Imports + +import paramiko + +class SFTP_Connection: + def __init__(self,host,port,user,key): + ''' + Initializes the Connection object and starts its host, port, user and key attributes. + Declaration: + SFTP_Connection_object = SFTP_Connection(host,port,user,key) + ''' + + self.host = host + self.port = port + self.user = user + self.key = key + self.client = None + + def open(self): + ''' + Uses the class attributes to make a connection + Usage: + SFTP_Connection_object = + ''' + self.client = paramiko.SSHClient() + self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) + self.client.connect(hostname = self.host, + port = self.port, + username = self.user, + password = self.key, + allow_agent=False, + look_for_keys=False) + + self.client = self.client.open_sftp() + + From 0fc21b90f351274541ab2fcdf3c0c6e4b05e75d8 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Fri, 11 Feb 2022 12:24:54 +0100 Subject: [PATCH 0019/1454] added a check_connection method --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5848093e..d12406fa 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [![install with Bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/recipes/nf-core/README.html) [![install with PyPI](https://img.shields.io/badge/install%20with-PyPI-blue.svg)](https://pypi.org/project/nf-core/) -A python package with helper tools for the relecov project. +A Python package with helper tools for the relecov project. ## Table of contents From 2410e0d35bc719e8173635a82e87e646ba4496f9 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Fri, 11 Feb 2022 12:30:24 +0100 Subject: [PATCH 0020/1454] Added docstrings --- relecov_tools/SFTP_connection_class.py | 55 ++++++++++++++++++++------ 1 file changed, 43 insertions(+), 12 deletions(-) diff --git a/relecov_tools/SFTP_connection_class.py b/relecov_tools/SFTP_connection_class.py index 0eb9c8b0..845a9d30 100644 --- a/relecov_tools/SFTP_connection_class.py +++ b/relecov_tools/SFTP_connection_class.py @@ -20,6 +20,7 @@ TO DO: -Check minimal required Python version +-Method to check connection ================================================================ END_OF_HEADER @@ -44,21 +45,51 @@ def __init__(self,host,port,user,key): self.key = key self.client = None - def open(self): + def check_connection(self): ''' - Uses the class attributes to make a connection + Check if there is a SFTP connection Usage: - SFTP_Connection_object = + SFTP_Connection_object.check_connection() + Return: + True if a connection still exists + False if connection doesnt exist (not established or timed out for instance) ''' - self.client = paramiko.SSHClient() - self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) - self.client.connect(hostname = self.host, - port = self.port, - username = self.user, - password = self.key, - allow_agent=False, - look_for_keys=False) + try: + self.client.getcwd() + return True + except: + return False + + def open_connection(self): + ''' + Uses the class attributes to make a SFTP connection + Usage: + SFTP_Connection_object.open_connection() + Return: + None (by now) + ''' + if self.check_connection(): + self.client = paramiko.SSHClient() + self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) + self.client.connect(hostname = self.host, + port = self.port, + username = self.user, + password = self.key, + allow_agent=False, + look_for_keys=False) + + self.client = self.client.open_sftp() - self.client = self.client.open_sftp() + + def close_connection(self): + ''' + Closes the SFTP connection if there is any + Usage: + SFTP_Connection_object.close_connection() + Return: + None (by now) + ''' + if self.check_connection(): + self.client.close() From 9a752a3db5c47ed5b3c42bc5410c56bc00a6d5b1 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Fri, 11 Feb 2022 13:15:04 +0100 Subject: [PATCH 0021/1454] indentation fixed, added little testing inside --- relecov_tools/SFTP_connection_class.py | 125 +++++++++++++++---------- 1 file changed, 73 insertions(+), 52 deletions(-) diff --git a/relecov_tools/SFTP_connection_class.py b/relecov_tools/SFTP_connection_class.py index 845a9d30..ba53597d 100644 --- a/relecov_tools/SFTP_connection_class.py +++ b/relecov_tools/SFTP_connection_class.py @@ -33,63 +33,84 @@ class SFTP_Connection: def __init__(self,host,port,user,key): - ''' - Initializes the Connection object and starts its host, port, user and key attributes. - Declaration: - SFTP_Connection_object = SFTP_Connection(host,port,user,key) - ''' - - self.host = host - self.port = port - self.user = user - self.key = key - self.client = None + ''' + Initializes the Connection object and starts its host, port, user and key attributes. + Declaration: + SFTP_Connection_object = SFTP_Connection(host,port,user,key) + ''' + self.host = host + self.port = port + self.user = user + self.key = key + self.client = None def check_connection(self): - ''' - Check if there is a SFTP connection - Usage: - SFTP_Connection_object.check_connection() - Return: - True if a connection still exists - False if connection doesnt exist (not established or timed out for instance) - ''' - try: - self.client.getcwd() - return True - except: - return False + ''' + Check if there is a SFTP connection + Usage: + SFTP_Connection_object.check_connection() + Return: + True if a connection still exists + False if connection doesnt exist (not established or timed out for instance) + ''' + try: + self.client.getcwd() + return True + except: + return False + def open_connection(self): - ''' - Uses the class attributes to make a SFTP connection - Usage: - SFTP_Connection_object.open_connection() - Return: - None (by now) - ''' - if self.check_connection(): - self.client = paramiko.SSHClient() - self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) - self.client.connect(hostname = self.host, - port = self.port, - username = self.user, - password = self.key, - allow_agent=False, - look_for_keys=False) - - self.client = self.client.open_sftp() - + ''' + Uses the class attributes to make a SFTP connection + Usage: + SFTP_Connection_object.open_connection() + Return: + True if connected succesfully + False if failed connection + ''' + if not self.check_connection(): + try: + self.client = paramiko.SSHClient() + self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) + self.client.connect(hostname = self.host, + port = self.port, + username = self.user, + password = self.key, + allow_agent=False, + look_for_keys=False) + self.client = self.client.open_sftp() + return True + except: + return False + def close_connection(self): - ''' - Closes the SFTP connection if there is any - Usage: - SFTP_Connection_object.close_connection() - Return: - None (by now) - ''' - if self.check_connection(): - self.client.close() + ''' + Closes the SFTP connection if there is any + Usage: + SFTP_Connection_object.close_connection() + Return: + -True if connection closed successfully + -False if connection closing failed + -None if no connection was established + ''' + if self.check_connection(): + try: + self.client.close() + return True + except: + return False + +CLAVE = "RANDOM_KEY_FOR_TESTING" +HOST = 'RANDOM_SFTP_FOR_TESTING' +PUERTO = 420 +USUARIO = 'ARTURITO' +my_sftp = SFTP_Connection(HOST,PUERTO,USUARIO,CLAVE) +if not my_sftp.open_connection(): + print("No connection!") +else: + print(my_sftp.check_connection()) +print(my_sftp.client.listdir()) \ No newline at end of file From a1b8fab935cc73263396a827a113e3120f5cde74 Mon Sep 17 00:00:00 2001 From: GuilleGorines <60110848+GuilleGorines@users.noreply.github.com> Date: Fri, 11 Feb 2022 13:59:54 +0100 Subject: [PATCH 0022/1454] Update relecov_tools/SFTP_connection_class.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Sara Monzón --- relecov_tools/SFTP_connection_class.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/SFTP_connection_class.py b/relecov_tools/SFTP_connection_class.py index ba53597d..cbfcc128 100644 --- a/relecov_tools/SFTP_connection_class.py +++ b/relecov_tools/SFTP_connection_class.py @@ -31,7 +31,7 @@ import paramiko -class SFTP_Connection: +class SftpHandle: def __init__(self,host,port,user,key): ''' Initializes the Connection object and starts its host, port, user and key attributes. From d7267af4f6e3b13a69a11d7e796675541da8adf9 Mon Sep 17 00:00:00 2001 From: GuilleGorines <60110848+GuilleGorines@users.noreply.github.com> Date: Fri, 11 Feb 2022 14:00:17 +0100 Subject: [PATCH 0023/1454] Update relecov_tools/SFTP_connection_class.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Sara Monzón --- relecov_tools/SFTP_connection_class.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/SFTP_connection_class.py b/relecov_tools/SFTP_connection_class.py index cbfcc128..b44e1986 100644 --- a/relecov_tools/SFTP_connection_class.py +++ b/relecov_tools/SFTP_connection_class.py @@ -36,7 +36,7 @@ def __init__(self,host,port,user,key): ''' Initializes the Connection object and starts its host, port, user and key attributes. Declaration: - SFTP_Connection_object = SFTP_Connection(host,port,user,key) + sftp = SftpHandle(host,port,user,key) ''' self.host = host self.port = port From ba1f379991882b8128e0d494c78a040afd67bfc1 Mon Sep 17 00:00:00 2001 From: GuilleGorines <60110848+GuilleGorines@users.noreply.github.com> Date: Fri, 11 Feb 2022 14:00:34 +0100 Subject: [PATCH 0024/1454] Update relecov_tools/SFTP_connection_class.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Sara Monzón --- relecov_tools/SFTP_connection_class.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/SFTP_connection_class.py b/relecov_tools/SFTP_connection_class.py index b44e1986..2278401e 100644 --- a/relecov_tools/SFTP_connection_class.py +++ b/relecov_tools/SFTP_connection_class.py @@ -44,7 +44,7 @@ def __init__(self,host,port,user,key): self.key = key self.client = None - def check_connection(self): + def check(self): ''' Check if there is a SFTP connection Usage: From e98937e81f24c24cb45d372bfea2867295fb932f Mon Sep 17 00:00:00 2001 From: GuilleGorines <60110848+GuilleGorines@users.noreply.github.com> Date: Fri, 11 Feb 2022 14:00:41 +0100 Subject: [PATCH 0025/1454] Update relecov_tools/SFTP_connection_class.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Sara Monzón --- relecov_tools/SFTP_connection_class.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/SFTP_connection_class.py b/relecov_tools/SFTP_connection_class.py index 2278401e..cebcc078 100644 --- a/relecov_tools/SFTP_connection_class.py +++ b/relecov_tools/SFTP_connection_class.py @@ -48,7 +48,7 @@ def check(self): ''' Check if there is a SFTP connection Usage: - SFTP_Connection_object.check_connection() + sftp.check() Return: True if a connection still exists False if connection doesnt exist (not established or timed out for instance) From 4c168077845114aed2bf063c05f1827a689043c3 Mon Sep 17 00:00:00 2001 From: GuilleGorines <60110848+GuilleGorines@users.noreply.github.com> Date: Fri, 11 Feb 2022 14:00:50 +0100 Subject: [PATCH 0026/1454] Update relecov_tools/SFTP_connection_class.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Sara Monzón --- relecov_tools/SFTP_connection_class.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/SFTP_connection_class.py b/relecov_tools/SFTP_connection_class.py index cebcc078..23046893 100644 --- a/relecov_tools/SFTP_connection_class.py +++ b/relecov_tools/SFTP_connection_class.py @@ -60,7 +60,7 @@ def check(self): return False - def open_connection(self): + def open(self): ''' Uses the class attributes to make a SFTP connection Usage: From b1a940e54810584821ed3ba6bf8207e27744e6df Mon Sep 17 00:00:00 2001 From: GuilleGorines <60110848+GuilleGorines@users.noreply.github.com> Date: Fri, 11 Feb 2022 14:00:58 +0100 Subject: [PATCH 0027/1454] Update relecov_tools/SFTP_connection_class.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Sara Monzón --- relecov_tools/SFTP_connection_class.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/SFTP_connection_class.py b/relecov_tools/SFTP_connection_class.py index 23046893..c4de2e33 100644 --- a/relecov_tools/SFTP_connection_class.py +++ b/relecov_tools/SFTP_connection_class.py @@ -69,7 +69,7 @@ def open(self): True if connected succesfully False if failed connection ''' - if not self.check_connection(): + if not self.check(): try: self.client = paramiko.SSHClient() self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) From bebb0e5daf4b062597bc0180d83a91b9af0acdd7 Mon Sep 17 00:00:00 2001 From: GuilleGorines <60110848+GuilleGorines@users.noreply.github.com> Date: Fri, 11 Feb 2022 14:01:05 +0100 Subject: [PATCH 0028/1454] Update relecov_tools/SFTP_connection_class.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Sara Monzón --- relecov_tools/SFTP_connection_class.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/SFTP_connection_class.py b/relecov_tools/SFTP_connection_class.py index c4de2e33..91cb06bf 100644 --- a/relecov_tools/SFTP_connection_class.py +++ b/relecov_tools/SFTP_connection_class.py @@ -108,7 +108,7 @@ def close_connection(self): USUARIO = 'ARTURITO' my_sftp = SFTP_Connection(HOST,PUERTO,USUARIO,CLAVE) -if not my_sftp.open_connection(): +if not my_sftp.open(): print("No connection!") else: print(my_sftp.check_connection()) From 8b373141f7dea8785b8838da5e77e46db4a45ecc Mon Sep 17 00:00:00 2001 From: GuilleGorines <60110848+GuilleGorines@users.noreply.github.com> Date: Fri, 11 Feb 2022 14:01:22 +0100 Subject: [PATCH 0029/1454] Update relecov_tools/SFTP_connection_class.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Sara Monzón --- relecov_tools/SFTP_connection_class.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/SFTP_connection_class.py b/relecov_tools/SFTP_connection_class.py index 91cb06bf..8b0308ae 100644 --- a/relecov_tools/SFTP_connection_class.py +++ b/relecov_tools/SFTP_connection_class.py @@ -111,6 +111,6 @@ def close_connection(self): if not my_sftp.open(): print("No connection!") else: - print(my_sftp.check_connection()) + print(my_sftp.check()) print(my_sftp.client.listdir()) \ No newline at end of file From 1830f1eb4a78848d1748d22fb58e92fd9bdd4591 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Fri, 11 Feb 2022 14:03:07 +0100 Subject: [PATCH 0030/1454] description change (abs minimal) --- relecov_tools/SFTP_connection_class.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/SFTP_connection_class.py b/relecov_tools/SFTP_connection_class.py index ba53597d..6a6cca98 100644 --- a/relecov_tools/SFTP_connection_class.py +++ b/relecov_tools/SFTP_connection_class.py @@ -11,7 +11,7 @@ REVISED BY: guillermo.gorines@urjc.es DESCRIPTION: - Includes the SFTP connection class, and its methods. + Includes the SFTP connection class, and its associated methods. REQUIREMENTS: -Python From 261880649c667f6a042ca69bac03bb40c4838e94 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Fri, 11 Feb 2022 14:08:33 +0100 Subject: [PATCH 0031/1454] adjustments based on comments --- relecov_tools/SFTP_connection_class.py | 26 ++++++++++++++++++-------- 1 file changed, 18 insertions(+), 8 deletions(-) diff --git a/relecov_tools/SFTP_connection_class.py b/relecov_tools/SFTP_connection_class.py index 87922536..7b6d2e01 100644 --- a/relecov_tools/SFTP_connection_class.py +++ b/relecov_tools/SFTP_connection_class.py @@ -20,7 +20,7 @@ TO DO: -Check minimal required Python version --Method to check connection +-Delete testing inside this script ================================================================ END_OF_HEADER @@ -30,6 +30,7 @@ # Imports import paramiko +import sys class SftpHandle: def __init__(self,host,port,user,key): @@ -64,7 +65,7 @@ def open(self): ''' Uses the class attributes to make a SFTP connection Usage: - SFTP_Connection_object.open_connection() + sftp.open() Return: True if connected succesfully False if failed connection @@ -80,37 +81,46 @@ def open(self): allow_agent=False, look_for_keys=False) - self.client = self.client.open_sftp() + self.client = self.client.open() + return True except: return False - def close_connection(self): + def close(self): ''' Closes the SFTP connection if there is any Usage: - SFTP_Connection_object.close_connection() + sftp.close() Return: -True if connection closed successfully -False if connection closing failed -None if no connection was established ''' - if self.check_connection(): + if self.check(): try: self.client.close() return True except: return False - + +if __name__ == '__main__': + sys.exit(main()) + + + +# TESTING ZONE, must be deleted later CLAVE = "RANDOM_KEY_FOR_TESTING" HOST = 'RANDOM_SFTP_FOR_TESTING' PUERTO = 420 USUARIO = 'ARTURITO' -my_sftp = SFTP_Connection(HOST,PUERTO,USUARIO,CLAVE) +my_sftp = SftpHandle(HOST,PUERTO,USUARIO,CLAVE) if not my_sftp.open(): print("No connection!") else: print(my_sftp.check()) +# testing the client attribute +# works fine by now print(my_sftp.client.listdir()) \ No newline at end of file From 42f8e2e508fb2d8934a20a90dad196c23311ea7e Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Feb 2022 19:52:17 +0100 Subject: [PATCH 0032/1454] . --- relecov_tools/__main__.py | 41 +++++++++++++++++++ .../{read_excel.py => read_metadata.py} | 0 2 files changed, 41 insertions(+) rename relecov_tools/{read_excel.py => read_metadata.py} (100%) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index e69de29b..fa2b084f 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -0,0 +1,41 @@ +#!/usr/bin/env python + +from click.types import File +from rich import print +from rich.prompt import Confirm +import click +import rich.console +import rich.logging +import rich.traceback +import sys + +def run_relecov_workflow(): + # Set up rich stderr console + stderr = rich.console.Console(stderr=True, force_terminal=nf_core.utils.rich_force_colors()) + + # Set up the rich traceback + rich.traceback.install(console=stderr, width=200, word_wrap=True, extra_lines=1) + + # Print nf-core header + stderr.print("\n[green]{},--.[grey39]/[green],-.".format(" " * 42), highlight=False) + stderr.print("[blue] ___ __ __ __ ___ [green]/,-._.--~\\", highlight=False) + stderr.print("[green] `._,._,'\n", highlight=False) + stderr.print("[grey39] nf-core/tools version {}".format(nf_core.__version__), highlight=False) + try: + + # Lanch the click cli + nf_core_cli() + + + + +@click.group(cls=CustomHelpOrder) +@click.version_option(nf_core.__version__) +@click.option("-v", "--verbose", is_flag=True, default=False, help="Print verbose output to the console.") +@click.option("-l", "--log-file", help="Save a verbose log to a file.", metavar="") +def nf_core_cli(verbose, log_file): + + # Set the base logger to output DEBUG + log.setLevel(logging.DEBUG) + + diff --git a/relecov_tools/read_excel.py b/relecov_tools/read_metadata.py similarity index 100% rename from relecov_tools/read_excel.py rename to relecov_tools/read_metadata.py From 34c99d87ef13718a6788cc6e0390c5af9a9fd989 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Feb 2022 22:17:32 +0100 Subject: [PATCH 0033/1454] Understanding how is working 'click' and rich packages for handling the menu options --- relecov_tools/__main__.py | 151 ++++++++++++++++++++++++++++++--- relecov_tools/list.py | 5 ++ relecov_tools/read_metadata.py | 38 +++++++++ relecov_tools/utils.py | 9 ++ 4 files changed, 191 insertions(+), 12 deletions(-) create mode 100644 relecov_tools/list.py diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index fa2b084f..263cd02c 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -8,34 +8,161 @@ import rich.logging import rich.traceback import sys +import os +import utils +#import nf_core +# conda install -c conda-forge click +# conda install -c conda-forge rich -def run_relecov_workflow(): +def run_bu_isciii(): # Set up rich stderr console - stderr = rich.console.Console(stderr=True, force_terminal=nf_core.utils.rich_force_colors()) + stderr = rich.console.Console(stderr=True, force_terminal=utils.rich_force_colors()) # Set up the rich traceback rich.traceback.install(console=stderr, width=200, word_wrap=True, extra_lines=1) # Print nf-core header - stderr.print("\n[green]{},--.[grey39]/[green],-.".format(" " * 42), highlight=False) - stderr.print("[blue] ___ __ __ __ ___ [green]/,-._.--~\\", highlight=False) - stderr.print("[green] `._,._,'\n", highlight=False) - stderr.print("[grey39] nf-core/tools version {}".format(nf_core.__version__), highlight=False) + #stderr.print("\n[green]{},--.[grey39]/[green],-.".format(" " * 42), highlight=False) + stderr.print("[blue] ___ ___ ___ ___ ___ ___ ____ ", highlight=False) + stderr.print("[blue] \ |-[grey39]-| [blue] | \ | | | | | | | | ", highlight=False) + stderr.print("[blue] \ \ [grey39]/ [blue] |__ / | | ___ | |__ | | | | ", highlight=False) + stderr.print("[blue] / [grey39] / [blue] \ | \ | | | | | | | | ", highlight=False) + stderr.print("[blue] / [grey39] |-[blue]-| |__ / |___| _|__ ___| |___ _|_ _|_ _|_ ", highlight=False) + + + #stderr.print("[green] `._,._,'\n", highlight=False) + __version__ = '0.0.1' + stderr.print("[grey39] BU-ISCIII-tools version {}".format(__version__), highlight=False) try: - - # Lanch the click cli - nf_core_cli() + pass + except: + pass + + # Lanch the click cli + bu_isciii_cli() + + + +# Customise the order of subcommands for --help +class CustomHelpOrder(click.Group): + def __init__(self, *args, **kwargs): + self.help_priorities = {} + super(CustomHelpOrder, self).__init__(*args, **kwargs) + + def get_help(self, ctx): + self.list_commands = self.list_commands_for_help + return super(CustomHelpOrder, self).get_help(ctx) + + def list_commands_for_help(self, ctx): + """reorder the list of commands when listing the help""" + commands = super(CustomHelpOrder, self).list_commands(ctx) + return (c[1] for c in sorted((self.help_priorities.get(command, 1000), command) for command in commands)) + + def command(self, *args, **kwargs): + """Behaves the same as `click.Group.command()` except capture + a priority for listing command names in help. + """ + help_priority = kwargs.pop("help_priority", 1000) + help_priorities = self.help_priorities + def decorator(f): + cmd = super(CustomHelpOrder, self).command(*args, **kwargs)(f) + help_priorities[cmd.name] = help_priority + return cmd + return decorator @click.group(cls=CustomHelpOrder) -@click.version_option(nf_core.__version__) +#@click.version_option(nf_core.__version__) @click.option("-v", "--verbose", is_flag=True, default=False, help="Print verbose output to the console.") @click.option("-l", "--log-file", help="Save a verbose log to a file.", metavar="") -def nf_core_cli(verbose, log_file): +def bu_isciii_cli(verbose, log_file): # Set the base logger to output DEBUG log.setLevel(logging.DEBUG) + + # Set up logs to the console + log.addHandler( + rich.logging.RichHandler( + level=logging.DEBUG if verbose else logging.INFO, + console=rich.console.Console(stderr=True, force_terminal=nf_core.utils.rich_force_colors()), + show_time=False, + markup=True, + ) + ) + + # Set up logs to a file if we asked for one + if log_file: + log_fh = logging.FileHandler(log_file, encoding="utf-8") + log_fh.setLevel(logging.DEBUG) + log_fh.setFormatter(logging.Formatter("[%(asctime)s] %(name)-20s [%(levelname)-7s] %(message)s")) + log.addHandler(log_fh) + +# pipeline list +@bu_isciii_cli.command(help_priority=1) +@click.argument("keywords", required=False, nargs=-1, metavar="") +@click.option( + "-s", + "--sort", + type=click.Choice(["release", "pulled", "name", "stars"]), + default="release", + help="How to sort listed pipelines", +) +@click.option("--json", is_flag=True, default=False, help="Print full output as JSON") +@click.option("--show-archived", is_flag=True, default=False, help="Print archived workflows") +def list(keywords, sort, json, show_archived): + """ + List available bu-isciii workflows used for relecov. + Checks the web for a list of nf-core pipelines with their latest releases. + Shows which nf-core pipelines you have pulled locally and whether they are up to date. + """ + print(nf_core.list.list_workflows(keywords, sort, json, show_archived)) + + +# sftp +@bu_isciii_cli.command(help_priority=2) +@click.argument("pipeline", required=False, metavar="") +@click.option("-r", "--revision", help="Release/branch/SHA of the project to run (if remote)") +@click.option("-i", "--id", help="ID for web-gui launch parameter set") +@click.option( + "-c", "--command-only", is_flag=True, default=False, help="Create Nextflow command with params (no params file)" +) +@click.option( + "-o", + "--params-out", + type=click.Path(), + default=os.path.join(os.getcwd(), "nf-params.json"), + help="Path to save run parameters file", +) +def sftp(pipeline, id, revision, command_only, params_in, params_out, save_all, show_hidden, url): + ''' + Download files located in sftp server. + + ''' + print(nf_core.list.list_workflows(keywords, sort, json, show_archived)) + +# metadata +@bu_isciii_cli.command(help_priority=3) +@click.argument("pipeline", required=False, metavar="") +@click.option("-r", "--revision", help="Release/branch/SHA of the project to run (if remote)") +@click.option("-i", "--id", help="ID for web-gui launch parameter set") +@click.option( + "-c", "--command-only", is_flag=True, default=False, help="Create Nextflow command with params (no params file)" +) +@click.option( + "-o", + "--params-out", + type=click.Path(), + default=os.path.join(os.getcwd(), "nf-params.json"), + help="Path to save run parameters file", +) +def metadata(pipeline, id, revision, command_only, params_in, params_out, save_all, show_hidden, url): + ''' + Read Metadata . + + ''' + print(nf_core.list.list_workflows(keywords, sort, json, show_archived)) - +if __name__ == "__main__": + run_bu_isciii() diff --git a/relecov_tools/list.py b/relecov_tools/list.py new file mode 100644 index 00000000..6193b25e --- /dev/null +++ b/relecov_tools/list.py @@ -0,0 +1,5 @@ +#!/usr/bin/env python +"""Lists available nf-core pipelines and versions.""" +import requests +import rich.console +import rich.table diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index e69de29b..a9babb7b 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -0,0 +1,38 @@ +#!/usr/bin/env python + +class ReadMetadata(): + def __init__(): + self.origin_file = file + slef.metadata = {} + + +# reade_metadata +def read_metadata_workflow(self): + def __init__ (self, ): + + ''' + Description : Starts the read metada workflow + ''' + + # Perform workflow details + +wb_file = openpyxl.load_workbook(arguments.inputFile, data_only=True) +ws_metadata_lab = wb_file['METADATA_LAB'] +heading = [] +for cell in ws_metadata_lab[1]: + heading.append(cell.value) + + +for row in islice(ws_metadata_lab.values,1,ws_metadata_lab.max_row): + sample_data_row = {} + for idx in range(len(heading)): + if 'date' in heading[idx]: + sample_data_row[heading[idx]] = row[idx].strftime('%d/%m/%Y') + else: + sample_data_row[heading[idx]] = row[idx] + try: + validate(instance=sample_data_row,schema=json_phage_plus_schema) + except: + print('Unsuccessful validation for sample ' , sample_data_row['sample_name']) + + continue diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 0bc334b4..c3e4bf76 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -10,3 +10,12 @@ def file_exists(file_to_check): if os.path.isfile(file_to_check): return True return False + + +def rich_force_colors(): + """ + Check if any environment variables are set to force Rich to use coloured output + """ + if os.getenv("GITHUB_ACTIONS") or os.getenv("FORCE_COLOR") or os.getenv("PY_COLORS"): + return True + return None From 4dd1d5ee850bd3252502ef6a5210d90084c6d271 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 14 Feb 2022 18:07:51 +0100 Subject: [PATCH 0034/1454] creating the methods for metadata class --- relecov_tools/read_metadata.py | 37 +++++++++++++++++++++++++++++++--- 1 file changed, 34 insertions(+), 3 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index a9babb7b..fc21d4ac 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -1,10 +1,12 @@ #!/usr/bin/env python -class ReadMetadata(): +class RelecovMetadata(): def __init__(): self.origin_file = file - slef.metadata = {} - + self.metadata = {} + self.isklims_db = iskylims_db + self.relecov_db = relecov_db + # reade_metadata def read_metadata_workflow(self): @@ -16,6 +18,35 @@ def __init__ (self, ): # Perform workflow details + +def check_new_metadata(folder): + """ Check if there is a new metadata to be processed + + folder Directory to be checked + """ + pass + +def fetch_metadata_file(folder, file_name): + """ Fetch the metadata file + folder Directory to fetch metadata file + file_name metadata file name + """ + pass + + +def add_extra_data (metadata_file, extra_data, result_metadata): + """ Add the additional information that must be included in final metadata + metadata Origin metadata file + extra_data additional data to be included + result_metadata final metadata after adding the additional data + """ + pass + +def store_in_database() + + + + wb_file = openpyxl.load_workbook(arguments.inputFile, data_only=True) ws_metadata_lab = wb_file['METADATA_LAB'] heading = [] From 81a1c654f0d7be9420e4b2ba61f2ef93ad0e3ac2 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 14 Feb 2022 18:08:15 +0100 Subject: [PATCH 0035/1454] creating the methods for metadata class --- relecov_tools/read_metadata.py | 27 +++++++++++++++++++++++---- 1 file changed, 23 insertions(+), 4 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index fc21d4ac..aabf818d 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -4,9 +4,9 @@ class RelecovMetadata(): def __init__(): self.origin_file = file self.metadata = {} - self.isklims_db = iskylims_db - self.relecov_db = relecov_db - + self.isklims_url = iskylims_url + self.relecov_url = relecov_url + # reade_metadata def read_metadata_workflow(self): @@ -33,6 +33,9 @@ def fetch_metadata_file(folder, file_name): """ pass + def validate_metadata_sample(row_sample): + """ Validate sample information + def add_extra_data (metadata_file, extra_data, result_metadata): """ Add the additional information that must be included in final metadata @@ -42,7 +45,23 @@ def add_extra_data (metadata_file, extra_data, result_metadata): """ pass -def store_in_database() +def request_information(external_url, request): + """ Get information from external database server using Rest API + + external_url + request + """ + pass + +def store_information (external_url, request, data): + """ Update information + + """ + pass + + + + From 1db8931e4fedc594634c94e9e97e47527c5fa30f Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 16 Feb 2022 15:52:03 +0100 Subject: [PATCH 0036/1454] cambios en schemas --- schema/ena_v01.json | 301 ++++++++------ schema/gisaid_V0.json | 148 +++++-- schema/phage_V0.json | 827 ++++++++++++++++++++++++++++++-------- schema/phage_plus_V0.json | 406 ++++++++++++------- 4 files changed, 1207 insertions(+), 475 deletions(-) diff --git a/schema/ena_v01.json b/schema/ena_v01.json index 3696df41..72bf14e6 100644 --- a/schema/ena_v01.json +++ b/schema/ena_v01.json @@ -25,39 +25,39 @@ "type": "object", "properties": { "sample_name": { - "examples": ["prov_rona_99"], - "ontology": "GENEPIO_0000079", - "type": "string", - "description": "The user-defined name for the sample.", - "clasification":"Database Identifiers", - "genepio_label":"sequencing run sample identifier", + "examples": ["prov_rona_99"], + "ontology": "GENEPIO:0001123", + "type": "string", + "description": "The user-defined name for the sample.", + "clasification":"Database Identifiers", + "label":"Collecting Sample id" }, "collecting_institution": { - "examples": ["Public Health Agency of Canada"], - "ontology": "GENEPIO_0001651", - "type": "string", - "description": "The name of the agency that collected the original sample.", - "genepio_label":"INSDC institution code", + "examples": ["Public Health Agency of Canada"], + "ontology": "GENEPIO:0001153", + "type": "string", + "description": "Name of the institution to which the person collecting the specimen belongs. Format: Institute Name, Institute Address", + "label":"Collecting Institution" }, "collection_date": { - "examples": ["19/03/2020"], + "examples": ["3/19/2020"], "ontology": "GENEPIO:0001174", "type": "string", - "description": "The date on which the sample was collected. ", - "format": "date", - "genepio_label":"", - + "description": "The date on which the sample was collected.", + "format":"date", + "classification":"Sample collection and processing", + "label":"Sample Collection Date" }, "receipt_date": { - "examples": ["20/03/2020"], + "examples": ["3/21/2020"], "ontology": "GENEPIO:0001179", "type": "string", "description": "The date on which the sample was received.", - "format": "date", - "genepio_label":"", - + "format":"date", + "clasification":"Sample collection and processing", + "label":"Sample Received Date" }, "geographic_location_(country_and/or_sea)": { "Enums": [ @@ -338,11 +338,12 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "GENEPIO_0000118", + "ontology": "GENEPIO:0001181 ", "type": "string", "description": "The country of origin of the sample.", "examples": ["South Africa [GAZ:00001094]"], - "genepio_label":"specimen collection location - country", + "clasification":"Sample collection and processing", + "label":"Geo Loc Autonomic Country" }, "geographic location (region and locality)": { @@ -350,7 +351,8 @@ "type": "string", "description": "The county/region of origin of the sample.", "examples": ["Derbyshire"], - "genepio_label":"", + "clasification":"Sample collection and processing", + "label":"Geo Loc Province" }, "geographic location (latitude)": { @@ -358,7 +360,8 @@ "type": "string", "description": "The latitude coordinates of the geographical location of sample collection.", "examples": ["38.98 N"], - "genepio_label":"", + "clasification":"Sample collection and processing", + "label":"Geo Loc Latitude", }, "geographic location (longitude)": { @@ -366,25 +369,8 @@ "type": "string", "description": "The longitude coordinates of the geographical location of sample collection.", "examples": ["77.11 W"], - "genepio_label":"", - - }, - "scientific_name": { - "Enums": [ - "Coronaviridae [NCBITaxon:11118]", - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001191", - "type": "string", - "description": "Taxonomic name of the organism.", - "examples": ["Severe acute respiratory syndrome coronavirus 2 "], - "genepio_label":"", - + "clasification":"Sample collection and processing", + "label":"Geo Loc Longitude" }, "isolate": { "ontology": "GENEPIO:0001644", @@ -392,6 +378,8 @@ "description": "Identifier of the specific isolate.", "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"], "genepio_label":"isolate identifier", + "clasification":"Sample collection and processing", + "label":"Isolate" }, "purpose_sampling": { @@ -422,9 +410,58 @@ "type": "string", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", "examples": ["Blood [UBERON:0000178]"], - "genepio_label":"", + "classification":"Sample collection and processing", + "label":"Organism Substance" }, + "isolation source non-host-associated": { + "Enums": [ + "Air vent [ENVO:03501208]", + "Banknote [ENVO:00003896]", + "Bed rail [ENVO:03501209]", + "Building Floor [ENVO:01000486]", + "Cloth [ENVO:02000058]", + "Control Panel [ENVO:03501210]", + "Door [ENVO:03501220]", + "Door Handle [ENVO:03501211]", + "Face Mask [OBI:0002787]", + "Face Shield [OBI:0002791]", + "Food [FOODON:00002403]", + "Food Packaging [FOODON:03490100]", + "Glass [ENVO:01000481]", + "Handrail [ENVO:03501212]", + "Hospital Gown [OBI:0002796]", + "Light Switch [ENVO:03501213]", + "Locker [ENVO:03501214]", + "N95 Mask [OBI:0002790]", + "Nurse Call Button [ENVO:03501215]", + "Paper [ENVO:03501256]", + "Particulate Matter [ENVO:01000060]", + "Plastic [ENVO:01000404]", + "PPE Gown [GENEPIO:0100025]", + "Sewage [ENVO:00002018]", + "Sink [ENVO:01000990]", + "Soil [ENVO:00001998]", + "Stainless Steel [ENVO:03501216]", + "Tissue Paper [ENVO:03501217]", + "Toilet Bowl [ENVO:03501218]", + "Water [ENVO:00002006]", + "Wastewater [ENVO:00002001]", + "Window [ENVO:03501219]", + "Wood [ENVO:00002040]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001223", + "type": "string", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "examples": ["Face Mask [OBI:0002787]"], + "clasification":"Sample collection and processing", + "label":"Environmental Material" + }, "host common name": { "Enums": [ "Human [NCBITaxon:9606]", @@ -446,11 +483,12 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "GENEPIO_0001724", + "ontology": "GENEPIO:0001386", "type": "string", "description": "The commonly used name of the host.", "examples": ["Human [NCBITaxon:9606]"], - "genepio_label":"subject organism common name", + "classification":"Host information", + "label":"Host Common Name" }, "host scientific name": { @@ -477,11 +515,12 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "GENEPIO_0001567", + "ontology": "GENEPIO:0001387", "type": "string", "description": "The taxonomic, or scientific name of the host.", "examples": ["Homo sapiens [NCBITaxon:9606]"], - "genepio_label":"subject organism (host) taxonomic species", + "clasification":"Host information", + "label":"Host Scientific Name" }, "host_health_state": { @@ -521,95 +560,125 @@ }, "type exposure": { "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO:0001417", "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", "clasification":"Host information", - "genepio_label":"", + "label":"Outbreak Exposure Event Location" }, "subject exposure duration": { "examples": ["e.g. Patient infected while traveling in …."], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", "clasification":"Host information", - "genepio_label":"", + "label":"Additional Host Information" }, "instrument_model": { - "Enums": ["454 Genome Sequencer [GENEPIO:0001937]", - "454 Genome Sequence 20 [OBI:0000689]", - "454 Genome Sequencer FLX [OBI:0000702]", - "454 Genome Sequencer FLX Titanium [GENEPIO:0001936]", - "454 Genome Sequencer Junior [GENEPIO:0001938]", - "AB SOLiD System [OBI:0000696]", - "SOLiD 3 Plus System [OBI:0002007]", - "SOLiD 4 [OBI:0002024]", - "SOLiD 4hq System [GENPIO:0001928]", - "SOLiD 5500 [GENPIO:0001929]", - "SOLiD 5500xl [GENPIO:0001930]", - "SOLiD PI System [GENPIO:0001931]", - "SOLiD System 2.0 [GENPIO:0001932]", - "SOLiD System 3.0 [GENPIO:0001933]", - "HeliScope Single Molecule Sequencer [OBI:0000717]", - "Illumina Genome Analyzer II [OBI:0000703]", - "Genome Analyzer IIe [OBI:0002027]", - "Genome Analyzer IIx [OBI:0002000]", - "Illumina HiSeq Sequencer [GENPIO:0001939]", - "Illumina HiSeq 1000 [OBI:0002022]", - "Illumina HiSeq 2000 [OBI:0002001]", - "Illumina HiSeq 2500 [OBI:0002002]", - "Illumina HiSeq 3000 [OBI:0002048]", - "Illumina HiSeq 4000 [OBI:0002049]", - "Ion Torrent PGM [GENPIO:0001935]", - "MiSeq [OBI:0002003]", - "NextSeq 500 [OBI:0002021]", - "PacBio RS II [OBI:0002012]", + "Enums": [ + "Illumina sequencing instrument [GENEPIO:0100105]", + "Illumina Genome Analyzer [GENEPIO:0100106]", + "Illumina Genome Analyzer II [GENEPIO:0100107]", + "Illumina Genome Analyzer IIx [GENEPIO:0100108]", + "Illumina HiScanSQ [GENEPIO:0100109]", + "Illumina HiSeq [GENEPIO:0100110]", + "Illumina HiSeq X [GENEPIO:0100111]", + "Illumina HiSeq X Five [GENEPIO:0100112]", + "Illumina HiSeq X Ten [GENEPIO:0100113]", + "Illumina HiSeq 1000 [GENEPIO:0100114]", + "Illumina HiSeq 1500 [GENEPIO:0100115]", + "Illumina HiSeq 2000 [GENEPIO:0100116]", + "Illumina HiSeq 2500 [GENEPIO:0100117]", + "Illumina HiSeq 3000 [GENEPIO:0100118]", + "Illumina HiSeq 4000 [GENEPIO:0100119]", + "Illumina iSeq [GENEPIO:0100120]", + "Illumina iSeq 100 [GENEPIO:0100121]", + "Illumina NovaSeq [GENEPIO:0100122]", + "Illumina NovaSeq 6000 [GENEPIO:0100123]", + "Illumina MiniSeq [GENEPIO:0100124]", + "Illumina MiSeq [GENEPIO:0100125]", + "Illumina NextSeq [GENEPIO:0100126]", + "Illumina NextSeq 500 [GENEPIO:0100127]", + "Illumina NextSeq 550 [GENEPIO:0100128]", + "Illumina NextSeq 2000 [GENEPIO:0100129]", + "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", + "PacBio RS [GENEPIO:0100131]", + "PacBio RS II [GENEPIO:0100132]", + "PacBio Sequel [GENEPIO:0100133]", + "PacBio Sequel II [GENEPIO:0100134]", + "Ion Torrent sequencing instrument [GENEPIO:0100135]", + "Ion Torrent PGM [GENEPIO:0100136]", + "Ion Torrent Proton [GENEPIO:0100137]", + "Ion Torrent S5 XL [GENEPIO:0100138]", + "Ion Torrent S5 [GENEPIO:0100139]", + "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", + "Oxford Nanopore GridION [GENEPIO:0100141]", + "Oxford Nanopore MinION [GENEPIO:0100142]", + "Oxford Nanopore PromethION [GENEPIO:0100143]", + "BGI Genomics sequencing instrument [GENEPIO:0100144]", + "BGI SEQ-500 [GENEPIO:0100145]", + "MGI sequencing instrument [GENEPIO:0100146]", + "MGI DNBSEQ-T7 [GENEPIO:0100147]", + "MGI DNBSEQ-G400 [GENEPIO:0100148]", + "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", + "MGI DNBSEQ-G50 [GENEPIO:0100150]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" ], - "ontology": "GENEPIO_0001921", + "ontology": "GENEPIO:0001452", "type": "string", "description": "The model of the sequencing instrument used.", - "examples": ["Oxford Nanopore MinION "], - "genepio_label":"sequencing instrument model", - + "examples": ["Oxford Nanopore MinION [GENEPIO:0100142]"], + "classification":"Sequencing", + "label":"Sequencing Instrument Model" }, "instrument_platform ": { "examples": ["MinIon"], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "The model of the sequencing instrument used.", - "genepio_label":"", - - }, - "file_name": { - "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], - "ontology": "GENEPIO:0001476", - "type": "string", - "description": "The user-specified filename of the r1 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", - "genepio_label":"", - - }, - "tax_id": { + "label":"Sequencing Platforms " + }, + "file_name": { + "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], + "ontology": "GENEPIO:0001476", + "type": "string", + "description": "The user-specified filename of the r1 FASTQ file.", + "clasification":"Bioinformatics and QC metrics", + "label":"Sequence file R1 fastq" + }, + "tax_id": { "examples": ["probably 2697049 in all cases"], "ontology": "GENEPIO:0001156", "type": "string", "description": "The NCBITaxon identifier for the organism being sequenced.", "clasification":"Sample collection and processing", - "genepio_label":"", - - }, - "scientific_name": { + "genepio_label":"" + }, + "scientific_name": { + "Enums": [ + "Coronaviridae [NCBITaxon:11118]", + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The taxonomic name of the organism.", - "clasification":"Sample collection and processing", - "genepio_label":"", - - }, - "common_name": { + "ontology": "GENEPIO:0001191", + "type": "string", + "description": "The taxonomic name of the organism.", + "clasification":"Sample collection and processing", + "classification":"Sample collection and processing", + "label":"Organism" + }, + "common_name": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", @@ -617,8 +686,8 @@ "clasification":"Sample collection and processing", "genepio_label":"", - }, - "sample_description": { + }, + "sample_description": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", @@ -626,15 +695,15 @@ "clasification":"Sample collection and processing", "genepio_label":"", - }, - "sample_storage_conditions": { + }, + "sample_storage_conditions": { "examples": ["24 degrees celsius"], "ontology": "NCIT_C115535", "type": "string", "description": "The name and version of a particular protocol used for sampling.", "clasification":"Sample collection and processing" - }, - "library_source": { + }, + "library_source": { "Enums": ["5-methycytidine antibody method [GENPIO:0001941]", "CAGE method [GENPIO:0001942]", "CF-H method [GENPIO:0001943]", diff --git a/schema/gisaid_V0.json b/schema/gisaid_V0.json index 7c01894b..c03fd1a3 100644 --- a/schema/gisaid_V0.json +++ b/schema/gisaid_V0.json @@ -5,7 +5,7 @@ "virus_name", "submitter", "originating_lab", - "address", + "collecting_address", "collection_date", "location", "host", @@ -18,60 +18,74 @@ "properties": { "type": { "examples": ["betacoronavirus"], - "ontology": "GENEPIO:0001156", + "ontology": "NCBITaxon:694002", "type": "string", - "description": "default must remain betacoronavirus", - "clasification":"Database Identifiers", + "description": "default must remain 'betacoronavirus'", + "clasification":"Database Identifiers" }, "virus_name": { - "examples": ["e.g. hCoV-19/Netherlands/Gelderland-01/2020 (Must be FASTA-Header from the FASTA file all_sequences.fasta)"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The user-defined GISAID virus name assigned to the sequence.", - "clasification":"Database Identifiers", + "examples": ["hCoV-19/Canada/prov_rona_99/2020"], + "ontology": "GENEPIO:0100282", + "type": "string", + "description": "The user-defined GISAID virus name assigned to the sequence.", + "clasification":"Database Identifiers", + "label":"GISAID Virus Name" }, "submitter": { - "examples": ["Public Health Agency of Canada"], - "ontology": "GENEPIO:0001156", + "examples": [""], + "ontology": "0", "type": "string", - "description": "enter your GISAID-Username", - "clasification":"Database Identifiers", + "description": "", + "clasification":"enter your GISAID-Username", + "label":"GISAID Username" }, "originating_lab": { - "examples": [""], - "ontology": "GENEPIO:0001156", + "examples": ["Public Health Agency of Canada"], + "ontology": "GENEPIO:0001153", "type": "string", - "description": "Where the clinical specimen or virus isolate was first obtained", - "clasification":"Sample collection and processing", + "description": "The name of the agency that collected the original sample.", + "label":"Collecting Institution" }, - "address": { - "examples": [""], - "ontology": "GENEPIO:0001156", + "collecting_address": { + "examples": ["655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada"], + "ontology": "GENEPIO:0001158", "type": "string", "description": "The mailing address of the agency submitting the sample.", "clasification":"Sample collection and processing", + "label":"Collecting Institution Address" }, - "collection_date": { - "examples": [""], - "ontology": "GENEPIO:0001156", + "submitting_address": { + "examples": ["123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"], + "ontology": "GENEPIO:0001167", "type": "string", - "description": "Date in the format YYYY or YYYY-MM or YYYY-MM-DD. Caution: collection date may be considered public health identifiable information. If this date is considered identifiable, it is acceptable to add 'jitter' to the collection date by adding or subtracting a calendar day (acceptable by GISAID). Do not change the collection date in your original records. Alternatively, ”received date” may be used as a substitute in the data you share. The date should be provided in ISO 8601 standard format YYYY-MM-DD.", - "format":"date", + "description": "The mailing address of the agency submitting the sequence.", "clasification":"Sample collection and processing", + "label":"Submitting Institution Address" + }, + "collection_date": { + "examples": ["3/19/2020"], + "ontology": "GENEPIO:0001174", + "type": "string", + "description": "The date on which the sample was collected.", + "format":"date", + "classification":"Sample collection and processing", + "label":"Sample Collection Date" }, "location": { "examples": ["e.g. Europe / Germany / Bavaria / Munich"], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO:0001181 ", "type": "string", "description": "The country of origin of the sample.", "clasification":"Sample collection and processing", + "label":"Geo Loc Autonomic Country" }, "host": { "examples": ["e.g. Human, Environment, Canine, Manis javanica, Rhinolophus affinis, etc"], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO:0001387", "type": "string", "description": "The taxonomic, or scientific name of the host.", "clasification":"Host information", + "label":"Host Scientific Name" }, "patient_age": { "Enums": [ @@ -96,7 +110,39 @@ "ontology": "GENEPIO:0001394", "type": "string", "description": "The age category of the host at the time of sampling.", - "clasification":"Host information", + "clasification":"Host information" + }, + "specimen_source": { + "Enums": [ + "Blood [UBERON:0000178]", + "Fluid [UBERON:0006314]", + "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", + "Fluid (Pericardial) [UBERON:0002409]", + "Fluid (Pleural) [UBERON:0001087]", + "Fluid (Vaginal) [UBERON:0036243]", + "Fluid (Amniotic) [UBERON:0000173]", + "Saliva [UBERON:0001836]", + "Tissue [UBERON:0000479]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001211", + "type": "string", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "examples": ["Blood [UBERON:0000178]"], + "classification":"Sample collection and processing", + "label":"Organism Substance" + }, + "Assembly method": { + "examples": ["Ivar"], + "ontology": "GENEPIO:0001463", + "type": "string", + "description": "The name of software used to generate the consensus sequence.", + "clasification":"Bioinformatics and QC metrics", + "label":"Consensus sequence software name" }, "gender": { "Enums": [ @@ -120,10 +166,27 @@ }, "sequencing_technology": { "examples": ["e.g. Illumina Miseq, Sanger, Nanopore MinION, Ion Torrent, etc."], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO:0001452", "type": "string", "description": "The model of the sequencing instrument used.", - "clasification":"Sequencing", + "classification":"Sequencing", + "label":"Sequencing Instrument Model" + }, + "authors": { + "examples": [""], + "ontology": "GENEPIO:0001517", + "type": "string", + "description": "", + "clasification":"Contributor Acknowledgement", + "label":"Authors" + }, + "coverage": { + "examples": ["400x"], + "ontology": "GENEPIO:0001474", + "type": "string", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "clasification":"Bioinformatics and QC metrics", + "label":"Depth of coverage value " }, "fasta_filename": { "examples": ["e.g. all_sequences.fasta not c:\users\meier\docs\all_sequences.fasta"], @@ -134,10 +197,11 @@ }, "additional_host_information": { "examples": ["e.g. Patient infected while traveling in …."], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", "clasification":"Host information", + "label":"Additional Host Information" }, "Last vaccinated": { "examples": ["e.g. 04/09/2021"], @@ -149,18 +213,34 @@ }, "outbreak": { "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO:0001417", "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", "clasification":"Host information", + "label":"Outbreak Exposure Event Location" }, "Sampling Strategy": { "examples": ["e.g. Sentinel surveillance (ILI), Sentinel surveillance (ARI), Sentinel surveillance (SARI), Non-sentinel-surveillance (hospital), Non-sentinel-surveillance (GP network), Longitudinal sampling on same patient(s), S gene dropout"], - "ontology": "GENEPIO:", + "ontology": "GENEPIO:0001445", "type": "string", "description": "The reason that the sample was sequenced.", - "clasification":"Sequencing", + "classification":"Sequencing", + "label":"Purpose of Sequencing" }, + "submitting_lab_sequence_id": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "Sample ID given by the submitting laboratory", + "clasification":"Database Identifiers" + }, + "submitting_lab": { + "examples": ["Centers for Disease Control and Prevention"], + "ontology": "GENEPIO:0001159", + "type": "string", + "description": "The name of the agency that generated the sequence.", + "label":"Submitting Institution" + } } } diff --git a/schema/phage_V0.json b/schema/phage_V0.json index bf7c2597..9155f85a 100644 --- a/schema/phage_V0.json +++ b/schema/phage_V0.json @@ -22,13 +22,16 @@ "ontology": "GENEPIO:0001156", "type": "string", "description": "The email address of the contact responsible for follow-up regarding the sample.", - "format": "email" + "clasification":"Sample collection and processing", + "label":"Collecting Institution Email" }, "depth_of_coverage_value": { + "examples": ["400x"], "ontology": "GENEPIO:0001474", - "type": "number", + "type": "string", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "examples": [400.0] + "clasification":"Bioinformatics and QC metrics", + "label":"Depth of coverage value " }, "exposure_details": { "ontology": "GENEPIO:0001431", @@ -37,10 +40,12 @@ "examples": ["Host role - Other: Bus Driver"] }, "breadth_of_coverage_value": { + "examples": ["95%"], "ontology": "GENEPIO:0001472", - "type": "number", + "type": "string", "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", - "examples": [0.95] + "clasification":"Bioinformatics and QC metrics", + "label":"Breadth of coverage value" }, "most_recent_travel_departure_date": { "examples": ["16/03/2020"], @@ -50,13 +55,37 @@ "format": "date" }, "sequencing_protocol": { - "ontology": "GENEPIO:0001454", - "type": "string", - "description": "The protocol used to generate the sequence.", - "examples": [ - "Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits." - ] - }, + "examples": ["Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits."], + "ontology": "GENEPIO:0001454", + "type": "string", + "description": "The protocol used to generate the sequence.", + "clasification":"Sequencing", + "label":"Sequencing Protocol" + }, + "%Ns": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing", + "label":"%Ns" + }, + "Number_of_variants_(AF_greater_75%)": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing", + "label":"Number of variants (AF greater 75%)" + }, + "Numer_of_variants_with_effect": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing", + "label":"Numer of variants with effect" + }, "host_age_bin": { "Enums": [ "0 - 9 [GENEPIO:0100049]", @@ -101,20 +130,27 @@ "ontology": "GENEPIO:0001211", "type": "string", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "examples": ["Blood [UBERON:0000178]"] + "examples": ["Blood [UBERON:0000178]"], + "classification":"Sample collection and processing", + "label":"Organism Substance" + }, "sample_collection_date": { - "examples": ["19/03/2020"], + "examples": ["3/19/2020"], "ontology": "GENEPIO:0001174", "type": "string", - "description": "The date on which the sample was collected. ", - "format": "date" + "description": "The date on which the sample was collected.", + "format":"date", + "classification":"Sample collection and processing", + "label":"Sample Collection Date" }, - "diagnostic_pcr_ct_value_2": { + "diagnostic_pcr_Ct_value_2": { + "examples": ["36"], "ontology": "GENEPIO:0001512", - "type": "integer", + "type": "string", "description": "The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "examples": [36] + "clasification":"Pathogen diagnostic testing", + "label":"Diagnostic Pcr Ct Value-2" }, "number_of_vaccine_doses_received": { "ontology": "GENEPIO:0001406", @@ -149,7 +185,9 @@ "ontology": "GENEPIO:0001255", "type": "string", "description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.", - "examples": ["Vero E6 Cell Line [BTO:0004755]"] + "examples": ["Vero E6 Cell Line [BTO:0004755]"], + "classification":"Sample collection and processing", + "label":"Lab passage Host" }, "anatomical_part": { "Enums": [ @@ -186,7 +224,9 @@ "ontology": "GENEPIO:0001214", "type": "string", "description": "An anatomical part of an organism e.g. oropharynx. ", - "examples": ["Nasopharynx (NP) [UBERON:0001728]"] + "examples": ["Nasopharynx (NP) [UBERON:0001728]"], + "classification":"Sample collection and processing", + "label":"Anatomical Structure" }, "host_health_outcome": { "Enums": [ @@ -205,24 +245,38 @@ "description": "Disease outcome in the host.", "examples": ["Recovered [NCIT:C49498]"] }, + "rna_extraction_protocol": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"Rna Extraction Protocol" + }, "sequencing_date": { "examples": ["22/06/2020"], "ontology": "GENEPIO:0001447", "type": "string", "description": "The date the sample was sequenced.", - "format": "date" + "format": "date", + "clasification":"Sequencing", + "label":"Sequencing date" }, "passage_number": { "ontology": "GENEPIO:0001261", "type": "integer", "description": "Number of passages.", - "examples": [3] + "examples": [3], + "clasification":"Sample collection and processing", + "label":"Passage Number" }, "ns_per_100_kbp": { + "examples": ["300"], "ontology": "GENEPIO:0001484", - "type": "integer", + "type": "string", "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", - "examples": [300] + "clasification":"Bioinformatics and QC metrics", + "label":"Ns per 100 kbp" }, "case_id": { "ontology": "GENEPIO:0100281", @@ -231,11 +285,12 @@ "examples": ["ABCD1234"] }, "biosample_accession": { - "pattern": "^SAM(D|N|E([AG]?))[0-9]+", + "examples": ["SAMN14180202"], "ontology": "GENEPIO:0001139", "type": "string", "description": "The identifier assigned to a BioSample in INSDC archives.", - "examples": ["SAMN14180202"] + "clasification":"Database Identifiers", + "label":"Biosample accession ENA" }, "last_dose_vacicnation_date": { "examples": ["09/04/2021"], @@ -245,12 +300,76 @@ "format": "date" }, "bioinformatics_protocol": { + "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], "ontology": "GENEPIO:0001489", "type": "string", - "description": "The name and version number of the bioinformatics protocol used.", - "examples": [ - "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" - ] + "description": "The name of the bioinformatics protocol used.", + "clasification":"Bioinformatics and QC metrics", + "label":"Bioinformatics protocol" + }, + "if_bioinformatic_protocol_is_other_specify": { + "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], + "ontology": "0", + "type": "string", + "description": "The name of the bioinformatics protocol used.", + "clasification":"Bioinformatics and QC metrics", + "label":"If bioinformatic protocol Is Other, Specify" + }, + "bioinformatic_protocol_version": { + "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], + "ontology": "0", + "type": "string", + "description": "The version number of the bioinformatics protocol used.", + "clasification":"Bioinformatics and QC metrics", + "label":"bioinformatics protocol version" + }, + "preprocessing": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Preprocessing" + }, + "if_preprocessing_other": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"If preprocessing Is Other, Specify" + }, + "preprocessing_params": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Preprocessing params" + }, + "mapping": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Lineage and Variant information", + "label":"Mapping" + }, + "mapping_params": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Lineage and Variant information", + "label":"Mapping params" + }, + "commercial/open-source/both": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Commercial/Open-source/both" }, "prior_sars_cov_2_antiviral_treatment": { "Enums": [ @@ -311,7 +430,9 @@ "ontology": "GENEPIO:0001510", "type": "string", "description": "The name of the gene used in the diagnostic RT-PCR test.", - "examples": ["RdRp gene (nsp12) [GENEPIO:0100168]"] + "examples": ["RdRp gene (nsp12) [GENEPIO:0100168]"], + "classification":"Pathogen diagnostic testing", + "label":"Gene Name 2" }, "body_product": { "Enums": [ @@ -332,7 +453,9 @@ "ontology": "GENEPIO:0001216", "type": "string", "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", - "examples": ["Feces [UBERON:0001988]"] + "examples": ["Feces [UBERON:0001988]"], + "classification":"Sample collection and processing", + "label":"Body product" }, "host_age": { "ontology": "GENEPIO:0001392", @@ -377,7 +500,9 @@ "ontology": "GENEPIO:0001234", "type": "string", "description": "The instrument or container used to collect the sample e.g. swab.", - "examples": ["Swab [GENEPIO:0100027]"] + "examples": ["Swab [GENEPIO:0100027]"], + "clasification":"Sample collection and processing", + "label":"Collection Device" }, "purpose_of_sequencing": { "Enums": [ @@ -414,25 +539,33 @@ "ontology": "GENEPIO:0001445", "type": "string", "description": "The reason that the sample was sequenced.", - "examples": ["Baseline surveillance (random sampling) [GENEPIO:0100005]"] + "examples": ["Baseline surveillance (random sampling) [GENEPIO:0100005]"], + "classification":"Sequencing", + "label":"Purpose of Sequencing" }, "raw_sequence_data_processing_method": { + "examples": ["Porechop 0.2.3"], "ontology": "GENEPIO:0001458", "type": "string", "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", - "examples": ["Porechop 0.2.3,Porechop 0.2.3"] + "clasification":"Bioinformatics and QC metrics", + "label":"Raw sequence data processin method" }, "sequence_submitter_contact_address": { + "examples": ["123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"], "ontology": "GENEPIO:0001167", "type": "string", "description": "The mailing address of the agency submitting the sequence.", - "examples": ["123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"] + "clasification":"Sample collection and processing", + "label":"Submitting Institution Address" }, "depth_of_coverage_threshold": { - "ontology": "GENEPIO:0001475", - "type": "number", + "examples": ["100x"], + "ontology": "GENEPIO:0001475", + "type": "string", "description": "The threshold used as a cut-off for the depth of coverage.", - "examples": [100.0] + "clasification":"Bioinformatics and QC metrics", + "label":"Depth of coverage threshold" }, "specimen_processing": { "Enums": [ @@ -448,19 +581,17 @@ "ontology": "GENEPIO:0001253", "type": "string", "description": "Any processing applied to the sample during or after receiving the sample. ", - "examples": ["Virus Passage [GENEPIO:0100039]"] - }, - "flow_cell_barcode": { - "ontology": "GENEPIO:0001451", - "type": "string", - "description": "The barcode of the flow cell used for sequencing.", - "examples": ["FAB06069"] + "examples": ["Virus Passage [GENEPIO:0100039]"], + "classification":"Sample collection and processing", + "label":"Specimen Processing" }, "r1_fastq_filename": { + "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], "ontology": "GENEPIO:0001476", "type": "string", "description": "The user-specified filename of the r1 FASTQ file.", - "examples": ["ABC123_S1_L001_R1_001.fastq.gz"] + "clasification":"Bioinformatics and QC metrics", + "label":"Sequence file R1 fastq" }, "destination_of_most_recent_travel_city": { "ontology": "GENEPIO:0001411", @@ -469,19 +600,77 @@ "examples": ["New York City"] }, "r1_fastq_filepath": { + "examples": ["/User/Documents/RespLab/Data/"], "ontology": "GENEPIO:0001478", "type": "string", "description": "The filepath of the r1 FASTQ file.", - "examples": [ - "/User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz" - ] + "clasification":"Bioinformatics and QC metrics", + "label":"Filepath R1 fastq" }, "library_id": { "ontology": "GENEPIO:0001448", "type": "string", "description": "The user-specified identifier for the library prepared for sequencing.", - "examples": ["XYZ_123345"] - }, + "examples": ["XYZ_123345"], + "clasification":"Sequencing", + "labe":"Library Id" + }, + "enrichment_protocol": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"Enrichment_protocol" + }, + "if_enrichment_protocol_is_other_specify": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"If Enrichment Protocol Is Other, Specify" + }, + "if_consensus_other": { + "examples": ["1.3"], + "ontology": "0", + "type": "string", + "description": "The version of the software used to generate the consensus sequence.", + "clasification":"Bioinformatics and QC metrics", + "label":"If consensus Is Other, Specify" + }, + "if_mapping_other": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Lineage and Variant information", + "label":"If mapping Is Other, Specify" + }, + "amplicon protocol": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"Amplicon Protocol" + }, + "if_amplicon_protocol_if_other_especify": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "labe":"If Amplicon Protocol If Other, Especify" + }, + "amplicon_version": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"Amplicon Version" + }, "host_vaccination_status": { "Enums": [ "Fully Vaccinated [GENEPIO:0100100]", @@ -502,27 +691,49 @@ "ontology": "OBI:0001621", "type": "string", "description": "The longitude coordinates of the geographical location of sample collection.", - "examples": ["77.11 W"] + "examples": ["77.11 W"], + "clasification":"Sample collection and processing", + "label":"Geo Loc Longitude" }, "genbank_ena_ddbj_accession": { - "pattern": "^([a-zA-Z]{2})\\d*.\\d{1}", + "examples": ["MN908947.3"], "ontology": "GENEPIO:0001145", "type": "string", "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", - "examples": ["MN908947.3"] + "clasification":"Database Identifiers", + "label":"GenBank/ENA/DDBJ accession" }, "bioproject_accession": { - "pattern": "^PRJ(N|E|D)([a-zA-Z]?)[0-9]+*", + "examples": ["PRJNA12345"], "ontology": "GENEPIO:0001136", "type": "string", - "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs. ", - "examples": ["PRJNA12345"] + "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", + "clasification":"Database Identifiers", + "label":"Bioproject accession ENA" }, - "lineage_clade_analysis_software_name": { + "lineage/clade_analysis_software_name": { + "examples": ["Pangolin"], "ontology": "GENEPIO:0001501", "type": "string", "description": "The name of the software used to determine the lineage/clade.", - "examples": ["Pangolin"] + "clasification":"Lineage and Variant information", + "label":"lineage/clade analysis software name" + }, + "analysis_author": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Contributor Acknowledgement", + "label":"Analysis Authors" + }, + "if_lineage_identification_other": { + "examples": ["Other than Pangolin"], + "ontology": "0", + "type": "string", + "description": "The name of the software used to determine the lineage/clade.", + "clasification":"Lineage and Variant information", + "label":"If lineage identification Is Other, Specify" }, "location_of_exposure_geo_loc_name_country": { "Enums": [ @@ -803,7 +1014,7 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "GENEPIO:0001410", + "ontology": "GENEPIO:0001181", "type": "string", "description": "The country where the host was likely exposed to the causative agent of the illness.", "examples": ["South Africa [GAZ:00001094]"] @@ -822,22 +1033,44 @@ "format": "date" }, "library_preparation_kit": { - "ontology": "GENEPIO:0001450", - "type": "string", - "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", - "examples": ["Nextera XT"] + "examples": ["Nextera XT"], + "ontology": "GENEPIO:0001450", + "type": "string", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "clasification":"Sequencing", + "label":"Library Preparation Kit" + }, + "flow_cell_barcode": { + "examples": ["FAB06069"], + "ontology": "GENEPIO:0001451", + "type": "string", + "description": "The barcode of the flow cell used for sequencing.", + "clasification":"Sequencing", + "label":"Flow Cell Barcode" + }, + "library_kit": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"Library Kit" }, "fast5_filename": { + "examples": ["batch1a_sequences.fast5"], "ontology": "GENEPIO:0001480", "type": "string", "description": "The user-specified filename of the FAST5 file.", - "examples": ["batch1a_sequences.fast5"] + "clasification":"Bioinformatics and QC metrics", + "label":"Filename fast5" }, - "diagnostic_pcr_ct_value_1": { + "diagnostic_pcr_Ct_value_1": { + "examples": ["21"], "ontology": "GENEPIO:0001509", - "type": "integer", + "type": "string", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "examples": [21] + "clasification":"Pathogen diagnostic testing", + "label":"Diagnostic Pcr Ct Value 1" }, "collection_method": { "Enums": [ @@ -871,7 +1104,9 @@ "ontology": "GENEPIO:0001241", "type": "string", "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", - "examples": ["Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]"] + "examples": ["Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]"], + "clasification":"Sample collection and processing", + "label":"Collection Method" }, "geo_loc_name_county_region": { "ontology": "GENEPIO:0100280", @@ -880,18 +1115,28 @@ "examples": ["Derbyshire"] }, "consensus_genome_length": { + "examples": ["38677"], "ontology": "GENEPIO:0001483", - "type": "integer", + "type": "string", "description": "Size of the assembled genome described as the number of base pairs.", - "examples": [38677] + "clasification":"Bioinformatics and QC metrics", + "label":"Consensus genome length" }, "r2_fastq_filepath": { + "examples": ["/User/Documents/RespLab/Data/"], "ontology": "GENEPIO:0001479", "type": "string", "description": "The filepath of the r2 FASTQ file.", - "examples": [ - "/User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz" - ] + "clasification":"Bioinformatics and QC metrics", + "label":"Filepath R2 fastq" + }, + "consensus_criteria": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Consensus criteria" }, "destination_of_most_recent_travel_state_province_territory": { "ontology": "GENEPIO:0001412", @@ -899,12 +1144,22 @@ "description": "The name of the province that was the destination of most recent travel.", "examples": ["California"] }, - "sample_received_date": { - "examples": ["20/03/2020"], + "reception_date": { + "examples": ["3/21/2020"], "ontology": "GENEPIO:0001179", "type": "string", "description": "The date on which the sample was received.", - "format": "date" + "format":"date", + "clasification":"Sample collection and processing", + "label":"Sample Received Date" + }, + "quality_control_metrics": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Quality control metrics " }, "host_common_name": { "Enums": [ @@ -930,13 +1185,17 @@ "ontology": "GENEPIO:0001386", "type": "string", "description": "The commonly used name of the host.", - "examples": ["Human [NCBITaxon:9606]"] + "examples": ["Human [NCBITaxon:9606]"], + "classification":"Host information", + "label":"Host Common Name" }, "geo_loc_name_state_province_territory": { "ontology": "GENEPIO:0001185", "type": "string", "description": "The state/province/territory of origin of the sample.", - "examples": ["Western Cape"] + "examples": ["Western Cape"], + "classification":"Sample collection and processing", + "label":"Geo Loc Autonomic Community" }, "lineage_clade_analysis_software_version": { "ontology": "GENEPIO:0001502", @@ -951,17 +1210,28 @@ "examples": ["BCxy123"] }, "sra_accession": { - "pattern": "^(SRR|ERR|DRR)[0-9]+", - "ontology": "GENEPIO:0001142", + "examples": ["SRR11177792"], + "ontology": "GENEPIO:0001142", + "type": "string", + "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", + "clasification":"Database Identifiers", + "label":"SRA accession" + }, + "author_submitter": { + "examples": [""], + "ontology": "0", "type": "string", - "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "examples": ["SRR11177792"] + "description": "", + "clasification":"Contributor Acknowledgement", + "label":"Author Submitter" }, "authors": { + "examples": [""], "ontology": "GENEPIO:0001517", "type": "string", - "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", - "examples": ["Tejinder Singh, Fei Hu, Johnny Blogs"] + "description": "", + "clasification":"Contributor Acknowledgement", + "label":"Authors" }, "host_role": { "Enums": [ @@ -1013,12 +1283,37 @@ "description": "The name of the consensus sequence.", "examples": ["ncov123assembly3"] }, + "assembly": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Assembly" + }, + "if_assembly_other": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"If assembly Is Other, Specify" + }, + "assembly_params": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Assambly params" + }, "gisaid_accession": { - "pattern": "^EPI_ISL_\\d*", - "ontology": "GENEPIO:0001147", + "examples": ["hCoV-19/Canada/prov_rona_99/2020"], + "ontology": "GENEPIO:0100282", "type": "string", - "description": "The GISAID accession number assigned to the sequence.", - "examples": ["EPI_ISL_123456"] + "description": "The user-defined GISAID virus name assigned to the sequence.", + "clasification":"Database Identifiers", + "label":"GISAID Virus Name" }, "geo_loc_name_country": { "Enums": [ @@ -1302,19 +1597,24 @@ "ontology": "GENEPIO:0001181", "type": "string", "description": "The country of origin of the sample.", - "examples": ["South Africa [GAZ:00001094]"] + "examples": ["South Africa [GAZ:00001094]"], + "label":"Geo Loc Autonomic Country" }, "consensus_sequence_filepath": { + "examples": ["/User/Documents/RespLab/Data/ncov123assembly.fasta"], "ontology": "GENEPIO:0001462", "type": "string", "description": "The filepath of the consesnsus sequence file.", - "examples": ["/User/Documents/RespLab/Data/ncov123assembly.fasta"] + "clasification":"Bioinformatics and QC metrics", + "label":"Consensus sequence filepath" }, "number_of_base_pairs_sequenced": { + "examples": ["387566"], "ontology": "GENEPIO:0001482", - "type": "integer", + "type": "string", "description": "The number of total base pairs generated by the sequencing process.", - "examples": [387566] + "clasification":"Bioinformatics and QC metrics", + "label":"Number of base pairs sequenced " }, "destination_of_most_recent_travel_country": { "ontology": "GENEPIO:0001413", @@ -1323,10 +1623,12 @@ "examples": ["United Kingdom"] }, "fast5_filepath": { + "examples": ["/User/Documents/RespLab/Data/"], "ontology": "GENEPIO:0001481", "type": "string", "description": "The filepath of the FAST5 file.", - "examples": ["/User/Documents/RespLab/Data/rona123assembly.fast5"] + "clasification":"Bioinformatics and QC metrics", + "label":"Filepath fast5" }, "culture_collection": { "ontology": "GENEPIO:0100284", @@ -1334,31 +1636,62 @@ "description": "The name of the source collection and unique culture identifier. ", "examples": ["/culture_collection=\"ATCC:26370\""] }, + "was_phix_used?": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"Was Phix Used" + }, + "number_of_samples_in_run": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"Number Of Samples In Run" + }, "amplicon_size": { - "ontology": "GENEPIO:0001449", - "type": "string", - "description": "The length of the amplicon generated by PCR amplification.", - "examples": ["300bp"] + "examples": ["300bp"], + "ontology": "GENEPIO:0001449", + "type": "string", + "description": "The length of the amplicon generated by PCR amplification.", + "clasification":"Sequencing", + "label":"Amplicon Size" + }, + "flowcell_kit": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "labe":"Flowcell Kit" }, "sample_collector_contact_address": { + "examples": ["655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada"], "ontology": "GENEPIO:0001158", "type": "string", "description": "The mailing address of the agency submitting the sample.", - "examples": ["655 Lab St,Vancouver, British Columbia, V5N 2A2, Canada"] + "clasification":"Sample collection and processing", + "label":"Collecting Institution Address" }, "collection_protocol": { "ontology": "GENEPIO:0001243", "type": "string", "description": "The name and version of a particular protocol used for sampling.", - "examples": ["SC2SamplingProtocol 1.2"] + "examples": ["SC2SamplingProtocol 1.2"], + "clasification":"Sample collection and processing", + "label":"Collection Protocol" + }, "variant_evidence": { - "ontology": "GENEPIO:0001504", + "examples": ["lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)"], + "ontology": "GENEPIO:0001504", "type": "string", "description": "The evidence used to make the variant determination.", - "examples": [ - "lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)" - ] + "clasification":"Lineage and Variant information", + "label":"Variant evidence" }, "most_recent_travel_return_date": { "examples": ["26/04/2020"], @@ -1384,6 +1717,21 @@ "description": "The exposure transmission contact type.", "examples": ["Direct (human-to-human contact) [TRANS:0000001]"] }, + "runID": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"RunID" + }, + "sequencing_instrument_platform": { + "examples": ["MinIon"], + "ontology": "0", + "type": "string", + "description": "The model of the sequencing instrument used.", + "label":"Sequencing Platforms " + }, "prior_sars_cov_2_infection": { "Enums": [ "Prior infection [GENEPIO:0100234]", @@ -1406,10 +1754,12 @@ "examples": ["hCoV-19/Canada/prov_rona_99/2020"] }, "specimen_collector_sample_id": { + "examples": ["prov_rona_99"], "ontology": "GENEPIO:0001123", "type": "string", - "description": "The user-defined name for the sample. ", - "examples": ["prov_rona_99"] + "description": "The user-defined name for the sample.", + "clasification":"Database Identifiers", + "label": "Collecting Sample id" }, "host_scientific_name": { "Enums": [ @@ -1438,7 +1788,9 @@ "ontology": "GENEPIO:0001387", "type": "string", "description": "The taxonomic, or scientific name of the host.", - "examples": ["Homo sapiens [NCBITaxon:9606]"] + "examples": ["Homo sapiens [NCBITaxon:9606]"], + "clasification":"Host information", + "label":"Host Scientific Name" }, "host_disease": { "Enums": [ @@ -1459,28 +1811,79 @@ "type": "string", "description": "Description of how organism was passaged.", "examples": [ - "AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain." - ] + "AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain.",], + "clasification":"Sample collection and processing", + "label":"Passage Method" + }, + "%qc_filtered": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing", + "label":"%qc filtered" + }, + "%reads_host": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing", + "label":"%reads host" + }, + "%reads_virus": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing", + "label":"%reads virus" + }, + "%unmapped": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing", + "label":"%unmapped" + }, + "%genome _greater_10x": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing", + "label":"% genome greater 10x" + }, + "mean_depth_of_coverage_value": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing", + "label":"mean depth of coverage value" }, "symptom_onset_date": { - "examples": ["16/03/2020"], - "ontology": "GENEPIO:0001399", - "type": "string", - "description": "The date on which the symptoms began or were first noted.", - "format": "date" - }, - "r2_fastq_filename": { - "ontology": "GENEPIO:0001477", - "type": "string", - "description": "The user-specified filename of the r2 FASTQ file.", - "examples": ["ABC123_S1_L001_R2_001.fastq.gz"] + "examples": ["16/03/2020"], + "ontology": "GENEPIO:0001399", + "type": "string", + "description": "The date on which the symptoms began or were first noted.", + "format": "date" + }, + "r2 fastq filename": { + "examples": ["ABC123_S1_L001_R2_001.fastq.gz"], + "ontology": "GENEPIO:0001477", + "type": "string", + "description": "The user-specified filename of the r2 FASTQ file.", + "clasification":"Bioinformatics and QC metrics", + "label":"Sequence file R2 fastq" }, "prior_sars_cov_2_infection_date": { - "examples": ["23/01/2021"], - "ontology": "GENEPIO:0001437", - "type": "string", - "description": "The date of diagnosis of the prior SARS-CoV-2 infection.", - "format": "date" + "examples": ["23/01/2021"], + "ontology": "GENEPIO:0001437", + "type": "string", + "description": "The date of diagnosis of the prior SARS-CoV-2 infection.", + "format": "date" }, "exposure_event": { "Enums": [ @@ -1511,10 +1914,12 @@ "examples": ["Mass Gathering [GENEPIO:0100237]"] }, "sequencing_kit_number": { - "ontology": "GENEPIO:0001455", - "type": "string", - "description": "The manufacturer's kit number.", - "examples": ["AB456XYZ789"] + "examples": ["AB456XYZ789"], + "ontology": "GENEPIO:0001455", + "type": "string", + "description": "The manufacturer's kit number.", + "clasification":"Sequencing", + "label":"Sequencing Kit Number" }, "purpose_of_sampling_details": { "ontology": "GENEPIO:0001200", @@ -1547,17 +1952,21 @@ "description": "The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection.", "examples": ["Remdesivir"] }, - "diagnostic_pcr_protocol_2": { - "ontology": "GENEPIO:0001511", + "diagnostic_pcr_protocol_1": { + "examples": ["PCREGene 2.0"], + "ontology": "GENEPIO:0001508", "type": "string", "description": "The name and version number of the protocol used for diagnostic marker amplification.", - "examples": ["PCRRdRpGene 3.0"] + "clasification":"Pathogen diagnostic testing", + "label":"Diagnostic Pcr Protocol 1" }, - "diagnostic_pcr_protocol_1": { - "ontology": "GENEPIO:0001508", + "diagnostic_pcr_protocol_2": { + "examples": ["PCRRdRpGene 3.0"], + "ontology": "GENEPIO:0001511", "type": "string", "description": "The name and version number of the protocol used for diagnostic marker amplification.", - "examples": ["PCREGene 2.0"] + "clasification":"Pathogen diagnostic testing", + "label":"Diagnostic Pcr Protocol 2" }, "host_specimen_voucher": { "ontology": "GENEPIO:0100283", @@ -1692,20 +2101,34 @@ "ontology": "GENEPIO:0001507", "type": "string", "description": "The name of the gene used in the diagnostic RT-PCR test.", - "examples": ["E gene (orf4) [GENEPIO:0100151]"] + "examples": ["E gene (orf4) [GENEPIO:0100151]"], + "classification":"Pathogen diagnostic testing", + "label":"Gene Name 1" + }, + "Protocol_SARS-CoV-2_detection": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing", + "label":"Protocol SARS-CoV-2 detection" }, "consensus_sequence_software_name": { + "examples": ["Ivar"], "ontology": "GENEPIO:0001463", "type": "string", "description": "The name of software used to generate the consensus sequence.", - "examples": ["Ivar"] + "clasification":"Bioinformatics and QC metrics", + "label":"Consensus sequence software name" }, "reference_genome_accession": { + "examples": [""], "ontology": "GENEPIO:0001485", "type": "string", - "description": "A persistent, unique identifier of a genome database entry.", - "examples": ["NC_045512.2"] - }, + "description": "", + "clasification":"Pathogen diagnostic testing", + "label":"reference genome accession" + }, "host_residence_geo_loc_name_country": { "Enums": [ "Afghanistan [GAZ:00006882]", @@ -1996,11 +2419,13 @@ "description": "Travel history in last six months.", "examples": ["Canada, Vancouver, USA, Seattle, Italy, Milan"] }, - "consensus_sequence_software_version": { - "ontology": "GENEPIO:0001469", + "lineage/clade_analysis_software_version": { + "examples": ["2.1.10"], + "ontology":"GENEPIO:0001502", "type": "string", - "description": "The version of the software used to generate the consensus sequence.", - "examples": ["1.3"] + "description": "The version of the software used to determine the lineage/clade.", + "clasification":"Lineage and Variant information", + "label":"Lineage/clade analysis software version" }, "complications": { "Enums": [ @@ -2097,14 +2522,17 @@ "ontology": "GENEPIO:0001189", "type": "string", "description": "The city of origin of the sample.", - "examples": ["Vancouver"] + "examples": ["Vancouver"], + "clasification":"Sample collection and processing", + "label":"Geo Loc City" }, - "umbrella_bioproject_accession": { - "pattern": "^PRJ(N|E|D)([a-zA-Z]?)[0-9]+*", - "ontology": "GENEPIO:0001133", + "bioproject umbrella accession": { + "examples": ["PRJNA623807"], + "ontology": "GENEPIO:0001133", "type": "string", - "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs. ", - "examples": ["PRJNA623807"] + "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", + "clasification":"Database Identifiers", + "label":"umbrella bioproject accession", }, "biomaterial_extracted": { "Enums": [ @@ -2121,7 +2549,9 @@ "ontology": "GENEPIO:0001266", "type": "string", "description": "The biomaterial extracted from samples for the purpose of sequencing.", - "examples": ["RNA (Total) [OBI:0000895]"] + "examples": ["RNA (Total) [OBI:0000895]"], + "classification":"Sample collection and processing", + "label":"Biomaterial Extracted" }, "host_age_unit": { "Enums": [ @@ -2142,7 +2572,9 @@ "ontology": "OBI:0001620", "type": "string", "description": "The latitude coordinates of the geographical location of sample collection.", - "examples": ["38.98 N"] + "examples": ["38.98 N"], + "clasification":"Sample collection and processing", + "label":"Geo Loc Latitude", }, "environmental_material": { "Enums": [ @@ -2188,14 +2620,17 @@ "ontology": "GENEPIO:0001223", "type": "string", "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", - "examples": ["Face Mask [OBI:0002787]"] + "examples": ["Face Mask [OBI:0002787]"], + "clasification":"Sample collection and processing", + "label":"Environmental Material" }, "sequence_submitter_contact_email": { "examples": ["RespLab@lab.ca"], "ontology": "GENEPIO:0001165", "type": "string", "description": "The email address of the contact responsible for follow-up regarding the sequence.", - "format": "email" + "clasification":"Sample collection and processing", + "label":"Submitting Institution Email" }, "environmental_site": { "Enums": [ @@ -2229,7 +2664,9 @@ "ontology": "GENEPIO:0001232", "type": "string", "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", - "examples": ["Hospital [ENVO:00002173]"] + "examples": ["Hospital [ENVO:00002173]"], + "classification":"Sample collection and processing", + "label":"Anthropogenic Geographic Feature" }, "pre_existing_conditions_and_risk_factors": { "Enums": [ @@ -2351,7 +2788,33 @@ "ontology": "GENEPIO:0001503", "type": "string", "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", - "examples": ["Variant of Concern (VOC) [GENEPIO:0100083]"] + "examples": ["Variant of Concern (VOC) [GENEPIO:0100083]"], + "classification":"Lineage and Variant information", + "label":"Variant designation" + }, + "variant_calling": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Variant Calling" + }, + "if_variant_calling_other": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"If variant calling Is Other, Specify" + }, + "variant_calling_params": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Variant Calling params" }, "sample_collected_in_quarantine": { "Enums": [ @@ -2369,10 +2832,11 @@ "examples": ["Yes [NCIT:C49488]"] }, "sample_collected_by": { + "examples": ["Public Health Agency of Canada"], "ontology": "GENEPIO:0001153", "type": "string", "description": "The name of the agency that collected the original sample.", - "examples": ["Public Health Agency of Canada"] + "label":"Collecting Institution" }, "sequencing_instrument": { "Enums": [ @@ -2431,7 +2895,9 @@ "ontology": "GENEPIO:0001452", "type": "string", "description": "The model of the sequencing instrument used.", - "examples": ["Oxford Nanopore MinION [GENEPIO:0100142]"] + "examples": ["Oxford Nanopore MinION [GENEPIO:0100142]"], + "classification":"Sequencing", + "label":"Sequencing Instrument Model" }, "host_health_status_details": { "Enums": [ @@ -2457,7 +2923,9 @@ "ontology": "GENEPIO:0001644", "type": "string", "description": "Identifier of the specific isolate.", - "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"] + "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"], + "clasification":"Sample collection and processing", + "label":"Isolate" }, "host_health_state": { "Enums": [ @@ -2580,18 +3048,20 @@ ] }, "dehosting_method": { + "examples": ["Nanostripper"], "ontology": "GENEPIO:0001459", "type": "string", "description": "The method used to remove host reads from the pathogen sequence.", - "examples": ["Nanostripper"] + "clasification":"Bioinformatics and QC metrics", + "label":"Dehosting Method" }, "amplicon_pcr_primer_scheme": { - "ontology": "GENEPIO:0001456", - "type": "string", - "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", - "examples": [ - "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv" - ] + "examples": ["https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv"], + "ontology": "GENEPIO:0001456", + "type": "string", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "clasification":"Sequencing", + "label":"Amplicon Pcr Primer Scheme" }, "vaccine_name": { "ontology": "GENEPIO:0001405", @@ -2634,19 +3104,24 @@ "ontology": "GENEPIO:0001446", "type": "string", "description": "The description of why the sample was sequenced providing specific details.", - "examples": ["Screened for S gene target failure (S dropout)"] + "examples": ["Screened for S gene target failure (S dropout)"], + "clasification":"Sequencing", + "label":"Purpose Of Sequencing Details" }, "sequence_submitted_by": { + "examples": ["Centers for Disease Control and Prevention"], "ontology": "GENEPIO:0001159", "type": "string", "description": "The name of the agency that generated the sequence.", - "examples": ["Centers for Disease Control and Prevention"] + "label":"Submitting Institution" }, "sequencing_protocol_name": { - "ontology": "GENEPIO:0001453", - "type": "string", - "description": "The name and version number of the sequencing protocol used.", - "examples": ["1D_DNA_MinION, ARTIC Network Protocol V3"] + "examples": ["1D_DNA_MinION, ARTIC Network Protocol V3"], + "ontology": "GENEPIO:0001453", + "type": "string", + "description": "The name and version number of the sequencing protocol used.", + "clasification":"Sequencing", + "label":"Sequencing Protocol Name" }, "prior_sars_cov_2_infection_isolate": { "ontology": "GENEPIO:0001436", @@ -2669,7 +3144,9 @@ "description": "Taxonomic name of the organism.", "examples": [ "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]" - ] + ], + "classification":"Sample collection and processing", + "label":"Organism" }, "purpose_of_sampling": { "Enums": [ diff --git a/schema/phage_plus_V0.json b/schema/phage_plus_V0.json index 8e6b5528..58b45e9e 100644 --- a/schema/phage_plus_V0.json +++ b/schema/phage_plus_V0.json @@ -326,13 +326,17 @@ "ontology": "GENEPIO:0001181", "type": "string", "description": "The country of origin of the sample.", - "examples": ["South Africa [GAZ:00001094]"] + "examples": ["South Africa [GAZ:00001094]"], + "classification":"Sample collection and processing", + "label":"Geo Loc Autonomic Country" }, "geo_loc_state": { "examples": ["Western Cape"], "ontology": "GENEPIO:0001185", "type": "string", - "description": "The state/province/territory of origin of the sample." + "description": "The state/province/territory of origin of the sample.", + "classification":"Sample collection and processing", + "label":"Geo Loc Autonomic Community" }, "organism": { "Enums": [ @@ -348,15 +352,18 @@ "type": "string", "description": "Taxonomic name of the organism.", "examples": [ - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]" - ] + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", + ], + "classification":"Sample collection and processing", + "label":"Organism" }, "isolate": { "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"], "ontology": "GENEPIO:0001644", "type": "string", "description": "Identifier of the specific isolate.", - "clasification":"Sample collection and processing" + "clasification":"Sample collection and processing", + "label":"Isolate" }, "host_scientific_name": { "Enums": [ @@ -385,7 +392,9 @@ "ontology": "GENEPIO:0001387", "type": "string", "description": "The taxonomic, or scientific name of the host.", - "examples": ["Homo sapiens [NCBITaxon:9606]"] + "examples": ["Homo sapiens [NCBITaxon:9606]"], + "clasification":"Host information", + "label":"Host Scientific Name" }, "host_disease": { "Enums": [ @@ -458,13 +467,16 @@ "ontology": "GENEPIO:0001452", "type": "string", "description": "The model of the sequencing instrument used.", - "examples": ["Oxford Nanopore MinION [GENEPIO:0100142]"] + "examples": ["Oxford Nanopore MinION [GENEPIO:0100142]"], + "classification":"Sequencing", + "label":"Sequencing Instrument Model" }, "sequencing_instrument_platform": { "examples": ["MinIon"], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", - "description": "The model of the sequencing instrument used." + "description": "The model of the sequencing instrument used.", + "label":"Sequencing Platforms " }, "consensus_sequence_software_name": { "examples": ["Ivar"], @@ -590,28 +602,32 @@ "ontology": "GENEPIO:0100280", "type": "string", "description": "The county/region of origin of the sample.", - "clasification":"Sample collection and processing" + "clasification":"Sample collection and processing", + "label":"Geo Loc Province" }, "geo_loc_city": { "examples": ["Vancouver"], "ontology": "GENEPIO:0001189", "type": "string", "description": "The city of origin of the sample.", - "clasification":"Sample collection and processing" + "clasification":"Sample collection and processing", + "label":"Geo Loc City" }, "geo_loc_latitude": { "examples": ["38.98 N"], - "ontology": "GENEPIO:0001156", + "ontology": "OBI:0001620", "type": "string", "description": "The latitude coordinates of the geographical location of sample collection.", - "clasification":"Sample collection and processing" + "clasification":"Sample collection and processing", + "label":"Geo Loc Latitude", }, "geo_loc_longitude": { "examples": ["77.11 W"], "ontology": "OBI:0001621", "type": "string", "description": "The longitude coordinates of the geographical location of sample collection.", - "clasification":"Sample collection and processing" + "clasification":"Sample collection and processing", + "label":"Geo Loc Longitude" }, "anatomical_material": { "Enums": [ @@ -633,7 +649,9 @@ "ontology": "GENEPIO:0001211", "type": "string", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "examples": ["Blood [UBERON:0000178]"] + "examples": ["Blood [UBERON:0000178]"], + "classification":"Sample collection and processing", + "label":"Organism Substance" }, "anatomical_part": { "Enums": [ @@ -670,7 +688,9 @@ "ontology": "GENEPIO:0001214", "type": "string", "description": "An anatomical part of an organism e.g. oropharynx. ", - "examples": ["Nasopharynx (NP) [UBERON:0001728]"] + "examples": ["Nasopharynx (NP) [UBERON:0001728]"], + "classification":"Sample collection and processing", + "label":"Anatomical Structure" }, "body_product": { "Enums": [ @@ -691,7 +711,9 @@ "ontology": "GENEPIO:0001216", "type": "string", "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", - "examples": ["Feces [UBERON:0001988]"] + "examples": ["Feces [UBERON:0001988]"], + "classification":"Sample collection and processing", + "label":"Body product" }, "environmental_material": { "Enums": [ @@ -737,7 +759,9 @@ "ontology": "GENEPIO:0001223", "type": "string", "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", - "examples": ["Face Mask [OBI:0002787]"] + "examples": ["Face Mask [OBI:0002787]"], + "clasification":"Sample collection and processing", + "label":"Environmental Material" }, "environmental_site": { "Enums": [ @@ -771,7 +795,9 @@ "ontology": "GENEPIO:0001232", "type": "string", "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", - "examples": ["Hospital [ENVO:00002173]"] + "examples": ["Hospital [ENVO:00002173]"], + "classification":"Sample collection and processing", + "label":"Anthropogenic Geographic Feature" }, "collection_device": { "Enums": [ @@ -801,7 +827,9 @@ "ontology": "GENEPIO:0001234", "type": "string", "description": "The instrument or container used to collect the sample e.g. swab.", - "examples": ["Swab [GENEPIO:0100027]"] + "examples": ["Swab [GENEPIO:0100027]"], + "clasification":"Sample collection and processing", + "label":"Collection Device" }, "collection_method": { "Enums": [ @@ -835,14 +863,17 @@ "ontology": "GENEPIO:0001241", "type": "string", "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", - "examples": ["Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]"] + "examples": ["Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]"], + "clasification":"Sample collection and processing", + "label":"Collection Method" }, "collection_protocol": { "examples": ["SC2SamplingProtocol 1.2"], "ontology": "GENEPIO:0001243", "type": "string", "description": "The name and version of a particular protocol used for sampling.", - "clasification":"Sample collection and processing" + "clasification":"Sample collection and processing", + "label":"Collection Protocol" }, "specimen_processing": { "Enums": [ @@ -858,7 +889,9 @@ "ontology": "GENEPIO:0001253", "type": "string", "description": "Any processing applied to the sample during or after receiving the sample. ", - "examples": ["Virus Passage [GENEPIO:0100039]"] + "examples": ["Virus Passage [GENEPIO:0100039]"], + "classification":"Sample collection and processing", + "label":"Specimen Processing" }, "lab_host": { "Enums": [ @@ -887,21 +920,25 @@ "ontology": "GENEPIO:0001255", "type": "string", "description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.", - "examples": ["Vero E6 Cell Line [BTO:0004755]"] + "examples": ["Vero E6 Cell Line [BTO:0004755]"], + "classification":"Sample collection and processing", + "label":"Lab passage Host" }, "passage_number": { "examples": ["3"], "ontology": "GENEPIO:0001261", "type": "string", "description": "Number of passages.", - "clasification":"Sample collection and processing" + "clasification":"Sample collection and processing", + "label":"Passage Number" }, "passage_method": { "examples": ["AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain."], "ontology": "GENEPIO:0001264", "type": "string", "description": "Description of how organism was passaged.", - "clasification":"Sample collection and processing" + "clasification":"Sample collection and processing", + "label":"Passage Method" }, "biomaterial_extracted": { "Enums": [ @@ -918,7 +955,9 @@ "ontology": "GENEPIO:0001266", "type": "string", "description": "The biomaterial extracted from samples for the purpose of sequencing.", - "examples": ["RNA (Total) [OBI:0000895]"] + "examples": ["RNA (Total) [OBI:0000895]"], + "classification":"Sample collection and processing", + "label":"Biomaterial Extracted" }, "tax_id": { "examples": ["probably 2697049 in all cases"], @@ -980,21 +1019,25 @@ "ontology": "GENEPIO:0001386", "type": "string", "description": "The commonly used name of the host.", - "examples": ["Human [NCBITaxon:9606]"] + "examples": ["Human [NCBITaxon:9606]"], + "classification":"Host information", + "label":"Host Common Name" }, "outbreak": { "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO:0001417", "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information" + "clasification":"Host information", + "label":"Outbreak Exposure Event Location" }, "additional_host_information": { "examples": ["e.g. Patient infected while traveling in …."], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information" + "clasification":"Host information", + "label":"Additional Host Information" }, "purpose_of_sequencing": { "Enums": [ @@ -1031,7 +1074,9 @@ "ontology": "GENEPIO:0001445", "type": "string", "description": "The reason that the sample was sequenced.", - "examples": ["Baseline surveillance (random sampling) [GENEPIO:0100005]"] + "examples": ["Baseline surveillance (random sampling) [GENEPIO:0100005]"], + "classification":"Sequencing", + "label":"Purpose of Sequencing" }, "purpose_of_sequencing_details": { "Enums": [ @@ -1054,7 +1099,9 @@ "ontology": "GENEPIO:0001446", "type": "string", "description": "The description of why the sample was sequenced providing specific details.", - "examples": ["Screened for S gene target failure (S dropout)"] + "examples": ["Screened for S gene target failure (S dropout)"], + "clasification":"Sequencing", + "label":"Purpose Of Sequencing Details" }, "sequencing_date": { "examples": ["4/26/2021"], @@ -1062,155 +1109,168 @@ "type": "string", "description": "The date the sample was sequenced.", "format":"date", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Sequencing date" }, - "rna_extraction_Protocol": { + "rna_extraction_protocol": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Rna Extraction Protocol" }, "library_kit": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Library Kit" }, "library_id": { "examples": ["XYZ_123345"], "ontology": "GENEPIO:0001448", "type": "string", "description": "The user-specified identifier for the library prepared for sequencing.", - "clasification":"Sequencing" + "clasification":"Sequencing", + "labe":"Library Id" }, "enrichment_protocol": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Enrichment_protocol" }, "if_enrichment_protocol_is_other_specify": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"If Enrichment Protocol Is Other, Specify" }, "amplicon protocol": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Amplicon Protocol" }, "if_amplicon_protocol_if_other_especify": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Sequencing" + "clasification":"Sequencing", + "labe":"If Amplicon Protocol If Other, Especify" }, - "amplicon_version": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Amplicon Version" }, "amplicon_size": { "examples": ["300bp"], "ontology": "GENEPIO:0001449", "type": "string", "description": "The length of the amplicon generated by PCR amplification.", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Amplicon Size" }, - "was_phix_used?": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Was Phix Used" }, - "number_of_samples_in_run": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Number Of Samples In Run" }, - "flowcell_kit": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Sequencing" + "clasification":"Sequencing", + "labe":"Flowcell Kit" }, - "runID": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"RunID" }, - "sequencing_platforms": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Sequencing Platforms " }, - "library_preparation_kit": { "examples": ["Nextera XT"], "ontology": "GENEPIO:0001450", "type": "string", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Library Preparation Kit" }, - "flow_cell_barcode": { "examples": ["FAB06069"], "ontology": "GENEPIO:0001451", "type": "string", "description": "The barcode of the flow cell used for sequencing.", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Flow Cell Barcode" }, "sequencing_protocol_name": { "examples": ["1D_DNA_MinION, ARTIC Network Protocol V3"], "ontology": "GENEPIO:0001453", "type": "string", "description": "The name and version number of the sequencing protocol used.", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Sequencing Protocol Name" }, "sequencing_protocol": { "examples": ["Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits."], "ontology": "GENEPIO:0001454", "type": "string", "description": "The protocol used to generate the sequence.", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Sequencing Protocol" }, "sequencing_kit_number": { "examples": ["AB456XYZ789"], "ontology": "GENEPIO:0001455", "type": "string", "description": "The manufacturer's kit number.", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Sequencing Kit Number" }, "amplicon_pcr_primer_scheme": { "examples": ["https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv"], "ontology": "GENEPIO:0001456", "type": "string", "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Amplicon Pcr Primer Scheme" }, "library_source": { "examples": ["METAGENOMIC"], @@ -1254,293 +1314,333 @@ "description": "", "clasification":"Sequencing" }, - "raw_sequence_data_processing_method": { "examples": ["Porechop 0.2.3"], "ontology": "GENEPIO:0001458", "type": "string", "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Raw sequence data processin method" }, "dehosting_method": { "examples": ["Nanostripper"], "ontology": "GENEPIO:0001459", "type": "string", "description": "The method used to remove host reads from the pathogen sequence.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Dehosting Method" }, "assembly": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Assembly" }, "if_assembly_other": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"If assembly Is Other, Specify" }, "assembly_params": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Assambly params" }, - "variant_Calling": { + "variant_calling": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Variant Calling" }, - "if_variant_Calling_other": { + "if_variant_calling_other": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"If variant calling Is Other, Specify" }, - "variant_Calling_params": { + "variant_calling_params": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Variant Calling params" }, "consensus_sequence_filepath": { "examples": ["/User/Documents/RespLab/Data/ncov123assembly.fasta"], "ontology": "GENEPIO:0001462", "type": "string", "description": "The filepath of the consesnsus sequence file.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Consensus sequence filepath" }, "consensus_sequence_software_name": { "examples": ["Ivar"], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO:0001463", "type": "string", "description": "The name of software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Consensus sequence software name" }, "if_consensus_other": { "examples": ["1.3"], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "The version of the software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"If consensus Is Other, Specify" }, "consensus_sequence_software_version": { "examples": ["1.3"], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO:0001469", "type": "string", "description": "The version of the software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Consensus sequence software version" }, "consensus_criteria": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Consensus criteria" }, "quality_control_metrics": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Quality control metrics " }, "breadth_of_coverage_value": { "examples": ["95%"], "ontology": "GENEPIO:0001472", "type": "string", "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Breadth of coverage value" }, "depth_of_coverage_value": { "examples": ["400x"], "ontology": "GENEPIO:0001474", "type": "string", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Depth of coverage value " }, "depth_of_coverage_threshold": { "examples": ["100x"], "ontology": "GENEPIO:0001475", "type": "string", "description": "The threshold used as a cut-off for the depth of coverage.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Depth of coverage threshold" }, "sequence_file_R1_fastq": { "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], "ontology": "GENEPIO:0001476", "type": "string", "description": "The user-specified filename of the r1 FASTQ file.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Sequence file R1 fastq" }, "sequence_file_R2_fastq": { "examples": ["ABC123_S1_L001_R2_001.fastq.gz"], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO:0001477", "type": "string", "description": "The user-specified filename of the r2 FASTQ file.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Sequence file R2 fastq" }, "r1_fastq_filepath": { "examples": ["/User/Documents/RespLab/Data/"], "ontology": "GENEPIO:0001478", "type": "string", "description": "The filepath of the r1 FASTQ file.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Filepath R1 fastq" }, "r2_fastq_filepath": { "examples": ["/User/Documents/RespLab/Data/"], "ontology": "GENEPIO:0001479", "type": "string", "description": "The filepath of the r2 FASTQ file.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Filepath R2 fastq" }, "fast5_filename": { "examples": ["batch1a_sequences.fast5"], "ontology": "GENEPIO:0001480", "type": "string", "description": "The user-specified filename of the FAST5 file.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Filename fast5" }, "fast5_filepath": { "examples": ["/User/Documents/RespLab/Data/"], "ontology": "GENEPIO:0001481", "type": "string", "description": "The filepath of the FAST5 file.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Filepath fast5" }, "number_of_base_pairs_sequenced": { "examples": ["387566"], "ontology": "GENEPIO:0001482", "type": "string", "description": "The number of total base pairs generated by the sequencing process.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Number of base pairs sequenced " }, "consensus_genome_length": { "examples": ["38677"], "ontology": "GENEPIO:0001483", "type": "string", "description": "Size of the assembled genome described as the number of base pairs.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Consensus genome length" }, "ns_per_100_kbp": { "examples": ["300"], "ontology": "GENEPIO:0001484", "type": "string", "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Ns per 100 kbp" }, "reference_genome_accession": { "examples": ["NC_045512.2"], "ontology": "GENEPIO:0001485", "type": "string", "description": "A persistent, unique identifier of a genome database entry.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Reference genome accession" }, "bioinformatics_protocol": { "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], "ontology": "GENEPIO:0001489", "type": "string", "description": "The name of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Bioinformatics protocol" }, "if_bioinformatic_protocol_is_other_specify": { "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "The name of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"If bioinformatic protocol Is Other, Specify" }, "bioinformatic_protocol_version": { "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "The version number of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"bioinformatics protocol version" }, "commercial/open-source/both": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Commercial/Open-source/both" }, "preprocessing": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Preprocessing" }, "if_preprocessing_other": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"If preprocessing Is Other, Specify" }, "preprocessing_params": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics" + "clasification":"Bioinformatics and QC metrics", + "label":"Preprocessing params" }, "mapping": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Lineage and Variant information" + "clasification":"Lineage and Variant information", + "label":"Mapping" }, "if_mapping_other": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Lineage and Variant information" + "clasification":"Lineage and Variant information", + "label":"If mapping Is Other, Specify" }, - "Mapping_params": { + "mapping_params": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Lineage and Variant information" + "clasification":"Lineage and Variant information", + "label":"Mapping params" }, "lineage/clade_name": { "examples": ["B.1.1.7"], "ontology": "GENEPIO:0001500", "type": "string", "description": "The name of the lineage or clade.", - "clasification":"Lineage and Variant information" + "clasification":"Lineage and Variant information", + "label":"Lineage/clade name" }, "lineage/clade_analysis_software_name": { "examples": ["Pangolin"], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO:0001501", "type": "string", "description": "The name of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information" + "clasification":"Lineage and Variant information", + "label":"lineage/clade analysis software name" }, "if_lineage_identification_other": { "examples": ["Other than Pangolin"], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "The name of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information" + "clasification":"Lineage and Variant information", + "label":"If lineage identification Is Other, Specify" }, "lineage/clade_analysis_software_version": { "examples": ["2.1.10"], "ontology":"GENEPIO:0001502", "type": "string", "description": "The version of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information" + "clasification":"Lineage and Variant information", + "label":"Lineage/clade analysis software version" }, "variant_designation": { "Enums": [ @@ -1551,14 +1651,17 @@ "ontology": "GENEPIO:0001503", "type": "string", "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", - "examples": ["Variant of Concern (VOC) [GENEPIO:0100083]"] + "examples": ["Variant of Concern (VOC) [GENEPIO:0100083]"], + "classification":"Lineage and Variant information", + "label":"Variant designation" }, "variant_evidence": { "examples": ["lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)"], "ontology": "GENEPIO:0001504", "type": "string", "description": "The evidence used to make the variant determination.", - "clasification":"Lineage and Variant information" + "clasification":"Lineage and Variant information", + "label":"Variant evidence" }, "gene_name_1": { "Enums": [ @@ -1604,14 +1707,17 @@ "ontology": "GENEPIO:0001507", "type": "string", "description": "The name of the gene used in the diagnostic RT-PCR test.", - "examples": ["E gene (orf4) [GENEPIO:0100151]"] + "examples": ["E gene (orf4) [GENEPIO:0100151]"], + "classification":"Pathogen diagnostic testing", + "label":"Gene Name 1" }, "Protocol_SARS-CoV-2_detection": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing" + "clasification":"Pathogen diagnostic testing", + "label":"Protocol SARS-CoV-2 detection" }, "%qc_filtered": { "examples": [""], From b666ddaee9ab93ce4f59fd0f4b1d6ef02b5b5066 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 18 Feb 2022 12:54:26 +0100 Subject: [PATCH 0037/1454] update schemas --- schema/ena_v01.json | 486 ++++++++++++++++++-------------------- schema/phage_plus_V0.json | 416 ++++++++++++++++++-------------- 2 files changed, 464 insertions(+), 438 deletions(-) diff --git a/schema/ena_v01.json b/schema/ena_v01.json index 72bf14e6..d63f9093 100644 --- a/schema/ena_v01.json +++ b/schema/ena_v01.json @@ -653,12 +653,12 @@ "label":"Sequence file R1 fastq" }, "tax_id": { - "examples": ["probably 2697049 in all cases"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The NCBITaxon identifier for the organism being sequenced.", - "clasification":"Sample collection and processing", - "genepio_label":"" + "examples": ["probably 2697049 in all cases"], + "ontology": "GENEPIO_0001724", + "type": "string", + "description": "The NCBITaxon identifier for the organism being sequenced.", + "clasification":"Sample collection and processing", + "label":"Tax ID" }, "scientific_name": { "Enums": [ @@ -679,13 +679,12 @@ "label":"Organism" }, "common_name": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The common name of the organism.", - "clasification":"Sample collection and processing", - "genepio_label":"", - + "examples": [""], + "ontology": "BU_ISCIII:003", + "type": "string", + "description": "The common name of the organism.", + "clasification":"Sample collection and processing", + "label":"Common name" }, "sample_description": { "examples": [""], @@ -729,20 +728,20 @@ "other library method [GENPIO:0001964]", "size fractionation method [GENPIO:0001963]", ], - "examples": ["METAGENOMIC"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Molecule type used to make the library.", - "clasification":"Sequencing", + "examples": ["METAGENOMIC"], + "ontology": "GENEPIO_0001965", + "type": "string", + "description": "Molecule type used to make the library.", + "clasification":"Sequencing", + "label":"Source material" }, "library_selection": { "examples": ["RANDOM PCR"], - "ontology": "GENPIO_0001940", - "type": "string", - "description": "Library capture method.", - "clasification":"Sequencing", - "genepio_label":"library selection", - + "ontology": "GENPIO_0001940", + "type": "string", + "description": "Library capture method.", + "clasification":"Sequencing", + "label":"Capture method" }, "library_strategy": { "Enums": ["Bisultife-Seq strategy [GENPIO:0001975]", @@ -771,17 +770,15 @@ "type": "string", "description": "Overall sequencing strategy or approach.", "clasification":"Sequencing", - "genepio_label":"library strategy", - + "label":"Sequencing technique" }, "library_layout": { "examples": ["PAIRED"], - "ontology":"GENPIO_0000001", + "ontology":"BU_ISCIII:007", "type": "string", "description": "Single or paired.", "clasification":"Sequencing", - "genepio_label":"library library_layout", - + "label":"Library Layout" }, "library_name": { "examples": ["e.g P17157_1007"], @@ -789,351 +786,320 @@ "type": "string", "description": "The submitter's name for this library.", "clasification":"Sequencing", - "genepio_label":"Library Name", + "label":"Library Name" }, "nominal_length ": { "examples": ["350"], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO_0000076", "type": "string", "description": "", "clasification":"Sequencing", - "genepio_label":"", - + "label":"Nominal Length" }, "analysis_accession": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO_0001145", "type": "string", "description": "", "clasification":"Submission ENA", - "genepio_label":"", - + "label":"Analysis Accession" + }, + "read_length": { + "examples": [""], + "ontology": "STATO_0000064", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Read length" }, "study_accession": { "examples": ["e.g PRJEB39632"], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO_0001136", "type": "string", "description": "", "clasification":"Submission ENA", - "genepio_label":"", - - }, - "secondary_study_accession": { + "label":"Study accession" + }, + "secondary_study_accession": { "examples": ["e.g ERP123173"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:012", "type": "string", "description": "", "clasification":"Submission ENA", - "genepio_label":"", - - }, - "sample_accession": { + "label":"Secondary study accession" + }, + "sample_accession": { "examples": ["e.g SAMEA7098096"], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO_0001139", "type": "string", "description": "", "clasification":"Submission ENA", - "genepio_label":"", - - }, - "secondary_sample_accession": { + "label":"Sample accession" + }, + "secondary_sample_accession": { "examples": ["e.g ERS4858671"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:014", "type": "string", "description": "", "clasification":"Submission ENA", - "genepio_label":"", - - }, - "experiment_accession": { + "label":"Secondary sample accession" + }, + "experiment_accession": { "examples": ["e.g ERX4331406"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:015", "type": "string", "description": "", "clasification":"Submission ENA", - "genepio_label":"", - + "label":"Experiment Accession" }, "run_accession": { "examples": ["e.g ERX4331406"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:016", "type": "string", "description": "", "clasification":"Submission ENA", - "genepio_label":"", - + "label":"Run Accession" }, "submission_accession": { "examples": ["e.g ERA2794974"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:017", "type": "string", "description": "", "clasification":"Submission ENA", - "genepio_label":"", - + "label":"Submission accession" }, "read_count": { "examples": ["e.g 837055"], - "ontology": "GENEPIO:0001156", + "ontology": "STATO_0000064", "type": "string", "description": "", "clasification":"Submission ENA", - "genepio_label":"", - + "label":"Read count" }, "base_count": { - "examples": ["e.g 503907110"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g 503907110"], + "ontology": "UO_0000244", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Base count" }, "center_name": { - "examples": [" KAROLINSKA INSITUTET"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The name of the institution", - "clasification":"Sample collection and processing", - "genepio_label":"", - + "examples": [" KAROLINSKA INSITUTET"], + "ontology": "NCIT_C19983", + "type": "string", + "description": "The name of the institution", + "clasification":"Sample collection and processing", + "label":"Center Name" }, "first_public": { "examples": ["e.g 2020-08-07"], - "ontology": "GENEPIO:0001156", + "ontology": "NCIT_C142711", "type": "string", "description": "", "clasification":"Submission ENA", - "genepio_label":"", - - }, - "last_updated": { + "label":"First Public date" + }, + "last_updated": { "examples": ["e.g 2020-07-29"], - "ontology": "GENEPIO:0001156", + "ontology": "OMIABIS_0001005", "type": "string", "description": "", "clasification":"Submission ENA", - "format":"date", - "genepio_label":"", - - }, - "experiment_title": { + "format":"Last Updated" + }, + "experiment_title": { "examples": ["e.g Illumina MiSeq paired end sequencing"], - "ontology": "GENEPIO:0001156", + "ontology": "ORNASEQ_0000004", "type": "string", "description": "", "clasification":"Submission ENA", - "genepio_label":"", - - }, - "study_title": { - "examples": ["e.g SARS-CoV-2 genomes from late April in Stockholm"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "label":"Experiment title" + }, + "study_title": { + "examples": ["e.g SARS-CoV-2 genomes from late April in Stockholm"], + "ontology": "OPMI_0000380", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Study title" }, "study_alias": { - "examples": ["e.g Sweden"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g Sweden"], + "ontology": "SIO_001066", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Study alias" }, "experiment_alias": { - "examples": ["e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092"], + "ontology": "NCIT_C42790", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Experiment alias" }, "run_alias": { - "examples": ["e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], + "ontology": "NCIT_C47911", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Run Alias" }, "fastq_bytes": { - "examples": ["e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], + "ontology": "NCIT_C48047", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Fastq bytes" }, "fastq_md5": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": [""], + "ontology": "MS_1000568", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Fastq md5" }, "fastq_ftp": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": [""], + "ontology": "PRIDE_0000469", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Fastq ftp" }, "fastq_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], + "ontology": "BU_ISCIII:032", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Fastq aspera" }, "fastq_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], + "ontology": "ENVO_01000807", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Fastq galaxy" }, "submitted_bytes": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], + "ontology": "NCIT_C172872", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted bytes " }, "submitted_md5": { - "examples": ["e.g 139853010;166270048"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g 139853010;166270048"], + "ontology": "BU_ISCIII:035", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted md5" }, "submitted_ftp": { - "examples": ["e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a"], + "ontology": "BU_ISCIII:036", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted ftp" }, "submitted_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], + "ontology": "BU_ISCIII:037", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted aspera" }, "submitted_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], + "ontology": "BU_ISCIII:038", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted Galaxy" }, "submitted_format": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], + "ontology": "BU_ISCIII:039", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted Format" }, "sra_bytes": { - "examples": ["e.g FASTQ;FASTQ"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g FASTQ;FASTQ"], + "ontology": "BU_ISCIII:040", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"SRA bytes" }, "sra_md5": { - "examples": ["e.g 260236789"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g 260236789"], + "ontology": "BU_ISCIII:041", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"SRA md5" }, "sra_ftp": { - "examples": ["e.g 2cf0d467d6dc4ae0a5473774d54c059c"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g 2cf0d467d6dc4ae0a5473774d54c059c"], + "ontology": "BU_ISCIII:042", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"SRA ftp" }, "sra_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385"], + "ontology": "BU_ISCIII:043", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"SRA aspera" }, "sra_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385"], + "ontology": "BU_ISCIII:044", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"SRA galaxy" }, "broker_name": { - "examples": ["P17157_1007"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": ["P17157_1007"], + "ontology": "BU_ISCIII:045", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Broker Name" }, "nominal_sdev": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - + "examples": [""], + "ontology": "STATO_0000237", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Nominal sdev" }, "first_created": { - "examples": ["e.g 2020-08-07"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, + "examples": ["e.g 2020-08-07"], + "ontology": "NCIT_C164483", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"First created date" + } } } diff --git a/schema/phage_plus_V0.json b/schema/phage_plus_V0.json index 58b45e9e..4d0bc178 100644 --- a/schema/phage_plus_V0.json +++ b/schema/phage_plus_V0.json @@ -961,33 +961,28 @@ }, "tax_id": { "examples": ["probably 2697049 in all cases"], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO_0001800", "type": "string", "description": "The NCBITaxon identifier for the organism being sequenced.", - "clasification":"Sample collection and processing" - }, - "scientific_name": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The taxonomic name of the organism.", - "clasification":"Sample collection and processing" + "clasification":"Sample collection and processing", + "label":"Tax ID" }, "common_name": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:003", "type": "string", "description": "The common name of the organism.", - "clasification":"Sample collection and processing" + "clasification":"Sample collection and processing", + "label":"Common name" }, "center_name": { "examples": [" KAROLINSKA INSITUTET"], - "ontology": "GENEPIO:0001156", + "ontology": "NCIT_C19983", "type": "string", "description": "The name of the institution", - "clasification":"Sample collection and processing" + "clasification":"Sample collection and processing", + "label":"Center Name" }, - "virus_id": { "examples": [""], "ontology": "GENEPIO:0001156", @@ -1272,47 +1267,66 @@ "clasification":"Sequencing", "label":"Amplicon Pcr Primer Scheme" }, - "library_source": { - "examples": ["METAGENOMIC"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Molecule type used to make the library.", - "clasification":"Sequencing" - }, "library_selection": { - "examples": ["RANDOM PCR"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Library capture method.", - "clasification":"Sequencing" + "examples": ["RANDOM PCR"], + "ontology": "GENPIO_0001940", + "type": "string", + "description": "Library capture method.", + "clasification":"Sequencing", + "label":"Capture method" }, "library_strategy": { + "Enums": ["Bisultife-Seq strategy [GENPIO:0001975]", + "CTS strategy [GENPIO:0001978]", + "ChIP-Seq strategy [GENPIO:0001979]", + "DNase-Hypersensitivity strategy [GENPIO:0001980]", + "EST strategy [GENPIO:0001981]", + "FL-cDNA strategy [GENPIO:0001983]", + "MB-Seq strategy [GENPIO:0001984]", + "MNase-Seq strategy [GENPIO:0001985]", + "MRE-Seq strategy [GENPIO:0001986]", + "MeDIP-Seq strategy [GENPIO:0001987]", + "RNA-Seq strategy [GENPIO:0001990]", + "WCS strategy [GENPIO:0001991]", + "WGS strategy [GENPIO:0001992]", + "WXS strategy [GENPIO:0001993]", + "amplicon strategy [GENPIO:0001974]", + "clone end strategy [GENPIO:0001976]", + "clone strategy [GENPIO:0001977]", + "finishing strategy [GENPIO:0001982]", + "other library strategy [GENPIO:0001988]", + "pool clone strategy [GENPIO:0001989]", + ], "examples": ["WGS"], - "ontology": "GENEPIO:0001156", + "ontology": "GENPIO_0001973", "type": "string", "description": "Overall sequencing strategy or approach.", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Sequencing technique" }, "library_layout": { "examples": ["PAIRED"], - "ontology": "GENEPIO:0001156", + "ontology":"BU_ISCIII:007", "type": "string", "description": "Single or paired.", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Library Layout" }, "library_name": { "examples": ["P17157_1007"], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO_0001995", "type": "string", "description": "Name of the used library", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"LibraryName" }, "nominal_length ": { "examples": ["350"], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO_0000076", "type": "string", "description": "", - "clasification":"Sequencing" + "clasification":"Sequencing", + "label":"Nominal Length" }, "raw_sequence_data_processing_method": { "examples": ["Porechop 0.2.3"], @@ -1721,87 +1735,99 @@ }, "%qc_filtered": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing" + "clasification":"Pathogen diagnostic testing", + "label":"%qc filtered" }, "%reads_host": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing" + "clasification":"Pathogen diagnostic testing", + "label":"%reads host" }, "%reads_virus": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing" + "clasification":"Pathogen diagnostic testing", + "label":"%reads virus" }, "%unmapped": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing" + "clasification":"Pathogen diagnostic testing", + "label":"%unmapped" }, - "% genome _greater_10x": { + "%genome _greater_10x": { "examples": [""], "ontology": "GENEPIO:0001156", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing" + "clasification":"Pathogen diagnostic testing", + "label":"% genome greater 10x" }, "mean_depth_of_coverage_value": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing" + "clasification":"Pathogen diagnostic testing", + "label":"mean depth of coverage value" }, "%Ns": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing" + "clasification":"Pathogen diagnostic testing", + "label":"%Ns" }, "Number_of_variants_(AF_greater_75%)": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing" + "clasification":"Pathogen diagnostic testing", + "label":"Number of variants (AF greater 75%)" }, "Numer_of_variants_with_effect": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing" + "clasification":"Pathogen diagnostic testing", + "label":"Numer of variants with effect" }, "reference_genome_accession": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO:0001485", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing" + "clasification":"Pathogen diagnostic testing", + "label":"reference genome accession" }, "diagnostic_pcr_protocol_1": { "examples": ["PCREGene 2.0"], "ontology": "GENEPIO:0001508", "type": "string", "description": "The name and version number of the protocol used for diagnostic marker amplification.", - "clasification":"Pathogen diagnostic testing" + "clasification":"Pathogen diagnostic testing", + "label":"Diagnostic Pcr Protocol 1" }, "diagnostic_pcr_Ct_value_1": { "examples": ["21"], "ontology": "GENEPIO:0001509", "type": "string", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "clasification":"Pathogen diagnostic testing" + "clasification":"Pathogen diagnostic testing", + "label":"Diagnostic Pcr Ct Value 1" }, "gene_name_2": { "Enums": [ @@ -1847,35 +1873,41 @@ "ontology": "GENEPIO:0001510", "type": "string", "description": "The name of the gene used in the diagnostic RT-PCR test.", - "examples": ["RdRp gene (nsp12) [GENEPIO:0100168]"] + "examples": ["RdRp gene (nsp12) [GENEPIO:0100168]"], + "classification":"Pathogen diagnostic testing", + "label":"Gene Name 2" }, "diagnostic_pcr_protocol_2": { "examples": ["PCRRdRpGene 3.0"], "ontology": "GENEPIO:0001511", "type": "string", "description": "The name and version number of the protocol used for diagnostic marker amplification.", - "clasification":"Pathogen diagnostic testing" + "clasification":"Pathogen diagnostic testing", + "label":"Diagnostic Pcr Protocol 2" }, "diagnostic_pcr_Ct_value_2": { "examples": ["36"], "ontology": "GENEPIO:0001512", "type": "string", "description": "The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "clasification":"Pathogen diagnostic testing" + "clasification":"Pathogen diagnostic testing", + "label":"Diagnostic Pcr Ct Value-2" }, "analysis_author": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Contributor Acknowledgement" + "clasification":"Contributor Acknowledgement", + "label":"Analysis Authors" }, "author_submitter": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "", - "clasification":"Contributor Acknowledgement" + "clasification":"Contributor Acknowledgement", + "label":"Author Submitter" }, "submitter": { "examples": [""], @@ -1889,7 +1921,8 @@ "ontology": "GENEPIO:0001517", "type": "string", "description": "", - "clasification":"Contributor Acknowledgement" + "clasification":"Contributor Acknowledgement", + "label":"Authors" }, "tax_id": { "examples": [""], @@ -1898,13 +1931,6 @@ "description": "", "clasification":"Sample collection and processing" }, - "scientific_name": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sample collection and processing" - }, "common_name": { "examples": [""], "ontology": "GENEPIO:0001156", @@ -1913,39 +1939,37 @@ "clasification":"Sample collection and processing" }, "library_source": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - "library_selection": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - "library_strategy": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - "library_layout": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - "library_name": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" + "Enums": ["5-methycytidine antibody method [GENPIO:0001941]", + "CAGE method [GENPIO:0001942]", + "CF-H method [GENPIO:0001943]", + "CF-M method ]GENPIO:0001944]", + "CF-S method [GENPIO:0001945]", + "CF-T method [GENPIO:0001946]", + "ChIP method ]GENPIO:0001947]", + "DNAse method [GENPIO:0001948]", + "HMPR method [GENPIO:0001949]", + "Hybrid Selection Method [GENPIO:0001950]", + "MBD2 protein methyl-CpG binding domain method [GENPIO:0001951]", + "MF method [GENPIO:0001952]", + "MNase method [GENPIO:0001953]", + "MSLL method [GENPIO:0001954]", + "PCR method [GENPIO:0001955]", + "RACE method [GENPIO:0001956]", + "RANDOM PCR method [GENPIO:0001957]", + "RANDOM method [GENPIO:0001958]", + "RT-PCR method [GENPIO:0001959]", + "Reduced Representation method [GENPIO:0001960]", + "Resctriction Digest method [GENPIO:0001961]", + "cDNA method [GENPIO:0001962]", + "other library method [GENPIO:0001964]", + "size fractionation method [GENPIO:0001963]", + ], + "examples": ["METAGENOMIC"], + "ontology": "GENEPIO_0001965", + "type": "string", + "description": "Molecule type used to make the library.", + "clasification":"Sequencing", + "label":"Source material" }, "nominal_length": { "examples": [""], @@ -1956,263 +1980,299 @@ }, "analysis_accession": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO_0001145", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Analysis Accession" }, "study_accession": { "examples": ["e.g PRJEB39632"], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO_0001136", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Study accession" }, "secondary_study_accession": { "examples": ["e.g ERP123173"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:012", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Secondary study accession" }, "sample_accession": { "examples": ["e.g SAMEA7098096"], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO_0001139", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Sample accession" }, "secondary_sample_accession": { "examples": ["e.g ERS4858671"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:014", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Secondary sample accession" }, "experiment_accession": { "examples": ["e.g ERX4331406"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:015", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Experiment Accession" }, "run_accession": { "examples": ["e.g ERX4331406"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:016", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Run Accession" }, "submission_accession": { "examples": ["e.g ERA2794974"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:017", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Submission Accession" }, "read_count": { "examples": ["e.g 837055"], - "ontology": "GENEPIO:0001156", + "ontology": "STATO_0000064", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Read count" }, "read_length": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "STATO_0000064", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Read length" }, "base_count": { "examples": ["e.g 503907110"], - "ontology": "GENEPIO:0001156", + "ontology": "UO_0000244", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Base count" }, "first_public": { "examples": ["e.g 2020-08-07"], - "ontology": "GENEPIO:0001156", + "ontology": "NCIT_C142711", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"First Public date" }, "last_updated": { "examples": ["e.g 2020-07-29"], - "ontology": "GENEPIO:0001156", + "ontology": "OMIABIS_0001005", "type": "string", "description": "", "clasification":"Submission ENA", - "format":"date" + "format":"Last Updated" }, "experiment_title": { "examples": ["e.g Illumina MiSeq paired end sequencing"], - "ontology": "GENEPIO:0001156", + "ontology": "ORNASEQ_0000004", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Experiment title" }, "study_title": { "examples": ["e.g SARS-CoV-2 genomes from late April in Stockholm"], - "ontology": "GENEPIO:0001156", + "ontology": "OPMI_0000380", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Study title" }, "study_alias": { "examples": ["e.g Sweden"], - "ontology": "GENEPIO:0001156", + "ontology": "SIO_001066", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Study alias" }, "experiment_alias": { "examples": ["e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092"], - "ontology": "GENEPIO:0001156", + "ontology": "NCIT_C42790", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Experiment alias" }, "run_alias": { "examples": ["e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "GENEPIO:0001156", + "ontology": "NCIT_C47911", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Run Alias" }, "fastq_bytes": { "examples": ["e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "GENEPIO:0001156", + "ontology": "NCIT_C48047", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Fastq bytes" }, "fastq_md5": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "MS_1000568", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Fastq md5" }, "fastq_ftp": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "PRIDE_0000469", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Fastq ftp" }, "fastq_aspera": { "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:032", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Fastq aspera" }, "fastq_galaxy": { "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "GENEPIO:0001156", + "ontology": "ENVO_01000807", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Fastq galaxy" }, "submitted_bytes": { "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "GENEPIO:0001156", + "ontology": "NCIT_C172872", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Submitted bytes " }, "submitted_md5": { "examples": ["e.g 139853010;166270048"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:035", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Submitted md5" }, "submitted_ftp": { "examples": ["e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:036", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Submitted ftp" }, "submitted_aspera": { "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:037", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Submitted aspera" }, "submitted_galaxy": { "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:038", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Submitted Galaxy" }, "submitted_format": { "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:039", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Submitted Format" }, "sra_bytes": { "examples": ["e.g FASTQ;FASTQ"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:040", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"SRA bytes" }, "sra_md5": { "examples": ["e.g 260236789"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:041", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"SRA md5" }, "sra_ftp": { "examples": ["e.g 2cf0d467d6dc4ae0a5473774d54c059c"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:042", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"SRA ftp" }, "sra_aspera": { "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:043", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"SRA aspera" }, "sra_galaxy": { "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:044", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"SRA galaxy" }, "broker_name": { "examples": ["P17157_1007"], - "ontology": "GENEPIO:0001156", + "ontology": "BU_ISCIII:045", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Broker Name" }, "nominal_sdev": { "examples": [""], - "ontology": "GENEPIO:0001156", + "ontology": "STATO_0000237", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"Nominal sdev" }, "first_created": { "examples": ["e.g 2020-08-07"], - "ontology": "GENEPIO:0001156", + "ontology": "NCIT_C164483", "type": "string", "description": "", - "clasification":"Submission ENA" + "clasification":"Submission ENA", + "label":"First created date" }, "type": { "examples": ["betacoronavirus"], From 99f9053ad2027599a2ddadd89a8c014c87a14a6b Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 28 Feb 2022 13:51:22 +0100 Subject: [PATCH 0038/1454] schemas with all labels and ontologies ID --- schema/ena_v01.json | 2304 ++++++++++++------------ schema/phage_V0.json | 1400 +++++++++------ schema/phage_plus_V0.json | 3548 ++++++++++++++++++++----------------- 3 files changed, 4025 insertions(+), 3227 deletions(-) diff --git a/schema/ena_v01.json b/schema/ena_v01.json index d63f9093..d90e3a47 100644 --- a/schema/ena_v01.json +++ b/schema/ena_v01.json @@ -1,1105 +1,1203 @@ { - "$schema": "http://json-schema.org/draft/2019-09/schema#", - "required": [ - "sample_name", - "collecting_institution", - "geographic_location_(country_and/or_sea)", - "isolate", - "host_scientific_name", - "host_common_name", - "host_health_state", - "host_sex", - "host_subject_id", - "instrument_model", - "file_name", - "sample_name", - "tax_id", - "scientific_name", - "common_name", - "sample_description", - "library_source", - "library_selection", - "library_strategy", - "library_layout" - ], - "type": "object", - "properties": { - "sample_name": { - "examples": ["prov_rona_99"], - "ontology": "GENEPIO:0001123", - "type": "string", - "description": "The user-defined name for the sample.", - "clasification":"Database Identifiers", - "label":"Collecting Sample id" - - }, - "collecting_institution": { - "examples": ["Public Health Agency of Canada"], - "ontology": "GENEPIO:0001153", - "type": "string", - "description": "Name of the institution to which the person collecting the specimen belongs. Format: Institute Name, Institute Address", - "label":"Collecting Institution" - - }, - "collection_date": { - "examples": ["3/19/2020"], - "ontology": "GENEPIO:0001174", - "type": "string", - "description": "The date on which the sample was collected.", - "format":"date", - "classification":"Sample collection and processing", - "label":"Sample Collection Date" - }, - "receipt_date": { - "examples": ["3/21/2020"], - "ontology": "GENEPIO:0001179", - "type": "string", - "description": "The date on which the sample was received.", - "format":"date", - "clasification":"Sample collection and processing", - "label":"Sample Received Date" - }, - "geographic_location_(country_and/or_sea)": { - "Enums": [ - "Afghanistan [GAZ:00006882]", - "Albania [GAZ:00002953]", - "Algeria [GAZ:00000563]", - "American Samoa [GAZ:00003957]", - "Andorra [GAZ:00002948]", - "Angola [GAZ:00001095]", - "Anguilla [GAZ:00009159]", - "Antarctica [GAZ:00000462]", - "Antigua and Barbuda [GAZ:00006883]", - "Argentina [GAZ:00002928]", - "Armenia [GAZ:00004094]", - "Aruba [GAZ:00004025]", - "Ashmore and Cartier Islands [GAZ:00005901]", - "Australia [GAZ:00000463]", - "Austria [GAZ:00002942]", - "Azerbaijan [GAZ:00004941]", - "Bahamas [GAZ:00002733]", - "Bahrain [GAZ:00005281]", - "Baker Island [GAZ:00007117]", - "Bangladesh [GAZ:00003750]", - "Barbados [GAZ:00001251]", - "Bassas da India [GAZ:00005810]", - "Belarus [GAZ:00006886]", - "Belgium [GAZ:00002938]", - "Belize [GAZ:00002934]", - "Benin [GAZ:00000904]", - "Bermuda [GAZ:00001264]", - "Bhutan [GAZ:00003920]", - "Bolivia [GAZ:00002511]", - "Borneo [GAZ:00025355]", - "Bosnia and Herzegovina [GAZ:00006887]", - "Botswana [GAZ:00001097]", - "Bouvet Island [GAZ:00001453]", - "Brazil [GAZ:00002828]", - "British Virgin Islands [GAZ:00003961]", - "Brunei [GAZ:00003901]", - "Bulgaria [GAZ:00002950]", - "Burkina Faso [GAZ:00000905]", - "Burundi [GAZ:00001090]", - "Cambodia [GAZ:00006888]", - "Cameroon [GAZ:00001093]", - "Canada [GAZ:00002560]", - "Cape Verde [GAZ:00001227]", - "Cayman Islands [GAZ:00003986]", - "Central African Republic [GAZ:00001089]", - "Chad [GAZ:00000586]", - "Chile [GAZ:00002825]", - "China [GAZ:00002845]", - "Christmas Island [GAZ:00005915]", - "Clipperton Island [GAZ:00005838]", - "Cocos Islands [GAZ:00009721]", - "Colombia [GAZ:00002929]", - "Comoros [GAZ:00005820]", - "Cook Islands [GAZ:00053798]", - "Coral Sea Islands [GAZ:00005917]", - "Costa Rica [GAZ:00002901]", - "Cote d'Ivoire [GAZ:00000906]", - "Croatia [GAZ:00002719]", - "Cuba [GAZ:00003762]", - "Curacao [GAZ:00012582]", - "Cyprus [GAZ:00004006]", - "Czech Republic [GAZ:00002954]", - "Democratic Republic of the Congo [GAZ:00001086]", - "Denmark [GAZ:00005852]", - "Djibouti [GAZ:00000582]", - "Dominica [GAZ:00006890]", - "Dominican Republic [GAZ:00003952]", - "Ecuador [GAZ:00002912]", - "Egypt [GAZ:00003934]", - "El Salvador [GAZ:00002935]", - "Equatorial Guinea [GAZ:00001091]", - "Eritrea [GAZ:00000581]", - "Estonia [GAZ:00002959]", - "Eswatini [GAZ:00001099]", - "Ethiopia [GAZ:00000567]", - "Europa Island [GAZ:00005811]", - "Falkland Islands (Islas Malvinas) [GAZ:00001412]", - "Faroe Islands [GAZ:00059206]", - "Fiji [GAZ:00006891]", - "Finland [GAZ:00002937]", - "France [GAZ:00003940]", - "French Guiana [GAZ:00002516]", - "French Polynesia [GAZ:00002918]", - "French Southern and Antarctic Lands [GAZ:00003753]", - "Gabon [GAZ:00001092]", - "Gambia [GAZ:00000907]", - "Gaza Strip [GAZ:00009571]", - "Georgia [GAZ:00004942]", - "Germany [GAZ:00002646]", - "Ghana [GAZ:00000908]", - "Gibraltar [GAZ:00003987]", - "Glorioso Islands [GAZ:00005808]", - "Greece [GAZ:00002945]", - "Greenland [GAZ:00001507]", - "Grenada [GAZ:02000573]", - "Guadeloupe [GAZ:00067142]", - "Guam [GAZ:00003706]", - "Guatemala [GAZ:00002936]", - "Guernsey [GAZ:00001550]", - "Guinea [GAZ:00000909]", - "Guinea-Bissau [GAZ:00000910]", - "Guyana [GAZ:00002522]", - "Haiti [GAZ:00003953]", - "Heard Island and McDonald Islands [GAZ:00009718]", - "Honduras [GAZ:00002894]", - "Hong Kong [GAZ:00003203]", - "Howland Island [GAZ:00007120]", - "Hungary [GAZ:00002952]", - "Iceland [GAZ:00000843]", - "India [GAZ:00002839]", - "Indonesia [GAZ:00003727]", - "Iran [GAZ:00004474]", - "Iraq [GAZ:00004483]", - "Ireland [GAZ:00002943]", - "Isle of Man [GAZ:00052477]", - "Israel [GAZ:00002476]", - "Italy [GAZ:00002650]", - "Jamaica [GAZ:00003781]", - "Jan Mayen [GAZ:00005853]", - "Japan [GAZ:00002747]", - "Jarvis Island [GAZ:00007118]", - "Jersey [GAZ:00001551]", - "Johnston Atoll [GAZ:00007114]", - "Jordan [GAZ:00002473]", - "Juan de Nova Island [GAZ:00005809]", - "Kazakhstan [GAZ:00004999]", - "Kenya [GAZ:00001101]", - "Kerguelen Archipelago [GAZ:00005682]", - "Kingman Reef [GAZ:00007116]", - "Kiribati [GAZ:00006894]", - "Kosovo [GAZ:00011337]", - "Kuwait [GAZ:00005285]", - "Kyrgyzstan [GAZ:00006893]", - "Laos [GAZ:00006889]", - "Latvia [GAZ:00002958]", - "Lebanon [GAZ:00002478]", - "Lesotho [GAZ:00001098]", - "Liberia [GAZ:00000911]", - "Libya [GAZ:00000566]", - "Liechtenstein [GAZ:00003858]", - "Line Islands [GAZ:00007144]", - "Lithuania [GAZ:00002960]", - "Luxembourg [GAZ:00002947]", - "Macau [GAZ:00003202]", - "Madagascar [GAZ:00001108]", - "Malawi [GAZ:00001105]", - "Malaysia [GAZ:00003902]", - "Maldives [GAZ:00006924]", - "Mali [GAZ:00000584]", - "Malta [GAZ:00004017]", - "Marshall Islands [GAZ:00007161]", - "Martinique [GAZ:00067143]", - "Mauritania [GAZ:00000583]", - "Mauritius [GAZ:00003745]", - "Mayotte [GAZ:00003943]", - "Mexico [GAZ:00002852]", - "Micronesia [GAZ:00005862]", - "Midway Islands [GAZ:00007112]", - "Moldova [GAZ:00003897]", - "Monaco [GAZ:00003857]", - "Mongolia [GAZ:00008744]", - "Montenegro [GAZ:00006898]", - "Montserrat [GAZ:00003988]", - "Morocco [GAZ:00000565]", - "Mozambique [GAZ:00001100]", - "Myanmar [GAZ:00006899]", - "Namibia [GAZ:00001096]", - "Nauru [GAZ:00006900]", - "Navassa Island [GAZ:00007119]", - "Nepal [GAZ:00004399]", - "Netherlands [GAZ:00002946]", - "New Caledonia [GAZ:00005206]", - "New Zealand [GAZ:00000469]", - "Nicaragua [GAZ:00002978]", - "Niger [GAZ:00000585]", - "Nigeria [GAZ:00000912]", - "Niue [GAZ:00006902]", - "Norfolk Island [GAZ:00005908]", - "North Korea [GAZ:00002801]", - "North Macedonia [GAZ:00006895]", - "North Sea [GAZ:00002284]", - "Northern Mariana Islands [GAZ:00003958]", - "Norway [GAZ:00002699]", - "Oman [GAZ:00005283]", - "Pakistan [GAZ:00005246]", - "Palau [GAZ:00006905]", - "Panama [GAZ:00002892]", - "Papua New Guinea [GAZ:00003922]", - "Paracel Islands [GAZ:00010832]", - "Paraguay [GAZ:00002933]", - "Peru [GAZ:00002932]", - "Philippines [GAZ:00004525]", - "Pitcairn Islands [GAZ:00005867]", - "Poland [GAZ:00002939]", - "Portugal [GAZ:00004126]", - "Puerto Rico [GAZ:00006935]", - "Qatar [GAZ:00005286]", - "Republic of the Congo [GAZ:00001088]", - "Reunion [GAZ:00003945]", - "Romania [GAZ:00002951]", - "Ross Sea [GAZ:00023304]", - "Russia [GAZ:00002721]", - "Rwanda [GAZ:00001087]", - "Saint Helena [GAZ:00000849]", - "Saint Kitts and Nevis [GAZ:00006906]", - "Saint Lucia [GAZ:00006909]", - "Saint Pierre and Miquelon [GAZ:00003942]", - "Saint Martin [GAZ:00005841]", - "Saint Vincent and the Grenadines [GAZ:02000565]", - "Samoa [GAZ:00006910]", - "San Marino [GAZ:00003102]", - "Sao Tome and Principe [GAZ:00006927]", - "Saudi Arabia [GAZ:00005279]", - "Senegal [GAZ:00000913]", - "Serbia [GAZ:00002957]", - "Seychelles [GAZ:00006922]", - "Sierra Leone [GAZ:00000914]", - "Singapore [GAZ:00003923]", - "Sint Maarten [GAZ:00012579]", - "Slovakia [GAZ:00002956]", - "Slovenia [GAZ:00002955]", - "Solomon Islands [GAZ:00005275]", - "Somalia [GAZ:00001104]", - "South Africa [GAZ:00001094]", - "South Georgia and the South Sandwich Islands [GAZ:00003990]", - "South Korea [GAZ:00002802]", - "South Sudan [GAZ:00233439]", - "Spain [GAZ:00003936]", - "Spratly Islands [GAZ:00010831]", - "Sri Lanka [GAZ:00003924]", - "State of Palestine [GAZ:00002475]", - "Sudan [GAZ:00000560]", - "Suriname [GAZ:00002525]", - "Svalbard [GAZ:00005396]", - "Swaziland [GAZ:00001099]", - "Sweden [GAZ:00002729]", - "Switzerland [GAZ:00002941]", - "Syria [GAZ:00002474]", - "Taiwan [GAZ:00005341]", - "Tajikistan [GAZ:00006912]", - "Tanzania [GAZ:00001103]", - "Thailand [GAZ:00003744]", - "Timor-Leste [GAZ:00006913]", - "Togo [GAZ:00000915]", - "Tokelau [GAZ:00260188]", - "Tonga [GAZ:00006916]", - "Trinidad and Tobago [GAZ:00003767]", - "Tromelin Island [GAZ:00005812]", - "Tunisia [GAZ:00000562]", - "Turkey [GAZ:00000558]", - "Turkmenistan [GAZ:00005018]", - "Turks and Caicos Islands [GAZ:00003955]", - "Tuvalu [GAZ:00009715]", - "USA [GAZ:00002459]", - "Uganda [GAZ:00001102]", - "Ukraine [GAZ:00002724]", - "United Arab Emirates [GAZ:00005282]", - "United Kingdom [GAZ:00002637]", - "Uruguay [GAZ:00002930]", - "Uzbekistan [GAZ:00004979]", - "Vanuatu [GAZ:00006918]", - "Venezuela [GAZ:00002931]", - "Viet Nam [GAZ:00003756]", - "Virgin Islands [GAZ:00003959]", - "Wake Island [GAZ:00007111]", - "Wallis and Futuna [GAZ:00007191]", - "West Bank [GAZ:00009572]", - "Western Sahara [GAZ:00000564]", - "Yemen [GAZ:00005284]", - "Zambia [GAZ:00001107]", - "Zimbabwe [GAZ:00001106]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001181 ", - "type": "string", - "description": "The country of origin of the sample.", - "examples": ["South Africa [GAZ:00001094]"], - "clasification":"Sample collection and processing", - "label":"Geo Loc Autonomic Country" - - }, - "geographic location (region and locality)": { - "ontology": "GENEPIO:0100280", - "type": "string", - "description": "The county/region of origin of the sample.", - "examples": ["Derbyshire"], - "clasification":"Sample collection and processing", - "label":"Geo Loc Province" - - }, - "geographic location (latitude)": { - "ontology": "OBI:0001620", - "type": "string", - "description": "The latitude coordinates of the geographical location of sample collection.", - "examples": ["38.98 N"], - "clasification":"Sample collection and processing", - "label":"Geo Loc Latitude", - - }, - "geographic location (longitude)": { - "ontology": "OBI:0001621", - "type": "string", - "description": "The longitude coordinates of the geographical location of sample collection.", - "examples": ["77.11 W"], - "clasification":"Sample collection and processing", - "label":"Geo Loc Longitude" - }, - "isolate": { - "ontology": "GENEPIO:0001644", - "type": "string", - "description": "Identifier of the specific isolate.", - "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"], - "genepio_label":"isolate identifier", - "clasification":"Sample collection and processing", - "label":"Isolate" - - }, - "purpose_sampling": { - "examples": ["Diagnostic testing"], - "ontology": "NCIT_C146997", - "type": "string", - "description": "The reason that the sample was collected.", - "clasification":"Sample collection and processing" - }, - "isolation source host-associated": { - "Enums": [ - "Blood [UBERON:0000178]", - "Fluid [UBERON:0006314]", - "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", - "Fluid (Pericardial) [UBERON:0002409]", - "Fluid (Pleural) [UBERON:0001087]", - "Fluid (Vaginal) [UBERON:0036243]", - "Fluid (Amniotic) [UBERON:0000173]", - "Saliva [UBERON:0001836]", - "Tissue [UBERON:0000479]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001211", - "type": "string", - "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "examples": ["Blood [UBERON:0000178]"], - "classification":"Sample collection and processing", - "label":"Organism Substance" - - }, - "isolation source non-host-associated": { - "Enums": [ - "Air vent [ENVO:03501208]", - "Banknote [ENVO:00003896]", - "Bed rail [ENVO:03501209]", - "Building Floor [ENVO:01000486]", - "Cloth [ENVO:02000058]", - "Control Panel [ENVO:03501210]", - "Door [ENVO:03501220]", - "Door Handle [ENVO:03501211]", - "Face Mask [OBI:0002787]", - "Face Shield [OBI:0002791]", - "Food [FOODON:00002403]", - "Food Packaging [FOODON:03490100]", - "Glass [ENVO:01000481]", - "Handrail [ENVO:03501212]", - "Hospital Gown [OBI:0002796]", - "Light Switch [ENVO:03501213]", - "Locker [ENVO:03501214]", - "N95 Mask [OBI:0002790]", - "Nurse Call Button [ENVO:03501215]", - "Paper [ENVO:03501256]", - "Particulate Matter [ENVO:01000060]", - "Plastic [ENVO:01000404]", - "PPE Gown [GENEPIO:0100025]", - "Sewage [ENVO:00002018]", - "Sink [ENVO:01000990]", - "Soil [ENVO:00001998]", - "Stainless Steel [ENVO:03501216]", - "Tissue Paper [ENVO:03501217]", - "Toilet Bowl [ENVO:03501218]", - "Water [ENVO:00002006]", - "Wastewater [ENVO:00002001]", - "Window [ENVO:03501219]", - "Wood [ENVO:00002040]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001223", - "type": "string", - "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", - "examples": ["Face Mask [OBI:0002787]"], - "clasification":"Sample collection and processing", - "label":"Environmental Material" - }, - "host common name": { - "Enums": [ - "Human [NCBITaxon:9606]", - "Bat [NCBITaxon:9397]", - "Cat [NCBITaxon:9685]", - "Chicken [NCBITaxon:9031]", - "Civet [NCBITaxon:9673]", - "Cow [NCBITaxon:9913]", - "Dog [NCBITaxon:9615]", - "Lion [NCBITaxon:9689]", - "Mink [NCBITaxon:452646]", - "Pangolin [NCBITaxon:9973]", - "Pig [NCBITaxon:9825]", - "Pigeon [NCBITaxon:8930]", - "Tiger [NCBITaxon:9694]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001386", - "type": "string", - "description": "The commonly used name of the host.", - "examples": ["Human [NCBITaxon:9606]"], - "classification":"Host information", - "label":"Host Common Name" - - }, - "host scientific name": { - "Enums": [ - "Bos taurus [NCBITaxon:9913]", - "Canis lupus familiaris [NCBITaxon:9615]", - "Chiroptera [NCBITaxon:9397]", - "Columbidae [NCBITaxon:8930]", - "Felis catus [NCBITaxon:9685]", - "Gallus gallus [NCBITaxon:9031]", - "Homo sapiens [NCBITaxon:9606]", - "Manis [NCBITaxon:9973]", - "Manis javanica [NCBITaxon:9974]", - "Neovison vison [NCBITaxon:452646]", - "Panthera leo [NCBITaxon:9689]", - "Panthera tigris [NCBITaxon:9694]", - "Rhinolophidae [NCBITaxon:58055]", - "Rhinolophus affinis [NCBITaxon:59477]", - "Sus scrofa domesticus [NCBITaxon:9825]", - "Viverridae [NCBITaxon:9673]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001387", - "type": "string", - "description": "The taxonomic, or scientific name of the host.", - "examples": ["Homo sapiens [NCBITaxon:9606]"], - "clasification":"Host information", - "label":"Host Scientific Name" - - }, - "host_health_state": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Health status of the host at the time of sample collection.", - "clasification":"Host information", - "genepio_label":"", - - }, - "host_age": { - "examples": ["e.g. 65 or 7 months, or unknown. Caution: the host age may be considered public health identifiable information. Consult the data steward before sharing. If the information is unknown or can not be shared, put unknown"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Patient age", - "clasification":"Host information" - }, - - "host_sex": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Gender or sex of the host.", - "clasification":"Host information", - "genepio_label":"", - - }, - "host_subject_id": { - "examples": ["e.g. #131"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "a unique identifier by which each subject can be referred to, de-identified.", - "clasification":"Host information", - "genepio_label":"", - - }, - "type exposure": { - "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], - "ontology": "GENEPIO:0001417", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", - "label":"Outbreak Exposure Event Location" - - }, - "subject exposure duration": { - "examples": ["e.g. Patient infected while traveling in …."], - "ontology": "0", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", - "label":"Additional Host Information" - - }, - "instrument_model": { - "Enums": [ - "Illumina sequencing instrument [GENEPIO:0100105]", - "Illumina Genome Analyzer [GENEPIO:0100106]", - "Illumina Genome Analyzer II [GENEPIO:0100107]", - "Illumina Genome Analyzer IIx [GENEPIO:0100108]", - "Illumina HiScanSQ [GENEPIO:0100109]", - "Illumina HiSeq [GENEPIO:0100110]", - "Illumina HiSeq X [GENEPIO:0100111]", - "Illumina HiSeq X Five [GENEPIO:0100112]", - "Illumina HiSeq X Ten [GENEPIO:0100113]", - "Illumina HiSeq 1000 [GENEPIO:0100114]", - "Illumina HiSeq 1500 [GENEPIO:0100115]", - "Illumina HiSeq 2000 [GENEPIO:0100116]", - "Illumina HiSeq 2500 [GENEPIO:0100117]", - "Illumina HiSeq 3000 [GENEPIO:0100118]", - "Illumina HiSeq 4000 [GENEPIO:0100119]", - "Illumina iSeq [GENEPIO:0100120]", - "Illumina iSeq 100 [GENEPIO:0100121]", - "Illumina NovaSeq [GENEPIO:0100122]", - "Illumina NovaSeq 6000 [GENEPIO:0100123]", - "Illumina MiniSeq [GENEPIO:0100124]", - "Illumina MiSeq [GENEPIO:0100125]", - "Illumina NextSeq [GENEPIO:0100126]", - "Illumina NextSeq 500 [GENEPIO:0100127]", - "Illumina NextSeq 550 [GENEPIO:0100128]", - "Illumina NextSeq 2000 [GENEPIO:0100129]", - "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", - "PacBio RS [GENEPIO:0100131]", - "PacBio RS II [GENEPIO:0100132]", - "PacBio Sequel [GENEPIO:0100133]", - "PacBio Sequel II [GENEPIO:0100134]", - "Ion Torrent sequencing instrument [GENEPIO:0100135]", - "Ion Torrent PGM [GENEPIO:0100136]", - "Ion Torrent Proton [GENEPIO:0100137]", - "Ion Torrent S5 XL [GENEPIO:0100138]", - "Ion Torrent S5 [GENEPIO:0100139]", - "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", - "Oxford Nanopore GridION [GENEPIO:0100141]", - "Oxford Nanopore MinION [GENEPIO:0100142]", - "Oxford Nanopore PromethION [GENEPIO:0100143]", - "BGI Genomics sequencing instrument [GENEPIO:0100144]", - "BGI SEQ-500 [GENEPIO:0100145]", - "MGI sequencing instrument [GENEPIO:0100146]", - "MGI DNBSEQ-T7 [GENEPIO:0100147]", - "MGI DNBSEQ-G400 [GENEPIO:0100148]", - "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", - "MGI DNBSEQ-G50 [GENEPIO:0100150]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001452", - "type": "string", - "description": "The model of the sequencing instrument used.", - "examples": ["Oxford Nanopore MinION [GENEPIO:0100142]"], - "classification":"Sequencing", - "label":"Sequencing Instrument Model" - }, - "instrument_platform ": { - "examples": ["MinIon"], - "ontology": "0", - "type": "string", - "description": "The model of the sequencing instrument used.", - "label":"Sequencing Platforms " - }, - "file_name": { - "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], - "ontology": "GENEPIO:0001476", - "type": "string", - "description": "The user-specified filename of the r1 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Sequence file R1 fastq" - }, - "tax_id": { - "examples": ["probably 2697049 in all cases"], - "ontology": "GENEPIO_0001724", - "type": "string", - "description": "The NCBITaxon identifier for the organism being sequenced.", - "clasification":"Sample collection and processing", - "label":"Tax ID" - }, - "scientific_name": { - "Enums": [ - "Coronaviridae [NCBITaxon:11118]", - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "examples": [""], - "ontology": "GENEPIO:0001191", - "type": "string", - "description": "The taxonomic name of the organism.", - "clasification":"Sample collection and processing", - "classification":"Sample collection and processing", - "label":"Organism" - }, - "common_name": { - "examples": [""], - "ontology": "BU_ISCIII:003", - "type": "string", - "description": "The common name of the organism.", - "clasification":"Sample collection and processing", - "label":"Common name" - }, - "sample_description": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Free text description of the sample.", - "clasification":"Sample collection and processing", - "genepio_label":"", - - }, - "sample_storage_conditions": { - "examples": ["24 degrees celsius"], - "ontology": "NCIT_C115535", - "type": "string", - "description": "The name and version of a particular protocol used for sampling.", - "clasification":"Sample collection and processing" - }, - "library_source": { - "Enums": ["5-methycytidine antibody method [GENPIO:0001941]", - "CAGE method [GENPIO:0001942]", - "CF-H method [GENPIO:0001943]", - "CF-M method ]GENPIO:0001944]", - "CF-S method [GENPIO:0001945]", - "CF-T method [GENPIO:0001946]", - "ChIP method ]GENPIO:0001947]", - "DNAse method [GENPIO:0001948]", - "HMPR method [GENPIO:0001949]", - "Hybrid Selection Method [GENPIO:0001950]", - "MBD2 protein methyl-CpG binding domain method [GENPIO:0001951]", - "MF method [GENPIO:0001952]", - "MNase method [GENPIO:0001953]", - "MSLL method [GENPIO:0001954]", - "PCR method [GENPIO:0001955]", - "RACE method [GENPIO:0001956]", - "RANDOM PCR method [GENPIO:0001957]", - "RANDOM method [GENPIO:0001958]", - "RT-PCR method [GENPIO:0001959]", - "Reduced Representation method [GENPIO:0001960]", - "Resctriction Digest method [GENPIO:0001961]", - "cDNA method [GENPIO:0001962]", - "other library method [GENPIO:0001964]", - "size fractionation method [GENPIO:0001963]", - ], - "examples": ["METAGENOMIC"], - "ontology": "GENEPIO_0001965", - "type": "string", - "description": "Molecule type used to make the library.", - "clasification":"Sequencing", - "label":"Source material" - }, - "library_selection": { - "examples": ["RANDOM PCR"], - "ontology": "GENPIO_0001940", - "type": "string", - "description": "Library capture method.", - "clasification":"Sequencing", - "label":"Capture method" - }, - "library_strategy": { - "Enums": ["Bisultife-Seq strategy [GENPIO:0001975]", - "CTS strategy [GENPIO:0001978]", - "ChIP-Seq strategy [GENPIO:0001979]", - "DNase-Hypersensitivity strategy [GENPIO:0001980]", - "EST strategy [GENPIO:0001981]", - "FL-cDNA strategy [GENPIO:0001983]", - "MB-Seq strategy [GENPIO:0001984]", - "MNase-Seq strategy [GENPIO:0001985]", - "MRE-Seq strategy [GENPIO:0001986]", - "MeDIP-Seq strategy [GENPIO:0001987]", - "RNA-Seq strategy [GENPIO:0001990]", - "WCS strategy [GENPIO:0001991]", - "WGS strategy [GENPIO:0001992]", - "WXS strategy [GENPIO:0001993]", - "amplicon strategy [GENPIO:0001974]", - "clone end strategy [GENPIO:0001976]", - "clone strategy [GENPIO:0001977]", - "finishing strategy [GENPIO:0001982]", - "other library strategy [GENPIO:0001988]", - "pool clone strategy [GENPIO:0001989]", - ], - "examples": ["WGS"], - "ontology": "GENPIO_0001973", - "type": "string", - "description": "Overall sequencing strategy or approach.", - "clasification":"Sequencing", - "label":"Sequencing technique" - }, - "library_layout": { - "examples": ["PAIRED"], - "ontology":"BU_ISCIII:007", - "type": "string", - "description": "Single or paired.", - "clasification":"Sequencing", - "label":"Library Layout" - }, - "library_name": { - "examples": ["e.g P17157_1007"], - "ontology": "GENEPIO_0001995", - "type": "string", - "description": "The submitter's name for this library.", - "clasification":"Sequencing", - "label":"Library Name" - }, - "nominal_length ": { - "examples": ["350"], - "ontology": "GENEPIO_0000076", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Nominal Length" - }, - "analysis_accession": { - "examples": [""], - "ontology": "GENEPIO_0001145", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Analysis Accession" - }, - "read_length": { - "examples": [""], - "ontology": "STATO_0000064", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Read length" - }, - "study_accession": { - "examples": ["e.g PRJEB39632"], - "ontology": "GENEPIO_0001136", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Study accession" - }, - "secondary_study_accession": { - "examples": ["e.g ERP123173"], - "ontology": "BU_ISCIII:012", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Secondary study accession" - }, - "sample_accession": { - "examples": ["e.g SAMEA7098096"], - "ontology": "GENEPIO_0001139", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Sample accession" - }, - "secondary_sample_accession": { - "examples": ["e.g ERS4858671"], - "ontology": "BU_ISCIII:014", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Secondary sample accession" - }, - "experiment_accession": { - "examples": ["e.g ERX4331406"], - "ontology": "BU_ISCIII:015", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Experiment Accession" - }, - "run_accession": { - "examples": ["e.g ERX4331406"], - "ontology": "BU_ISCIII:016", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Run Accession" - }, - "submission_accession": { - "examples": ["e.g ERA2794974"], - "ontology": "BU_ISCIII:017", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submission accession" - }, - "read_count": { - "examples": ["e.g 837055"], - "ontology": "STATO_0000064", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Read count" - }, - "base_count": { - "examples": ["e.g 503907110"], - "ontology": "UO_0000244", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Base count" - }, - "center_name": { - "examples": [" KAROLINSKA INSITUTET"], - "ontology": "NCIT_C19983", - "type": "string", - "description": "The name of the institution", - "clasification":"Sample collection and processing", - "label":"Center Name" - }, - "first_public": { - "examples": ["e.g 2020-08-07"], - "ontology": "NCIT_C142711", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"First Public date" - }, - "last_updated": { - "examples": ["e.g 2020-07-29"], - "ontology": "OMIABIS_0001005", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "format":"Last Updated" - }, - "experiment_title": { - "examples": ["e.g Illumina MiSeq paired end sequencing"], - "ontology": "ORNASEQ_0000004", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Experiment title" - }, - "study_title": { - "examples": ["e.g SARS-CoV-2 genomes from late April in Stockholm"], - "ontology": "OPMI_0000380", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Study title" - }, - "study_alias": { - "examples": ["e.g Sweden"], - "ontology": "SIO_001066", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Study alias" - }, - "experiment_alias": { - "examples": ["e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092"], - "ontology": "NCIT_C42790", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Experiment alias" - }, - "run_alias": { - "examples": ["e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "NCIT_C47911", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Run Alias" - }, - "fastq_bytes": { - "examples": ["e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "NCIT_C48047", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq bytes" - }, - "fastq_md5": { - "examples": [""], - "ontology": "MS_1000568", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq md5" - }, - "fastq_ftp": { - "examples": [""], - "ontology": "PRIDE_0000469", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq ftp" - }, - "fastq_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "BU_ISCIII:032", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq aspera" - }, - "fastq_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "ENVO_01000807", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq galaxy" - }, - "submitted_bytes": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "NCIT_C172872", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted bytes " - }, - "submitted_md5": { - "examples": ["e.g 139853010;166270048"], - "ontology": "BU_ISCIII:035", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted md5" - }, - "submitted_ftp": { - "examples": ["e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a"], - "ontology": "BU_ISCIII:036", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted ftp" - }, - "submitted_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "BU_ISCIII:037", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted aspera" - }, - "submitted_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "BU_ISCIII:038", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted Galaxy" - }, - "submitted_format": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "BU_ISCIII:039", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted Format" - }, - "sra_bytes": { - "examples": ["e.g FASTQ;FASTQ"], - "ontology": "BU_ISCIII:040", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA bytes" - }, - "sra_md5": { - "examples": ["e.g 260236789"], - "ontology": "BU_ISCIII:041", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA md5" - }, - "sra_ftp": { - "examples": ["e.g 2cf0d467d6dc4ae0a5473774d54c059c"], - "ontology": "BU_ISCIII:042", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA ftp" - }, - "sra_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385"], - "ontology": "BU_ISCIII:043", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA aspera" - }, - "sra_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385"], - "ontology": "BU_ISCIII:044", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA galaxy" - }, - "broker_name": { - "examples": ["P17157_1007"], - "ontology": "BU_ISCIII:045", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Broker Name" - }, - "nominal_sdev": { - "examples": [""], - "ontology": "STATO_0000237", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Nominal sdev" - }, - "first_created": { - "examples": ["e.g 2020-08-07"], - "ontology": "NCIT_C164483", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"First created date" - } - + "$schema": "http://json-schema.org/draft/2019-09/schema#", + "required": [ + "sample_name", + "collecting_institution", + "geographic_location_(country_and/or_sea)", + "isolate", + "host_scientific_name", + "host_common_name", + "host_subject_id", + "instrument_model", + "file_name", + "sample_name", + "tax_id", + "scientific_name", + "common_name", + "sample_description", + "library_source", + "library_selection", + "library_strategy", + "library_layout" + ], + "type": "object", + "properties": { + "sample_name": { + "examples": [ + "prov_rona_99" + ], + "ontology": "GENEPIO:0001123", + "type": "string", + "description": "The user-defined name for the sample.", + "clasification": "Database Identifiers", + "label": "Collecting Sample id" + }, + "collecting_institution": { + "examples": [ + "Public Health Agency of Canada" + ], + "ontology": "GENEPIO:0001153", + "type": "string", + "description": "Name of the institution to which the person collecting the specimen belongs. Format: Institute Name, Institute Address", + "label": "Originating Laboratory" + }, + "collection_date": { + "examples": [ + "3/19/2020" + ], + "ontology": "GENEPIO:0001174", + "type": "string", + "description": "The date on which the sample was collected.", + "format": "date", + "classification": "Sample collection and processing", + "label": "Sample Collection Date" + }, + "receipt_date": { + "examples": [ + "3/21/2020" + ], + "ontology": "GENEPIO:0001179", + "type": "string", + "description": "The date on which the sample was received.", + "format": "date", + "clasification": "Sample collection and processing", + "label": "Sample Received Date" + }, + "geographic_location_(country_and/or_sea)": { + "Enums": [ + "Afghanistan [GAZ:00006882]", + "Albania [GAZ:00002953]", + "Algeria [GAZ:00000563]", + "American Samoa [GAZ:00003957]", + "Andorra [GAZ:00002948]", + "Angola [GAZ:00001095]", + "Anguilla [GAZ:00009159]", + "Antarctica [GAZ:00000462]", + "Antigua and Barbuda [GAZ:00006883]", + "Argentina [GAZ:00002928]", + "Armenia [GAZ:00004094]", + "Aruba [GAZ:00004025]", + "Ashmore and Cartier Islands [GAZ:00005901]", + "Australia [GAZ:00000463]", + "Austria [GAZ:00002942]", + "Azerbaijan [GAZ:00004941]", + "Bahamas [GAZ:00002733]", + "Bahrain [GAZ:00005281]", + "Baker Island [GAZ:00007117]", + "Bangladesh [GAZ:00003750]", + "Barbados [GAZ:00001251]", + "Bassas da India [GAZ:00005810]", + "Belarus [GAZ:00006886]", + "Belgium [GAZ:00002938]", + "Belize [GAZ:00002934]", + "Benin [GAZ:00000904]", + "Bermuda [GAZ:00001264]", + "Bhutan [GAZ:00003920]", + "Bolivia [GAZ:00002511]", + "Borneo [GAZ:00025355]", + "Bosnia and Herzegovina [GAZ:00006887]", + "Botswana [GAZ:00001097]", + "Bouvet Island [GAZ:00001453]", + "Brazil [GAZ:00002828]", + "British Virgin Islands [GAZ:00003961]", + "Brunei [GAZ:00003901]", + "Bulgaria [GAZ:00002950]", + "Burkina Faso [GAZ:00000905]", + "Burundi [GAZ:00001090]", + "Cambodia [GAZ:00006888]", + "Cameroon [GAZ:00001093]", + "Canada [GAZ:00002560]", + "Cape Verde [GAZ:00001227]", + "Cayman Islands [GAZ:00003986]", + "Central African Republic [GAZ:00001089]", + "Chad [GAZ:00000586]", + "Chile [GAZ:00002825]", + "China [GAZ:00002845]", + "Christmas Island [GAZ:00005915]", + "Clipperton Island [GAZ:00005838]", + "Cocos Islands [GAZ:00009721]", + "Colombia [GAZ:00002929]", + "Comoros [GAZ:00005820]", + "Cook Islands [GAZ:00053798]", + "Coral Sea Islands [GAZ:00005917]", + "Costa Rica [GAZ:00002901]", + "Cote d'Ivoire [GAZ:00000906]", + "Croatia [GAZ:00002719]", + "Cuba [GAZ:00003762]", + "Curacao [GAZ:00012582]", + "Cyprus [GAZ:00004006]", + "Czech Republic [GAZ:00002954]", + "Democratic Republic of the Congo [GAZ:00001086]", + "Denmark [GAZ:00005852]", + "Djibouti [GAZ:00000582]", + "Dominica [GAZ:00006890]", + "Dominican Republic [GAZ:00003952]", + "Ecuador [GAZ:00002912]", + "Egypt [GAZ:00003934]", + "El Salvador [GAZ:00002935]", + "Equatorial Guinea [GAZ:00001091]", + "Eritrea [GAZ:00000581]", + "Estonia [GAZ:00002959]", + "Eswatini [GAZ:00001099]", + "Ethiopia [GAZ:00000567]", + "Europa Island [GAZ:00005811]", + "Falkland Islands (Islas Malvinas) [GAZ:00001412]", + "Faroe Islands [GAZ:00059206]", + "Fiji [GAZ:00006891]", + "Finland [GAZ:00002937]", + "France [GAZ:00003940]", + "French Guiana [GAZ:00002516]", + "French Polynesia [GAZ:00002918]", + "French Southern and Antarctic Lands [GAZ:00003753]", + "Gabon [GAZ:00001092]", + "Gambia [GAZ:00000907]", + "Gaza Strip [GAZ:00009571]", + "Georgia [GAZ:00004942]", + "Germany [GAZ:00002646]", + "Ghana [GAZ:00000908]", + "Gibraltar [GAZ:00003987]", + "Glorioso Islands [GAZ:00005808]", + "Greece [GAZ:00002945]", + "Greenland [GAZ:00001507]", + "Grenada [GAZ:02000573]", + "Guadeloupe [GAZ:00067142]", + "Guam [GAZ:00003706]", + "Guatemala [GAZ:00002936]", + "Guernsey [GAZ:00001550]", + "Guinea [GAZ:00000909]", + "Guinea-Bissau [GAZ:00000910]", + "Guyana [GAZ:00002522]", + "Haiti [GAZ:00003953]", + "Heard Island and McDonald Islands [GAZ:00009718]", + "Honduras [GAZ:00002894]", + "Hong Kong [GAZ:00003203]", + "Howland Island [GAZ:00007120]", + "Hungary [GAZ:00002952]", + "Iceland [GAZ:00000843]", + "India [GAZ:00002839]", + "Indonesia [GAZ:00003727]", + "Iran [GAZ:00004474]", + "Iraq [GAZ:00004483]", + "Ireland [GAZ:00002943]", + "Isle of Man [GAZ:00052477]", + "Israel [GAZ:00002476]", + "Italy [GAZ:00002650]", + "Jamaica [GAZ:00003781]", + "Jan Mayen [GAZ:00005853]", + "Japan [GAZ:00002747]", + "Jarvis Island [GAZ:00007118]", + "Jersey [GAZ:00001551]", + "Johnston Atoll [GAZ:00007114]", + "Jordan [GAZ:00002473]", + "Juan de Nova Island [GAZ:00005809]", + "Kazakhstan [GAZ:00004999]", + "Kenya [GAZ:00001101]", + "Kerguelen Archipelago [GAZ:00005682]", + "Kingman Reef [GAZ:00007116]", + "Kiribati [GAZ:00006894]", + "Kosovo [GAZ:00011337]", + "Kuwait [GAZ:00005285]", + "Kyrgyzstan [GAZ:00006893]", + "Laos [GAZ:00006889]", + "Latvia [GAZ:00002958]", + "Lebanon [GAZ:00002478]", + "Lesotho [GAZ:00001098]", + "Liberia [GAZ:00000911]", + "Libya [GAZ:00000566]", + "Liechtenstein [GAZ:00003858]", + "Line Islands [GAZ:00007144]", + "Lithuania [GAZ:00002960]", + "Luxembourg [GAZ:00002947]", + "Macau [GAZ:00003202]", + "Madagascar [GAZ:00001108]", + "Malawi [GAZ:00001105]", + "Malaysia [GAZ:00003902]", + "Maldives [GAZ:00006924]", + "Mali [GAZ:00000584]", + "Malta [GAZ:00004017]", + "Marshall Islands [GAZ:00007161]", + "Martinique [GAZ:00067143]", + "Mauritania [GAZ:00000583]", + "Mauritius [GAZ:00003745]", + "Mayotte [GAZ:00003943]", + "Mexico [GAZ:00002852]", + "Micronesia [GAZ:00005862]", + "Midway Islands [GAZ:00007112]", + "Moldova [GAZ:00003897]", + "Monaco [GAZ:00003857]", + "Mongolia [GAZ:00008744]", + "Montenegro [GAZ:00006898]", + "Montserrat [GAZ:00003988]", + "Morocco [GAZ:00000565]", + "Mozambique [GAZ:00001100]", + "Myanmar [GAZ:00006899]", + "Namibia [GAZ:00001096]", + "Nauru [GAZ:00006900]", + "Navassa Island [GAZ:00007119]", + "Nepal [GAZ:00004399]", + "Netherlands [GAZ:00002946]", + "New Caledonia [GAZ:00005206]", + "New Zealand [GAZ:00000469]", + "Nicaragua [GAZ:00002978]", + "Niger [GAZ:00000585]", + "Nigeria [GAZ:00000912]", + "Niue [GAZ:00006902]", + "Norfolk Island [GAZ:00005908]", + "North Korea [GAZ:00002801]", + "North Macedonia [GAZ:00006895]", + "North Sea [GAZ:00002284]", + "Northern Mariana Islands [GAZ:00003958]", + "Norway [GAZ:00002699]", + "Oman [GAZ:00005283]", + "Pakistan [GAZ:00005246]", + "Palau [GAZ:00006905]", + "Panama [GAZ:00002892]", + "Papua New Guinea [GAZ:00003922]", + "Paracel Islands [GAZ:00010832]", + "Paraguay [GAZ:00002933]", + "Peru [GAZ:00002932]", + "Philippines [GAZ:00004525]", + "Pitcairn Islands [GAZ:00005867]", + "Poland [GAZ:00002939]", + "Portugal [GAZ:00004126]", + "Puerto Rico [GAZ:00006935]", + "Qatar [GAZ:00005286]", + "Republic of the Congo [GAZ:00001088]", + "Reunion [GAZ:00003945]", + "Romania [GAZ:00002951]", + "Ross Sea [GAZ:00023304]", + "Russia [GAZ:00002721]", + "Rwanda [GAZ:00001087]", + "Saint Helena [GAZ:00000849]", + "Saint Kitts and Nevis [GAZ:00006906]", + "Saint Lucia [GAZ:00006909]", + "Saint Pierre and Miquelon [GAZ:00003942]", + "Saint Martin [GAZ:00005841]", + "Saint Vincent and the Grenadines [GAZ:02000565]", + "Samoa [GAZ:00006910]", + "San Marino [GAZ:00003102]", + "Sao Tome and Principe [GAZ:00006927]", + "Saudi Arabia [GAZ:00005279]", + "Senegal [GAZ:00000913]", + "Serbia [GAZ:00002957]", + "Seychelles [GAZ:00006922]", + "Sierra Leone [GAZ:00000914]", + "Singapore [GAZ:00003923]", + "Sint Maarten [GAZ:00012579]", + "Slovakia [GAZ:00002956]", + "Slovenia [GAZ:00002955]", + "Solomon Islands [GAZ:00005275]", + "Somalia [GAZ:00001104]", + "South Africa [GAZ:00001094]", + "South Georgia and the South Sandwich Islands [GAZ:00003990]", + "South Korea [GAZ:00002802]", + "South Sudan [GAZ:00233439]", + "Spain [GAZ:00003936]", + "Spratly Islands [GAZ:00010831]", + "Sri Lanka [GAZ:00003924]", + "State of Palestine [GAZ:00002475]", + "Sudan [GAZ:00000560]", + "Suriname [GAZ:00002525]", + "Svalbard [GAZ:00005396]", + "Swaziland [GAZ:00001099]", + "Sweden [GAZ:00002729]", + "Switzerland [GAZ:00002941]", + "Syria [GAZ:00002474]", + "Taiwan [GAZ:00005341]", + "Tajikistan [GAZ:00006912]", + "Tanzania [GAZ:00001103]", + "Thailand [GAZ:00003744]", + "Timor-Leste [GAZ:00006913]", + "Togo [GAZ:00000915]", + "Tokelau [GAZ:00260188]", + "Tonga [GAZ:00006916]", + "Trinidad and Tobago [GAZ:00003767]", + "Tromelin Island [GAZ:00005812]", + "Tunisia [GAZ:00000562]", + "Turkey [GAZ:00000558]", + "Turkmenistan [GAZ:00005018]", + "Turks and Caicos Islands [GAZ:00003955]", + "Tuvalu [GAZ:00009715]", + "USA [GAZ:00002459]", + "Uganda [GAZ:00001102]", + "Ukraine [GAZ:00002724]", + "United Arab Emirates [GAZ:00005282]", + "United Kingdom [GAZ:00002637]", + "Uruguay [GAZ:00002930]", + "Uzbekistan [GAZ:00004979]", + "Vanuatu [GAZ:00006918]", + "Venezuela [GAZ:00002931]", + "Viet Nam [GAZ:00003756]", + "Virgin Islands [GAZ:00003959]", + "Wake Island [GAZ:00007111]", + "Wallis and Futuna [GAZ:00007191]", + "West Bank [GAZ:00009572]", + "Western Sahara [GAZ:00000564]", + "Yemen [GAZ:00005284]", + "Zambia [GAZ:00001107]", + "Zimbabwe [GAZ:00001106]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001181 ", + "type": "string", + "description": "The country of origin of the sample.", + "examples": [ + "South Africa [GAZ:00001094]" + ], + "clasification": "Sample collection and processing", + "label": "Geo Loc Autonomic Country" + }, + "geographic location (region and locality)": { + "ontology": "GENEPIO:0100280", + "type": "string", + "description": "The county/region of origin of the sample.", + "examples": [ + "Derbyshire" + ], + "clasification": "Sample collection and processing", + "label": "Geo Loc Province" + }, + "geographic location (latitude)": { + "ontology": "OBI:0001620", + "type": "string", + "description": "The latitude coordinates of the geographical location of sample collection.", + "examples": [ + "38.98 N" + ], + "clasification": "Sample collection and processing", + "label": "Geo Loc Latitude", + }, + "geographic location (longitude)": { + "ontology": "OBI:0001621", + "type": "string", + "description": "The longitude coordinates of the geographical location of sample collection.", + "examples": [ + "77.11 W" + ], + "clasification": "Sample collection and processing", + "label": "Geo Loc Longitude" + }, + "isolate": { + "ontology": "GENEPIO:0001644", + "type": "string", + "description": "Identifier of the specific isolate.", + "examples": [ + "SARS-CoV-2/human/USA/CA-CDPH-001/2020" + ], + "genepio_label": "isolate identifier", + "clasification": "Sample collection and processing", + "label": "Isolate" + }, + "purpose_sampling": { + "examples": [ + "Diagnostic testing" + ], + "ontology": "NCIT_C146997", + "type": "string", + "description": "The reason that the sample was collected.", + "clasification": "Sample collection and processing" + }, + "isolation source host-associated": { + "Enums": [ + "Blood [UBERON:0000178]", + "Fluid [UBERON:0006314]", + "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", + "Fluid (Pericardial) [UBERON:0002409]", + "Fluid (Pleural) [UBERON:0001087]", + "Fluid (Vaginal) [UBERON:0036243]", + "Fluid (Amniotic) [UBERON:0000173]", + "Saliva [UBERON:0001836]", + "Tissue [UBERON:0000479]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001211", + "type": "string", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "examples": [ + "Blood [UBERON:0000178]" + ], + "classification": "Sample collection and processing", + "label": "Organism Substance" + }, + "isolation source non-host-associated": { + "Enums": [ + "Air vent [ENVO:03501208]", + "Banknote [ENVO:00003896]", + "Bed rail [ENVO:03501209]", + "Building Floor [ENVO:01000486]", + "Cloth [ENVO:02000058]", + "Control Panel [ENVO:03501210]", + "Door [ENVO:03501220]", + "Door Handle [ENVO:03501211]", + "Face Mask [OBI:0002787]", + "Face Shield [OBI:0002791]", + "Food [FOODON:00002403]", + "Food Packaging [FOODON:03490100]", + "Glass [ENVO:01000481]", + "Handrail [ENVO:03501212]", + "Hospital Gown [OBI:0002796]", + "Light Switch [ENVO:03501213]", + "Locker [ENVO:03501214]", + "N95 Mask [OBI:0002790]", + "Nurse Call Button [ENVO:03501215]", + "Paper [ENVO:03501256]", + "Particulate Matter [ENVO:01000060]", + "Plastic [ENVO:01000404]", + "PPE Gown [GENEPIO:0100025]", + "Sewage [ENVO:00002018]", + "Sink [ENVO:01000990]", + "Soil [ENVO:00001998]", + "Stainless Steel [ENVO:03501216]", + "Tissue Paper [ENVO:03501217]", + "Toilet Bowl [ENVO:03501218]", + "Water [ENVO:00002006]", + "Wastewater [ENVO:00002001]", + "Window [ENVO:03501219]", + "Wood [ENVO:00002040]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001223", + "type": "string", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "examples": [ + "Face Mask [OBI:0002787]" + ], + "clasification": "Sample collection and processing", + "label": "Environmental Material" + }, + "host common name": { + "Enums": [ + "Human [NCBITaxon:9606]", + "Bat [NCBITaxon:9397]", + "Cat [NCBITaxon:9685]", + "Chicken [NCBITaxon:9031]", + "Civet [NCBITaxon:9673]", + "Cow [NCBITaxon:9913]", + "Dog [NCBITaxon:9615]", + "Lion [NCBITaxon:9689]", + "Mink [NCBITaxon:452646]", + "Pangolin [NCBITaxon:9973]", + "Pig [NCBITaxon:9825]", + "Pigeon [NCBITaxon:8930]", + "Tiger [NCBITaxon:9694]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001386", + "type": "string", + "description": "The commonly used name of the host.", + "examples": [ + "Human [NCBITaxon:9606]" + ], + "classification": "Host information", + "label": "Host Common Name" + }, + "host scientific name": { + "Enums": [ + "Bos taurus [NCBITaxon:9913]", + "Canis lupus familiaris [NCBITaxon:9615]", + "Chiroptera [NCBITaxon:9397]", + "Columbidae [NCBITaxon:8930]", + "Felis catus [NCBITaxon:9685]", + "Gallus gallus [NCBITaxon:9031]", + "Homo sapiens [NCBITaxon:9606]", + "Manis [NCBITaxon:9973]", + "Manis javanica [NCBITaxon:9974]", + "Neovison vison [NCBITaxon:452646]", + "Panthera leo [NCBITaxon:9689]", + "Panthera tigris [NCBITaxon:9694]", + "Rhinolophidae [NCBITaxon:58055]", + "Rhinolophus affinis [NCBITaxon:59477]", + "Sus scrofa domesticus [NCBITaxon:9825]", + "Viverridae [NCBITaxon:9673]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001387", + "type": "string", + "description": "The taxonomic, or scientific name of the host.", + "examples": [ + "Homo sapiens [NCBITaxon:9606]" + ], + "clasification": "Host information", + "label": "Host Scientific Name" + }, + "host_subject_id": { + "examples": [ + "e.g. #131" + ], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "a unique identifier by which each subject can be referred to, de-identified.", + "clasification": "Host information", + "genepio_label": "", + }, + "type exposure": { + "examples": [ + "Date, Location e.g. type of gathering, Family cluster, etc." + ], + "ontology": "GENEPIO:0001417", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification": "Host information", + "label": "Outbreak Exposure Event Location" + }, + "subject exposure duration": { + "examples": [ + "e.g. Patient infected while traveling in …." + ], + "ontology": "GENEPIO_0001268", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification": "Host information", + "label": "Additional Host Information" + }, + "instrument_model": { + "Enums": [ + "Illumina sequencing instrument [GENEPIO:0100105]", + "Illumina Genome Analyzer [GENEPIO:0100106]", + "Illumina Genome Analyzer II [GENEPIO:0100107]", + "Illumina Genome Analyzer IIx [GENEPIO:0100108]", + "Illumina HiScanSQ [GENEPIO:0100109]", + "Illumina HiSeq [GENEPIO:0100110]", + "Illumina HiSeq X [GENEPIO:0100111]", + "Illumina HiSeq X Five [GENEPIO:0100112]", + "Illumina HiSeq X Ten [GENEPIO:0100113]", + "Illumina HiSeq 1000 [GENEPIO:0100114]", + "Illumina HiSeq 1500 [GENEPIO:0100115]", + "Illumina HiSeq 2000 [GENEPIO:0100116]", + "Illumina HiSeq 2500 [GENEPIO:0100117]", + "Illumina HiSeq 3000 [GENEPIO:0100118]", + "Illumina HiSeq 4000 [GENEPIO:0100119]", + "Illumina iSeq [GENEPIO:0100120]", + "Illumina iSeq 100 [GENEPIO:0100121]", + "Illumina NovaSeq [GENEPIO:0100122]", + "Illumina NovaSeq 6000 [GENEPIO:0100123]", + "Illumina MiniSeq [GENEPIO:0100124]", + "Illumina MiSeq [GENEPIO:0100125]", + "Illumina NextSeq [GENEPIO:0100126]", + "Illumina NextSeq 500 [GENEPIO:0100127]", + "Illumina NextSeq 550 [GENEPIO:0100128]", + "Illumina NextSeq 2000 [GENEPIO:0100129]", + "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", + "PacBio RS [GENEPIO:0100131]", + "PacBio RS II [GENEPIO:0100132]", + "PacBio Sequel [GENEPIO:0100133]", + "PacBio Sequel II [GENEPIO:0100134]", + "Ion Torrent sequencing instrument [GENEPIO:0100135]", + "Ion Torrent PGM [GENEPIO:0100136]", + "Ion Torrent Proton [GENEPIO:0100137]", + "Ion Torrent S5 XL [GENEPIO:0100138]", + "Ion Torrent S5 [GENEPIO:0100139]", + "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", + "Oxford Nanopore GridION [GENEPIO:0100141]", + "Oxford Nanopore MinION [GENEPIO:0100142]", + "Oxford Nanopore PromethION [GENEPIO:0100143]", + "BGI Genomics sequencing instrument [GENEPIO:0100144]", + "BGI SEQ-500 [GENEPIO:0100145]", + "MGI sequencing instrument [GENEPIO:0100146]", + "MGI DNBSEQ-T7 [GENEPIO:0100147]", + "MGI DNBSEQ-G400 [GENEPIO:0100148]", + "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", + "MGI DNBSEQ-G50 [GENEPIO:0100150]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001452", + "type": "string", + "description": "The model of the sequencing instrument used.", + "examples": [ + "Oxford Nanopore MinION [GENEPIO:0100142]" + ], + "classification": "Sequencing", + "label": "Sequencing Instrument Model" + }, + "instrument_platform": { + "examples": [ + "MinIon" + ], + "ontology": "GENEPIO_0000071", + "type": "string", + "description": "The model of the sequencing instrument used.", + "label": "Sequencing Platforms " + }, + "file_name": { + "examples": [ + "ABC123_S1_L001_R1_001.fastq.gz" + ], + "ontology": "GENEPIO:0001476", + "type": "string", + "description": "The user-specified filename of the r1 FASTQ file.", + "clasification": "Bioinformatics and QC metrics", + "label": "Sequence file R1 fastq" + }, + "tax_id": { + "examples": [ + "probably 2697049 in all cases" + ], + "ontology": "GENEPIO_0001724", + "type": "string", + "description": "The NCBITaxon identifier for the organism being sequenced.", + "clasification": "Sample collection and processing", + "label": "Tax ID" + }, + "scientific_name": { + "Enums": [ + "Coronaviridae [NCBITaxon:11118]", + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "examples": [ + "" + ], + "ontology": "GENEPIO:0001191", + "type": "string", + "description": "The taxonomic name of the organism.", + "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", + "label": "Organism" + }, + "common_name": { + "examples": [ + "" + ], + "ontology": "NCIT:C164471", + "type": "string", + "description": "The common name of the organism.", + "clasification": "Sample collection and processing", + "label": "Common name" + }, + "sample_description": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Free text description of the sample.", + "clasification": "Sample collection and processing", + "genepio_label": "", + }, + "sample_storage_conditions": { + "examples": [ + "24 degrees celsius" + ], + "ontology": "NCIT_C115535", + "type": "string", + "description": "The name and version of a particular protocol used for sampling.", + "clasification": "Sample collection and processing" + }, + "library_source": { + "Enums": [ + "5-methycytidine antibody method [GENPIO:0001941]", + "CAGE method [GENPIO:0001942]", + "CF-H method [GENPIO:0001943]", + "CF-M method ]GENPIO:0001944]", + "CF-S method [GENPIO:0001945]", + "CF-T method [GENPIO:0001946]", + "ChIP method ]GENPIO:0001947]", + "DNAse method [GENPIO:0001948]", + "HMPR method [GENPIO:0001949]", + "Hybrid Selection Method [GENPIO:0001950]", + "MBD2 protein methyl-CpG binding domain method [GENPIO:0001951]", + "MF method [GENPIO:0001952]", + "MNase method [GENPIO:0001953]", + "MSLL method [GENPIO:0001954]", + "PCR method [GENPIO:0001955]", + "RACE method [GENPIO:0001956]", + "RANDOM PCR method [GENPIO:0001957]", + "RANDOM method [GENPIO:0001958]", + "RT-PCR method [GENPIO:0001959]", + "Reduced Representation method [GENPIO:0001960]", + "Resctriction Digest method [GENPIO:0001961]", + "cDNA method [GENPIO:0001962]", + "other library method [GENPIO:0001964]", + "size fractionation method [GENPIO:0001963]", + ], + "examples": [ + "METAGENOMIC" + ], + "ontology": "GENEPIO_0001965", + "type": "string", + "description": "Molecule type used to make the library.", + "clasification": "Sequencing", + "label": "Source material" + }, + "library_selection": { + "examples": [ + "RANDOM PCR" + ], + "ontology": "GENPIO_0001940", + "type": "string", + "description": "Library capture method.", + "clasification": "Sequencing", + "label": "Capture method" + }, + "library_strategy": { + "Enums": [ + "Bisultife-Seq strategy [GENPIO:0001975]", + "CTS strategy [GENPIO:0001978]", + "ChIP-Seq strategy [GENPIO:0001979]", + "DNase-Hypersensitivity strategy [GENPIO:0001980]", + "EST strategy [GENPIO:0001981]", + "FL-cDNA strategy [GENPIO:0001983]", + "MB-Seq strategy [GENPIO:0001984]", + "MNase-Seq strategy [GENPIO:0001985]", + "MRE-Seq strategy [GENPIO:0001986]", + "MeDIP-Seq strategy [GENPIO:0001987]", + "RNA-Seq strategy [GENPIO:0001990]", + "WCS strategy [GENPIO:0001991]", + "WGS strategy [GENPIO:0001992]", + "WXS strategy [GENPIO:0001993]", + "amplicon strategy [GENPIO:0001974]", + "clone end strategy [GENPIO:0001976]", + "clone strategy [GENPIO:0001977]", + "finishing strategy [GENPIO:0001982]", + "other library strategy [GENPIO:0001988]", + "pool clone strategy [GENPIO:0001989]", + ], + "examples": [ + "WGS" + ], + "ontology": "GENPIO_0001973", + "type": "string", + "description": "Overall sequencing strategy or approach.", + "clasification": "Sequencing", + "label": "Sequencing technique" + }, + "library_layout": { + "examples": [ + "PAIRED" + ], + "ontology": "BU_ISCIII:007", + "type": "string", + "description": "Single or paired.", + "clasification": "Sequencing", + "label": "Library Layout" + }, + "library_name": { + "examples": [ + "e.g P17157_1007" + ], + "ontology": "GENEPIO_0001995", + "type": "string", + "description": "The submitter's name for this library.", + "clasification": "Sequencing", + "label": "Library Name" + }, + "nominal_length ": { + "examples": [ + "350" + ], + "ontology": "GENEPIO_0000076", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Nominal Length" + }, + "analysis_accession": { + "examples": [ + "" + ], + "ontology": "GENEPIO_0001145", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Analysis Accession" + }, + "read_length": { + "examples": [ + "" + ], + "ontology": "STATO_0000064", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Read length" + }, + "study_accession": { + "examples": [ + "e.g PRJEB39632" + ], + "ontology": "GENEPIO_0001136", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Study accession" + }, + "secondary_study_accession": { + "examples": [ + "e.g ERP123173" + ], + "ontology": "BU_ISCIII:012", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Secondary study accession" + }, + "sample_accession": { + "examples": [ + "e.g SAMEA7098096" + ], + "ontology": "GENEPIO_0001139", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Sample accession" + }, + "secondary_sample_accession": { + "examples": [ + "e.g ERS4858671" + ], + "ontology": "BU_ISCIII:014", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Secondary sample accession" + }, + "experiment_accession": { + "examples": [ + "e.g ERX4331406" + ], + "ontology": "BU_ISCIII:015", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Experiment Accession" + }, + "run_accession": { + "examples": [ + "e.g ERX4331406" + ], + "ontology": "BU_ISCIII:016", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Run Accession" + }, + "submission_accession": { + "examples": [ + "e.g ERA2794974" + ], + "ontology": "BU_ISCIII:017", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Submission accession" + }, + "read_count": { + "examples": [ + "e.g 837055" + ], + "ontology": "STATO_0000064", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Read count" + }, + "base_count": { + "examples": [ + "e.g 503907110" + ], + "ontology": "UO_0000244", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Base count" + }, + "center_name": { + "examples": [ + " KAROLINSKA INSITUTET" + ], + "ontology": "NCIT_C19983", + "type": "string", + "description": "The name of the institution", + "clasification": "Sample collection and processing", + "label": "Center Name" + }, + "first_public": { + "examples": [ + "e.g 2020-08-07" + ], + "ontology": "NCIT_C142711", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "First Public date" + }, + "last_updated": { + "examples": [ + "e.g 2020-07-29" + ], + "ontology": "OMIABIS_0001005", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "format": "Last Updated" + }, + "experiment_title": { + "examples": [ + "e.g Illumina MiSeq paired end sequencing" + ], + "ontology": "ORNASEQ_0000004", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Experiment title" + }, + "study_title": { + "examples": [ + "e.g SARS-CoV-2 genomes from late April in Stockholm" + ], + "ontology": "OPMI_0000380", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Study title" + }, + "study_alias": { + "examples": [ + "e.g Sweden" + ], + "ontology": "SIO_001066", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Study alias" + }, + "experiment_alias": { + "examples": [ + "e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092" + ], + "ontology": "NCIT_C42790", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Experiment alias" + }, + "run_alias": { + "examples": [ + "e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1" + ], + "ontology": "NCIT_C47911", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Run Alias" + }, + "fastq_bytes": { + "examples": [ + "e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1" + ], + "ontology": "NCIT_C48047", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Fastq bytes" + }, + "fastq_md5": { + "examples": [ + "" + ], + "ontology": "MS_1000568", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Fastq md5" + }, + "fastq_ftp": { + "examples": [ + "" + ], + "ontology": "PRIDE_0000469", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Fastq ftp" + }, + "fastq_aspera": { + "examples": [ + "e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz" + ], + "ontology": "BU_ISCIII:032", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Fastq aspera" + }, + "fastq_galaxy": { + "examples": [ + "e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz" + ], + "ontology": "ENVO_01000807", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Fastq galaxy" + }, + "submitted_bytes": { + "examples": [ + "e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz" + ], + "ontology": "NCIT_C172872", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Submitted bytes " + }, + "submitted_md5": { + "examples": [ + "e.g 139853010;166270048" + ], + "ontology": "BU_ISCIII:035", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Submitted md5" + }, + "submitted_ftp": { + "examples": [ + "e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a" + ], + "ontology": "BU_ISCIII:036", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Submitted ftp" + }, + "submitted_aspera": { + "examples": [ + "e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz" + ], + "ontology": "BU_ISCIII:037", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Submitted aspera" + }, + "submitted_galaxy": { + "examples": [ + "e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz" + ], + "ontology": "BU_ISCIII:038", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Submitted Galaxy" + }, + "submitted_format": { + "examples": [ + "e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz" + ], + "ontology": "BU_ISCIII:039", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Submitted Format" + }, + "sra_bytes": { + "examples": [ + "e.g FASTQ;FASTQ" + ], + "ontology": "BU_ISCIII:040", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "SRA bytes" + }, + "sra_md5": { + "examples": [ + "e.g 260236789" + ], + "ontology": "BU_ISCIII:041", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "SRA md5" + }, + "sra_ftp": { + "examples": [ + "e.g 2cf0d467d6dc4ae0a5473774d54c059c" + ], + "ontology": "BU_ISCIII:042", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "SRA ftp" + }, + "sra_aspera": { + "examples": [ + "e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385" + ], + "ontology": "BU_ISCIII:043", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "SRA aspera" + }, + "sra_galaxy": { + "examples": [ + "e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385" + ], + "ontology": "BU_ISCIII:044", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "SRA galaxy" + }, + "broker_name": { + "examples": [ + "P17157_1007" + ], + "ontology": "BU_ISCIII:045", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Broker Name" + }, + "nominal_sdev": { + "examples": [ + "" + ], + "ontology": "STATO_0000237", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Nominal sdev" + }, + "first_created": { + "examples": [ + "e.g 2020-08-07" + ], + "ontology": "NCIT_C164483", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "First created date" } -} + } +} \ No newline at end of file diff --git a/schema/phage_V0.json b/schema/phage_V0.json index 9155f85a..7da4dbf1 100644 --- a/schema/phage_V0.json +++ b/schema/phage_V0.json @@ -18,74 +18,114 @@ "type": "object", "properties": { "sample_collector_contact_email": { - "examples": ["johnnyblogs@lab.ca"], - "ontology": "GENEPIO:0001156", + "examples": [ + "johnnyblogs@lab.ca" + ], + "ontology": "OBI:0001890", "type": "string", "description": "The email address of the contact responsible for follow-up regarding the sample.", - "clasification":"Sample collection and processing", - "label":"Collecting Institution Email" + "clasification": "Sample collection and processing", + "label": "Originating Laboratory Email" }, "depth_of_coverage_value": { - "examples": ["400x"], + "examples": [ + "400x" + ], "ontology": "GENEPIO:0001474", "type": "string", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Depth of coverage value " + "clasification": "Bioinformatics and QC metrics", + "label": "Depth of coverage value " }, "exposure_details": { "ontology": "GENEPIO:0001431", "type": "string", "description": "Additional host exposure information.", - "examples": ["Host role - Other: Bus Driver"] + "examples": [ + "Host role - Other: Bus Driver" + ] }, "breadth_of_coverage_value": { - "examples": ["95%"], + "examples": [ + "95%" + ], "ontology": "GENEPIO:0001472", "type": "string", "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", - "clasification":"Bioinformatics and QC metrics", - "label":"Breadth of coverage value" + "clasification": "Bioinformatics and QC metrics", + "label": "Breadth of coverage value" }, "most_recent_travel_departure_date": { - "examples": ["16/03/2020"], + "examples": [ + "16/03/2020" + ], "ontology": "GENEPIO:0001414", "type": "string", "description": "The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.", "format": "date" }, "sequencing_protocol": { - "examples": ["Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits."], - "ontology": "GENEPIO:0001454", - "type": "string", - "description": "The protocol used to generate the sequence.", - "clasification":"Sequencing", - "label":"Sequencing Protocol" + "examples": [ + "Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits." + ], + "ontology": "GENEPIO:0001454", + "type": "string", + "description": "The protocol used to generate the sequence.", + "clasification": "Sequencing", + "label": "Sequencing Protocol" }, "%Ns": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"%Ns" + "clasification": "Pathogen diagnostic testing", + "label": "%Ns" + }, + "shipping_date": { + "examples": [ + "3/20/2020" + ], + "ontology": "0", + "type": "string", + "description": "The date on which the sample was sent.", + "format": "date", + "clasification": "Sample collection and processing", + "label": "Shipping Date" + }, + "results_emission_date": { + "examples": [ + "3/23/2020" + ], + "ontology": "NCIT_C142672", + "type": "string", + "description": "The date on which the results were emitted.", + "format": "date", + "clasification": "Sample collection and processing", + "label": "Results Emission Date" }, "Number_of_variants_(AF_greater_75%)": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"Number of variants (AF greater 75%)" + "clasification": "Pathogen diagnostic testing", + "label": "Number of variants (AF greater 75%)" }, "Numer_of_variants_with_effect": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"Numer of variants with effect" - }, + "clasification": "Pathogen diagnostic testing", + "label": "Numer of variants with effect" + }, "host_age_bin": { "Enums": [ "0 - 9 [GENEPIO:0100049]", @@ -108,7 +148,9 @@ "ontology": "GENEPIO:0001394", "type": "string", "description": "The age category of the host at the time of sampling.", - "examples": ["50 - 59 [GENEPIO:0100054]"] + "examples": [ + "50 - 59 [GENEPIO:0100054]" + ] }, "anatomical_material": { "Enums": [ @@ -130,33 +172,40 @@ "ontology": "GENEPIO:0001211", "type": "string", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "examples": ["Blood [UBERON:0000178]"], - "classification":"Sample collection and processing", - "label":"Organism Substance" - + "examples": [ + "Blood [UBERON:0000178]" + ], + "classification": "Sample collection and processing", + "label": "Organism Substance" }, "sample_collection_date": { - "examples": ["3/19/2020"], + "examples": [ + "3/19/2020" + ], "ontology": "GENEPIO:0001174", "type": "string", "description": "The date on which the sample was collected.", - "format":"date", - "classification":"Sample collection and processing", - "label":"Sample Collection Date" + "format": "date", + "classification": "Sample collection and processing", + "label": "Sample Collection Date" }, "diagnostic_pcr_Ct_value_2": { - "examples": ["36"], + "examples": [ + "36" + ], "ontology": "GENEPIO:0001512", "type": "string", "description": "The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "clasification":"Pathogen diagnostic testing", - "label":"Diagnostic Pcr Ct Value-2" + "clasification": "Pathogen diagnostic testing", + "label": "Diagnostic Pcr Ct Value-2" }, "number_of_vaccine_doses_received": { "ontology": "GENEPIO:0001406", "type": "integer", "description": "The number of doses of the vaccine recived by the host.", - "examples": [2] + "examples": [ + 2 + ] }, "lab_host": { "Enums": [ @@ -185,9 +234,11 @@ "ontology": "GENEPIO:0001255", "type": "string", "description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.", - "examples": ["Vero E6 Cell Line [BTO:0004755]"], - "classification":"Sample collection and processing", - "label":"Lab passage Host" + "examples": [ + "Vero E6 Cell Line [BTO:0004755]" + ], + "classification": "Sample collection and processing", + "label": "Lab passage Host" }, "anatomical_part": { "Enums": [ @@ -224,9 +275,11 @@ "ontology": "GENEPIO:0001214", "type": "string", "description": "An anatomical part of an organism e.g. oropharynx. ", - "examples": ["Nasopharynx (NP) [UBERON:0001728]"], - "classification":"Sample collection and processing", - "label":"Anatomical Structure" + "examples": [ + "Nasopharynx (NP) [UBERON:0001728]" + ], + "classification": "Sample collection and processing", + "label": "Anatomical Structure" }, "host_health_outcome": { "Enums": [ @@ -243,133 +296,167 @@ "ontology": "GENEPIO:0001390", "type": "string", "description": "Disease outcome in the host.", - "examples": ["Recovered [NCIT:C49498]"] + "examples": [ + "Recovered [NCIT:C49498]" + ] }, "rna_extraction_protocol": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Rna Extraction Protocol" + "examples": [ + "" + ], + "ontology": "OBI_0302884", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Rna Extraction Protocol" }, "sequencing_date": { - "examples": ["22/06/2020"], + "examples": [ + "22/06/2020" + ], "ontology": "GENEPIO:0001447", "type": "string", "description": "The date the sample was sequenced.", "format": "date", - "clasification":"Sequencing", - "label":"Sequencing date" + "clasification": "Sequencing", + "label": "Sequencing date" }, "passage_number": { "ontology": "GENEPIO:0001261", "type": "integer", "description": "Number of passages.", - "examples": [3], - "clasification":"Sample collection and processing", - "label":"Passage Number" + "examples": [ + 3 + ], + "clasification": "Sample collection and processing", + "label": "Passage Number" }, "ns_per_100_kbp": { - "examples": ["300"], + "examples": [ + "300" + ], "ontology": "GENEPIO:0001484", "type": "string", "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Ns per 100 kbp" + "clasification": "Bioinformatics and QC metrics", + "label": "Ns per 100 kbp" }, "case_id": { "ontology": "GENEPIO:0100281", "type": "string", "description": "The identifier used to specify an epidemiologically detected case of disease.", - "examples": ["ABCD1234"] + "examples": [ + "ABCD1234" + ] }, "biosample_accession": { - "examples": ["SAMN14180202"], + "examples": [ + "SAMN14180202" + ], "ontology": "GENEPIO:0001139", "type": "string", "description": "The identifier assigned to a BioSample in INSDC archives.", - "clasification":"Database Identifiers", - "label":"Biosample accession ENA" + "clasification": "Database Identifiers", + "label": "Biosample accession ENA" }, "last_dose_vacicnation_date": { - "examples": ["09/04/2021"], + "examples": [ + "09/04/2021" + ], "ontology": "GENEPIO:0001408", "type": "string", "description": "The date the host received their last dose of vaccine.", "format": "date" }, "bioinformatics_protocol": { - "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], + "examples": [ + "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" + ], "ontology": "GENEPIO:0001489", "type": "string", "description": "The name of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics", - "label":"Bioinformatics protocol" + "clasification": "Bioinformatics and QC metrics", + "label": "Bioinformatics protocol" }, "if_bioinformatic_protocol_is_other_specify": { - "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], + "examples": [ + "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" + ], "ontology": "0", "type": "string", "description": "The name of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics", - "label":"If bioinformatic protocol Is Other, Specify" + "clasification": "Bioinformatics and QC metrics", + "label": "If bioinformatic protocol Is Other, Specify" }, "bioinformatic_protocol_version": { - "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], - "ontology": "0", + "examples": [ + "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" + ], + "ontology": "NCIT:C93490", "type": "string", "description": "The version number of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics", - "label":"bioinformatics protocol version" + "clasification": "Bioinformatics and QC metrics", + "label": "bioinformatics protocol version" }, "preprocessing": { - "examples": [""], - "ontology": "0", + "examples": [ + "" + ], + "ontology": "MS_1002386", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Preprocessing" + "clasification": "Bioinformatics and QC metrics", + "label": "Preprocessing" }, "if_preprocessing_other": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"If preprocessing Is Other, Specify" + "clasification": "Bioinformatics and QC metrics", + "label": "If preprocessing Is Other, Specify" }, "preprocessing_params": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Preprocessing params" + "clasification": "Bioinformatics and QC metrics", + "label": "Preprocessing params" }, "mapping": { - "examples": [""], - "ontology": "0", + "examples": [ + "" + ], + "ontology": "topic:0102", "type": "string", "description": "", - "clasification":"Lineage and Variant information", - "label":"Mapping" + "clasification": "Lineage and Variant information", + "label": "Mapping" }, "mapping_params": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Lineage and Variant information", - "label":"Mapping params" + "clasification": "Lineage and Variant information", + "label": "Mapping params" }, "commercial/open-source/both": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Commercial/Open-source/both" + "clasification": "Bioinformatics and QC metrics", + "label": "Commercial/Open-source/both" }, "prior_sars_cov_2_antiviral_treatment": { "Enums": [ @@ -384,7 +471,9 @@ "ontology": "GENEPIO:0001438", "type": "string", "description": "Whether there was prior SARS-CoV-2 treatment with an antiviral agent.", - "examples": ["Prior antiviral treatment [GENEPIO:0100037]"] + "examples": [ + "Prior antiviral treatment [GENEPIO:0100037]" + ] }, "gene_name_2": { "Enums": [ @@ -430,9 +519,11 @@ "ontology": "GENEPIO:0001510", "type": "string", "description": "The name of the gene used in the diagnostic RT-PCR test.", - "examples": ["RdRp gene (nsp12) [GENEPIO:0100168]"], - "classification":"Pathogen diagnostic testing", - "label":"Gene Name 2" + "examples": [ + "RdRp gene (nsp12) [GENEPIO:0100168]" + ], + "classification": "Pathogen diagnostic testing", + "label": "Gene Name 2" }, "body_product": { "Enums": [ @@ -453,24 +544,35 @@ "ontology": "GENEPIO:0001216", "type": "string", "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", - "examples": ["Feces [UBERON:0001988]"], - "classification":"Sample collection and processing", - "label":"Body product" + "examples": [ + "Feces [UBERON:0001988]" + ], + "classification": "Sample collection and processing", + "label": "Body product" }, "host_age": { "ontology": "GENEPIO:0001392", "anyOf": [ - { "type": "integer" }, - { "pattern": "\\d+-\\d+", "type": "string" } + { + "type": "integer" + }, + { + "pattern": "\\d+-\\d+", + "type": "string" + } ], "description": "Age of host at the time of sampling.", - "examples": [79] + "examples": [ + 79 + ] }, "host_ethnicity": { "ontology": "GECKO:0000061", "type": "string", "description": "The self-identified ethnicity(ies) of the host.", - "examples": ["Indigenous, European"] + "examples": [ + "Indigenous, European" + ] }, "collection_device": { "Enums": [ @@ -500,9 +602,11 @@ "ontology": "GENEPIO:0001234", "type": "string", "description": "The instrument or container used to collect the sample e.g. swab.", - "examples": ["Swab [GENEPIO:0100027]"], - "clasification":"Sample collection and processing", - "label":"Collection Device" + "examples": [ + "Swab [GENEPIO:0100027]" + ], + "clasification": "Sample collection and processing", + "label": "Collection Device" }, "purpose_of_sequencing": { "Enums": [ @@ -539,33 +643,41 @@ "ontology": "GENEPIO:0001445", "type": "string", "description": "The reason that the sample was sequenced.", - "examples": ["Baseline surveillance (random sampling) [GENEPIO:0100005]"], - "classification":"Sequencing", - "label":"Purpose of Sequencing" + "examples": [ + "Baseline surveillance (random sampling) [GENEPIO:0100005]" + ], + "classification": "Sequencing", + "label": "Purpose of Sequencing" }, "raw_sequence_data_processing_method": { - "examples": ["Porechop 0.2.3"], + "examples": [ + "Porechop 0.2.3" + ], "ontology": "GENEPIO:0001458", "type": "string", "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", - "clasification":"Bioinformatics and QC metrics", - "label":"Raw sequence data processin method" + "clasification": "Bioinformatics and QC metrics", + "label": "Raw sequence data processin method" }, "sequence_submitter_contact_address": { - "examples": ["123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"], + "examples": [ + "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" + ], "ontology": "GENEPIO:0001167", "type": "string", "description": "The mailing address of the agency submitting the sequence.", - "clasification":"Sample collection and processing", - "label":"Submitting Institution Address" + "clasification": "Sample collection and processing", + "label": "Submitting Institution Address" }, "depth_of_coverage_threshold": { - "examples": ["100x"], - "ontology": "GENEPIO:0001475", + "examples": [ + "100x" + ], + "ontology": "GENEPIO:0001475", "type": "string", "description": "The threshold used as a cut-off for the depth of coverage.", - "clasification":"Bioinformatics and QC metrics", - "label":"Depth of coverage threshold" + "clasification": "Bioinformatics and QC metrics", + "label": "Depth of coverage threshold" }, "specimen_processing": { "Enums": [ @@ -581,96 +693,120 @@ "ontology": "GENEPIO:0001253", "type": "string", "description": "Any processing applied to the sample during or after receiving the sample. ", - "examples": ["Virus Passage [GENEPIO:0100039]"], - "classification":"Sample collection and processing", - "label":"Specimen Processing" + "examples": [ + "Virus Passage [GENEPIO:0100039]" + ], + "classification": "Sample collection and processing", + "label": "Specimen Processing" }, "r1_fastq_filename": { - "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], + "examples": [ + "ABC123_S1_L001_R1_001.fastq.gz" + ], "ontology": "GENEPIO:0001476", "type": "string", "description": "The user-specified filename of the r1 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Sequence file R1 fastq" + "clasification": "Bioinformatics and QC metrics", + "label": "Sequence file R1 fastq" }, "destination_of_most_recent_travel_city": { "ontology": "GENEPIO:0001411", "type": "string", "description": "The name of the city that was the destination of most recent travel.", - "examples": ["New York City"] + "examples": [ + "New York City" + ] }, "r1_fastq_filepath": { - "examples": ["/User/Documents/RespLab/Data/"], + "examples": [ + "/User/Documents/RespLab/Data/" + ], "ontology": "GENEPIO:0001478", "type": "string", "description": "The filepath of the r1 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Filepath R1 fastq" + "clasification": "Bioinformatics and QC metrics", + "label": "Filepath R1 fastq" }, "library_id": { "ontology": "GENEPIO:0001448", "type": "string", "description": "The user-specified identifier for the library prepared for sequencing.", - "examples": ["XYZ_123345"], - "clasification":"Sequencing", - "labe":"Library Id" + "examples": [ + "XYZ_123345" + ], + "clasification": "Sequencing", + "labe": "Library Id" }, "enrichment_protocol": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Enrichment_protocol" + "examples": [ + "" + ], + "ontology": "EFO_0009089", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Enrichment_protocol" }, "if_enrichment_protocol_is_other_specify": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"If Enrichment Protocol Is Other, Specify" + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "If Enrichment Protocol Is Other, Specify" }, "if_consensus_other": { - "examples": ["1.3"], + "examples": [ + "1.3" + ], "ontology": "0", "type": "string", "description": "The version of the software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"If consensus Is Other, Specify" + "clasification": "Bioinformatics and QC metrics", + "label": "If consensus Is Other, Specify" }, "if_mapping_other": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Lineage and Variant information", - "label":"If mapping Is Other, Specify" + "clasification": "Lineage and Variant information", + "label": "If mapping Is Other, Specify" }, "amplicon protocol": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Amplicon Protocol" + "examples": [ + "" + ], + "ontology": "EFO_0003747", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Amplicon Protocol" }, "if_amplicon_protocol_if_other_especify": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "labe":"If Amplicon Protocol If Other, Especify" + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Sequencing", + "labe": "If Amplicon Protocol If Other, Especify" }, "amplicon_version": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Amplicon Version" - }, + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Amplicon Version" + }, "host_vaccination_status": { "Enums": [ "Fully Vaccinated [GENEPIO:0100100]", @@ -685,55 +821,69 @@ "ontology": "GENEPIO:0001404", "type": "string", "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", - "examples": ["Fully Vaccinated [GENEPIO:0100100]"] + "examples": [ + "Fully Vaccinated [GENEPIO:0100100]" + ] }, "geo_loc_longitude": { "ontology": "OBI:0001621", "type": "string", "description": "The longitude coordinates of the geographical location of sample collection.", - "examples": ["77.11 W"], - "clasification":"Sample collection and processing", - "label":"Geo Loc Longitude" + "examples": [ + "77.11 W" + ], + "clasification": "Sample collection and processing", + "label": "Geo Loc Longitude" }, "genbank_ena_ddbj_accession": { - "examples": ["MN908947.3"], + "examples": [ + "MN908947.3" + ], "ontology": "GENEPIO:0001145", "type": "string", "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", - "clasification":"Database Identifiers", - "label":"GenBank/ENA/DDBJ accession" + "clasification": "Database Identifiers", + "label": "GenBank/ENA/DDBJ accession" }, "bioproject_accession": { - "examples": ["PRJNA12345"], + "examples": [ + "PRJNA12345" + ], "ontology": "GENEPIO:0001136", "type": "string", "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", - "clasification":"Database Identifiers", - "label":"Bioproject accession ENA" + "clasification": "Database Identifiers", + "label": "Bioproject accession ENA" }, "lineage/clade_analysis_software_name": { - "examples": ["Pangolin"], + "examples": [ + "Pangolin" + ], "ontology": "GENEPIO:0001501", "type": "string", "description": "The name of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information", - "label":"lineage/clade analysis software name" + "clasification": "Lineage and Variant information", + "label": "lineage/clade analysis software name" }, "analysis_author": { - "examples": [""], - "ontology": "0", + "examples": [ + "" + ], + "ontology": "NCIT:C42781", "type": "string", "description": "", - "clasification":"Contributor Acknowledgement", - "label":"Analysis Authors" + "clasification": "Contributor Acknowledgement", + "label": "Analysis Authors" }, "if_lineage_identification_other": { - "examples": ["Other than Pangolin"], + "examples": [ + "Other than Pangolin" + ], "ontology": "0", "type": "string", "description": "The name of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information", - "label":"If lineage identification Is Other, Specify" + "clasification": "Lineage and Variant information", + "label": "If lineage identification Is Other, Specify" }, "location_of_exposure_geo_loc_name_country": { "Enums": [ @@ -1017,60 +1167,76 @@ "ontology": "GENEPIO:0001181", "type": "string", "description": "The country where the host was likely exposed to the causative agent of the illness.", - "examples": ["South Africa [GAZ:00001094]"] + "examples": [ + "South Africa [GAZ:00001094]" + ] }, "sample_plan_name": { "ontology": "GENEPIO:0100285", "type": "string", "description": "The name of the sample plan implemented for sample collection.", - "examples": ["CanCOGeN Sampling Strategy 1.0"] + "examples": [ + "CanCOGeN Sampling Strategy 1.0" + ] }, "prior_sars_cov_2_antiviral_treatment_date": { - "examples": ["28/01/2021"], + "examples": [ + "28/01/2021" + ], "ontology": "GENEPIO:0001440", "type": "string", "description": "The date treatment was first administered during the prior SARS-CoV-2 infection.", "format": "date" }, "library_preparation_kit": { - "examples": ["Nextera XT"], - "ontology": "GENEPIO:0001450", - "type": "string", - "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", - "clasification":"Sequencing", - "label":"Library Preparation Kit" + "examples": [ + "Nextera XT" + ], + "ontology": "GENEPIO:0001450", + "type": "string", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "clasification": "Sequencing", + "label": "Library Preparation Kit" }, "flow_cell_barcode": { - "examples": ["FAB06069"], - "ontology": "GENEPIO:0001451", - "type": "string", - "description": "The barcode of the flow cell used for sequencing.", - "clasification":"Sequencing", - "label":"Flow Cell Barcode" + "examples": [ + "FAB06069" + ], + "ontology": "GENEPIO:0001451", + "type": "string", + "description": "The barcode of the flow cell used for sequencing.", + "clasification": "Sequencing", + "label": "Flow Cell Barcode" }, "library_kit": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Library Kit" + "examples": [ + "" + ], + "ontology": "GENEPIO_0000085", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Library Kit" }, "fast5_filename": { - "examples": ["batch1a_sequences.fast5"], + "examples": [ + "batch1a_sequences.fast5" + ], "ontology": "GENEPIO:0001480", "type": "string", "description": "The user-specified filename of the FAST5 file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Filename fast5" + "clasification": "Bioinformatics and QC metrics", + "label": "Filename fast5" }, "diagnostic_pcr_Ct_value_1": { - "examples": ["21"], + "examples": [ + "21" + ], "ontology": "GENEPIO:0001509", "type": "string", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "clasification":"Pathogen diagnostic testing", - "label":"Diagnostic Pcr Ct Value 1" + "clasification": "Pathogen diagnostic testing", + "label": "Diagnostic Pcr Ct Value 1" }, "collection_method": { "Enums": [ @@ -1104,62 +1270,78 @@ "ontology": "GENEPIO:0001241", "type": "string", "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", - "examples": ["Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]"], - "clasification":"Sample collection and processing", - "label":"Collection Method" + "examples": [ + "Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]" + ], + "clasification": "Sample collection and processing", + "label": "Collection Method" }, "geo_loc_name_county_region": { "ontology": "GENEPIO:0100280", "type": "string", "description": "The county/region of origin of the sample.", - "examples": ["Derbyshire"] + "examples": [ + "Derbyshire" + ] }, "consensus_genome_length": { - "examples": ["38677"], + "examples": [ + "38677" + ], "ontology": "GENEPIO:0001483", "type": "string", "description": "Size of the assembled genome described as the number of base pairs.", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus genome length" + "clasification": "Bioinformatics and QC metrics", + "label": "Consensus genome length" }, "r2_fastq_filepath": { - "examples": ["/User/Documents/RespLab/Data/"], + "examples": [ + "/User/Documents/RespLab/Data/" + ], "ontology": "GENEPIO:0001479", "type": "string", "description": "The filepath of the r2 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Filepath R2 fastq" + "clasification": "Bioinformatics and QC metrics", + "label": "Filepath R2 fastq" }, "consensus_criteria": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus criteria" + "clasification": "Bioinformatics and QC metrics", + "label": "Consensus criteria" }, "destination_of_most_recent_travel_state_province_territory": { "ontology": "GENEPIO:0001412", "type": "string", "description": "The name of the province that was the destination of most recent travel.", - "examples": ["California"] + "examples": [ + "California" + ] }, "reception_date": { - "examples": ["3/21/2020"], + "examples": [ + "3/21/2020" + ], "ontology": "GENEPIO:0001179", "type": "string", "description": "The date on which the sample was received.", - "format":"date", - "clasification":"Sample collection and processing", - "label":"Sample Received Date" + "format": "date", + "clasification": "Sample collection and processing", + "label": "Sample Received Date" }, "quality_control_metrics": { - "examples": [""], - "ontology": "0", + "examples": [ + "" + ], + "ontology": "data_3914", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Quality control metrics " + "clasification": "Bioinformatics and QC metrics", + "label": "Quality control metrics " }, "host_common_name": { "Enums": [ @@ -1185,53 +1367,67 @@ "ontology": "GENEPIO:0001386", "type": "string", "description": "The commonly used name of the host.", - "examples": ["Human [NCBITaxon:9606]"], - "classification":"Host information", - "label":"Host Common Name" + "examples": [ + "Human [NCBITaxon:9606]" + ], + "classification": "Host information", + "label": "Host Common Name" }, "geo_loc_name_state_province_territory": { "ontology": "GENEPIO:0001185", "type": "string", "description": "The state/province/territory of origin of the sample.", - "examples": ["Western Cape"], - "classification":"Sample collection and processing", - "label":"Geo Loc Autonomic Community" + "examples": [ + "Western Cape" + ], + "classification": "Sample collection and processing", + "label": "Geo Loc Autonomic Community" }, "lineage_clade_analysis_software_version": { "ontology": "GENEPIO:0001502", "type": "string", "description": "The version of the software used to determine the lineage/clade.", - "examples": ["2.1.10"] + "examples": [ + "2.1.10" + ] }, "host_subject_id": { "ontology": "GENEPIO:0001398", "type": "string", "description": "A unique identifier by which each host can be referred to e.g. #131", - "examples": ["BCxy123"] + "examples": [ + "BCxy123" + ] }, "sra_accession": { - "examples": ["SRR11177792"], - "ontology": "GENEPIO:0001142", - "type": "string", - "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "clasification":"Database Identifiers", - "label":"SRA accession" + "examples": [ + "SRR11177792" + ], + "ontology": "GENEPIO:0001142", + "type": "string", + "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", + "clasification": "Database Identifiers", + "label": "SRA accession" }, "author_submitter": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Contributor Acknowledgement", - "label":"Author Submitter" + "clasification": "Contributor Acknowledgement", + "label": "Author Submitter" }, "authors": { - "examples": [""], + "examples": [ + "" + ], "ontology": "GENEPIO:0001517", "type": "string", "description": "", - "clasification":"Contributor Acknowledgement", - "label":"Authors" + "clasification": "Contributor Acknowledgement", + "label": "Authors" }, "host_role": { "Enums": [ @@ -1275,45 +1471,57 @@ "ontology": "GENEPIO:0001419", "type": "string", "description": "The role of the host in relation to the exposure setting.", - "examples": ["Patient [OMRSE:00000030]"] + "examples": [ + "Patient [OMRSE:00000030]" + ] }, "consensus_sequence_name": { "ontology": "GENEPIO:0001460", "type": "string", "description": "The name of the consensus sequence.", - "examples": ["ncov123assembly3"] + "examples": [ + "ncov123assembly3" + ] }, "assembly": { - "examples": [""], - "ontology": "0", + "examples": [ + "" + ], + "ontology": "NCIT_C63548", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Assembly" + "clasification": "Bioinformatics and QC metrics", + "label": "Assembly" }, "if_assembly_other": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"If assembly Is Other, Specify" + "clasification": "Bioinformatics and QC metrics", + "label": "If assembly Is Other, Specify" }, "assembly_params": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Assambly params" + "clasification": "Bioinformatics and QC metrics", + "label": "Assambly params" }, "gisaid_accession": { - "examples": ["hCoV-19/Canada/prov_rona_99/2020"], + "examples": [ + "hCoV-19/Canada/prov_rona_99/2020" + ], "ontology": "GENEPIO:0100282", "type": "string", "description": "The user-defined GISAID virus name assigned to the sequence.", - "clasification":"Database Identifiers", - "label":"GISAID Virus Name" + "clasification": "Database Identifiers", + "label": "GISAID Virus Name" }, "geo_loc_name_country": { "Enums": [ @@ -1597,104 +1805,131 @@ "ontology": "GENEPIO:0001181", "type": "string", "description": "The country of origin of the sample.", - "examples": ["South Africa [GAZ:00001094]"], - "label":"Geo Loc Autonomic Country" + "examples": [ + "South Africa [GAZ:00001094]" + ], + "label": "Geo Loc Autonomic Country" }, "consensus_sequence_filepath": { - "examples": ["/User/Documents/RespLab/Data/ncov123assembly.fasta"], + "examples": [ + "/User/Documents/RespLab/Data/ncov123assembly.fasta" + ], "ontology": "GENEPIO:0001462", "type": "string", "description": "The filepath of the consesnsus sequence file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus sequence filepath" + "clasification": "Bioinformatics and QC metrics", + "label": "Consensus sequence filepath" }, "number_of_base_pairs_sequenced": { - "examples": ["387566"], + "examples": [ + "387566" + ], "ontology": "GENEPIO:0001482", "type": "string", "description": "The number of total base pairs generated by the sequencing process.", - "clasification":"Bioinformatics and QC metrics", - "label":"Number of base pairs sequenced " + "clasification": "Bioinformatics and QC metrics", + "label": "Number of base pairs sequenced " }, "destination_of_most_recent_travel_country": { "ontology": "GENEPIO:0001413", "type": "string", "description": "The name of the country that was the destination of most recent travel.", - "examples": ["United Kingdom"] + "examples": [ + "United Kingdom" + ] }, "fast5_filepath": { - "examples": ["/User/Documents/RespLab/Data/"], + "examples": [ + "/User/Documents/RespLab/Data/" + ], "ontology": "GENEPIO:0001481", "type": "string", "description": "The filepath of the FAST5 file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Filepath fast5" + "clasification": "Bioinformatics and QC metrics", + "label": "Filepath fast5" }, "culture_collection": { "ontology": "GENEPIO:0100284", "type": "string", "description": "The name of the source collection and unique culture identifier. ", - "examples": ["/culture_collection=\"ATCC:26370\""] + "examples": [ + "/culture_collection=\"ATCC:26370\"" + ] }, "was_phix_used?": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Was Phix Used" + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Was Phix Used" }, "number_of_samples_in_run": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Number Of Samples In Run" + "examples": [ + "" + ], + "ontology": "KISAO_0000326", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Number Of Samples In Run" }, "amplicon_size": { - "examples": ["300bp"], - "ontology": "GENEPIO:0001449", - "type": "string", - "description": "The length of the amplicon generated by PCR amplification.", - "clasification":"Sequencing", - "label":"Amplicon Size" + "examples": [ + "300bp" + ], + "ontology": "GENEPIO:0001449", + "type": "string", + "description": "The length of the amplicon generated by PCR amplification.", + "clasification": "Sequencing", + "label": "Amplicon Size" }, "flowcell_kit": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "labe":"Flowcell Kit" + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Sequencing", + "labe": "Flowcell Kit" }, "sample_collector_contact_address": { - "examples": ["655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada"], + "examples": [ + "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" + ], "ontology": "GENEPIO:0001158", "type": "string", "description": "The mailing address of the agency submitting the sample.", - "clasification":"Sample collection and processing", - "label":"Collecting Institution Address" + "clasification": "Sample collection and processing", + "label": "Originating Laboratory Address" }, "collection_protocol": { "ontology": "GENEPIO:0001243", "type": "string", "description": "The name and version of a particular protocol used for sampling.", - "examples": ["SC2SamplingProtocol 1.2"], - "clasification":"Sample collection and processing", - "label":"Collection Protocol" - + "examples": [ + "SC2SamplingProtocol 1.2" + ], + "clasification": "Sample collection and processing", + "label": "Collection Protocol" }, "variant_evidence": { - "examples": ["lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)"], - "ontology": "GENEPIO:0001504", + "examples": [ + "lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)" + ], + "ontology": "GENEPIO:0001504", "type": "string", "description": "The evidence used to make the variant determination.", - "clasification":"Lineage and Variant information", - "label":"Variant evidence" + "clasification": "Lineage and Variant information", + "label": "Variant evidence" }, "most_recent_travel_return_date": { - "examples": ["26/04/2020"], + "examples": [ + "26/04/2020" + ], "ontology": "GENEPIO:0001415", "type": "string", "description": "The date of a person's most recent return to some residence from a journey originating at that residence.", @@ -1715,23 +1950,29 @@ "ontology": "GENEPIO:0001418", "type": "string", "description": "The exposure transmission contact type.", - "examples": ["Direct (human-to-human contact) [TRANS:0000001]"] + "examples": [ + "Direct (human-to-human contact) [TRANS:0000001]" + ] }, "runID": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"RunID" + "examples": [ + "" + ], + "ontology": "NCIT_C117058", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "RunID" }, "sequencing_instrument_platform": { - "examples": ["MinIon"], - "ontology": "0", - "type": "string", - "description": "The model of the sequencing instrument used.", - "label":"Sequencing Platforms " - }, + "examples": [ + "MinIon" + ], + "ontology": "GENEPIO_0000071", + "type": "string", + "description": "The model of the sequencing instrument used.", + "label": "Sequencing Platforms " + }, "prior_sars_cov_2_infection": { "Enums": [ "Prior infection [GENEPIO:0100234]", @@ -1745,20 +1986,28 @@ "ontology": "GENEPIO:0001435", "type": "string", "description": "Whether there was prior SARS-CoV-2 infection.", - "examples": ["Prior infection [GENEPIO:0100234]"] + "examples": [ + "Prior infection [GENEPIO:0100234]" + ] }, "gisaid_virus_name": { "ontology": "GENEPIO:0100282", "type": "string", "description": "The user-defined GISAID virus name assigned to the sequence.", - "examples": ["hCoV-19/Canada/prov_rona_99/2020"] + "examples": [ + "hCoV-19/Canada/prov_rona_99/2020" + ], + "clasification": "Database Identifiers", + "label": "GISAID Virus Name" }, "specimen_collector_sample_id": { - "examples": ["prov_rona_99"], + "examples": [ + "prov_rona_99" + ], "ontology": "GENEPIO:0001123", "type": "string", "description": "The user-defined name for the sample.", - "clasification":"Database Identifiers", + "clasification": "Database Identifiers", "label": "Collecting Sample id" }, "host_scientific_name": { @@ -1788,9 +2037,11 @@ "ontology": "GENEPIO:0001387", "type": "string", "description": "The taxonomic, or scientific name of the host.", - "examples": ["Homo sapiens [NCBITaxon:9606]"], - "clasification":"Host information", - "label":"Host Scientific Name" + "examples": [ + "Homo sapiens [NCBITaxon:9606]" + ], + "clasification": "Host information", + "label": "Host Scientific Name" }, "host_disease": { "Enums": [ @@ -1804,86 +2055,107 @@ "ontology": "GENEPIO:0001391", "type": "string", "description": "The name of the disease experienced by the host.", - "examples": ["COVID-19 [MONDO:0100096]"] + "examples": [ + "COVID-19 [MONDO:0100096]" + ] }, "passage_method": { "ontology": "GENEPIO:0001264", "type": "string", "description": "Description of how organism was passaged.", "examples": [ - "AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain.",], - "clasification":"Sample collection and processing", - "label":"Passage Method" + "AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain.", + ], + "clasification": "Sample collection and processing", + "label": "Passage Method" }, "%qc_filtered": { - "examples": [""], + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Pathogen diagnostic testing", + "label": "%qc filtered" + }, + "%reads_host": { + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"%qc filtered" - }, - "%reads_host": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"%reads host" + "clasification": "Pathogen diagnostic testing", + "label": "%reads host" }, "%reads_virus": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"%reads virus" + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Pathogen diagnostic testing", + "label": "%reads virus" }, "%unmapped": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"%unmapped" + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Pathogen diagnostic testing", + "label": "%unmapped" }, "%genome _greater_10x": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"% genome greater 10x" + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Pathogen diagnostic testing", + "label": "% genome greater 10x" }, "mean_depth_of_coverage_value": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"mean depth of coverage value" + "examples": [ + "" + ], + "ontology": "NCIT:C167285", + "type": "string", + "description": "", + "clasification": "Pathogen diagnostic testing", + "label": "mean depth of coverage value" }, "symptom_onset_date": { - "examples": ["16/03/2020"], - "ontology": "GENEPIO:0001399", - "type": "string", - "description": "The date on which the symptoms began or were first noted.", - "format": "date" + "examples": [ + "16/03/2020" + ], + "ontology": "GENEPIO:0001399", + "type": "string", + "description": "The date on which the symptoms began or were first noted.", + "format": "date" }, "r2 fastq filename": { - "examples": ["ABC123_S1_L001_R2_001.fastq.gz"], - "ontology": "GENEPIO:0001477", - "type": "string", - "description": "The user-specified filename of the r2 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Sequence file R2 fastq" + "examples": [ + "ABC123_S1_L001_R2_001.fastq.gz" + ], + "ontology": "GENEPIO:0001477", + "type": "string", + "description": "The user-specified filename of the r2 FASTQ file.", + "clasification": "Bioinformatics and QC metrics", + "label": "Sequence file R2 fastq" }, "prior_sars_cov_2_infection_date": { - "examples": ["23/01/2021"], - "ontology": "GENEPIO:0001437", - "type": "string", - "description": "The date of diagnosis of the prior SARS-CoV-2 infection.", - "format": "date" + "examples": [ + "23/01/2021" + ], + "ontology": "GENEPIO:0001437", + "type": "string", + "description": "The date of diagnosis of the prior SARS-CoV-2 infection.", + "format": "date" }, "exposure_event": { "Enums": [ @@ -1911,21 +2183,27 @@ "ontology": "GENEPIO:0001417", "type": "string", "description": "Event leading to exposure.", - "examples": ["Mass Gathering [GENEPIO:0100237]"] + "examples": [ + "Mass Gathering [GENEPIO:0100237]" + ] }, "sequencing_kit_number": { - "examples": ["AB456XYZ789"], - "ontology": "GENEPIO:0001455", - "type": "string", - "description": "The manufacturer's kit number.", - "clasification":"Sequencing", - "label":"Sequencing Kit Number" + "examples": [ + "AB456XYZ789" + ], + "ontology": "GENEPIO:0001455", + "type": "string", + "description": "The manufacturer's kit number.", + "clasification": "Sequencing", + "label": "Sequencing Kit Number" }, "purpose_of_sampling_details": { "ontology": "GENEPIO:0001200", "type": "string", "description": "Further details pertaining to the reason the sample was collected.", - "examples": ["Screening of bat specimens in museum collections."] + "examples": [ + "Screening of bat specimens in museum collections." + ] }, "host_gender": { "Enums": [ @@ -1944,29 +2222,37 @@ "ontology": "GENEPIO:0001395", "type": "string", "description": "The gender of the host at the time of sample collection.", - "examples": ["Male [NCIT:C46109]"] + "examples": [ + "Male [NCIT:C46109]" + ] }, "prior_sars_cov_2_antiviral_treatment_agent": { "ontology": "GENEPIO:0001439", "type": "string", "description": "The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection.", - "examples": ["Remdesivir"] + "examples": [ + "Remdesivir" + ] }, "diagnostic_pcr_protocol_1": { - "examples": ["PCREGene 2.0"], + "examples": [ + "PCREGene 2.0" + ], "ontology": "GENEPIO:0001508", "type": "string", "description": "The name and version number of the protocol used for diagnostic marker amplification.", - "clasification":"Pathogen diagnostic testing", - "label":"Diagnostic Pcr Protocol 1" + "clasification": "Pathogen diagnostic testing", + "label": "Diagnostic Pcr Protocol 1" }, "diagnostic_pcr_protocol_2": { - "examples": ["PCRRdRpGene 3.0"], + "examples": [ + "PCRRdRpGene 3.0" + ], "ontology": "GENEPIO:0001511", "type": "string", "description": "The name and version number of the protocol used for diagnostic marker amplification.", - "clasification":"Pathogen diagnostic testing", - "label":"Diagnostic Pcr Protocol 2" + "clasification": "Pathogen diagnostic testing", + "label": "Diagnostic Pcr Protocol 2" }, "host_specimen_voucher": { "ontology": "GENEPIO:0100283", @@ -2049,13 +2335,17 @@ "ontology": "GENEPIO:0001428", "type": "string", "description": "The setting leading to exposure.", - "examples": ["Healthcare Setting [GENEPIO:0100201]"] + "examples": [ + "Healthcare Setting [GENEPIO:0100201]" + ] }, "lineage_clade_name": { "ontology": "GENEPIO:0001500", "type": "string", "description": "The name of the lineage or clade.", - "examples": ["B.1.1.7"] + "examples": [ + "B.1.1.7" + ] }, "gene_name_1": { "Enums": [ @@ -2101,34 +2391,42 @@ "ontology": "GENEPIO:0001507", "type": "string", "description": "The name of the gene used in the diagnostic RT-PCR test.", - "examples": ["E gene (orf4) [GENEPIO:0100151]"], - "classification":"Pathogen diagnostic testing", - "label":"Gene Name 1" + "examples": [ + "E gene (orf4) [GENEPIO:0100151]" + ], + "classification": "Pathogen diagnostic testing", + "label": "Gene Name 1" }, "Protocol_SARS-CoV-2_detection": { - "examples": [""], - "ontology": "0", + "examples": [ + "" + ], + "ontology": "CIDO_0020274", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"Protocol SARS-CoV-2 detection" + "clasification": "Pathogen diagnostic testing", + "label": "Protocol SARS-CoV-2 detection" }, "consensus_sequence_software_name": { - "examples": ["Ivar"], + "examples": [ + "Ivar" + ], "ontology": "GENEPIO:0001463", "type": "string", "description": "The name of software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus sequence software name" + "clasification": "Bioinformatics and QC metrics", + "label": "Consensus sequence software name" }, "reference_genome_accession": { - "examples": [""], + "examples": [ + "" + ], "ontology": "GENEPIO:0001485", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"reference genome accession" - }, + "clasification": "Pathogen diagnostic testing", + "label": "reference genome accession" + }, "host_residence_geo_loc_name_country": { "Enums": [ "Afghanistan [GAZ:00006882]", @@ -2411,21 +2709,27 @@ "ontology": "GENEPIO:0001396", "type": "string", "description": "The country where the host resides.", - "examples": ["South Africa [GAZ:00001094]"] + "examples": [ + "South Africa [GAZ:00001094]" + ] }, "travel_history": { "ontology": "GENEPIO:0001416", "type": "string", "description": "Travel history in last six months.", - "examples": ["Canada, Vancouver, USA, Seattle, Italy, Milan"] + "examples": [ + "Canada, Vancouver, USA, Seattle, Italy, Milan" + ] }, "lineage/clade_analysis_software_version": { - "examples": ["2.1.10"], - "ontology":"GENEPIO:0001502", + "examples": [ + "2.1.10" + ], + "ontology": "GENEPIO:0001502", "type": "string", "description": "The version of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information", - "label":"Lineage/clade analysis software version" + "clasification": "Lineage and Variant information", + "label": "Lineage/clade analysis software version" }, "complications": { "Enums": [ @@ -2516,23 +2820,29 @@ "ontology": "GENEPIO:0001402", "type": "string", "description": "Patient medical complications that are believed to have occurred as a result of host disease.", - "examples": ["Acute respiratory failure [MONDO:0001208]"] + "examples": [ + "Acute respiratory failure [MONDO:0001208]" + ] }, "geo_loc_name_city": { "ontology": "GENEPIO:0001189", "type": "string", "description": "The city of origin of the sample.", - "examples": ["Vancouver"], - "clasification":"Sample collection and processing", - "label":"Geo Loc City" + "examples": [ + "Vancouver" + ], + "clasification": "Sample collection and processing", + "label": "Geo Loc City" }, "bioproject umbrella accession": { - "examples": ["PRJNA623807"], - "ontology": "GENEPIO:0001133", + "examples": [ + "PRJNA623807" + ], + "ontology": "GENEPIO:0001133", "type": "string", "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", - "clasification":"Database Identifiers", - "label":"umbrella bioproject accession", + "clasification": "Database Identifiers", + "label": "umbrella bioproject accession", }, "biomaterial_extracted": { "Enums": [ @@ -2549,9 +2859,11 @@ "ontology": "GENEPIO:0001266", "type": "string", "description": "The biomaterial extracted from samples for the purpose of sequencing.", - "examples": ["RNA (Total) [OBI:0000895]"], - "classification":"Sample collection and processing", - "label":"Biomaterial Extracted" + "examples": [ + "RNA (Total) [OBI:0000895]" + ], + "classification": "Sample collection and processing", + "label": "Biomaterial Extracted" }, "host_age_unit": { "Enums": [ @@ -2566,15 +2878,19 @@ "ontology": "GENEPIO:0001393", "type": "string", "description": "The units used to measure the host's age.", - "examples": ["years [UO:0000036]"] + "examples": [ + "years [UO:0000036]" + ] }, "geo_loc_latitude": { "ontology": "OBI:0001620", "type": "string", "description": "The latitude coordinates of the geographical location of sample collection.", - "examples": ["38.98 N"], - "clasification":"Sample collection and processing", - "label":"Geo Loc Latitude", + "examples": [ + "38.98 N" + ], + "clasification": "Sample collection and processing", + "label": "Geo Loc Latitude", }, "environmental_material": { "Enums": [ @@ -2620,17 +2936,21 @@ "ontology": "GENEPIO:0001223", "type": "string", "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", - "examples": ["Face Mask [OBI:0002787]"], - "clasification":"Sample collection and processing", - "label":"Environmental Material" + "examples": [ + "Face Mask [OBI:0002787]" + ], + "clasification": "Sample collection and processing", + "label": "Environmental Material" }, "sequence_submitter_contact_email": { - "examples": ["RespLab@lab.ca"], + "examples": [ + "RespLab@lab.ca" + ], "ontology": "GENEPIO:0001165", "type": "string", "description": "The email address of the contact responsible for follow-up regarding the sequence.", - "clasification":"Sample collection and processing", - "label":"Submitting Institution Email" + "clasification": "Sample collection and processing", + "label": "Submitting Institution Email" }, "environmental_site": { "Enums": [ @@ -2664,9 +2984,11 @@ "ontology": "GENEPIO:0001232", "type": "string", "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", - "examples": ["Hospital [ENVO:00002173]"], - "classification":"Sample collection and processing", - "label":"Anthropogenic Geographic Feature" + "examples": [ + "Hospital [ENVO:00002173]" + ], + "classification": "Sample collection and processing", + "label": "Anthropogenic Geographic Feature" }, "pre_existing_conditions_and_risk_factors": { "Enums": [ @@ -2770,10 +3092,14 @@ "ontology": "GENEPIO:0001401", "type": "string", "description": "Patient pre-existing conditions and risk factors.\nPre-existing condition: A medical condition that existed prior to the current infection.\nRisk Factor: A variable associated with an increased risk of disease or infection.", - "examples": ["Asthma [HP:0002099]"] + "examples": [ + "Asthma [HP:0002099]" + ] }, "first_dose_vaccination_date": { - "examples": ["26/02/2021"], + "examples": [ + "26/02/2021" + ], "ontology": "GENEPIO:0001407", "type": "string", "description": "The date the host was first vaccinated.", @@ -2788,33 +3114,41 @@ "ontology": "GENEPIO:0001503", "type": "string", "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", - "examples": ["Variant of Concern (VOC) [GENEPIO:0100083]"], - "classification":"Lineage and Variant information", - "label":"Variant designation" + "examples": [ + "Variant of Concern (VOC) [GENEPIO:0100083]" + ], + "classification": "Lineage and Variant information", + "label": "Variant designation" }, "variant_calling": { - "examples": [""], - "ontology": "0", + "examples": [ + "" + ], + "ontology": "operation_3227", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Variant Calling" + "clasification": "Bioinformatics and QC metrics", + "label": "Variant Calling" }, "if_variant_calling_other": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"If variant calling Is Other, Specify" + "clasification": "Bioinformatics and QC metrics", + "label": "If variant calling Is Other, Specify" }, "variant_calling_params": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Variant Calling params" + "clasification": "Bioinformatics and QC metrics", + "label": "Variant Calling params" }, "sample_collected_in_quarantine": { "Enums": [ @@ -2829,14 +3163,18 @@ "ontology": "GENEPIO:0100277", "type": "string", "description": "Whether the sample was collected from an individual in quarantine.", - "examples": ["Yes [NCIT:C49488]"] + "examples": [ + "Yes [NCIT:C49488]" + ] }, "sample_collected_by": { - "examples": ["Public Health Agency of Canada"], + "examples": [ + "Public Health Agency of Canada" + ], "ontology": "GENEPIO:0001153", "type": "string", "description": "The name of the agency that collected the original sample.", - "label":"Collecting Institution" + "label": "Originating Laboratory" }, "sequencing_instrument": { "Enums": [ @@ -2895,9 +3233,11 @@ "ontology": "GENEPIO:0001452", "type": "string", "description": "The model of the sequencing instrument used.", - "examples": ["Oxford Nanopore MinION [GENEPIO:0100142]"], - "classification":"Sequencing", - "label":"Sequencing Instrument Model" + "examples": [ + "Oxford Nanopore MinION [GENEPIO:0100142]" + ], + "classification": "Sequencing", + "label": "Sequencing Instrument Model" }, "host_health_status_details": { "Enums": [ @@ -2917,15 +3257,19 @@ "ontology": "GENEPIO:0001389", "type": "string", "description": "Further details pertaining to the health or disease status of the host at time of collection.", - "examples": ["Hospitalized (ICU) [GENEPIO:0100046]"] + "examples": [ + "Hospitalized (ICU) [GENEPIO:0100046]" + ] }, "isolate": { "ontology": "GENEPIO:0001644", "type": "string", "description": "Identifier of the specific isolate.", - "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"], - "clasification":"Sample collection and processing", - "label":"Isolate" + "examples": [ + "SARS-CoV-2/human/USA/CA-CDPH-001/2020" + ], + "clasification": "Sample collection and processing", + "label": "Isolate" }, "host_health_state": { "Enums": [ @@ -2943,7 +3287,9 @@ "ontology": "GENEPIO:0001388", "type": "string", "description": "Health status of the host at the time of sample collection.", - "examples": ["Asymptomatic [NCIT:C3833]"] + "examples": [ + "Asymptomatic [NCIT:C3833]" + ] }, "signs_and_symptoms": { "Enums": [ @@ -3048,26 +3394,32 @@ ] }, "dehosting_method": { - "examples": ["Nanostripper"], + "examples": [ + "Nanostripper" + ], "ontology": "GENEPIO:0001459", "type": "string", "description": "The method used to remove host reads from the pathogen sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Dehosting Method" + "clasification": "Bioinformatics and QC metrics", + "label": "Dehosting Method" }, "amplicon_pcr_primer_scheme": { - "examples": ["https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv"], - "ontology": "GENEPIO:0001456", - "type": "string", - "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", - "clasification":"Sequencing", - "label":"Amplicon Pcr Primer Scheme" + "examples": [ + "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv" + ], + "ontology": "GENEPIO:0001456", + "type": "string", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "clasification": "Sequencing", + "label": "Amplicon Pcr Primer Scheme" }, "vaccine_name": { "ontology": "GENEPIO:0001405", "type": "string", "description": "The name of the vaccine(s) administered.", - "examples": ["BNT162b2, Pfizer-BioNTech"] + "examples": [ + "BNT162b2, Pfizer-BioNTech" + ] }, "data_abstraction_details": { "ontology": "GENEPIO:0100278", @@ -3081,7 +3433,9 @@ "ontology": "GENEPIO:0001461", "type": "string", "description": "The name of the consensus sequence file.", - "examples": ["ncov123assembly.fasta"] + "examples": [ + "ncov123assembly.fasta" + ] }, "purpose_of_sequencing_details": { "Enums": [ @@ -3104,30 +3458,38 @@ "ontology": "GENEPIO:0001446", "type": "string", "description": "The description of why the sample was sequenced providing specific details.", - "examples": ["Screened for S gene target failure (S dropout)"], - "clasification":"Sequencing", - "label":"Purpose Of Sequencing Details" + "examples": [ + "Screened for S gene target failure (S dropout)" + ], + "clasification": "Sequencing", + "label": "Purpose Of Sequencing Details" }, "sequence_submitted_by": { - "examples": ["Centers for Disease Control and Prevention"], + "examples": [ + "Centers for Disease Control and Prevention" + ], "ontology": "GENEPIO:0001159", "type": "string", "description": "The name of the agency that generated the sequence.", - "label":"Submitting Institution" + "label": "Submitting Institution" }, "sequencing_protocol_name": { - "examples": ["1D_DNA_MinION, ARTIC Network Protocol V3"], - "ontology": "GENEPIO:0001453", - "type": "string", - "description": "The name and version number of the sequencing protocol used.", - "clasification":"Sequencing", - "label":"Sequencing Protocol Name" + "examples": [ + "1D_DNA_MinION, ARTIC Network Protocol V3" + ], + "ontology": "GENEPIO:0001453", + "type": "string", + "description": "The name and version number of the sequencing protocol used.", + "clasification": "Sequencing", + "label": "Sequencing Protocol Name" }, "prior_sars_cov_2_infection_isolate": { "ontology": "GENEPIO:0001436", "type": "string", "description": "The identifier of the isolate found in the prior SARS-CoV-2 infection.", - "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"] + "examples": [ + "SARS-CoV-2/human/USA/CA-CDPH-001/2020" + ] }, "organism": { "Enums": [ @@ -3145,8 +3507,8 @@ "examples": [ "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]" ], - "classification":"Sample collection and processing", - "label":"Organism" + "classification": "Sample collection and processing", + "label": "Organism" }, "purpose_of_sampling": { "Enums": [ @@ -3164,7 +3526,9 @@ "ontology": "GENEPIO:0001198", "type": "string", "description": "The reason that the sample was collected.", - "examples": ["Diagnostic Testing [GENEPIO:0100002]"] + "examples": [ + "Diagnostic Testing [GENEPIO:0100002]" + ] } } -} +} \ No newline at end of file diff --git a/schema/phage_plus_V0.json b/schema/phage_plus_V0.json index 4d0bc178..5418e8e9 100644 --- a/schema/phage_plus_V0.json +++ b/schema/phage_plus_V0.json @@ -19,2267 +19,2603 @@ "type": "object", "properties": { "sample_name": { - "examples": ["prov_rona_99"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The user-defined name for the sample.", - "clasification":"Database Identifiers" + "examples": [ + "prov_rona_99" + ], + "ontology": "0", + "type": "string", + "description": "The user-defined name for the sample.", + "clasification": "Database Identifiers", + "label": "Collecting Sample id" }, "collecting_institution": { - "examples": ["Public Health Agency of Canada"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The name of the agency that collected the original sample." + "examples": [ + "Public Health Agency of Canada" + ], + "ontology": "GENEPIO:0001153", + "type": "string", + "description": "The name of the agency that collected the original sample.", + "label": "Originating Laboratory" }, "submitting_institution": { - "examples": ["Centers for Disease Control and Prevention"], - "ontology": "GENEPIO:0001159", - "type": "string", - "description": "The name of the agency that generated the sequence." + "examples": [ + "Centers for Disease Control and Prevention" + ], + "ontology": "GENEPIO:0001159", + "type": "string", + "description": "The name of the agency that generated the sequence." }, "sample_collection_date": { - "examples": ["3/19/2020"], - "ontology": "GENEPIO:0001174", - "type": "string", - "description": "The date on which the sample was collected.", - "format":"date" + "examples": [ + "3/19/2020" + ], + "ontology": "GENEPIO:0001174", + "type": "string", + "description": "The date on which the sample was collected.", + "format": "date" }, "geo_loc_name_country": { - "Enums": [ - "Afghanistan [GAZ:00006882]", - "Albania [GAZ:00002953]", - "Algeria [GAZ:00000563]", - "American Samoa [GAZ:00003957]", - "Andorra [GAZ:00002948]", - "Angola [GAZ:00001095]", - "Anguilla [GAZ:00009159]", - "Antarctica [GAZ:00000462]", - "Antigua and Barbuda [GAZ:00006883]", - "Argentina [GAZ:00002928]", - "Armenia [GAZ:00004094]", - "Aruba [GAZ:00004025]", - "Ashmore and Cartier Islands [GAZ:00005901]", - "Australia [GAZ:00000463]", - "Austria [GAZ:00002942]", - "Azerbaijan [GAZ:00004941]", - "Bahamas [GAZ:00002733]", - "Bahrain [GAZ:00005281]", - "Baker Island [GAZ:00007117]", - "Bangladesh [GAZ:00003750]", - "Barbados [GAZ:00001251]", - "Bassas da India [GAZ:00005810]", - "Belarus [GAZ:00006886]", - "Belgium [GAZ:00002938]", - "Belize [GAZ:00002934]", - "Benin [GAZ:00000904]", - "Bermuda [GAZ:00001264]", - "Bhutan [GAZ:00003920]", - "Bolivia [GAZ:00002511]", - "Borneo [GAZ:00025355]", - "Bosnia and Herzegovina [GAZ:00006887]", - "Botswana [GAZ:00001097]", - "Bouvet Island [GAZ:00001453]", - "Brazil [GAZ:00002828]", - "British Virgin Islands [GAZ:00003961]", - "Brunei [GAZ:00003901]", - "Bulgaria [GAZ:00002950]", - "Burkina Faso [GAZ:00000905]", - "Burundi [GAZ:00001090]", - "Cambodia [GAZ:00006888]", - "Cameroon [GAZ:00001093]", - "Canada [GAZ:00002560]", - "Cape Verde [GAZ:00001227]", - "Cayman Islands [GAZ:00003986]", - "Central African Republic [GAZ:00001089]", - "Chad [GAZ:00000586]", - "Chile [GAZ:00002825]", - "China [GAZ:00002845]", - "Christmas Island [GAZ:00005915]", - "Clipperton Island [GAZ:00005838]", - "Cocos Islands [GAZ:00009721]", - "Colombia [GAZ:00002929]", - "Comoros [GAZ:00005820]", - "Cook Islands [GAZ:00053798]", - "Coral Sea Islands [GAZ:00005917]", - "Costa Rica [GAZ:00002901]", - "Cote d'Ivoire [GAZ:00000906]", - "Croatia [GAZ:00002719]", - "Cuba [GAZ:00003762]", - "Curacao [GAZ:00012582]", - "Cyprus [GAZ:00004006]", - "Czech Republic [GAZ:00002954]", - "Democratic Republic of the Congo [GAZ:00001086]", - "Denmark [GAZ:00005852]", - "Djibouti [GAZ:00000582]", - "Dominica [GAZ:00006890]", - "Dominican Republic [GAZ:00003952]", - "Ecuador [GAZ:00002912]", - "Egypt [GAZ:00003934]", - "El Salvador [GAZ:00002935]", - "Equatorial Guinea [GAZ:00001091]", - "Eritrea [GAZ:00000581]", - "Estonia [GAZ:00002959]", - "Eswatini [GAZ:00001099]", - "Ethiopia [GAZ:00000567]", - "Europa Island [GAZ:00005811]", - "Falkland Islands (Islas Malvinas) [GAZ:00001412]", - "Faroe Islands [GAZ:00059206]", - "Fiji [GAZ:00006891]", - "Finland [GAZ:00002937]", - "France [GAZ:00003940]", - "French Guiana [GAZ:00002516]", - "French Polynesia [GAZ:00002918]", - "French Southern and Antarctic Lands [GAZ:00003753]", - "Gabon [GAZ:00001092]", - "Gambia [GAZ:00000907]", - "Gaza Strip [GAZ:00009571]", - "Georgia [GAZ:00004942]", - "Germany [GAZ:00002646]", - "Ghana [GAZ:00000908]", - "Gibraltar [GAZ:00003987]", - "Glorioso Islands [GAZ:00005808]", - "Greece [GAZ:00002945]", - "Greenland [GAZ:00001507]", - "Grenada [GAZ:02000573]", - "Guadeloupe [GAZ:00067142]", - "Guam [GAZ:00003706]", - "Guatemala [GAZ:00002936]", - "Guernsey [GAZ:00001550]", - "Guinea [GAZ:00000909]", - "Guinea-Bissau [GAZ:00000910]", - "Guyana [GAZ:00002522]", - "Haiti [GAZ:00003953]", - "Heard Island and McDonald Islands [GAZ:00009718]", - "Honduras [GAZ:00002894]", - "Hong Kong [GAZ:00003203]", - "Howland Island [GAZ:00007120]", - "Hungary [GAZ:00002952]", - "Iceland [GAZ:00000843]", - "India [GAZ:00002839]", - "Indonesia [GAZ:00003727]", - "Iran [GAZ:00004474]", - "Iraq [GAZ:00004483]", - "Ireland [GAZ:00002943]", - "Isle of Man [GAZ:00052477]", - "Israel [GAZ:00002476]", - "Italy [GAZ:00002650]", - "Jamaica [GAZ:00003781]", - "Jan Mayen [GAZ:00005853]", - "Japan [GAZ:00002747]", - "Jarvis Island [GAZ:00007118]", - "Jersey [GAZ:00001551]", - "Johnston Atoll [GAZ:00007114]", - "Jordan [GAZ:00002473]", - "Juan de Nova Island [GAZ:00005809]", - "Kazakhstan [GAZ:00004999]", - "Kenya [GAZ:00001101]", - "Kerguelen Archipelago [GAZ:00005682]", - "Kingman Reef [GAZ:00007116]", - "Kiribati [GAZ:00006894]", - "Kosovo [GAZ:00011337]", - "Kuwait [GAZ:00005285]", - "Kyrgyzstan [GAZ:00006893]", - "Laos [GAZ:00006889]", - "Latvia [GAZ:00002958]", - "Lebanon [GAZ:00002478]", - "Lesotho [GAZ:00001098]", - "Liberia [GAZ:00000911]", - "Libya [GAZ:00000566]", - "Liechtenstein [GAZ:00003858]", - "Line Islands [GAZ:00007144]", - "Lithuania [GAZ:00002960]", - "Luxembourg [GAZ:00002947]", - "Macau [GAZ:00003202]", - "Madagascar [GAZ:00001108]", - "Malawi [GAZ:00001105]", - "Malaysia [GAZ:00003902]", - "Maldives [GAZ:00006924]", - "Mali [GAZ:00000584]", - "Malta [GAZ:00004017]", - "Marshall Islands [GAZ:00007161]", - "Martinique [GAZ:00067143]", - "Mauritania [GAZ:00000583]", - "Mauritius [GAZ:00003745]", - "Mayotte [GAZ:00003943]", - "Mexico [GAZ:00002852]", - "Micronesia [GAZ:00005862]", - "Midway Islands [GAZ:00007112]", - "Moldova [GAZ:00003897]", - "Monaco [GAZ:00003857]", - "Mongolia [GAZ:00008744]", - "Montenegro [GAZ:00006898]", - "Montserrat [GAZ:00003988]", - "Morocco [GAZ:00000565]", - "Mozambique [GAZ:00001100]", - "Myanmar [GAZ:00006899]", - "Namibia [GAZ:00001096]", - "Nauru [GAZ:00006900]", - "Navassa Island [GAZ:00007119]", - "Nepal [GAZ:00004399]", - "Netherlands [GAZ:00002946]", - "New Caledonia [GAZ:00005206]", - "New Zealand [GAZ:00000469]", - "Nicaragua [GAZ:00002978]", - "Niger [GAZ:00000585]", - "Nigeria [GAZ:00000912]", - "Niue [GAZ:00006902]", - "Norfolk Island [GAZ:00005908]", - "North Korea [GAZ:00002801]", - "North Macedonia [GAZ:00006895]", - "North Sea [GAZ:00002284]", - "Northern Mariana Islands [GAZ:00003958]", - "Norway [GAZ:00002699]", - "Oman [GAZ:00005283]", - "Pakistan [GAZ:00005246]", - "Palau [GAZ:00006905]", - "Panama [GAZ:00002892]", - "Papua New Guinea [GAZ:00003922]", - "Paracel Islands [GAZ:00010832]", - "Paraguay [GAZ:00002933]", - "Peru [GAZ:00002932]", - "Philippines [GAZ:00004525]", - "Pitcairn Islands [GAZ:00005867]", - "Poland [GAZ:00002939]", - "Portugal [GAZ:00004126]", - "Puerto Rico [GAZ:00006935]", - "Qatar [GAZ:00005286]", - "Republic of the Congo [GAZ:00001088]", - "Reunion [GAZ:00003945]", - "Romania [GAZ:00002951]", - "Ross Sea [GAZ:00023304]", - "Russia [GAZ:00002721]", - "Rwanda [GAZ:00001087]", - "Saint Helena [GAZ:00000849]", - "Saint Kitts and Nevis [GAZ:00006906]", - "Saint Lucia [GAZ:00006909]", - "Saint Pierre and Miquelon [GAZ:00003942]", - "Saint Martin [GAZ:00005841]", - "Saint Vincent and the Grenadines [GAZ:02000565]", - "Samoa [GAZ:00006910]", - "San Marino [GAZ:00003102]", - "Sao Tome and Principe [GAZ:00006927]", - "Saudi Arabia [GAZ:00005279]", - "Senegal [GAZ:00000913]", - "Serbia [GAZ:00002957]", - "Seychelles [GAZ:00006922]", - "Sierra Leone [GAZ:00000914]", - "Singapore [GAZ:00003923]", - "Sint Maarten [GAZ:00012579]", - "Slovakia [GAZ:00002956]", - "Slovenia [GAZ:00002955]", - "Solomon Islands [GAZ:00005275]", - "Somalia [GAZ:00001104]", - "South Africa [GAZ:00001094]", - "South Georgia and the South Sandwich Islands [GAZ:00003990]", - "South Korea [GAZ:00002802]", - "South Sudan [GAZ:00233439]", - "Spain [GAZ:00003936]", - "Spratly Islands [GAZ:00010831]", - "Sri Lanka [GAZ:00003924]", - "State of Palestine [GAZ:00002475]", - "Sudan [GAZ:00000560]", - "Suriname [GAZ:00002525]", - "Svalbard [GAZ:00005396]", - "Swaziland [GAZ:00001099]", - "Sweden [GAZ:00002729]", - "Switzerland [GAZ:00002941]", - "Syria [GAZ:00002474]", - "Taiwan [GAZ:00005341]", - "Tajikistan [GAZ:00006912]", - "Tanzania [GAZ:00001103]", - "Thailand [GAZ:00003744]", - "Timor-Leste [GAZ:00006913]", - "Togo [GAZ:00000915]", - "Tokelau [GAZ:00260188]", - "Tonga [GAZ:00006916]", - "Trinidad and Tobago [GAZ:00003767]", - "Tromelin Island [GAZ:00005812]", - "Tunisia [GAZ:00000562]", - "Turkey [GAZ:00000558]", - "Turkmenistan [GAZ:00005018]", - "Turks and Caicos Islands [GAZ:00003955]", - "Tuvalu [GAZ:00009715]", - "USA [GAZ:00002459]", - "Uganda [GAZ:00001102]", - "Ukraine [GAZ:00002724]", - "United Arab Emirates [GAZ:00005282]", - "United Kingdom [GAZ:00002637]", - "Uruguay [GAZ:00002930]", - "Uzbekistan [GAZ:00004979]", - "Vanuatu [GAZ:00006918]", - "Venezuela [GAZ:00002931]", - "Viet Nam [GAZ:00003756]", - "Virgin Islands [GAZ:00003959]", - "Wake Island [GAZ:00007111]", - "Wallis and Futuna [GAZ:00007191]", - "West Bank [GAZ:00009572]", - "Western Sahara [GAZ:00000564]", - "Yemen [GAZ:00005284]", - "Zambia [GAZ:00001107]", - "Zimbabwe [GAZ:00001106]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001181", - "type": "string", - "description": "The country of origin of the sample.", - "examples": ["South Africa [GAZ:00001094]"], - "classification":"Sample collection and processing", - "label":"Geo Loc Autonomic Country" + "Enums": [ + "Afghanistan [GAZ:00006882]", + "Albania [GAZ:00002953]", + "Algeria [GAZ:00000563]", + "American Samoa [GAZ:00003957]", + "Andorra [GAZ:00002948]", + "Angola [GAZ:00001095]", + "Anguilla [GAZ:00009159]", + "Antarctica [GAZ:00000462]", + "Antigua and Barbuda [GAZ:00006883]", + "Argentina [GAZ:00002928]", + "Armenia [GAZ:00004094]", + "Aruba [GAZ:00004025]", + "Ashmore and Cartier Islands [GAZ:00005901]", + "Australia [GAZ:00000463]", + "Austria [GAZ:00002942]", + "Azerbaijan [GAZ:00004941]", + "Bahamas [GAZ:00002733]", + "Bahrain [GAZ:00005281]", + "Baker Island [GAZ:00007117]", + "Bangladesh [GAZ:00003750]", + "Barbados [GAZ:00001251]", + "Bassas da India [GAZ:00005810]", + "Belarus [GAZ:00006886]", + "Belgium [GAZ:00002938]", + "Belize [GAZ:00002934]", + "Benin [GAZ:00000904]", + "Bermuda [GAZ:00001264]", + "Bhutan [GAZ:00003920]", + "Bolivia [GAZ:00002511]", + "Borneo [GAZ:00025355]", + "Bosnia and Herzegovina [GAZ:00006887]", + "Botswana [GAZ:00001097]", + "Bouvet Island [GAZ:00001453]", + "Brazil [GAZ:00002828]", + "British Virgin Islands [GAZ:00003961]", + "Brunei [GAZ:00003901]", + "Bulgaria [GAZ:00002950]", + "Burkina Faso [GAZ:00000905]", + "Burundi [GAZ:00001090]", + "Cambodia [GAZ:00006888]", + "Cameroon [GAZ:00001093]", + "Canada [GAZ:00002560]", + "Cape Verde [GAZ:00001227]", + "Cayman Islands [GAZ:00003986]", + "Central African Republic [GAZ:00001089]", + "Chad [GAZ:00000586]", + "Chile [GAZ:00002825]", + "China [GAZ:00002845]", + "Christmas Island [GAZ:00005915]", + "Clipperton Island [GAZ:00005838]", + "Cocos Islands [GAZ:00009721]", + "Colombia [GAZ:00002929]", + "Comoros [GAZ:00005820]", + "Cook Islands [GAZ:00053798]", + "Coral Sea Islands [GAZ:00005917]", + "Costa Rica [GAZ:00002901]", + "Cote d'Ivoire [GAZ:00000906]", + "Croatia [GAZ:00002719]", + "Cuba [GAZ:00003762]", + "Curacao [GAZ:00012582]", + "Cyprus [GAZ:00004006]", + "Czech Republic [GAZ:00002954]", + "Democratic Republic of the Congo [GAZ:00001086]", + "Denmark [GAZ:00005852]", + "Djibouti [GAZ:00000582]", + "Dominica [GAZ:00006890]", + "Dominican Republic [GAZ:00003952]", + "Ecuador [GAZ:00002912]", + "Egypt [GAZ:00003934]", + "El Salvador [GAZ:00002935]", + "Equatorial Guinea [GAZ:00001091]", + "Eritrea [GAZ:00000581]", + "Estonia [GAZ:00002959]", + "Eswatini [GAZ:00001099]", + "Ethiopia [GAZ:00000567]", + "Europa Island [GAZ:00005811]", + "Falkland Islands (Islas Malvinas) [GAZ:00001412]", + "Faroe Islands [GAZ:00059206]", + "Fiji [GAZ:00006891]", + "Finland [GAZ:00002937]", + "France [GAZ:00003940]", + "French Guiana [GAZ:00002516]", + "French Polynesia [GAZ:00002918]", + "French Southern and Antarctic Lands [GAZ:00003753]", + "Gabon [GAZ:00001092]", + "Gambia [GAZ:00000907]", + "Gaza Strip [GAZ:00009571]", + "Georgia [GAZ:00004942]", + "Germany [GAZ:00002646]", + "Ghana [GAZ:00000908]", + "Gibraltar [GAZ:00003987]", + "Glorioso Islands [GAZ:00005808]", + "Greece [GAZ:00002945]", + "Greenland [GAZ:00001507]", + "Grenada [GAZ:02000573]", + "Guadeloupe [GAZ:00067142]", + "Guam [GAZ:00003706]", + "Guatemala [GAZ:00002936]", + "Guernsey [GAZ:00001550]", + "Guinea [GAZ:00000909]", + "Guinea-Bissau [GAZ:00000910]", + "Guyana [GAZ:00002522]", + "Haiti [GAZ:00003953]", + "Heard Island and McDonald Islands [GAZ:00009718]", + "Honduras [GAZ:00002894]", + "Hong Kong [GAZ:00003203]", + "Howland Island [GAZ:00007120]", + "Hungary [GAZ:00002952]", + "Iceland [GAZ:00000843]", + "India [GAZ:00002839]", + "Indonesia [GAZ:00003727]", + "Iran [GAZ:00004474]", + "Iraq [GAZ:00004483]", + "Ireland [GAZ:00002943]", + "Isle of Man [GAZ:00052477]", + "Israel [GAZ:00002476]", + "Italy [GAZ:00002650]", + "Jamaica [GAZ:00003781]", + "Jan Mayen [GAZ:00005853]", + "Japan [GAZ:00002747]", + "Jarvis Island [GAZ:00007118]", + "Jersey [GAZ:00001551]", + "Johnston Atoll [GAZ:00007114]", + "Jordan [GAZ:00002473]", + "Juan de Nova Island [GAZ:00005809]", + "Kazakhstan [GAZ:00004999]", + "Kenya [GAZ:00001101]", + "Kerguelen Archipelago [GAZ:00005682]", + "Kingman Reef [GAZ:00007116]", + "Kiribati [GAZ:00006894]", + "Kosovo [GAZ:00011337]", + "Kuwait [GAZ:00005285]", + "Kyrgyzstan [GAZ:00006893]", + "Laos [GAZ:00006889]", + "Latvia [GAZ:00002958]", + "Lebanon [GAZ:00002478]", + "Lesotho [GAZ:00001098]", + "Liberia [GAZ:00000911]", + "Libya [GAZ:00000566]", + "Liechtenstein [GAZ:00003858]", + "Line Islands [GAZ:00007144]", + "Lithuania [GAZ:00002960]", + "Luxembourg [GAZ:00002947]", + "Macau [GAZ:00003202]", + "Madagascar [GAZ:00001108]", + "Malawi [GAZ:00001105]", + "Malaysia [GAZ:00003902]", + "Maldives [GAZ:00006924]", + "Mali [GAZ:00000584]", + "Malta [GAZ:00004017]", + "Marshall Islands [GAZ:00007161]", + "Martinique [GAZ:00067143]", + "Mauritania [GAZ:00000583]", + "Mauritius [GAZ:00003745]", + "Mayotte [GAZ:00003943]", + "Mexico [GAZ:00002852]", + "Micronesia [GAZ:00005862]", + "Midway Islands [GAZ:00007112]", + "Moldova [GAZ:00003897]", + "Monaco [GAZ:00003857]", + "Mongolia [GAZ:00008744]", + "Montenegro [GAZ:00006898]", + "Montserrat [GAZ:00003988]", + "Morocco [GAZ:00000565]", + "Mozambique [GAZ:00001100]", + "Myanmar [GAZ:00006899]", + "Namibia [GAZ:00001096]", + "Nauru [GAZ:00006900]", + "Navassa Island [GAZ:00007119]", + "Nepal [GAZ:00004399]", + "Netherlands [GAZ:00002946]", + "New Caledonia [GAZ:00005206]", + "New Zealand [GAZ:00000469]", + "Nicaragua [GAZ:00002978]", + "Niger [GAZ:00000585]", + "Nigeria [GAZ:00000912]", + "Niue [GAZ:00006902]", + "Norfolk Island [GAZ:00005908]", + "North Korea [GAZ:00002801]", + "North Macedonia [GAZ:00006895]", + "North Sea [GAZ:00002284]", + "Northern Mariana Islands [GAZ:00003958]", + "Norway [GAZ:00002699]", + "Oman [GAZ:00005283]", + "Pakistan [GAZ:00005246]", + "Palau [GAZ:00006905]", + "Panama [GAZ:00002892]", + "Papua New Guinea [GAZ:00003922]", + "Paracel Islands [GAZ:00010832]", + "Paraguay [GAZ:00002933]", + "Peru [GAZ:00002932]", + "Philippines [GAZ:00004525]", + "Pitcairn Islands [GAZ:00005867]", + "Poland [GAZ:00002939]", + "Portugal [GAZ:00004126]", + "Puerto Rico [GAZ:00006935]", + "Qatar [GAZ:00005286]", + "Republic of the Congo [GAZ:00001088]", + "Reunion [GAZ:00003945]", + "Romania [GAZ:00002951]", + "Ross Sea [GAZ:00023304]", + "Russia [GAZ:00002721]", + "Rwanda [GAZ:00001087]", + "Saint Helena [GAZ:00000849]", + "Saint Kitts and Nevis [GAZ:00006906]", + "Saint Lucia [GAZ:00006909]", + "Saint Pierre and Miquelon [GAZ:00003942]", + "Saint Martin [GAZ:00005841]", + "Saint Vincent and the Grenadines [GAZ:02000565]", + "Samoa [GAZ:00006910]", + "San Marino [GAZ:00003102]", + "Sao Tome and Principe [GAZ:00006927]", + "Saudi Arabia [GAZ:00005279]", + "Senegal [GAZ:00000913]", + "Serbia [GAZ:00002957]", + "Seychelles [GAZ:00006922]", + "Sierra Leone [GAZ:00000914]", + "Singapore [GAZ:00003923]", + "Sint Maarten [GAZ:00012579]", + "Slovakia [GAZ:00002956]", + "Slovenia [GAZ:00002955]", + "Solomon Islands [GAZ:00005275]", + "Somalia [GAZ:00001104]", + "South Africa [GAZ:00001094]", + "South Georgia and the South Sandwich Islands [GAZ:00003990]", + "South Korea [GAZ:00002802]", + "South Sudan [GAZ:00233439]", + "Spain [GAZ:00003936]", + "Spratly Islands [GAZ:00010831]", + "Sri Lanka [GAZ:00003924]", + "State of Palestine [GAZ:00002475]", + "Sudan [GAZ:00000560]", + "Suriname [GAZ:00002525]", + "Svalbard [GAZ:00005396]", + "Swaziland [GAZ:00001099]", + "Sweden [GAZ:00002729]", + "Switzerland [GAZ:00002941]", + "Syria [GAZ:00002474]", + "Taiwan [GAZ:00005341]", + "Tajikistan [GAZ:00006912]", + "Tanzania [GAZ:00001103]", + "Thailand [GAZ:00003744]", + "Timor-Leste [GAZ:00006913]", + "Togo [GAZ:00000915]", + "Tokelau [GAZ:00260188]", + "Tonga [GAZ:00006916]", + "Trinidad and Tobago [GAZ:00003767]", + "Tromelin Island [GAZ:00005812]", + "Tunisia [GAZ:00000562]", + "Turkey [GAZ:00000558]", + "Turkmenistan [GAZ:00005018]", + "Turks and Caicos Islands [GAZ:00003955]", + "Tuvalu [GAZ:00009715]", + "USA [GAZ:00002459]", + "Uganda [GAZ:00001102]", + "Ukraine [GAZ:00002724]", + "United Arab Emirates [GAZ:00005282]", + "United Kingdom [GAZ:00002637]", + "Uruguay [GAZ:00002930]", + "Uzbekistan [GAZ:00004979]", + "Vanuatu [GAZ:00006918]", + "Venezuela [GAZ:00002931]", + "Viet Nam [GAZ:00003756]", + "Virgin Islands [GAZ:00003959]", + "Wake Island [GAZ:00007111]", + "Wallis and Futuna [GAZ:00007191]", + "West Bank [GAZ:00009572]", + "Western Sahara [GAZ:00000564]", + "Yemen [GAZ:00005284]", + "Zambia [GAZ:00001107]", + "Zimbabwe [GAZ:00001106]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001181", + "type": "string", + "description": "The country of origin of the sample.", + "examples": [ + "South Africa [GAZ:00001094]" + ], + "classification": "Sample collection and processing", + "label": "Geo Loc Autonomic Country" }, "geo_loc_state": { - "examples": ["Western Cape"], - "ontology": "GENEPIO:0001185", - "type": "string", - "description": "The state/province/territory of origin of the sample.", - "classification":"Sample collection and processing", - "label":"Geo Loc Autonomic Community" + "examples": [ + "Western Cape" + ], + "ontology": "GENEPIO:0001185", + "type": "string", + "description": "The state/province/territory of origin of the sample.", + "classification": "Sample collection and processing", + "label": "Geo Loc Autonomic Community" }, "organism": { - "Enums": [ - "Coronaviridae [NCBITaxon:11118]", - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001191", - "type": "string", - "description": "Taxonomic name of the organism.", - "examples": [ - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", - ], - "classification":"Sample collection and processing", - "label":"Organism" + "Enums": [ + "Coronaviridae [NCBITaxon:11118]", + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001191", + "type": "string", + "description": "Taxonomic name of the organism.", + "examples": [ + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", + ], + "classification": "Sample collection and processing", + "label": "Organism" }, "isolate": { - "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"], - "ontology": "GENEPIO:0001644", - "type": "string", - "description": "Identifier of the specific isolate.", - "clasification":"Sample collection and processing", - "label":"Isolate" + "examples": [ + "SARS-CoV-2/human/USA/CA-CDPH-001/2020" + ], + "ontology": "GENEPIO:0001644", + "type": "string", + "description": "Identifier of the specific isolate.", + "clasification": "Sample collection and processing", + "label": "Isolate" }, "host_scientific_name": { - "Enums": [ - "Bos taurus [NCBITaxon:9913]", - "Canis lupus familiaris [NCBITaxon:9615]", - "Chiroptera [NCBITaxon:9397]", - "Columbidae [NCBITaxon:8930]", - "Felis catus [NCBITaxon:9685]", - "Gallus gallus [NCBITaxon:9031]", - "Homo sapiens [NCBITaxon:9606]", - "Manis [NCBITaxon:9973]", - "Manis javanica [NCBITaxon:9974]", - "Neovison vison [NCBITaxon:452646]", - "Panthera leo [NCBITaxon:9689]", - "Panthera tigris [NCBITaxon:9694]", - "Rhinolophidae [NCBITaxon:58055]", - "Rhinolophus affinis [NCBITaxon:59477]", - "Sus scrofa domesticus [NCBITaxon:9825]", - "Viverridae [NCBITaxon:9673]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001387", - "type": "string", - "description": "The taxonomic, or scientific name of the host.", - "examples": ["Homo sapiens [NCBITaxon:9606]"], - "clasification":"Host information", - "label":"Host Scientific Name" + "Enums": [ + "Bos taurus [NCBITaxon:9913]", + "Canis lupus familiaris [NCBITaxon:9615]", + "Chiroptera [NCBITaxon:9397]", + "Columbidae [NCBITaxon:8930]", + "Felis catus [NCBITaxon:9685]", + "Gallus gallus [NCBITaxon:9031]", + "Homo sapiens [NCBITaxon:9606]", + "Manis [NCBITaxon:9973]", + "Manis javanica [NCBITaxon:9974]", + "Neovison vison [NCBITaxon:452646]", + "Panthera leo [NCBITaxon:9689]", + "Panthera tigris [NCBITaxon:9694]", + "Rhinolophidae [NCBITaxon:58055]", + "Rhinolophus affinis [NCBITaxon:59477]", + "Sus scrofa domesticus [NCBITaxon:9825]", + "Viverridae [NCBITaxon:9673]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001387", + "type": "string", + "description": "The taxonomic, or scientific name of the host.", + "examples": [ + "Homo sapiens [NCBITaxon:9606]" + ], + "clasification": "Host information", + "label": "Host Scientific Name" }, "host_disease": { - "Enums": [ - "COVID-19 [MONDO:0100096]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001391", - "type": "string", - "description": "The name of the disease experienced by the host.", - "examples": ["COVID-19 [MONDO:0100096]"] + "Enums": [ + "COVID-19 [MONDO:0100096]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001391", + "type": "string", + "description": "The name of the disease experienced by the host.", + "examples": [ + "COVID-19 [MONDO:0100096]" + ] }, "sequencing_instrument_model": { - "Enums": [ - "Illumina sequencing instrument [GENEPIO:0100105]", - "Illumina Genome Analyzer [GENEPIO:0100106]", - "Illumina Genome Analyzer II [GENEPIO:0100107]", - "Illumina Genome Analyzer IIx [GENEPIO:0100108]", - "Illumina HiScanSQ [GENEPIO:0100109]", - "Illumina HiSeq [GENEPIO:0100110]", - "Illumina HiSeq X [GENEPIO:0100111]", - "Illumina HiSeq X Five [GENEPIO:0100112]", - "Illumina HiSeq X Ten [GENEPIO:0100113]", - "Illumina HiSeq 1000 [GENEPIO:0100114]", - "Illumina HiSeq 1500 [GENEPIO:0100115]", - "Illumina HiSeq 2000 [GENEPIO:0100116]", - "Illumina HiSeq 2500 [GENEPIO:0100117]", - "Illumina HiSeq 3000 [GENEPIO:0100118]", - "Illumina HiSeq 4000 [GENEPIO:0100119]", - "Illumina iSeq [GENEPIO:0100120]", - "Illumina iSeq 100 [GENEPIO:0100121]", - "Illumina NovaSeq [GENEPIO:0100122]", - "Illumina NovaSeq 6000 [GENEPIO:0100123]", - "Illumina MiniSeq [GENEPIO:0100124]", - "Illumina MiSeq [GENEPIO:0100125]", - "Illumina NextSeq [GENEPIO:0100126]", - "Illumina NextSeq 500 [GENEPIO:0100127]", - "Illumina NextSeq 550 [GENEPIO:0100128]", - "Illumina NextSeq 2000 [GENEPIO:0100129]", - "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", - "PacBio RS [GENEPIO:0100131]", - "PacBio RS II [GENEPIO:0100132]", - "PacBio Sequel [GENEPIO:0100133]", - "PacBio Sequel II [GENEPIO:0100134]", - "Ion Torrent sequencing instrument [GENEPIO:0100135]", - "Ion Torrent PGM [GENEPIO:0100136]", - "Ion Torrent Proton [GENEPIO:0100137]", - "Ion Torrent S5 XL [GENEPIO:0100138]", - "Ion Torrent S5 [GENEPIO:0100139]", - "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", - "Oxford Nanopore GridION [GENEPIO:0100141]", - "Oxford Nanopore MinION [GENEPIO:0100142]", - "Oxford Nanopore PromethION [GENEPIO:0100143]", - "BGI Genomics sequencing instrument [GENEPIO:0100144]", - "BGI SEQ-500 [GENEPIO:0100145]", - "MGI sequencing instrument [GENEPIO:0100146]", - "MGI DNBSEQ-T7 [GENEPIO:0100147]", - "MGI DNBSEQ-G400 [GENEPIO:0100148]", - "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", - "MGI DNBSEQ-G50 [GENEPIO:0100150]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001452", - "type": "string", - "description": "The model of the sequencing instrument used.", - "examples": ["Oxford Nanopore MinION [GENEPIO:0100142]"], - "classification":"Sequencing", - "label":"Sequencing Instrument Model" + "Enums": [ + "Illumina sequencing instrument [GENEPIO:0100105]", + "Illumina Genome Analyzer [GENEPIO:0100106]", + "Illumina Genome Analyzer II [GENEPIO:0100107]", + "Illumina Genome Analyzer IIx [GENEPIO:0100108]", + "Illumina HiScanSQ [GENEPIO:0100109]", + "Illumina HiSeq [GENEPIO:0100110]", + "Illumina HiSeq X [GENEPIO:0100111]", + "Illumina HiSeq X Five [GENEPIO:0100112]", + "Illumina HiSeq X Ten [GENEPIO:0100113]", + "Illumina HiSeq 1000 [GENEPIO:0100114]", + "Illumina HiSeq 1500 [GENEPIO:0100115]", + "Illumina HiSeq 2000 [GENEPIO:0100116]", + "Illumina HiSeq 2500 [GENEPIO:0100117]", + "Illumina HiSeq 3000 [GENEPIO:0100118]", + "Illumina HiSeq 4000 [GENEPIO:0100119]", + "Illumina iSeq [GENEPIO:0100120]", + "Illumina iSeq 100 [GENEPIO:0100121]", + "Illumina NovaSeq [GENEPIO:0100122]", + "Illumina NovaSeq 6000 [GENEPIO:0100123]", + "Illumina MiniSeq [GENEPIO:0100124]", + "Illumina MiSeq [GENEPIO:0100125]", + "Illumina NextSeq [GENEPIO:0100126]", + "Illumina NextSeq 500 [GENEPIO:0100127]", + "Illumina NextSeq 550 [GENEPIO:0100128]", + "Illumina NextSeq 2000 [GENEPIO:0100129]", + "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", + "PacBio RS [GENEPIO:0100131]", + "PacBio RS II [GENEPIO:0100132]", + "PacBio Sequel [GENEPIO:0100133]", + "PacBio Sequel II [GENEPIO:0100134]", + "Ion Torrent sequencing instrument [GENEPIO:0100135]", + "Ion Torrent PGM [GENEPIO:0100136]", + "Ion Torrent Proton [GENEPIO:0100137]", + "Ion Torrent S5 XL [GENEPIO:0100138]", + "Ion Torrent S5 [GENEPIO:0100139]", + "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", + "Oxford Nanopore GridION [GENEPIO:0100141]", + "Oxford Nanopore MinION [GENEPIO:0100142]", + "Oxford Nanopore PromethION [GENEPIO:0100143]", + "BGI Genomics sequencing instrument [GENEPIO:0100144]", + "BGI SEQ-500 [GENEPIO:0100145]", + "MGI sequencing instrument [GENEPIO:0100146]", + "MGI DNBSEQ-T7 [GENEPIO:0100147]", + "MGI DNBSEQ-G400 [GENEPIO:0100148]", + "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", + "MGI DNBSEQ-G50 [GENEPIO:0100150]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001452", + "type": "string", + "description": "The model of the sequencing instrument used.", + "examples": [ + "Oxford Nanopore MinION [GENEPIO:0100142]" + ], + "classification": "Sequencing", + "label": "Sequencing Instrument Model" }, "sequencing_instrument_platform": { - "examples": ["MinIon"], - "ontology": "0", - "type": "string", - "description": "The model of the sequencing instrument used.", - "label":"Sequencing Platforms " - }, - "consensus_sequence_software_name": { - "examples": ["Ivar"], - "ontology": "GENEPIO:0001463", - "type": "string", - "description": "The name of software used to generate the consensus sequence." - }, - "consensus_sequence_software_version": { - "examples": ["1.3"], - "ontology": "GENEPIO:0001469", - "type": "string", - "description": "The version of the software used to generate the consensus sequence." + "examples": [ + "MinIon" + ], + "ontology": "GENEPIO_0000071", + "type": "string", + "description": "The model of the sequencing instrument used.", + "label": "Sequencing Platforms " }, "submitting_lab_sequence_id": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Sample ID given by the submitting laboratory" + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "Sample ID given by the submitting laboratory" }, "bioproject_umbrella_accession_ENA": { - "examples": ["PRJNA623807"], - "ontology": "GENEPIO:0001133", - "type": "string", - "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", - "clasification":"Database Identifiers" + "examples": [ + "PRJNA623807" + ], + "ontology": "GENEPIO:0001133", + "type": "string", + "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", + "clasification": "Database Identifiers" }, - "bioproject_accession_ENA": { - "examples": ["PRJNA12345"], - "ontology": "GENEPIO:0001156", + "bioproject_accession_ENA": { + "examples": [ + "PRJNA12345" + ], + "ontology": "GENEPIO:0001136", "type": "string", "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", - "clasification":"Database Identifiers" + "clasification": "Database Identifiers", + "label": "Bioproject accession ENA" }, "biosample_accession_ENA": { - "examples": ["SAMN14180202"], - "ontology": "GENEPIO:0001139", - "type": "string", - "description": "The identifier assigned to a BioSample in INSDC archives.", - "clasification":"Database Identifiers" - }, + "examples": [ + "SAMN14180202" + ], + "ontology": "GENEPIO:0001139", + "type": "string", + "description": "The identifier assigned to a BioSample in INSDC archives.", + "clasification": "Database Identifiers" + }, "sra_accession": { - "examples": ["SRR11177792"], - "ontology": "GENEPIO:0001142", - "type": "string", - "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "clasification":"Database Identifiers" - }, + "examples": [ + "SRR11177792" + ], + "ontology": "GENEPIO:0001142", + "type": "string", + "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", + "clasification": "Database Identifiers" + }, "genBank/ENA/DDBJ_accession": { - "examples": ["MN908947.3"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", - "clasification":"Database Identifiers" - }, + "examples": [ + "MN908947.3" + ], + "ontology": "GENEPIO_0001145", + "type": "string", + "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", + "clasification": "Database Identifiers", + "label": "GenBank/ENA/DDBJ accession" + }, "gisaid_accession": { - "examples": ["EPI_ISL_123456"], - "ontology": "GENEPIO:0001147", - "type": "string", - "description": "The GISAID accession number assigned to the sequence.", - "clasification":"Database Identifiers" - }, + "examples": [ + "EPI_ISL_123456" + ], + "ontology": "GENEPIO:0001147", + "type": "string", + "description": "The GISAID accession number assigned to the sequence.", + "clasification": "Database Identifiers", + "label": "GISAID Virus Name" + }, "virus_name": { - "examples": ["hCoV-19/Canada/prov_rona_99/2020"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The user-defined GISAID virus name assigned to the sequence.", - "clasification":"Database Identifiers" - }, + "examples": [ + "hCoV-19/Canada/prov_rona_99/2020" + ], + "ontology": "GENEPIO:0100282", + "type": "string", + "description": "The user-defined GISAID virus name assigned to the sequence.", + "clasification": "Database Identifiers" + }, "collecting_institution_email": { - "examples": ["johnnyblogs@lab.ca"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The email address of the contact responsible for follow-up regarding the sample.", - "clasification":"Sample collection and processing" - }, + "examples": [ + "johnnyblogs@lab.ca" + ], + "ontology": "OBI:0001890", + "type": "string", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "clasification": "Sample collection and processing", + "label": "Originating Laboratory Email" + }, "collecting_institution_address": { - "examples": ["655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada"], - "ontology": "GENEPIO:0001158", - "type": "string", - "description": "The mailing address of the agency submitting the sample.", - "clasification":"Sample collection and processing" - }, + "examples": [ + "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" + ], + "ontology": "GENEPIO:0001158", + "type": "string", + "description": "The mailing address of the agency submitting the sample.", + "clasification": "Originating Laboratory Address" + }, "submitting_institution_email": { - "examples": ["RespLab@lab.ca"], + "examples": [ + "RespLab@lab.ca" + ], "ontology": "GENEPIO:0001165", "type": "string", "description": "The email address of the contact responsible for follow-up regarding the sequence.", - "clasification":"Sample collection and processing" - }, + "clasification": "Sample collection and processing" + }, "submitting_institution_address": { - "examples": ["123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"], - "ontology": "GENEPIO:0001156", + "examples": [ + "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" + ], + "ontology": "0", "type": "string", "description": "The mailing address of the agency submitting the sequence.", - "clasification":"Sample collection and processing" - }, + "clasification": "Sample collection and processing" + }, "sample_received_date": { - "examples": ["3/21/2020"], + "examples": [ + "3/21/2020" + ], "ontology": "GENEPIO:0001179", "type": "string", "description": "The date on which the sample was received.", - "format":"date", - "clasification":"Sample collection and processing" - }, + "format": "date", + "clasification": "Sample collection and processing" + }, "shipping_date": { - "examples": ["3/20/2020"], - "ontology": "GENEPIO:0001156", + "examples": [ + "3/20/2020" + ], + "ontology": "0", "type": "string", "description": "The date on which the sample was sent.", - "format":"date", - "clasification":"Sample collection and processing" - }, + "format": "date", + "clasification": "Sample collection and processing", + "label": "Shipping Date" + }, "results_emission_date": { - "examples": ["3/23/2020"], - "ontology": "GENEPIO:0001156", + "examples": [ + "3/23/2020" + ], + "ontology": "NCIT_C142672", "type": "string", "description": "The date on which the results were emitted.", - "format":"date", - "clasification":"Sample collection and processing" - }, + "format": "date", + "clasification": "Sample collection and processing", + "label": "Results Emission Date" + }, "geo_loc_region": { - "examples": ["Derbyshire"], + "examples": [ + "Derbyshire" + ], "ontology": "GENEPIO:0100280", "type": "string", "description": "The county/region of origin of the sample.", - "clasification":"Sample collection and processing", - "label":"Geo Loc Province" - }, + "clasification": "Sample collection and processing", + "label": "Geo Loc Province" + }, "geo_loc_city": { - "examples": ["Vancouver"], + "examples": [ + "Vancouver" + ], "ontology": "GENEPIO:0001189", "type": "string", "description": "The city of origin of the sample.", - "clasification":"Sample collection and processing", - "label":"Geo Loc City" - }, + "clasification": "Sample collection and processing", + "label": "Geo Loc City" + }, "geo_loc_latitude": { - "examples": ["38.98 N"], + "examples": [ + "38.98 N" + ], "ontology": "OBI:0001620", "type": "string", "description": "The latitude coordinates of the geographical location of sample collection.", - "clasification":"Sample collection and processing", - "label":"Geo Loc Latitude", - }, + "clasification": "Sample collection and processing", + "label": "Geo Loc Latitude", + }, "geo_loc_longitude": { - "examples": ["77.11 W"], + "examples": [ + "77.11 W" + ], "ontology": "OBI:0001621", "type": "string", "description": "The longitude coordinates of the geographical location of sample collection.", - "clasification":"Sample collection and processing", - "label":"Geo Loc Longitude" - }, + "clasification": "Sample collection and processing", + "label": "Geo Loc Longitude" + }, "anatomical_material": { - "Enums": [ - "Blood [UBERON:0000178]", - "Fluid [UBERON:0006314]", - "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", - "Fluid (Pericardial) [UBERON:0002409]", - "Fluid (Pleural) [UBERON:0001087]", - "Fluid (Vaginal) [UBERON:0036243]", - "Fluid (Amniotic) [UBERON:0000173]", - "Saliva [UBERON:0001836]", - "Tissue [UBERON:0000479]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001211", - "type": "string", - "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "examples": ["Blood [UBERON:0000178]"], - "classification":"Sample collection and processing", - "label":"Organism Substance" - }, - "anatomical_part": { "Enums": [ - "Anus [UBERON:0001245]", - "Duodenum [UBERON:0002114]", - "Eye [UBERON:0000970]", - "Intestine [UBERON:0000160]", - "Lower respiratory tract [UBERON:0001558]", - "Bronchus [UBERON:0002185]", - "Lung [UBERON:0002048]", - "Bronchiole [UBERON:0002186]", - "Alveolar sac [UBERON:0002169]", - "Pleural sac [UBERON:0009778]", - "Pleural cavity [UBERON:0002402]", - "Trachea [UBERON:0003126]", - "Rectum [UBERON:0001052]", - "Skin [UBERON:0001003]", - "Stomach [UBERON:0000945]", - "Upper respiratory tract [UBERON:0001557]", - "Anterior Nares [UBERON:2001427]", - "Esophagus [UBERON:0001043]", - "Ethmoid sinus [UBERON:0002453]", - "Nasal Cavity [UBERON:0001707]", - "Middle Nasal Turbinate [UBERON:0005921]", - "Inferior Nasal Turbinate [UBERON:0005922]", - "Nasopharynx (NP) [UBERON:0001728]", - "Oropharynx (OP) [UBERON:0001729]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" + "Blood [UBERON:0000178]", + "Fluid [UBERON:0006314]", + "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", + "Fluid (Pericardial) [UBERON:0002409]", + "Fluid (Pleural) [UBERON:0001087]", + "Fluid (Vaginal) [UBERON:0036243]", + "Fluid (Amniotic) [UBERON:0000173]", + "Saliva [UBERON:0001836]", + "Tissue [UBERON:0000479]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001211", + "type": "string", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "examples": [ + "Blood [UBERON:0000178]" + ], + "classification": "Sample collection and processing", + "label": "Organism Substance" + }, + "anatomical_part": { + "Enums": [ + "Anus [UBERON:0001245]", + "Duodenum [UBERON:0002114]", + "Eye [UBERON:0000970]", + "Intestine [UBERON:0000160]", + "Lower respiratory tract [UBERON:0001558]", + "Bronchus [UBERON:0002185]", + "Lung [UBERON:0002048]", + "Bronchiole [UBERON:0002186]", + "Alveolar sac [UBERON:0002169]", + "Pleural sac [UBERON:0009778]", + "Pleural cavity [UBERON:0002402]", + "Trachea [UBERON:0003126]", + "Rectum [UBERON:0001052]", + "Skin [UBERON:0001003]", + "Stomach [UBERON:0000945]", + "Upper respiratory tract [UBERON:0001557]", + "Anterior Nares [UBERON:2001427]", + "Esophagus [UBERON:0001043]", + "Ethmoid sinus [UBERON:0002453]", + "Nasal Cavity [UBERON:0001707]", + "Middle Nasal Turbinate [UBERON:0005921]", + "Inferior Nasal Turbinate [UBERON:0005922]", + "Nasopharynx (NP) [UBERON:0001728]", + "Oropharynx (OP) [UBERON:0001729]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" ], "ontology": "GENEPIO:0001214", "type": "string", "description": "An anatomical part of an organism e.g. oropharynx. ", - "examples": ["Nasopharynx (NP) [UBERON:0001728]"], - "classification":"Sample collection and processing", - "label":"Anatomical Structure" + "examples": [ + "Nasopharynx (NP) [UBERON:0001728]" + ], + "classification": "Sample collection and processing", + "label": "Anatomical Structure" }, "body_product": { - "Enums": [ - "Breast Milk [UBERON:0001913]", - "Feces [UBERON:0001988]", - "Mucus [UBERON:0000912]", - "Semen [UBERON:0006530]", - "Sputum [UBERON:0007311]", - "Sweat [UBERON:0001089]", - "Tear [UBERON:0001827]", - "Urine [UBERON:0001088]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001216", - "type": "string", - "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", - "examples": ["Feces [UBERON:0001988]"], - "classification":"Sample collection and processing", - "label":"Body product" + "Enums": [ + "Breast Milk [UBERON:0001913]", + "Feces [UBERON:0001988]", + "Mucus [UBERON:0000912]", + "Semen [UBERON:0006530]", + "Sputum [UBERON:0007311]", + "Sweat [UBERON:0001089]", + "Tear [UBERON:0001827]", + "Urine [UBERON:0001088]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001216", + "type": "string", + "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", + "examples": [ + "Feces [UBERON:0001988]" + ], + "classification": "Sample collection and processing", + "label": "Body product" }, "environmental_material": { - "Enums": [ - "Air vent [ENVO:03501208]", - "Banknote [ENVO:00003896]", - "Bed rail [ENVO:03501209]", - "Building Floor [ENVO:01000486]", - "Cloth [ENVO:02000058]", - "Control Panel [ENVO:03501210]", - "Door [ENVO:03501220]", - "Door Handle [ENVO:03501211]", - "Face Mask [OBI:0002787]", - "Face Shield [OBI:0002791]", - "Food [FOODON:00002403]", - "Food Packaging [FOODON:03490100]", - "Glass [ENVO:01000481]", - "Handrail [ENVO:03501212]", - "Hospital Gown [OBI:0002796]", - "Light Switch [ENVO:03501213]", - "Locker [ENVO:03501214]", - "N95 Mask [OBI:0002790]", - "Nurse Call Button [ENVO:03501215]", - "Paper [ENVO:03501256]", - "Particulate Matter [ENVO:01000060]", - "Plastic [ENVO:01000404]", - "PPE Gown [GENEPIO:0100025]", - "Sewage [ENVO:00002018]", - "Sink [ENVO:01000990]", - "Soil [ENVO:00001998]", - "Stainless Steel [ENVO:03501216]", - "Tissue Paper [ENVO:03501217]", - "Toilet Bowl [ENVO:03501218]", - "Water [ENVO:00002006]", - "Wastewater [ENVO:00002001]", - "Window [ENVO:03501219]", - "Wood [ENVO:00002040]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001223", - "type": "string", - "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", - "examples": ["Face Mask [OBI:0002787]"], - "clasification":"Sample collection and processing", - "label":"Environmental Material" + "Enums": [ + "Air vent [ENVO:03501208]", + "Banknote [ENVO:00003896]", + "Bed rail [ENVO:03501209]", + "Building Floor [ENVO:01000486]", + "Cloth [ENVO:02000058]", + "Control Panel [ENVO:03501210]", + "Door [ENVO:03501220]", + "Door Handle [ENVO:03501211]", + "Face Mask [OBI:0002787]", + "Face Shield [OBI:0002791]", + "Food [FOODON:00002403]", + "Food Packaging [FOODON:03490100]", + "Glass [ENVO:01000481]", + "Handrail [ENVO:03501212]", + "Hospital Gown [OBI:0002796]", + "Light Switch [ENVO:03501213]", + "Locker [ENVO:03501214]", + "N95 Mask [OBI:0002790]", + "Nurse Call Button [ENVO:03501215]", + "Paper [ENVO:03501256]", + "Particulate Matter [ENVO:01000060]", + "Plastic [ENVO:01000404]", + "PPE Gown [GENEPIO:0100025]", + "Sewage [ENVO:00002018]", + "Sink [ENVO:01000990]", + "Soil [ENVO:00001998]", + "Stainless Steel [ENVO:03501216]", + "Tissue Paper [ENVO:03501217]", + "Toilet Bowl [ENVO:03501218]", + "Water [ENVO:00002006]", + "Wastewater [ENVO:00002001]", + "Window [ENVO:03501219]", + "Wood [ENVO:00002040]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001223", + "type": "string", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "examples": [ + "Face Mask [OBI:0002787]" + ], + "clasification": "Sample collection and processing", + "label": "Environmental Material" }, "environmental_site": { - "Enums": [ - "Acute care facility [ENVO:03501135]", - "Animal house [ENVO:00003040]", - "Bathroom [ENVO:01000422]", - "Clinical assessment centre [ENVO:03501136]", - "Conference venue [ENVO:03501127]", - "Corridor [ENVO:03501121]", - "Daycare [ENVO:01000927]", - "Emergency room (ER) [ENVO:03501145]", - "Family practice clinic [ENVO:03501186]", - "Group home [ENVO:03501196]", - "Homeless shelter [ENVO:03501133]", - "Hospital [ENVO:00002173]", - "Intensive Care Unit (ICU) [ENVO:03501152]", - "Long Term Care Facility [ENVO:03501194]", - "Patient room [ENVO:03501180]", - "Prison [ENVO:03501204]", - "Production Facility [ENVO:01000536]", - "School [ENVO:03501130]", - "Sewage Plant [ENVO:00003043]", - "Subway train [ENVO:03501109]", - "Wet market [ENVO:03501198]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001232", - "type": "string", - "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", - "examples": ["Hospital [ENVO:00002173]"], - "classification":"Sample collection and processing", - "label":"Anthropogenic Geographic Feature" + "Enums": [ + "Acute care facility [ENVO:03501135]", + "Animal house [ENVO:00003040]", + "Bathroom [ENVO:01000422]", + "Clinical assessment centre [ENVO:03501136]", + "Conference venue [ENVO:03501127]", + "Corridor [ENVO:03501121]", + "Daycare [ENVO:01000927]", + "Emergency room (ER) [ENVO:03501145]", + "Family practice clinic [ENVO:03501186]", + "Group home [ENVO:03501196]", + "Homeless shelter [ENVO:03501133]", + "Hospital [ENVO:00002173]", + "Intensive Care Unit (ICU) [ENVO:03501152]", + "Long Term Care Facility [ENVO:03501194]", + "Patient room [ENVO:03501180]", + "Prison [ENVO:03501204]", + "Production Facility [ENVO:01000536]", + "School [ENVO:03501130]", + "Sewage Plant [ENVO:00003043]", + "Subway train [ENVO:03501109]", + "Wet market [ENVO:03501198]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001232", + "type": "string", + "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", + "examples": [ + "Hospital [ENVO:00002173]" + ], + "classification": "Sample collection and processing", + "label": "Anthropogenic Geographic Feature" }, "collection_device": { - "Enums": [ - "Air filter [ENVO:00003968]", - "Blood Collection Tube [OBI:0002859]", - "Bronchoscope [OBI:0002826]", - "Collection Container [OBI:0002088]", - "Collection Cup [GENEPIO:0100026]", - "Fibrobronchoscope Brush [OBI:0002825]", - "Filter [GENEPIO:0100103]", - "Fine Needle [OBI:0002827]", - "Microcapillary tube [OBI:0002858]", - "Micropipette [OBI:0001128]", - "Needle [OBI:0000436]", - "Serum Collection Tube [OBI:0002860]", - "Sputum Collection Tube [OBI:0002861]", - "Suction Catheter [OBI:0002831]", - "Swab [GENEPIO:0100027]", - "Urine Collection Tube [OBI:0002862]", - "Virus Transport Medium [OBI:0002866]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001234", - "type": "string", - "description": "The instrument or container used to collect the sample e.g. swab.", - "examples": ["Swab [GENEPIO:0100027]"], - "clasification":"Sample collection and processing", - "label":"Collection Device" + "Enums": [ + "Air filter [ENVO:00003968]", + "Blood Collection Tube [OBI:0002859]", + "Bronchoscope [OBI:0002826]", + "Collection Container [OBI:0002088]", + "Collection Cup [GENEPIO:0100026]", + "Fibrobronchoscope Brush [OBI:0002825]", + "Filter [GENEPIO:0100103]", + "Fine Needle [OBI:0002827]", + "Microcapillary tube [OBI:0002858]", + "Micropipette [OBI:0001128]", + "Needle [OBI:0000436]", + "Serum Collection Tube [OBI:0002860]", + "Sputum Collection Tube [OBI:0002861]", + "Suction Catheter [OBI:0002831]", + "Swab [GENEPIO:0100027]", + "Urine Collection Tube [OBI:0002862]", + "Virus Transport Medium [OBI:0002866]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001234", + "type": "string", + "description": "The instrument or container used to collect the sample e.g. swab.", + "examples": [ + "Swab [GENEPIO:0100027]" + ], + "clasification": "Sample collection and processing", + "label": "Collection Device" }, "collection_method": { - "Enums": [ - "Amniocentesis [NCIT:C52009]", - "Aspiration [NCIT:C15631]", - "Suprapubic Aspiration [GENEPIO:0100028]", - "Tracheal Aspiration [GENEPIO:0100029]", - "Vacuum Aspiration [GENEPIO:0100030]", - "Biopsy [OBI:0002650]", - "Needle Biopsy [OBI:0002651]", - "Filtration [OBI:0302885]", - "Air Filtration [GENEPIO:0100031]", - "Lavage [OBI:0600044]", - "Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]", - "Gastric Lavage [GENEPIO:0100033]", - "Lumbar Puncture [NCIT:C15327]", - "Necropsy [MMO:0000344]", - "Phlebotomy [NCIT:C28221]", - "Rinsing [GENEPIO:0002116]", - "Saline gargle (mouth rinse and gargle) [GENEPIO:0100034]", - "Scraping [GENEPIO:0100035]", - "Swabbing [GENEPIO:0002117]", - "Finger Prick [GENEPIO:0100036]", - "Washout Tear Collection [GENEPIO:0100038]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001241", - "type": "string", - "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", - "examples": ["Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]"], - "clasification":"Sample collection and processing", - "label":"Collection Method" + "Enums": [ + "Amniocentesis [NCIT:C52009]", + "Aspiration [NCIT:C15631]", + "Suprapubic Aspiration [GENEPIO:0100028]", + "Tracheal Aspiration [GENEPIO:0100029]", + "Vacuum Aspiration [GENEPIO:0100030]", + "Biopsy [OBI:0002650]", + "Needle Biopsy [OBI:0002651]", + "Filtration [OBI:0302885]", + "Air Filtration [GENEPIO:0100031]", + "Lavage [OBI:0600044]", + "Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]", + "Gastric Lavage [GENEPIO:0100033]", + "Lumbar Puncture [NCIT:C15327]", + "Necropsy [MMO:0000344]", + "Phlebotomy [NCIT:C28221]", + "Rinsing [GENEPIO:0002116]", + "Saline gargle (mouth rinse and gargle) [GENEPIO:0100034]", + "Scraping [GENEPIO:0100035]", + "Swabbing [GENEPIO:0002117]", + "Finger Prick [GENEPIO:0100036]", + "Washout Tear Collection [GENEPIO:0100038]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001241", + "type": "string", + "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", + "examples": [ + "Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]" + ], + "clasification": "Sample collection and processing", + "label": "Collection Method" }, "collection_protocol": { - "examples": ["SC2SamplingProtocol 1.2"], - "ontology": "GENEPIO:0001243", - "type": "string", - "description": "The name and version of a particular protocol used for sampling.", - "clasification":"Sample collection and processing", - "label":"Collection Protocol" + "examples": [ + "SC2SamplingProtocol 1.2" + ], + "ontology": "GENEPIO:0001243", + "type": "string", + "description": "The name and version of a particular protocol used for sampling.", + "clasification": "Sample collection and processing", + "label": "Collection Protocol" }, "specimen_processing": { - "Enums": [ - "Virus Passage [GENEPIO:0100039]", - "RNA Re-Extraction (Post RT-PCR) [GENEPIO:0100040]", - "Specimens Pooled [OBI:0600016]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001253", - "type": "string", - "description": "Any processing applied to the sample during or after receiving the sample. ", - "examples": ["Virus Passage [GENEPIO:0100039]"], - "classification":"Sample collection and processing", - "label":"Specimen Processing" + "Enums": [ + "Virus Passage [GENEPIO:0100039]", + "RNA Re-Extraction (Post RT-PCR) [GENEPIO:0100040]", + "Specimens Pooled [OBI:0600016]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001253", + "type": "string", + "description": "Any processing applied to the sample during or after receiving the sample. ", + "examples": [ + "Virus Passage [GENEPIO:0100039]" + ], + "classification": "Sample collection and processing", + "label": "Specimen Processing" }, "lab_host": { - "Enums": [ - "293/ACE2 Cell Line [GENEPIO:0100041]", - "Caco2 Cell Line [BTO:0000195]", - "Calu3 Cell Line [BTO:0002750]", - "EFK3B Cell Line [GENEPIO:0100042]", - "HEK293T Cell Line [BTO:0002181]", - "HRCE Cell Line [GENEPIO:0100043]", - "Huh7 Cell Line [BTO:0001950]", - "LLCMk2 Cell Line [CLO:0007330]", - "MDBK Cell Line [BTO:0000836]", - "NHBE Cell Line [BTO:0002924]", - "PK-15 Cell Line [BTO:0001865]", - "RK-13 Cell Line [BTO:0002909]", - "U251 Cell Line [BTO:0002035]", - "Vero Cell Line [BTO:0001444]", - "Vero E6 Cell Line [BTO:0004755]", - "Vero E6/TMPRSS2 Cell Line [GENEPIO:0100044]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001255", - "type": "string", - "description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.", - "examples": ["Vero E6 Cell Line [BTO:0004755]"], - "classification":"Sample collection and processing", - "label":"Lab passage Host" + "Enums": [ + "293/ACE2 Cell Line [GENEPIO:0100041]", + "Caco2 Cell Line [BTO:0000195]", + "Calu3 Cell Line [BTO:0002750]", + "EFK3B Cell Line [GENEPIO:0100042]", + "HEK293T Cell Line [BTO:0002181]", + "HRCE Cell Line [GENEPIO:0100043]", + "Huh7 Cell Line [BTO:0001950]", + "LLCMk2 Cell Line [CLO:0007330]", + "MDBK Cell Line [BTO:0000836]", + "NHBE Cell Line [BTO:0002924]", + "PK-15 Cell Line [BTO:0001865]", + "RK-13 Cell Line [BTO:0002909]", + "U251 Cell Line [BTO:0002035]", + "Vero Cell Line [BTO:0001444]", + "Vero E6 Cell Line [BTO:0004755]", + "Vero E6/TMPRSS2 Cell Line [GENEPIO:0100044]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001255", + "type": "string", + "description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.", + "examples": [ + "Vero E6 Cell Line [BTO:0004755]" + ], + "classification": "Sample collection and processing", + "label": "Lab passage Host" }, "passage_number": { - "examples": ["3"], - "ontology": "GENEPIO:0001261", - "type": "string", - "description": "Number of passages.", - "clasification":"Sample collection and processing", - "label":"Passage Number" + "examples": [ + "3" + ], + "ontology": "GENEPIO:0001261", + "type": "string", + "description": "Number of passages.", + "clasification": "Sample collection and processing", + "label": "Passage Number" }, "passage_method": { - "examples": ["AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain."], - "ontology": "GENEPIO:0001264", - "type": "string", - "description": "Description of how organism was passaged.", - "clasification":"Sample collection and processing", - "label":"Passage Method" + "examples": [ + "AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain." + ], + "ontology": "GENEPIO:0001264", + "type": "string", + "description": "Description of how organism was passaged.", + "clasification": "Sample collection and processing", + "label": "Passage Method" }, "biomaterial_extracted": { - "Enums": [ - "mRNA (cDNA) [OBI:0002754]", - "RNA (Total) [OBI:0000895]", - "RNA (Poly-A) [OBI:0000869]", - "RNA (Ribo-Depleted) [OBI:0002627]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001266", - "type": "string", - "description": "The biomaterial extracted from samples for the purpose of sequencing.", - "examples": ["RNA (Total) [OBI:0000895]"], - "classification":"Sample collection and processing", - "label":"Biomaterial Extracted" + "Enums": [ + "mRNA (cDNA) [OBI:0002754]", + "RNA (Total) [OBI:0000895]", + "RNA (Poly-A) [OBI:0000869]", + "RNA (Ribo-Depleted) [OBI:0002627]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001266", + "type": "string", + "description": "The biomaterial extracted from samples for the purpose of sequencing.", + "examples": [ + "RNA (Total) [OBI:0000895]" + ], + "classification": "Sample collection and processing", + "label": "Biomaterial Extracted" }, "tax_id": { - "examples": ["probably 2697049 in all cases"], - "ontology": "GENEPIO_0001800", - "type": "string", - "description": "The NCBITaxon identifier for the organism being sequenced.", - "clasification":"Sample collection and processing", - "label":"Tax ID" - }, - "common_name": { - "examples": [""], - "ontology": "BU_ISCIII:003", - "type": "string", - "description": "The common name of the organism.", - "clasification":"Sample collection and processing", - "label":"Common name" + "examples": [ + "probably 2697049 in all cases" + ], + "ontology": "GENEPIO_0001800", + "type": "string", + "description": "The NCBITaxon identifier for the organism being sequenced.", + "clasification": "Sample collection and processing", + "label": "Tax ID" }, "center_name": { - "examples": [" KAROLINSKA INSITUTET"], - "ontology": "NCIT_C19983", - "type": "string", - "description": "The name of the institution", - "clasification":"Sample collection and processing", - "label":"Center Name" - }, - "virus_id": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The user-defined name for the sample.", - "clasification":"Database Identifiers" + "examples": [ + " KAROLINSKA INSITUTET" + ], + "ontology": "NCIT_C19983", + "type": "string", + "description": "The name of the institution", + "clasification": "Sample collection and processing", + "label": "Center Name" }, "host_common_name": { - "Enums": [ - "Human [NCBITaxon:9606]", - "Bat [NCBITaxon:9397]", - "Cat [NCBITaxon:9685]", - "Chicken [NCBITaxon:9031]", - "Civet [NCBITaxon:9673]", - "Cow [NCBITaxon:9913]", - "Dog [NCBITaxon:9615]", - "Lion [NCBITaxon:9689]", - "Mink [NCBITaxon:452646]", - "Pangolin [NCBITaxon:9973]", - "Pig [NCBITaxon:9825]", - "Pigeon [NCBITaxon:8930]", - "Tiger [NCBITaxon:9694]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001386", - "type": "string", - "description": "The commonly used name of the host.", - "examples": ["Human [NCBITaxon:9606]"], - "classification":"Host information", - "label":"Host Common Name" + "Enums": [ + "Human [NCBITaxon:9606]", + "Bat [NCBITaxon:9397]", + "Cat [NCBITaxon:9685]", + "Chicken [NCBITaxon:9031]", + "Civet [NCBITaxon:9673]", + "Cow [NCBITaxon:9913]", + "Dog [NCBITaxon:9615]", + "Lion [NCBITaxon:9689]", + "Mink [NCBITaxon:452646]", + "Pangolin [NCBITaxon:9973]", + "Pig [NCBITaxon:9825]", + "Pigeon [NCBITaxon:8930]", + "Tiger [NCBITaxon:9694]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001386", + "type": "string", + "description": "The commonly used name of the host.", + "examples": [ + "Human [NCBITaxon:9606]" + ], + "classification": "Host information", + "label": "Host Common Name" }, "outbreak": { - "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], - "ontology": "GENEPIO:0001417", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", - "label":"Outbreak Exposure Event Location" + "examples": [ + "Date, Location e.g. type of gathering, Family cluster, etc." + ], + "ontology": "GENEPIO:0001417", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification": "Host information", + "label": "Outbreak Exposure Event Location" }, "additional_host_information": { - "examples": ["e.g. Patient infected while traveling in …."], - "ontology": "0", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", - "label":"Additional Host Information" + "examples": [ + "e.g. Patient infected while traveling in …." + ], + "ontology": "GENEPIO_0001268", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification": "Host information", + "label": "Additional Host Information" }, "purpose_of_sequencing": { - "Enums": [ - "Baseline surveillance (random sampling) [GENEPIO:0100005]", - "Targeted surveillance (non-random sampling) [GENEPIO:0100006]", - "Priority surveillance projects [GENEPIO:0100007]", - "Screening for Variants of Concern (VOC) [GENEPIO:0100008]", - "Sample has epidemiological link to Variant of Concern (VoC) [GENEPIO:0100273]", - "Sample has epidemiological link to Omicron Variant [GENEPIO:0100274]", - "Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]", - "Re-infection surveillance [GENEPIO:0100010]", - "Vaccine escape surveillance [GENEPIO:0100011]", - "Travel-associated surveillance [GENEPIO:0100012]", - "Domestic travel surveillance [GENEPIO:0100013]", - "Interstate/ interprovincial travel surveillance [GENEPIO:0100275]", - "Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276]", - "International travel surveillance [GENEPIO:0100014]", - "Surveillance of international border crossing by air travel or ground transport [GENEPIO:0100015]", - "Surveillance of international border crossing by air travel [GENEPIO:0100016]", - "Surveillance of international border crossing by ground transport [GENEPIO:0100017]", - "Surveillance from international worker testing [GENEPIO:0100018]", - "Cluster/Outbreak investigation [GENEPIO:0100019]", - "Multi-jurisdictional outbreak investigation [GENEPIO:0100020]", - "Intra-jurisdictional outbreak investigation [GENEPIO:0100021]", - "Research [GENEPIO:0100022]", - "Viral passage experiment [GENEPIO:0100023]", - "Protocol testing [GENEPIO:0100024]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001445", - "type": "string", - "description": "The reason that the sample was sequenced.", - "examples": ["Baseline surveillance (random sampling) [GENEPIO:0100005]"], - "classification":"Sequencing", - "label":"Purpose of Sequencing" + "Enums": [ + "Baseline surveillance (random sampling) [GENEPIO:0100005]", + "Targeted surveillance (non-random sampling) [GENEPIO:0100006]", + "Priority surveillance projects [GENEPIO:0100007]", + "Screening for Variants of Concern (VOC) [GENEPIO:0100008]", + "Sample has epidemiological link to Variant of Concern (VoC) [GENEPIO:0100273]", + "Sample has epidemiological link to Omicron Variant [GENEPIO:0100274]", + "Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]", + "Re-infection surveillance [GENEPIO:0100010]", + "Vaccine escape surveillance [GENEPIO:0100011]", + "Travel-associated surveillance [GENEPIO:0100012]", + "Domestic travel surveillance [GENEPIO:0100013]", + "Interstate/ interprovincial travel surveillance [GENEPIO:0100275]", + "Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276]", + "International travel surveillance [GENEPIO:0100014]", + "Surveillance of international border crossing by air travel or ground transport [GENEPIO:0100015]", + "Surveillance of international border crossing by air travel [GENEPIO:0100016]", + "Surveillance of international border crossing by ground transport [GENEPIO:0100017]", + "Surveillance from international worker testing [GENEPIO:0100018]", + "Cluster/Outbreak investigation [GENEPIO:0100019]", + "Multi-jurisdictional outbreak investigation [GENEPIO:0100020]", + "Intra-jurisdictional outbreak investigation [GENEPIO:0100021]", + "Research [GENEPIO:0100022]", + "Viral passage experiment [GENEPIO:0100023]", + "Protocol testing [GENEPIO:0100024]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001445", + "type": "string", + "description": "The reason that the sample was sequenced.", + "examples": [ + "Baseline surveillance (random sampling) [GENEPIO:0100005]" + ], + "classification": "Sequencing", + "label": "Purpose of Sequencing" }, "purpose_of_sequencing_details": { - "Enums": [ - "Screened for S gene target failure (S dropout)", - "Screened for mink variants", - "Screened for B.1.1.7 variant", - "Screened for B.1.135 variant", - "Screened for P.1 variant", - "Screened due to travel history", - "Screened due to close contact with infected individual", - "Assessing public health control measures", - "Determining early introductions and spread", - "Investigating airline-related exposures", - "Investigating temporary foreign worker", - "Investigating remote regions", - "Investigating health care workers", - "Investigating schools/universities", - "Investigating reinfection" - ], - "ontology": "GENEPIO:0001446", - "type": "string", - "description": "The description of why the sample was sequenced providing specific details.", - "examples": ["Screened for S gene target failure (S dropout)"], - "clasification":"Sequencing", - "label":"Purpose Of Sequencing Details" + "Enums": [ + "Screened for S gene target failure (S dropout)", + "Screened for mink variants", + "Screened for B.1.1.7 variant", + "Screened for B.1.135 variant", + "Screened for P.1 variant", + "Screened due to travel history", + "Screened due to close contact with infected individual", + "Assessing public health control measures", + "Determining early introductions and spread", + "Investigating airline-related exposures", + "Investigating temporary foreign worker", + "Investigating remote regions", + "Investigating health care workers", + "Investigating schools/universities", + "Investigating reinfection" + ], + "ontology": "GENEPIO:0001446", + "type": "string", + "description": "The description of why the sample was sequenced providing specific details.", + "examples": [ + "Screened for S gene target failure (S dropout)" + ], + "clasification": "Sequencing", + "label": "Purpose Of Sequencing Details" }, "sequencing_date": { - "examples": ["4/26/2021"], - "ontology": "GENEPIO:0001447", - "type": "string", - "description": "The date the sample was sequenced.", - "format":"date", - "clasification":"Sequencing", - "label":"Sequencing date" + "examples": [ + "4/26/2021" + ], + "ontology": "GENEPIO:0001447", + "type": "string", + "description": "The date the sample was sequenced.", + "format": "date", + "clasification": "Sequencing", + "label": "Sequencing date" }, "rna_extraction_protocol": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Rna Extraction Protocol" + "examples": [ + "" + ], + "ontology": "OBI_0302884", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Rna Extraction Protocol" }, "library_kit": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Library Kit" + "examples": [ + "" + ], + "ontology": "GENEPIO_0000085", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Library Kit" }, "library_id": { - "examples": ["XYZ_123345"], - "ontology": "GENEPIO:0001448", - "type": "string", - "description": "The user-specified identifier for the library prepared for sequencing.", - "clasification":"Sequencing", - "labe":"Library Id" + "examples": [ + "XYZ_123345" + ], + "ontology": "GENEPIO:0001448", + "type": "string", + "description": "The user-specified identifier for the library prepared for sequencing.", + "clasification": "Sequencing", + "labe": "Library Id" }, "enrichment_protocol": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Enrichment_protocol" + "examples": [ + "" + ], + "ontology": "EFO_0009089", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Enrichment_protocol" }, "if_enrichment_protocol_is_other_specify": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"If Enrichment Protocol Is Other, Specify" + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "If Enrichment Protocol Is Other, Specify" }, "amplicon protocol": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Amplicon Protocol" + "examples": [ + "" + ], + "ontology": "EFO_0003747", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Amplicon Protocol" }, "if_amplicon_protocol_if_other_especify": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "labe":"If Amplicon Protocol If Other, Especify" + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Sequencing", + "labe": "If Amplicon Protocol If Other, Especify" }, "amplicon_version": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Amplicon Version" + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Amplicon Version" }, "amplicon_size": { - "examples": ["300bp"], - "ontology": "GENEPIO:0001449", - "type": "string", - "description": "The length of the amplicon generated by PCR amplification.", - "clasification":"Sequencing", - "label":"Amplicon Size" + "examples": [ + "300bp" + ], + "ontology": "GENEPIO:0001449", + "type": "string", + "description": "The length of the amplicon generated by PCR amplification.", + "clasification": "Sequencing", + "label": "Amplicon Size" }, "was_phix_used?": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Was Phix Used" + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Was Phix Used" }, "number_of_samples_in_run": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Number Of Samples In Run" + "examples": [ + "" + ], + "ontology": "KISAO_0000326", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Number Of Samples In Run" }, "flowcell_kit": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "labe":"Flowcell Kit" + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Sequencing", + "labe": "Flowcell Kit" }, "runID": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"RunID" + "examples": [ + "" + ], + "ontology": "NCIT_C117058", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "RunID" }, "sequencing_platforms": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Sequencing Platforms " + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Sequencing Platforms " }, "library_preparation_kit": { - "examples": ["Nextera XT"], - "ontology": "GENEPIO:0001450", - "type": "string", - "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", - "clasification":"Sequencing", - "label":"Library Preparation Kit" + "examples": [ + "Nextera XT" + ], + "ontology": "GENEPIO:0001450", + "type": "string", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "clasification": "Sequencing", + "label": "Library Preparation Kit" }, "flow_cell_barcode": { - "examples": ["FAB06069"], - "ontology": "GENEPIO:0001451", - "type": "string", - "description": "The barcode of the flow cell used for sequencing.", - "clasification":"Sequencing", - "label":"Flow Cell Barcode" + "examples": [ + "FAB06069" + ], + "ontology": "GENEPIO:0001451", + "type": "string", + "description": "The barcode of the flow cell used for sequencing.", + "clasification": "Sequencing", + "label": "Flow Cell Barcode" }, "sequencing_protocol_name": { - "examples": ["1D_DNA_MinION, ARTIC Network Protocol V3"], - "ontology": "GENEPIO:0001453", - "type": "string", - "description": "The name and version number of the sequencing protocol used.", - "clasification":"Sequencing", - "label":"Sequencing Protocol Name" + "examples": [ + "1D_DNA_MinION, ARTIC Network Protocol V3" + ], + "ontology": "GENEPIO:0001453", + "type": "string", + "description": "The name and version number of the sequencing protocol used.", + "clasification": "Sequencing", + "label": "Sequencing Protocol Name" }, "sequencing_protocol": { - "examples": ["Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits."], - "ontology": "GENEPIO:0001454", - "type": "string", - "description": "The protocol used to generate the sequence.", - "clasification":"Sequencing", - "label":"Sequencing Protocol" + "examples": [ + "Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits." + ], + "ontology": "GENEPIO:0001454", + "type": "string", + "description": "The protocol used to generate the sequence.", + "clasification": "Sequencing", + "label": "Sequencing Protocol" }, "sequencing_kit_number": { - "examples": ["AB456XYZ789"], - "ontology": "GENEPIO:0001455", - "type": "string", - "description": "The manufacturer's kit number.", - "clasification":"Sequencing", - "label":"Sequencing Kit Number" + "examples": [ + "AB456XYZ789" + ], + "ontology": "GENEPIO:0001455", + "type": "string", + "description": "The manufacturer's kit number.", + "clasification": "Sequencing", + "label": "Sequencing Kit Number" }, "amplicon_pcr_primer_scheme": { - "examples": ["https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv"], - "ontology": "GENEPIO:0001456", - "type": "string", - "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", - "clasification":"Sequencing", - "label":"Amplicon Pcr Primer Scheme" + "examples": [ + "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv" + ], + "ontology": "GENEPIO:0001456", + "type": "string", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "clasification": "Sequencing", + "label": "Amplicon Pcr Primer Scheme" }, "library_selection": { - "examples": ["RANDOM PCR"], - "ontology": "GENPIO_0001940", - "type": "string", - "description": "Library capture method.", - "clasification":"Sequencing", - "label":"Capture method" + "examples": [ + "RANDOM PCR" + ], + "ontology": "GENPIO_0001940", + "type": "string", + "description": "Library capture method.", + "clasification": "Sequencing", + "label": "Capture method" }, "library_strategy": { - "Enums": ["Bisultife-Seq strategy [GENPIO:0001975]", - "CTS strategy [GENPIO:0001978]", - "ChIP-Seq strategy [GENPIO:0001979]", - "DNase-Hypersensitivity strategy [GENPIO:0001980]", - "EST strategy [GENPIO:0001981]", - "FL-cDNA strategy [GENPIO:0001983]", - "MB-Seq strategy [GENPIO:0001984]", - "MNase-Seq strategy [GENPIO:0001985]", - "MRE-Seq strategy [GENPIO:0001986]", - "MeDIP-Seq strategy [GENPIO:0001987]", - "RNA-Seq strategy [GENPIO:0001990]", - "WCS strategy [GENPIO:0001991]", - "WGS strategy [GENPIO:0001992]", - "WXS strategy [GENPIO:0001993]", - "amplicon strategy [GENPIO:0001974]", - "clone end strategy [GENPIO:0001976]", - "clone strategy [GENPIO:0001977]", - "finishing strategy [GENPIO:0001982]", - "other library strategy [GENPIO:0001988]", - "pool clone strategy [GENPIO:0001989]", - ], - "examples": ["WGS"], - "ontology": "GENPIO_0001973", - "type": "string", - "description": "Overall sequencing strategy or approach.", - "clasification":"Sequencing", - "label":"Sequencing technique" + "Enums": [ + "Bisultife-Seq strategy [GENPIO:0001975]", + "CTS strategy [GENPIO:0001978]", + "ChIP-Seq strategy [GENPIO:0001979]", + "DNase-Hypersensitivity strategy [GENPIO:0001980]", + "EST strategy [GENPIO:0001981]", + "FL-cDNA strategy [GENPIO:0001983]", + "MB-Seq strategy [GENPIO:0001984]", + "MNase-Seq strategy [GENPIO:0001985]", + "MRE-Seq strategy [GENPIO:0001986]", + "MeDIP-Seq strategy [GENPIO:0001987]", + "RNA-Seq strategy [GENPIO:0001990]", + "WCS strategy [GENPIO:0001991]", + "WGS strategy [GENPIO:0001992]", + "WXS strategy [GENPIO:0001993]", + "amplicon strategy [GENPIO:0001974]", + "clone end strategy [GENPIO:0001976]", + "clone strategy [GENPIO:0001977]", + "finishing strategy [GENPIO:0001982]", + "other library strategy [GENPIO:0001988]", + "pool clone strategy [GENPIO:0001989]", + ], + "examples": [ + "WGS" + ], + "ontology": "GENPIO_0001973", + "type": "string", + "description": "Overall sequencing strategy or approach.", + "clasification": "Sequencing", + "label": "Sequencing technique" }, "library_layout": { - "examples": ["PAIRED"], - "ontology":"BU_ISCIII:007", - "type": "string", - "description": "Single or paired.", - "clasification":"Sequencing", - "label":"Library Layout" + "examples": [ + "PAIRED" + ], + "ontology": "BU_ISCIII:007", + "type": "string", + "description": "Single or paired.", + "clasification": "Sequencing", + "label": "Library Layout" }, "library_name": { - "examples": ["P17157_1007"], - "ontology": "GENEPIO_0001995", - "type": "string", - "description": "Name of the used library", - "clasification":"Sequencing", - "label":"LibraryName" + "examples": [ + "P17157_1007" + ], + "ontology": "GENEPIO_0001995", + "type": "string", + "description": "Name of the used library", + "clasification": "Sequencing", + "label": "LibraryName" }, "nominal_length ": { - "examples": ["350"], - "ontology": "GENEPIO_0000076", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Nominal Length" + "examples": [ + "350" + ], + "ontology": "GENEPIO_0000076", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Nominal Length" }, "raw_sequence_data_processing_method": { - "examples": ["Porechop 0.2.3"], + "examples": [ + "Porechop 0.2.3" + ], "ontology": "GENEPIO:0001458", "type": "string", "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", - "clasification":"Bioinformatics and QC metrics", - "label":"Raw sequence data processin method" + "clasification": "Bioinformatics and QC metrics", + "label": "Raw sequence data processin method" }, "dehosting_method": { - "examples": ["Nanostripper"], + "examples": [ + "Nanostripper" + ], "ontology": "GENEPIO:0001459", "type": "string", "description": "The method used to remove host reads from the pathogen sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Dehosting Method" + "clasification": "Bioinformatics and QC metrics", + "label": "Dehosting Method" }, "assembly": { - "examples": [""], - "ontology": "0", + "examples": [ + "" + ], + "ontology": "NCIT_C63548", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Assembly" + "clasification": "Bioinformatics and QC metrics", + "label": "Assembly" }, "if_assembly_other": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"If assembly Is Other, Specify" + "clasification": "Bioinformatics and QC metrics", + "label": "If assembly Is Other, Specify" }, "assembly_params": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Assambly params" + "clasification": "Bioinformatics and QC metrics", + "label": "Assambly params" }, "variant_calling": { - "examples": [""], - "ontology": "0", + "examples": [ + "" + ], + "ontology": "operation_3227", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Variant Calling" + "clasification": "Bioinformatics and QC metrics", + "label": "Variant Calling" }, - "if_variant_calling_other": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"If variant calling Is Other, Specify" + "if_variant_calling_other": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Bioinformatics and QC metrics", + "label": "If variant calling Is Other, Specify" }, "variant_calling_params": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Variant Calling params" + "clasification": "Bioinformatics and QC metrics", + "label": "Variant Calling params" }, "consensus_sequence_filepath": { - "examples": ["/User/Documents/RespLab/Data/ncov123assembly.fasta"], + "examples": [ + "/User/Documents/RespLab/Data/ncov123assembly.fasta" + ], "ontology": "GENEPIO:0001462", "type": "string", "description": "The filepath of the consesnsus sequence file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus sequence filepath" + "clasification": "Bioinformatics and QC metrics", + "label": "Consensus sequence filepath" }, "consensus_sequence_software_name": { - "examples": ["Ivar"], + "examples": [ + "Ivar" + ], "ontology": "GENEPIO:0001463", "type": "string", "description": "The name of software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus sequence software name" + "clasification": "Bioinformatics and QC metrics", + "label": "Consensus sequence software name" }, "if_consensus_other": { - "examples": ["1.3"], + "examples": [ + "1.3" + ], "ontology": "0", "type": "string", "description": "The version of the software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"If consensus Is Other, Specify" + "clasification": "Bioinformatics and QC metrics", + "label": "If consensus Is Other, Specify" }, "consensus_sequence_software_version": { - "examples": ["1.3"], + "examples": [ + "1.3" + ], "ontology": "GENEPIO:0001469", "type": "string", "description": "The version of the software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus sequence software version" + "clasification": "Bioinformatics and QC metrics", + "label": "Consensus sequence software version" }, "consensus_criteria": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus criteria" + "clasification": "Bioinformatics and QC metrics", + "label": "Consensus criteria" }, "quality_control_metrics": { - "examples": [""], - "ontology": "0", + "examples": [ + "" + ], + "ontology": "data_3914", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Quality control metrics " + "clasification": "Bioinformatics and QC metrics", + "label": "Quality control metrics " }, "breadth_of_coverage_value": { - "examples": ["95%"], + "examples": [ + "95%" + ], "ontology": "GENEPIO:0001472", "type": "string", "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", - "clasification":"Bioinformatics and QC metrics", - "label":"Breadth of coverage value" + "clasification": "Bioinformatics and QC metrics", + "label": "Breadth of coverage value" }, "depth_of_coverage_value": { - "examples": ["400x"], + "examples": [ + "400x" + ], "ontology": "GENEPIO:0001474", "type": "string", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Depth of coverage value " + "clasification": "Bioinformatics and QC metrics", + "label": "Depth of coverage value " }, "depth_of_coverage_threshold": { - "examples": ["100x"], - "ontology": "GENEPIO:0001475", + "examples": [ + "100x" + ], + "ontology": "GENEPIO:0001475", "type": "string", "description": "The threshold used as a cut-off for the depth of coverage.", - "clasification":"Bioinformatics and QC metrics", - "label":"Depth of coverage threshold" + "clasification": "Bioinformatics and QC metrics", + "label": "Depth of coverage threshold" }, "sequence_file_R1_fastq": { - "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], + "examples": [ + "ABC123_S1_L001_R1_001.fastq.gz" + ], "ontology": "GENEPIO:0001476", "type": "string", "description": "The user-specified filename of the r1 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Sequence file R1 fastq" + "clasification": "Bioinformatics and QC metrics", + "label": "Sequence file R1 fastq" }, "sequence_file_R2_fastq": { - "examples": ["ABC123_S1_L001_R2_001.fastq.gz"], + "examples": [ + "ABC123_S1_L001_R2_001.fastq.gz" + ], "ontology": "GENEPIO:0001477", "type": "string", "description": "The user-specified filename of the r2 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Sequence file R2 fastq" + "clasification": "Bioinformatics and QC metrics", + "label": "Sequence file R2 fastq" }, "r1_fastq_filepath": { - "examples": ["/User/Documents/RespLab/Data/"], + "examples": [ + "/User/Documents/RespLab/Data/" + ], "ontology": "GENEPIO:0001478", "type": "string", "description": "The filepath of the r1 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Filepath R1 fastq" + "clasification": "Bioinformatics and QC metrics", + "label": "Filepath R1 fastq" }, "r2_fastq_filepath": { - "examples": ["/User/Documents/RespLab/Data/"], + "examples": [ + "/User/Documents/RespLab/Data/" + ], "ontology": "GENEPIO:0001479", "type": "string", "description": "The filepath of the r2 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Filepath R2 fastq" + "clasification": "Bioinformatics and QC metrics", + "label": "Filepath R2 fastq" }, "fast5_filename": { - "examples": ["batch1a_sequences.fast5"], + "examples": [ + "batch1a_sequences.fast5" + ], "ontology": "GENEPIO:0001480", "type": "string", "description": "The user-specified filename of the FAST5 file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Filename fast5" + "clasification": "Bioinformatics and QC metrics", + "label": "Filename fast5" }, "fast5_filepath": { - "examples": ["/User/Documents/RespLab/Data/"], + "examples": [ + "/User/Documents/RespLab/Data/" + ], "ontology": "GENEPIO:0001481", "type": "string", "description": "The filepath of the FAST5 file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Filepath fast5" + "clasification": "Bioinformatics and QC metrics", + "label": "Filepath fast5" }, "number_of_base_pairs_sequenced": { - "examples": ["387566"], + "examples": [ + "387566" + ], "ontology": "GENEPIO:0001482", "type": "string", "description": "The number of total base pairs generated by the sequencing process.", - "clasification":"Bioinformatics and QC metrics", - "label":"Number of base pairs sequenced " + "clasification": "Bioinformatics and QC metrics", + "label": "Number of base pairs sequenced " }, "consensus_genome_length": { - "examples": ["38677"], + "examples": [ + "38677" + ], "ontology": "GENEPIO:0001483", "type": "string", "description": "Size of the assembled genome described as the number of base pairs.", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus genome length" + "clasification": "Bioinformatics and QC metrics", + "label": "Consensus genome length" }, "ns_per_100_kbp": { - "examples": ["300"], + "examples": [ + "300" + ], "ontology": "GENEPIO:0001484", "type": "string", "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Ns per 100 kbp" + "clasification": "Bioinformatics and QC metrics", + "label": "Ns per 100 kbp" }, "reference_genome_accession": { - "examples": ["NC_045512.2"], + "examples": [ + "NC_045512.2" + ], "ontology": "GENEPIO:0001485", "type": "string", "description": "A persistent, unique identifier of a genome database entry.", - "clasification":"Bioinformatics and QC metrics", - "label":"Reference genome accession" + "clasification": "Bioinformatics and QC metrics", + "label": "Reference genome accession" }, "bioinformatics_protocol": { - "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], + "examples": [ + "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" + ], "ontology": "GENEPIO:0001489", "type": "string", "description": "The name of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics", - "label":"Bioinformatics protocol" + "clasification": "Bioinformatics and QC metrics", + "label": "Bioinformatics protocol" }, "if_bioinformatic_protocol_is_other_specify": { - "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], + "examples": [ + "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" + ], "ontology": "0", "type": "string", "description": "The name of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics", - "label":"If bioinformatic protocol Is Other, Specify" + "clasification": "Bioinformatics and QC metrics", + "label": "If bioinformatic protocol Is Other, Specify" }, "bioinformatic_protocol_version": { - "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], - "ontology": "0", + "examples": [ + "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" + ], + "ontology": "NCIT:C93490", "type": "string", "description": "The version number of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics", - "label":"bioinformatics protocol version" + "clasification": "Bioinformatics and QC metrics", + "label": "bioinformatics protocol version" }, "commercial/open-source/both": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Commercial/Open-source/both" + "clasification": "Bioinformatics and QC metrics", + "label": "Commercial/Open-source/both" }, "preprocessing": { - "examples": [""], - "ontology": "0", + "examples": [ + "" + ], + "ontology": "MS_1002386", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Preprocessing" + "clasification": "Bioinformatics and QC metrics", + "label": "Preprocessing" }, "if_preprocessing_other": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"If preprocessing Is Other, Specify" + "clasification": "Bioinformatics and QC metrics", + "label": "If preprocessing Is Other, Specify" }, "preprocessing_params": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Preprocessing params" + "clasification": "Bioinformatics and QC metrics", + "label": "Preprocessing params" }, "mapping": { - "examples": [""], - "ontology": "0", + "examples": [ + "" + ], + "ontology": "topic:0102", "type": "string", "description": "", - "clasification":"Lineage and Variant information", - "label":"Mapping" + "clasification": "Lineage and Variant information", + "label": "Mapping" }, "if_mapping_other": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Lineage and Variant information", - "label":"If mapping Is Other, Specify" + "clasification": "Lineage and Variant information", + "label": "If mapping Is Other, Specify" }, "mapping_params": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Lineage and Variant information", - "label":"Mapping params" + "clasification": "Lineage and Variant information", + "label": "Mapping params" }, "lineage/clade_name": { - "examples": ["B.1.1.7"], + "examples": [ + "B.1.1.7" + ], "ontology": "GENEPIO:0001500", "type": "string", "description": "The name of the lineage or clade.", - "clasification":"Lineage and Variant information", - "label":"Lineage/clade name" + "clasification": "Lineage and Variant information", + "label": "Lineage/clade name" }, "lineage/clade_analysis_software_name": { - "examples": ["Pangolin"], + "examples": [ + "Pangolin" + ], "ontology": "GENEPIO:0001501", "type": "string", "description": "The name of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information", - "label":"lineage/clade analysis software name" + "clasification": "Lineage and Variant information", + "label": "lineage/clade analysis software name" }, "if_lineage_identification_other": { - "examples": ["Other than Pangolin"], + "examples": [ + "Other than Pangolin" + ], "ontology": "0", "type": "string", "description": "The name of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information", - "label":"If lineage identification Is Other, Specify" + "clasification": "Lineage and Variant information", + "label": "If lineage identification Is Other, Specify" }, "lineage/clade_analysis_software_version": { - "examples": ["2.1.10"], - "ontology":"GENEPIO:0001502", + "examples": [ + "2.1.10" + ], + "ontology": "GENEPIO:0001502", "type": "string", "description": "The version of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information", - "label":"Lineage/clade analysis software version" + "clasification": "Lineage and Variant information", + "label": "Lineage/clade analysis software version" }, "variant_designation": { - "Enums": [ - "Variant of Interest (VOI) [GENEPIO:0100082]", - "Variant of Concern (VOC) [GENEPIO:0100083]", - "Variant Under Monitoring (VUM) [GENEPIO:0100279]" - ], - "ontology": "GENEPIO:0001503", - "type": "string", - "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", - "examples": ["Variant of Concern (VOC) [GENEPIO:0100083]"], - "classification":"Lineage and Variant information", - "label":"Variant designation" + "Enums": [ + "Variant of Interest (VOI) [GENEPIO:0100082]", + "Variant of Concern (VOC) [GENEPIO:0100083]", + "Variant Under Monitoring (VUM) [GENEPIO:0100279]" + ], + "ontology": "GENEPIO:0001503", + "type": "string", + "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", + "examples": [ + "Variant of Concern (VOC) [GENEPIO:0100083]" + ], + "classification": "Lineage and Variant information", + "label": "Variant designation" }, "variant_evidence": { - "examples": ["lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)"], - "ontology": "GENEPIO:0001504", + "examples": [ + "lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)" + ], + "ontology": "GENEPIO:0001504", "type": "string", "description": "The evidence used to make the variant determination.", - "clasification":"Lineage and Variant information", - "label":"Variant evidence" + "clasification": "Lineage and Variant information", + "label": "Variant evidence" }, "gene_name_1": { - "Enums": [ - "E gene (orf4) [GENEPIO:0100151]", - "M gene (orf5) [GENEPIO:0100152]", - "N gene (orf9) [GENEPIO:0100153]", - "Spike gene (orf2) [GENEPIO:0100154]", - "orf1ab (rep) [GENEPIO:0100155]", - "orf1a (pp1a) [GENEPIO:0100156]", - "nsp11 [GENEPIO:0100157]", - "nsp1 [GENEPIO:0100158]", - "nsp2 [GENEPIO:0100159]", - "nsp3 [GENEPIO:0100160]", - "nsp4 [GENEPIO:0100161]", - "nsp5 [GENEPIO:0100162]", - "nsp6 [GENEPIO:0100163]", - "nsp7 [GENEPIO:0100164]", - "nsp8 [GENEPIO:0100165]", - "nsp9 [GENEPIO:0100166]", - "nsp10 [GENEPIO:0100167]", - "RdRp gene (nsp12) [GENEPIO:0100168]", - "hel gene (nsp13) [GENEPIO:0100169]", - "exoN gene (nsp14) [GENEPIO:0100170]", - "nsp15 [GENEPIO:0100171]", - "nsp16 [GENEPIO:0100172]", - "orf3a [GENEPIO:0100173]", - "orf3b [GENEPIO:0100174]", - "orf6 (ns6) [GENEPIO:0100175]", - "orf7a [GENEPIO:0100176]", - "orf7b (ns7b) [GENEPIO:0100177]", - "orf8 (ns8) [GENEPIO:0100178]", - "orf9b [GENEPIO:0100179]", - "orf9c [GENEPIO:0100180]", - "orf10 [GENEPIO:0100181]", - "orf14 [GENEPIO:0100182]", - "SARS-COV-2 5' UTR [GENEPIO:0100183]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001507", - "type": "string", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "examples": ["E gene (orf4) [GENEPIO:0100151]"], - "classification":"Pathogen diagnostic testing", - "label":"Gene Name 1" + "Enums": [ + "E gene (orf4) [GENEPIO:0100151]", + "M gene (orf5) [GENEPIO:0100152]", + "N gene (orf9) [GENEPIO:0100153]", + "Spike gene (orf2) [GENEPIO:0100154]", + "orf1ab (rep) [GENEPIO:0100155]", + "orf1a (pp1a) [GENEPIO:0100156]", + "nsp11 [GENEPIO:0100157]", + "nsp1 [GENEPIO:0100158]", + "nsp2 [GENEPIO:0100159]", + "nsp3 [GENEPIO:0100160]", + "nsp4 [GENEPIO:0100161]", + "nsp5 [GENEPIO:0100162]", + "nsp6 [GENEPIO:0100163]", + "nsp7 [GENEPIO:0100164]", + "nsp8 [GENEPIO:0100165]", + "nsp9 [GENEPIO:0100166]", + "nsp10 [GENEPIO:0100167]", + "RdRp gene (nsp12) [GENEPIO:0100168]", + "hel gene (nsp13) [GENEPIO:0100169]", + "exoN gene (nsp14) [GENEPIO:0100170]", + "nsp15 [GENEPIO:0100171]", + "nsp16 [GENEPIO:0100172]", + "orf3a [GENEPIO:0100173]", + "orf3b [GENEPIO:0100174]", + "orf6 (ns6) [GENEPIO:0100175]", + "orf7a [GENEPIO:0100176]", + "orf7b (ns7b) [GENEPIO:0100177]", + "orf8 (ns8) [GENEPIO:0100178]", + "orf9b [GENEPIO:0100179]", + "orf9c [GENEPIO:0100180]", + "orf10 [GENEPIO:0100181]", + "orf14 [GENEPIO:0100182]", + "SARS-COV-2 5' UTR [GENEPIO:0100183]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001507", + "type": "string", + "description": "The name of the gene used in the diagnostic RT-PCR test.", + "examples": [ + "E gene (orf4) [GENEPIO:0100151]" + ], + "classification": "Pathogen diagnostic testing", + "label": "Gene Name 1" }, "Protocol_SARS-CoV-2_detection": { - "examples": [""], - "ontology": "0", + "examples": [ + "" + ], + "ontology": "CIDO_0020274", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"Protocol SARS-CoV-2 detection" + "clasification": "Pathogen diagnostic testing", + "label": "Protocol SARS-CoV-2 detection" }, "%qc_filtered": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"%qc filtered" + "clasification": "Pathogen diagnostic testing", + "label": "%qc filtered" }, "%reads_host": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"%reads host" + "clasification": "Pathogen diagnostic testing", + "label": "%reads host" }, "%reads_virus": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"%reads virus" + "clasification": "Pathogen diagnostic testing", + "label": "%reads virus" }, "%unmapped": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"%unmapped" + "clasification": "Pathogen diagnostic testing", + "label": "%unmapped" }, "%genome _greater_10x": { - "examples": [""], - "ontology": "GENEPIO:0001156", + "examples": [ + "" + ], + "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"% genome greater 10x" + "clasification": "Pathogen diagnostic testing", + "label": "% genome greater 10x" }, "mean_depth_of_coverage_value": { - "examples": [""], - "ontology": "0", + "examples": [ + "" + ], + "ontology": "NCIT:C167285", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"mean depth of coverage value" + "clasification": "Pathogen diagnostic testing", + "label": "mean depth of coverage value" }, "%Ns": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"%Ns" + "clasification": "Pathogen diagnostic testing", + "label": "%Ns" }, "Number_of_variants_(AF_greater_75%)": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"Number of variants (AF greater 75%)" + "clasification": "Pathogen diagnostic testing", + "label": "Number of variants (AF greater 75%)" }, "Numer_of_variants_with_effect": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"Numer of variants with effect" + "clasification": "Pathogen diagnostic testing", + "label": "Numer of variants with effect" }, "reference_genome_accession": { - "examples": [""], + "examples": [ + "" + ], "ontology": "GENEPIO:0001485", "type": "string", "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"reference genome accession" + "clasification": "Pathogen diagnostic testing", + "label": "reference genome accession" }, "diagnostic_pcr_protocol_1": { - "examples": ["PCREGene 2.0"], + "examples": [ + "PCREGene 2.0" + ], "ontology": "GENEPIO:0001508", "type": "string", "description": "The name and version number of the protocol used for diagnostic marker amplification.", - "clasification":"Pathogen diagnostic testing", - "label":"Diagnostic Pcr Protocol 1" + "clasification": "Pathogen diagnostic testing", + "label": "Diagnostic Pcr Protocol 1" }, "diagnostic_pcr_Ct_value_1": { - "examples": ["21"], + "examples": [ + "21" + ], "ontology": "GENEPIO:0001509", "type": "string", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "clasification":"Pathogen diagnostic testing", - "label":"Diagnostic Pcr Ct Value 1" + "clasification": "Pathogen diagnostic testing", + "label": "Diagnostic Pcr Ct Value 1" }, "gene_name_2": { - "Enums": [ - "E gene (orf4) [GENEPIO:0100151]", - "M gene (orf5) [GENEPIO:0100152]", - "N gene (orf9) [GENEPIO:0100153]", - "Spike gene (orf2) [GENEPIO:0100154]", - "orf1ab (rep) [GENEPIO:0100155]", - "orf1a (pp1a) [GENEPIO:0100156]", - "nsp11 [GENEPIO:0100157]", - "nsp1 [GENEPIO:0100158]", - "nsp2 [GENEPIO:0100159]", - "nsp3 [GENEPIO:0100160]", - "nsp4 [GENEPIO:0100161]", - "nsp5 [GENEPIO:0100162]", - "nsp6 [GENEPIO:0100163]", - "nsp7 [GENEPIO:0100164]", - "nsp8 [GENEPIO:0100165]", - "nsp9 [GENEPIO:0100166]", - "nsp10 [GENEPIO:0100167]", - "RdRp gene (nsp12) [GENEPIO:0100168]", - "hel gene (nsp13) [GENEPIO:0100169]", - "exoN gene (nsp14) [GENEPIO:0100170]", - "nsp15 [GENEPIO:0100171]", - "nsp16 [GENEPIO:0100172]", - "orf3a [GENEPIO:0100173]", - "orf3b [GENEPIO:0100174]", - "orf6 (ns6) [GENEPIO:0100175]", - "orf7a [GENEPIO:0100176]", - "orf7b (ns7b) [GENEPIO:0100177]", - "orf8 (ns8) [GENEPIO:0100178]", - "orf9b [GENEPIO:0100179]", - "orf9c [GENEPIO:0100180]", - "orf10 [GENEPIO:0100181]", - "orf14 [GENEPIO:0100182]", - "SARS-COV-2 5' UTR [GENEPIO:0100183]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001510", - "type": "string", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "examples": ["RdRp gene (nsp12) [GENEPIO:0100168]"], - "classification":"Pathogen diagnostic testing", - "label":"Gene Name 2" + "Enums": [ + "E gene (orf4) [GENEPIO:0100151]", + "M gene (orf5) [GENEPIO:0100152]", + "N gene (orf9) [GENEPIO:0100153]", + "Spike gene (orf2) [GENEPIO:0100154]", + "orf1ab (rep) [GENEPIO:0100155]", + "orf1a (pp1a) [GENEPIO:0100156]", + "nsp11 [GENEPIO:0100157]", + "nsp1 [GENEPIO:0100158]", + "nsp2 [GENEPIO:0100159]", + "nsp3 [GENEPIO:0100160]", + "nsp4 [GENEPIO:0100161]", + "nsp5 [GENEPIO:0100162]", + "nsp6 [GENEPIO:0100163]", + "nsp7 [GENEPIO:0100164]", + "nsp8 [GENEPIO:0100165]", + "nsp9 [GENEPIO:0100166]", + "nsp10 [GENEPIO:0100167]", + "RdRp gene (nsp12) [GENEPIO:0100168]", + "hel gene (nsp13) [GENEPIO:0100169]", + "exoN gene (nsp14) [GENEPIO:0100170]", + "nsp15 [GENEPIO:0100171]", + "nsp16 [GENEPIO:0100172]", + "orf3a [GENEPIO:0100173]", + "orf3b [GENEPIO:0100174]", + "orf6 (ns6) [GENEPIO:0100175]", + "orf7a [GENEPIO:0100176]", + "orf7b (ns7b) [GENEPIO:0100177]", + "orf8 (ns8) [GENEPIO:0100178]", + "orf9b [GENEPIO:0100179]", + "orf9c [GENEPIO:0100180]", + "orf10 [GENEPIO:0100181]", + "orf14 [GENEPIO:0100182]", + "SARS-COV-2 5' UTR [GENEPIO:0100183]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided 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"Broker Name" }, "nominal_sdev": { - "examples": [""], + "examples": [ + "" + ], "ontology": "STATO_0000237", "type": "string", "description": "", - "clasification":"Submission ENA", - "label":"Nominal sdev" + "clasification": "Submission ENA", + "label": "Nominal sdev" }, "first_created": { - "examples": ["e.g 2020-08-07"], + "examples": [ + "e.g 2020-08-07" + ], "ontology": "NCIT_C164483", "type": "string", "description": "", - "clasification":"Submission ENA", - "label":"First created date" + "clasification": "Submission ENA", + "label": "First created date" }, "type": { - "examples": ["betacoronavirus"], - "ontology": "GENEPIO:0001156", + "examples": [ + "betacoronavirus" + ], + "ontology": "NCIT:C25284", "type": "string", "description": "default must remain 'betacoronavirus'", - "clasification":"Database Identifiers" + "clasification": "Database Identifiers" } } -} +} \ No newline at end of file From 45b1001e9fd8777e5ebc4e8965c8edcfa0328dfb Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 1 Mar 2022 13:50:37 +0100 Subject: [PATCH 0039/1454] deleted utils from test --- {schema => relecov_tools/schema}/ena_v01.json | 0 {schema => relecov_tools/schema}/genepio.owl | 0 {schema => relecov_tools/schema}/gisaid_V0.json | 0 {schema => relecov_tools/schema}/phage_V0.json | 0 {schema => relecov_tools/schema}/phage_plus_V0.json | 0 {test => relecov_tools}/validation_jsons.py | 0 test/__init__.py | 6 ++++++ 7 files changed, 6 insertions(+) rename {schema => relecov_tools/schema}/ena_v01.json (100%) rename {schema => relecov_tools/schema}/genepio.owl (100%) rename {schema => relecov_tools/schema}/gisaid_V0.json (100%) rename {schema => relecov_tools/schema}/phage_V0.json (100%) rename {schema => relecov_tools/schema}/phage_plus_V0.json (100%) rename {test => relecov_tools}/validation_jsons.py (100%) diff --git a/schema/ena_v01.json b/relecov_tools/schema/ena_v01.json similarity index 100% rename from schema/ena_v01.json rename to relecov_tools/schema/ena_v01.json diff --git a/schema/genepio.owl b/relecov_tools/schema/genepio.owl similarity index 100% rename from schema/genepio.owl rename to relecov_tools/schema/genepio.owl diff --git a/schema/gisaid_V0.json b/relecov_tools/schema/gisaid_V0.json similarity index 100% rename from schema/gisaid_V0.json rename to relecov_tools/schema/gisaid_V0.json diff --git a/schema/phage_V0.json b/relecov_tools/schema/phage_V0.json similarity index 100% rename from schema/phage_V0.json rename to relecov_tools/schema/phage_V0.json diff --git a/schema/phage_plus_V0.json b/relecov_tools/schema/phage_plus_V0.json similarity index 100% rename from schema/phage_plus_V0.json rename to relecov_tools/schema/phage_plus_V0.json diff --git a/test/validation_jsons.py b/relecov_tools/validation_jsons.py similarity index 100% rename from test/validation_jsons.py rename to relecov_tools/validation_jsons.py diff --git a/test/__init__.py b/test/__init__.py index e69de29b..a58e0b83 100644 --- a/test/__init__.py +++ b/test/__init__.py @@ -0,0 +1,6 @@ +""" Main relecov package file. +""" + +import pkg_resources + +__version__ = pkg_resources.get_distribution("relecov").version From d0f1080ace548413797ee3653139b2ec6150340f Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 1 Mar 2022 14:04:57 +0100 Subject: [PATCH 0040/1454] restructuring --- .../RESULTADOS 1er CONTROL CALIDAD-HERA.xlsx | Bin 0 -> 95683 bytes example_data/metadata_lab_dummy.xlsx | Bin 0 -> 74149 bytes .../samples/programmatic/._samples.xml | Bin 0 -> 212 bytes relecov_tools/schema/gisaid_V0.json | 251 +++++++++++------- relecov_tools/validation_jsons.py | 155 ++++++----- 5 files changed, 238 insertions(+), 168 deletions(-) create mode 100644 example_data/RESULTADOS 1er CONTROL CALIDAD-HERA.xlsx create mode 100644 example_data/metadata_lab_dummy.xlsx create mode 100644 example_data/samples/programmatic/._samples.xml diff --git a/example_data/RESULTADOS 1er CONTROL CALIDAD-HERA.xlsx 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z{<8V&UjN6#VL!4gP5zYS`va1HW%$Vqox1Ojhs@R)|o50+1L3ClDI}@gg7w@vi_e5x_AdBnYYuq+J^qI7A5ADWagzZ6zUroSQuKH8Jeb;r&(B7J7*N-=cZblxHwxn lS(;hux*3|A>6#cA8tXbbn!4&58kv|myO@}mx|kU=004fSA2a{} literal 0 HcmV?d00001 diff --git a/relecov_tools/schema/gisaid_V0.json b/relecov_tools/schema/gisaid_V0.json index c03fd1a3..9c8181ba 100644 --- a/relecov_tools/schema/gisaid_V0.json +++ b/relecov_tools/schema/gisaid_V0.json @@ -12,80 +12,108 @@ "patient_age", "gender", "sequencing_technology", - "fasta_filename", + "fasta_filename" ], "type": "object", "properties": { "type": { - "examples": ["betacoronavirus"], + "examples": [ + "betacoronavirus" + ], "ontology": "NCBITaxon:694002", "type": "string", "description": "default must remain 'betacoronavirus'", - "clasification":"Database Identifiers" + "clasification": "Database Identifiers" + }, + "sample_name": { + "examples": [ + "prov_rona_99" + ], + "ontology": "0", + "type": "string", + "description": "The user-defined name for the sample.", + "clasification": "Database Identifiers", + "label": "Collecting Sample id" }, "virus_name": { - "examples": ["hCoV-19/Canada/prov_rona_99/2020"], - "ontology": "GENEPIO:0100282", - "type": "string", - "description": "The user-defined GISAID virus name assigned to the sequence.", - "clasification":"Database Identifiers", - "label":"GISAID Virus Name" + "examples": [ + "hCoV-19/Canada/prov_rona_99/2020" + ], + "ontology": "GENEPIO:0100282", + "type": "string", + "description": "The user-defined GISAID virus name assigned to the sequence.", + "clasification": "Database Identifiers", + "label": "GISAID Virus Name" }, "submitter": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "", - "clasification":"enter your GISAID-Username", - "label":"GISAID Username" + "clasification": "enter your GISAID-Username", + "label": "GISAID Username" }, "originating_lab": { - "examples": ["Public Health Agency of Canada"], + "examples": [ + "Public Health Agency of Canada" + ], "ontology": "GENEPIO:0001153", "type": "string", "description": "The name of the agency that collected the original sample.", - "label":"Collecting Institution" + "label": "Originating Laboratory" }, "collecting_address": { - "examples": ["655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada"], + "examples": [ + "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" + ], "ontology": "GENEPIO:0001158", "type": "string", "description": "The mailing address of the agency submitting the sample.", - "clasification":"Sample collection and processing", - "label":"Collecting Institution Address" + "clasification": "Sample collection and processing", + "label": "Originating Laboratory Address" }, "submitting_address": { - "examples": ["123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"], + "examples": [ + "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" + ], "ontology": "GENEPIO:0001167", "type": "string", "description": "The mailing address of the agency submitting the sequence.", - "clasification":"Sample collection and processing", - "label":"Submitting Institution Address" + "clasification": "Sample collection and processing", + "label": "Submitting Institution Address" }, "collection_date": { - "examples": ["3/19/2020"], - "ontology": "GENEPIO:0001174", - "type": "string", - "description": "The date on which the sample was collected.", - "format":"date", - "classification":"Sample collection and processing", - "label":"Sample Collection Date" + "examples": [ + "3/19/2020" + ], + "ontology": "GENEPIO:0001174", + "type": "string", + "description": "The date on which the sample was collected.", + "format": "date", + "classification": "Sample collection and processing", + "label": "Sample Collection Date" }, "location": { - "examples": ["e.g. Europe / Germany / Bavaria / Munich"], + "examples": [ + "e.g. Europe / Germany / Bavaria / Munich" + ], "ontology": "GENEPIO:0001181 ", "type": "string", "description": "The country of origin of the sample.", - "clasification":"Sample collection and processing", - "label":"Geo Loc Autonomic Country" + "clasification": "Sample collection and processing", + "label": "Geo Loc Autonomic Country" }, "host": { - "examples": ["e.g. Human, Environment, Canine, Manis javanica, Rhinolophus affinis, etc"], + "examples": [ + "e.g. Human, Environment, Canine, Manis javanica, Rhinolophus affinis, etc" + ], "ontology": "GENEPIO:0001387", "type": "string", "description": "The taxonomic, or scientific name of the host.", - "clasification":"Host information", - "label":"Host Scientific Name" + "clasification": "Host information", + "label": "Host Scientific Name" }, "patient_age": { "Enums": [ @@ -106,43 +134,49 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "examples": ["50 - 59 [GENEPIO:0100054]"], + "examples": [ + "50 - 59 [GENEPIO:0100054]" + ], "ontology": "GENEPIO:0001394", "type": "string", "description": "The age category of the host at the time of sampling.", - "clasification":"Host information" + "clasification": "Host information" }, "specimen_source": { "Enums": [ - "Blood [UBERON:0000178]", - "Fluid [UBERON:0006314]", - "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", - "Fluid (Pericardial) [UBERON:0002409]", - "Fluid (Pleural) [UBERON:0001087]", - "Fluid (Vaginal) [UBERON:0036243]", - "Fluid (Amniotic) [UBERON:0000173]", - "Saliva [UBERON:0001836]", - "Tissue [UBERON:0000479]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" + "Blood [UBERON:0000178]", + "Fluid [UBERON:0006314]", + "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", + "Fluid (Pericardial) [UBERON:0002409]", + "Fluid (Pleural) [UBERON:0001087]", + "Fluid (Vaginal) [UBERON:0036243]", + "Fluid (Amniotic) [UBERON:0000173]", + "Saliva [UBERON:0001836]", + "Tissue [UBERON:0000479]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" ], "ontology": "GENEPIO:0001211", "type": "string", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "examples": ["Blood [UBERON:0000178]"], - "classification":"Sample collection and processing", - "label":"Organism Substance" + "examples": [ + "Blood [UBERON:0000178]" + ], + "classification": "Sample collection and processing", + "label": "Organism Substance" }, "Assembly method": { - "examples": ["Ivar"], + "examples": [ + "Ivar" + ], "ontology": "GENEPIO:0001463", "type": "string", "description": "The name of software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus sequence software name" + "clasification": "Bioinformatics and QC metrics", + "label": "Consensus sequence software name" }, "gender": { "Enums": [ @@ -158,89 +192,110 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "examples": ["Male [NCIT:C46109]"], + "examples": [ + "Male [NCIT:C46109]" + ], "ontology": "GENEPIO:0001395", "type": "string", "description": "The gender of the host at the time of sample collection.", - "clasification":"Host information", + "clasification": "Host information", }, "sequencing_technology": { - "examples": ["e.g. Illumina Miseq, Sanger, Nanopore MinION, Ion Torrent, etc."], + "examples": [ + "e.g. Illumina Miseq, Sanger, Nanopore MinION, Ion Torrent, etc." + ], "ontology": "GENEPIO:0001452", "type": "string", "description": "The model of the sequencing instrument used.", - "classification":"Sequencing", - "label":"Sequencing Instrument Model" + "classification": "Sequencing", + "label": "Sequencing Instrument Model" }, "authors": { - "examples": [""], + "examples": [ + "" + ], "ontology": "GENEPIO:0001517", "type": "string", "description": "", - "clasification":"Contributor Acknowledgement", - "label":"Authors" + "clasification": "Contributor Acknowledgement", + "label": "Authors" }, "coverage": { - "examples": ["400x"], + "examples": [ + "400x" + ], "ontology": "GENEPIO:0001474", "type": "string", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Depth of coverage value " + "clasification": "Bioinformatics and QC metrics", + "label": "Depth of coverage value " }, "fasta_filename": { - "examples": ["e.g. all_sequences.fasta not c:\users\meier\docs\all_sequences.fasta"], + "examples": [ + "" + ], "ontology": "GENEPIO:0001156", "type": "string", "description": "Filename that contains the sequence without path", - "clasification":"Bioinformatics and QC metrics", + "clasification": "Bioinformatics and QC metrics", }, "additional_host_information": { - "examples": ["e.g. Patient infected while traveling in …."], - "ontology": "0", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", - "label":"Additional Host Information" + "examples": [ + "e.g. Patient infected while traveling in …." + ], + "ontology": "GENEPIO_0001268", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification": "Host information", + "label": "Additional Host Information" }, "Last vaccinated": { - "examples": ["e.g. 04/09/2021"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The date the host received their last dose of vaccine.", - "format":"date", - "clasification":"Host information", + "examples": [ + "e.g. 04/09/2021" + ], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The date the host received their last dose of vaccine.", + "format": "date", + "clasification": "Host information", }, "outbreak": { - "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], - "ontology": "GENEPIO:0001417", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", - "label":"Outbreak Exposure Event Location" + "examples": [ + "Date, Location e.g. type of gathering, Family cluster, etc." + ], + "ontology": "GENEPIO:0001417", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification": "Host information", + "label": "Outbreak Exposure Event Location" }, "Sampling Strategy": { - "examples": ["e.g. Sentinel surveillance (ILI), Sentinel surveillance (ARI), Sentinel surveillance (SARI), Non-sentinel-surveillance (hospital), Non-sentinel-surveillance (GP network), Longitudinal sampling on same patient(s), S gene dropout"], - "ontology": "GENEPIO:0001445", - "type": "string", - "description": "The reason that the sample was sequenced.", - "classification":"Sequencing", - "label":"Purpose of Sequencing" + "examples": [ + "e.g. Sentinel surveillance (ILI), Sentinel surveillance (ARI), Sentinel surveillance (SARI), Non-sentinel-surveillance (hospital), Non-sentinel-surveillance (GP network), Longitudinal sampling on same patient(s), S gene dropout" + ], + "ontology": "GENEPIO:0001445", + "type": "string", + "description": "The reason that the sample was sequenced.", + "classification": "Sequencing", + "label": "Purpose of Sequencing" }, "submitting_lab_sequence_id": { - "examples": [""], + "examples": [ + "" + ], "ontology": "0", "type": "string", "description": "Sample ID given by the submitting laboratory", - "clasification":"Database Identifiers" + "clasification": "Database Identifiers" }, "submitting_lab": { - "examples": ["Centers for Disease Control and Prevention"], + "examples": [ + "Centers for Disease Control and Prevention" + ], "ontology": "GENEPIO:0001159", "type": "string", "description": "The name of the agency that generated the sequence.", - "label":"Submitting Institution" + "label": "Submitting Institution" } } - -} +} \ No newline at end of file diff --git a/relecov_tools/validation_jsons.py b/relecov_tools/validation_jsons.py index bd9e2172..ea153826 100644 --- a/relecov_tools/validation_jsons.py +++ b/relecov_tools/validation_jsons.py @@ -1,43 +1,48 @@ #!/usr/bin/env python from jsonschema import validate from jsonschema import Draft202012Validator -import json ,sys +import json, sys from openpyxl import Workbook import openpyxl from itertools import islice +import argparse + +# import test.utils + from utils import * -''' + +""" References: genepio.owl https://github.com/GenEpiO/genepio/blob/master/genepio.owl -''' +""" -class PhagePlusSchema : - def __init__ (self, schema): + +class PhagePlusSchema: + def __init__(self, schema): self.schema = schema self.ontology = {} - for key , values in schema['properties'].items(): - self.ontology[values['ontology']] = key - + for key, values in schema["properties"].items(): + self.ontology[values["ontology"]] = key - def get_gontology(self,property_item): - ''' + def get_gontology(self, property_item): + """ Description: The function return the geontology value for a property in the schema Input: property_item # property name to fetch its geontology Return: Return ontology value or None - ''' + """ try: - return self.schema['properties'][property_item]['ontology'] + return self.schema["properties"][property_item]["ontology"] except: return None def maping_schemas_based_on_geontology(mapped_to_schema): - ''' + """ Description: The function return a dictionnary with the properties of the mapped_to_schema as key and properties of phagePlusSchema as value @@ -45,11 +50,11 @@ def maping_schemas_based_on_geontology(mapped_to_schema): mapped_to_schema # json schema to be mapped Return: mapped_dict contains as key the property in the mapped_to_schema and value de property in the self.schema - ''' + """ mapped_dict = OrderedDict() - for key, values in mapped_to_schema['properties'].items(): + for key, values in mapped_to_schema["properties"].items(): try: - mapped_dict[key] = self.ontology[values['ontology']] + mapped_dict[key] = self.ontology[values["ontology"]] except: # There is no exact match on ontology. Search for the parent # to be implemented later @@ -57,12 +62,11 @@ def maping_schemas_based_on_geontology(mapped_to_schema): return mapped_dict -class PhagePlusData : - def __init__ (self,data, json_schema): +class PhagePlusData: + def __init__(self, data, json_schema): self.data = data self.schema = json_schema - def convert_json(schema): pass @@ -76,9 +80,8 @@ def map_sample_to_schema(mapped_structure): return map_sample_dict - -def check_arg (args=None) : - ''' +def check_arg(args=None): + """ The function is used for parsing the input parameters form the command line using the standard python package argparse. The package itself is handling the validation and the return errors messages @@ -86,91 +89,103 @@ def check_arg (args=None) : args # Contains the arguments from the command line Return: parser.parse_args() # The variable contains the valid parameters - ''' - parser = argparse.ArgumentParser(prog = 'validation_jsons.py', - formatter_class=argparse.RawDescriptionHelpFormatter, - description= 'Read the excel input user files and store them in the LIMS') - - parser.add_argument('-v', '--version', action='version', version='%(prog)s 0.0.1') - parser.add_argument('-p', '--phagePlusSchema' , required = True, - help='file where the phage plus schema is located') - parser.add_argument('-i', '--inputFile', required =True, - help='Execl file with the user collected data') - parser.add_argument('-c', '--convertedSchema', required = True, - help='schema to be mapped') + """ + parser = argparse.ArgumentParser( + prog="validation_jsons.py", + formatter_class=argparse.RawDescriptionHelpFormatter, + description="Read the excel input user files and store them in the LIMS", + ) + + parser.add_argument("-v", "--version", action="version", version="%(prog)s 0.0.1") + parser.add_argument( + "-p", + "--phagePlusSchema", + required=True, + help="file where the phage plus schema is located", + ) + parser.add_argument( + "-i", + "--inputFile", + required=True, + help="Execl file with the user collected data", + ) + parser.add_argument( + "-c", "--convertedSchema", required=True, help="schema to be mapped" + ) return parser.parse_args() - -data ={"sample_name":'s1', "collecting_institution" :'inst2', - "submitting_institution":'sub', - "sample_collection_date": '12/02/2022', - "geo_loc_country":'Afghanistan', - "geo_loc_state":'Western', - "organism":'Coronaviridae', - "isolate":'SARS-CoV-2/', - "host_scientific_name":'Bos taurus', - "host_disease":'Homo sapiens', - "sequencing_instrument_model" :'COVID-19', - "sequencing_instrument_platform": 'Illumina sequencing instrument', - "consensus_sequence_software_name":'MinIon', - "consensus_sequence_software_version":'Ivar' +data = { + "sample_name": "s1", + "collecting_institution": "inst2", + "submitting_institution": "sub", + "sample_collection_date": "12/02/2022", + "geo_loc_country": "Afghanistan", + "geo_loc_state": "Western", + "organism": "Coronaviridae", + "isolate": "SARS-CoV-2/", + "host_scientific_name": "Bos taurus", + "host_disease": "Homo sapiens", + "sequencing_instrument_model": "COVID-19", + "sequencing_instrument_platform": "Illumina sequencing instrument", + "consensus_sequence_software_name": "MinIon", + "consensus_sequence_software_version": "Ivar", } -if __name__ == '__main__': - if len (sys.argv) == 1 : - print('Usage: validation_jsons.py [ARGUMENTS] ') - print('Try validation_jsons.py --help for more information.') +if __name__ == "__main__": + if len(sys.argv) == 1: + print("Usage: validation_jsons.py [ARGUMENTS] ") + print("Try validation_jsons.py --help for more information.") exit(2) arguments = check_arg(sys.argv[1:]) - if not check_if_file_exists(arguments.phagePlusSchema): - print('phage plus schema file does not exist\n') + if not test.utils.file_exists(arguments.phagePlusSchema): + print("phage plus schema file does not exist\n") exit(2) - if not check_if_file_exists(arguments.inputFile): - print('excel file does not exist\n') + if not test.utils.file_exists(arguments.inputFile): + print("excel file does not exist\n") exit(2) - if not check_if_file_exists(arguments.convertedSchema): - print('file for converting schema does not exist\n') + if not test.utils.file_exists(arguments.convertedSchema): + print("file for converting schema does not exist\n") exit(2) # schema_file = open('/home/lchapado/Projects/Proyecto_ERA/relecov-tools/schema/phage_plus_V0.json') schema_file = open(arguments.phagePlusSchema) - json_phage_plus_schema = json.load(schema_file) try: Draft202012Validator.check_schema(json_phage_plus_schema) except: - print('Invalid schema') + print("Invalid schema") exit(1) phage_plus_schema = PhagePlusSchema(json_phage_plus_schema) sample_list = [] wb_file = openpyxl.load_workbook(arguments.inputFile, data_only=True) - ws_metadata_lab = wb_file['METADATA_LAB'] + ws_metadata_lab = wb_file["METADATA_LAB"] heading = [] for cell in ws_metadata_lab[1]: heading.append(cell.value) - for row in islice(ws_metadata_lab.values,1,ws_metadata_lab.max_row): + for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row): sample_data_row = {} for idx in range(len(heading)): - if 'date' in heading[idx]: - sample_data_row[heading[idx]] = row[idx].strftime('%d/%m/%Y') + if "date" in heading[idx]: + sample_data_row[heading[idx]] = row[idx].strftime("%d/%m/%Y") else: sample_data_row[heading[idx]] = row[idx] try: - validate(instance=sample_data_row,schema=json_phage_plus_schema) + validate(instance=sample_data_row, schema=json_phage_plus_schema) except: - print('Unsuccessful validation for sample ' , sample_data_row['sample_name']) + print("Unsuccessful validation for sample ", sample_data_row["sample_name"]) continue - sample_list.append(PhagePlusData(sample_data_row,phage_plus_schema)) + sample_list.append(PhagePlusData(sample_data_row, phage_plus_schema)) # create the information mapped to the new schema - mapped_structure = phage_plus_schema.maping_schemas_based_on_geontology(arguments.convertedSchema) + mapped_structure = phage_plus_schema.maping_schemas_based_on_geontology( + arguments.convertedSchema + ) mapped_sample_list = [] for sample in sample_list: mapped_sample_list.append(map_sample_to_schema(mapped_structure)) - - print('Completed') + print("Completed") From 36812ef01d4fd58621e017753fd5aa823205f283 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 1 Mar 2022 14:07:28 +0100 Subject: [PATCH 0041/1454] added python_lint.yml --- .github/workflows/python_lint.yml | 37 +++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 .github/workflows/python_lint.yml diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml new file mode 100644 index 00000000..31edb167 --- /dev/null +++ b/.github/workflows/python_lint.yml @@ -0,0 +1,37 @@ +name: python_lint + +on: + push: + paths: + - '**.py' + pull_request: + paths: + - '**.py' + +jobs: + flake8_py3: + runs-on: ubuntu-latest + steps: + - name: Setup Python + uses: actions/setup-python@v1 + with: + python-version: 3.9.10 + architecture: x64 + - name: Checkout PyTorch + uses: actions/checkout@master + - name: Install flake8 + run: pip install flake8 + - name: Run flake8 + uses: suo/flake8-github-action@releases/v1 + with: + checkName: 'flake8_py3' # NOTE: this needs to be the same as the job name + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + + black_lint: + runs-on: ubuntu-latest + steps: + - name: Setup + uses: actions/checkout@v2 + - name: Check code lints with Black + uses: psf/black@stable From f55f0909378bec14365dd80ab8e77d76b1c35836 Mon Sep 17 00:00:00 2001 From: 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create mode 100644 MANIFEST.in delete mode 100644 example_data/RESULTADOS 1er CONTROL CALIDAD-HERA.xlsx delete mode 100644 example_data/metadata_lab_dummy.xlsx delete mode 100644 example_data/samples/programmatic/._samples.xml rename {test => relecov_tools/test}/mapping_V0.py (100%) rename {test => relecov_tools/test}/mapping_V2.py (100%) rename {test => relecov_tools/test}/my_test_file.xlsx (100%) rename {test => relecov_tools/test}/owl_parsing.py (100%) create mode 100644 requirements.txt create mode 100644 setup.py delete mode 100644 test/__init__.py create mode 100644 tox.ini diff --git a/.gitignore b/.gitignore index b6e47617..08cefe8a 100644 --- a/.gitignore +++ b/.gitignore @@ -127,3 +127,6 @@ dmypy.json # Pyre type checker .pyre/ + +# (Ad-hoc files) +.nextflow* diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 00000000..67263199 --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,6 @@ +include LICENSE +include README.md +graft bu_isciii/templates +graft bu_isciii/schemas 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z{<8V&UjN6#VL!4gP5zYS`va1HW%$Vqox1Ojhs@R)|o50+1L3ClDI}@gg7w@vi_e5x_AdBnYYuq+J^qI7A5ADWagzZ6zUroSQuKH8Jeb;r&(B7J7*N-=cZblxHwxn lS(;hux*3|A>6#cA8tXbbn!4&58kv|myO@}mx|kU=004fSA2a{} diff --git a/test/mapping_V0.py b/relecov_tools/test/mapping_V0.py similarity index 100% rename from test/mapping_V0.py rename to relecov_tools/test/mapping_V0.py diff --git a/test/mapping_V2.py b/relecov_tools/test/mapping_V2.py similarity index 100% rename from test/mapping_V2.py rename to relecov_tools/test/mapping_V2.py diff --git a/test/my_test_file.xlsx b/relecov_tools/test/my_test_file.xlsx similarity index 100% rename from test/my_test_file.xlsx rename to relecov_tools/test/my_test_file.xlsx diff --git a/test/owl_parsing.py b/relecov_tools/test/owl_parsing.py similarity index 100% rename from test/owl_parsing.py rename to relecov_tools/test/owl_parsing.py diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 00000000..36e731a6 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,10 @@ +click +questionary +jinja2 +jsonschema +packaging +prompt_toolkit>=3.0.3 +rich>=10.0.0 +sysrsync==1.0.1 +requests==2.27.1 +markdown==3.3.6 \ No newline at end of file diff --git a/setup.py b/setup.py new file mode 100644 index 00000000..22c87dbd --- /dev/null +++ b/setup.py @@ -0,0 +1,36 @@ +#!/usr/bin/env python + +from setuptools import setup, find_packages + +version = "0.0.1" + +with open("README.md") as f: + readme = f.read() + +with open("requirements.txt") as f: + required = f.read().splitlines() + +setup( + name="bu-isciii", + version=version, + description="Tools for managing and resolution of buisciii services.", + long_description=readme, + long_description_content_type="text/markdown", + keywords=[ + "buisciii", + "bioinformatics", + "pipeline", + "sequencing", + "NGS", + "next generation sequencing", + ], + author="Sara Monzon", + author_email="smonzon@isciii.es", + url="https://github.com/BU-ISCIII/buisciii-tools", + license="GNU GENERAL PUBLIC LICENSE v.3", + entry_points={"console_scripts": ["bu-isciii=bu_isciii.__main__:run_bu_isciii"]}, + install_requires=required, + packages=find_packages(exclude=("docs")), + include_package_data=True, + zip_safe=False, +) diff --git a/test/__init__.py b/test/__init__.py deleted file mode 100644 index a58e0b83..00000000 --- a/test/__init__.py +++ /dev/null @@ -1,6 +0,0 @@ -""" Main relecov package file. -""" - -import pkg_resources - -__version__ = pkg_resources.get_distribution("relecov").version diff --git a/tox.ini b/tox.ini new file mode 100644 index 00000000..bdace909 --- /dev/null +++ b/tox.ini @@ -0,0 +1,6 @@ +## According to black coding style: https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html +[flake8] +max-line-length = 88 +... +select = C,E,F,W,B,B950 +extend-ignore = E203, E501, W605 From 334b3f3666612884649b249bd1f55d9bbacae03d Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 1 Mar 2022 14:22:37 +0100 Subject: [PATCH 0045/1454] deleted main --- __main__.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 __main__.py diff --git a/__main__.py b/__main__.py deleted file mode 100644 index e69de29b..00000000 From 91edc2988df0eb3f916fe52246263113c5f14ba1 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 1 Mar 2022 15:34:31 +0100 Subject: [PATCH 0046/1454] deleted mapping files from erika --- relecov_tools/test/mapping_V0.py | 47 - relecov_tools/test/mapping_V2.py | 3302 ------------------------------ 2 files changed, 3349 deletions(-) delete mode 100644 relecov_tools/test/mapping_V0.py delete mode 100644 relecov_tools/test/mapping_V2.py diff --git a/relecov_tools/test/mapping_V0.py b/relecov_tools/test/mapping_V0.py deleted file mode 100644 index fbaed99c..00000000 --- a/relecov_tools/test/mapping_V0.py +++ /dev/null @@ -1,47 +0,0 @@ -import json -from types import SimpleNamespace - -module_path = str(Path.cwd().parents[0]) -module_path - -# %cd .. - -# + -import sys -from pathlib import Path - -# in jupyter (lab / notebook), based on notebook path -module_path = str(Path.cwd().parents[0]) -# in standard python -#module_path = str(Path.cwd(__file__).parents[0] / "py") - -#if module_path not in sys.path: -# sys.path.append(module_path) - -#from modules import preparations -#import tools -# - - -module_path - -schema_file = open('/Users/erika/Desktop/BU-ISCIII/Relecov/ECDC-HERA/JSON SCHEMA/26_ENERO/ena_v01.json') - -# + -import json - -# Opening JSON file -f = open('ena_v01.json') - -# returns JSON object as -# a dictionary -data = json.load(f) - - - -# Closing file -f.close() -# - - -# Parse JSON into an object with attributes corresponding to dict keys. -x = json.loads(fage_plus_schema, object_hook=lambda d: SimpleNamespace(**d)) -#print(x.name, x.hometown.name, x.hometown.id) diff --git a/relecov_tools/test/mapping_V2.py b/relecov_tools/test/mapping_V2.py deleted file mode 100644 index 5de020cc..00000000 --- a/relecov_tools/test/mapping_V2.py +++ /dev/null @@ -1,3302 +0,0 @@ -# -*- coding: utf-8 -*- -import pandas as pd - -import json -from types import SimpleNamespace -import sys -from pathlib import Path -import json - -pd.set_option('display.max_columns', None) -pd.set_option('display.max_rows', None) - -ENA_schema = { - "$schema": "http://json-schema.org/draft/2019-09/schema#", - "required": [ - "sample_name", - "collecting_institution", - "geographic_location_(country_and/or_sea)", - "isolate", - "host_scientific_name", - "host_common_name", - "host_health_state", - "host_sex", - "host_subject_id", - "instrument_model", - "file_name", - "sample_name", - "tax_id", - "scientific_name", - "common_name", - "sample_description", - "library_source", - "library_selection", - "library_strategy", - "library_layout" - ], - "type": "object", - "properties": { - "sample_name": { - "examples": ["prov_rona_99"], - "ontology": "GENEPIO_0000079", - "type": "string", - "description": "The user-defined name for the sample.", - "clasification":"Database Identifiers", - "genepio_label":"sequencing run sample identifier", - - }, - "collecting_institution": { - "examples": ["Public Health Agency of Canada"], - "ontology": "GENEPIO_0001651", - "type": "string", - "description": "The name of the agency that collected the original sample.", - "genepio_label":"INSDC institution code", - - }, - "collection_date": { - "examples": ["19/03/2020"], - "ontology": "GENEPIO:0001174", - "type": "string", - "description": "The date on which the sample was collected. ", - "format": "date", - "genepio_label":"", - - }, - "receipt_date": { - "examples": ["20/03/2020"], - "ontology": "GENEPIO:0001179", - "type": "string", - "description": "The date on which the sample was received.", - "format": "date", - "genepio_label":"", - - }, - "geographic_location_(country_and/or_sea)": { - "Enums": [ - "Afghanistan [GAZ:00006882]", - "Albania [GAZ:00002953]", - "Algeria [GAZ:00000563]", - "American Samoa [GAZ:00003957]", - "Andorra [GAZ:00002948]", - "Angola [GAZ:00001095]", - "Anguilla [GAZ:00009159]", - "Antarctica [GAZ:00000462]", - "Antigua and Barbuda [GAZ:00006883]", - "Argentina [GAZ:00002928]", - "Armenia [GAZ:00004094]", - "Aruba [GAZ:00004025]", - "Ashmore and Cartier Islands [GAZ:00005901]", - "Australia [GAZ:00000463]", - "Austria [GAZ:00002942]", - "Azerbaijan [GAZ:00004941]", - "Bahamas [GAZ:00002733]", - "Bahrain [GAZ:00005281]", - "Baker Island [GAZ:00007117]", - "Bangladesh [GAZ:00003750]", - "Barbados [GAZ:00001251]", - "Bassas da India [GAZ:00005810]", - "Belarus [GAZ:00006886]", - "Belgium [GAZ:00002938]", - "Belize [GAZ:00002934]", - "Benin [GAZ:00000904]", - "Bermuda [GAZ:00001264]", - "Bhutan [GAZ:00003920]", - "Bolivia [GAZ:00002511]", - "Borneo [GAZ:00025355]", - "Bosnia and Herzegovina [GAZ:00006887]", - "Botswana [GAZ:00001097]", - "Bouvet Island [GAZ:00001453]", - "Brazil [GAZ:00002828]", - "British Virgin Islands [GAZ:00003961]", - "Brunei [GAZ:00003901]", - "Bulgaria [GAZ:00002950]", - "Burkina Faso [GAZ:00000905]", - "Burundi [GAZ:00001090]", - "Cambodia [GAZ:00006888]", - "Cameroon [GAZ:00001093]", - "Canada [GAZ:00002560]", - "Cape Verde [GAZ:00001227]", - "Cayman Islands [GAZ:00003986]", - "Central African Republic [GAZ:00001089]", - "Chad [GAZ:00000586]", - "Chile [GAZ:00002825]", - "China [GAZ:00002845]", - "Christmas Island [GAZ:00005915]", - "Clipperton Island [GAZ:00005838]", - "Cocos Islands [GAZ:00009721]", - "Colombia [GAZ:00002929]", - "Comoros [GAZ:00005820]", - "Cook Islands [GAZ:00053798]", - "Coral Sea Islands [GAZ:00005917]", - "Costa Rica [GAZ:00002901]", - "Cote d'Ivoire [GAZ:00000906]", - "Croatia [GAZ:00002719]", - "Cuba [GAZ:00003762]", - "Curacao [GAZ:00012582]", - "Cyprus [GAZ:00004006]", - "Czech Republic [GAZ:00002954]", - "Democratic Republic of the Congo [GAZ:00001086]", - "Denmark [GAZ:00005852]", - "Djibouti [GAZ:00000582]", - "Dominica [GAZ:00006890]", - "Dominican Republic [GAZ:00003952]", - "Ecuador [GAZ:00002912]", - "Egypt [GAZ:00003934]", - "El Salvador [GAZ:00002935]", - "Equatorial Guinea [GAZ:00001091]", - "Eritrea [GAZ:00000581]", - "Estonia [GAZ:00002959]", - "Eswatini [GAZ:00001099]", - "Ethiopia [GAZ:00000567]", - "Europa Island [GAZ:00005811]", - "Falkland Islands (Islas Malvinas) [GAZ:00001412]", - "Faroe Islands [GAZ:00059206]", - "Fiji [GAZ:00006891]", - "Finland [GAZ:00002937]", - "France [GAZ:00003940]", - "French Guiana [GAZ:00002516]", - "French Polynesia [GAZ:00002918]", - "French Southern and Antarctic Lands [GAZ:00003753]", - "Gabon [GAZ:00001092]", - "Gambia [GAZ:00000907]", - "Gaza Strip [GAZ:00009571]", - "Georgia [GAZ:00004942]", - "Germany [GAZ:00002646]", - "Ghana [GAZ:00000908]", - "Gibraltar [GAZ:00003987]", - "Glorioso Islands [GAZ:00005808]", - "Greece [GAZ:00002945]", - "Greenland [GAZ:00001507]", - "Grenada [GAZ:02000573]", - "Guadeloupe [GAZ:00067142]", - "Guam [GAZ:00003706]", - "Guatemala [GAZ:00002936]", - "Guernsey [GAZ:00001550]", - "Guinea [GAZ:00000909]", - "Guinea-Bissau [GAZ:00000910]", - "Guyana [GAZ:00002522]", - "Haiti [GAZ:00003953]", - "Heard Island and McDonald Islands [GAZ:00009718]", - "Honduras [GAZ:00002894]", - "Hong Kong [GAZ:00003203]", - "Howland Island [GAZ:00007120]", - "Hungary [GAZ:00002952]", - "Iceland [GAZ:00000843]", - "India [GAZ:00002839]", - "Indonesia [GAZ:00003727]", - "Iran [GAZ:00004474]", - "Iraq [GAZ:00004483]", - "Ireland [GAZ:00002943]", - "Isle of Man [GAZ:00052477]", - "Israel [GAZ:00002476]", - "Italy [GAZ:00002650]", - "Jamaica [GAZ:00003781]", - "Jan Mayen [GAZ:00005853]", - "Japan [GAZ:00002747]", - "Jarvis Island [GAZ:00007118]", - "Jersey [GAZ:00001551]", - "Johnston Atoll [GAZ:00007114]", - "Jordan [GAZ:00002473]", - "Juan de Nova Island [GAZ:00005809]", - "Kazakhstan [GAZ:00004999]", - "Kenya [GAZ:00001101]", - "Kerguelen Archipelago [GAZ:00005682]", - "Kingman Reef [GAZ:00007116]", - "Kiribati [GAZ:00006894]", - "Kosovo [GAZ:00011337]", - "Kuwait [GAZ:00005285]", - "Kyrgyzstan [GAZ:00006893]", - "Laos [GAZ:00006889]", - "Latvia [GAZ:00002958]", - "Lebanon [GAZ:00002478]", - "Lesotho [GAZ:00001098]", - "Liberia [GAZ:00000911]", - "Libya [GAZ:00000566]", - "Liechtenstein [GAZ:00003858]", - "Line Islands [GAZ:00007144]", - "Lithuania [GAZ:00002960]", - "Luxembourg [GAZ:00002947]", - "Macau [GAZ:00003202]", - "Madagascar [GAZ:00001108]", - "Malawi [GAZ:00001105]", - "Malaysia [GAZ:00003902]", - "Maldives [GAZ:00006924]", - "Mali [GAZ:00000584]", - "Malta [GAZ:00004017]", - "Marshall Islands [GAZ:00007161]", - "Martinique [GAZ:00067143]", - "Mauritania [GAZ:00000583]", - "Mauritius [GAZ:00003745]", - "Mayotte [GAZ:00003943]", - "Mexico [GAZ:00002852]", - "Micronesia [GAZ:00005862]", - "Midway Islands [GAZ:00007112]", - "Moldova [GAZ:00003897]", - "Monaco [GAZ:00003857]", - "Mongolia [GAZ:00008744]", - "Montenegro [GAZ:00006898]", - "Montserrat [GAZ:00003988]", - "Morocco [GAZ:00000565]", - "Mozambique [GAZ:00001100]", - "Myanmar [GAZ:00006899]", - "Namibia [GAZ:00001096]", - "Nauru [GAZ:00006900]", - "Navassa Island [GAZ:00007119]", - "Nepal [GAZ:00004399]", - "Netherlands [GAZ:00002946]", - "New Caledonia [GAZ:00005206]", - "New Zealand [GAZ:00000469]", - "Nicaragua [GAZ:00002978]", - "Niger [GAZ:00000585]", - "Nigeria [GAZ:00000912]", - "Niue [GAZ:00006902]", - "Norfolk Island [GAZ:00005908]", - "North Korea [GAZ:00002801]", - "North Macedonia [GAZ:00006895]", - "North Sea [GAZ:00002284]", - "Northern Mariana Islands [GAZ:00003958]", - "Norway [GAZ:00002699]", - "Oman [GAZ:00005283]", - "Pakistan [GAZ:00005246]", - "Palau [GAZ:00006905]", - "Panama [GAZ:00002892]", - "Papua New Guinea [GAZ:00003922]", - "Paracel Islands [GAZ:00010832]", - "Paraguay [GAZ:00002933]", - "Peru [GAZ:00002932]", - "Philippines [GAZ:00004525]", - "Pitcairn Islands [GAZ:00005867]", - "Poland [GAZ:00002939]", - "Portugal [GAZ:00004126]", - "Puerto Rico [GAZ:00006935]", - "Qatar [GAZ:00005286]", - "Republic of the Congo [GAZ:00001088]", - "Reunion [GAZ:00003945]", - "Romania [GAZ:00002951]", - "Ross Sea [GAZ:00023304]", - "Russia [GAZ:00002721]", - "Rwanda [GAZ:00001087]", - "Saint Helena [GAZ:00000849]", - "Saint Kitts and Nevis [GAZ:00006906]", - "Saint Lucia [GAZ:00006909]", - "Saint Pierre and Miquelon [GAZ:00003942]", - "Saint Martin [GAZ:00005841]", - "Saint Vincent and the Grenadines [GAZ:02000565]", - "Samoa [GAZ:00006910]", - "San Marino [GAZ:00003102]", - "Sao Tome and Principe [GAZ:00006927]", - "Saudi Arabia [GAZ:00005279]", - "Senegal [GAZ:00000913]", - "Serbia [GAZ:00002957]", - "Seychelles [GAZ:00006922]", - "Sierra Leone [GAZ:00000914]", - "Singapore [GAZ:00003923]", - "Sint Maarten [GAZ:00012579]", - "Slovakia [GAZ:00002956]", - "Slovenia [GAZ:00002955]", - "Solomon Islands [GAZ:00005275]", - "Somalia [GAZ:00001104]", - "South Africa [GAZ:00001094]", - "South Georgia and the South Sandwich Islands [GAZ:00003990]", - "South Korea [GAZ:00002802]", - "South Sudan [GAZ:00233439]", - "Spain [GAZ:00003936]", - "Spratly Islands [GAZ:00010831]", - "Sri Lanka [GAZ:00003924]", - "State of Palestine [GAZ:00002475]", - "Sudan [GAZ:00000560]", - "Suriname [GAZ:00002525]", - "Svalbard [GAZ:00005396]", - "Swaziland [GAZ:00001099]", - "Sweden [GAZ:00002729]", - "Switzerland [GAZ:00002941]", - "Syria [GAZ:00002474]", - "Taiwan [GAZ:00005341]", - "Tajikistan [GAZ:00006912]", - "Tanzania [GAZ:00001103]", - "Thailand [GAZ:00003744]", - "Timor-Leste [GAZ:00006913]", - "Togo [GAZ:00000915]", - "Tokelau [GAZ:00260188]", - "Tonga [GAZ:00006916]", - "Trinidad and Tobago [GAZ:00003767]", - "Tromelin Island [GAZ:00005812]", - "Tunisia [GAZ:00000562]", - "Turkey [GAZ:00000558]", - "Turkmenistan [GAZ:00005018]", - "Turks and Caicos Islands [GAZ:00003955]", - "Tuvalu [GAZ:00009715]", - "USA [GAZ:00002459]", - "Uganda [GAZ:00001102]", - "Ukraine [GAZ:00002724]", - "United Arab Emirates [GAZ:00005282]", - "United Kingdom [GAZ:00002637]", - "Uruguay [GAZ:00002930]", - "Uzbekistan [GAZ:00004979]", - "Vanuatu [GAZ:00006918]", - "Venezuela [GAZ:00002931]", - "Viet Nam [GAZ:00003756]", - "Virgin Islands [GAZ:00003959]", - "Wake Island [GAZ:00007111]", - "Wallis and Futuna [GAZ:00007191]", - "West Bank [GAZ:00009572]", - "Western Sahara [GAZ:00000564]", - "Yemen [GAZ:00005284]", - "Zambia [GAZ:00001107]", - "Zimbabwe [GAZ:00001106]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO_0000118", - "type": "string", - "description": "The country of origin of the sample.", - "examples": ["South Africa [GAZ:00001094]"], - "genepio_label":"specimen collection location - country", - - }, - "geographic location (region and locality)": { - "ontology": "GENEPIO:0100280", - "type": "string", - "description": "The county/region of origin of the sample.", - "examples": ["Derbyshire"], - "genepio_label":"", - - }, - "geographic location (latitude)": { - "ontology": "OBI:0001620", - "type": "string", - "description": "The latitude coordinates of the geographical location of sample collection.", - "examples": ["38.98 N"], - "genepio_label":"", - - }, - "geographic location (longitude)": { - "ontology": "OBI:0001621", - "type": "string", - "description": "The longitude coordinates of the geographical location of sample collection.", - "examples": ["77.11 W"], - "genepio_label":"", - - }, - "scientific_name": { - "Enums": [ - "Coronaviridae [NCBITaxon:11118]", - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001191", - "type": "string", - "description": "Taxonomic name of the organism.", - "examples": ["Severe acute respiratory syndrome coronavirus 2 "], - "genepio_label":"", - - }, - "isolate": { - "ontology": "GENEPIO:0001644", - "type": "string", - "description": "Identifier of the specific isolate.", - "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"], - "genepio_label":"isolate identifier", - - }, - "purpose_sampling": { - "examples": ["Diagnostic testing"], - "ontology": "NCIT_C146997", - "type": "string", - "description": "The reason that the sample was collected.", - "clasification":"Sample collection and processing" - }, - "isolation source host-associated": { - "Enums": [ - "Blood [UBERON:0000178]", - "Fluid [UBERON:0006314]", - "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", - "Fluid (Pericardial) [UBERON:0002409]", - "Fluid (Pleural) [UBERON:0001087]", - "Fluid (Vaginal) [UBERON:0036243]", - "Fluid (Amniotic) [UBERON:0000173]", - "Saliva [UBERON:0001836]", - "Tissue [UBERON:0000479]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001211", - "type": "string", - "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "examples": ["Blood [UBERON:0000178]"], - "genepio_label":"", - - }, - "host common name": { - "Enums": [ - "Human [NCBITaxon:9606]", - "Bat [NCBITaxon:9397]", - "Cat [NCBITaxon:9685]", - "Chicken [NCBITaxon:9031]", - "Civet [NCBITaxon:9673]", - "Cow [NCBITaxon:9913]", - "Dog [NCBITaxon:9615]", - "Lion [NCBITaxon:9689]", - "Mink [NCBITaxon:452646]", - "Pangolin [NCBITaxon:9973]", - "Pig [NCBITaxon:9825]", - "Pigeon [NCBITaxon:8930]", - "Tiger [NCBITaxon:9694]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO_0001724", - "type": "string", - "description": "The commonly used name of the host.", - "examples": ["Human [NCBITaxon:9606]"], - "genepio_label":"subject organism common name", - - }, - "host scientific name": { - "Enums": [ - "Bos taurus [NCBITaxon:9913]", - "Canis lupus familiaris [NCBITaxon:9615]", - "Chiroptera [NCBITaxon:9397]", - "Columbidae [NCBITaxon:8930]", - "Felis catus [NCBITaxon:9685]", - "Gallus gallus [NCBITaxon:9031]", - "Homo sapiens [NCBITaxon:9606]", - "Manis [NCBITaxon:9973]", - "Manis javanica [NCBITaxon:9974]", - "Neovison vison [NCBITaxon:452646]", - "Panthera leo [NCBITaxon:9689]", - "Panthera tigris [NCBITaxon:9694]", - "Rhinolophidae [NCBITaxon:58055]", - "Rhinolophus affinis [NCBITaxon:59477]", - "Sus scrofa domesticus [NCBITaxon:9825]", - "Viverridae [NCBITaxon:9673]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO_0001567", - "type": "string", - "description": "The taxonomic, or scientific name of the host.", - "examples": ["Homo sapiens [NCBITaxon:9606]"], - "genepio_label":"subject organism (host) taxonomic species", - - }, - "host_health_state": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Health status of the host at the time of sample collection.", - "clasification":"Host information", - "genepio_label":"", - - }, - "host_age": { - "examples": ["e.g. 65 or 7 months, or unknown. Caution: the host age may be considered public health identifiable information. Consult the data steward before sharing. If the information is unknown or can not be shared, put unknown"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Patient age", - "clasification":"Host information" - }, - - "host_sex": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Gender or sex of the host.", - "clasification":"Host information", - "genepio_label":"", - - }, - "host_subject_id": { - "examples": ["e.g. #131"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "a unique identifier by which each subject can be referred to, de-identified.", - "clasification":"Host information", - "genepio_label":"", - - }, - "type exposure": { - "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", - "genepio_label":"", - - }, - "subject exposure duration": { - "examples": ["e.g. Patient infected while traveling in …."], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", - "genepio_label":"", - - }, - "instrument_model": { - "Enums": ["454 Genome Sequencer [GENEPIO:0001937]", - "454 Genome Sequence 20 [OBI:0000689]", - "454 Genome Sequencer FLX [OBI:0000702]", - "454 Genome Sequencer FLX Titanium [GENEPIO:0001936]", - "454 Genome Sequencer Junior [GENEPIO:0001938]", - "AB SOLiD System [OBI:0000696]", - "SOLiD 3 Plus System [OBI:0002007]", - "SOLiD 4 [OBI:0002024]", - "SOLiD 4hq System [GENPIO:0001928]", - "SOLiD 5500 [GENPIO:0001929]", - "SOLiD 5500xl [GENPIO:0001930]", - "SOLiD PI System [GENPIO:0001931]", - "SOLiD System 2.0 [GENPIO:0001932]", - "SOLiD System 3.0 [GENPIO:0001933]", - "HeliScope Single Molecule Sequencer [OBI:0000717]", - "Illumina Genome Analyzer II [OBI:0000703]", - "Genome Analyzer IIe [OBI:0002027]", - "Genome Analyzer IIx [OBI:0002000]", - "Illumina HiSeq Sequencer [GENPIO:0001939]", - "Illumina HiSeq 1000 [OBI:0002022]", - "Illumina HiSeq 2000 [OBI:0002001]", - "Illumina HiSeq 2500 [OBI:0002002]", - "Illumina HiSeq 3000 [OBI:0002048]", - "Illumina HiSeq 4000 [OBI:0002049]", - "Ion Torrent PGM [GENPIO:0001935]", - "MiSeq [OBI:0002003]", - "NextSeq 500 [OBI:0002021]", - "PacBio RS II [OBI:0002012]", - ], - "ontology": "GENEPIO_0001921", - "type": "string", - "description": "The model of the sequencing instrument used.", - "examples": ["Oxford Nanopore MinION "], - "genepio_label":"sequencing instrument model", - - }, - "instrument_platform ": { - "examples": ["MinIon"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The model of the sequencing instrument used.", - "genepio_label":"", - - }, - "file_name": { - "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], - "ontology": "GENEPIO:0001476", - "type": "string", - "description": "The user-specified filename of the r1 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", - "genepio_label":"", - - }, - "tax_id": { - "examples": ["probably 2697049 in all cases"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The NCBITaxon identifier for the organism being sequenced.", - "clasification":"Sample collection and processing", - "genepio_label":"", - - }, - "scientific_name": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The taxonomic name of the organism.", - "clasification":"Sample collection and processing", - "genepio_label":"", - - }, - "common_name": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The common name of the organism.", - "clasification":"Sample collection and processing", - "genepio_label":"", - - }, - "sample_description": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Free text description of the sample.", - "clasification":"Sample collection and processing", - "genepio_label":"", - - }, - "sample_storage_conditions": { - "examples": ["24 degrees celsius"], - "ontology": "NCIT_C115535", - "type": "string", - "description": "The name and version of a particular protocol used for sampling.", - "clasification":"Sample collection and processing" - }, - "library_source": { - "Enums": ["5-methycytidine antibody method [GENPIO:0001941]", - "CAGE method [GENPIO:0001942]", - "CF-H method [GENPIO:0001943]", - "CF-M method ]GENPIO:0001944]", - "CF-S method [GENPIO:0001945]", - "CF-T method [GENPIO:0001946]", - "ChIP method ]GENPIO:0001947]", - "DNAse method [GENPIO:0001948]", - "HMPR method [GENPIO:0001949]", - "Hybrid Selection Method [GENPIO:0001950]", - "MBD2 protein methyl-CpG binding domain method [GENPIO:0001951]", - "MF method [GENPIO:0001952]", - "MNase method [GENPIO:0001953]", - "MSLL method [GENPIO:0001954]", - "PCR method [GENPIO:0001955]", - "RACE method [GENPIO:0001956]", - "RANDOM PCR method [GENPIO:0001957]", - "RANDOM method [GENPIO:0001958]", - "RT-PCR method [GENPIO:0001959]", - "Reduced Representation method [GENPIO:0001960]", - "Resctriction Digest method [GENPIO:0001961]", - "cDNA method [GENPIO:0001962]", - "other library method [GENPIO:0001964]", - "size fractionation method [GENPIO:0001963]", - ], - "examples": ["METAGENOMIC"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Molecule type used to make the library.", - "clasification":"Sequencing", - }, - "library_selection": { - "examples": ["RANDOM PCR"], - "ontology": "GENPIO_0001940", - "type": "string", - "description": "Library capture method.", - "clasification":"Sequencing", - "genepio_label":"library selection", - - }, - "library_strategy": { - "Enums": ["Bisultife-Seq strategy [GENPIO:0001975]", - "CTS strategy [GENPIO:0001978]", - "ChIP-Seq strategy [GENPIO:0001979]", - "DNase-Hypersensitivity strategy [GENPIO:0001980]", - "EST strategy [GENPIO:0001981]", - "FL-cDNA strategy [GENPIO:0001983]", - "MB-Seq strategy [GENPIO:0001984]", - "MNase-Seq strategy [GENPIO:0001985]", - "MRE-Seq strategy [GENPIO:0001986]", - "MeDIP-Seq strategy [GENPIO:0001987]", - "RNA-Seq strategy [GENPIO:0001990]", - "WCS strategy [GENPIO:0001991]", - "WGS strategy [GENPIO:0001992]", - "WXS strategy [GENPIO:0001993]", - "amplicon strategy [GENPIO:0001974]", - "clone end strategy [GENPIO:0001976]", - "clone strategy [GENPIO:0001977]", - "finishing strategy [GENPIO:0001982]", - "other library strategy [GENPIO:0001988]", - "pool clone strategy [GENPIO:0001989]", - ], - "examples": ["WGS"], - "ontology": "GENPIO_0001973", - "type": "string", - "description": "Overall sequencing strategy or approach.", - "clasification":"Sequencing", - "genepio_label":"library strategy", - - }, - "library_layout": { - "examples": ["PAIRED"], - "ontology":"GENPIO_0000001", - "type": "string", - "description": "Single or paired.", - "clasification":"Sequencing", - "genepio_label":"library library_layout", - - }, - "library_name": { - "examples": ["e.g P17157_1007"], - "ontology": "GENEPIO_0001995", - "type": "string", - "description": "The submitter's name for this library.", - "clasification":"Sequencing", - "genepio_label":"Library Name", - }, - "nominal_length ": { - "examples": ["350"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing", - "genepio_label":"", - - }, - "analysis_accession": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "study_accession": { - "examples": ["e.g PRJEB39632"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "secondary_study_accession": { - "examples": ["e.g ERP123173"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "sample_accession": { - "examples": ["e.g SAMEA7098096"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "secondary_sample_accession": { - "examples": ["e.g ERS4858671"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "experiment_accession": { - "examples": ["e.g ERX4331406"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "run_accession": { - "examples": ["e.g ERX4331406"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "submission_accession": { - "examples": ["e.g ERA2794974"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "read_count": { - "examples": ["e.g 837055"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "base_count": { - "examples": ["e.g 503907110"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "center_name": { - "examples": [" KAROLINSKA INSITUTET"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The name of the institution", - "clasification":"Sample collection and processing", - "genepio_label":"", - - }, - "first_public": { - "examples": ["e.g 2020-08-07"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "last_updated": { - "examples": ["e.g 2020-07-29"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "format":"date", - "genepio_label":"", - - }, - "experiment_title": { - "examples": ["e.g Illumina MiSeq paired end sequencing"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "study_title": { - "examples": ["e.g SARS-CoV-2 genomes from late April in Stockholm"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "study_alias": { - "examples": ["e.g Sweden"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "experiment_alias": { - "examples": ["e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "run_alias": { - "examples": ["e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "fastq_bytes": { - "examples": ["e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "fastq_md5": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "fastq_ftp": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "fastq_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "fastq_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "submitted_bytes": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "submitted_md5": { - "examples": ["e.g 139853010;166270048"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "submitted_ftp": { - "examples": ["e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "submitted_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "submitted_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "submitted_format": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "sra_bytes": { - "examples": ["e.g FASTQ;FASTQ"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "sra_md5": { - "examples": ["e.g 260236789"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "sra_ftp": { - "examples": ["e.g 2cf0d467d6dc4ae0a5473774d54c059c"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "sra_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "sra_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "broker_name": { - "examples": ["P17157_1007"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "nominal_sdev": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - "first_created": { - "examples": ["e.g 2020-08-07"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "genepio_label":"", - - }, - - } -} - - -phage_schema= { - "$schema": "http://json-schema.org/draft/2020-12/schema", - "required": [ - "sample_name", - "collecting_institution", - "submitting_institution", - "sample_collection_date", - "geo_loc_country", - "geo_loc_state", - "organism", - "isolate", - "host_scientific_name", - "host_disease", - "sequencing_instrument_model", - "sequencing_instrument_platform", - "consensus_sequence_software_name", - "consensus_sequence_software_version" - ], - "type": "object", - "properties": { - "sample_name": { - "examples": ["prov_rona_99"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The user-defined name for the sample.", - "clasification":"Database Identifiers" - }, - "collecting_institution": { - "examples": ["Public Health Agency of Canada"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The name of the agency that collected the original sample." - }, - "submitting_institution": { - "examples": ["Centers for Disease Control and Prevention"], - "ontology": "GENEPIO:0001159", - "type": "string", - "description": "The name of the agency that generated the sequence." - }, - "sample_collection_date": { - "examples": ["3/19/2020"], - "ontology": "GENEPIO:0001174", - "type": "string", - "description": "The date on which the sample was collected.", - "format":"date" - }, - "geo_loc_country": { - "Enums": [ - "Afghanistan [GAZ:00006882]", - "Albania [GAZ:00002953]", - "Algeria [GAZ:00000563]", - "American Samoa [GAZ:00003957]", - "Andorra [GAZ:00002948]", - "Angola [GAZ:00001095]", - "Anguilla [GAZ:00009159]", - "Antarctica [GAZ:00000462]", - "Antigua and Barbuda [GAZ:00006883]", - "Argentina [GAZ:00002928]", - "Armenia [GAZ:00004094]", - "Aruba [GAZ:00004025]", - "Ashmore and Cartier Islands [GAZ:00005901]", - "Australia [GAZ:00000463]", - "Austria [GAZ:00002942]", - "Azerbaijan [GAZ:00004941]", - "Bahamas [GAZ:00002733]", - "Bahrain [GAZ:00005281]", - "Baker Island [GAZ:00007117]", - "Bangladesh [GAZ:00003750]", - "Barbados [GAZ:00001251]", - "Bassas da India [GAZ:00005810]", - "Belarus [GAZ:00006886]", - "Belgium [GAZ:00002938]", - "Belize [GAZ:00002934]", - "Benin [GAZ:00000904]", - "Bermuda [GAZ:00001264]", - "Bhutan [GAZ:00003920]", - "Bolivia [GAZ:00002511]", - "Borneo [GAZ:00025355]", - "Bosnia and Herzegovina [GAZ:00006887]", - "Botswana [GAZ:00001097]", - "Bouvet Island [GAZ:00001453]", - "Brazil [GAZ:00002828]", - "British Virgin Islands [GAZ:00003961]", - "Brunei [GAZ:00003901]", - "Bulgaria [GAZ:00002950]", - "Burkina Faso [GAZ:00000905]", - "Burundi [GAZ:00001090]", - "Cambodia [GAZ:00006888]", - "Cameroon [GAZ:00001093]", - "Canada [GAZ:00002560]", - "Cape Verde [GAZ:00001227]", - "Cayman Islands [GAZ:00003986]", - "Central African Republic [GAZ:00001089]", - "Chad [GAZ:00000586]", - "Chile [GAZ:00002825]", - "China [GAZ:00002845]", - "Christmas Island [GAZ:00005915]", - "Clipperton Island [GAZ:00005838]", - "Cocos Islands [GAZ:00009721]", - "Colombia [GAZ:00002929]", - "Comoros [GAZ:00005820]", - "Cook Islands [GAZ:00053798]", - "Coral Sea Islands [GAZ:00005917]", - "Costa Rica [GAZ:00002901]", - "Cote d'Ivoire [GAZ:00000906]", - "Croatia [GAZ:00002719]", - "Cuba [GAZ:00003762]", - "Curacao [GAZ:00012582]", - "Cyprus [GAZ:00004006]", - "Czech Republic [GAZ:00002954]", - "Democratic Republic of the Congo [GAZ:00001086]", - "Denmark [GAZ:00005852]", - "Djibouti [GAZ:00000582]", - "Dominica [GAZ:00006890]", - "Dominican Republic [GAZ:00003952]", - "Ecuador [GAZ:00002912]", - "Egypt [GAZ:00003934]", - "El Salvador [GAZ:00002935]", - "Equatorial Guinea [GAZ:00001091]", - "Eritrea [GAZ:00000581]", - "Estonia [GAZ:00002959]", - "Eswatini [GAZ:00001099]", - "Ethiopia [GAZ:00000567]", - "Europa Island [GAZ:00005811]", - "Falkland Islands (Islas Malvinas) [GAZ:00001412]", - "Faroe Islands [GAZ:00059206]", - "Fiji [GAZ:00006891]", - "Finland [GAZ:00002937]", - "France [GAZ:00003940]", - "French Guiana [GAZ:00002516]", - "French Polynesia [GAZ:00002918]", - "French Southern and Antarctic Lands [GAZ:00003753]", - "Gabon [GAZ:00001092]", - "Gambia [GAZ:00000907]", - "Gaza Strip [GAZ:00009571]", - "Georgia [GAZ:00004942]", - "Germany [GAZ:00002646]", - "Ghana [GAZ:00000908]", - "Gibraltar [GAZ:00003987]", - "Glorioso Islands [GAZ:00005808]", - "Greece [GAZ:00002945]", - "Greenland [GAZ:00001507]", - "Grenada [GAZ:02000573]", - "Guadeloupe [GAZ:00067142]", - "Guam [GAZ:00003706]", - "Guatemala [GAZ:00002936]", - "Guernsey [GAZ:00001550]", - "Guinea [GAZ:00000909]", - "Guinea-Bissau [GAZ:00000910]", - "Guyana [GAZ:00002522]", - "Haiti [GAZ:00003953]", - "Heard Island and McDonald Islands [GAZ:00009718]", - "Honduras [GAZ:00002894]", - "Hong Kong [GAZ:00003203]", - "Howland Island [GAZ:00007120]", - "Hungary [GAZ:00002952]", - "Iceland [GAZ:00000843]", - "India [GAZ:00002839]", - "Indonesia [GAZ:00003727]", - "Iran [GAZ:00004474]", - "Iraq [GAZ:00004483]", - "Ireland [GAZ:00002943]", - "Isle of Man [GAZ:00052477]", - "Israel [GAZ:00002476]", - "Italy [GAZ:00002650]", - "Jamaica [GAZ:00003781]", - "Jan Mayen [GAZ:00005853]", - "Japan [GAZ:00002747]", - "Jarvis Island [GAZ:00007118]", - "Jersey [GAZ:00001551]", - "Johnston Atoll [GAZ:00007114]", - "Jordan [GAZ:00002473]", - "Juan de Nova Island [GAZ:00005809]", - "Kazakhstan [GAZ:00004999]", - "Kenya [GAZ:00001101]", - "Kerguelen Archipelago [GAZ:00005682]", - "Kingman Reef [GAZ:00007116]", - "Kiribati [GAZ:00006894]", - "Kosovo [GAZ:00011337]", - "Kuwait [GAZ:00005285]", - "Kyrgyzstan [GAZ:00006893]", - "Laos [GAZ:00006889]", - "Latvia [GAZ:00002958]", - "Lebanon [GAZ:00002478]", - "Lesotho [GAZ:00001098]", - "Liberia [GAZ:00000911]", - "Libya [GAZ:00000566]", - "Liechtenstein [GAZ:00003858]", - "Line Islands [GAZ:00007144]", - "Lithuania [GAZ:00002960]", - "Luxembourg [GAZ:00002947]", - "Macau [GAZ:00003202]", - "Madagascar [GAZ:00001108]", - "Malawi [GAZ:00001105]", - "Malaysia [GAZ:00003902]", - "Maldives [GAZ:00006924]", - "Mali [GAZ:00000584]", - "Malta [GAZ:00004017]", - "Marshall Islands [GAZ:00007161]", - "Martinique [GAZ:00067143]", - "Mauritania [GAZ:00000583]", - "Mauritius [GAZ:00003745]", - "Mayotte [GAZ:00003943]", - "Mexico [GAZ:00002852]", - "Micronesia [GAZ:00005862]", - "Midway Islands [GAZ:00007112]", - "Moldova [GAZ:00003897]", - "Monaco [GAZ:00003857]", - "Mongolia [GAZ:00008744]", - "Montenegro [GAZ:00006898]", - "Montserrat [GAZ:00003988]", - "Morocco [GAZ:00000565]", - "Mozambique [GAZ:00001100]", - "Myanmar [GAZ:00006899]", - "Namibia [GAZ:00001096]", - "Nauru [GAZ:00006900]", - "Navassa Island [GAZ:00007119]", - "Nepal [GAZ:00004399]", - "Netherlands [GAZ:00002946]", - "New Caledonia [GAZ:00005206]", - "New Zealand [GAZ:00000469]", - "Nicaragua [GAZ:00002978]", - "Niger [GAZ:00000585]", - "Nigeria [GAZ:00000912]", - "Niue [GAZ:00006902]", - "Norfolk Island [GAZ:00005908]", - "North Korea [GAZ:00002801]", - "North Macedonia [GAZ:00006895]", - "North Sea [GAZ:00002284]", - "Northern Mariana Islands [GAZ:00003958]", - "Norway [GAZ:00002699]", - "Oman [GAZ:00005283]", - "Pakistan [GAZ:00005246]", - "Palau [GAZ:00006905]", - "Panama [GAZ:00002892]", - "Papua New Guinea [GAZ:00003922]", - "Paracel Islands [GAZ:00010832]", - "Paraguay [GAZ:00002933]", - "Peru [GAZ:00002932]", - "Philippines [GAZ:00004525]", - "Pitcairn Islands [GAZ:00005867]", - "Poland [GAZ:00002939]", - "Portugal [GAZ:00004126]", - "Puerto Rico [GAZ:00006935]", - "Qatar [GAZ:00005286]", - "Republic of the Congo [GAZ:00001088]", - "Reunion [GAZ:00003945]", - "Romania [GAZ:00002951]", - "Ross Sea [GAZ:00023304]", - "Russia [GAZ:00002721]", - "Rwanda [GAZ:00001087]", - "Saint Helena [GAZ:00000849]", - "Saint Kitts and Nevis [GAZ:00006906]", - "Saint Lucia [GAZ:00006909]", - "Saint Pierre and Miquelon [GAZ:00003942]", - "Saint Martin [GAZ:00005841]", - "Saint Vincent and the Grenadines [GAZ:02000565]", - "Samoa [GAZ:00006910]", - "San Marino [GAZ:00003102]", - "Sao Tome and Principe [GAZ:00006927]", - "Saudi Arabia [GAZ:00005279]", - "Senegal [GAZ:00000913]", - "Serbia [GAZ:00002957]", - "Seychelles [GAZ:00006922]", - "Sierra Leone [GAZ:00000914]", - "Singapore [GAZ:00003923]", - "Sint Maarten [GAZ:00012579]", - "Slovakia [GAZ:00002956]", - "Slovenia [GAZ:00002955]", - "Solomon Islands [GAZ:00005275]", - "Somalia [GAZ:00001104]", - "South Africa [GAZ:00001094]", - "South Georgia and the South Sandwich Islands [GAZ:00003990]", - "South Korea [GAZ:00002802]", - "South Sudan [GAZ:00233439]", - "Spain [GAZ:00003936]", - "Spratly Islands [GAZ:00010831]", - "Sri Lanka [GAZ:00003924]", - "State of Palestine [GAZ:00002475]", - "Sudan [GAZ:00000560]", - "Suriname [GAZ:00002525]", - "Svalbard [GAZ:00005396]", - "Swaziland [GAZ:00001099]", - "Sweden [GAZ:00002729]", - "Switzerland [GAZ:00002941]", - "Syria [GAZ:00002474]", - "Taiwan [GAZ:00005341]", - "Tajikistan [GAZ:00006912]", - "Tanzania [GAZ:00001103]", - "Thailand [GAZ:00003744]", - "Timor-Leste [GAZ:00006913]", - "Togo [GAZ:00000915]", - "Tokelau [GAZ:00260188]", - "Tonga [GAZ:00006916]", - "Trinidad and Tobago [GAZ:00003767]", - "Tromelin Island [GAZ:00005812]", - "Tunisia [GAZ:00000562]", - "Turkey [GAZ:00000558]", - "Turkmenistan [GAZ:00005018]", - "Turks and Caicos Islands [GAZ:00003955]", - "Tuvalu [GAZ:00009715]", - "USA [GAZ:00002459]", - "Uganda [GAZ:00001102]", - "Ukraine [GAZ:00002724]", - "United Arab Emirates [GAZ:00005282]", - "United Kingdom [GAZ:00002637]", - "Uruguay [GAZ:00002930]", - "Uzbekistan [GAZ:00004979]", - "Vanuatu [GAZ:00006918]", - "Venezuela [GAZ:00002931]", - "Viet Nam [GAZ:00003756]", - "Virgin Islands [GAZ:00003959]", - "Wake Island [GAZ:00007111]", - "Wallis and Futuna [GAZ:00007191]", - "West Bank [GAZ:00009572]", - "Western Sahara [GAZ:00000564]", - "Yemen [GAZ:00005284]", - "Zambia [GAZ:00001107]", - "Zimbabwe [GAZ:00001106]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001181", - "type": "string", - "description": "The country of origin of the sample.", - "examples": ["South Africa [GAZ:00001094]"] - }, - "geo_loc_state": { - "examples": ["Western Cape"], - "ontology": "GENEPIO:0001185", - "type": "string", - "description": "The state/province/territory of origin of the sample." - }, - "organism": { - "Enums": [ - "Coronaviridae [NCBITaxon:11118]", - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001191", - "type": "string", - "description": "Taxonomic name of the organism.", - "examples": [ - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]" - ] - }, - "isolate": { - "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"], - "ontology": "GENEPIO:0001644", - "type": "string", - "description": "Identifier of the specific isolate.", - "clasification":"Sample collection and processing" - }, - "purpose_sampling": { - "examples": ["Diagnostic testing"], - "ontology": "NCIT_C146997", - "type": "string", - "description": "The reason that the sample was collected.", - "clasification":"Sample collection and processing" - }, - "host_scientific_name": { - "Enums": [ - "Bos taurus [NCBITaxon:9913]", - "Canis lupus familiaris [NCBITaxon:9615]", - "Chiroptera [NCBITaxon:9397]", - "Columbidae [NCBITaxon:8930]", - "Felis catus [NCBITaxon:9685]", - "Gallus gallus [NCBITaxon:9031]", - "Homo sapiens [NCBITaxon:9606]", - "Manis [NCBITaxon:9973]", - "Manis javanica [NCBITaxon:9974]", - "Neovison vison [NCBITaxon:452646]", - "Panthera leo [NCBITaxon:9689]", - "Panthera tigris [NCBITaxon:9694]", - "Rhinolophidae [NCBITaxon:58055]", - "Rhinolophus affinis [NCBITaxon:59477]", - "Sus scrofa domesticus [NCBITaxon:9825]", - "Viverridae [NCBITaxon:9673]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001387", - "type": "string", - "description": "The taxonomic, or scientific name of the host.", - "examples": ["Homo sapiens [NCBITaxon:9606]"] - }, - "host_health_state": { - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Health status of the host at the time of sample collection.", - }, - "host_gender": { - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Gender or sex of the host.", - }, - "host_subject_id": { - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "a unique identifier by which each subject can be referred to, de-identified, e.g. #131", - }, - - "host_disease": { - "Enums": [ - "COVID-19 [MONDO:0100096]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001391", - "type": "string", - "description": "The name of the disease experienced by the host.", - "examples": ["COVID-19 [MONDO:0100096]"] - }, - "sequencing_instrument_model": { - "Enums": [ - "Illumina sequencing instrument [GENEPIO:0100105]", - "Illumina Genome Analyzer [GENEPIO:0100106]", - "Illumina Genome Analyzer II [GENEPIO:0100107]", - "Illumina Genome Analyzer IIx [GENEPIO:0100108]", - "Illumina HiScanSQ [GENEPIO:0100109]", - "Illumina HiSeq [GENEPIO:0100110]", - "Illumina HiSeq X [GENEPIO:0100111]", - "Illumina HiSeq X Five [GENEPIO:0100112]", - "Illumina HiSeq X Ten [GENEPIO:0100113]", - "Illumina HiSeq 1000 [GENEPIO:0100114]", - "Illumina HiSeq 1500 [GENEPIO:0100115]", - "Illumina HiSeq 2000 [GENEPIO:0100116]", - "Illumina HiSeq 2500 [GENEPIO:0100117]", - "Illumina HiSeq 3000 [GENEPIO:0100118]", - "Illumina HiSeq 4000 [GENEPIO:0100119]", - "Illumina iSeq [GENEPIO:0100120]", - "Illumina iSeq 100 [GENEPIO:0100121]", - "Illumina NovaSeq [GENEPIO:0100122]", - "Illumina NovaSeq 6000 [GENEPIO:0100123]", - "Illumina MiniSeq [GENEPIO:0100124]", - "Illumina MiSeq [GENEPIO:0100125]", - "Illumina NextSeq [GENEPIO:0100126]", - "Illumina NextSeq 500 [GENEPIO:0100127]", - "Illumina NextSeq 550 [GENEPIO:0100128]", - "Illumina NextSeq 2000 [GENEPIO:0100129]", - "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", - "PacBio RS [GENEPIO:0100131]", - "PacBio RS II [GENEPIO:0100132]", - "PacBio Sequel [GENEPIO:0100133]", - "PacBio Sequel II [GENEPIO:0100134]", - "Ion Torrent sequencing instrument [GENEPIO:0100135]", - "Ion Torrent PGM [GENEPIO:0100136]", - "Ion Torrent Proton [GENEPIO:0100137]", - "Ion Torrent S5 XL [GENEPIO:0100138]", - "Ion Torrent S5 [GENEPIO:0100139]", - "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", - "Oxford Nanopore GridION [GENEPIO:0100141]", - "Oxford Nanopore MinION [GENEPIO:0100142]", - "Oxford Nanopore PromethION [GENEPIO:0100143]", - "BGI Genomics sequencing instrument [GENEPIO:0100144]", - "BGI SEQ-500 [GENEPIO:0100145]", - "MGI sequencing instrument [GENEPIO:0100146]", - "MGI DNBSEQ-T7 [GENEPIO:0100147]", - "MGI DNBSEQ-G400 [GENEPIO:0100148]", - "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", - "MGI DNBSEQ-G50 [GENEPIO:0100150]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001452", - "type": "string", - "description": "The model of the sequencing instrument used.", - "examples": ["Oxford Nanopore MinION [GENEPIO:0100142]"] - }, - "sequencing_instrument_platform": { - "examples": ["MinIon"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The model of the sequencing instrument used." - }, - "consensus_sequence_software_name": { - "examples": ["Ivar"], - "ontology": "GENEPIO:0001463", - "type": "string", - "description": "The name of software used to generate the consensus sequence." - }, - "consensus_sequence_software_version": { - "examples": ["1.3"], - "ontology": "GENEPIO:0001469", - "type": "string", - "description": "The version of the software used to generate the consensus sequence." - }, - "submitting_lab_sequence_id": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Sample ID given by the submitting laboratory" - }, - "bioproject_umbrella_accession_ENA": { - "examples": ["PRJNA623807"], - "ontology": "GENEPIO:0001133", - "type": "string", - "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", - "clasification":"Database Identifiers" - }, - "bioproject_accession_ENA": { - "examples": ["PRJNA12345"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", - "clasification":"Database Identifiers" - }, - "biosample_accession_ENA": { - "examples": ["SAMN14180202"], - "ontology": "GENEPIO:0001139", - "type": "string", - "description": "The identifier assigned to a BioSample in INSDC archives.", - "clasification":"Database Identifiers" - }, - "sra_accession": { - "examples": ["SRR11177792"], - "ontology": "GENEPIO:0001142", - "type": "string", - "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "clasification":"Database Identifiers" - }, - "genBank/ENA/DDBJ_accession": { - "examples": ["MN908947.3"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", - "clasification":"Database Identifiers" - }, - "gisaid_accession": { - "examples": ["EPI_ISL_123456"], - "ontology": "GENEPIO:0001147", - "type": "string", - "description": "The GISAID accession number assigned to the sequence.", - "clasification":"Database Identifiers" - }, - "virus_name": { - "examples": ["hCoV-19/Canada/prov_rona_99/2020"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The user-defined GISAID virus name assigned to the sequence.", - "clasification":"Database Identifiers" - }, - "collecting_institution_email": { - "examples": ["johnnyblogs@lab.ca"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The email address of the contact responsible for follow-up regarding the sample.", - "clasification":"Sample collection and processing" - }, - "collecting_institution_address": { - "examples": ["655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada"], - "ontology": "GENEPIO:0001158", - "type": "string", - "description": "The mailing address of the agency submitting the sample.", - "clasification":"Sample collection and processing" - }, - "submitting_institution_email": { - "examples": ["RespLab@lab.ca"], - "ontology": "GENEPIO:0001165", - "type": "string", - "description": "The email address of the contact responsible for follow-up regarding the sequence.", - "clasification":"Sample collection and processing" - }, - "submitting_institution_address": { - "examples": ["123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The mailing address of the agency submitting the sequence.", - "clasification":"Sample collection and processing" - }, - "sample_received_date": { - "examples": ["3/21/2020"], - "ontology": "GENEPIO:0001179", - "type": "string", - "description": "The date on which the sample was received.", - "format":"date", - "clasification":"Sample collection and processing" - }, - "results_emission_date": { - "examples": ["3/23/2020"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The date on which the results were emitted.", - "format":"date", - "clasification":"Sample collection and processing" - }, - "geo_loc_region": { - "examples": ["Derbyshire"], - "ontology": "GENEPIO:0100280", - "type": "string", - "description": "The county/region of origin of the sample.", - "clasification":"Sample collection and processing" - }, - "geo_loc_city": { - "examples": ["Vancouver"], - "ontology": "GENEPIO:0001189", - "type": "string", - "description": "The city of origin of the sample.", - "clasification":"Sample collection and processing" - }, - "geo_loc_latitude": { - "examples": ["38.98 N"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The latitude coordinates of the geographical location of sample collection.", - "clasification":"Sample collection and processing" - }, - "geo_loc_longitude": { - "examples": ["77.11 W"], - "ontology": "OBI:0001621", - "type": "string", - "description": "The longitude coordinates of the geographical location of sample collection.", - "clasification":"Sample collection and processing" - }, - "anatomical_material": { - "Enums": [ - "Blood [UBERON:0000178]", - "Fluid [UBERON:0006314]", - "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", - "Fluid (Pericardial) [UBERON:0002409]", - "Fluid (Pleural) [UBERON:0001087]", - "Fluid (Vaginal) [UBERON:0036243]", - "Fluid (Amniotic) [UBERON:0000173]", - "Saliva [UBERON:0001836]", - "Tissue [UBERON:0000479]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001211", - "type": "string", - "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "examples": ["Blood [UBERON:0000178]"] - }, - "anatomical_part": { - "Enums": [ - "Anus [UBERON:0001245]", - "Duodenum [UBERON:0002114]", - "Eye [UBERON:0000970]", - "Intestine [UBERON:0000160]", - "Lower respiratory tract [UBERON:0001558]", - "Bronchus [UBERON:0002185]", - "Lung [UBERON:0002048]", - "Bronchiole [UBERON:0002186]", - "Alveolar sac [UBERON:0002169]", - "Pleural sac [UBERON:0009778]", - "Pleural cavity [UBERON:0002402]", - "Trachea [UBERON:0003126]", - "Rectum [UBERON:0001052]", - "Skin [UBERON:0001003]", - "Stomach [UBERON:0000945]", - "Upper respiratory tract [UBERON:0001557]", - "Anterior Nares [UBERON:2001427]", - "Esophagus [UBERON:0001043]", - "Ethmoid sinus [UBERON:0002453]", - "Nasal Cavity [UBERON:0001707]", - "Middle Nasal Turbinate [UBERON:0005921]", - "Inferior Nasal Turbinate [UBERON:0005922]", - "Nasopharynx (NP) [UBERON:0001728]", - "Oropharynx (OP) [UBERON:0001729]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001214", - "type": "string", - "description": "An anatomical part of an organism e.g. oropharynx. ", - "examples": ["Nasopharynx (NP) [UBERON:0001728]"] - }, - "body_product": { - "Enums": [ - "Breast Milk [UBERON:0001913]", - "Feces [UBERON:0001988]", - "Mucus [UBERON:0000912]", - "Semen [UBERON:0006530]", - "Sputum [UBERON:0007311]", - "Sweat [UBERON:0001089]", - "Tear [UBERON:0001827]", - "Urine [UBERON:0001088]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001216", - "type": "string", - "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", - "examples": ["Feces [UBERON:0001988]"] - }, - "environmental_material": { - "Enums": [ - "Air vent [ENVO:03501208]", - "Banknote [ENVO:00003896]", - "Bed rail [ENVO:03501209]", - "Building Floor [ENVO:01000486]", - "Cloth [ENVO:02000058]", - "Control Panel [ENVO:03501210]", - "Door [ENVO:03501220]", - "Door Handle [ENVO:03501211]", - "Face Mask [OBI:0002787]", - "Face Shield [OBI:0002791]", - "Food [FOODON:00002403]", - "Food Packaging [FOODON:03490100]", - "Glass [ENVO:01000481]", - "Handrail [ENVO:03501212]", - "Hospital Gown [OBI:0002796]", - "Light Switch [ENVO:03501213]", - "Locker [ENVO:03501214]", - "N95 Mask [OBI:0002790]", - "Nurse Call Button [ENVO:03501215]", - "Paper [ENVO:03501256]", - "Particulate Matter [ENVO:01000060]", - "Plastic [ENVO:01000404]", - "PPE Gown [GENEPIO:0100025]", - "Sewage [ENVO:00002018]", - "Sink [ENVO:01000990]", - "Soil [ENVO:00001998]", - "Stainless Steel [ENVO:03501216]", - "Tissue Paper [ENVO:03501217]", - "Toilet Bowl [ENVO:03501218]", - "Water [ENVO:00002006]", - "Wastewater [ENVO:00002001]", - "Window [ENVO:03501219]", - "Wood [ENVO:00002040]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001223", - "type": "string", - "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", - "examples": ["Face Mask [OBI:0002787]"] - }, - "environmental_site": { - "Enums": [ - "Acute care facility [ENVO:03501135]", - "Animal house [ENVO:00003040]", - "Bathroom [ENVO:01000422]", - "Clinical assessment centre [ENVO:03501136]", - "Conference venue [ENVO:03501127]", - "Corridor [ENVO:03501121]", - "Daycare [ENVO:01000927]", - "Emergency room (ER) [ENVO:03501145]", - "Family practice clinic [ENVO:03501186]", - "Group home [ENVO:03501196]", - "Homeless shelter [ENVO:03501133]", - "Hospital [ENVO:00002173]", - "Intensive Care Unit (ICU) [ENVO:03501152]", - "Long Term Care Facility [ENVO:03501194]", - "Patient room [ENVO:03501180]", - "Prison [ENVO:03501204]", - "Production Facility [ENVO:01000536]", - "School [ENVO:03501130]", - "Sewage Plant [ENVO:00003043]", - "Subway train [ENVO:03501109]", - "Wet market [ENVO:03501198]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001232", - "type": "string", - "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", - "examples": ["Hospital [ENVO:00002173]"] - }, - "collection_device": { - "Enums": [ - "Air filter [ENVO:00003968]", - "Blood Collection Tube [OBI:0002859]", - "Bronchoscope [OBI:0002826]", - "Collection Container [OBI:0002088]", - "Collection Cup [GENEPIO:0100026]", - "Fibrobronchoscope Brush [OBI:0002825]", - "Filter [GENEPIO:0100103]", - "Fine Needle [OBI:0002827]", - "Microcapillary tube [OBI:0002858]", - "Micropipette [OBI:0001128]", - "Needle [OBI:0000436]", - "Serum Collection Tube [OBI:0002860]", - "Sputum Collection Tube [OBI:0002861]", - "Suction Catheter [OBI:0002831]", - "Swab [GENEPIO:0100027]", - "Urine Collection Tube [OBI:0002862]", - "Virus Transport Medium [OBI:0002866]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001234", - "type": "string", - "description": "The instrument or container used to collect the sample e.g. swab.", - "examples": ["Swab [GENEPIO:0100027]"] - }, - "collection_method": { - "Enums": [ - "Amniocentesis [NCIT:C52009]", - "Aspiration [NCIT:C15631]", - "Suprapubic Aspiration [GENEPIO:0100028]", - "Tracheal Aspiration [GENEPIO:0100029]", - "Vacuum Aspiration [GENEPIO:0100030]", - "Biopsy [OBI:0002650]", - "Needle Biopsy [OBI:0002651]", - "Filtration [OBI:0302885]", - "Air Filtration [GENEPIO:0100031]", - "Lavage [OBI:0600044]", - "Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]", - "Gastric Lavage [GENEPIO:0100033]", - "Lumbar Puncture [NCIT:C15327]", - "Necropsy [MMO:0000344]", - "Phlebotomy [NCIT:C28221]", - "Rinsing [GENEPIO:0002116]", - "Saline gargle (mouth rinse and gargle) [GENEPIO:0100034]", - "Scraping [GENEPIO:0100035]", - "Swabbing [GENEPIO:0002117]", - "Finger Prick [GENEPIO:0100036]", - "Washout Tear Collection [GENEPIO:0100038]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001241", - "type": "string", - "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", - "examples": ["Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]"] - }, - "collection_protocol": { - "examples": ["SC2SamplingProtocol 1.2"], - "ontology": "GENEPIO:0001243", - "type": "string", - "description": "Conditions at which sample was stored, usually storage temperature, duration and location", - "clasification":"Sample collection and processing" - }, - "sample_storage_conditions": { - "examples": ["24 degrees celsius"], - "ontology": "NCIT_C115535", - "type": "string", - "description": "The name and version of a particular protocol used for sampling.", - "clasification":"Sample collection and processing" - }, - "specimen_processing": { - "Enums": [ - "Virus Passage [GENEPIO:0100039]", - "RNA Re-Extraction (Post RT-PCR) [GENEPIO:0100040]", - "Specimens Pooled [OBI:0600016]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001253", - "type": "string", - "description": "Any processing applied to the sample during or after receiving the sample. ", - "examples": ["Virus Passage [GENEPIO:0100039]"] - }, - "lab_host": { - "Enums": [ - "293/ACE2 Cell Line [GENEPIO:0100041]", - "Caco2 Cell Line [BTO:0000195]", - "Calu3 Cell Line [BTO:0002750]", - "EFK3B Cell Line [GENEPIO:0100042]", - "HEK293T Cell Line [BTO:0002181]", - "HRCE Cell Line [GENEPIO:0100043]", - "Huh7 Cell Line [BTO:0001950]", - "LLCMk2 Cell Line [CLO:0007330]", - "MDBK Cell Line [BTO:0000836]", - "NHBE Cell Line [BTO:0002924]", - "PK-15 Cell Line [BTO:0001865]", - "RK-13 Cell Line [BTO:0002909]", - "U251 Cell Line [BTO:0002035]", - "Vero Cell Line [BTO:0001444]", - "Vero E6 Cell Line [BTO:0004755]", - "Vero E6/TMPRSS2 Cell Line [GENEPIO:0100044]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001255", - "type": "string", - "description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.", - "examples": ["Vero E6 Cell Line [BTO:0004755]"] - }, - "passage_number": { - "examples": ["3"], - "ontology": "GENEPIO:0001261", - "type": "string", - "description": "Number of passages.", - "clasification":"Sample collection and processing" - }, - "passage_method": { - "examples": ["AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain."], - "ontology": "GENEPIO:0001264", - "type": "string", - "description": "Description of how organism was passaged.", - "clasification":"Sample collection and processing" - }, - "biomaterial_extracted": { - "Enums": [ - "mRNA (cDNA) [OBI:0002754]", - "RNA (Total) [OBI:0000895]", - "RNA (Poly-A) [OBI:0000869]", - "RNA (Ribo-Depleted) [OBI:0002627]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001266", - "type": "string", - "description": "The biomaterial extracted from samples for the purpose of sequencing.", - "examples": ["RNA (Total) [OBI:0000895]"] - }, - "tax_id": { - "examples": ["probably 2697049 in all cases"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The NCBITaxon identifier for the organism being sequenced.", - "clasification":"Sample collection and processing" - }, - "scientific_name": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The taxonomic name of the organism.", - "clasification":"Sample collection and processing" - }, - "common_name": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The common name of the organism.", - "clasification":"Sample collection and processing" - }, - "sample_description": { - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Free text description of the sample.", - "clasification":"Sample collection and processing" - }, - - "center_name": { - "examples": [" KAROLINSKA INSITUTET"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The name of the institution", - "clasification":"Sample collection and processing" - }, - - "virus_id": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The user-defined name for the sample.", - "clasification":"Database Identifiers" - }, - "host_common_name": { - "Enums": [ - "Human [NCBITaxon:9606]", - "Bat [NCBITaxon:9397]", - "Cat [NCBITaxon:9685]", - "Chicken [NCBITaxon:9031]", - "Civet [NCBITaxon:9673]", - "Cow [NCBITaxon:9913]", - "Dog [NCBITaxon:9615]", - "Lion [NCBITaxon:9689]", - "Mink [NCBITaxon:452646]", - "Pangolin [NCBITaxon:9973]", - "Pig [NCBITaxon:9825]", - "Pigeon [NCBITaxon:8930]", - "Tiger [NCBITaxon:9694]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001386", - "type": "string", - "description": "The commonly used name of the host.", - "examples": ["Human [NCBITaxon:9606]"] - }, - "outbreak": { - "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information" - }, - "additional_host_information": { - "examples": ["e.g. Patient infected while traveling in …."], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information" - }, - "host_age": { - "examples": ["e.g. 65 or 7 months, or unknown. Caution: the host age may be considered public health identifiable information. Consult the data steward before sharing. If the information is unknown or can not be shared, put unknown"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Patient age", - "clasification":"Host information" - }, - "host_age_unit": { - "examples": ["years"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The units used to measure the host's age.", - "clasification":"Host information" - }, - "host_age_bin": { - "examples": ["20-30"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The age category of the host at the time of sampling.", - "clasification":"Host information" - }, - "host_gender": { - "examples": ["Male, Female, or unknown.Caution: the host gender may be considered public health identifiable information. Consult the data steward before sharing. If the information is unknown or can not be shared, put unknown"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Gender", - "clasification":"Host information" - }, - "purpose_of_sequencing": { - "Enums": [ - "Baseline surveillance (random sampling) [GENEPIO:0100005]", - "Targeted surveillance (non-random sampling) [GENEPIO:0100006]", - "Priority surveillance projects [GENEPIO:0100007]", - "Screening for Variants of Concern (VOC) [GENEPIO:0100008]", - "Sample has epidemiological link to Variant of Concern (VoC) [GENEPIO:0100273]", - "Sample has epidemiological link to Omicron Variant [GENEPIO:0100274]", - "Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]", - "Re-infection surveillance [GENEPIO:0100010]", - "Vaccine escape surveillance [GENEPIO:0100011]", - "Travel-associated surveillance [GENEPIO:0100012]", - "Domestic travel surveillance [GENEPIO:0100013]", - "Interstate/ interprovincial travel surveillance [GENEPIO:0100275]", - "Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276]", - "International travel surveillance [GENEPIO:0100014]", - "Surveillance of international border crossing by air travel or ground transport [GENEPIO:0100015]", - "Surveillance of international border crossing by air travel [GENEPIO:0100016]", - "Surveillance of international border crossing by ground transport [GENEPIO:0100017]", - "Surveillance from international worker testing [GENEPIO:0100018]", - "Cluster/Outbreak investigation [GENEPIO:0100019]", - "Multi-jurisdictional outbreak investigation [GENEPIO:0100020]", - "Intra-jurisdictional outbreak investigation [GENEPIO:0100021]", - "Research [GENEPIO:0100022]", - "Viral passage experiment [GENEPIO:0100023]", - "Protocol testing [GENEPIO:0100024]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001445", - "type": "string", - "description": "The reason that the sample was sequenced.", - "examples": ["Baseline surveillance (random sampling) [GENEPIO:0100005]"] - }, - "purpose_of_sequencing_details": { - "Enums": [ - "Screened for S gene target failure (S dropout)", - "Screened for mink variants", - "Screened for B.1.1.7 variant", - "Screened for B.1.135 variant", - "Screened for P.1 variant", - "Screened due to travel history", - "Screened due to close contact with infected individual", - "Assessing public health control measures", - "Determining early introductions and spread", - "Investigating airline-related exposures", - "Investigating temporary foreign worker", - "Investigating remote regions", - "Investigating health care workers", - "Investigating schools/universities", - "Investigating reinfection" - ], - "ontology": "GENEPIO:0001446", - "type": "string", - "description": "The description of why the sample was sequenced providing specific details.", - "examples": ["Screened for S gene target failure (S dropout)"] - }, - "sequencing_date": { - "examples": ["4/26/2021"], - "ontology": "GENEPIO:0001447", - "type": "string", - "description": "The date the sample was sequenced.", - "format":"date", - "clasification":"Sequencing" - }, - "rna_extraction_Protocol": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - "library_kit": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - "library_name": { - "examples": ["e.g P17157_1007"], - "ontology": "GENEPIO_0001995", - "type": "string", - "description": "The submitter's name for this library.", - "clasification":"Sequencing", - "genepio_label":"Library Name", - }, - "enrichment_protocol": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - "if_enrichment_protocol_is_other_specify": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - "amplicon protocol": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - "if_amplicon_protocol_if_other_especify": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - - "amplicon_version": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - "amplicon_size": { - "examples": ["300bp"], - "ontology": "GENEPIO:0001449", - "type": "string", - "description": "The length of the amplicon generated by PCR amplification.", - "clasification":"Sequencing" - }, - - "was_phix_used?": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - - "number_of_samples_in_run": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - - "flowcell_kit": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - - "runID": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - - "sequencing_platforms": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - - "library_preparation_kit": { - "examples": ["Nextera XT"], - "ontology": "GENEPIO:0001450", - "type": "string", - "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", - "clasification":"Sequencing" - }, - - "flow_cell_barcode": { - "examples": ["FAB06069"], - "ontology": "GENEPIO:0001451", - "type": "string", - "description": "The barcode of the flow cell used for sequencing.", - "clasification":"Sequencing" - }, - "sequencing_protocol_name": { - "examples": ["1D_DNA_MinION, ARTIC Network Protocol V3"], - "ontology": "GENEPIO:0001453", - "type": "string", - "description": "The name and version number of the sequencing protocol used.", - "clasification":"Sequencing" - }, - "sequencing_protocol": { - "examples": ["Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits."], - "ontology": "GENEPIO:0001454", - "type": "string", - "description": "The protocol used to generate the sequence.", - "clasification":"Sequencing" - }, - "sequencing_kit_number": { - "examples": ["AB456XYZ789"], - "ontology": "GENEPIO:0001455", - "type": "string", - "description": "The manufacturer's kit number.", - "clasification":"Sequencing" - }, - "amplicon_pcr_primer_scheme": { - "examples": ["https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv"], - "ontology": "GENEPIO:0001456", - "type": "string", - "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", - "clasification":"Sequencing" - }, - "library_source": { - "examples": ["METAGENOMIC"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Molecule type used to make the library.", - "clasification":"Sequencing" - }, - "library_selection": { - "examples": ["RANDOM PCR"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Library capture method.", - "clasification":"Sequencing" - }, - "library_strategy": { - "examples": ["WGS"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Overall sequencing strategy or approach.", - "clasification":"Sequencing" - }, - "library_layout": { - "examples": ["PAIRED"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Single or paired.", - "clasification":"Sequencing" - }, - "library_name": { - "examples": ["P17157_1007"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Name of the used library", - "clasification":"Sequencing" - }, - "nominal_length ": { - "examples": ["350"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - - "raw_sequence_data_processing_method": { - "examples": ["Porechop 0.2.3"], - "ontology": "GENEPIO:0001458", - "type": "string", - "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", - "clasification":"Bioinformatics and QC metrics" - }, - "dehosting_method": { - "examples": ["Nanostripper"], - "ontology": "GENEPIO:0001459", - "type": "string", - "description": "The method used to remove host reads from the pathogen sequence.", - "clasification":"Bioinformatics and QC metrics" - }, - "assembly": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics" - }, - "if_assembly_other": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics" - }, - "assembly_params": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics" - }, - "variant_Calling": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics" - }, - "if_variant_Calling_other": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics" - }, - "variant_Calling_params": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics" - }, - "consensus_sequence_filepath": { - "examples": ["/User/Documents/RespLab/Data/ncov123assembly.fasta"], - "ontology": "GENEPIO:0001462", - "type": "string", - "description": "The filepath of the consesnsus sequence file.", - "clasification":"Bioinformatics and QC metrics" - }, - "consensus_sequence_software_name": { - "examples": ["Ivar"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The name of software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics" - }, - "if_consensus_other": { - "examples": ["1.3"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The version of the software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics" - }, - "consensus_sequence_software_version": { - "examples": ["1.3"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The version of the software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics" - }, - "consensus_criteria": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics" - }, - "quality_control_metrics": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics" - }, - "breadth_of_coverage_value": { - "examples": ["95%"], - "ontology": "GENEPIO:0001472", - "type": "string", - "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", - "clasification":"Bioinformatics and QC metrics" - }, - "depth_of_coverage_value": { - "examples": ["400x"], - "ontology": "GENEPIO:0001474", - "type": "string", - "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "clasification":"Bioinformatics and QC metrics" - }, - "depth_of_coverage_threshold": { - "examples": ["100x"], - "ontology": "GENEPIO:0001475", - "type": "string", - "description": "The threshold used as a cut-off for the depth of coverage.", - "clasification":"Bioinformatics and QC metrics" - }, - "sequence_file_R1_fastq": { - "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], - "ontology": "GENEPIO:0001476", - "type": "string", - "description": "The user-specified filename of the r1 FASTQ file.", - "clasification":"Bioinformatics and QC metrics" - }, - "sequence_file_R2_fastq": { - "examples": ["ABC123_S1_L001_R2_001.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The user-specified filename of the r2 FASTQ file.", - "clasification":"Bioinformatics and QC metrics" - }, - "r1_fastq_filepath": { - "examples": ["/User/Documents/RespLab/Data/"], - "ontology": "GENEPIO:0001478", - "type": "string", - "description": "The filepath of the r1 FASTQ file.", - "clasification":"Bioinformatics and QC metrics" - }, - "r2_fastq_filepath": { - "examples": ["/User/Documents/RespLab/Data/"], - "ontology": "GENEPIO:0001479", - "type": "string", - "description": "The filepath of the r2 FASTQ file.", - "clasification":"Bioinformatics and QC metrics" - }, - "fast5_filename": { - "examples": ["batch1a_sequences.fast5"], - "ontology": "GENEPIO:0001480", - "type": "string", - "description": "The user-specified filename of the FAST5 file.", - "clasification":"Bioinformatics and QC metrics" - }, - "fast5_filepath": { - "examples": ["/User/Documents/RespLab/Data/"], - "ontology": "GENEPIO:0001481", - "type": "string", - "description": "The filepath of the FAST5 file.", - "clasification":"Bioinformatics and QC metrics" - }, - "number_of_base_pairs_sequenced": { - "examples": ["387566"], - "ontology": "GENEPIO:0001482", - "type": "string", - "description": "The number of total base pairs generated by the sequencing process.", - "clasification":"Bioinformatics and QC metrics" - }, - "consensus_genome_length": { - "examples": ["38677"], - "ontology": "GENEPIO:0001483", - "type": "string", - "description": "Size of the assembled genome described as the number of base pairs.", - "clasification":"Bioinformatics and QC metrics" - }, - "ns_per_100_kbp": { - "examples": ["300"], - "ontology": "GENEPIO:0001484", - "type": "string", - "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", - "clasification":"Bioinformatics and QC metrics" - }, - "reference_genome_accession": { - "examples": ["NC_045512.2"], - "ontology": "GENEPIO:0001485", - "type": "string", - "description": "A persistent, unique identifier of a genome database entry.", - "clasification":"Bioinformatics and QC metrics" - }, - "bioinformatics_protocol": { - "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], - "ontology": "GENEPIO:0001489", - "type": "string", - "description": "The name of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics" - }, - "if_bioinformatic_protocol_is_other_specify": { - "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The name of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics" - }, - "bioinformatic_protocol_version": { - "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The version number of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics" - }, - "commercial/open-source/both": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics" - }, - "preprocessing": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics" - }, - "if_preprocessing_other": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics" - }, - "preprocessing_params": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics" - }, - "mapping": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Lineage and Variant information" - }, - "if_mapping_other": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Lineage and Variant information" - }, - "Mapping_params": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Lineage and Variant information" - }, - "lineage/clade_name": { - "examples": ["B.1.1.7"], - "ontology": "GENEPIO:0001500", - "type": "string", - "description": "The name of the lineage or clade.", - "clasification":"Lineage and Variant information" - }, - "lineage/clade_analysis_software_name": { - "examples": ["Pangolin"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The name of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information" - }, - "if_lineage_identification_other": { - "examples": ["Other than Pangolin"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The name of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information" - }, - "lineage/clade_analysis_software_version": { - "examples": ["2.1.10"], - "ontology":"GENEPIO:0001502", - "type": "string", - "description": "The version of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information" - }, - "variant_designation": { - "Enums": [ - "Variant of Interest (VOI) [GENEPIO:0100082]", - "Variant of Concern (VOC) [GENEPIO:0100083]", - "Variant Under Monitoring (VUM) [GENEPIO:0100279]" - ], - "ontology": "GENEPIO:0001503", - "type": "string", - "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", - "examples": ["Variant of Concern (VOC) [GENEPIO:0100083]"] - }, - "variant_evidence": { - "examples": ["lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)"], - "ontology": "GENEPIO:0001504", - "type": "string", - "description": "The evidence used to make the variant determination.", - "clasification":"Lineage and Variant information" - }, - "gene_name_1": { - "Enums": [ - "E gene (orf4) [GENEPIO:0100151]", - "M gene (orf5) [GENEPIO:0100152]", - "N gene (orf9) [GENEPIO:0100153]", - "Spike gene (orf2) [GENEPIO:0100154]", - "orf1ab (rep) [GENEPIO:0100155]", - "orf1a (pp1a) [GENEPIO:0100156]", - "nsp11 [GENEPIO:0100157]", - "nsp1 [GENEPIO:0100158]", - "nsp2 [GENEPIO:0100159]", - "nsp3 [GENEPIO:0100160]", - "nsp4 [GENEPIO:0100161]", - "nsp5 [GENEPIO:0100162]", - "nsp6 [GENEPIO:0100163]", - "nsp7 [GENEPIO:0100164]", - "nsp8 [GENEPIO:0100165]", - "nsp9 [GENEPIO:0100166]", - "nsp10 [GENEPIO:0100167]", - "RdRp gene (nsp12) [GENEPIO:0100168]", - "hel gene (nsp13) [GENEPIO:0100169]", - "exoN gene (nsp14) [GENEPIO:0100170]", - "nsp15 [GENEPIO:0100171]", - "nsp16 [GENEPIO:0100172]", - "orf3a [GENEPIO:0100173]", - "orf3b [GENEPIO:0100174]", - "orf6 (ns6) [GENEPIO:0100175]", - "orf7a [GENEPIO:0100176]", - "orf7b (ns7b) [GENEPIO:0100177]", - "orf8 (ns8) [GENEPIO:0100178]", - "orf9b [GENEPIO:0100179]", - "orf9c [GENEPIO:0100180]", - "orf10 [GENEPIO:0100181]", - "orf14 [GENEPIO:0100182]", - "SARS-COV-2 5' UTR [GENEPIO:0100183]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001507", - "type": "string", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "examples": ["E gene (orf4) [GENEPIO:0100151]"] - }, - "Protocol_SARS-CoV-2_detection": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing" - }, - "%qc_filtered": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing" - }, - "%reads_host": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing" - }, - "%reads_virus": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing" - }, - "%unmapped": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing" - }, - "% genome _greater_10x": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing" - }, - "mean_depth_of_coverage_value": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing" - }, - "%Ns": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing" - }, - "Number_of_variants_(AF_greater_75%)": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing" - }, - "Numer_of_variants_with_effect": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing" - }, - "reference_genome_accession": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing" - }, - "diagnostic_pcr_protocol_1": { - "examples": ["PCREGene 2.0"], - "ontology": "GENEPIO:0001508", - "type": "string", - "description": "The name and version number of the protocol used for diagnostic marker amplification.", - "clasification":"Pathogen diagnostic testing" - }, - "diagnostic_pcr_Ct_value_1": { - "examples": ["21"], - "ontology": "GENEPIO:0001509", - "type": "string", - "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "clasification":"Pathogen diagnostic testing" - }, - "gene_name_2": { - "Enums": [ - "E gene (orf4) [GENEPIO:0100151]", - "M gene (orf5) [GENEPIO:0100152]", - "N gene (orf9) [GENEPIO:0100153]", - "Spike gene (orf2) [GENEPIO:0100154]", - "orf1ab (rep) [GENEPIO:0100155]", - "orf1a (pp1a) [GENEPIO:0100156]", - "nsp11 [GENEPIO:0100157]", - "nsp1 [GENEPIO:0100158]", - "nsp2 [GENEPIO:0100159]", - "nsp3 [GENEPIO:0100160]", - "nsp4 [GENEPIO:0100161]", - "nsp5 [GENEPIO:0100162]", - "nsp6 [GENEPIO:0100163]", - "nsp7 [GENEPIO:0100164]", - "nsp8 [GENEPIO:0100165]", - "nsp9 [GENEPIO:0100166]", - "nsp10 [GENEPIO:0100167]", - "RdRp gene (nsp12) [GENEPIO:0100168]", - "hel gene (nsp13) [GENEPIO:0100169]", - "exoN gene (nsp14) [GENEPIO:0100170]", - "nsp15 [GENEPIO:0100171]", - "nsp16 [GENEPIO:0100172]", - "orf3a [GENEPIO:0100173]", - "orf3b [GENEPIO:0100174]", - "orf6 (ns6) [GENEPIO:0100175]", - "orf7a [GENEPIO:0100176]", - "orf7b (ns7b) [GENEPIO:0100177]", - "orf8 (ns8) [GENEPIO:0100178]", - "orf9b [GENEPIO:0100179]", - "orf9c [GENEPIO:0100180]", - "orf10 [GENEPIO:0100181]", - "orf14 [GENEPIO:0100182]", - "SARS-COV-2 5' UTR [GENEPIO:0100183]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001510", - "type": "string", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "examples": ["RdRp gene (nsp12) [GENEPIO:0100168]"] - }, - "diagnostic_pcr_protocol_2": { - "examples": ["PCRRdRpGene 3.0"], - "ontology": "GENEPIO:0001511", - "type": "string", - "description": "The name and version number of the protocol used for diagnostic marker amplification.", - "clasification":"Pathogen diagnostic testing" - }, - "diagnostic_pcr_Ct_value_2": { - "examples": ["36"], - "ontology": "GENEPIO:0001512", - "type": "string", - "description": "The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "clasification":"Pathogen diagnostic testing" - }, - "analysis_author": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Contributor Acknowledgement" - }, - "author_submitter": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Contributor Acknowledgement" - }, - "submitter": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"enter your GISAID-Username" - }, - "authors": { - "examples": [""], - "ontology": "GENEPIO:0001517", - "type": "string", - "description": "", - "clasification":"Contributor Acknowledgement" - }, - "tax_id": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sample collection and processing" - }, - "scientific_name": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sample collection and processing" - }, - "common_name": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sample collection and processing" - }, - "library_source": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - "library_selection": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - "library_strategy": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - "library_layout": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - "library_name": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - "nominal_length": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - "analysis_accession": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "study_accession": { - "examples": ["e.g PRJEB39632"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "secondary_study_accession": { - "examples": ["e.g ERP123173"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "sample_accession": { - "examples": ["e.g SAMEA7098096"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "secondary_sample_accession": { - "examples": ["e.g ERS4858671"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "experiment_accession": { - "examples": ["e.g ERX4331406"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "run_accession": { - "examples": ["e.g ERX4331406"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "submission_accession": { - "examples": ["e.g ERA2794974"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "read_count": { - "examples": ["e.g 837055"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "read_length": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "base_count": { - "examples": ["e.g 503907110"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "first_public": { - "examples": ["e.g 2020-08-07"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "last_updated": { - "examples": ["e.g 2020-07-29"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "format":"date" - }, - "experiment_title": { - "examples": ["e.g Illumina MiSeq paired end sequencing"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "study_title": { - "examples": ["e.g SARS-CoV-2 genomes from late April in Stockholm"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "study_alias": { - "examples": ["e.g Sweden"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "experiment_alias": { - "examples": ["e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "run_alias": { - "examples": ["e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "fastq_bytes": { - "examples": ["e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "fastq_md5": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "fastq_ftp": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "fastq_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "fastq_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "submitted_bytes": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "submitted_md5": { - "examples": ["e.g 139853010;166270048"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "submitted_ftp": { - "examples": ["e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "submitted_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "submitted_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "submitted_format": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "sra_bytes": { - "examples": ["e.g FASTQ;FASTQ"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "sra_md5": { - "examples": ["e.g 260236789"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "sra_ftp": { - "examples": ["e.g 2cf0d467d6dc4ae0a5473774d54c059c"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "sra_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "sra_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "broker_name": { - "examples": ["P17157_1007"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "nominal_sdev": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "first_created": { - "examples": ["e.g 2020-08-07"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Submission ENA" - }, - "type": { - "examples": ["betacoronavirus"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "default must remain 'betacoronavirus'", - "clasification":"Database Identifiers" - } - } -} - - -ENA_schema.keys() - -properties = ENA_schema['properties'] - -properties_phage = phage_schema['properties'] - -phage_df = pd.DataFrame.from_dict(properties_phage) - -ENA_df = pd.DataFrame.from_dict(properties) - -ENA_df.columns - -ENA_df['geographic_location_(country_and/or_sea)']['Enums']; - -p_col = phage_df.columns -lista_phage = p_col.tolist() - -ENA_col = ENA_df.columns -lista_ENA = ENA_col.tolist() - -# + - -df = pd.DataFrame(lista_phage, columns = ['PHA4GE']) - -# + - -df_2 = pd.DataFrame(lista_ENA, columns = ['ENA']) -# - - -#result = pd.concat([df, df_2], axis=1) -#result = df.merge(df_2, left_on ='PHA4GE', right_on = "ENA") -#result = df.merge(df_2, left_on=None) -result = df.join(df_2) - -result - -phage_df - - From 11acbc638e90875038095c0f0619b47e14dbdc9e Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 1 Mar 2022 15:43:57 +0100 Subject: [PATCH 0047/1454] linting for main --- relecov_tools/__main__.py | 146 +++++++++++++++++++++++++++++--------- 1 file changed, 111 insertions(+), 35 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 263cd02c..d872692f 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -1,38 +1,58 @@ #!/usr/bin/env python -from click.types import File +# from click.types import File from rich import print -from rich.prompt import Confirm + +# from rich.prompt import Confirm import click import rich.console import rich.logging import rich.traceback -import sys + +# import sys import os import utils -#import nf_core + +# import nf_core # conda install -c conda-forge click # conda install -c conda-forge rich + def run_bu_isciii(): - # Set up rich stderr console + # Set up rich stderr console stderr = rich.console.Console(stderr=True, force_terminal=utils.rich_force_colors()) # Set up the rich traceback rich.traceback.install(console=stderr, width=200, word_wrap=True, extra_lines=1) # Print nf-core header - #stderr.print("\n[green]{},--.[grey39]/[green],-.".format(" " * 42), highlight=False) - stderr.print("[blue] ___ ___ ___ ___ ___ ___ ____ ", highlight=False) - stderr.print("[blue] \ |-[grey39]-| [blue] | \ | | | | | | | | ", highlight=False) - stderr.print("[blue] \ \ [grey39]/ [blue] |__ / | | ___ | |__ | | | | ", highlight=False) - stderr.print("[blue] / [grey39] / [blue] \ | \ | | | | | | | | ", highlight=False) - stderr.print("[blue] / [grey39] |-[blue]-| |__ / |___| _|__ ___| |___ _|_ _|_ _|_ ", highlight=False) - + # stderr.print("\n[green]{},--.[grey39]/[green],-.".format(" " * 42), highlight=False) + stderr.print( + "[blue] ___ ___ ___ ___ ___ ___ ____ ", + highlight=False, + ) + stderr.print( + "[blue] \ |-[grey39]-| [blue] | \ | | | | | | | | ", + highlight=False, + ) + stderr.print( + "[blue] \ \ [grey39]/ [blue] |__ / | | ___ | |__ | | | | ", + highlight=False, + ) + stderr.print( + "[blue] / [grey39] / [blue] \ | \ | | | | | | | | ", + highlight=False, + ) + stderr.print( + "[blue] / [grey39] |-[blue]-| |__ / |___| _|__ ___| |___ _|_ _|_ _|_ ", + highlight=False, + ) - #stderr.print("[green] `._,._,'\n", highlight=False) - __version__ = '0.0.1' - stderr.print("[grey39] BU-ISCIII-tools version {}".format(__version__), highlight=False) + # stderr.print("[green] `._,._,'\n", highlight=False) + __version__ = "0.0.1" + stderr.print( + "[grey39] BU-ISCIII-tools version {}".format(__version__), highlight=False + ) try: pass except: @@ -42,7 +62,6 @@ def run_bu_isciii(): bu_isciii_cli() - # Customise the order of subcommands for --help class CustomHelpOrder(click.Group): def __init__(self, *args, **kwargs): @@ -56,7 +75,13 @@ def get_help(self, ctx): def list_commands_for_help(self, ctx): """reorder the list of commands when listing the help""" commands = super(CustomHelpOrder, self).list_commands(ctx) - return (c[1] for c in sorted((self.help_priorities.get(command, 1000), command) for command in commands)) + return ( + c[1] + for c in sorted( + (self.help_priorities.get(command, 1000), command) + for command in commands + ) + ) def command(self, *args, **kwargs): """Behaves the same as `click.Group.command()` except capture @@ -74,19 +99,29 @@ def decorator(f): @click.group(cls=CustomHelpOrder) -#@click.version_option(nf_core.__version__) -@click.option("-v", "--verbose", is_flag=True, default=False, help="Print verbose output to the console.") -@click.option("-l", "--log-file", help="Save a verbose log to a file.", metavar="") +# @click.version_option(nf_core.__version__) +@click.option( + "-v", + "--verbose", + is_flag=True, + default=False, + help="Print verbose output to the console.", +) +@click.option( + "-l", "--log-file", help="Save a verbose log to a file.", metavar="" +) def bu_isciii_cli(verbose, log_file): # Set the base logger to output DEBUG log.setLevel(logging.DEBUG) - # Set up logs to the console + # Set up logs to the console log.addHandler( rich.logging.RichHandler( level=logging.DEBUG if verbose else logging.INFO, - console=rich.console.Console(stderr=True, force_terminal=nf_core.utils.rich_force_colors()), + console=rich.console.Console( + stderr=True, force_terminal=nf_core.utils.rich_force_colors() + ), show_time=False, markup=True, ) @@ -96,9 +131,14 @@ def bu_isciii_cli(verbose, log_file): if log_file: log_fh = logging.FileHandler(log_file, encoding="utf-8") log_fh.setLevel(logging.DEBUG) - log_fh.setFormatter(logging.Formatter("[%(asctime)s] %(name)-20s [%(levelname)-7s] %(message)s")) + log_fh.setFormatter( + logging.Formatter( + "[%(asctime)s] %(name)-20s [%(levelname)-7s] %(message)s" + ) + ) log.addHandler(log_fh) + # pipeline list @bu_isciii_cli.command(help_priority=1) @click.argument("keywords", required=False, nargs=-1, metavar="") @@ -110,7 +150,9 @@ def bu_isciii_cli(verbose, log_file): help="How to sort listed pipelines", ) @click.option("--json", is_flag=True, default=False, help="Print full output as JSON") -@click.option("--show-archived", is_flag=True, default=False, help="Print archived workflows") +@click.option( + "--show-archived", is_flag=True, default=False, help="Print archived workflows" +) def list(keywords, sort, json, show_archived): """ List available bu-isciii workflows used for relecov. @@ -123,10 +165,16 @@ def list(keywords, sort, json, show_archived): # sftp @bu_isciii_cli.command(help_priority=2) @click.argument("pipeline", required=False, metavar="") -@click.option("-r", "--revision", help="Release/branch/SHA of the project to run (if remote)") +@click.option( + "-r", "--revision", help="Release/branch/SHA of the project to run (if remote)" +) @click.option("-i", "--id", help="ID for web-gui launch parameter set") @click.option( - "-c", "--command-only", is_flag=True, default=False, help="Create Nextflow command with params (no params file)" + "-c", + "--command-only", + is_flag=True, + default=False, + help="Create Nextflow command with params (no params file)", ) @click.option( "-o", @@ -135,20 +183,37 @@ def list(keywords, sort, json, show_archived): default=os.path.join(os.getcwd(), "nf-params.json"), help="Path to save run parameters file", ) -def sftp(pipeline, id, revision, command_only, params_in, params_out, save_all, show_hidden, url): - ''' +def sftp( + pipeline, + id, + revision, + command_only, + params_in, + params_out, + save_all, + show_hidden, + url, +): + """ Download files located in sftp server. - ''' + """ print(nf_core.list.list_workflows(keywords, sort, json, show_archived)) + # metadata @bu_isciii_cli.command(help_priority=3) @click.argument("pipeline", required=False, metavar="") -@click.option("-r", "--revision", help="Release/branch/SHA of the project to run (if remote)") +@click.option( + "-r", "--revision", help="Release/branch/SHA of the project to run (if remote)" +) @click.option("-i", "--id", help="ID for web-gui launch parameter set") @click.option( - "-c", "--command-only", is_flag=True, default=False, help="Create Nextflow command with params (no params file)" + "-c", + "--command-only", + is_flag=True, + default=False, + help="Create Nextflow command with params (no params file)", ) @click.option( "-o", @@ -157,12 +222,23 @@ def sftp(pipeline, id, revision, command_only, params_in, params_out, save_all, default=os.path.join(os.getcwd(), "nf-params.json"), help="Path to save run parameters file", ) -def metadata(pipeline, id, revision, command_only, params_in, params_out, save_all, show_hidden, url): - ''' +def metadata( + pipeline, + id, + revision, + command_only, + params_in, + params_out, + save_all, + show_hidden, + url, +): + """ Read Metadata . - ''' + """ print(nf_core.list.list_workflows(keywords, sort, json, show_archived)) - + + if __name__ == "__main__": run_bu_isciii() From 68b92361397a14ef41a5ceee026274238b5a0e51 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 1 Mar 2022 16:40:01 +0100 Subject: [PATCH 0048/1454] working on validation_json --- sftp_download.sh => relecov-tools | 0 relecov_tools/__init__.py | 2 +- relecov_tools/read_metadata.py | 57 ++++++++++++++++--------------- relecov_tools/validation_jsons.py | 12 ++++--- 4 files changed, 37 insertions(+), 34 deletions(-) rename sftp_download.sh => relecov-tools (100%) diff --git a/sftp_download.sh b/relecov-tools similarity index 100% rename from sftp_download.sh rename to relecov-tools diff --git a/relecov_tools/__init__.py b/relecov_tools/__init__.py index a58e0b83..c94a25ee 100644 --- a/relecov_tools/__init__.py +++ b/relecov_tools/__init__.py @@ -3,4 +3,4 @@ import pkg_resources -__version__ = pkg_resources.get_distribution("relecov").version +__version__ = pkg_resources.get_distribution("bu_isciii").version diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index aabf818d..fbbecfc2 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -1,6 +1,7 @@ #!/usr/bin/env python -class RelecovMetadata(): + +class RelecovMetadata: def __init__(): self.origin_file = file self.metadata = {} @@ -8,81 +9,81 @@ def __init__(): self.relecov_url = relecov_url -# reade_metadata +# read_metadata + + def read_metadata_workflow(self): - def __init__ (self, ): + def __init__( + self, + ): - ''' - Description : Starts the read metada workflow - ''' + """ + Description : Starts the read metada workflow + """ # Perform workflow details def check_new_metadata(folder): - """ Check if there is a new metadata to be processed + """Check if there is a new metadata to be processed folder Directory to be checked """ pass + def fetch_metadata_file(folder, file_name): - """ Fetch the metadata file + """Fetch the metadata file folder Directory to fetch metadata file file_name metadata file name """ pass - def validate_metadata_sample(row_sample): - """ Validate sample information +def validate_metadata_sample(row_sample): + """Validate sample information""" -def add_extra_data (metadata_file, extra_data, result_metadata): - """ Add the additional information that must be included in final metadata + +def add_extra_data(metadata_file, extra_data, result_metadata): + """Add the additional information that must be included in final metadata metadata Origin metadata file extra_data additional data to be included result_metadata final metadata after adding the additional data """ pass + def request_information(external_url, request): - """ Get information from external database server using Rest API + """Get information from external database server using Rest API external_url request """ pass -def store_information (external_url, request, data): - """ Update information - """ +def store_information(external_url, request, data): + """Update information""" pass - - - - - - wb_file = openpyxl.load_workbook(arguments.inputFile, data_only=True) -ws_metadata_lab = wb_file['METADATA_LAB'] +ws_metadata_lab = wb_file["METADATA_LAB"] heading = [] for cell in ws_metadata_lab[1]: heading.append(cell.value) -for row in islice(ws_metadata_lab.values,1,ws_metadata_lab.max_row): +for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row): sample_data_row = {} for idx in range(len(heading)): - if 'date' in heading[idx]: - sample_data_row[heading[idx]] = row[idx].strftime('%d/%m/%Y') + if "date" in heading[idx]: + sample_data_row[heading[idx]] = row[idx].strftime("%d/%m/%Y") else: sample_data_row[heading[idx]] = row[idx] try: - validate(instance=sample_data_row,schema=json_phage_plus_schema) + validate(instance=sample_data_row, schema=json_phage_plus_schema) except: - print('Unsuccessful validation for sample ' , sample_data_row['sample_name']) + print("Unsuccessful validation for sample ", sample_data_row["sample_name"]) continue diff --git a/relecov_tools/validation_jsons.py b/relecov_tools/validation_jsons.py index ea153826..486355c1 100644 --- a/relecov_tools/validation_jsons.py +++ b/relecov_tools/validation_jsons.py @@ -7,9 +7,11 @@ from itertools import islice import argparse -# import test.utils +import utils -from utils import * +# import relecov_tools.utils + +# from utils import * """ @@ -139,13 +141,13 @@ def check_arg(args=None): print("Try validation_jsons.py --help for more information.") exit(2) arguments = check_arg(sys.argv[1:]) - if not test.utils.file_exists(arguments.phagePlusSchema): + if not utils.file_exists(arguments.phagePlusSchema): print("phage plus schema file does not exist\n") exit(2) - if not test.utils.file_exists(arguments.inputFile): + if not utils.file_exists(arguments.inputFile): print("excel file does not exist\n") exit(2) - if not test.utils.file_exists(arguments.convertedSchema): + if not utils.file_exists(arguments.convertedSchema): print("file for converting schema does not exist\n") exit(2) # schema_file = open('/home/lchapado/Projects/Proyecto_ERA/relecov-tools/schema/phage_plus_V0.json') From 9fe53c00f0487e864a1aba5eb47f82e9194496d1 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 2 Mar 2022 12:03:59 +0100 Subject: [PATCH 0049/1454] fixed schemas --- relecov_tools/schema/ena_v01.json | 12 ++++++------ relecov_tools/schema/gisaid_V0.json | 8 ++++---- relecov_tools/schema/phage_V0.json | 8 ++++---- relecov_tools/schema/phage_plus_V0.json | 24 ++++++++---------------- 4 files changed, 22 insertions(+), 30 deletions(-) diff --git a/relecov_tools/schema/ena_v01.json b/relecov_tools/schema/ena_v01.json index d90e3a47..f3a7eb9c 100644 --- a/relecov_tools/schema/ena_v01.json +++ b/relecov_tools/schema/ena_v01.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft/2019-09/schema#", + "schema": "ENA", "required": [ "sample_name", "collecting_institution", @@ -369,7 +369,7 @@ "38.98 N" ], "clasification": "Sample collection and processing", - "label": "Geo Loc Latitude", + "label": "Geo Loc Latitude" }, "geographic location (longitude)": { "ontology": "OBI:0001621", @@ -548,7 +548,7 @@ "type": "string", "description": "a unique identifier by which each subject can be referred to, de-identified.", "clasification": "Host information", - "genepio_label": "", + "genepio_label": "" }, "type exposure": { "examples": [ @@ -700,7 +700,7 @@ "type": "string", "description": "Free text description of the sample.", "clasification": "Sample collection and processing", - "genepio_label": "", + "genepio_label": "" }, "sample_storage_conditions": { "examples": [ @@ -736,7 +736,7 @@ "Resctriction Digest method [GENPIO:0001961]", "cDNA method [GENPIO:0001962]", "other library method [GENPIO:0001964]", - "size fractionation method [GENPIO:0001963]", + "size fractionation method [GENPIO:0001963]" ], "examples": [ "METAGENOMIC" @@ -778,7 +778,7 @@ "clone strategy [GENPIO:0001977]", "finishing strategy [GENPIO:0001982]", "other library strategy [GENPIO:0001988]", - "pool clone strategy [GENPIO:0001989]", + "pool clone strategy [GENPIO:0001989]" ], "examples": [ "WGS" diff --git a/relecov_tools/schema/gisaid_V0.json b/relecov_tools/schema/gisaid_V0.json index 9c8181ba..08ad14d9 100644 --- a/relecov_tools/schema/gisaid_V0.json +++ b/relecov_tools/schema/gisaid_V0.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft/2022-01/gisaid_schema#", + "schema": "GISAID#", "required": [ "type", "virus_name", @@ -198,7 +198,7 @@ "ontology": "GENEPIO:0001395", "type": "string", "description": "The gender of the host at the time of sample collection.", - "clasification": "Host information", + "clasification": "Host information" }, "sequencing_technology": { "examples": [ @@ -237,7 +237,7 @@ "ontology": "GENEPIO:0001156", "type": "string", "description": "Filename that contains the sequence without path", - "clasification": "Bioinformatics and QC metrics", + "clasification": "Bioinformatics and QC metrics" }, "additional_host_information": { "examples": [ @@ -257,7 +257,7 @@ "type": "string", "description": "The date the host received their last dose of vaccine.", "format": "date", - "clasification": "Host information", + "clasification": "Host information" }, "outbreak": { "examples": [ diff --git a/relecov_tools/schema/phage_V0.json b/relecov_tools/schema/phage_V0.json index 7da4dbf1..cd6f3b15 100644 --- a/relecov_tools/schema/phage_V0.json +++ b/relecov_tools/schema/phage_V0.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft/2019-09/schema#", + "schema": "PHAGE", "required": [ "sequence_submitted_by", "sample_collected_by", @@ -2064,7 +2064,7 @@ "type": "string", "description": "Description of how organism was passaged.", "examples": [ - "AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain.", + "AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain." ], "clasification": "Sample collection and processing", "label": "Passage Method" @@ -2842,7 +2842,7 @@ "type": "string", "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", "clasification": "Database Identifiers", - "label": "umbrella bioproject accession", + "label": "umbrella bioproject accession" }, "biomaterial_extracted": { "Enums": [ @@ -2890,7 +2890,7 @@ "38.98 N" ], "clasification": "Sample collection and processing", - "label": "Geo Loc Latitude", + "label": "Geo Loc Latitude" }, "environmental_material": { "Enums": [ diff --git a/relecov_tools/schema/phage_plus_V0.json b/relecov_tools/schema/phage_plus_V0.json index 5418e8e9..2edfd062 100644 --- a/relecov_tools/schema/phage_plus_V0.json +++ b/relecov_tools/schema/phage_plus_V0.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft/2020-12/schema", + "schema": "PHAGE_PLUS", "required": [ "sample_name", "collecting_institution", @@ -366,7 +366,7 @@ "type": "string", "description": "Taxonomic name of the organism.", "examples": [ - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]" ], "classification": "Sample collection and processing", "label": "Organism" @@ -673,7 +673,7 @@ "type": "string", "description": "The latitude coordinates of the geographical location of sample collection.", "clasification": "Sample collection and processing", - "label": "Geo Loc Latitude", + "label": "Geo Loc Latitude" }, "geo_loc_longitude": { "examples": [ @@ -1421,7 +1421,7 @@ "clone strategy [GENPIO:0001977]", "finishing strategy [GENPIO:0001982]", "other library strategy [GENPIO:0001988]", - "pool clone strategy [GENPIO:0001989]", + "pool clone strategy [GENPIO:0001989]" ], "examples": [ "WGS" @@ -2047,16 +2047,6 @@ "clasification": "Pathogen diagnostic testing", "label": "Numer of variants with effect" }, - "reference_genome_accession": { - "examples": [ - "" - ], - "ontology": "GENEPIO:0001485", - "type": "string", - "description": "", - "clasification": "Pathogen diagnostic testing", - "label": "reference genome accession" - }, "diagnostic_pcr_protocol_1": { "examples": [ "PCREGene 2.0" @@ -2187,7 +2177,9 @@ "label": "Authors" }, "common_name": { - "examples": "", + "examples": [ + "" + ], "ontology": "NCIT:C164471", "type": "string", "description": "", @@ -2218,7 +2210,7 @@ "Resctriction Digest method [GENPIO:0001961]", "cDNA method [GENPIO:0001962]", "other library method [GENPIO:0001964]", - "size fractionation method [GENPIO:0001963]", + "size fractionation method [GENPIO:0001963]" ], "examples": [ "METAGENOMIC" From 881d163ede59124a3f452951c939559936015c0e Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 3 Mar 2022 10:43:10 +0100 Subject: [PATCH 0050/1454] deleted files --- .../RESULTADOS 1er CONTROL CALIDAD-HERA.xlsx | Bin 95683 -> 0 bytes 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zXe)YL7N{i6{IO6$*OO%8;Bb|rw3q>#cVJN9wl^LVqI!j5DVUzCDj^+XvyG>jQcI7G z^M|w^@XO|#nwaI8X`)K6Mt-|mU5!+F)=dM|2`yzjhf%IgA~ARB^gcokV!Zso9U>1z zu#D?jR5OH*J}X$$++R`b0b?*vt^#dam?mr*X1P0p*Uv}$I)jyGp{MVYzx33&i=4?r z2Ru#6JCeI{GwI*oLRVIXeAc~%Li(5N(5NFM=OYZ?w`GF^YFa0i(;~yoZ!l2s09I9w z4SgWbPQ;`d3yZhjSX56wHSCI37Id|DtOT!ujOb%)4mKPoATJ2BYr&Ax<{kJInkm=T zvA&|h;Drj-KR4_os5kVb;ZL1mPo0f4-5p>~23N6aMzzhTSk0btF_yBs_W6PyP5HgY zdBM)lx5IKblCI+O=!NGXho%-T2NKy+vE7oW>MAh(n)PwO-soDY(pnO8CO%V631YXZ zPLa3APPms`A78x9aMMXW#JH4VPnIyu(}vrsD4~mk*5NCsg?srjS=rvsu|F9EILts8 z8=zE4&3;md+p~!s?bd+9)^kw8`)DOlf4bWr$X%%mOA`V{Zljk}3n3Dp3uPniJiT~| zB~A_7Ha6rX3zN9h-Ixq{oTaBQOliM2q>;w-*W({OF~RhVQlOv_QcWDqGl6&U7)3lD zy|CSe^20drL3z3yflxS&!-B1ECe>7lrelHX+G&}6>y6^sxC?rB{O?5ute7u9?qz&0 zr#@P^ePO-dvP#rp=5X8s%xGnB%ec`olvYmbgAIHuxRWfBr4cSO@BfYN-0)_>Wh&L8 z{w?|zn`pj?=LutOSDA@EToHJT%8JfUowI{JzTdlA) Date: Fri, 4 Mar 2022 14:10:51 +0100 Subject: [PATCH 0052/1454] added mapping_file.json --- relecov_tools/schema/ena_v01.json | 5 +- relecov_tools/schema/mapping_file.json | 28 ++++ relecov_tools/schema/small_schema.json | 200 ++++++++++++++++++++++++- 3 files changed, 229 insertions(+), 4 deletions(-) create mode 100644 relecov_tools/schema/mapping_file.json diff --git a/relecov_tools/schema/ena_v01.json b/relecov_tools/schema/ena_v01.json index f3a7eb9c..2c757cff 100644 --- a/relecov_tools/schema/ena_v01.json +++ b/relecov_tools/schema/ena_v01.json @@ -10,7 +10,6 @@ "host_subject_id", "instrument_model", "file_name", - "sample_name", "tax_id", "scientific_name", "common_name", @@ -548,7 +547,7 @@ "type": "string", "description": "a unique identifier by which each subject can be referred to, de-identified.", "clasification": "Host information", - "genepio_label": "" + "label": "Host Subject Id" }, "type exposure": { "examples": [ @@ -700,7 +699,7 @@ "type": "string", "description": "Free text description of the sample.", "clasification": "Sample collection and processing", - "genepio_label": "" + "label": "Sample Description" }, "sample_storage_conditions": { "examples": [ diff --git a/relecov_tools/schema/mapping_file.json b/relecov_tools/schema/mapping_file.json new file mode 100644 index 00000000..801ac7de --- /dev/null +++ b/relecov_tools/schema/mapping_file.json @@ -0,0 +1,28 @@ +{ + "Collecting Sample id": "sample_name", + "Originating Laboratory": "collecting_institution", + "Submitting Institution": "submitting_institution", + "Sample Collection Date": "sample_collection_date", + "geo_loc_country": "geo_loc_country", + "geo_loc_state": "geo_loc_state", + "organism": "organism", + "isolate": "isolate", + "host_scientific_name": "host_scientific_name", + "Host Common Name": "host_common_name", + "host_disease": "host_disease", + "Sequencing Instrument Model": "sequencing_instrument_model", + "Sequencing Platforms": "sequencing_instrument_platform", + "consensus_sequence_software_name": "consensus_sequence_software_name", + "consensus_sequence_software_version": "consensus_sequence_software_version", + "file_name": "file_name", + "tax_id": "tax_id", + "sample_description": "sample_description", + "Library Source": "library_source", + "Library Selection": "library_selection", + "Library Strategy": "library_strategy", + "Library Layout": "library_layout", + "type": "type", + "GISAID Virus Name": "virus_name", + "GISAID Id": "submitter", + "Originating Laboratory Address": "collecting_institution_address" +} \ No newline at end of file diff --git a/relecov_tools/schema/small_schema.json b/relecov_tools/schema/small_schema.json index 7b3c62d5..5c9630ac 100644 --- a/relecov_tools/schema/small_schema.json +++ b/relecov_tools/schema/small_schema.json @@ -10,11 +10,23 @@ "organism", "isolate", "host_scientific_name", + "host_common_name", "host_disease", "sequencing_instrument_model", "sequencing_instrument_platform", "consensus_sequence_software_name", - "consensus_sequence_software_version" + "consensus_sequence_software_version", + "file_name", + "tax_id", + "sample_description", + "library_source", + "library_selection", + "library_strategy", + "library_layout", + "type", + "virus_name", + "submitter", + "collecting_institution_address" ], "type": "object", "properties": { @@ -521,6 +533,192 @@ "description": "The version of the software used to generate the consensus sequence.", "clasification": "Bioinformatics and QC metrics", "label": "Consensus sequence software version" + }, + "host_common_name": { + "Enums": [ + "Human [NCBITaxon:9606]", + "Bat [NCBITaxon:9397]", + "Cat [NCBITaxon:9685]", + "Chicken [NCBITaxon:9031]", + "Civet [NCBITaxon:9673]", + "Cow [NCBITaxon:9913]", + "Dog [NCBITaxon:9615]", + "Lion [NCBITaxon:9689]", + "Mink [NCBITaxon:452646]", + "Pangolin [NCBITaxon:9973]", + "Pig [NCBITaxon:9825]", + "Pigeon [NCBITaxon:8930]", + "Tiger [NCBITaxon:9694]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001386", + "type": "string", + "description": "The commonly used name of the host.", + "examples": [ + "Human [NCBITaxon:9606]" + ], + "classification": "Host information", + "label": "Host Common Name" + }, + "file_name": { + "examples": [ + "ABC123_S1_L001_R1_001.fastq.gz" + ], + "ontology": "GENEPIO:0001476", + "type": "string", + "description": "The user-specified filename of the r1 FASTQ file.", + "clasification": "Bioinformatics and QC metrics", + "label": "Sequence file R1 fastq" + }, + "tax_id": { + "examples": [ + "probably 2697049 in all cases" + ], + "ontology": "GENEPIO_0001724", + "type": "string", + "description": "The NCBITaxon identifier for the organism being sequenced.", + "clasification": "Sample collection and processing", + "label": "Tax ID" + }, + "sample_description": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Free text description of the sample.", + "clasification": "Sample collection and processing", + "label": "Sample Description" + }, + "library_source": { + "Enums": [ + "5-methycytidine antibody method [GENPIO:0001941]", + "CAGE method [GENPIO:0001942]", + "CF-H method [GENPIO:0001943]", + "CF-M method ]GENPIO:0001944]", + "CF-S method [GENPIO:0001945]", + "CF-T method [GENPIO:0001946]", + "ChIP method ]GENPIO:0001947]", + "DNAse method [GENPIO:0001948]", + "HMPR method [GENPIO:0001949]", + "Hybrid Selection Method [GENPIO:0001950]", + "MBD2 protein methyl-CpG binding domain method [GENPIO:0001951]", + "MF method [GENPIO:0001952]", + "MNase method [GENPIO:0001953]", + "MSLL method [GENPIO:0001954]", + "PCR method [GENPIO:0001955]", + "RACE method [GENPIO:0001956]", + "RANDOM PCR method [GENPIO:0001957]", + "RANDOM method [GENPIO:0001958]", + "RT-PCR method [GENPIO:0001959]", + "Reduced Representation method [GENPIO:0001960]", + "Resctriction Digest method [GENPIO:0001961]", + "cDNA method [GENPIO:0001962]", + "other library method [GENPIO:0001964]", + "size fractionation method [GENPIO:0001963]" + ], + "examples": [ + "METAGENOMIC" + ], + "ontology": "GENEPIO_0001965", + "type": "string", + "description": "Molecule type used to make the library.", + "clasification": "Sequencing", + "label": "Source material" + }, + "library_selection": { + "examples": [ + "RANDOM PCR" + ], + "ontology": "GENPIO_0001940", + "type": "string", + "description": "Library capture method.", + "clasification": "Sequencing", + "label": "Capture method" + }, + "library_strategy": { + "Enums": [ + "Bisultife-Seq strategy [GENPIO:0001975]", + "CTS strategy [GENPIO:0001978]", + "ChIP-Seq strategy [GENPIO:0001979]", + "DNase-Hypersensitivity strategy [GENPIO:0001980]", + "EST strategy [GENPIO:0001981]", + "FL-cDNA strategy [GENPIO:0001983]", + "MB-Seq strategy [GENPIO:0001984]", + "MNase-Seq strategy [GENPIO:0001985]", + "MRE-Seq strategy [GENPIO:0001986]", + "MeDIP-Seq strategy [GENPIO:0001987]", + "RNA-Seq strategy [GENPIO:0001990]", + "WCS strategy [GENPIO:0001991]", + "WGS strategy [GENPIO:0001992]", + "WXS strategy [GENPIO:0001993]", + "amplicon strategy [GENPIO:0001974]", + "clone end strategy [GENPIO:0001976]", + "clone strategy [GENPIO:0001977]", + "finishing strategy [GENPIO:0001982]", + "other library strategy [GENPIO:0001988]", + "pool clone strategy [GENPIO:0001989]" + ], + "examples": [ + "WGS" + ], + "ontology": "GENPIO_0001973", + "type": "string", + "description": "Overall sequencing strategy or approach.", + "clasification": "Sequencing", + "label": "Sequencing technique" + }, + "library_layout": { + "examples": [ + "PAIRED" + ], + "ontology": "BU_ISCIII:007", + "type": "string", + "description": "Single or paired.", + "clasification": "Sequencing", + "label": "Library Layout" + }, + "type": { + "examples": [ + "betacoronavirus" + ], + "ontology": "NCBITaxon:694002", + "type": "string", + "description": "default must remain 'betacoronavirus'", + "clasification": "Database Identifiers" + }, + "virus_name": { + "examples": [ + "hCoV-19/Canada/prov_rona_99/2020" + ], + "ontology": "GENEPIO:0100282", + "type": "string", + "description": "The user-defined GISAID virus name assigned to the sequence.", + "clasification": "Database Identifiers", + "label": "GISAID Virus Name" + }, + "submitter": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "enter your GISAID-Username", + "label": "GISAID Username" + }, + "collecting_institution_address": { + "examples": [ + "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" + ], + "ontology": "GENEPIO:0001158", + "type": "string", + "description": "The mailing address of the agency submitting the sample.", + "clasification": "Originating Laboratory Address" } } } \ No newline at end of file From 9e8f4ffbe3a3bfa81d8f36d7840444dd05302936 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 7 Mar 2022 10:24:00 +0100 Subject: [PATCH 0053/1454] changes from last days --- relecov_tools/SFTP_connection_class.py | 60 +-- .../.~lock.dummy_data_small.xlsx# | 1 - .../example_data/dummy_data_small.xlsx | Bin 5305 -> 6032 bytes relecov_tools/pruebas.ipynb | 341 +++++++++++++++++- relecov_tools/schema/mapping_file.json | 5 +- relecov_tools/schema/small_schema.json | 35 +- relecov_tools/validation_jsons.py | 21 +- 7 files changed, 425 insertions(+), 38 deletions(-) delete mode 100644 relecov_tools/example_data/.~lock.dummy_data_small.xlsx# diff --git a/relecov_tools/SFTP_connection_class.py b/relecov_tools/SFTP_connection_class.py index 7b6d2e01..7a706b8b 100644 --- a/relecov_tools/SFTP_connection_class.py +++ b/relecov_tools/SFTP_connection_class.py @@ -1,4 +1,4 @@ -''' +""" ============================================================= HEADER ============================================================= @@ -25,70 +25,72 @@ ================================================================ END_OF_HEADER ================================================================ -''' +""" # Imports import paramiko import sys + class SftpHandle: - def __init__(self,host,port,user,key): - ''' + def __init__(self, host, port, user, key): + """ Initializes the Connection object and starts its host, port, user and key attributes. Declaration: sftp = SftpHandle(host,port,user,key) - ''' + """ self.host = host self.port = port self.user = user self.key = key - self.client = None - + self.client = None + def check(self): - ''' + """ Check if there is a SFTP connection Usage: sftp.check() Return: True if a connection still exists False if connection doesnt exist (not established or timed out for instance) - ''' + """ try: self.client.getcwd() return True except: return False - - + def open(self): - ''' + """ Uses the class attributes to make a SFTP connection Usage: sftp.open() Return: True if connected succesfully False if failed connection - ''' + """ if not self.check(): try: self.client = paramiko.SSHClient() self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) - self.client.connect(hostname = self.host, - port = self.port, - username = self.user, - password = self.key, - allow_agent=False, - look_for_keys=False) + self.client.connect( + hostname=self.host, + port=self.port, + username=self.user, + password=self.key, + allow_agent=False, + look_for_keys=False, + ) self.client = self.client.open() return True except: return False - + def close(self): - ''' + """ Closes the SFTP connection if there is any Usage: sftp.close() @@ -96,26 +98,26 @@ def close(self): -True if connection closed successfully -False if connection closing failed -None if no connection was established - ''' + """ if self.check(): - try: + try: self.client.close() return True except: return False -if __name__ == '__main__': - sys.exit(main()) +if __name__ == "__main__": + sys.exit(main()) # TESTING ZONE, must be deleted later CLAVE = "RANDOM_KEY_FOR_TESTING" -HOST = 'RANDOM_SFTP_FOR_TESTING' +HOST = "RANDOM_SFTP_FOR_TESTING" PUERTO = 420 -USUARIO = 'ARTURITO' +USUARIO = "ARTURITO" -my_sftp = SftpHandle(HOST,PUERTO,USUARIO,CLAVE) +my_sftp = SftpHandle(HOST, PUERTO, USUARIO, CLAVE) if not my_sftp.open(): print("No connection!") else: @@ -123,4 +125,4 @@ def close(self): # testing the client attribute # works fine by now -print(my_sftp.client.listdir()) \ No newline at end of file +print(my_sftp.client.listdir()) diff --git a/relecov_tools/example_data/.~lock.dummy_data_small.xlsx# b/relecov_tools/example_data/.~lock.dummy_data_small.xlsx# deleted file mode 100644 index d63cb8bb..00000000 --- a/relecov_tools/example_data/.~lock.dummy_data_small.xlsx# +++ /dev/null @@ -1 +0,0 @@ -,erika.kvalem,bioinfoadm-System-Product-Name,03.03.2022 16:17,file:///home/erika.kvalem/.config/libreoffice/4; \ No newline at end of file diff --git a/relecov_tools/example_data/dummy_data_small.xlsx b/relecov_tools/example_data/dummy_data_small.xlsx index b09e4718de663940b7b7897e9c3bb7d1f2542f2f..6d6ac571efca116473f88a2cd69487cc30c8468c 100644 GIT binary patch delta 3948 zcmZ8k1ys~s(_dg0Sh_*FyCemcd~hWMNokRM6qN4z6H6-~OT!ANbjkv{AT8b9jZ)Ge z2!bE@z2|v--h0kHcjnH_xpVKiGxHk^UxEm+jwTM63WSf34@!S#`<|Ev3+H-8b7R4< zZwRCv4nMG*N69cnCE`*EjxP-L;9y*t^9H;!KDUC)xZVdX*+64XbVrd5{*MOYLWkdGuN8{>~}F 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zkBPLv&i7k)jF@!tG&?x^BuVr%?{8;u8*}p4j&5Lelm#sRa@GzbVNQ#jaD*Rg{|79I Bs=)vN diff --git a/relecov_tools/pruebas.ipynb b/relecov_tools/pruebas.ipynb index 8fe6305f..3beeecc8 100644 --- a/relecov_tools/pruebas.ipynb +++ b/relecov_tools/pruebas.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 144, + "execution_count": 3, "id": "a99df8ae", "metadata": {}, "outputs": [], @@ -137,11 +137,346 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 63, "id": "72587d32", "metadata": {}, "outputs": [], - "source": [] + "source": [ + "heading =['Collecting Sample id', 'Originating Laboratory', 'Submitting Institution', 'Sample Collection Date', 'geo_loc_country', 'geo_loc_state', 'organism', 'isolate', 'host_scientific_name', 'Host Common Name', 'host_disease', 'Sequencing Instrument Model', 'Sequencing Platforms', 'consensus_sequence_software_name', 'consensus_sequence_software_version', 'file_name', 'tax_id', 'sample_description', 'Library Source', 'Library Selection', 'Library Strategy', 'Library Layout', 'type', 'GISAID Virus Name', 'GISAID Id', 'Originating Laboratory Address']\n" + ] + }, + { + "cell_type": "code", + "execution_count": 71, + "id": "7ea69469", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "26" + ] + }, + "execution_count": 71, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "len(heading)" + ] + }, + { + "cell_type": "code", + "execution_count": 64, + "id": "54afd367", + "metadata": {}, + "outputs": [], + "source": [ + "map_file = open(\"schema/mapping_file.json\")\n", + "mapping_file = json.load(map_file)" + ] + }, + { + "cell_type": "code", + "execution_count": 65, + "id": "3d1e0f63", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'Collecting Sample id': 'sample_name',\n", + " 'Originating Laboratory': 'collecting_institution',\n", + " 'Submitting Institution': 'submitting_institution',\n", + " 'Sample Collection Date': 'sample_collection_date',\n", + " 'geo_loc_country': 'geo_loc_country',\n", + " 'geo_loc_state': 'geo_loc_state',\n", + " 'organism': 'organism',\n", + " 'isolate': 'isolate',\n", + " 'host_scientific_name': 'host_scientific_name',\n", + " 'Host Common Name': 'host_common_name',\n", + " 'host_disease': 'host_disease',\n", + " 'Sequencing Instrument Model': 'sequencing_instrument_model',\n", + " 'Sequencing Platforms': 'sequencing_instrument_platform',\n", + " 'consensus_sequence_software_name': 'consensus_sequence_software_name',\n", + " 'consensus_sequence_software_version': 'consensus_sequence_software_version',\n", + " 'file_name': 'file_name',\n", + " 'tax_id': 'tax_id',\n", + " 'sample_description': 'sample_description',\n", + " 'Library Source': 'library_source',\n", + " 'Library Selection': 'library_selection',\n", + " 'Library Strategy': 'library_strategy',\n", + " 'Library Layout': 'library_layout',\n", + " 'type': 'type',\n", + " 'GISAID Virus Name': 'virus_name',\n", + " 'GISAID Id': 'submitter',\n", + " 'Originating Laboratory Address': 'collecting_address'}" + ] + }, + "execution_count": 65, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "mapping_file" + ] + }, + { + "cell_type": "code", + "execution_count": 54, + "id": "def77932", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'sample_name'" + ] + }, + "execution_count": 54, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "list(mapping_file.values())[0]" + ] + }, + { + "cell_type": "code", + "execution_count": 70, + "id": "34b84069", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "0\n", + "1\n", + "2\n", + "3\n", + "4\n", + "5\n", + "6\n", + "7\n", + "8\n", + "9\n", + "10\n", + "11\n", + "12\n", + "13\n", + "14\n", + "15\n", + "16\n", + "17\n", + "18\n", + "19\n", + "20\n", + "21\n", + "22\n", + "23\n", + "24\n", + "25\n" + ] + } + ], + "source": [ + "for i in range(len(heading)):\n", + " print(i)" + ] + }, + { + "cell_type": "code", + "execution_count": 72, + "id": "1caa1045", + "metadata": {}, + "outputs": [], + "source": [ + "for i in range(len(heading)):\n", + " if heading[i] in list(mapping_file.keys()):\n", + " index = list(mapping_file).index(heading[i])\n", + " heading[index] = list(mapping_file.values())[index]\n", + " \n", + " \n" + ] + }, + { + "cell_type": "code", + "execution_count": 73, + "id": "8ab4a0c2", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['sample_name',\n", + " 'collecting_institution',\n", + " 'submitting_institution',\n", + " 'sample_collection_date',\n", + " 'geo_loc_country',\n", + " 'geo_loc_state',\n", + " 'organism',\n", + " 'isolate',\n", + " 'host_scientific_name',\n", + " 'host_common_name',\n", + " 'host_disease',\n", + " 'sequencing_instrument_model',\n", + " 'sequencing_instrument_platform',\n", + " 'consensus_sequence_software_name',\n", + " 'consensus_sequence_software_version',\n", + " 'file_name',\n", + " 'tax_id',\n", + " 'sample_description',\n", + " 'library_source',\n", + " 'library_selection',\n", + " 'library_strategy',\n", + " 'library_layout',\n", + " 'type',\n", + " 'virus_name',\n", + " 'submitter',\n", + " 'collecting_address']" + ] + }, + "execution_count": 73, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "heading" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4689d46e", + "metadata": {}, + "outputs": [], + "source": [ + "dictionary = {'test':{1,3}, 'test2':{2}, 'test3':{2,3}}\n", + "\n", + "if 'test' in dictionary:\n", + " print(list(dictionary).index('test'))" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "id": "5ae4de88", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['Collecting Sample id',\n", + " 'Originating Laboratory',\n", + " 'Submitting Institution',\n", + " 'Sample Collection Date',\n", + " 'geo_loc_country',\n", + " 'geo_loc_state',\n", + " 'organism',\n", + " 'isolate',\n", + " 'host_scientific_name',\n", + " 'Host Common Name',\n", + " 'host_disease',\n", + " 'Sequencing Instrument Model',\n", + " 'Sequencing Platforms',\n", + " 'consensus_sequence_software_name',\n", + " 'consensus_sequence_software_version',\n", + " 'file_name',\n", + " 'tax_id',\n", + " 'sample_description',\n", + " 'Library Source',\n", + " 'Library Selection',\n", + " 'Library Strategy',\n", + " 'Library Layout',\n", + " 'type',\n", + " 'GISAID Virus Name',\n", + " 'GISAID Id',\n", + " 'Originating Laboratory Address']" + ] + }, + "execution_count": 27, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "heading" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b212e5ee", + "metadata": {}, + "outputs": [], + "source": [ + " 'sample_name',\n", + " 'collecting_institution',\n", + " 'submitting_institution',\n", + "'sample_collection_date',\n", + " 'geo_loc_country',\n", + " 'geo_loc_state',\n", + " 'organism',\n", + " 'isolate',\n", + " 'host_scientific_name',\n", + " 'host_common_name',\n", + " 'host_disease',\n", + " 'sequencing_instrument_model',\n", + " 'sequencing_instrument_platform',\n", + " 'consensus_sequence_software_name',\n", + " 'consensus_sequence_software_version',\n", + " 'file_name',\n", + " 'tax_id',\n", + " 'sample_description',\n", + " 'library_source',\n", + " 'library_selection',\n", + " 'library_strategy',\n", + " 'library_layout',\n", + " 'type',\n", + " 'virus_name',\n", + " 'submitter',\n", + " 'collecting_institution_address'],\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3124de94", + "metadata": {}, + "outputs": [], + "source": [ + "collecting_institution': 'Hospital Universitario de Basurto',\n", + "'collecting_institution_address': 'Avda. Montevideo, 18,Bilbao,Vizcaya, ',\n", + "'consensus_sequence_software_name': 'CLC Genomics Workbench 12',\n", + "'consensus_sequence_software_version': '. CLC Genomics Workbench 12,',\n", + "'file_name': 'filename2',\n", + "'geo_loc_country': 'Spain',\n", + "'geo_loc_state': 'Madrid',\n", + "'host_common_name': 'Human',\n", + "'host_disease': 'SARS-CoV2',\n", + "'host_scientific_name': 'Homo sapiens',\n", + "'isolate': 'SARS-CoV-2/human/USA/CA-CDPH-001/2020',\n", + "'library_layout': 'PAIRED',\n", + "'library_selection': 'RANDOM PCR',\n", + "'library_source': 'METAGENOMIC',\n", + "'library_strategy': 'WGS',\n", + "'organism': 'Severe acute respiratory syndrome coronavirus 2',\n", + "'sample_description': 'madnatory ENA description sample',\n", + "'sample_name': 'ID_001',\n", + "'sequencing_instrument_model': 'Illumina MiSeq',\n", + "'sequencing_instrument_platform': 'ILLUMINA',\n", + "'submitter': 'GISAID-Username',\n", + "'submitting_institution': 'Laboratorio de Microbiología de Bibao ',\n", + "'tax_id': 2697049,\n", + "'type': 'betacoronavirus',\n", + "'virus_name': 'hCoV-19/España/Vizcaya-01/2020'}\n", + "\n" + ] } ], "metadata": { diff --git a/relecov_tools/schema/mapping_file.json b/relecov_tools/schema/mapping_file.json index 801ac7de..8cd1d4af 100644 --- a/relecov_tools/schema/mapping_file.json +++ b/relecov_tools/schema/mapping_file.json @@ -24,5 +24,8 @@ "type": "type", "GISAID Virus Name": "virus_name", "GISAID Id": "submitter", - "Originating Laboratory Address": "collecting_institution_address" + "Originating Laboratory Address": "collecting_institution_address", + "broker_name": "broker_name", + "nominal_sdev": "nominal_sdev", + "first_created_date": "first_created_date" } \ No newline at end of file diff --git a/relecov_tools/schema/small_schema.json b/relecov_tools/schema/small_schema.json index 5c9630ac..a6218862 100644 --- a/relecov_tools/schema/small_schema.json +++ b/relecov_tools/schema/small_schema.json @@ -579,7 +579,10 @@ "probably 2697049 in all cases" ], "ontology": "GENEPIO_0001724", - "type": "string", + "type": [ + "number", + "string" + ], "description": "The NCBITaxon identifier for the organism being sequenced.", "clasification": "Sample collection and processing", "label": "Tax ID" @@ -719,6 +722,36 @@ "type": "string", "description": "The mailing address of the agency submitting the sample.", "clasification": "Originating Laboratory Address" + }, + "broker_name": { + "examples": [ + "P17157_1007" + ], + "ontology": "BU_ISCIII:045", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Broker Name" + }, + "nominal_sdev": { + "examples": [ + "" + ], + "ontology": "STATO_0000237", + "type": "number", + "description": "", + "clasification": "Submission ENA", + "label": "Nominal sdev" + }, + "first_created": { + "examples": [ + "e.g 2020-08-07" + ], + "ontology": "NCIT_C164483", + "format": "date", + "description": "", + "clasification": "Submission ENA", + "label": "First created date" } } } \ No newline at end of file diff --git a/relecov_tools/validation_jsons.py b/relecov_tools/validation_jsons.py index ac87dc1b..a1ceb9d2 100644 --- a/relecov_tools/validation_jsons.py +++ b/relecov_tools/validation_jsons.py @@ -120,6 +120,7 @@ def check_arg(args=None): return parser.parse_args() +""" data = { "sample_name": "s1", "collecting_institution": "inst2", @@ -136,6 +137,7 @@ def check_arg(args=None): "consensus_sequence_software_name": "MinIon", "consensus_sequence_software_version": "Ivar", } +""" if __name__ == "__main__": @@ -157,6 +159,8 @@ def check_arg(args=None): schema_file = open(arguments.phagePlusSchema) json_phage_plus_schema = json.load(schema_file) + map_file = open("schema/mapping_file.json") + mapping_file = json.load(map_file) try: Draft202012Validator.check_schema(json_phage_plus_schema) except: @@ -172,18 +176,29 @@ def check_arg(args=None): heading.append(cell.value) + for i in range(len(heading)): + if heading[i] in list(mapping_file.keys()): + index = list(mapping_file).index(heading[i]) + heading[index] = list(mapping_file.values())[index] + for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row): sample_data_row = {} for idx in range(len(heading)): if "date" in heading[idx]: - sample_data_row[heading[idx]] = row[idx].strftime("%d/%m/%Y") + try: + sample_data_row[heading[idx]] = row[idx].strftime("%d/%m/%Y") + except AttributeError: + pass else: sample_data_row[heading[idx]] = row[idx] try: + import pdb + + pdb.set_trace() validate( - instance=list(sample_data_row.keys()), - schema=json_phage_plus_schema["properties"], + instance=sample_data_row, + schema=json_phage_plus_schema, ) print("Success") except ValidationError: From 40fc3ebba15d1747bc511d441dec9bd83d6db387 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Mon, 7 Mar 2022 22:28:21 +0100 Subject: [PATCH 0054/1454] renamed sftp script --- relecov_tools/{SFTP_connection_class.py => sftp.py} | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) rename relecov_tools/{SFTP_connection_class.py => sftp.py} (98%) diff --git a/relecov_tools/SFTP_connection_class.py b/relecov_tools/sftp.py similarity index 98% rename from relecov_tools/SFTP_connection_class.py rename to relecov_tools/sftp.py index 7a706b8b..3a822d70 100644 --- a/relecov_tools/SFTP_connection_class.py +++ b/relecov_tools/sftp.py @@ -32,13 +32,12 @@ import paramiko import sys - class SftpHandle: def __init__(self, host, port, user, key): """ Initializes the Connection object and starts its host, port, user and key attributes. Declaration: - sftp = SftpHandle(host,port,user,key) + sftp = SftpHandle(host, port, user, key) """ self.host = host self.port = port @@ -106,6 +105,8 @@ def close(self): except: return False + def + if __name__ == "__main__": sys.exit(main()) From 3224530cd44a8ba193a8c1eef8c1181aec0d63eb Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Mon, 7 Mar 2022 22:28:49 +0100 Subject: [PATCH 0055/1454] started email module with basic tools --- relecov_tools/mail.py | 52 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 relecov_tools/mail.py diff --git a/relecov_tools/mail.py b/relecov_tools/mail.py new file mode 100644 index 00000000..794344b2 --- /dev/null +++ b/relecov_tools/mail.py @@ -0,0 +1,52 @@ +""" +============================================================= +HEADER +============================================================= +INSTITUTION: BU-ISCIII +AUTHOR: Guillermo J. Gorines Cordero +MAIL: guillermo.gorines@urjc.es +VERSION: 0 +CREATED: 7-3-2022 +REVISED: 7-3-2022 +REVISED BY: guillermo.gorines@urjc.es +DESCRIPTION: + + Includes the Email, and its associated methods. + +REQUIREMENTS: + -Python + +TO DO: + + +================================================================ +END_OF_HEADER +================================================================ +""" + +# Imports +import smtplib + +from email.mime.multipart import MIMEMultipart +from email.mime.text import MIMEText + +class Email: + def __init__(self, receiver, sender, password, subject): + self.receiver = receiver + self.sender = sender + self.password = password + self.subject = subject + self.text = "" + self.html = False + + def write_message(self, text): + self.message = text + return + + def send_message(self): + msg = MIMEMultipart('alternative') + msg['To'] = self.receiver + msg['From'] = self.sender + msg['Subject'] = self.subject + + s = smtplib.SMTP('localhost') From aff172312ee21bbf4b933cb95c9ba3686be4617e Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Mon, 7 Mar 2022 22:40:55 +0100 Subject: [PATCH 0056/1454] added send message module --- relecov_tools/mail.py | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/relecov_tools/mail.py b/relecov_tools/mail.py index 794344b2..983281aa 100644 --- a/relecov_tools/mail.py +++ b/relecov_tools/mail.py @@ -43,10 +43,24 @@ def write_message(self, text): self.message = text return + def generate_HTML(self): + pass + return + def send_message(self): msg = MIMEMultipart('alternative') msg['To'] = self.receiver msg['From'] = self.sender msg['Subject'] = self.subject - s = smtplib.SMTP('localhost') + text_part = MIMEText(self.text, 'plain') + msg.attach(text_part) + + if self.html: + html_part = MIMEText(self.html, 'html') + msg.attach(html_part) + + # open server, send email, close email + server = smtplib.SMTP('localhost') + server.sendmail(self.sender, self.receiver, msg.as_string()) + server.quit() \ No newline at end of file From cfc86c16f0846e0087cc67ae5f395f9df7f28a46 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Mon, 7 Mar 2022 22:41:08 +0100 Subject: [PATCH 0057/1454] linting-friendly changes --- relecov_tools/sftp.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index 3a822d70..5189f381 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -105,8 +105,9 @@ def close(self): except: return False - def - + def main(args): + pass + return if __name__ == "__main__": sys.exit(main()) From 4f55e95943e096a2f07838c0a2ac01455a1d8c68 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 8 Mar 2022 11:48:12 +0100 Subject: [PATCH 0058/1454] changes in schemas and validation module --- .../example_data/dummy_data_small.xlsx | Bin 6032 -> 7423 bytes relecov_tools/schema/ena_v01.json | 8 +- relecov_tools/schema/small_schema.json | 429 +++++++++++++++++- 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z=Pj(^e>FWuo?VRlkL#ax;9TkdV|YR_IZ!qlT`eMFM$rHC#h40qc49|LOfS38Mf^X} z!1#}75Gaxg!vyDr{W;{~*)Ym*CgLGlj4_<+!a4pY2@G)V^rpuo!8tFsi~YGIV{)FA Y@p)-t_+Q)QFkpt^{7{ASdIbXg3&I^-*Z=?k diff --git a/relecov_tools/schema/ena_v01.json b/relecov_tools/schema/ena_v01.json index 2c757cff..4a62fc38 100644 --- a/relecov_tools/schema/ena_v01.json +++ b/relecov_tools/schema/ena_v01.json @@ -790,7 +790,7 @@ }, "library_layout": { "examples": [ - "PAIRED" + "CTS strategy" ], "ontology": "BU_ISCIII:007", "type": "string", @@ -800,7 +800,7 @@ }, "library_name": { "examples": [ - "e.g P17157_1007" + "e.g PAIRED" ], "ontology": "GENEPIO_0001995", "type": "string", @@ -938,7 +938,7 @@ "clasification": "Sample collection and processing", "label": "Center Name" }, - "first_public": { + "first_public_date": { "examples": [ "e.g 2020-08-07" ], @@ -948,7 +948,7 @@ "clasification": "Submission ENA", "label": "First Public date" }, - "last_updated": { + "last_updated_date": { "examples": [ "e.g 2020-07-29" ], diff --git a/relecov_tools/schema/small_schema.json b/relecov_tools/schema/small_schema.json index a6218862..6f4f9786 100644 --- a/relecov_tools/schema/small_schema.json +++ b/relecov_tools/schema/small_schema.json @@ -587,6 +587,36 @@ "clasification": "Sample collection and processing", "label": "Tax ID" }, + "scientific_name": { + "Enums": [ + "Coronaviridae [NCBITaxon:11118]", + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "examples": [ + "" + ], + "ontology": "GENEPIO:0001191", + "type": "string", + "description": "The taxonomic name of the organism.", + "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", + "label": "Organism" + }, + "common_name": { + "examples": [ + "" + ], + "ontology": "NCIT:C164471", + "type": "string", + "description": "The common name of the organism.", + "clasification": "Sample collection and processing", + "label": "Common name" + }, "sample_description": { "examples": [ "" @@ -597,6 +627,15 @@ "clasification": "Sample collection and processing", "label": "Sample Description" }, + "sample_storage_conditions": { + "examples": [ + "24 degrees celsius" + ], + "ontology": "NCIT_C115535", + "type": "string", + "description": "The name and version of a particular protocol used for sampling.", + "clasification": "Sample collection and processing" + }, "library_source": { "Enums": [ "5-methycytidine antibody method [GENPIO:0001941]", @@ -677,7 +716,7 @@ }, "library_layout": { "examples": [ - "PAIRED" + "CTS strategy" ], "ontology": "BU_ISCIII:007", "type": "string", @@ -723,6 +762,394 @@ "description": "The mailing address of the agency submitting the sample.", "clasification": "Originating Laboratory Address" }, + "library_name": { + "examples": [ + "e.g PAIRED" + ], + "ontology": "GENEPIO_0001995", + "type": "string", + "description": "The submitter's name for this library.", + "clasification": "Sequencing", + "label": "Library Name" + }, + "nominal_length": { + "examples": [ + "350" + ], + "ontology": "GENEPIO_0000076", + "type": "number", + "description": "", + "clasification": "Sequencing", + "label": "Nominal Length" + }, + "analysis_accession": { + "examples": [ + "" + ], + "ontology": "GENEPIO_0001145", + "type": [ + "string", + "null" + ], + "description": "", + "clasification": "Submission ENA", + "label": "Analysis Accession" + }, + "read_length": { + "examples": [ + "" + ], + "ontology": "STATO_0000064", + "type": [ + "string", + "null" + ], + "description": "", + "clasification": "Submission ENA", + "label": "Read length" + }, + "study_accession": { + "examples": [ + "e.g PRJEB39632" + ], + "ontology": "GENEPIO_0001136", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Study accession" + }, + "secondary_study_accession": { + "examples": [ + "e.g ERP123173" + ], + "ontology": "BU_ISCIII:012", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Secondary study accession" + }, + "sample_accession": { + "examples": [ + "e.g SAMEA7098096" + ], + "ontology": "GENEPIO_0001139", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Sample accession" + }, + "secondary_sample_accession": { + "examples": [ + "e.g ERS4858671" + ], + "ontology": "BU_ISCIII:014", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Secondary sample accession" + }, + "experiment_accession": { + "examples": [ + "e.g ERX4331406" + ], + "ontology": "BU_ISCIII:015", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Experiment Accession" + }, + "run_accession": { + "examples": [ + "e.g ERX4331406" + ], + "ontology": "BU_ISCIII:016", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Run Accession" + }, + "submission_accession": { + "examples": [ + "e.g ERA2794974" + ], + "ontology": "BU_ISCIII:017", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Submission accession" + }, + "read_count": { + "examples": [ + "e.g 837055" + ], + "ontology": "STATO_0000064", + "type": [ + "string", + "number" + ], + "description": "", + "clasification": "Submission ENA", + "label": "Read count" + }, + "base_count": { + "examples": [ + "e.g 503907110" + ], + "ontology": "UO_0000244", + "type": [ + "string", + "number" + ], + "description": "", + "clasification": "Submission ENA", + "label": "Base count" + }, + "center_name": { + "examples": [ + " KAROLINSKA INSITUTET" + ], + "ontology": "NCIT_C19983", + "type": "string", + "description": "The name of the institution", + "clasification": "Sample collection and processing", + "label": "Center Name" + }, + "first_public_date": { + "examples": [ + "e.g 2020-08-07" + ], + "ontology": "NCIT_C142711", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "First Public date" + }, + "last_updated_date": { + "examples": [ + "e.g 2020-07-29" + ], + "ontology": "OMIABIS_0001005", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "format": "Last Updated" + }, + "experiment_title": { + "examples": [ + "e.g Illumina MiSeq paired end sequencing" + ], + "ontology": "ORNASEQ_0000004", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Experiment title" + }, + "study_title": { + "examples": [ + "e.g SARS-CoV-2 genomes from late April in Stockholm" + ], + "ontology": "OPMI_0000380", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Study title" + }, + "study_alias": { + "examples": [ + "e.g Sweden" + ], + "ontology": "SIO_001066", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Study alias" + }, + "experiment_alias": { + "examples": [ + "e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092" + ], + "ontology": "NCIT_C42790", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Experiment alias" + }, + "run_alias": { + "examples": [ + "e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1" + ], + "ontology": "NCIT_C47911", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Run Alias" + }, + "fastq_bytes": { + "examples": [ + "e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1" + ], + "ontology": "NCIT_C48047", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Fastq bytes" + }, + "fastq_md5": { + "examples": [ + "" + ], + "ontology": "MS_1000568", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Fastq md5" + }, + "fastq_ftp": { + "examples": [ + "" + ], + "ontology": "PRIDE_0000469", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Fastq ftp" + }, + "fastq_aspera": { + "examples": [ + "e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz" + ], + "ontology": "BU_ISCIII:032", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Fastq aspera" + }, + "fastq_galaxy": { + "examples": [ + "e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz" + ], + "ontology": "ENVO_01000807", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Fastq galaxy" + }, + "submitted_bytes": { + "examples": [ + "e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz" + ], + "ontology": "NCIT_C172872", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Submitted bytes " + }, + "submitted_md5": { + "examples": [ + "e.g 139853010;166270048" + ], + "ontology": "BU_ISCIII:035", + "type": [ + "string", + "number" + ], + "description": "", + "clasification": "Submission ENA", + "label": "Submitted md5" + }, + "submitted_ftp": { + "examples": [ + "e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a" + ], + "ontology": "BU_ISCIII:036", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Submitted ftp" + }, + "submitted_aspera": { + "examples": [ + "e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz" + ], + "ontology": "BU_ISCIII:037", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Submitted aspera" + }, + "submitted_galaxy": { + "examples": [ + "e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz" + ], + "ontology": "BU_ISCIII:038", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Submitted Galaxy" + }, + "submitted_format": { + "examples": [ + "e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz" + ], + "ontology": "BU_ISCIII:039", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Submitted Format" + }, + "sra_bytes": { + "examples": [ + "e.g FASTQ;FASTQ" + ], + "ontology": "BU_ISCIII:040", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "SRA bytes" + }, + "sra_md5": { + "examples": [ + "e.g 260236789" + ], + "ontology": "BU_ISCIII:041", + "type": [ + "string", + "number" + ], + "description": "", + "clasification": "Submission ENA", + "label": "SRA md5" + }, + "sra_ftp": { + "examples": [ + "e.g 2cf0d467d6dc4ae0a5473774d54c059c" + ], + "ontology": "BU_ISCIII:042", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "SRA ftp" + }, + "sra_aspera": { + "examples": [ + "e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385" + ], + "ontology": "BU_ISCIII:043", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "SRA aspera" + }, + "sra_galaxy": { + "examples": [ + "e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385" + ], + "ontology": "BU_ISCIII:044", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "SRA galaxy" + }, "broker_name": { "examples": [ "P17157_1007" diff --git a/relecov_tools/validation_jsons.py b/relecov_tools/validation_jsons.py index a1ceb9d2..12ff022c 100644 --- a/relecov_tools/validation_jsons.py +++ b/relecov_tools/validation_jsons.py @@ -1,5 +1,9 @@ #!/usr/bin/env python from logging import exception +from tkinter import E + +# from types import NoneType +import jsonschema from jsonschema import validate from jsonschema import Draft202012Validator import json, sys @@ -195,24 +199,34 @@ def check_arg(args=None): try: import pdb - pdb.set_trace() validate( instance=sample_data_row, schema=json_phage_plus_schema, ) print("Success") - except ValidationError: - - print( - "Unsuccessful validation for sample ", - sample_data_row["Collecting Sample id"], - ) + except jsonschema.ValidationError as e: + e continue # sample_list.append(PhagePlusData(sample_data_row, phage_plus_schema)) # create the information mapped to the new schema """ - + variable_errores = { + "sample":["jsonschema.exceptions.ValidationError: 2697049 is not of type 'string' + +Failed validating 'type' in schema['properties']['tax_id']: + {'clasification': 'Sample collection and processing', + 'description': 'The NCBITaxon identifier for the organism being ' + 'sequenced.', + 'examples': ['probably 2697049 in all cases'], + 'label': 'Tax ID', + 'ontology': 'GENEPIO_0001800', + 'type': 'string'} + +On instance['tax_id']: + 2697049 +"] + } mapped_structure = phage_plus_schema.maping_schemas_based_on_geontology( arguments.convertedSchema ) From bcc044a735a3beb595c687ac2fb17e1c33134351 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 8 Mar 2022 11:52:56 +0100 Subject: [PATCH 0059/1454] deleted pruebas files --- relecov_tools/prueba.py | 23 -- relecov_tools/pruebas.ipynb | 503 ------------------------------------ 2 files changed, 526 deletions(-) delete mode 100644 relecov_tools/prueba.py delete mode 100644 relecov_tools/pruebas.ipynb diff --git a/relecov_tools/prueba.py b/relecov_tools/prueba.py deleted file mode 100644 index c13f2d18..00000000 --- a/relecov_tools/prueba.py +++ /dev/null @@ -1,23 +0,0 @@ -import json -import openpyxl - - -def validateJsonFile(jsonFile): - try: - json.load(jsonFile) - - except ValueError as err: - print(err) - return False - return True - - -with open("schema/phage_plus_V0.json") as f: - print("Given JSON file is valid:", validateJsonFile) - - -sample_list = [] -wb_file = openpyxl.load_workbook("example_data/dummy_data.xlsx", data_only=True) -ws_metadata_lab = wb_file["METADATA_LAB"] -heading = [] -print(ws_metadata_lab) diff --git a/relecov_tools/pruebas.ipynb b/relecov_tools/pruebas.ipynb deleted file mode 100644 index 3beeecc8..00000000 --- a/relecov_tools/pruebas.ipynb +++ /dev/null @@ -1,503 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 3, - "id": "a99df8ae", - "metadata": {}, - "outputs": [], - "source": [ - "import json\n", - "import openpyxl" - ] - }, - { - "cell_type": "code", - "execution_count": 220, - "id": "dd64f661", - "metadata": {}, - "outputs": [], - "source": [ - "f = open(\"schema/small_schema.json\")\n", - "json_phage_plus_schema = json.load(f)" - ] - }, - { - "cell_type": "code", - "execution_count": 221, - "id": "9057ba90", - "metadata": {}, - "outputs": [], - "source": [ - "json_phage_plus_schema;" - ] - }, - { - "cell_type": "code", - "execution_count": 222, - "id": "97b35c6a", - "metadata": {}, - "outputs": [], - "source": [ - " wb_file = openpyxl.load_workbook(\"example_data/dummy_data_small.xlsx\", data_only=True)\n", - "ws_metadata_lab = wb_file[\"METADATA_LAB\"]\n", - "heading = []\n", - "for cell in ws_metadata_lab[1]:\n", - " heading.append(cell.value)\n" - ] - }, - { - "cell_type": "code", - "execution_count": 223, - "id": "986c372a", - "metadata": {}, - "outputs": [], - "source": [ - "heading;" - ] - }, - { - "cell_type": "code", - "execution_count": 224, - "id": "895b82c2", - "metadata": {}, - "outputs": [], - "source": [ - "for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row):\n", - " sample_data_row = {}\n", - " for idx in range(len(heading)):\n", - " if \"date\" in heading[idx]:\n", - " sample_data_row[heading[idx]] = row[idx].strftime(\"%d/%m/%Y\")\n", - " else:\n", - " sample_data_row[heading[idx]] = row[idx]\n", - " \n", - "fila = sample_data_row" - ] - }, - { - "cell_type": "code", - "execution_count": 225, - "id": "c441ba9d", - "metadata": {}, - "outputs": [], - "source": [ - "list(fila.keys());" - ] - }, - { - "cell_type": "code", - "execution_count": 226, - "id": "a2f1610b", - "metadata": {}, - "outputs": [], - "source": [ - "json_phage_plus_schema['properties'];" - ] - }, - { - "cell_type": "code", - "execution_count": 227, - "id": "2b3da23d", - "metadata": {}, - "outputs": [], - "source": [ - "instance = [{}, 3, \"foo\"]" - ] - }, - { - "cell_type": "code", - "execution_count": 228, - "id": "2b30fc71", - "metadata": {}, - "outputs": [], - "source": [ - "validate(instance = list(fila.keys()), schema =json_phage_plus_schema['properties']) " - ] - }, - { - "cell_type": "code", - "execution_count": 229, - "id": "cc3c4bac", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'prov_rona_99'" - ] - }, - "execution_count": 229, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "sample_data_row[\"Collecting Sample id\"]" - ] - }, - { - "cell_type": "code", - "execution_count": 63, - "id": "72587d32", - "metadata": {}, - "outputs": [], - "source": [ - "heading =['Collecting Sample id', 'Originating Laboratory', 'Submitting Institution', 'Sample Collection Date', 'geo_loc_country', 'geo_loc_state', 'organism', 'isolate', 'host_scientific_name', 'Host Common Name', 'host_disease', 'Sequencing Instrument Model', 'Sequencing Platforms', 'consensus_sequence_software_name', 'consensus_sequence_software_version', 'file_name', 'tax_id', 'sample_description', 'Library Source', 'Library Selection', 'Library Strategy', 'Library Layout', 'type', 'GISAID Virus Name', 'GISAID Id', 'Originating Laboratory Address']\n" - ] - }, - { - "cell_type": "code", - "execution_count": 71, - "id": "7ea69469", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "26" - ] - }, - "execution_count": 71, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "len(heading)" - ] - }, - { - "cell_type": "code", - "execution_count": 64, - "id": "54afd367", - "metadata": {}, - "outputs": [], - "source": [ - "map_file = open(\"schema/mapping_file.json\")\n", - "mapping_file = json.load(map_file)" - ] - }, - { - "cell_type": "code", - "execution_count": 65, - "id": "3d1e0f63", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'Collecting Sample id': 'sample_name',\n", - " 'Originating Laboratory': 'collecting_institution',\n", - " 'Submitting Institution': 'submitting_institution',\n", - " 'Sample Collection Date': 'sample_collection_date',\n", - " 'geo_loc_country': 'geo_loc_country',\n", - " 'geo_loc_state': 'geo_loc_state',\n", - " 'organism': 'organism',\n", - " 'isolate': 'isolate',\n", - " 'host_scientific_name': 'host_scientific_name',\n", - " 'Host Common Name': 'host_common_name',\n", - " 'host_disease': 'host_disease',\n", - " 'Sequencing Instrument Model': 'sequencing_instrument_model',\n", - " 'Sequencing Platforms': 'sequencing_instrument_platform',\n", - " 'consensus_sequence_software_name': 'consensus_sequence_software_name',\n", - " 'consensus_sequence_software_version': 'consensus_sequence_software_version',\n", - " 'file_name': 'file_name',\n", - " 'tax_id': 'tax_id',\n", - " 'sample_description': 'sample_description',\n", - " 'Library Source': 'library_source',\n", - " 'Library Selection': 'library_selection',\n", - " 'Library Strategy': 'library_strategy',\n", - " 'Library Layout': 'library_layout',\n", - " 'type': 'type',\n", - " 'GISAID Virus Name': 'virus_name',\n", - " 'GISAID Id': 'submitter',\n", - " 'Originating Laboratory Address': 'collecting_address'}" - ] - }, - "execution_count": 65, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "mapping_file" - ] - }, - { - "cell_type": "code", - "execution_count": 54, - "id": "def77932", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'sample_name'" - ] - }, - "execution_count": 54, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "list(mapping_file.values())[0]" - ] - }, - { - "cell_type": "code", - "execution_count": 70, - "id": "34b84069", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "0\n", - "1\n", - "2\n", - "3\n", - "4\n", - "5\n", - "6\n", - "7\n", - "8\n", - "9\n", - "10\n", - "11\n", - "12\n", - "13\n", - "14\n", - "15\n", - "16\n", - "17\n", - "18\n", - "19\n", - "20\n", - "21\n", - "22\n", - "23\n", - "24\n", - "25\n" - ] - } - ], - "source": [ - "for i in range(len(heading)):\n", - " print(i)" - ] - }, - { - "cell_type": "code", - "execution_count": 72, - "id": "1caa1045", - "metadata": {}, - "outputs": [], - "source": [ - "for i in range(len(heading)):\n", - " if heading[i] in list(mapping_file.keys()):\n", - " index = list(mapping_file).index(heading[i])\n", - " heading[index] = list(mapping_file.values())[index]\n", - " \n", - " \n" - ] - }, - { - "cell_type": "code", - "execution_count": 73, - "id": "8ab4a0c2", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['sample_name',\n", - " 'collecting_institution',\n", - " 'submitting_institution',\n", - " 'sample_collection_date',\n", - " 'geo_loc_country',\n", - " 'geo_loc_state',\n", - " 'organism',\n", - " 'isolate',\n", - " 'host_scientific_name',\n", - " 'host_common_name',\n", - " 'host_disease',\n", - " 'sequencing_instrument_model',\n", - " 'sequencing_instrument_platform',\n", - " 'consensus_sequence_software_name',\n", - " 'consensus_sequence_software_version',\n", - " 'file_name',\n", - " 'tax_id',\n", - " 'sample_description',\n", - " 'library_source',\n", - " 'library_selection',\n", - " 'library_strategy',\n", - " 'library_layout',\n", - " 'type',\n", - " 'virus_name',\n", - " 'submitter',\n", - " 'collecting_address']" - ] - }, - "execution_count": 73, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "heading" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "4689d46e", - "metadata": {}, - "outputs": [], - "source": [ - "dictionary = {'test':{1,3}, 'test2':{2}, 'test3':{2,3}}\n", - "\n", - "if 'test' in dictionary:\n", - " print(list(dictionary).index('test'))" - ] - }, - { - "cell_type": "code", - "execution_count": 27, - "id": "5ae4de88", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['Collecting Sample id',\n", - " 'Originating Laboratory',\n", - " 'Submitting Institution',\n", - " 'Sample Collection Date',\n", - " 'geo_loc_country',\n", - " 'geo_loc_state',\n", - " 'organism',\n", - " 'isolate',\n", - " 'host_scientific_name',\n", - " 'Host Common Name',\n", - " 'host_disease',\n", - " 'Sequencing Instrument Model',\n", - " 'Sequencing Platforms',\n", - " 'consensus_sequence_software_name',\n", - " 'consensus_sequence_software_version',\n", - " 'file_name',\n", - " 'tax_id',\n", - " 'sample_description',\n", - " 'Library Source',\n", - " 'Library Selection',\n", - " 'Library Strategy',\n", - " 'Library Layout',\n", - " 'type',\n", - " 'GISAID Virus Name',\n", - " 'GISAID Id',\n", - " 'Originating Laboratory Address']" - ] - }, - "execution_count": 27, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "heading" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "b212e5ee", - "metadata": {}, - "outputs": [], - "source": [ - " 'sample_name',\n", - " 'collecting_institution',\n", - " 'submitting_institution',\n", - "'sample_collection_date',\n", - " 'geo_loc_country',\n", - " 'geo_loc_state',\n", - " 'organism',\n", - " 'isolate',\n", - " 'host_scientific_name',\n", - " 'host_common_name',\n", - " 'host_disease',\n", - " 'sequencing_instrument_model',\n", - " 'sequencing_instrument_platform',\n", - " 'consensus_sequence_software_name',\n", - " 'consensus_sequence_software_version',\n", - " 'file_name',\n", - " 'tax_id',\n", - " 'sample_description',\n", - " 'library_source',\n", - " 'library_selection',\n", - " 'library_strategy',\n", - " 'library_layout',\n", - " 'type',\n", - " 'virus_name',\n", - " 'submitter',\n", - " 'collecting_institution_address'],\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "3124de94", - "metadata": {}, - "outputs": [], - "source": [ - "collecting_institution': 'Hospital Universitario de Basurto',\n", - "'collecting_institution_address': 'Avda. Montevideo, 18,Bilbao,Vizcaya, ',\n", - "'consensus_sequence_software_name': 'CLC Genomics Workbench 12',\n", - "'consensus_sequence_software_version': '. CLC Genomics Workbench 12,',\n", - "'file_name': 'filename2',\n", - "'geo_loc_country': 'Spain',\n", - "'geo_loc_state': 'Madrid',\n", - "'host_common_name': 'Human',\n", - "'host_disease': 'SARS-CoV2',\n", - "'host_scientific_name': 'Homo sapiens',\n", - "'isolate': 'SARS-CoV-2/human/USA/CA-CDPH-001/2020',\n", - "'library_layout': 'PAIRED',\n", - "'library_selection': 'RANDOM PCR',\n", - "'library_source': 'METAGENOMIC',\n", - "'library_strategy': 'WGS',\n", - "'organism': 'Severe acute respiratory syndrome coronavirus 2',\n", - "'sample_description': 'madnatory ENA description sample',\n", - "'sample_name': 'ID_001',\n", - "'sequencing_instrument_model': 'Illumina MiSeq',\n", - "'sequencing_instrument_platform': 'ILLUMINA',\n", - "'submitter': 'GISAID-Username',\n", - "'submitting_institution': 'Laboratorio de Microbiología de Bibao ',\n", - "'tax_id': 2697049,\n", - "'type': 'betacoronavirus',\n", - "'virus_name': 'hCoV-19/España/Vizcaya-01/2020'}\n", - "\n" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.9.5" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} From 68fddd165796c9653764a415951014b2d4f613e1 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 8 Mar 2022 13:06:16 +0100 Subject: [PATCH 0060/1454] Changed the heading to RELECOV --- relecov_tools/__main__.py | 146 +++++++++++++++++++++++++++----------- 1 file changed, 106 insertions(+), 40 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 263cd02c..f478ba73 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -7,42 +7,52 @@ import rich.console import rich.logging import rich.traceback -import sys import os import utils -#import nf_core -# conda install -c conda-forge click -# conda install -c conda-forge rich + +log = logging.getLogger() + def run_bu_isciii(): - # Set up rich stderr console + # Set up rich stderr console stderr = rich.console.Console(stderr=True, force_terminal=utils.rich_force_colors()) # Set up the rich traceback rich.traceback.install(console=stderr, width=200, word_wrap=True, extra_lines=1) # Print nf-core header - #stderr.print("\n[green]{},--.[grey39]/[green],-.".format(" " * 42), highlight=False) - stderr.print("[blue] ___ ___ ___ ___ ___ ___ ____ ", highlight=False) - stderr.print("[blue] \ |-[grey39]-| [blue] | \ | | | | | | | | ", highlight=False) - stderr.print("[blue] \ \ [grey39]/ [blue] |__ / | | ___ | |__ | | | | ", highlight=False) - stderr.print("[blue] / [grey39] / [blue] \ | \ | | | | | | | | ", highlight=False) - stderr.print("[blue] / [grey39] |-[blue]-| |__ / |___| _|__ ___| |___ _|_ _|_ _|_ ", highlight=False) - - - #stderr.print("[green] `._,._,'\n", highlight=False) - __version__ = '0.0.1' - stderr.print("[grey39] BU-ISCIII-tools version {}".format(__version__), highlight=False) - try: - pass - except: - pass + # stderr.print("\n[green]{},--.[grey39]/[green],-.".format(" " * 42), highlight=False) + stderr.print( + "[blue] ___ ___ ___ ___ ___ ", + highlight=False, + ) + stderr.print( + "[blue] \ |-[grey39]-| [blue] | \ | | | | | | \ / ", + highlight=False, + ) + stderr.print( + "[blue] \ \ [grey39]/ [blue] |__ / |__ | |___ | | | \ / ", + highlight=False, + ) + stderr.print( + "[blue] / [grey39] / [blue] \ | \ | | | | | | \ / ", + highlight=False, + ) + stderr.print( + "[blue] / [grey39] |-[blue]-| | \ |___ |___ |___ |___ |___| \/ ", + highlight=False, + ) + + # stderr.print("[green] `._,._,'\n", highlight=False) + __version__ = "0.0.1" + stderr.print( + "[grey39] RELECOV-tools version {}".format(__version__), highlight=False + ) # Lanch the click cli bu_isciii_cli() - # Customise the order of subcommands for --help class CustomHelpOrder(click.Group): def __init__(self, *args, **kwargs): @@ -56,7 +66,13 @@ def get_help(self, ctx): def list_commands_for_help(self, ctx): """reorder the list of commands when listing the help""" commands = super(CustomHelpOrder, self).list_commands(ctx) - return (c[1] for c in sorted((self.help_priorities.get(command, 1000), command) for command in commands)) + return ( + c[1] + for c in sorted( + (self.help_priorities.get(command, 1000), command) + for command in commands + ) + ) def command(self, *args, **kwargs): """Behaves the same as `click.Group.command()` except capture @@ -74,19 +90,28 @@ def decorator(f): @click.group(cls=CustomHelpOrder) -#@click.version_option(nf_core.__version__) -@click.option("-v", "--verbose", is_flag=True, default=False, help="Print verbose output to the console.") -@click.option("-l", "--log-file", help="Save a verbose log to a file.", metavar="") +@click.option( + "-v", + "--verbose", + is_flag=True, + default=False, + help="Print verbose output to the console.", +) +@click.option( + "-l", "--log-file", help="Save a verbose log to a file.", metavar="" +) def bu_isciii_cli(verbose, log_file): # Set the base logger to output DEBUG log.setLevel(logging.DEBUG) - # Set up logs to the console + # Set up logs to the console log.addHandler( rich.logging.RichHandler( level=logging.DEBUG if verbose else logging.INFO, - console=rich.console.Console(stderr=True, force_terminal=nf_core.utils.rich_force_colors()), + console=rich.console.Console( + stderr=True, force_terminal=nf_core.utils.rich_force_colors() + ), show_time=False, markup=True, ) @@ -96,9 +121,14 @@ def bu_isciii_cli(verbose, log_file): if log_file: log_fh = logging.FileHandler(log_file, encoding="utf-8") log_fh.setLevel(logging.DEBUG) - log_fh.setFormatter(logging.Formatter("[%(asctime)s] %(name)-20s [%(levelname)-7s] %(message)s")) + log_fh.setFormatter( + logging.Formatter( + "[%(asctime)s] %(name)-20s [%(levelname)-7s] %(message)s" + ) + ) log.addHandler(log_fh) + # pipeline list @bu_isciii_cli.command(help_priority=1) @click.argument("keywords", required=False, nargs=-1, metavar="") @@ -110,7 +140,9 @@ def bu_isciii_cli(verbose, log_file): help="How to sort listed pipelines", ) @click.option("--json", is_flag=True, default=False, help="Print full output as JSON") -@click.option("--show-archived", is_flag=True, default=False, help="Print archived workflows") +@click.option( + "--show-archived", is_flag=True, default=False, help="Print archived workflows" +) def list(keywords, sort, json, show_archived): """ List available bu-isciii workflows used for relecov. @@ -123,10 +155,16 @@ def list(keywords, sort, json, show_archived): # sftp @bu_isciii_cli.command(help_priority=2) @click.argument("pipeline", required=False, metavar="") -@click.option("-r", "--revision", help="Release/branch/SHA of the project to run (if remote)") +@click.option( + "-r", "--revision", help="Release/branch/SHA of the project to run (if remote)" +) @click.option("-i", "--id", help="ID for web-gui launch parameter set") @click.option( - "-c", "--command-only", is_flag=True, default=False, help="Create Nextflow command with params (no params file)" + "-c", + "--command-only", + is_flag=True, + default=False, + help="Create Nextflow command with params (no params file)", ) @click.option( "-o", @@ -135,20 +173,37 @@ def list(keywords, sort, json, show_archived): default=os.path.join(os.getcwd(), "nf-params.json"), help="Path to save run parameters file", ) -def sftp(pipeline, id, revision, command_only, params_in, params_out, save_all, show_hidden, url): - ''' +def sftp( + pipeline, + id, + revision, + command_only, + params_in, + params_out, + save_all, + show_hidden, + url, +): + """ Download files located in sftp server. - ''' + """ print(nf_core.list.list_workflows(keywords, sort, json, show_archived)) + # metadata @bu_isciii_cli.command(help_priority=3) @click.argument("pipeline", required=False, metavar="") -@click.option("-r", "--revision", help="Release/branch/SHA of the project to run (if remote)") +@click.option( + "-r", "--revision", help="Release/branch/SHA of the project to run (if remote)" +) @click.option("-i", "--id", help="ID for web-gui launch parameter set") @click.option( - "-c", "--command-only", is_flag=True, default=False, help="Create Nextflow command with params (no params file)" + "-c", + "--command-only", + is_flag=True, + default=False, + help="Create Nextflow command with params (no params file)", ) @click.option( "-o", @@ -157,12 +212,23 @@ def sftp(pipeline, id, revision, command_only, params_in, params_out, save_all, default=os.path.join(os.getcwd(), "nf-params.json"), help="Path to save run parameters file", ) -def metadata(pipeline, id, revision, command_only, params_in, params_out, save_all, show_hidden, url): - ''' +def metadata( + pipeline, + id, + revision, + command_only, + params_in, + params_out, + save_all, + show_hidden, + url, +): + """ Read Metadata . - ''' + """ print(nf_core.list.list_workflows(keywords, sort, json, show_archived)) - + + if __name__ == "__main__": run_bu_isciii() From 46cbf313576cdde8b806c96db3e4d24764b5fb6a Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 8 Mar 2022 14:01:31 +0100 Subject: [PATCH 0061/1454] Updating json schemas from merging bu-isciii --- schema/ena_v01.json | 1105 ++++++++++++++++++ schema/phage_plus_V0.json | 2285 +++++++++++++++++++++++++++++++++++++ test/validation_jsons.py | 176 +++ 3 files changed, 3566 insertions(+) create mode 100644 schema/ena_v01.json create mode 100644 schema/phage_plus_V0.json create mode 100644 test/validation_jsons.py diff --git a/schema/ena_v01.json b/schema/ena_v01.json new file mode 100644 index 00000000..d63f9093 --- /dev/null +++ b/schema/ena_v01.json @@ -0,0 +1,1105 @@ +{ + "$schema": "http://json-schema.org/draft/2019-09/schema#", + "required": [ + "sample_name", + "collecting_institution", + "geographic_location_(country_and/or_sea)", + "isolate", + "host_scientific_name", + "host_common_name", + "host_health_state", + "host_sex", + "host_subject_id", + "instrument_model", + "file_name", + "sample_name", + "tax_id", + "scientific_name", + "common_name", + "sample_description", + "library_source", + "library_selection", + "library_strategy", + "library_layout" + ], + "type": "object", + "properties": { + "sample_name": { + "examples": ["prov_rona_99"], + "ontology": "GENEPIO:0001123", + "type": "string", + "description": "The user-defined name for the sample.", + "clasification":"Database Identifiers", + "label":"Collecting Sample id" + + }, + "collecting_institution": { + "examples": ["Public Health Agency of Canada"], + "ontology": "GENEPIO:0001153", + "type": "string", + "description": "Name of the institution to which the person collecting the specimen belongs. Format: Institute Name, Institute Address", + "label":"Collecting Institution" + + }, + "collection_date": { + "examples": ["3/19/2020"], + "ontology": "GENEPIO:0001174", + "type": "string", + "description": "The date on which the sample was collected.", + "format":"date", + "classification":"Sample collection and processing", + "label":"Sample Collection Date" + }, + "receipt_date": { + "examples": ["3/21/2020"], + "ontology": "GENEPIO:0001179", + "type": "string", + "description": "The date on which the sample was received.", + "format":"date", + "clasification":"Sample collection and processing", + "label":"Sample Received Date" + }, + "geographic_location_(country_and/or_sea)": { + "Enums": [ + "Afghanistan [GAZ:00006882]", + "Albania [GAZ:00002953]", + "Algeria [GAZ:00000563]", + "American Samoa [GAZ:00003957]", + "Andorra [GAZ:00002948]", + "Angola [GAZ:00001095]", + "Anguilla [GAZ:00009159]", + "Antarctica [GAZ:00000462]", + "Antigua and Barbuda [GAZ:00006883]", + "Argentina [GAZ:00002928]", + "Armenia [GAZ:00004094]", + "Aruba [GAZ:00004025]", + "Ashmore and Cartier Islands [GAZ:00005901]", + "Australia [GAZ:00000463]", + "Austria [GAZ:00002942]", + "Azerbaijan [GAZ:00004941]", + "Bahamas [GAZ:00002733]", + "Bahrain [GAZ:00005281]", + "Baker Island [GAZ:00007117]", + "Bangladesh [GAZ:00003750]", + "Barbados [GAZ:00001251]", + "Bassas da India [GAZ:00005810]", + "Belarus [GAZ:00006886]", + "Belgium [GAZ:00002938]", + "Belize [GAZ:00002934]", + "Benin [GAZ:00000904]", + "Bermuda [GAZ:00001264]", + "Bhutan [GAZ:00003920]", + "Bolivia [GAZ:00002511]", + "Borneo [GAZ:00025355]", + "Bosnia and Herzegovina [GAZ:00006887]", + "Botswana [GAZ:00001097]", + "Bouvet Island [GAZ:00001453]", + "Brazil [GAZ:00002828]", + "British Virgin Islands [GAZ:00003961]", + "Brunei [GAZ:00003901]", + "Bulgaria [GAZ:00002950]", + "Burkina Faso [GAZ:00000905]", + "Burundi [GAZ:00001090]", + "Cambodia [GAZ:00006888]", + "Cameroon [GAZ:00001093]", + "Canada [GAZ:00002560]", + "Cape Verde [GAZ:00001227]", + "Cayman Islands [GAZ:00003986]", + "Central African Republic [GAZ:00001089]", + "Chad [GAZ:00000586]", + "Chile [GAZ:00002825]", + "China [GAZ:00002845]", + "Christmas Island [GAZ:00005915]", + "Clipperton Island [GAZ:00005838]", + "Cocos Islands [GAZ:00009721]", + "Colombia [GAZ:00002929]", + "Comoros [GAZ:00005820]", + "Cook Islands [GAZ:00053798]", + "Coral Sea Islands [GAZ:00005917]", + "Costa Rica [GAZ:00002901]", + "Cote d'Ivoire [GAZ:00000906]", + "Croatia [GAZ:00002719]", + "Cuba [GAZ:00003762]", + "Curacao [GAZ:00012582]", + "Cyprus [GAZ:00004006]", + "Czech Republic [GAZ:00002954]", + "Democratic Republic of the Congo [GAZ:00001086]", + "Denmark [GAZ:00005852]", + "Djibouti [GAZ:00000582]", + "Dominica [GAZ:00006890]", + "Dominican Republic [GAZ:00003952]", + "Ecuador [GAZ:00002912]", + "Egypt [GAZ:00003934]", + "El Salvador [GAZ:00002935]", + "Equatorial Guinea [GAZ:00001091]", + "Eritrea [GAZ:00000581]", + "Estonia [GAZ:00002959]", + "Eswatini [GAZ:00001099]", + "Ethiopia [GAZ:00000567]", + "Europa Island [GAZ:00005811]", + "Falkland Islands (Islas Malvinas) [GAZ:00001412]", + "Faroe Islands [GAZ:00059206]", + "Fiji [GAZ:00006891]", + "Finland [GAZ:00002937]", + "France [GAZ:00003940]", + "French Guiana [GAZ:00002516]", + "French Polynesia [GAZ:00002918]", + "French Southern and Antarctic Lands [GAZ:00003753]", + "Gabon [GAZ:00001092]", + "Gambia [GAZ:00000907]", + "Gaza Strip [GAZ:00009571]", + "Georgia [GAZ:00004942]", + "Germany [GAZ:00002646]", + "Ghana [GAZ:00000908]", + "Gibraltar [GAZ:00003987]", + "Glorioso Islands [GAZ:00005808]", + "Greece [GAZ:00002945]", + "Greenland [GAZ:00001507]", + "Grenada [GAZ:02000573]", + "Guadeloupe [GAZ:00067142]", + "Guam [GAZ:00003706]", + "Guatemala [GAZ:00002936]", + "Guernsey [GAZ:00001550]", + "Guinea [GAZ:00000909]", + "Guinea-Bissau [GAZ:00000910]", + "Guyana [GAZ:00002522]", + "Haiti [GAZ:00003953]", + "Heard Island and McDonald Islands [GAZ:00009718]", + "Honduras [GAZ:00002894]", + "Hong Kong [GAZ:00003203]", + "Howland Island [GAZ:00007120]", + "Hungary [GAZ:00002952]", + "Iceland [GAZ:00000843]", + "India [GAZ:00002839]", + "Indonesia [GAZ:00003727]", + "Iran [GAZ:00004474]", + "Iraq [GAZ:00004483]", + "Ireland [GAZ:00002943]", + "Isle of Man [GAZ:00052477]", + "Israel [GAZ:00002476]", + "Italy [GAZ:00002650]", + "Jamaica [GAZ:00003781]", + "Jan Mayen [GAZ:00005853]", + "Japan [GAZ:00002747]", + "Jarvis Island [GAZ:00007118]", + "Jersey [GAZ:00001551]", + "Johnston Atoll [GAZ:00007114]", + "Jordan [GAZ:00002473]", + "Juan de Nova Island [GAZ:00005809]", + "Kazakhstan [GAZ:00004999]", + "Kenya [GAZ:00001101]", + "Kerguelen Archipelago [GAZ:00005682]", + "Kingman Reef [GAZ:00007116]", + "Kiribati [GAZ:00006894]", + "Kosovo [GAZ:00011337]", + "Kuwait [GAZ:00005285]", + "Kyrgyzstan [GAZ:00006893]", + "Laos [GAZ:00006889]", + "Latvia [GAZ:00002958]", + "Lebanon [GAZ:00002478]", + "Lesotho [GAZ:00001098]", + "Liberia [GAZ:00000911]", + "Libya [GAZ:00000566]", + "Liechtenstein [GAZ:00003858]", + "Line Islands [GAZ:00007144]", + "Lithuania [GAZ:00002960]", + "Luxembourg [GAZ:00002947]", + "Macau [GAZ:00003202]", + "Madagascar [GAZ:00001108]", + "Malawi [GAZ:00001105]", + "Malaysia [GAZ:00003902]", + "Maldives [GAZ:00006924]", + "Mali [GAZ:00000584]", + "Malta [GAZ:00004017]", + "Marshall Islands [GAZ:00007161]", + "Martinique [GAZ:00067143]", + "Mauritania [GAZ:00000583]", + "Mauritius [GAZ:00003745]", + "Mayotte [GAZ:00003943]", + "Mexico [GAZ:00002852]", + "Micronesia [GAZ:00005862]", + "Midway Islands [GAZ:00007112]", + "Moldova [GAZ:00003897]", + "Monaco [GAZ:00003857]", + "Mongolia [GAZ:00008744]", + "Montenegro [GAZ:00006898]", + "Montserrat [GAZ:00003988]", + "Morocco [GAZ:00000565]", + "Mozambique [GAZ:00001100]", + "Myanmar [GAZ:00006899]", + "Namibia [GAZ:00001096]", + "Nauru [GAZ:00006900]", + "Navassa Island [GAZ:00007119]", + "Nepal [GAZ:00004399]", + "Netherlands [GAZ:00002946]", + "New Caledonia [GAZ:00005206]", + "New Zealand [GAZ:00000469]", + "Nicaragua [GAZ:00002978]", + "Niger [GAZ:00000585]", + "Nigeria [GAZ:00000912]", + "Niue [GAZ:00006902]", + "Norfolk Island [GAZ:00005908]", + "North Korea [GAZ:00002801]", + "North Macedonia [GAZ:00006895]", + "North Sea [GAZ:00002284]", + "Northern Mariana Islands [GAZ:00003958]", + "Norway [GAZ:00002699]", + "Oman [GAZ:00005283]", + "Pakistan [GAZ:00005246]", + "Palau [GAZ:00006905]", + "Panama [GAZ:00002892]", + "Papua New Guinea [GAZ:00003922]", + "Paracel Islands [GAZ:00010832]", + "Paraguay [GAZ:00002933]", + "Peru [GAZ:00002932]", + "Philippines [GAZ:00004525]", + "Pitcairn Islands [GAZ:00005867]", + "Poland [GAZ:00002939]", + "Portugal [GAZ:00004126]", + "Puerto Rico [GAZ:00006935]", + "Qatar [GAZ:00005286]", + "Republic of the Congo [GAZ:00001088]", + "Reunion [GAZ:00003945]", + "Romania [GAZ:00002951]", + "Ross Sea [GAZ:00023304]", + "Russia [GAZ:00002721]", + "Rwanda [GAZ:00001087]", + "Saint Helena [GAZ:00000849]", + "Saint Kitts and Nevis [GAZ:00006906]", + "Saint Lucia [GAZ:00006909]", + "Saint Pierre and Miquelon [GAZ:00003942]", + "Saint Martin [GAZ:00005841]", + "Saint Vincent and the Grenadines [GAZ:02000565]", + "Samoa [GAZ:00006910]", + "San Marino [GAZ:00003102]", + "Sao Tome and Principe [GAZ:00006927]", + "Saudi Arabia [GAZ:00005279]", + "Senegal [GAZ:00000913]", + "Serbia [GAZ:00002957]", + "Seychelles [GAZ:00006922]", + "Sierra Leone [GAZ:00000914]", + "Singapore [GAZ:00003923]", + "Sint Maarten [GAZ:00012579]", + "Slovakia [GAZ:00002956]", + "Slovenia [GAZ:00002955]", + "Solomon Islands [GAZ:00005275]", + "Somalia [GAZ:00001104]", + "South Africa [GAZ:00001094]", + "South Georgia and the South Sandwich Islands [GAZ:00003990]", + "South Korea [GAZ:00002802]", + "South Sudan [GAZ:00233439]", + "Spain [GAZ:00003936]", + "Spratly Islands [GAZ:00010831]", + "Sri Lanka [GAZ:00003924]", + "State of Palestine [GAZ:00002475]", + "Sudan [GAZ:00000560]", + "Suriname [GAZ:00002525]", + "Svalbard [GAZ:00005396]", + "Swaziland [GAZ:00001099]", + "Sweden [GAZ:00002729]", + "Switzerland [GAZ:00002941]", + "Syria [GAZ:00002474]", + "Taiwan [GAZ:00005341]", + "Tajikistan [GAZ:00006912]", + "Tanzania [GAZ:00001103]", + "Thailand [GAZ:00003744]", + "Timor-Leste [GAZ:00006913]", + "Togo [GAZ:00000915]", + "Tokelau [GAZ:00260188]", + "Tonga [GAZ:00006916]", + "Trinidad and Tobago [GAZ:00003767]", + "Tromelin Island [GAZ:00005812]", + "Tunisia [GAZ:00000562]", + "Turkey [GAZ:00000558]", + "Turkmenistan [GAZ:00005018]", + "Turks and Caicos Islands [GAZ:00003955]", + "Tuvalu [GAZ:00009715]", + "USA [GAZ:00002459]", + "Uganda [GAZ:00001102]", + "Ukraine [GAZ:00002724]", + "United Arab Emirates [GAZ:00005282]", + "United Kingdom [GAZ:00002637]", + "Uruguay [GAZ:00002930]", + "Uzbekistan [GAZ:00004979]", + "Vanuatu [GAZ:00006918]", + "Venezuela [GAZ:00002931]", + "Viet Nam [GAZ:00003756]", + "Virgin Islands [GAZ:00003959]", + "Wake Island [GAZ:00007111]", + "Wallis and Futuna [GAZ:00007191]", + "West Bank [GAZ:00009572]", + "Western Sahara [GAZ:00000564]", + "Yemen [GAZ:00005284]", + "Zambia [GAZ:00001107]", + "Zimbabwe [GAZ:00001106]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001181 ", + "type": "string", + "description": "The country of origin of the sample.", + "examples": ["South Africa [GAZ:00001094]"], + "clasification":"Sample collection and processing", + "label":"Geo Loc Autonomic Country" + + }, + "geographic location (region and locality)": { + "ontology": "GENEPIO:0100280", + "type": "string", + "description": "The county/region of origin of the sample.", + "examples": ["Derbyshire"], + "clasification":"Sample collection and processing", + "label":"Geo Loc Province" + + }, + "geographic location (latitude)": { + "ontology": "OBI:0001620", + "type": "string", + "description": "The latitude coordinates of the geographical location of sample collection.", + "examples": ["38.98 N"], + "clasification":"Sample collection and processing", + "label":"Geo Loc Latitude", + + }, + "geographic location (longitude)": { + "ontology": "OBI:0001621", + "type": "string", + "description": "The longitude coordinates of the geographical location of sample collection.", + "examples": ["77.11 W"], + "clasification":"Sample collection and processing", + "label":"Geo Loc Longitude" + }, + "isolate": { + "ontology": "GENEPIO:0001644", + "type": "string", + "description": "Identifier of the specific isolate.", + "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"], + "genepio_label":"isolate identifier", + "clasification":"Sample collection and processing", + "label":"Isolate" + + }, + "purpose_sampling": { + "examples": ["Diagnostic testing"], + "ontology": "NCIT_C146997", + "type": "string", + "description": "The reason that the sample was collected.", + "clasification":"Sample collection and processing" + }, + "isolation source host-associated": { + "Enums": [ + "Blood [UBERON:0000178]", + "Fluid [UBERON:0006314]", + "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", + "Fluid (Pericardial) [UBERON:0002409]", + "Fluid (Pleural) [UBERON:0001087]", + "Fluid (Vaginal) [UBERON:0036243]", + "Fluid (Amniotic) [UBERON:0000173]", + "Saliva [UBERON:0001836]", + "Tissue [UBERON:0000479]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001211", + "type": "string", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "examples": ["Blood [UBERON:0000178]"], + "classification":"Sample collection and processing", + "label":"Organism Substance" + + }, + "isolation source non-host-associated": { + "Enums": [ + "Air vent [ENVO:03501208]", + "Banknote [ENVO:00003896]", + "Bed rail [ENVO:03501209]", + "Building Floor [ENVO:01000486]", + "Cloth [ENVO:02000058]", + "Control Panel [ENVO:03501210]", + "Door [ENVO:03501220]", + "Door Handle [ENVO:03501211]", + "Face Mask [OBI:0002787]", + "Face Shield [OBI:0002791]", + "Food [FOODON:00002403]", + "Food Packaging [FOODON:03490100]", + "Glass [ENVO:01000481]", + "Handrail [ENVO:03501212]", + "Hospital Gown [OBI:0002796]", + "Light Switch [ENVO:03501213]", + "Locker [ENVO:03501214]", + "N95 Mask [OBI:0002790]", + "Nurse Call Button [ENVO:03501215]", + "Paper [ENVO:03501256]", + "Particulate Matter [ENVO:01000060]", + "Plastic [ENVO:01000404]", + "PPE Gown [GENEPIO:0100025]", + "Sewage [ENVO:00002018]", + "Sink [ENVO:01000990]", + "Soil [ENVO:00001998]", + "Stainless Steel [ENVO:03501216]", + "Tissue Paper [ENVO:03501217]", + "Toilet Bowl [ENVO:03501218]", + "Water [ENVO:00002006]", + "Wastewater [ENVO:00002001]", + "Window [ENVO:03501219]", + "Wood [ENVO:00002040]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001223", + "type": "string", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "examples": ["Face Mask [OBI:0002787]"], + "clasification":"Sample collection and processing", + "label":"Environmental Material" + }, + "host common name": { + "Enums": [ + "Human [NCBITaxon:9606]", + "Bat [NCBITaxon:9397]", + "Cat [NCBITaxon:9685]", + "Chicken [NCBITaxon:9031]", + "Civet [NCBITaxon:9673]", + "Cow [NCBITaxon:9913]", + "Dog [NCBITaxon:9615]", + "Lion [NCBITaxon:9689]", + "Mink [NCBITaxon:452646]", + "Pangolin [NCBITaxon:9973]", + "Pig [NCBITaxon:9825]", + "Pigeon [NCBITaxon:8930]", + "Tiger [NCBITaxon:9694]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001386", + "type": "string", + "description": "The commonly used name of the host.", + "examples": ["Human [NCBITaxon:9606]"], + "classification":"Host information", + "label":"Host Common Name" + + }, + "host scientific name": { + "Enums": [ + "Bos taurus [NCBITaxon:9913]", + "Canis lupus familiaris [NCBITaxon:9615]", + "Chiroptera [NCBITaxon:9397]", + "Columbidae [NCBITaxon:8930]", + "Felis catus [NCBITaxon:9685]", + "Gallus gallus [NCBITaxon:9031]", + "Homo sapiens [NCBITaxon:9606]", + "Manis [NCBITaxon:9973]", + "Manis javanica [NCBITaxon:9974]", + "Neovison vison [NCBITaxon:452646]", + "Panthera leo [NCBITaxon:9689]", + "Panthera tigris [NCBITaxon:9694]", + "Rhinolophidae [NCBITaxon:58055]", + "Rhinolophus affinis [NCBITaxon:59477]", + "Sus scrofa domesticus [NCBITaxon:9825]", + "Viverridae [NCBITaxon:9673]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001387", + "type": "string", + "description": "The taxonomic, or scientific name of the host.", + "examples": ["Homo sapiens [NCBITaxon:9606]"], + "clasification":"Host information", + "label":"Host Scientific Name" + + }, + "host_health_state": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Health status of the host at the time of sample collection.", + "clasification":"Host information", + "genepio_label":"", + + }, + "host_age": { + "examples": ["e.g. 65 or 7 months, or unknown. Caution: the host age may be considered public health identifiable information. Consult the data steward before sharing. If the information is unknown or can not be shared, put unknown"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Patient age", + "clasification":"Host information" + }, + + "host_sex": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Gender or sex of the host.", + "clasification":"Host information", + "genepio_label":"", + + }, + "host_subject_id": { + "examples": ["e.g. #131"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "a unique identifier by which each subject can be referred to, de-identified.", + "clasification":"Host information", + "genepio_label":"", + + }, + "type exposure": { + "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], + "ontology": "GENEPIO:0001417", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification":"Host information", + "label":"Outbreak Exposure Event Location" + + }, + "subject exposure duration": { + "examples": ["e.g. Patient infected while traveling in …."], + "ontology": "0", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification":"Host information", + "label":"Additional Host Information" + + }, + "instrument_model": { + "Enums": [ + "Illumina sequencing instrument [GENEPIO:0100105]", + "Illumina Genome Analyzer [GENEPIO:0100106]", + "Illumina Genome Analyzer II [GENEPIO:0100107]", + "Illumina Genome Analyzer IIx [GENEPIO:0100108]", + "Illumina HiScanSQ [GENEPIO:0100109]", + "Illumina HiSeq [GENEPIO:0100110]", + "Illumina HiSeq X [GENEPIO:0100111]", + "Illumina HiSeq X Five [GENEPIO:0100112]", + "Illumina HiSeq X Ten [GENEPIO:0100113]", + "Illumina HiSeq 1000 [GENEPIO:0100114]", + "Illumina HiSeq 1500 [GENEPIO:0100115]", + "Illumina HiSeq 2000 [GENEPIO:0100116]", + "Illumina HiSeq 2500 [GENEPIO:0100117]", + "Illumina HiSeq 3000 [GENEPIO:0100118]", + "Illumina HiSeq 4000 [GENEPIO:0100119]", + "Illumina iSeq [GENEPIO:0100120]", + "Illumina iSeq 100 [GENEPIO:0100121]", + "Illumina NovaSeq [GENEPIO:0100122]", + "Illumina NovaSeq 6000 [GENEPIO:0100123]", + "Illumina MiniSeq [GENEPIO:0100124]", + "Illumina MiSeq [GENEPIO:0100125]", + "Illumina NextSeq [GENEPIO:0100126]", + "Illumina NextSeq 500 [GENEPIO:0100127]", + "Illumina NextSeq 550 [GENEPIO:0100128]", + "Illumina NextSeq 2000 [GENEPIO:0100129]", + "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", + "PacBio RS [GENEPIO:0100131]", + "PacBio RS II [GENEPIO:0100132]", + "PacBio Sequel [GENEPIO:0100133]", + "PacBio Sequel II [GENEPIO:0100134]", + "Ion Torrent sequencing instrument [GENEPIO:0100135]", + "Ion Torrent PGM [GENEPIO:0100136]", + "Ion Torrent Proton [GENEPIO:0100137]", + "Ion Torrent S5 XL [GENEPIO:0100138]", + "Ion Torrent S5 [GENEPIO:0100139]", + "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", + "Oxford Nanopore GridION [GENEPIO:0100141]", + "Oxford Nanopore MinION [GENEPIO:0100142]", + "Oxford Nanopore PromethION [GENEPIO:0100143]", + "BGI Genomics sequencing instrument [GENEPIO:0100144]", + "BGI SEQ-500 [GENEPIO:0100145]", + "MGI sequencing instrument [GENEPIO:0100146]", + "MGI DNBSEQ-T7 [GENEPIO:0100147]", + "MGI DNBSEQ-G400 [GENEPIO:0100148]", + "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", + "MGI DNBSEQ-G50 [GENEPIO:0100150]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001452", + "type": "string", + "description": "The model of the sequencing instrument used.", + "examples": ["Oxford Nanopore MinION [GENEPIO:0100142]"], + "classification":"Sequencing", + "label":"Sequencing Instrument Model" + }, + "instrument_platform ": { + "examples": ["MinIon"], + "ontology": "0", + "type": "string", + "description": "The model of the sequencing instrument used.", + "label":"Sequencing Platforms " + }, + "file_name": { + "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], + "ontology": "GENEPIO:0001476", + "type": "string", + "description": "The user-specified filename of the r1 FASTQ file.", + "clasification":"Bioinformatics and QC metrics", + "label":"Sequence file R1 fastq" + }, + "tax_id": { + "examples": ["probably 2697049 in all cases"], + "ontology": "GENEPIO_0001724", + "type": "string", + "description": "The NCBITaxon identifier for the organism being sequenced.", + "clasification":"Sample collection and processing", + "label":"Tax ID" + }, + "scientific_name": { + "Enums": [ + "Coronaviridae [NCBITaxon:11118]", + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "examples": [""], + "ontology": "GENEPIO:0001191", + "type": "string", + "description": "The taxonomic name of the organism.", + "clasification":"Sample collection and processing", + "classification":"Sample collection and processing", + "label":"Organism" + }, + "common_name": { + "examples": [""], + "ontology": "BU_ISCIII:003", + "type": "string", + "description": "The common name of the organism.", + "clasification":"Sample collection and processing", + "label":"Common name" + }, + "sample_description": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Free text description of the sample.", + "clasification":"Sample collection and processing", + "genepio_label":"", + + }, + "sample_storage_conditions": { + "examples": ["24 degrees celsius"], + "ontology": "NCIT_C115535", + "type": "string", + "description": "The name and version of a particular protocol used for sampling.", + "clasification":"Sample collection and processing" + }, + "library_source": { + "Enums": ["5-methycytidine antibody method [GENPIO:0001941]", + "CAGE method [GENPIO:0001942]", + "CF-H method [GENPIO:0001943]", + "CF-M method ]GENPIO:0001944]", + "CF-S method [GENPIO:0001945]", + "CF-T method [GENPIO:0001946]", + "ChIP method ]GENPIO:0001947]", + "DNAse method [GENPIO:0001948]", + "HMPR method [GENPIO:0001949]", + "Hybrid Selection Method [GENPIO:0001950]", + "MBD2 protein methyl-CpG binding domain method [GENPIO:0001951]", + "MF method [GENPIO:0001952]", + "MNase method [GENPIO:0001953]", + "MSLL method [GENPIO:0001954]", + "PCR method [GENPIO:0001955]", + "RACE method [GENPIO:0001956]", + "RANDOM PCR method [GENPIO:0001957]", + "RANDOM method [GENPIO:0001958]", + "RT-PCR method [GENPIO:0001959]", + "Reduced Representation method [GENPIO:0001960]", + "Resctriction Digest method [GENPIO:0001961]", + "cDNA method [GENPIO:0001962]", + "other library method [GENPIO:0001964]", + "size fractionation method [GENPIO:0001963]", + ], + "examples": ["METAGENOMIC"], + "ontology": "GENEPIO_0001965", + "type": "string", + "description": "Molecule type used to make the library.", + "clasification":"Sequencing", + "label":"Source material" + }, + "library_selection": { + "examples": ["RANDOM PCR"], + "ontology": "GENPIO_0001940", + "type": "string", + "description": "Library capture method.", + "clasification":"Sequencing", + "label":"Capture method" + }, + "library_strategy": { + "Enums": ["Bisultife-Seq strategy [GENPIO:0001975]", + "CTS strategy [GENPIO:0001978]", + "ChIP-Seq strategy [GENPIO:0001979]", + "DNase-Hypersensitivity strategy [GENPIO:0001980]", + "EST strategy [GENPIO:0001981]", + "FL-cDNA strategy [GENPIO:0001983]", + "MB-Seq strategy [GENPIO:0001984]", + "MNase-Seq strategy [GENPIO:0001985]", + "MRE-Seq strategy [GENPIO:0001986]", + "MeDIP-Seq strategy [GENPIO:0001987]", + "RNA-Seq strategy [GENPIO:0001990]", + "WCS strategy [GENPIO:0001991]", + "WGS strategy [GENPIO:0001992]", + "WXS strategy [GENPIO:0001993]", + "amplicon strategy [GENPIO:0001974]", + "clone end strategy [GENPIO:0001976]", + "clone strategy [GENPIO:0001977]", + "finishing strategy [GENPIO:0001982]", + "other library strategy [GENPIO:0001988]", + "pool clone strategy [GENPIO:0001989]", + ], + "examples": ["WGS"], + "ontology": "GENPIO_0001973", + "type": "string", + "description": "Overall sequencing strategy or approach.", + "clasification":"Sequencing", + "label":"Sequencing technique" + }, + "library_layout": { + "examples": ["PAIRED"], + "ontology":"BU_ISCIII:007", + "type": "string", + "description": "Single or paired.", + "clasification":"Sequencing", + "label":"Library Layout" + }, + "library_name": { + "examples": ["e.g P17157_1007"], + "ontology": "GENEPIO_0001995", + "type": "string", + "description": "The submitter's name for this library.", + "clasification":"Sequencing", + "label":"Library Name" + }, + "nominal_length ": { + "examples": ["350"], + "ontology": "GENEPIO_0000076", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"Nominal Length" + }, + "analysis_accession": { + "examples": [""], + "ontology": "GENEPIO_0001145", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Analysis Accession" + }, + "read_length": { + "examples": [""], + "ontology": "STATO_0000064", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Read length" + }, + "study_accession": { + "examples": ["e.g PRJEB39632"], + "ontology": "GENEPIO_0001136", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Study accession" + }, + "secondary_study_accession": { + "examples": ["e.g ERP123173"], + "ontology": "BU_ISCIII:012", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Secondary study accession" + }, + "sample_accession": { + "examples": ["e.g SAMEA7098096"], + "ontology": "GENEPIO_0001139", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Sample accession" + }, + "secondary_sample_accession": { + "examples": ["e.g ERS4858671"], + "ontology": "BU_ISCIII:014", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Secondary sample accession" + }, + "experiment_accession": { + "examples": ["e.g ERX4331406"], + "ontology": "BU_ISCIII:015", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Experiment Accession" + }, + "run_accession": { + "examples": ["e.g ERX4331406"], + "ontology": "BU_ISCIII:016", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Run Accession" + }, + "submission_accession": { + "examples": ["e.g ERA2794974"], + "ontology": "BU_ISCIII:017", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submission accession" + }, + "read_count": { + "examples": ["e.g 837055"], + "ontology": "STATO_0000064", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Read count" + }, + "base_count": { + "examples": ["e.g 503907110"], + "ontology": "UO_0000244", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Base count" + }, + "center_name": { + "examples": [" KAROLINSKA INSITUTET"], + "ontology": "NCIT_C19983", + "type": "string", + "description": "The name of the institution", + "clasification":"Sample collection and processing", + "label":"Center Name" + }, + "first_public": { + "examples": ["e.g 2020-08-07"], + "ontology": "NCIT_C142711", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"First Public date" + }, + "last_updated": { + "examples": ["e.g 2020-07-29"], + "ontology": "OMIABIS_0001005", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "format":"Last Updated" + }, + "experiment_title": { + "examples": ["e.g Illumina MiSeq paired end sequencing"], + "ontology": "ORNASEQ_0000004", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Experiment title" + }, + "study_title": { + "examples": ["e.g SARS-CoV-2 genomes from late April in Stockholm"], + "ontology": "OPMI_0000380", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Study title" + }, + "study_alias": { + "examples": ["e.g Sweden"], + "ontology": "SIO_001066", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Study alias" + }, + "experiment_alias": { + "examples": ["e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092"], + "ontology": "NCIT_C42790", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Experiment alias" + }, + "run_alias": { + "examples": ["e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], + "ontology": "NCIT_C47911", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Run Alias" + }, + "fastq_bytes": { + "examples": ["e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], + "ontology": "NCIT_C48047", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Fastq bytes" + }, + "fastq_md5": { + "examples": [""], + "ontology": "MS_1000568", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Fastq md5" + }, + "fastq_ftp": { + "examples": [""], + "ontology": "PRIDE_0000469", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Fastq ftp" + }, + "fastq_aspera": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], + "ontology": "BU_ISCIII:032", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Fastq aspera" + }, + "fastq_galaxy": { + "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], + "ontology": "ENVO_01000807", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Fastq galaxy" + }, + "submitted_bytes": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], + "ontology": "NCIT_C172872", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted bytes " + }, + "submitted_md5": { + "examples": ["e.g 139853010;166270048"], + "ontology": "BU_ISCIII:035", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted md5" + }, + "submitted_ftp": { + "examples": ["e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a"], + "ontology": "BU_ISCIII:036", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted ftp" + }, + "submitted_aspera": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], + "ontology": "BU_ISCIII:037", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted aspera" + }, + "submitted_galaxy": { + "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], + "ontology": "BU_ISCIII:038", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted Galaxy" + }, + "submitted_format": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], + "ontology": "BU_ISCIII:039", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted Format" + }, + "sra_bytes": { + "examples": ["e.g FASTQ;FASTQ"], + "ontology": "BU_ISCIII:040", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"SRA bytes" + }, + "sra_md5": { + "examples": ["e.g 260236789"], + "ontology": "BU_ISCIII:041", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"SRA md5" + }, + "sra_ftp": { + "examples": ["e.g 2cf0d467d6dc4ae0a5473774d54c059c"], + "ontology": "BU_ISCIII:042", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"SRA ftp" + }, + "sra_aspera": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385"], + "ontology": "BU_ISCIII:043", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"SRA aspera" + }, + "sra_galaxy": { + "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385"], + "ontology": "BU_ISCIII:044", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"SRA galaxy" + }, + "broker_name": { + "examples": ["P17157_1007"], + "ontology": "BU_ISCIII:045", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Broker Name" + }, + "nominal_sdev": { + "examples": [""], + "ontology": "STATO_0000237", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Nominal sdev" + }, + "first_created": { + "examples": ["e.g 2020-08-07"], + "ontology": "NCIT_C164483", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"First created date" + } + + } +} diff --git a/schema/phage_plus_V0.json b/schema/phage_plus_V0.json new file mode 100644 index 00000000..4d0bc178 --- /dev/null +++ b/schema/phage_plus_V0.json @@ -0,0 +1,2285 @@ +{ + "$schema": "http://json-schema.org/draft/2020-12/schema", + "required": [ + "sample_name", + "collecting_institution", + "submitting_institution", + "sample_collection_date", + "geo_loc_country", + "geo_loc_state", + "organism", + "isolate", + "host_scientific_name", + "host_disease", + "sequencing_instrument_model", + "sequencing_instrument_platform", + "consensus_sequence_software_name", + "consensus_sequence_software_version" + ], + "type": "object", + "properties": { + "sample_name": { + "examples": ["prov_rona_99"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The user-defined name for the sample.", + "clasification":"Database Identifiers" + }, + "collecting_institution": { + "examples": ["Public Health Agency of Canada"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The name of the agency that collected the original sample." + }, + "submitting_institution": { + "examples": ["Centers for Disease Control and Prevention"], + "ontology": "GENEPIO:0001159", + "type": "string", + "description": "The name of the agency that generated the sequence." + }, + "sample_collection_date": { + "examples": ["3/19/2020"], + "ontology": "GENEPIO:0001174", + "type": "string", + "description": "The date on which the sample was collected.", + "format":"date" + }, + "geo_loc_name_country": { + "Enums": [ + "Afghanistan [GAZ:00006882]", + "Albania [GAZ:00002953]", + "Algeria [GAZ:00000563]", + "American Samoa [GAZ:00003957]", + "Andorra [GAZ:00002948]", + "Angola [GAZ:00001095]", + "Anguilla [GAZ:00009159]", + "Antarctica [GAZ:00000462]", + "Antigua and Barbuda [GAZ:00006883]", + "Argentina [GAZ:00002928]", + "Armenia [GAZ:00004094]", + "Aruba [GAZ:00004025]", + "Ashmore and Cartier Islands [GAZ:00005901]", + "Australia [GAZ:00000463]", + "Austria [GAZ:00002942]", + "Azerbaijan [GAZ:00004941]", + "Bahamas [GAZ:00002733]", + "Bahrain [GAZ:00005281]", + "Baker Island [GAZ:00007117]", + "Bangladesh [GAZ:00003750]", + "Barbados [GAZ:00001251]", + "Bassas da India [GAZ:00005810]", + "Belarus [GAZ:00006886]", + "Belgium [GAZ:00002938]", + "Belize [GAZ:00002934]", + "Benin [GAZ:00000904]", + "Bermuda [GAZ:00001264]", + "Bhutan [GAZ:00003920]", + "Bolivia [GAZ:00002511]", + "Borneo [GAZ:00025355]", + "Bosnia and Herzegovina [GAZ:00006887]", + "Botswana [GAZ:00001097]", + "Bouvet Island [GAZ:00001453]", + "Brazil [GAZ:00002828]", + "British Virgin Islands [GAZ:00003961]", + "Brunei [GAZ:00003901]", + "Bulgaria [GAZ:00002950]", + "Burkina Faso [GAZ:00000905]", + "Burundi [GAZ:00001090]", + "Cambodia [GAZ:00006888]", + "Cameroon [GAZ:00001093]", + "Canada [GAZ:00002560]", + "Cape Verde [GAZ:00001227]", + "Cayman Islands [GAZ:00003986]", + "Central African Republic [GAZ:00001089]", + "Chad [GAZ:00000586]", + "Chile [GAZ:00002825]", + "China [GAZ:00002845]", + "Christmas Island [GAZ:00005915]", + "Clipperton Island [GAZ:00005838]", + "Cocos Islands [GAZ:00009721]", + "Colombia [GAZ:00002929]", + "Comoros [GAZ:00005820]", + "Cook Islands [GAZ:00053798]", + "Coral Sea Islands [GAZ:00005917]", + "Costa Rica [GAZ:00002901]", + "Cote d'Ivoire [GAZ:00000906]", + "Croatia [GAZ:00002719]", + "Cuba [GAZ:00003762]", + "Curacao [GAZ:00012582]", + "Cyprus [GAZ:00004006]", + "Czech Republic [GAZ:00002954]", + "Democratic Republic of the Congo [GAZ:00001086]", + "Denmark [GAZ:00005852]", + "Djibouti [GAZ:00000582]", + "Dominica [GAZ:00006890]", + "Dominican Republic [GAZ:00003952]", + "Ecuador [GAZ:00002912]", + "Egypt [GAZ:00003934]", + "El Salvador [GAZ:00002935]", + "Equatorial Guinea [GAZ:00001091]", + "Eritrea [GAZ:00000581]", + "Estonia [GAZ:00002959]", + "Eswatini [GAZ:00001099]", + "Ethiopia [GAZ:00000567]", + "Europa Island [GAZ:00005811]", + "Falkland Islands (Islas Malvinas) [GAZ:00001412]", + "Faroe Islands [GAZ:00059206]", + "Fiji [GAZ:00006891]", + "Finland [GAZ:00002937]", + "France [GAZ:00003940]", + "French Guiana [GAZ:00002516]", + "French Polynesia [GAZ:00002918]", + "French Southern and Antarctic Lands [GAZ:00003753]", + "Gabon [GAZ:00001092]", + "Gambia [GAZ:00000907]", + "Gaza Strip [GAZ:00009571]", + "Georgia [GAZ:00004942]", + "Germany [GAZ:00002646]", + "Ghana [GAZ:00000908]", + "Gibraltar [GAZ:00003987]", + "Glorioso Islands [GAZ:00005808]", + "Greece [GAZ:00002945]", + "Greenland [GAZ:00001507]", + "Grenada [GAZ:02000573]", + "Guadeloupe [GAZ:00067142]", + "Guam [GAZ:00003706]", + "Guatemala [GAZ:00002936]", + "Guernsey [GAZ:00001550]", + "Guinea [GAZ:00000909]", + "Guinea-Bissau [GAZ:00000910]", + "Guyana [GAZ:00002522]", + "Haiti [GAZ:00003953]", + "Heard Island and McDonald Islands [GAZ:00009718]", + "Honduras [GAZ:00002894]", + "Hong Kong [GAZ:00003203]", + "Howland Island [GAZ:00007120]", + "Hungary [GAZ:00002952]", + "Iceland [GAZ:00000843]", + "India [GAZ:00002839]", + "Indonesia [GAZ:00003727]", + "Iran [GAZ:00004474]", + "Iraq [GAZ:00004483]", + "Ireland [GAZ:00002943]", + "Isle of Man [GAZ:00052477]", + "Israel [GAZ:00002476]", + "Italy [GAZ:00002650]", + "Jamaica [GAZ:00003781]", + "Jan Mayen [GAZ:00005853]", + "Japan [GAZ:00002747]", + "Jarvis Island [GAZ:00007118]", + "Jersey [GAZ:00001551]", + "Johnston Atoll [GAZ:00007114]", + "Jordan [GAZ:00002473]", + "Juan de Nova Island [GAZ:00005809]", + "Kazakhstan [GAZ:00004999]", + "Kenya [GAZ:00001101]", + "Kerguelen Archipelago [GAZ:00005682]", + "Kingman Reef [GAZ:00007116]", + "Kiribati [GAZ:00006894]", + "Kosovo [GAZ:00011337]", + "Kuwait [GAZ:00005285]", + "Kyrgyzstan [GAZ:00006893]", + "Laos [GAZ:00006889]", + "Latvia [GAZ:00002958]", + "Lebanon [GAZ:00002478]", + "Lesotho [GAZ:00001098]", + "Liberia [GAZ:00000911]", + "Libya [GAZ:00000566]", + "Liechtenstein [GAZ:00003858]", + "Line Islands [GAZ:00007144]", + "Lithuania [GAZ:00002960]", + "Luxembourg [GAZ:00002947]", + "Macau [GAZ:00003202]", + "Madagascar [GAZ:00001108]", + "Malawi [GAZ:00001105]", + "Malaysia [GAZ:00003902]", + "Maldives [GAZ:00006924]", + "Mali [GAZ:00000584]", + "Malta [GAZ:00004017]", + "Marshall Islands [GAZ:00007161]", + "Martinique [GAZ:00067143]", + "Mauritania [GAZ:00000583]", + "Mauritius [GAZ:00003745]", + "Mayotte [GAZ:00003943]", + "Mexico [GAZ:00002852]", + "Micronesia [GAZ:00005862]", + "Midway Islands [GAZ:00007112]", + "Moldova [GAZ:00003897]", + "Monaco [GAZ:00003857]", + "Mongolia [GAZ:00008744]", + "Montenegro [GAZ:00006898]", + "Montserrat [GAZ:00003988]", + "Morocco [GAZ:00000565]", + "Mozambique [GAZ:00001100]", + "Myanmar [GAZ:00006899]", + "Namibia [GAZ:00001096]", + "Nauru [GAZ:00006900]", + "Navassa Island [GAZ:00007119]", + "Nepal [GAZ:00004399]", + "Netherlands [GAZ:00002946]", + "New Caledonia [GAZ:00005206]", + "New Zealand [GAZ:00000469]", + "Nicaragua [GAZ:00002978]", + "Niger [GAZ:00000585]", + "Nigeria [GAZ:00000912]", + "Niue [GAZ:00006902]", + "Norfolk Island [GAZ:00005908]", + "North Korea [GAZ:00002801]", + "North Macedonia [GAZ:00006895]", + "North Sea [GAZ:00002284]", + "Northern Mariana Islands [GAZ:00003958]", + "Norway [GAZ:00002699]", + "Oman [GAZ:00005283]", + "Pakistan [GAZ:00005246]", + "Palau [GAZ:00006905]", + "Panama [GAZ:00002892]", + "Papua New Guinea [GAZ:00003922]", + "Paracel Islands [GAZ:00010832]", + "Paraguay [GAZ:00002933]", + "Peru [GAZ:00002932]", + "Philippines [GAZ:00004525]", + "Pitcairn Islands [GAZ:00005867]", + "Poland [GAZ:00002939]", + "Portugal [GAZ:00004126]", + "Puerto Rico [GAZ:00006935]", + "Qatar [GAZ:00005286]", + "Republic of the Congo [GAZ:00001088]", + "Reunion [GAZ:00003945]", + "Romania [GAZ:00002951]", + "Ross Sea [GAZ:00023304]", + "Russia [GAZ:00002721]", + "Rwanda [GAZ:00001087]", + "Saint Helena [GAZ:00000849]", + "Saint Kitts and Nevis [GAZ:00006906]", + "Saint Lucia [GAZ:00006909]", + "Saint Pierre and Miquelon [GAZ:00003942]", + "Saint Martin [GAZ:00005841]", + "Saint Vincent and the Grenadines [GAZ:02000565]", + "Samoa [GAZ:00006910]", + "San Marino [GAZ:00003102]", + "Sao Tome and Principe [GAZ:00006927]", + "Saudi Arabia [GAZ:00005279]", + "Senegal [GAZ:00000913]", + "Serbia [GAZ:00002957]", + "Seychelles [GAZ:00006922]", + "Sierra Leone [GAZ:00000914]", + "Singapore [GAZ:00003923]", + "Sint Maarten [GAZ:00012579]", + "Slovakia [GAZ:00002956]", + "Slovenia [GAZ:00002955]", + "Solomon Islands [GAZ:00005275]", + "Somalia [GAZ:00001104]", + "South Africa [GAZ:00001094]", + "South Georgia and the South Sandwich Islands [GAZ:00003990]", + "South Korea [GAZ:00002802]", + "South Sudan [GAZ:00233439]", + "Spain [GAZ:00003936]", + "Spratly Islands [GAZ:00010831]", + "Sri Lanka [GAZ:00003924]", + "State of Palestine [GAZ:00002475]", + "Sudan [GAZ:00000560]", + "Suriname [GAZ:00002525]", + "Svalbard [GAZ:00005396]", + "Swaziland [GAZ:00001099]", + "Sweden [GAZ:00002729]", + "Switzerland [GAZ:00002941]", + "Syria [GAZ:00002474]", + "Taiwan [GAZ:00005341]", + "Tajikistan [GAZ:00006912]", + "Tanzania [GAZ:00001103]", + "Thailand [GAZ:00003744]", + "Timor-Leste [GAZ:00006913]", + "Togo [GAZ:00000915]", + "Tokelau [GAZ:00260188]", + "Tonga [GAZ:00006916]", + "Trinidad and Tobago [GAZ:00003767]", + "Tromelin Island [GAZ:00005812]", + "Tunisia [GAZ:00000562]", + "Turkey [GAZ:00000558]", + "Turkmenistan [GAZ:00005018]", + "Turks and Caicos Islands [GAZ:00003955]", + "Tuvalu [GAZ:00009715]", + "USA [GAZ:00002459]", + "Uganda [GAZ:00001102]", + "Ukraine [GAZ:00002724]", + "United Arab Emirates [GAZ:00005282]", + "United Kingdom [GAZ:00002637]", + "Uruguay [GAZ:00002930]", + "Uzbekistan [GAZ:00004979]", + "Vanuatu [GAZ:00006918]", + "Venezuela [GAZ:00002931]", + "Viet Nam [GAZ:00003756]", + "Virgin Islands [GAZ:00003959]", + "Wake Island [GAZ:00007111]", + "Wallis and Futuna [GAZ:00007191]", + "West Bank [GAZ:00009572]", + "Western Sahara [GAZ:00000564]", + "Yemen [GAZ:00005284]", + "Zambia [GAZ:00001107]", + "Zimbabwe [GAZ:00001106]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001181", + "type": "string", + "description": "The country of origin of the sample.", + "examples": ["South Africa [GAZ:00001094]"], + "classification":"Sample collection and processing", + "label":"Geo Loc Autonomic Country" + }, + "geo_loc_state": { + "examples": ["Western Cape"], + "ontology": "GENEPIO:0001185", + "type": "string", + "description": "The state/province/territory of origin of the sample.", + "classification":"Sample collection and processing", + "label":"Geo Loc Autonomic Community" + }, + "organism": { + "Enums": [ + "Coronaviridae [NCBITaxon:11118]", + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001191", + "type": "string", + "description": "Taxonomic name of the organism.", + "examples": [ + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", + ], + "classification":"Sample collection and processing", + "label":"Organism" + }, + "isolate": { + "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"], + "ontology": "GENEPIO:0001644", + "type": "string", + "description": "Identifier of the specific isolate.", + "clasification":"Sample collection and processing", + "label":"Isolate" + }, + "host_scientific_name": { + "Enums": [ + "Bos taurus [NCBITaxon:9913]", + "Canis lupus familiaris [NCBITaxon:9615]", + "Chiroptera [NCBITaxon:9397]", + "Columbidae [NCBITaxon:8930]", + "Felis catus [NCBITaxon:9685]", + "Gallus gallus [NCBITaxon:9031]", + "Homo sapiens [NCBITaxon:9606]", + "Manis [NCBITaxon:9973]", + "Manis javanica [NCBITaxon:9974]", + "Neovison vison [NCBITaxon:452646]", + "Panthera leo [NCBITaxon:9689]", + "Panthera tigris [NCBITaxon:9694]", + "Rhinolophidae [NCBITaxon:58055]", + "Rhinolophus affinis [NCBITaxon:59477]", + "Sus scrofa domesticus [NCBITaxon:9825]", + "Viverridae [NCBITaxon:9673]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001387", + "type": "string", + "description": "The taxonomic, or scientific name of the host.", + "examples": ["Homo sapiens [NCBITaxon:9606]"], + "clasification":"Host information", + "label":"Host Scientific Name" + }, + "host_disease": { + "Enums": [ + "COVID-19 [MONDO:0100096]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001391", + "type": "string", + "description": "The name of the disease experienced by the host.", + "examples": ["COVID-19 [MONDO:0100096]"] + }, + "sequencing_instrument_model": { + "Enums": [ + "Illumina sequencing instrument [GENEPIO:0100105]", + "Illumina Genome Analyzer [GENEPIO:0100106]", + "Illumina Genome Analyzer II [GENEPIO:0100107]", + "Illumina Genome Analyzer IIx [GENEPIO:0100108]", + "Illumina HiScanSQ [GENEPIO:0100109]", + "Illumina HiSeq [GENEPIO:0100110]", + "Illumina HiSeq X [GENEPIO:0100111]", + "Illumina HiSeq X Five [GENEPIO:0100112]", + "Illumina HiSeq X Ten [GENEPIO:0100113]", + "Illumina HiSeq 1000 [GENEPIO:0100114]", + "Illumina HiSeq 1500 [GENEPIO:0100115]", + "Illumina HiSeq 2000 [GENEPIO:0100116]", + "Illumina HiSeq 2500 [GENEPIO:0100117]", + "Illumina HiSeq 3000 [GENEPIO:0100118]", + "Illumina HiSeq 4000 [GENEPIO:0100119]", + "Illumina iSeq [GENEPIO:0100120]", + "Illumina iSeq 100 [GENEPIO:0100121]", + "Illumina NovaSeq [GENEPIO:0100122]", + "Illumina NovaSeq 6000 [GENEPIO:0100123]", + "Illumina MiniSeq [GENEPIO:0100124]", + "Illumina MiSeq [GENEPIO:0100125]", + "Illumina NextSeq [GENEPIO:0100126]", + "Illumina NextSeq 500 [GENEPIO:0100127]", + "Illumina NextSeq 550 [GENEPIO:0100128]", + "Illumina NextSeq 2000 [GENEPIO:0100129]", + "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", + "PacBio RS [GENEPIO:0100131]", + "PacBio RS II [GENEPIO:0100132]", + "PacBio Sequel [GENEPIO:0100133]", + "PacBio Sequel II [GENEPIO:0100134]", + "Ion Torrent sequencing instrument [GENEPIO:0100135]", + "Ion Torrent PGM [GENEPIO:0100136]", + "Ion Torrent Proton [GENEPIO:0100137]", + "Ion Torrent S5 XL [GENEPIO:0100138]", + "Ion Torrent S5 [GENEPIO:0100139]", + "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", + "Oxford Nanopore GridION [GENEPIO:0100141]", + "Oxford Nanopore MinION [GENEPIO:0100142]", + "Oxford Nanopore PromethION [GENEPIO:0100143]", + "BGI Genomics sequencing instrument [GENEPIO:0100144]", + "BGI SEQ-500 [GENEPIO:0100145]", + "MGI sequencing instrument [GENEPIO:0100146]", + "MGI DNBSEQ-T7 [GENEPIO:0100147]", + "MGI DNBSEQ-G400 [GENEPIO:0100148]", + "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", + "MGI DNBSEQ-G50 [GENEPIO:0100150]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001452", + "type": "string", + "description": "The model of the sequencing instrument used.", + "examples": ["Oxford Nanopore MinION [GENEPIO:0100142]"], + "classification":"Sequencing", + "label":"Sequencing Instrument Model" + }, + "sequencing_instrument_platform": { + "examples": ["MinIon"], + "ontology": "0", + "type": "string", + "description": "The model of the sequencing instrument used.", + "label":"Sequencing Platforms " + }, + "consensus_sequence_software_name": { + "examples": ["Ivar"], + "ontology": "GENEPIO:0001463", + "type": "string", + "description": "The name of software used to generate the consensus sequence." + }, + "consensus_sequence_software_version": { + "examples": ["1.3"], + "ontology": "GENEPIO:0001469", + "type": "string", + "description": "The version of the software used to generate the consensus sequence." + }, + "submitting_lab_sequence_id": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Sample ID given by the submitting laboratory" + }, + "bioproject_umbrella_accession_ENA": { + "examples": ["PRJNA623807"], + "ontology": "GENEPIO:0001133", + "type": "string", + "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", + "clasification":"Database Identifiers" + }, + "bioproject_accession_ENA": { + "examples": ["PRJNA12345"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", + "clasification":"Database Identifiers" + }, + "biosample_accession_ENA": { + "examples": ["SAMN14180202"], + "ontology": "GENEPIO:0001139", + "type": "string", + "description": "The identifier assigned to a BioSample in INSDC archives.", + "clasification":"Database Identifiers" + }, + "sra_accession": { + "examples": ["SRR11177792"], + "ontology": "GENEPIO:0001142", + "type": "string", + "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", + "clasification":"Database Identifiers" + }, + "genBank/ENA/DDBJ_accession": { + "examples": ["MN908947.3"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", + "clasification":"Database Identifiers" + }, + "gisaid_accession": { + "examples": ["EPI_ISL_123456"], + "ontology": "GENEPIO:0001147", + "type": "string", + "description": "The GISAID accession number assigned to the sequence.", + "clasification":"Database Identifiers" + }, + "virus_name": { + "examples": ["hCoV-19/Canada/prov_rona_99/2020"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The user-defined GISAID virus name assigned to the sequence.", + "clasification":"Database Identifiers" + }, + "collecting_institution_email": { + "examples": ["johnnyblogs@lab.ca"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "clasification":"Sample collection and processing" + }, + "collecting_institution_address": { + "examples": ["655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada"], + "ontology": "GENEPIO:0001158", + "type": "string", + "description": "The mailing address of the agency submitting the sample.", + "clasification":"Sample collection and processing" + }, + "submitting_institution_email": { + "examples": ["RespLab@lab.ca"], + "ontology": "GENEPIO:0001165", + "type": "string", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "clasification":"Sample collection and processing" + }, + "submitting_institution_address": { + "examples": ["123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The mailing address of the agency submitting the sequence.", + "clasification":"Sample collection and processing" + }, + "sample_received_date": { + "examples": ["3/21/2020"], + "ontology": "GENEPIO:0001179", + "type": "string", + "description": "The date on which the sample was received.", + "format":"date", + "clasification":"Sample collection and processing" + }, + "shipping_date": { + "examples": ["3/20/2020"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The date on which the sample was sent.", + "format":"date", + "clasification":"Sample collection and processing" + }, + "results_emission_date": { + "examples": ["3/23/2020"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The date on which the results were emitted.", + "format":"date", + "clasification":"Sample collection and processing" + }, + "geo_loc_region": { + "examples": ["Derbyshire"], + "ontology": "GENEPIO:0100280", + "type": "string", + "description": "The county/region of origin of the sample.", + "clasification":"Sample collection and processing", + "label":"Geo Loc Province" + }, + "geo_loc_city": { + "examples": ["Vancouver"], + "ontology": "GENEPIO:0001189", + "type": "string", + "description": "The city of origin of the sample.", + "clasification":"Sample collection and processing", + "label":"Geo Loc City" + }, + "geo_loc_latitude": { + "examples": ["38.98 N"], + "ontology": "OBI:0001620", + "type": "string", + "description": "The latitude coordinates of the geographical location of sample collection.", + "clasification":"Sample collection and processing", + "label":"Geo Loc Latitude", + }, + "geo_loc_longitude": { + "examples": ["77.11 W"], + "ontology": "OBI:0001621", + "type": "string", + "description": "The longitude coordinates of the geographical location of sample collection.", + "clasification":"Sample collection and processing", + "label":"Geo Loc Longitude" + }, + "anatomical_material": { + "Enums": [ + "Blood [UBERON:0000178]", + "Fluid [UBERON:0006314]", + "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", + "Fluid (Pericardial) [UBERON:0002409]", + "Fluid (Pleural) [UBERON:0001087]", + "Fluid (Vaginal) [UBERON:0036243]", + "Fluid (Amniotic) [UBERON:0000173]", + "Saliva [UBERON:0001836]", + "Tissue [UBERON:0000479]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001211", + "type": "string", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "examples": ["Blood [UBERON:0000178]"], + "classification":"Sample collection and processing", + "label":"Organism Substance" + }, + "anatomical_part": { + "Enums": [ + "Anus [UBERON:0001245]", + "Duodenum [UBERON:0002114]", + "Eye [UBERON:0000970]", + "Intestine [UBERON:0000160]", + "Lower respiratory tract [UBERON:0001558]", + "Bronchus [UBERON:0002185]", + "Lung [UBERON:0002048]", + "Bronchiole [UBERON:0002186]", + "Alveolar sac [UBERON:0002169]", + "Pleural sac [UBERON:0009778]", + "Pleural cavity [UBERON:0002402]", + "Trachea [UBERON:0003126]", + "Rectum [UBERON:0001052]", + "Skin [UBERON:0001003]", + "Stomach [UBERON:0000945]", + "Upper respiratory tract [UBERON:0001557]", + "Anterior Nares [UBERON:2001427]", + "Esophagus [UBERON:0001043]", + "Ethmoid sinus [UBERON:0002453]", + "Nasal Cavity [UBERON:0001707]", + "Middle Nasal Turbinate [UBERON:0005921]", + "Inferior Nasal Turbinate [UBERON:0005922]", + "Nasopharynx (NP) [UBERON:0001728]", + "Oropharynx (OP) [UBERON:0001729]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001214", + "type": "string", + "description": "An anatomical part of an organism e.g. oropharynx. ", + "examples": ["Nasopharynx (NP) [UBERON:0001728]"], + "classification":"Sample collection and processing", + "label":"Anatomical Structure" + }, + "body_product": { + "Enums": [ + "Breast Milk [UBERON:0001913]", + "Feces [UBERON:0001988]", + "Mucus [UBERON:0000912]", + "Semen [UBERON:0006530]", + "Sputum [UBERON:0007311]", + "Sweat [UBERON:0001089]", + "Tear [UBERON:0001827]", + "Urine [UBERON:0001088]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001216", + "type": "string", + "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", + "examples": ["Feces [UBERON:0001988]"], + "classification":"Sample collection and processing", + "label":"Body product" + }, + "environmental_material": { + "Enums": [ + "Air vent [ENVO:03501208]", + "Banknote [ENVO:00003896]", + "Bed rail [ENVO:03501209]", + "Building Floor [ENVO:01000486]", + "Cloth [ENVO:02000058]", + "Control Panel [ENVO:03501210]", + "Door [ENVO:03501220]", + "Door Handle [ENVO:03501211]", + "Face Mask [OBI:0002787]", + "Face Shield [OBI:0002791]", + "Food [FOODON:00002403]", + "Food Packaging [FOODON:03490100]", + "Glass [ENVO:01000481]", + "Handrail [ENVO:03501212]", + "Hospital Gown [OBI:0002796]", + "Light Switch [ENVO:03501213]", + "Locker [ENVO:03501214]", + "N95 Mask [OBI:0002790]", + "Nurse Call Button [ENVO:03501215]", + "Paper [ENVO:03501256]", + "Particulate Matter [ENVO:01000060]", + "Plastic [ENVO:01000404]", + "PPE Gown [GENEPIO:0100025]", + "Sewage [ENVO:00002018]", + "Sink [ENVO:01000990]", + "Soil [ENVO:00001998]", + "Stainless Steel [ENVO:03501216]", + "Tissue Paper [ENVO:03501217]", + "Toilet Bowl [ENVO:03501218]", + "Water [ENVO:00002006]", + "Wastewater [ENVO:00002001]", + "Window [ENVO:03501219]", + "Wood [ENVO:00002040]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001223", + "type": "string", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "examples": ["Face Mask [OBI:0002787]"], + "clasification":"Sample collection and processing", + "label":"Environmental Material" + }, + "environmental_site": { + "Enums": [ + "Acute care facility [ENVO:03501135]", + "Animal house [ENVO:00003040]", + "Bathroom [ENVO:01000422]", + "Clinical assessment centre [ENVO:03501136]", + "Conference venue [ENVO:03501127]", + "Corridor [ENVO:03501121]", + "Daycare [ENVO:01000927]", + "Emergency room (ER) [ENVO:03501145]", + "Family practice clinic [ENVO:03501186]", + "Group home [ENVO:03501196]", + "Homeless shelter [ENVO:03501133]", + "Hospital [ENVO:00002173]", + "Intensive Care Unit (ICU) [ENVO:03501152]", + "Long Term Care Facility [ENVO:03501194]", + "Patient room [ENVO:03501180]", + "Prison [ENVO:03501204]", + "Production Facility [ENVO:01000536]", + "School [ENVO:03501130]", + "Sewage Plant [ENVO:00003043]", + "Subway train [ENVO:03501109]", + "Wet market [ENVO:03501198]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001232", + "type": "string", + "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", + "examples": ["Hospital [ENVO:00002173]"], + "classification":"Sample collection and processing", + "label":"Anthropogenic Geographic Feature" + }, + "collection_device": { + "Enums": [ + "Air filter [ENVO:00003968]", + "Blood Collection Tube [OBI:0002859]", + "Bronchoscope [OBI:0002826]", + "Collection Container [OBI:0002088]", + "Collection Cup [GENEPIO:0100026]", + "Fibrobronchoscope Brush [OBI:0002825]", + "Filter [GENEPIO:0100103]", + "Fine Needle [OBI:0002827]", + "Microcapillary tube [OBI:0002858]", + "Micropipette [OBI:0001128]", + "Needle [OBI:0000436]", + "Serum Collection Tube [OBI:0002860]", + "Sputum Collection Tube [OBI:0002861]", + "Suction Catheter [OBI:0002831]", + "Swab [GENEPIO:0100027]", + "Urine Collection Tube [OBI:0002862]", + "Virus Transport Medium [OBI:0002866]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001234", + "type": "string", + "description": "The instrument or container used to collect the sample e.g. swab.", + "examples": ["Swab [GENEPIO:0100027]"], + "clasification":"Sample collection and processing", + "label":"Collection Device" + }, + "collection_method": { + "Enums": [ + "Amniocentesis [NCIT:C52009]", + "Aspiration [NCIT:C15631]", + "Suprapubic Aspiration [GENEPIO:0100028]", + "Tracheal Aspiration [GENEPIO:0100029]", + "Vacuum Aspiration [GENEPIO:0100030]", + "Biopsy [OBI:0002650]", + "Needle Biopsy [OBI:0002651]", + "Filtration [OBI:0302885]", + "Air Filtration [GENEPIO:0100031]", + "Lavage [OBI:0600044]", + "Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]", + "Gastric Lavage [GENEPIO:0100033]", + "Lumbar Puncture [NCIT:C15327]", + "Necropsy [MMO:0000344]", + "Phlebotomy [NCIT:C28221]", + "Rinsing [GENEPIO:0002116]", + "Saline gargle (mouth rinse and gargle) [GENEPIO:0100034]", + "Scraping [GENEPIO:0100035]", + "Swabbing [GENEPIO:0002117]", + "Finger Prick [GENEPIO:0100036]", + "Washout Tear Collection [GENEPIO:0100038]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001241", + "type": "string", + "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", + "examples": ["Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]"], + "clasification":"Sample collection and processing", + "label":"Collection Method" + }, + "collection_protocol": { + "examples": ["SC2SamplingProtocol 1.2"], + "ontology": "GENEPIO:0001243", + "type": "string", + "description": "The name and version of a particular protocol used for sampling.", + "clasification":"Sample collection and processing", + "label":"Collection Protocol" + }, + "specimen_processing": { + "Enums": [ + "Virus Passage [GENEPIO:0100039]", + "RNA Re-Extraction (Post RT-PCR) [GENEPIO:0100040]", + "Specimens Pooled [OBI:0600016]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001253", + "type": "string", + "description": "Any processing applied to the sample during or after receiving the sample. ", + "examples": ["Virus Passage [GENEPIO:0100039]"], + "classification":"Sample collection and processing", + "label":"Specimen Processing" + }, + "lab_host": { + "Enums": [ + "293/ACE2 Cell Line [GENEPIO:0100041]", + "Caco2 Cell Line [BTO:0000195]", + "Calu3 Cell Line [BTO:0002750]", + "EFK3B Cell Line [GENEPIO:0100042]", + "HEK293T Cell Line [BTO:0002181]", + "HRCE Cell Line [GENEPIO:0100043]", + "Huh7 Cell Line [BTO:0001950]", + "LLCMk2 Cell Line [CLO:0007330]", + "MDBK Cell Line [BTO:0000836]", + "NHBE Cell Line [BTO:0002924]", + "PK-15 Cell Line [BTO:0001865]", + "RK-13 Cell Line [BTO:0002909]", + "U251 Cell Line [BTO:0002035]", + "Vero Cell Line [BTO:0001444]", + "Vero E6 Cell Line [BTO:0004755]", + "Vero E6/TMPRSS2 Cell Line [GENEPIO:0100044]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001255", + "type": "string", + "description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.", + "examples": ["Vero E6 Cell Line [BTO:0004755]"], + "classification":"Sample collection and processing", + "label":"Lab passage Host" + }, + "passage_number": { + "examples": ["3"], + "ontology": "GENEPIO:0001261", + "type": "string", + "description": "Number of passages.", + "clasification":"Sample collection and processing", + "label":"Passage Number" + }, + "passage_method": { + "examples": ["AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain."], + "ontology": "GENEPIO:0001264", + "type": "string", + "description": "Description of how organism was passaged.", + "clasification":"Sample collection and processing", + "label":"Passage Method" + }, + "biomaterial_extracted": { + "Enums": [ + "mRNA (cDNA) [OBI:0002754]", + "RNA (Total) [OBI:0000895]", + "RNA (Poly-A) [OBI:0000869]", + "RNA (Ribo-Depleted) [OBI:0002627]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001266", + "type": "string", + "description": "The biomaterial extracted from samples for the purpose of sequencing.", + "examples": ["RNA (Total) [OBI:0000895]"], + "classification":"Sample collection and processing", + "label":"Biomaterial Extracted" + }, + "tax_id": { + "examples": ["probably 2697049 in all cases"], + "ontology": "GENEPIO_0001800", + "type": "string", + "description": "The NCBITaxon identifier for the organism being sequenced.", + "clasification":"Sample collection and processing", + "label":"Tax ID" + }, + "common_name": { + "examples": [""], + "ontology": "BU_ISCIII:003", + "type": "string", + "description": "The common name of the organism.", + "clasification":"Sample collection and processing", + "label":"Common name" + }, + "center_name": { + "examples": [" KAROLINSKA INSITUTET"], + "ontology": "NCIT_C19983", + "type": "string", + "description": "The name of the institution", + "clasification":"Sample collection and processing", + "label":"Center Name" + }, + "virus_id": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "The user-defined name for the sample.", + "clasification":"Database Identifiers" + }, + "host_common_name": { + "Enums": [ + "Human [NCBITaxon:9606]", + "Bat [NCBITaxon:9397]", + "Cat [NCBITaxon:9685]", + "Chicken [NCBITaxon:9031]", + "Civet [NCBITaxon:9673]", + "Cow [NCBITaxon:9913]", + "Dog [NCBITaxon:9615]", + "Lion [NCBITaxon:9689]", + "Mink [NCBITaxon:452646]", + "Pangolin [NCBITaxon:9973]", + "Pig [NCBITaxon:9825]", + "Pigeon [NCBITaxon:8930]", + "Tiger [NCBITaxon:9694]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001386", + "type": "string", + "description": "The commonly used name of the host.", + "examples": ["Human [NCBITaxon:9606]"], + "classification":"Host information", + "label":"Host Common Name" + }, + "outbreak": { + "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], + "ontology": "GENEPIO:0001417", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification":"Host information", + "label":"Outbreak Exposure Event Location" + }, + "additional_host_information": { + "examples": ["e.g. Patient infected while traveling in …."], + "ontology": "0", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification":"Host information", + "label":"Additional Host Information" + }, + "purpose_of_sequencing": { + "Enums": [ + "Baseline surveillance (random sampling) [GENEPIO:0100005]", + "Targeted surveillance (non-random sampling) [GENEPIO:0100006]", + "Priority surveillance projects [GENEPIO:0100007]", + "Screening for Variants of Concern (VOC) [GENEPIO:0100008]", + "Sample has epidemiological link to Variant of Concern (VoC) [GENEPIO:0100273]", + "Sample has epidemiological link to Omicron Variant [GENEPIO:0100274]", + "Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]", + "Re-infection surveillance [GENEPIO:0100010]", + "Vaccine escape surveillance [GENEPIO:0100011]", + "Travel-associated surveillance [GENEPIO:0100012]", + "Domestic travel surveillance [GENEPIO:0100013]", + "Interstate/ interprovincial travel surveillance [GENEPIO:0100275]", + "Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276]", + "International travel surveillance [GENEPIO:0100014]", + "Surveillance of international border crossing by air travel or ground transport [GENEPIO:0100015]", + "Surveillance of international border crossing by air travel [GENEPIO:0100016]", + "Surveillance of international border crossing by ground transport [GENEPIO:0100017]", + "Surveillance from international worker testing [GENEPIO:0100018]", + "Cluster/Outbreak investigation [GENEPIO:0100019]", + "Multi-jurisdictional outbreak investigation [GENEPIO:0100020]", + "Intra-jurisdictional outbreak investigation [GENEPIO:0100021]", + "Research [GENEPIO:0100022]", + "Viral passage experiment [GENEPIO:0100023]", + "Protocol testing [GENEPIO:0100024]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001445", + "type": "string", + "description": "The reason that the sample was sequenced.", + "examples": ["Baseline surveillance (random sampling) [GENEPIO:0100005]"], + "classification":"Sequencing", + "label":"Purpose of Sequencing" + }, + "purpose_of_sequencing_details": { + "Enums": [ + "Screened for S gene target failure (S dropout)", + "Screened for mink variants", + "Screened for B.1.1.7 variant", + "Screened for B.1.135 variant", + "Screened for P.1 variant", + "Screened due to travel history", + "Screened due to close contact with infected individual", + "Assessing public health control measures", + "Determining early introductions and spread", + "Investigating airline-related exposures", + "Investigating temporary foreign worker", + "Investigating remote regions", + "Investigating health care workers", + "Investigating schools/universities", + "Investigating reinfection" + ], + "ontology": "GENEPIO:0001446", + "type": "string", + "description": "The description of why the sample was sequenced providing specific details.", + "examples": ["Screened for S gene target failure (S dropout)"], + "clasification":"Sequencing", + "label":"Purpose Of Sequencing Details" + }, + "sequencing_date": { + "examples": ["4/26/2021"], + "ontology": "GENEPIO:0001447", + "type": "string", + "description": "The date the sample was sequenced.", + "format":"date", + "clasification":"Sequencing", + "label":"Sequencing date" + }, + "rna_extraction_protocol": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"Rna Extraction Protocol" + }, + "library_kit": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"Library Kit" + }, + "library_id": { + "examples": ["XYZ_123345"], + "ontology": "GENEPIO:0001448", + "type": "string", + "description": "The user-specified identifier for the library prepared for sequencing.", + "clasification":"Sequencing", + "labe":"Library Id" + }, + "enrichment_protocol": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"Enrichment_protocol" + }, + "if_enrichment_protocol_is_other_specify": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"If Enrichment Protocol Is Other, Specify" + }, + "amplicon protocol": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"Amplicon Protocol" + }, + "if_amplicon_protocol_if_other_especify": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "labe":"If Amplicon Protocol If Other, Especify" + }, + "amplicon_version": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"Amplicon Version" + }, + "amplicon_size": { + "examples": ["300bp"], + "ontology": "GENEPIO:0001449", + "type": "string", + "description": "The length of the amplicon generated by PCR amplification.", + "clasification":"Sequencing", + "label":"Amplicon Size" + }, + "was_phix_used?": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"Was Phix Used" + }, + "number_of_samples_in_run": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"Number Of Samples In Run" + }, + "flowcell_kit": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "labe":"Flowcell Kit" + }, + "runID": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"RunID" + }, + "sequencing_platforms": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"Sequencing Platforms " + }, + "library_preparation_kit": { + "examples": ["Nextera XT"], + "ontology": "GENEPIO:0001450", + "type": "string", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "clasification":"Sequencing", + "label":"Library Preparation Kit" + }, + "flow_cell_barcode": { + "examples": ["FAB06069"], + "ontology": "GENEPIO:0001451", + "type": "string", + "description": "The barcode of the flow cell used for sequencing.", + "clasification":"Sequencing", + "label":"Flow Cell Barcode" + }, + "sequencing_protocol_name": { + "examples": ["1D_DNA_MinION, ARTIC Network Protocol V3"], + "ontology": "GENEPIO:0001453", + "type": "string", + "description": "The name and version number of the sequencing protocol used.", + "clasification":"Sequencing", + "label":"Sequencing Protocol Name" + }, + "sequencing_protocol": { + "examples": ["Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits."], + "ontology": "GENEPIO:0001454", + "type": "string", + "description": "The protocol used to generate the sequence.", + "clasification":"Sequencing", + "label":"Sequencing Protocol" + }, + "sequencing_kit_number": { + "examples": ["AB456XYZ789"], + "ontology": "GENEPIO:0001455", + "type": "string", + "description": "The manufacturer's kit number.", + "clasification":"Sequencing", + "label":"Sequencing Kit Number" + }, + "amplicon_pcr_primer_scheme": { + "examples": ["https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv"], + "ontology": "GENEPIO:0001456", + "type": "string", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "clasification":"Sequencing", + "label":"Amplicon Pcr Primer Scheme" + }, + "library_selection": { + "examples": ["RANDOM PCR"], + "ontology": "GENPIO_0001940", + "type": "string", + "description": "Library capture method.", + "clasification":"Sequencing", + "label":"Capture method" + }, + "library_strategy": { + "Enums": ["Bisultife-Seq strategy [GENPIO:0001975]", + "CTS strategy [GENPIO:0001978]", + "ChIP-Seq strategy [GENPIO:0001979]", + "DNase-Hypersensitivity strategy [GENPIO:0001980]", + "EST strategy [GENPIO:0001981]", + "FL-cDNA strategy [GENPIO:0001983]", + "MB-Seq strategy [GENPIO:0001984]", + "MNase-Seq strategy [GENPIO:0001985]", + "MRE-Seq strategy [GENPIO:0001986]", + "MeDIP-Seq strategy [GENPIO:0001987]", + "RNA-Seq strategy [GENPIO:0001990]", + "WCS strategy [GENPIO:0001991]", + "WGS strategy [GENPIO:0001992]", + "WXS strategy [GENPIO:0001993]", + "amplicon strategy [GENPIO:0001974]", + "clone end strategy [GENPIO:0001976]", + "clone strategy [GENPIO:0001977]", + "finishing strategy [GENPIO:0001982]", + "other library strategy [GENPIO:0001988]", + "pool clone strategy [GENPIO:0001989]", + ], + "examples": ["WGS"], + "ontology": "GENPIO_0001973", + "type": "string", + "description": "Overall sequencing strategy or approach.", + "clasification":"Sequencing", + "label":"Sequencing technique" + }, + "library_layout": { + "examples": ["PAIRED"], + "ontology":"BU_ISCIII:007", + "type": "string", + "description": "Single or paired.", + "clasification":"Sequencing", + "label":"Library Layout" + }, + "library_name": { + "examples": ["P17157_1007"], + "ontology": "GENEPIO_0001995", + "type": "string", + "description": "Name of the used library", + "clasification":"Sequencing", + "label":"LibraryName" + }, + "nominal_length ": { + "examples": ["350"], + "ontology": "GENEPIO_0000076", + "type": "string", + "description": "", + "clasification":"Sequencing", + "label":"Nominal Length" + }, + "raw_sequence_data_processing_method": { + "examples": ["Porechop 0.2.3"], + "ontology": "GENEPIO:0001458", + "type": "string", + "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "clasification":"Bioinformatics and QC metrics", + "label":"Raw sequence data processin method" + }, + "dehosting_method": { + "examples": ["Nanostripper"], + "ontology": "GENEPIO:0001459", + "type": "string", + "description": "The method used to remove host reads from the pathogen sequence.", + "clasification":"Bioinformatics and QC metrics", + "label":"Dehosting Method" + }, + "assembly": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Assembly" + }, + "if_assembly_other": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"If assembly Is Other, Specify" + }, + "assembly_params": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Assambly params" + }, + "variant_calling": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Variant Calling" + }, + "if_variant_calling_other": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"If variant calling Is Other, Specify" + }, + "variant_calling_params": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Variant Calling params" + }, + "consensus_sequence_filepath": { + "examples": ["/User/Documents/RespLab/Data/ncov123assembly.fasta"], + "ontology": "GENEPIO:0001462", + "type": "string", + "description": "The filepath of the consesnsus sequence file.", + "clasification":"Bioinformatics and QC metrics", + "label":"Consensus sequence filepath" + }, + "consensus_sequence_software_name": { + "examples": ["Ivar"], + "ontology": "GENEPIO:0001463", + "type": "string", + "description": "The name of software used to generate the consensus sequence.", + "clasification":"Bioinformatics and QC metrics", + "label":"Consensus sequence software name" + }, + "if_consensus_other": { + "examples": ["1.3"], + "ontology": "0", + "type": "string", + "description": "The version of the software used to generate the consensus sequence.", + "clasification":"Bioinformatics and QC metrics", + "label":"If consensus Is Other, Specify" + }, + "consensus_sequence_software_version": { + "examples": ["1.3"], + "ontology": "GENEPIO:0001469", + "type": "string", + "description": "The version of the software used to generate the consensus sequence.", + "clasification":"Bioinformatics and QC metrics", + "label":"Consensus sequence software version" + }, + "consensus_criteria": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Consensus criteria" + }, + "quality_control_metrics": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Quality control metrics " + }, + "breadth_of_coverage_value": { + "examples": ["95%"], + "ontology": "GENEPIO:0001472", + "type": "string", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "clasification":"Bioinformatics and QC metrics", + "label":"Breadth of coverage value" + }, + "depth_of_coverage_value": { + "examples": ["400x"], + "ontology": "GENEPIO:0001474", + "type": "string", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "clasification":"Bioinformatics and QC metrics", + "label":"Depth of coverage value " + }, + "depth_of_coverage_threshold": { + "examples": ["100x"], + "ontology": "GENEPIO:0001475", + "type": "string", + "description": "The threshold used as a cut-off for the depth of coverage.", + "clasification":"Bioinformatics and QC metrics", + "label":"Depth of coverage threshold" + }, + "sequence_file_R1_fastq": { + "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], + "ontology": "GENEPIO:0001476", + "type": "string", + "description": "The user-specified filename of the r1 FASTQ file.", + "clasification":"Bioinformatics and QC metrics", + "label":"Sequence file R1 fastq" + }, + "sequence_file_R2_fastq": { + "examples": ["ABC123_S1_L001_R2_001.fastq.gz"], + "ontology": "GENEPIO:0001477", + "type": "string", + "description": "The user-specified filename of the r2 FASTQ file.", + "clasification":"Bioinformatics and QC metrics", + "label":"Sequence file R2 fastq" + }, + "r1_fastq_filepath": { + "examples": ["/User/Documents/RespLab/Data/"], + "ontology": "GENEPIO:0001478", + "type": "string", + "description": "The filepath of the r1 FASTQ file.", + "clasification":"Bioinformatics and QC metrics", + "label":"Filepath R1 fastq" + }, + "r2_fastq_filepath": { + "examples": ["/User/Documents/RespLab/Data/"], + "ontology": "GENEPIO:0001479", + "type": "string", + "description": "The filepath of the r2 FASTQ file.", + "clasification":"Bioinformatics and QC metrics", + "label":"Filepath R2 fastq" + }, + "fast5_filename": { + "examples": ["batch1a_sequences.fast5"], + "ontology": "GENEPIO:0001480", + "type": "string", + "description": "The user-specified filename of the FAST5 file.", + "clasification":"Bioinformatics and QC metrics", + "label":"Filename fast5" + }, + "fast5_filepath": { + "examples": ["/User/Documents/RespLab/Data/"], + "ontology": "GENEPIO:0001481", + "type": "string", + "description": "The filepath of the FAST5 file.", + "clasification":"Bioinformatics and QC metrics", + "label":"Filepath fast5" + }, + "number_of_base_pairs_sequenced": { + "examples": ["387566"], + "ontology": "GENEPIO:0001482", + "type": "string", + "description": "The number of total base pairs generated by the sequencing process.", + "clasification":"Bioinformatics and QC metrics", + "label":"Number of base pairs sequenced " + }, + "consensus_genome_length": { + "examples": ["38677"], + "ontology": "GENEPIO:0001483", + "type": "string", + "description": "Size of the assembled genome described as the number of base pairs.", + "clasification":"Bioinformatics and QC metrics", + "label":"Consensus genome length" + }, + "ns_per_100_kbp": { + "examples": ["300"], + "ontology": "GENEPIO:0001484", + "type": "string", + "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", + "clasification":"Bioinformatics and QC metrics", + "label":"Ns per 100 kbp" + }, + "reference_genome_accession": { + "examples": ["NC_045512.2"], + "ontology": "GENEPIO:0001485", + "type": "string", + "description": "A persistent, unique identifier of a genome database entry.", + "clasification":"Bioinformatics and QC metrics", + "label":"Reference genome accession" + }, + "bioinformatics_protocol": { + "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], + "ontology": "GENEPIO:0001489", + "type": "string", + "description": "The name of the bioinformatics protocol used.", + "clasification":"Bioinformatics and QC metrics", + "label":"Bioinformatics protocol" + }, + "if_bioinformatic_protocol_is_other_specify": { + "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], + "ontology": "0", + "type": "string", + "description": "The name of the bioinformatics protocol used.", + "clasification":"Bioinformatics and QC metrics", + "label":"If bioinformatic protocol Is Other, Specify" + }, + "bioinformatic_protocol_version": { + "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], + "ontology": "0", + "type": "string", + "description": "The version number of the bioinformatics protocol used.", + "clasification":"Bioinformatics and QC metrics", + "label":"bioinformatics protocol version" + }, + "commercial/open-source/both": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Commercial/Open-source/both" + }, + "preprocessing": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Preprocessing" + }, + "if_preprocessing_other": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"If preprocessing Is Other, Specify" + }, + "preprocessing_params": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Bioinformatics and QC metrics", + "label":"Preprocessing params" + }, + "mapping": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Lineage and Variant information", + "label":"Mapping" + }, + "if_mapping_other": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Lineage and Variant information", + "label":"If mapping Is Other, Specify" + }, + "mapping_params": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Lineage and Variant information", + "label":"Mapping params" + }, + "lineage/clade_name": { + "examples": ["B.1.1.7"], + "ontology": "GENEPIO:0001500", + "type": "string", + "description": "The name of the lineage or clade.", + "clasification":"Lineage and Variant information", + "label":"Lineage/clade name" + }, + "lineage/clade_analysis_software_name": { + "examples": ["Pangolin"], + "ontology": "GENEPIO:0001501", + "type": "string", + "description": "The name of the software used to determine the lineage/clade.", + "clasification":"Lineage and Variant information", + "label":"lineage/clade analysis software name" + }, + "if_lineage_identification_other": { + "examples": ["Other than Pangolin"], + "ontology": "0", + "type": "string", + "description": "The name of the software used to determine the lineage/clade.", + "clasification":"Lineage and Variant information", + "label":"If lineage identification Is Other, Specify" + }, + "lineage/clade_analysis_software_version": { + "examples": ["2.1.10"], + "ontology":"GENEPIO:0001502", + "type": "string", + "description": "The version of the software used to determine the lineage/clade.", + "clasification":"Lineage and Variant information", + "label":"Lineage/clade analysis software version" + }, + "variant_designation": { + "Enums": [ + "Variant of Interest (VOI) [GENEPIO:0100082]", + "Variant of Concern (VOC) [GENEPIO:0100083]", + "Variant Under Monitoring (VUM) [GENEPIO:0100279]" + ], + "ontology": "GENEPIO:0001503", + "type": "string", + "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", + "examples": ["Variant of Concern (VOC) [GENEPIO:0100083]"], + "classification":"Lineage and Variant information", + "label":"Variant designation" + }, + "variant_evidence": { + "examples": ["lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)"], + "ontology": "GENEPIO:0001504", + "type": "string", + "description": "The evidence used to make the variant determination.", + "clasification":"Lineage and Variant information", + "label":"Variant evidence" + }, + "gene_name_1": { + "Enums": [ + "E gene (orf4) [GENEPIO:0100151]", + "M gene (orf5) [GENEPIO:0100152]", + "N gene (orf9) [GENEPIO:0100153]", + "Spike gene (orf2) [GENEPIO:0100154]", + "orf1ab (rep) [GENEPIO:0100155]", + "orf1a (pp1a) [GENEPIO:0100156]", + "nsp11 [GENEPIO:0100157]", + "nsp1 [GENEPIO:0100158]", + "nsp2 [GENEPIO:0100159]", + "nsp3 [GENEPIO:0100160]", + "nsp4 [GENEPIO:0100161]", + "nsp5 [GENEPIO:0100162]", + "nsp6 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+ "label":"%unmapped" + }, + "%genome _greater_10x": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing", + "label":"% genome greater 10x" + }, + "mean_depth_of_coverage_value": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing", + "label":"mean depth of coverage value" + }, + "%Ns": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing", + "label":"%Ns" + }, + "Number_of_variants_(AF_greater_75%)": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing", + "label":"Number of variants (AF greater 75%)" + }, + "Numer_of_variants_with_effect": { + "examples": [""], + "ontology": "0", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing", + "label":"Numer of variants with effect" + }, + "reference_genome_accession": { + "examples": [""], + "ontology": "GENEPIO:0001485", + "type": "string", + "description": "", + "clasification":"Pathogen diagnostic testing", + "label":"reference genome accession" + }, + "diagnostic_pcr_protocol_1": { + "examples": ["PCREGene 2.0"], + "ontology": "GENEPIO:0001508", + "type": "string", + "description": "The name and version number of the protocol used for diagnostic marker amplification.", + "clasification":"Pathogen diagnostic testing", + "label":"Diagnostic Pcr Protocol 1" + }, + "diagnostic_pcr_Ct_value_1": { + "examples": ["21"], + "ontology": "GENEPIO:0001509", + "type": "string", + "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "clasification":"Pathogen diagnostic testing", + "label":"Diagnostic Pcr Ct Value 1" + }, + "gene_name_2": { + "Enums": [ + "E gene (orf4) [GENEPIO:0100151]", + "M gene (orf5) [GENEPIO:0100152]", + "N gene (orf9) 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[GENPIO:0001962]", + "other library method [GENPIO:0001964]", + "size fractionation method [GENPIO:0001963]", + ], + "examples": ["METAGENOMIC"], + "ontology": "GENEPIO_0001965", + "type": "string", + "description": "Molecule type used to make the library.", + "clasification":"Sequencing", + "label":"Source material" + }, + "nominal_length": { + "examples": [""], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "", + "clasification":"Sequencing" + }, + "analysis_accession": { + "examples": [""], + "ontology": "GENEPIO_0001145", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Analysis Accession" + }, + "study_accession": { + "examples": ["e.g PRJEB39632"], + "ontology": "GENEPIO_0001136", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Study accession" + }, + "secondary_study_accession": { + "examples": ["e.g ERP123173"], + "ontology": "BU_ISCIII:012", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Secondary study accession" + }, + "sample_accession": { + "examples": ["e.g SAMEA7098096"], + "ontology": "GENEPIO_0001139", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Sample accession" + }, + "secondary_sample_accession": { + "examples": ["e.g ERS4858671"], + "ontology": "BU_ISCIII:014", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Secondary sample accession" + }, + "experiment_accession": { + "examples": ["e.g ERX4331406"], + "ontology": "BU_ISCIII:015", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Experiment Accession" + }, + "run_accession": { + "examples": ["e.g ERX4331406"], + "ontology": "BU_ISCIII:016", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Run Accession" + }, + "submission_accession": { + "examples": ["e.g ERA2794974"], + "ontology": 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+ "clasification":"Submission ENA", + "format":"Last Updated" + }, + "experiment_title": { + "examples": ["e.g Illumina MiSeq paired end sequencing"], + "ontology": "ORNASEQ_0000004", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Experiment title" + }, + "study_title": { + "examples": ["e.g SARS-CoV-2 genomes from late April in Stockholm"], + "ontology": "OPMI_0000380", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Study title" + }, + "study_alias": { + "examples": ["e.g Sweden"], + "ontology": "SIO_001066", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Study alias" + }, + "experiment_alias": { + "examples": ["e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092"], + "ontology": "NCIT_C42790", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Experiment alias" + }, + "run_alias": { + "examples": ["e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], + "ontology": "NCIT_C47911", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Run Alias" + }, + "fastq_bytes": { + "examples": ["e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], + "ontology": "NCIT_C48047", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Fastq bytes" + }, + "fastq_md5": { + "examples": [""], + "ontology": "MS_1000568", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Fastq md5" + }, + "fastq_ftp": { + "examples": [""], + "ontology": "PRIDE_0000469", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Fastq ftp" + }, + "fastq_aspera": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], + "ontology": "BU_ISCIII:032", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Fastq aspera" + }, + "fastq_galaxy": { + "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], + "ontology": "ENVO_01000807", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Fastq galaxy" + }, + "submitted_bytes": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], + "ontology": "NCIT_C172872", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted bytes " + }, + "submitted_md5": { + "examples": ["e.g 139853010;166270048"], + "ontology": "BU_ISCIII:035", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted md5" + }, + "submitted_ftp": { + "examples": ["e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a"], + "ontology": "BU_ISCIII:036", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted ftp" + }, + "submitted_aspera": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], + "ontology": "BU_ISCIII:037", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted aspera" + }, + "submitted_galaxy": { + "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], + "ontology": "BU_ISCIII:038", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted Galaxy" + }, + "submitted_format": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], + "ontology": "BU_ISCIII:039", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Submitted Format" + }, + "sra_bytes": { + "examples": ["e.g FASTQ;FASTQ"], + "ontology": "BU_ISCIII:040", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"SRA bytes" + }, + "sra_md5": { + "examples": ["e.g 260236789"], + "ontology": "BU_ISCIII:041", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"SRA md5" + }, + "sra_ftp": { + "examples": ["e.g 2cf0d467d6dc4ae0a5473774d54c059c"], + "ontology": "BU_ISCIII:042", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"SRA ftp" + }, + "sra_aspera": { + "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385"], + "ontology": "BU_ISCIII:043", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"SRA aspera" + }, + "sra_galaxy": { + "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385"], + "ontology": "BU_ISCIII:044", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"SRA galaxy" + }, + "broker_name": { + "examples": ["P17157_1007"], + "ontology": "BU_ISCIII:045", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Broker Name" + }, + "nominal_sdev": { + "examples": [""], + "ontology": "STATO_0000237", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"Nominal sdev" + }, + "first_created": { + "examples": ["e.g 2020-08-07"], + "ontology": "NCIT_C164483", + "type": "string", + "description": "", + "clasification":"Submission ENA", + "label":"First created date" + }, + "type": { + "examples": ["betacoronavirus"], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "default must remain 'betacoronavirus'", + "clasification":"Database Identifiers" + } + } +} diff --git a/test/validation_jsons.py b/test/validation_jsons.py new file mode 100644 index 00000000..bd9e2172 --- /dev/null +++ b/test/validation_jsons.py @@ -0,0 +1,176 @@ +#!/usr/bin/env python +from jsonschema import validate +from jsonschema import Draft202012Validator +import json ,sys +from openpyxl import Workbook +import openpyxl +from itertools import islice +from utils import * + +''' +References: + genepio.owl https://github.com/GenEpiO/genepio/blob/master/genepio.owl + + +''' + +class PhagePlusSchema : + def __init__ (self, schema): + self.schema = schema + self.ontology = {} + for key , values in schema['properties'].items(): + self.ontology[values['ontology']] = key + + + def get_gontology(self,property_item): + ''' + Description: + The function return the geontology value for a property in the schema + Input: + property_item # property name to fetch its geontology + Return: + Return ontology value or None + ''' + try: + return self.schema['properties'][property_item]['ontology'] + except: + return None + + def maping_schemas_based_on_geontology(mapped_to_schema): + ''' + Description: + The function return a dictionnary with the properties of the mapped_to_schema as key and + properties of phagePlusSchema as value + Input: + mapped_to_schema # json schema to be mapped + Return: + mapped_dict contains as key the property in the mapped_to_schema and value de property in the self.schema + ''' + mapped_dict = OrderedDict() + for key, values in mapped_to_schema['properties'].items(): + try: + mapped_dict[key] = self.ontology[values['ontology']] + except: + # There is no exact match on ontology. Search for the parent + # to be implemented later + pass + return mapped_dict + + +class PhagePlusData : + def __init__ (self,data, json_schema): + self.data = data + self.schema = json_schema + + + def convert_json(schema): + pass + + def get_data(self, field): + return self.data[field] + + def map_sample_to_schema(mapped_structure): + map_sample_dict = OrderedDict() + for item, value in mapped_structure.items: + mapped_sample_list[item] = self.data[value] + return map_sample_dict + + + +def check_arg (args=None) : + ''' + The function is used for parsing the input parameters form the command line + using the standard python package argparse. The package itself is handling + the validation and the return errors messages + Input: + args # Contains the arguments from the command line + Return: + parser.parse_args() # The variable contains the valid parameters + ''' + parser = argparse.ArgumentParser(prog = 'validation_jsons.py', + formatter_class=argparse.RawDescriptionHelpFormatter, + description= 'Read the excel input user files and store them in the LIMS') + + parser.add_argument('-v', '--version', action='version', version='%(prog)s 0.0.1') + parser.add_argument('-p', '--phagePlusSchema' , required = True, + help='file where the phage plus schema is located') + parser.add_argument('-i', '--inputFile', required =True, + help='Execl file with the user collected data') + parser.add_argument('-c', '--convertedSchema', required = True, + help='schema to be mapped') + return parser.parse_args() + + + +data ={"sample_name":'s1', "collecting_institution" :'inst2', + "submitting_institution":'sub', + "sample_collection_date": '12/02/2022', + "geo_loc_country":'Afghanistan', + "geo_loc_state":'Western', + "organism":'Coronaviridae', + "isolate":'SARS-CoV-2/', + "host_scientific_name":'Bos taurus', + "host_disease":'Homo sapiens', + "sequencing_instrument_model" :'COVID-19', + "sequencing_instrument_platform": 'Illumina sequencing instrument', + "consensus_sequence_software_name":'MinIon', + "consensus_sequence_software_version":'Ivar' +} + + +if __name__ == '__main__': + if len (sys.argv) == 1 : + print('Usage: validation_jsons.py [ARGUMENTS] ') + print('Try validation_jsons.py --help for more information.') + exit(2) + arguments = check_arg(sys.argv[1:]) + if not check_if_file_exists(arguments.phagePlusSchema): + print('phage plus schema file does not exist\n') + exit(2) + if not check_if_file_exists(arguments.inputFile): + print('excel file does not exist\n') + exit(2) + if not check_if_file_exists(arguments.convertedSchema): + print('file for converting schema does not exist\n') + exit(2) + # schema_file = open('/home/lchapado/Projects/Proyecto_ERA/relecov-tools/schema/phage_plus_V0.json') + schema_file = open(arguments.phagePlusSchema) + + + json_phage_plus_schema = json.load(schema_file) + try: + Draft202012Validator.check_schema(json_phage_plus_schema) + except: + print('Invalid schema') + exit(1) + phage_plus_schema = PhagePlusSchema(json_phage_plus_schema) + + sample_list = [] + wb_file = openpyxl.load_workbook(arguments.inputFile, data_only=True) + ws_metadata_lab = wb_file['METADATA_LAB'] + heading = [] + for cell in ws_metadata_lab[1]: + heading.append(cell.value) + + for row in islice(ws_metadata_lab.values,1,ws_metadata_lab.max_row): + sample_data_row = {} + for idx in range(len(heading)): + if 'date' in heading[idx]: + sample_data_row[heading[idx]] = row[idx].strftime('%d/%m/%Y') + else: + sample_data_row[heading[idx]] = row[idx] + try: + validate(instance=sample_data_row,schema=json_phage_plus_schema) + except: + print('Unsuccessful validation for sample ' , sample_data_row['sample_name']) + + continue + sample_list.append(PhagePlusData(sample_data_row,phage_plus_schema)) + # create the information mapped to the new schema + mapped_structure = phage_plus_schema.maping_schemas_based_on_geontology(arguments.convertedSchema) + mapped_sample_list = [] + for sample in sample_list: + mapped_sample_list.append(map_sample_to_schema(mapped_structure)) + + + print('Completed') From 7c493c80a72f0609ac9411e3a2f316ec9afa4b8b Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 8 Mar 2022 15:07:43 +0100 Subject: [PATCH 0062/1454] Fixing liting issues --- relecov_tools/utils.py | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index c3e4bf76..db44b8bd 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -1,12 +1,13 @@ import os + def file_exists(file_to_check): - ''' + """ Input: file_to_check # file name to check if exists Return: True if exists - ''' + """ if os.path.isfile(file_to_check): return True return False @@ -16,6 +17,10 @@ def rich_force_colors(): """ Check if any environment variables are set to force Rich to use coloured output """ - if os.getenv("GITHUB_ACTIONS") or os.getenv("FORCE_COLOR") or os.getenv("PY_COLORS"): + if ( + os.getenv("GITHUB_ACTIONS") + or os.getenv("FORCE_COLOR") + or os.getenv("PY_COLORS") + ): return True return None From ead9507d5e812a59f46c3595ed80e5ea2e28b2b9 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 8 Mar 2022 15:31:47 +0100 Subject: [PATCH 0063/1454] include functions for rich console --- relecov_tools/utils.py | 76 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 76 insertions(+) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index db44b8bd..6c60d99a 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -1,4 +1,10 @@ +#!/usr/bin/env python +""" +Common utility function for bu-isciii package. +""" import os +import rich +import questionary def file_exists(file_to_check): @@ -24,3 +30,73 @@ def rich_force_colors(): ): return True return None + + +stderr = rich.console.Console( + stderr=True, style="dim", highlight=False, force_terminal=rich_force_colors() +) + + +def prompt_resolution_id(): + stderr.print( + "Specify the name resolution id for the service you want to create. You can obtain this from iSkyLIMS. eg. SRVCNM584.1" + ) + resolution_id = questionary.text("Resolution id").unsafe_ask() + return resolution_id + + +def prompt_service_dir_path(): + stderr.print("Service path to copy to execution temporal directory") + source = questionary.path("Source path").unsafe_ask() + return source + + +def prompt_tmp_dir_path(): + stderr.print("Temporal directory destination to execute sercive") + source = questionary.path("Source path").unsafe_ask() + return source + + +def prompt_source_path(): + stderr.print("Directory containing files cd to transfer") + source = questionary.path("Source path").unsafe_ask() + return source + + +def prompt_destination_path(): + stderr.print("Directory to which the files will be transfered") + destination = questionary.path("Destination path").unsafe_ask() + return destination + + +def prompt_selection(msg, choices): + selection = questionary.select(msg, choices=choices).unsafe_ask() + return selection + + +def prompt_path(msg): + source = questionary.path(msg).unsafe_ask() + return source + + +def prompt_yn_question(msg): + confirmation = questionary.confirm(msg).unsafe_ask() + return confirmation + + +def prompt_skip_folder_creation(): + stderr.print("Do you want to skip folder creation? (Y/N)") + confirmation = questionary.confirm("Skip?", default=False).unsafe_ask() + return confirmation + + +def get_service_ids(services_requested): + service_id_list = [] + for services in services_requested: + service_id_list.append(services["serviceId"]) + service_id_list.append("all") + stderr.print("Which selected service do you want to manage?") + services_sel = [prompt_selection("Service label:", service_id_list)] + if services_sel == "all": + services_sel == service_id_list + return services_sel From 3aa1758c08e4537b6cc0540258d966c55722617b Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 8 Mar 2022 16:24:36 +0100 Subject: [PATCH 0064/1454] removing references to bu-isciii and nf-core --- relecov_tools/__main__.py | 67 +++++++++++++++------------------------ 1 file changed, 26 insertions(+), 41 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 739301a4..82b4b4d2 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -1,5 +1,7 @@ #!/usr/bin/env python - +import os +import utils +import logging # from click.types import File from rich import print @@ -8,14 +10,14 @@ import rich.console import rich.logging import rich.traceback -import os -import utils -log = logging.getLogger() +import relecov_tools.read_metadata + +log = logging.getLogger() -def run_bu_isciii(): +def run_relecov_tools(): # Set up rich stderr console stderr = rich.console.Console(stderr=True, force_terminal=utils.rich_force_colors()) @@ -52,7 +54,7 @@ def run_bu_isciii(): ) # Lanch the click cli - bu_isciii_cli() + relecov_tools_cli() # Customise the order of subcommands for --help @@ -92,7 +94,7 @@ def decorator(f): @click.group(cls=CustomHelpOrder) -# @click.version_option(nf_core.__version__) +@click.version_option(relecov_tools.__version__) @click.option( "-v", "--verbose", @@ -103,23 +105,11 @@ def decorator(f): @click.option( "-l", "--log-file", help="Save a verbose log to a file.", metavar="" ) -def bu_isciii_cli(verbose, log_file): +def relecov_tools_cli(verbose, log_file): # Set the base logger to output DEBUG log.setLevel(logging.DEBUG) - # Set up logs to the console - log.addHandler( - rich.logging.RichHandler( - level=logging.DEBUG if verbose else logging.INFO, - console=rich.console.Console( - stderr=True, force_terminal=nf_core.utils.rich_force_colors() - ), - show_time=False, - markup=True, - ) - ) - # Set up logs to a file if we asked for one if log_file: log_fh = logging.FileHandler(log_file, encoding="utf-8") @@ -133,7 +123,7 @@ def bu_isciii_cli(verbose, log_file): # pipeline list -@bu_isciii_cli.command(help_priority=1) +@relecov_tools_cli.command(help_priority=1) @click.argument("keywords", required=False, nargs=-1, metavar="") @click.option( "-s", @@ -156,7 +146,7 @@ def list(keywords, sort, json, show_archived): # sftp -@bu_isciii_cli.command(help_priority=2) +@relecov_tools_cli.command(help_priority=2) @click.argument("pipeline", required=False, metavar="") @click.option( "-r", "--revision", help="Release/branch/SHA of the project to run (if remote)" @@ -191,14 +181,16 @@ def sftp( Download files located in sftp server. """ - print(nf_core.list.list_workflows(keywords, sort, json, show_archived)) - # metadata -@bu_isciii_cli.command(help_priority=3) -@click.argument("pipeline", required=False, metavar="") +@relecov_tools_cli.command(help_priority=3) +# @click.option("metadata_file", required=False, metavar="") @click.option( - "-r", "--revision", help="Release/branch/SHA of the project to run (if remote)" + "-m", + "--metadata_file", + type=click.Path(), + default=None, + help="file containing metadata" ) @click.option("-i", "--id", help="ID for web-gui launch parameter set") @click.option( @@ -215,23 +207,16 @@ def sftp( default=os.path.join(os.getcwd(), "nf-params.json"), help="Path to save run parameters file", ) -def metadata( - pipeline, - id, - revision, - command_only, - params_in, - params_out, - save_all, - show_hidden, - url, +def read_metadata( + metadata_file ): """ - Read Metadata . - + Create the json complaining the relecov schema from the Metadata file. """ - print(nf_core.list.list_workflows(keywords, sort, json, show_archived)) + new_metadata = relecov_tools.read_metadata.RelecovMetadata(metadata_file) + relecov_json = new_metadata.create_json() + return relecov_json if __name__ == "__main__": - run_bu_isciii() + run_relecov_tools() From 0b5220281a21c22871d3a6ac820d8bc9165f62c1 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 8 Mar 2022 16:25:05 +0100 Subject: [PATCH 0065/1454] removing references to services and resolutions --- relecov_tools/utils.py | 26 -------------------------- 1 file changed, 26 deletions(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 6c60d99a..91545f41 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -37,20 +37,6 @@ def rich_force_colors(): ) -def prompt_resolution_id(): - stderr.print( - "Specify the name resolution id for the service you want to create. You can obtain this from iSkyLIMS. eg. SRVCNM584.1" - ) - resolution_id = questionary.text("Resolution id").unsafe_ask() - return resolution_id - - -def prompt_service_dir_path(): - stderr.print("Service path to copy to execution temporal directory") - source = questionary.path("Source path").unsafe_ask() - return source - - def prompt_tmp_dir_path(): stderr.print("Temporal directory destination to execute sercive") source = questionary.path("Source path").unsafe_ask() @@ -88,15 +74,3 @@ def prompt_skip_folder_creation(): stderr.print("Do you want to skip folder creation? (Y/N)") confirmation = questionary.confirm("Skip?", default=False).unsafe_ask() return confirmation - - -def get_service_ids(services_requested): - service_id_list = [] - for services in services_requested: - service_id_list.append(services["serviceId"]) - service_id_list.append("all") - stderr.print("Which selected service do you want to manage?") - services_sel = [prompt_selection("Service label:", service_id_list)] - if services_sel == "all": - services_sel == service_id_list - return services_sel From 91153e72ab88b3a46cb60a5b08129d355aa9196f Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 8 Mar 2022 16:30:41 +0100 Subject: [PATCH 0066/1454] removing litting issues --- relecov_tools/__main__.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 82b4b4d2..d9d08978 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -3,7 +3,7 @@ import utils import logging # from click.types import File -from rich import print +# from rich import print # from rich.prompt import Confirm import click @@ -142,7 +142,7 @@ def list(keywords, sort, json, show_archived): Checks the web for a list of nf-core pipelines with their latest releases. Shows which nf-core pipelines you have pulled locally and whether they are up to date. """ - print(nf_core.list.list_workflows(keywords, sort, json, show_archived)) + pass # sftp @@ -182,6 +182,7 @@ def sftp( """ + # metadata @relecov_tools_cli.command(help_priority=3) # @click.option("metadata_file", required=False, metavar="") From 55db1c8b930f1e7eb7b3c4603976d118e7e266e0 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 8 Mar 2022 19:25:08 +0100 Subject: [PATCH 0067/1454] creating the commit to merge the pull request form bu-isciii --- relecov_tools/__main__.py | 1 - relecov_tools/read_metadata.py | 43 +++++++++++++++++++--------------- 2 files changed, 24 insertions(+), 20 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index d9d08978..9f7a6f5a 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -11,7 +11,6 @@ import rich.logging import rich.traceback - import relecov_tools.read_metadata log = logging.getLogger() diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index fbbecfc2..655fae76 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -1,25 +1,26 @@ #!/usr/bin/env python +import relecov_tools.utils + class RelecovMetadata: - def __init__(): - self.origin_file = file - self.metadata = {} - self.isklims_url = iskylims_url - self.relecov_url = relecov_url + def __init__( + self, + excel_file=None, + inpuf_folder=None, + ): + if excel_file is None: + self.excel_file = relecov_tools.prompt_path( + msg="Select the excel file which contains metadata" + ) + else: + self.excel_file = excel_file -# read_metadata +# read_metadata -def read_metadata_workflow(self): - def __init__( - self, - ): - """ - Description : Starts the read metada workflow - """ # Perform workflow details @@ -37,7 +38,12 @@ def fetch_metadata_file(folder, file_name): folder Directory to fetch metadata file file_name metadata file name """ - pass + wb_file = openpyxl.load_workbook(file_name, data_only=True) + ws_metadata_lab = wb_file["METADATA_LAB"] + heading = [] + for cell in ws_metadata_lab[1]: + heading.append(cell.value) + def validate_metadata_sample(row_sample): @@ -67,12 +73,11 @@ def store_information(external_url, request, data): pass -wb_file = openpyxl.load_workbook(arguments.inputFile, data_only=True) -ws_metadata_lab = wb_file["METADATA_LAB"] -heading = [] -for cell in ws_metadata_lab[1]: - heading.append(cell.value) +def read_metadata_workflow(self): + """ + Description : Starts the read metada workflow + """ for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row): sample_data_row = {} From 7616ea908e9d3b8cc23d7bdf83b32445def1d291 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 8 Mar 2022 20:06:15 +0100 Subject: [PATCH 0068/1454] files modification to create relecov_tools package --- relecov_tools/__main__.py | 56 +++++++++++++++++++++++++--------- relecov_tools/read_metadata.py | 39 +++++++++++++++-------- relecov_tools/utils.py | 6 ++-- setup.py | 6 ++-- 4 files changed, 73 insertions(+), 34 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 9f7a6f5a..e820bc73 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -1,6 +1,5 @@ #!/usr/bin/env python import os -import utils import logging # from click.types import File # from rich import print @@ -11,6 +10,7 @@ import rich.logging import rich.traceback +import relecov_tools.utils import relecov_tools.read_metadata log = logging.getLogger() @@ -18,7 +18,7 @@ def run_relecov_tools(): # Set up rich stderr console - stderr = rich.console.Console(stderr=True, force_terminal=utils.rich_force_colors()) + stderr = rich.console.Console(stderr=True, force_terminal=relecov_tools.utils.rich_force_colors()) # Set up the rich traceback rich.traceback.install(console=stderr, width=200, word_wrap=True, extra_lines=1) @@ -166,20 +166,14 @@ def list(keywords, sort, json, show_archived): help="Path to save run parameters file", ) def sftp( - pipeline, - id, - revision, - command_only, - params_in, - params_out, - save_all, - show_hidden, - url, + host, + port, + user, + passwd ): - """ - Download files located in sftp server. - - """ + """Download files located in sftp server.""" + sftp_connection = relecov_tools.sftp.SftpHandle(host, port, user, passwd) + sftp_connection.open() # metadata @@ -218,5 +212,37 @@ def read_metadata( return relecov_json +# validation +@relecov_tools_cli.command(help_priority=4) +@click.argument("pipeline", required=False, metavar="") +@click.option( + "-r", "--revision", help="Release/branch/SHA of the project to run (if remote)" +) +@click.option("-i", "--id", help="ID for web-gui launch parameter set") +@click.option( + "-c", + "--command-only", + is_flag=True, + default=False, + help="Create Nextflow command with params (no params file)", +) +@click.option( + "-o", + "--params-out", + type=click.Path(), + default=os.path.join(os.getcwd(), "nf-params.json"), + help="Path to save run parameters file", +) +def validation( + host, + port, + user, + passwd +): + """Download files located in sftp server.""" + relecov_json = relecov_tools.validation_jsons.ValidationJson(host, port, user, passwd) + relecov_json.open() + + if __name__ == "__main__": run_relecov_tools() diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 655fae76..464bfc31 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -1,5 +1,7 @@ #!/usr/bin/env python - +from itertools import islice +from openpyxl import Workbook +import openpyxl import relecov_tools.utils @@ -78,17 +80,28 @@ def read_metadata_workflow(self): """ Description : Starts the read metada workflow """ + sample_list = [] + wb_file = openpyxl.load_workbook(arguments.inputFile, data_only=True) + ws_metadata_lab = wb_file["METADATA_LAB"] + heading = [] + for cell in ws_metadata_lab[1]: -for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row): - sample_data_row = {} - for idx in range(len(heading)): - if "date" in heading[idx]: - sample_data_row[heading[idx]] = row[idx].strftime("%d/%m/%Y") - else: - sample_data_row[heading[idx]] = row[idx] - try: - validate(instance=sample_data_row, schema=json_phage_plus_schema) - except: - print("Unsuccessful validation for sample ", sample_data_row["sample_name"]) + heading.append(cell.value) - continue + for i in range(len(heading)): + if heading[i] in list(mapping_file.keys()): + index = list(mapping_file).index(heading[i]) + heading[index] = list(mapping_file.values())[index] + for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row): + sample_data_row = {} + for idx in range(len(heading)): + if "date" in heading[idx]: + sample_data_row[heading[idx]] = row[idx].strftime("%d/%m/%Y") + else: + sample_data_row[heading[idx]] = row[idx] + try: + validate(instance=sample_data_row, schema=json_phage_plus_schema) + except: + print("Unsuccessful validation for sample ", sample_data_row["sample_name"]) + + continue diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 91545f41..ba4e219b 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -1,9 +1,9 @@ #!/usr/bin/env python """ -Common utility function for bu-isciii package. +Common utility function for relecov_tools package. """ import os -import rich +from rich.console import Console import questionary @@ -32,7 +32,7 @@ def rich_force_colors(): return None -stderr = rich.console.Console( +stderr = Console( stderr=True, style="dim", highlight=False, force_terminal=rich_force_colors() ) diff --git a/setup.py b/setup.py index 22c87dbd..efd977a6 100644 --- a/setup.py +++ b/setup.py @@ -11,7 +11,7 @@ required = f.read().splitlines() setup( - name="bu-isciii", + name="relecov_tools", version=version, description="Tools for managing and resolution of buisciii services.", long_description=readme, @@ -26,9 +26,9 @@ ], author="Sara Monzon", author_email="smonzon@isciii.es", - url="https://github.com/BU-ISCIII/buisciii-tools", + url="https://github.com/BU-ISCIII/relecov_tools", license="GNU GENERAL PUBLIC LICENSE v.3", - entry_points={"console_scripts": ["bu-isciii=bu_isciii.__main__:run_bu_isciii"]}, + entry_points={"console_scripts": ["relecov_tools=relecov_tools.__main__:run_relecov_tools"]}, install_requires=required, packages=find_packages(exclude=("docs")), include_package_data=True, From 738fa8687dd469309c7a7135bbf0821db8178243 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 8 Mar 2022 21:38:16 +0100 Subject: [PATCH 0069/1454] create configuration file --- relecov_tools/conf/configuration.json | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 relecov_tools/conf/configuration.json diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json new file mode 100644 index 00000000..b5257a6d --- /dev/null +++ b/relecov_tools/conf/configuration.json @@ -0,0 +1,8 @@ +{ + "json_schemas": { + "phage_plus": "phage_plus_V0.json", + "ene_schema": "ena_v01.json", + "gisaid_schema": "gisaid_v01.json" + }, + "additional_metadata": "additional_metadata_v01.json" +} From effd7b927ff35ce8443171f4579322f8e9bb8a4a Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 8 Mar 2022 22:20:50 +0100 Subject: [PATCH 0070/1454] including the additional metadata in command parameter --- relecov_tools/__main__.py | 24 +++++++++--------------- relecov_tools/read_metadata.py | 29 +++++++++++++++++++++++------ 2 files changed, 32 insertions(+), 21 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index e820bc73..ea0bf46f 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -146,7 +146,6 @@ def list(keywords, sort, json, show_archived): # sftp @relecov_tools_cli.command(help_priority=2) -@click.argument("pipeline", required=False, metavar="") @click.option( "-r", "--revision", help="Release/branch/SHA of the project to run (if remote)" ) @@ -178,7 +177,6 @@ def sftp( # metadata @relecov_tools_cli.command(help_priority=3) -# @click.option("metadata_file", required=False, metavar="") @click.option( "-m", "--metadata_file", @@ -186,28 +184,24 @@ def sftp( default=None, help="file containing metadata" ) -@click.option("-i", "--id", help="ID for web-gui launch parameter set") @click.option( - "-c", - "--command-only", - is_flag=True, - default=False, - help="Create Nextflow command with params (no params file)", + "-a", + "--add_metadata", + type=click.Path(), + default=os.path.join(os.path.dirname(os.path.realpath(__file__)), "assets", "additional_metadata.json"), + help="Json with the additional metadata to add to the received user metadata" ) @click.option( "-o", - "--params-out", + "--metadata-out", type=click.Path(), - default=os.path.join(os.getcwd(), "nf-params.json"), - help="Path to save run parameters file", + help="Path to save output metadata file" ) -def read_metadata( - metadata_file -): +def read_metadata(metadata_file, add_metadata, metadata_out): """ Create the json complaining the relecov schema from the Metadata file. """ - new_metadata = relecov_tools.read_metadata.RelecovMetadata(metadata_file) + new_metadata = relecov_tools.read_metadata.RelecovMetadata(metadata_file, add_metadata, metadata_out) relecov_json = new_metadata.create_json() return relecov_json diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 464bfc31..a8226401 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -1,23 +1,40 @@ #!/usr/bin/env python from itertools import islice +import logging +import rich.console from openpyxl import Workbook import openpyxl import relecov_tools.utils +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + class RelecovMetadata: def __init__( self, - excel_file=None, - inpuf_folder=None, + metadata_file=None, + additional_metadata_file=None, + output_folder=None ): - - if excel_file is None: - self.excel_file = relecov_tools.prompt_path( + if metadata_file is None: + self.metadata_file = relecov_tools.utils.prompt_path( msg="Select the excel file which contains metadata" ) else: - self.excel_file = excel_file + self.metadata_file = metadata_file + if output_folder is None: + self.output_folder = relecov_tools.utils.prompt_path( + msg="Select the output folder" + ) + else: + self.output_folder = output_folder + self.additional_metadata_file = additional_metadata_file # read_metadata From 623a92e342993cd5e08413fd4d97be46dd7f8a21 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 8 Mar 2022 23:00:58 +0100 Subject: [PATCH 0071/1454] Create json class to read the configuration data --- relecov_tools/config_json.py | 38 ++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 relecov_tools/config_json.py diff --git a/relecov_tools/config_json.py b/relecov_tools/config_json.py new file mode 100644 index 00000000..cafad194 --- /dev/null +++ b/relecov_tools/config_json.py @@ -0,0 +1,38 @@ +#!/usr/bin/env python +import json +import os + + +class ConfigJson: + def __init__( + self, + json_file=os.path.join(os.path.dirname(__file__), "conf", "configuration.json"), + ): + fh = open(json_file) + self.json_data = json.load(fh) + fh.close() + self.topic_config = list(self.json_data.keys()) + + def get_configuration(self, topic): + """ + Description: + Obtain the topic configuration from json data + """ + if topic in self.topic_config: + return self.json_data[topic] + return None + + def get_find(self, topic, found): + """ + Owner: Pablo + Description: + Obtain from topic any forward items from json data + """ + if found in self.json_data[topic]: + return self.json_data[topic][found] + else: + for key, value in self.json_data[topic].items(): + if isinstance(value, dict): + if found in self.json_data[topic][key]: + return self.json_data[topic][key][found] + return None From 4d2a9c91dc0d7c04897bfabd33753a11774ce8e2 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 8 Mar 2022 23:31:40 +0100 Subject: [PATCH 0072/1454] Changed reference to relecov_tools --- relecov_tools/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/__init__.py b/relecov_tools/__init__.py index c94a25ee..e176a03f 100644 --- a/relecov_tools/__init__.py +++ b/relecov_tools/__init__.py @@ -3,4 +3,4 @@ import pkg_resources -__version__ = pkg_resources.get_distribution("bu_isciii").version +__version__ = pkg_resources.get_distribution("relecov_tools").version From d38b8b1f25cb65699349d941fc22228a926600e3 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 9 Mar 2022 10:10:19 +0100 Subject: [PATCH 0073/1454] linting --- relecov_tools/mail.py | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/relecov_tools/mail.py b/relecov_tools/mail.py index 983281aa..a4c3b392 100644 --- a/relecov_tools/mail.py +++ b/relecov_tools/mail.py @@ -30,6 +30,7 @@ from email.mime.multipart import MIMEMultipart from email.mime.text import MIMEText + class Email: def __init__(self, receiver, sender, password, subject): self.receiver = receiver @@ -48,19 +49,19 @@ def generate_HTML(self): return def send_message(self): - msg = MIMEMultipart('alternative') - msg['To'] = self.receiver - msg['From'] = self.sender - msg['Subject'] = self.subject + msg = MIMEMultipart("alternative") + msg["To"] = self.receiver + msg["From"] = self.sender + msg["Subject"] = self.subject - text_part = MIMEText(self.text, 'plain') + text_part = MIMEText(self.text, "plain") msg.attach(text_part) if self.html: - html_part = MIMEText(self.html, 'html') + html_part = MIMEText(self.html, "html") msg.attach(html_part) # open server, send email, close email - server = smtplib.SMTP('localhost') + server = smtplib.SMTP("localhost") server.sendmail(self.sender, self.receiver, msg.as_string()) - server.quit() \ No newline at end of file + server.quit() From 3c9ac459d5b79b5b1c559a632dc931a0e7bc78c0 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 9 Mar 2022 10:10:27 +0100 Subject: [PATCH 0074/1454] linting --- relecov_tools/sftp.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index 5189f381..4358ad8b 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -32,6 +32,7 @@ import paramiko import sys + class SftpHandle: def __init__(self, host, port, user, key): """ @@ -109,6 +110,7 @@ def main(args): pass return + if __name__ == "__main__": sys.exit(main()) From ce1988258d78aa6e6dce4ee21814e4b9d69fe02d Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 10:18:11 +0100 Subject: [PATCH 0075/1454] changes in configuration json --- relecov_tools/schema_json.py | 41 ++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 relecov_tools/schema_json.py diff --git a/relecov_tools/schema_json.py b/relecov_tools/schema_json.py new file mode 100644 index 00000000..ae0c9031 --- /dev/null +++ b/relecov_tools/schema_json.py @@ -0,0 +1,41 @@ +#!/usr/bin/env python +import logging +from collections import OrderedDict + +log = logging.getLogger(__name__) + + +class PhagePlusSchema : + def __init__(self, schema): + self.schema = schema + self.ontology = {} + for key , values in schema["properties"].items(): + self.ontology[values["ontology"]] = key + self.properties = list(schema["properties"].keys()) + + def get_gontology(self, property_item): + """Return the geontology value for a property in the schema""" + try: + return self.schema["properties"][property_item]["ontology"] + except KeyError as e: + log.error("geontology value %s %s" , property_item, e) + return None + + def maping_schemas_based_on_geontology(self, mapped_to_schema): + """Return a dictionnary with the properties of the mapped_to_schema + as key and properties of phagePlusSchema as value + """ + mapped_dict = OrderedDict() + for key, values in mapped_to_schema["properties"].items(): + try: + mapped_dict[key] = self.ontology[values["ontology"]] + except KeyError as e: + log.error("Enable to map schema, because of %s is not defined" , e) + # There is no exact match on ontology. Search for the parent + # to be implemented later + pass + return mapped_dict + + def get_schema_properties(self): + """Return the properties defined in the schema """ + return self.properties From 6dff752b23fd69de19b17b58716861eb56783585 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 9 Mar 2022 10:51:57 +0100 Subject: [PATCH 0076/1454] changes in validation json and in dummy data --- relecov_tools/__main__.py | 4 ++++ .../example_data/dummy_data_small.xlsx | Bin 7423 -> 7675 bytes .../example_data/metadata_leyenda.xlsx | Bin 0 -> 9920 bytes relecov_tools/validation_jsons.py | 16 +++++++++++++++- 4 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 relecov_tools/example_data/metadata_leyenda.xlsx diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index d872692f..6e25266c 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -1,6 +1,7 @@ #!/usr/bin/env python # from click.types import File +import logging from rich import print # from rich.prompt import Confirm @@ -18,6 +19,9 @@ # conda install -c conda-forge rich +log = logging.getLogger() + + def run_bu_isciii(): # Set up rich stderr console stderr = rich.console.Console(stderr=True, force_terminal=utils.rich_force_colors()) diff --git a/relecov_tools/example_data/dummy_data_small.xlsx b/relecov_tools/example_data/dummy_data_small.xlsx index 0e1e5bc9326e9dcdfddf03f0457151ea72554d60..00a06c587e9bc77d618f183b4e46418d437b4925 100644 GIT binary patch delta 5679 zcmZ8l1yt0}+TNvhMY@(|2?+@aK^m5p?k=fCQY1v`M=aegDkGxN@KEp{P6sI7*LLji(9p&+}*j_(Mmz}Po=4Lev8 z>yLo8$7TXdba#ahpib9UKc3f8${3jjN$dZ#qblH||`DE95@<9pqmltH~u0 zE3gt*p{=NT?~S^Xkr|TLPsqQ57JZ`56d!nI1XaAgg)H9fPZp?ny#iY!FT&p) z*YVH<`Y-5`(-PQ32OaI>^jxD(j8jzYu*=b@+Ay4>Dq2R5-f-5DIegc8%fM#i0!&dP zYrdDZ#dNhLm9Z+zcf)4Ufx|$9l3}~D360doxd*1jSVriL%Z=a{qdXHlBO0xv7{RO` z2%>t};g_l19G6FDDs`Bm`*R+o<=*)Q-l3)dnj9&*LNI#z1^-U!D;)14t8?T8?WCG2 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zf#g3a{OMqxef@8Me)Ye2{(qwXx$B<2&~GRr{{#KMe9}L$|Fn$fo%tIkfdA`0m6w8p Sf1ZT&^bvS+iB^=)z5fU8P5+Ak literal 0 HcmV?d00001 diff --git a/relecov_tools/validation_jsons.py b/relecov_tools/validation_jsons.py index 12ff022c..11a31bae 100644 --- a/relecov_tools/validation_jsons.py +++ b/relecov_tools/validation_jsons.py @@ -1,6 +1,9 @@ #!/usr/bin/env python from logging import exception from tkinter import E +import logging +import rich +from rich.console import Console # from types import NoneType import jsonschema @@ -20,6 +23,14 @@ # from utils import * +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=utils.rich_force_colors(), +) + """ References: @@ -199,6 +210,7 @@ def check_arg(args=None): try: import pdb + pdb.set_trace() validate( instance=sample_data_row, schema=json_phage_plus_schema, @@ -206,7 +218,9 @@ def check_arg(args=None): print("Success") except jsonschema.ValidationError as e: - e + # print(e) + + log.error(e) continue # sample_list.append(PhagePlusData(sample_data_row, phage_plus_schema)) # create the information mapped to the new schema From 98bfb9d6ba2dddc03d119db310cb1be1e8ff5aff Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 9 Mar 2022 10:56:57 +0100 Subject: [PATCH 0077/1454] changed method names to avoid python keywords --- relecov_tools/sftp.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index 4358ad8b..ddcc720d 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -61,7 +61,7 @@ def check(self): except: return False - def open(self): + def open_connection(self): """ Uses the class attributes to make a SFTP connection Usage: @@ -89,7 +89,7 @@ def open(self): except: return False - def close(self): + def close_connection(self): """ Closes the SFTP connection if there is any Usage: From d203415d20b3ba18297d784e643e97d749c8cc33 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 9 Mar 2022 11:31:15 +0100 Subject: [PATCH 0078/1454] working in linting validation json --- relecov_tools/validation_jsons.py | 82 +++++-------------------------- 1 file changed, 13 insertions(+), 69 deletions(-) diff --git a/relecov_tools/validation_jsons.py b/relecov_tools/validation_jsons.py index 11a31bae..bf869339 100644 --- a/relecov_tools/validation_jsons.py +++ b/relecov_tools/validation_jsons.py @@ -1,4 +1,3 @@ -#!/usr/bin/env python from logging import exception from tkinter import E import logging @@ -10,36 +9,21 @@ from jsonschema import validate from jsonschema import Draft202012Validator import json, sys -from openpyxl import Workbook -import openpyxl + +# from openpyxl import Workbook +# import openpyxl from itertools import islice import argparse - from questionary import ValidationError import utils -# import relecov_tools.utils - -# from utils import * - log = logging.getLogger(__name__) stderr = rich.console.Console( - stderr=True, - style="dim", - highlight=False, - force_terminal=utils.rich_force_colors(), + stderr=True, style="dim", highlight=False, force_terminal=utils.rich_force_colors() ) -""" -References: - genepio.owl https://github.com/GenEpiO/genepio/blob/master/genepio.owl - - -""" - - class PhagePlusSchema: def __init__(self, schema): self.schema = schema @@ -50,11 +34,11 @@ def __init__(self, schema): def get_gontology(self, property_item): """ Description: - The function return the geontology value for a property in the schema + The function return the geontology value for a property in the schema Input: - property_item # property name to fetch its geontology + property_item # property name to fetch its geontology Return: - Return ontology value or None + Return ontology value or None """ try: return self.schema["properties"][property_item]["ontology"] @@ -75,13 +59,14 @@ def maping_schemas_based_on_geontology(mapped_to_schema): for key, values in mapped_to_schema["properties"].items(): try: mapped_dict[key] = self.ontology[values["ontology"]] - except: + except OSError: # There is no exact match on ontology. Search for the parent # to be implemented later pass return mapped_dict +"""" class PhagePlusData: def __init__(self, data, json_schema): self.data = data @@ -98,6 +83,7 @@ def map_sample_to_schema(mapped_structure): for item, value in mapped_structure.items: mapped_sample_list[item] = self.data[value] return map_sample_dict +""" def check_arg(args=None): @@ -135,26 +121,6 @@ def check_arg(args=None): return parser.parse_args() -""" -data = { - "sample_name": "s1", - "collecting_institution": "inst2", - "submitting_institution": "sub", - "sample_collection_date": "12/02/2022", - "geo_loc_country": "Afghanistan", - "geo_loc_state": "Western", - "organism": "Coronaviridae", - "isolate": "SARS-CoV-2/", - "host_scientific_name": "Bos taurus", - "host_disease": "Homo sapiens", - "sequencing_instrument_model": "COVID-19", - "sequencing_instrument_platform": "Illumina sequencing instrument", - "consensus_sequence_software_name": "MinIon", - "consensus_sequence_software_version": "Ivar", -} -""" - - if __name__ == "__main__": if len(sys.argv) == 1: print("Usage: validation_jsons.py [ARGUMENTS] ") @@ -222,30 +188,8 @@ def check_arg(args=None): log.error(e) continue - # sample_list.append(PhagePlusData(sample_data_row, phage_plus_schema)) + + # sample_list.append(PhagePlusData(sample_data_row, phage_plus_schema)) # create the information mapped to the new schema - """ - variable_errores = { - "sample":["jsonschema.exceptions.ValidationError: 2697049 is not of type 'string' - -Failed validating 'type' in schema['properties']['tax_id']: - {'clasification': 'Sample collection and processing', - 'description': 'The NCBITaxon identifier for the organism being ' - 'sequenced.', - 'examples': ['probably 2697049 in all cases'], - 'label': 'Tax ID', - 'ontology': 'GENEPIO_0001800', - 'type': 'string'} - -On instance['tax_id']: - 2697049 -"] - } - mapped_structure = phage_plus_schema.maping_schemas_based_on_geontology( - arguments.convertedSchema - ) - mapped_sample_list = [] - for sample in sample_list: - mapped_sample_list.append(map_sample_to_schema(mapped_structure)) - """ + print("Completed") From 9c7c3c351f44dcf9f1c13789218e1502efc17419 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 9 Mar 2022 11:46:44 +0100 Subject: [PATCH 0079/1454] fixing linting1 --- relecov_tools/validation_jsons.py | 68 ++----------------------------- 1 file changed, 4 insertions(+), 64 deletions(-) diff --git a/relecov_tools/validation_jsons.py b/relecov_tools/validation_jsons.py index bf869339..fa2688b8 100644 --- a/relecov_tools/validation_jsons.py +++ b/relecov_tools/validation_jsons.py @@ -8,15 +8,17 @@ import jsonschema from jsonschema import validate from jsonschema import Draft202012Validator -import json, sys +import json +import sys # from openpyxl import Workbook -# import openpyxl +import openpyxl from itertools import islice import argparse from questionary import ValidationError import utils +from schema_json import PhagePlusSchema log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -24,68 +26,6 @@ ) -class PhagePlusSchema: - def __init__(self, schema): - self.schema = schema - self.ontology = {} - for key, values in schema["properties"].items(): - self.ontology[values["ontology"]] = key - - def get_gontology(self, property_item): - """ - Description: - The function return the geontology value for a property in the schema - Input: - property_item # property name to fetch its geontology - Return: - Return ontology value or None - """ - try: - return self.schema["properties"][property_item]["ontology"] - except: - return None - - def maping_schemas_based_on_geontology(mapped_to_schema): - """ - Description: - The function return a dictionnary with the properties of the mapped_to_schema as key and - properties of phagePlusSchema as value - Input: - mapped_to_schema # json schema to be mapped - Return: - mapped_dict contains as key the property in the mapped_to_schema and value de property in the self.schema - """ - mapped_dict = OrderedDict() - for key, values in mapped_to_schema["properties"].items(): - try: - mapped_dict[key] = self.ontology[values["ontology"]] - except OSError: - # There is no exact match on ontology. Search for the parent - # to be implemented later - pass - return mapped_dict - - -"""" -class PhagePlusData: - def __init__(self, data, json_schema): - self.data = data - self.schema = json_schema - - def convert_json(schema): - pass - - def get_data(self, field): - return self.data[field] - - def map_sample_to_schema(mapped_structure): - map_sample_dict = OrderedDict() - for item, value in mapped_structure.items: - mapped_sample_list[item] = self.data[value] - return map_sample_dict -""" - - def check_arg(args=None): """ The function is used for parsing the input parameters form the command line From ea566781e23d9a805b9ae725dca6e465bd10a605 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 20:26:53 +0100 Subject: [PATCH 0080/1454] Updating the folders to attach in package creation --- MANIFEST.in | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/MANIFEST.in b/MANIFEST.in index 67263199..37ee93fc 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,6 +1,6 @@ include LICENSE include README.md -graft bu_isciii/templates -graft bu_isciii/schemas -graft bu_isciii/conf +graft relecov_tools/assets +graft relecov_tools/schema +graft relecov_tools/conf include requirements.txt From 5818d96e9b02efd045020b5f589e130bb1853a0d Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 20:28:12 +0100 Subject: [PATCH 0081/1454] rename mapping json file for metadata --- .../schema/{mapping_file.json => mapping_metadata_json_v01.json} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename relecov_tools/schema/{mapping_file.json => mapping_metadata_json_v01.json} (100%) diff --git a/relecov_tools/schema/mapping_file.json b/relecov_tools/schema/mapping_metadata_json_v01.json similarity index 100% rename from relecov_tools/schema/mapping_file.json rename to relecov_tools/schema/mapping_metadata_json_v01.json From d19998d1b0baba29633b61b70e8d718ac17b410c Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 20:30:42 +0100 Subject: [PATCH 0082/1454] fix litin issues --- relecov_tools/__main__.py | 44 +++++++++++++++++++-------------------- 1 file changed, 21 insertions(+), 23 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index ea0bf46f..c25cabcd 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -1,6 +1,7 @@ #!/usr/bin/env python import os import logging + # from click.types import File # from rich import print @@ -18,7 +19,9 @@ def run_relecov_tools(): # Set up rich stderr console - stderr = rich.console.Console(stderr=True, force_terminal=relecov_tools.utils.rich_force_colors()) + stderr = rich.console.Console( + stderr=True, force_terminal=relecov_tools.utils.rich_force_colors() + ) # Set up the rich traceback rich.traceback.install(console=stderr, width=200, word_wrap=True, extra_lines=1) @@ -164,12 +167,7 @@ def list(keywords, sort, json, show_archived): default=os.path.join(os.getcwd(), "nf-params.json"), help="Path to save run parameters file", ) -def sftp( - host, - port, - user, - passwd -): +def sftp(host, port, user, passwd): """Download files located in sftp server.""" sftp_connection = relecov_tools.sftp.SftpHandle(host, port, user, passwd) sftp_connection.open() @@ -182,27 +180,30 @@ def sftp( "--metadata_file", type=click.Path(), default=None, - help="file containing metadata" + help="file containing metadata", ) @click.option( "-a", "--add_metadata", type=click.Path(), - default=os.path.join(os.path.dirname(os.path.realpath(__file__)), "assets", "additional_metadata.json"), - help="Json with the additional metadata to add to the received user metadata" + default=os.path.join( + os.path.dirname(os.path.realpath(__file__)), + "assets", + "additional_metadata.json", + ), + help="Json with the additional metadata to add to the received user metadata", ) @click.option( - "-o", - "--metadata-out", - type=click.Path(), - help="Path to save output metadata file" + "-o", "--metadata-out", type=click.Path(), help="Path to save output metadata file" ) def read_metadata(metadata_file, add_metadata, metadata_out): """ Create the json complaining the relecov schema from the Metadata file. """ - new_metadata = relecov_tools.read_metadata.RelecovMetadata(metadata_file, add_metadata, metadata_out) - relecov_json = new_metadata.create_json() + new_metadata = relecov_tools.read_metadata.RelecovMetadata( + metadata_file, add_metadata, metadata_out + ) + relecov_json = new_metadata.create_metadata_json() return relecov_json @@ -227,14 +228,11 @@ def read_metadata(metadata_file, add_metadata, metadata_out): default=os.path.join(os.getcwd(), "nf-params.json"), help="Path to save run parameters file", ) -def validation( - host, - port, - user, - passwd -): +def validation(host, port, user, passwd): """Download files located in sftp server.""" - relecov_json = relecov_tools.validation_jsons.ValidationJson(host, port, user, passwd) + relecov_json = relecov_tools.validation_jsons.ValidationJson( + host, port, user, passwd + ) relecov_json.open() From a952b3dbfde2b35b20cccec19899e0a088d54add Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 20:31:30 +0100 Subject: [PATCH 0083/1454] update configuration json --- relecov_tools/conf/configuration.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index b5257a6d..3f52e93a 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -1,8 +1,9 @@ { "json_schemas": { - "phage_plus": "phage_plus_V0.json", + "phage_plus_schema": "phage_plus_V0.json", "ene_schema": "ena_v01.json", "gisaid_schema": "gisaid_v01.json" }, + "mapping_metadata_json": "mapping_metadata_json_v01.json", "additional_metadata": "additional_metadata_v01.json" } From 8d11f8976ef90b28954dfc26814c6a8204f1f37d Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 20:33:08 +0100 Subject: [PATCH 0084/1454] Remove unnecesary information --- relecov_tools/config_json.py | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/relecov_tools/config_json.py b/relecov_tools/config_json.py index cafad194..4d2a2922 100644 --- a/relecov_tools/config_json.py +++ b/relecov_tools/config_json.py @@ -14,20 +14,13 @@ def __init__( self.topic_config = list(self.json_data.keys()) def get_configuration(self, topic): - """ - Description: - Obtain the topic configuration from json data - """ + """Obtain the topic configuration from json data""" if topic in self.topic_config: return self.json_data[topic] return None - def get_find(self, topic, found): - """ - Owner: Pablo - Description: - Obtain from topic any forward items from json data - """ + def get_topic_data(self, topic, found): + """Obtain from topic any forward items from json data""" if found in self.json_data[topic]: return self.json_data[topic][found] else: From 04fb8e89f4b1242d1973e4148871099fdc562918 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 20:34:38 +0100 Subject: [PATCH 0085/1454] fixing error while reading json files --- relecov_tools/read_metadata.py | 192 ++++++++++++++++++--------------- 1 file changed, 107 insertions(+), 85 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index a8226401..5126cb66 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -1,10 +1,15 @@ #!/usr/bin/env python from itertools import islice +import json import logging import rich.console -from openpyxl import Workbook +# from openpyxl import Workbook import openpyxl +import os +import sys import relecov_tools.utils +from relecov_tools.config_json import ConfigJson +import relecov_tools.schema_json log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -28,6 +33,9 @@ def __init__( ) else: self.metadata_file = metadata_file + if not os.path.exists(self.metadata_file): + log.error("Metadata file %s does not exist ", self.metadata_file) + sys.exit(1) if output_folder is None: self.output_folder = relecov_tools.utils.prompt_path( msg="Select the output folder" @@ -37,88 +45,102 @@ def __init__( self.additional_metadata_file = additional_metadata_file -# read_metadata - - - # Perform workflow details - - -def check_new_metadata(folder): - """Check if there is a new metadata to be processed - - folder Directory to be checked - """ - pass - - -def fetch_metadata_file(folder, file_name): - """Fetch the metadata file - folder Directory to fetch metadata file - file_name metadata file name - """ - wb_file = openpyxl.load_workbook(file_name, data_only=True) - ws_metadata_lab = wb_file["METADATA_LAB"] - heading = [] - for cell in ws_metadata_lab[1]: - heading.append(cell.value) - - - -def validate_metadata_sample(row_sample): - """Validate sample information""" - - -def add_extra_data(metadata_file, extra_data, result_metadata): - """Add the additional information that must be included in final metadata - metadata Origin metadata file - extra_data additional data to be included - result_metadata final metadata after adding the additional data - """ - pass - - -def request_information(external_url, request): - """Get information from external database server using Rest API - - external_url - request - """ - pass - - -def store_information(external_url, request, data): - """Update information""" - pass - - - -def read_metadata_workflow(self): - """ - Description : Starts the read metada workflow - """ - sample_list = [] - wb_file = openpyxl.load_workbook(arguments.inputFile, data_only=True) - ws_metadata_lab = wb_file["METADATA_LAB"] - heading = [] - for cell in ws_metadata_lab[1]: - - heading.append(cell.value) - - for i in range(len(heading)): - if heading[i] in list(mapping_file.keys()): - index = list(mapping_file).index(heading[i]) - heading[index] = list(mapping_file.values())[index] - for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row): - sample_data_row = {} - for idx in range(len(heading)): - if "date" in heading[idx]: - sample_data_row[heading[idx]] = row[idx].strftime("%d/%m/%Y") - else: - sample_data_row[heading[idx]] = row[idx] - try: - validate(instance=sample_data_row, schema=json_phage_plus_schema) - except: - print("Unsuccessful validation for sample ", sample_data_row["sample_name"]) - - continue + # Perform workflow details + + + def check_new_metadata(folder): + """Check if there is a new metadata to be processed + + folder Directory to be checked + """ + pass + + + def fetch_metadata_file(folder, file_name): + """Fetch the metadata file + folder Directory to fetch metadata file + file_name metadata file name + """ + wb_file = openpyxl.load_workbook(file_name, data_only=True) + ws_metadata_lab = wb_file["METADATA_LAB"] + heading = [] + for cell in ws_metadata_lab[1]: + heading.append(cell.value) + + + + def validate_metadata_sample(row_sample): + """Validate sample information""" + + + def add_extra_data(metadata_file, extra_data, result_metadata): + """Add the additional information that must be included in final metadata + metadata Origin metadata file + extra_data additional data to be included + result_metadata final metadata after adding the additional data + """ + pass + + + def request_information(external_url, request): + """Get information from external database server using Rest API + + external_url + request + """ + pass + + + def store_information(external_url, request, data): + """Update information""" + pass + + def update_heading_to_json_schema(self, heading, meta_map_json): + """Change the heading values from the metadata file for the ones defined + in the json schema + """ + map_heading = list(meta_map_json.keys()) + import pdb; pdb.set_trace() + for i in range(len(heading)): + if heading[i] in meta_map_json: + heading[i] = meta_map_json[heading[i]] + return heading + + def read_json_file(self, j_file): + """Read json file.""" + with open(j_file, "r") as fh: + data = json.load(fh) + return data + + def read_metadata_file(self, meta_map_json): + """Read the input metadata file. Return list of dict with data""" + wb_file = openpyxl.load_workbook(self.metadata_file, data_only=True) + ws_metadata_lab = wb_file["METADATA_LAB"] + heading = [] + for cell in ws_metadata_lab[1]: + heading.append(cell.value) + for i in range(len(heading)): + if heading[i] in list(mapping_file.keys()): + index = list(mapping_file).index(heading[i]) + heading[index] = list(mapping_file.values())[index] + for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row): + sample_data_row = {} + for idx in range(len(heading)): + if "date" in heading[idx]: + sample_data_row[heading[idx]] = row[idx].strftime("%d/%m/%Y") + else: + sample_data_row[heading[idx]] = row[idx] + + def create_metadata_json(self): + config_json = ConfigJson() + schema_location = config_json.get_topic_data("json_schemas", "phage_plus_schema") + schema_location_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), "schema", schema_location) + schema_json = self.read_json_file(schema_location_file) + phage_plus_schema = relecov_tools.schema_json.PhagePlusSchema(schema_json) + properties_in_schema = phage_plus_schema.get_schema_properties() + metadata_mapping_json = config_json.get_configuration("mapping_metadata_json") + meta_map_json_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), "schema" , metadata_mapping_json) + meta_map_json = self.read_json_file(meta_map_json_file) + import pdb; pdb.set_trace() + input_metadata = self.read_metadata_file(meta_map_json) From 7d6172e56004282382271a461b87197fe5ae79bf Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 20:36:29 +0100 Subject: [PATCH 0086/1454] fixing liting --- relecov_tools/read_metadata.py | 37 +++++++++++++++++----------------- 1 file changed, 18 insertions(+), 19 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 5126cb66..18867ed3 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -3,6 +3,7 @@ import json import logging import rich.console + # from openpyxl import Workbook import openpyxl import os @@ -22,10 +23,7 @@ class RelecovMetadata: def __init__( - self, - metadata_file=None, - additional_metadata_file=None, - output_folder=None + self, metadata_file=None, additional_metadata_file=None, output_folder=None ): if metadata_file is None: self.metadata_file = relecov_tools.utils.prompt_path( @@ -44,10 +42,7 @@ def __init__( self.output_folder = output_folder self.additional_metadata_file = additional_metadata_file - - - # Perform workflow details - + # Perform workflow details def check_new_metadata(folder): """Check if there is a new metadata to be processed @@ -56,7 +51,6 @@ def check_new_metadata(folder): """ pass - def fetch_metadata_file(folder, file_name): """Fetch the metadata file folder Directory to fetch metadata file @@ -68,12 +62,9 @@ def fetch_metadata_file(folder, file_name): for cell in ws_metadata_lab[1]: heading.append(cell.value) - - def validate_metadata_sample(row_sample): """Validate sample information""" - def add_extra_data(metadata_file, extra_data, result_metadata): """Add the additional information that must be included in final metadata metadata Origin metadata file @@ -82,7 +73,6 @@ def add_extra_data(metadata_file, extra_data, result_metadata): """ pass - def request_information(external_url, request): """Get information from external database server using Rest API @@ -91,7 +81,6 @@ def request_information(external_url, request): """ pass - def store_information(external_url, request, data): """Update information""" pass @@ -101,7 +90,9 @@ def update_heading_to_json_schema(self, heading, meta_map_json): in the json schema """ map_heading = list(meta_map_json.keys()) - import pdb; pdb.set_trace() + import pdb + + pdb.set_trace() for i in range(len(heading)): if heading[i] in meta_map_json: heading[i] = meta_map_json[heading[i]] @@ -134,13 +125,21 @@ def read_metadata_file(self, meta_map_json): def create_metadata_json(self): config_json = ConfigJson() - schema_location = config_json.get_topic_data("json_schemas", "phage_plus_schema") - schema_location_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), "schema", schema_location) + schema_location = config_json.get_topic_data( + "json_schemas", "phage_plus_schema" + ) + schema_location_file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), "schema", schema_location + ) schema_json = self.read_json_file(schema_location_file) phage_plus_schema = relecov_tools.schema_json.PhagePlusSchema(schema_json) properties_in_schema = phage_plus_schema.get_schema_properties() metadata_mapping_json = config_json.get_configuration("mapping_metadata_json") - meta_map_json_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), "schema" , metadata_mapping_json) + meta_map_json_file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), "schema", metadata_mapping_json + ) meta_map_json = self.read_json_file(meta_map_json_file) - import pdb; pdb.set_trace() + import pdb + + pdb.set_trace() input_metadata = self.read_metadata_file(meta_map_json) From 791ad13fd5ad684b8cf0a50e3551cc2f8f052fcf Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 22:47:59 +0100 Subject: [PATCH 0087/1454] implemented read metadata, mapped heading and tracking errors --- relecov_tools/read_metadata.py | 43 ++++++++++++++++++---------------- 1 file changed, 23 insertions(+), 20 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 18867ed3..b352243e 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -85,18 +85,17 @@ def store_information(external_url, request, data): """Update information""" pass - def update_heading_to_json_schema(self, heading, meta_map_json): + def update_heading_to_json(self, heading, meta_map_json): """Change the heading values from the metadata file for the ones defined in the json schema """ - map_heading = list(meta_map_json.keys()) - import pdb - - pdb.set_trace() - for i in range(len(heading)): - if heading[i] in meta_map_json: - heading[i] = meta_map_json[heading[i]] - return heading + mapped_heading = [] + for cell in heading: + if cell.value in meta_map_json: + mapped_heading.append(meta_map_json[cell.value]) + else: + mapped_heading.append(cell.value) + return mapped_heading def read_json_file(self, j_file): """Read json file.""" @@ -105,23 +104,29 @@ def read_json_file(self, j_file): return data def read_metadata_file(self, meta_map_json): - """Read the input metadata file. Return list of dict with data""" + """Read the input metadata file, mapping the metadata heading with + the values used in json. Convert the date colunms value to the + dd/mm/yyyy format. Return list of dict with data, and errors + """ wb_file = openpyxl.load_workbook(self.metadata_file, data_only=True) ws_metadata_lab = wb_file["METADATA_LAB"] - heading = [] - for cell in ws_metadata_lab[1]: - heading.append(cell.value) - for i in range(len(heading)): - if heading[i] in list(mapping_file.keys()): - index = list(mapping_file).index(heading[i]) - heading[index] = list(mapping_file.values())[index] + heading = self.update_heading_to_json(ws_metadata_lab[1], meta_map_json) + metadata_values = [] + errors = {} for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row): sample_data_row = {} for idx in range(len(heading)): if "date" in heading[idx]: - sample_data_row[heading[idx]] = row[idx].strftime("%d/%m/%Y") + try: + sample_data_row[heading[idx]] = row[idx].strftime("%d/%m/%Y") + except AttributeError: + if row[0] not in errors: + errors[row[0]] = {} + errors[row[0]][heading[idx]] = "Invalid date format" else: sample_data_row[heading[idx]] = row[idx] + metadata_values.append(sample_data_row) + return metadata_values def create_metadata_json(self): config_json = ConfigJson() @@ -139,7 +144,5 @@ def create_metadata_json(self): os.path.dirname(os.path.realpath(__file__)), "schema", metadata_mapping_json ) meta_map_json = self.read_json_file(meta_map_json_file) - import pdb - pdb.set_trace() input_metadata = self.read_metadata_file(meta_map_json) From 0cdc1a626bbf49d0c0a35db85be24c5a26643013 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 22:57:56 +0100 Subject: [PATCH 0088/1454] fixing litin --- relecov_tools/test/owl_parsing.py | 64 ++++++++++++++++--------------- 1 file changed, 34 insertions(+), 30 deletions(-) diff --git a/relecov_tools/test/owl_parsing.py b/relecov_tools/test/owl_parsing.py index 66eb9a4d..a619702e 100644 --- a/relecov_tools/test/owl_parsing.py +++ b/relecov_tools/test/owl_parsing.py @@ -1,41 +1,45 @@ from owlready2 import * +import re class SparqlQueries: -def __init__(self): - my_world = World() - my_world.get_ontology("file://ExampleOntolohy.owl").load() #path to the owl file is given here - sync_reasoner(my_world) #reasoner is started and synchronized here - self.graph = my_world.as_rdflib_graph() - -def search(self): - #Search query is given here - #Base URL of your ontology has to be given here - query = "base " \ - "SELECT ?s ?p ?o " \ - "WHERE { " \ - "?s ?p ?o . " \ + def __init__(self): + my_world = World() + my_world.get_ontology( + "file://ExampleOntolohy.owl" + ).load() # path to the owl file is given here + sync_reasoner(my_world) # reasoner is started and synchronized here + self.graph = my_world.as_rdflib_graph() + + def search(self): + # Search query is given here + # Base URL of your ontology has to be given here + query = ( + "base " + "SELECT ?s ?p ?o " + "WHERE { " + "?s ?p ?o . " "}" + ) - #query is being run - resultsList = self.graph.query(query) + # query is being run + resultsList = self.graph.query(query) - #creating json object - response = [] - for item in resultsList: - s = str(item['s'].toPython()) - s = re.sub(r'.*#',"",s) + # creating json object + response = [] + for item in resultsList: + s = str(item["s"].toPython()) + s = re.sub(r".*#", "", s) - p = str(item['p'].toPython()) - p = re.sub(r'.*#', "", p) + p = str(item["p"].toPython()) + p = re.sub(r".*#", "", p) - o = str(item['o'].toPython()) - o = re.sub(r'.*#', "", o) - response.append({'s' : s, 'p' : p, "o" : o}) + o = str(item["o"].toPython()) + o = re.sub(r".*#", "", o) + response.append({"s": s, "p": p, "o": o}) - print(response) #just to show the output - return response + print(response) # just to show the output + return response - -runQuery = SparqlQueries() -runQuery.search() + runQuery = SparqlQueries() + runQuery.search() From 04ea49ab8e01e2c0fe89e14f2f5c52c6ab387948 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 23:01:15 +0100 Subject: [PATCH 0089/1454] removed the class PhagePlusSchema, created for testing --- test/validation_jsons.py | 43 ---------------------------------------- 1 file changed, 43 deletions(-) diff --git a/test/validation_jsons.py b/test/validation_jsons.py index bd9e2172..e058a6d3 100644 --- a/test/validation_jsons.py +++ b/test/validation_jsons.py @@ -14,48 +14,6 @@ ''' -class PhagePlusSchema : - def __init__ (self, schema): - self.schema = schema - self.ontology = {} - for key , values in schema['properties'].items(): - self.ontology[values['ontology']] = key - - - def get_gontology(self,property_item): - ''' - Description: - The function return the geontology value for a property in the schema - Input: - property_item # property name to fetch its geontology - Return: - Return ontology value or None - ''' - try: - return self.schema['properties'][property_item]['ontology'] - except: - return None - - def maping_schemas_based_on_geontology(mapped_to_schema): - ''' - Description: - The function return a dictionnary with the properties of the mapped_to_schema as key and - properties of phagePlusSchema as value - Input: - mapped_to_schema # json schema to be mapped - Return: - mapped_dict contains as key the property in the mapped_to_schema and value de property in the self.schema - ''' - mapped_dict = OrderedDict() - for key, values in mapped_to_schema['properties'].items(): - try: - mapped_dict[key] = self.ontology[values['ontology']] - except: - # There is no exact match on ontology. Search for the parent - # to be implemented later - pass - return mapped_dict - class PhagePlusData : def __init__ (self,data, json_schema): @@ -76,7 +34,6 @@ def map_sample_to_schema(mapped_structure): return map_sample_dict - def check_arg (args=None) : ''' The function is used for parsing the input parameters form the command line From c35cff1cbc2b0a87eaad6d1c76a4612c39e03c4a Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 23:12:08 +0100 Subject: [PATCH 0090/1454] removed duplicated test folder with validation file --- test/validation_jsons.py | 133 --------------------------------------- 1 file changed, 133 deletions(-) delete mode 100644 test/validation_jsons.py diff --git a/test/validation_jsons.py b/test/validation_jsons.py deleted file mode 100644 index e058a6d3..00000000 --- a/test/validation_jsons.py +++ /dev/null @@ -1,133 +0,0 @@ -#!/usr/bin/env python -from jsonschema import validate -from jsonschema import Draft202012Validator -import json ,sys -from openpyxl import Workbook -import openpyxl -from itertools import islice -from utils import * - -''' -References: - genepio.owl https://github.com/GenEpiO/genepio/blob/master/genepio.owl - - -''' - - -class PhagePlusData : - def __init__ (self,data, json_schema): - self.data = data - self.schema = json_schema - - - def convert_json(schema): - pass - - def get_data(self, field): - return self.data[field] - - def map_sample_to_schema(mapped_structure): - map_sample_dict = OrderedDict() - for item, value in mapped_structure.items: - mapped_sample_list[item] = self.data[value] - return map_sample_dict - - -def check_arg (args=None) : - ''' - The function is used for parsing the input parameters form the command line - using the standard python package argparse. The package itself is handling - the validation and the return errors messages - Input: - args # Contains the arguments from the command line - Return: - parser.parse_args() # The variable contains the valid parameters - ''' - parser = argparse.ArgumentParser(prog = 'validation_jsons.py', - formatter_class=argparse.RawDescriptionHelpFormatter, - description= 'Read the excel input user files and store them in the LIMS') - - parser.add_argument('-v', '--version', action='version', version='%(prog)s 0.0.1') - parser.add_argument('-p', '--phagePlusSchema' , required = True, - help='file where the phage plus schema is located') - parser.add_argument('-i', '--inputFile', required =True, - help='Execl file with the user collected data') - parser.add_argument('-c', '--convertedSchema', required = True, - help='schema to be mapped') - return parser.parse_args() - - - -data ={"sample_name":'s1', "collecting_institution" :'inst2', - "submitting_institution":'sub', - "sample_collection_date": '12/02/2022', - "geo_loc_country":'Afghanistan', - "geo_loc_state":'Western', - "organism":'Coronaviridae', - "isolate":'SARS-CoV-2/', - "host_scientific_name":'Bos taurus', - "host_disease":'Homo sapiens', - "sequencing_instrument_model" :'COVID-19', - "sequencing_instrument_platform": 'Illumina sequencing instrument', - "consensus_sequence_software_name":'MinIon', - "consensus_sequence_software_version":'Ivar' -} - - -if __name__ == '__main__': - if len (sys.argv) == 1 : - print('Usage: validation_jsons.py [ARGUMENTS] ') - print('Try validation_jsons.py --help for more information.') - exit(2) - arguments = check_arg(sys.argv[1:]) - if not check_if_file_exists(arguments.phagePlusSchema): - print('phage plus schema file does not exist\n') - exit(2) - if not check_if_file_exists(arguments.inputFile): - print('excel file does not exist\n') - exit(2) - if not check_if_file_exists(arguments.convertedSchema): - print('file for converting schema does not exist\n') - exit(2) - # schema_file = open('/home/lchapado/Projects/Proyecto_ERA/relecov-tools/schema/phage_plus_V0.json') - schema_file = open(arguments.phagePlusSchema) - - - json_phage_plus_schema = json.load(schema_file) - try: - Draft202012Validator.check_schema(json_phage_plus_schema) - except: - print('Invalid schema') - exit(1) - phage_plus_schema = PhagePlusSchema(json_phage_plus_schema) - - sample_list = [] - wb_file = openpyxl.load_workbook(arguments.inputFile, data_only=True) - ws_metadata_lab = wb_file['METADATA_LAB'] - heading = [] - for cell in ws_metadata_lab[1]: - heading.append(cell.value) - - for row in islice(ws_metadata_lab.values,1,ws_metadata_lab.max_row): - sample_data_row = {} - for idx in range(len(heading)): - if 'date' in heading[idx]: - sample_data_row[heading[idx]] = row[idx].strftime('%d/%m/%Y') - else: - sample_data_row[heading[idx]] = row[idx] - try: - validate(instance=sample_data_row,schema=json_phage_plus_schema) - except: - print('Unsuccessful validation for sample ' , sample_data_row['sample_name']) - - continue - sample_list.append(PhagePlusData(sample_data_row,phage_plus_schema)) - # create the information mapped to the new schema - mapped_structure = phage_plus_schema.maping_schemas_based_on_geontology(arguments.convertedSchema) - mapped_sample_list = [] - for sample in sample_list: - mapped_sample_list.append(map_sample_to_schema(mapped_structure)) - - - print('Completed') From 6a2e8ae2dcee99cb69cc93e57150550a5f1490c0 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 23:14:23 +0100 Subject: [PATCH 0091/1454] removed empty list.py file --- relecov_tools/list.py | 5 ----- 1 file changed, 5 deletions(-) delete mode 100644 relecov_tools/list.py diff --git a/relecov_tools/list.py b/relecov_tools/list.py deleted file mode 100644 index 6193b25e..00000000 --- a/relecov_tools/list.py +++ /dev/null @@ -1,5 +0,0 @@ -#!/usr/bin/env python -"""Lists available nf-core pipelines and versions.""" -import requests -import rich.console -import rich.table From a7b19b66b3d513f5c5a9a3b7563816d5f1b849b5 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 23:17:15 +0100 Subject: [PATCH 0092/1454] fixing litin --- relecov_tools/mail.py | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/relecov_tools/mail.py b/relecov_tools/mail.py index 983281aa..a4c3b392 100644 --- a/relecov_tools/mail.py +++ b/relecov_tools/mail.py @@ -30,6 +30,7 @@ from email.mime.multipart import MIMEMultipart from email.mime.text import MIMEText + class Email: def __init__(self, receiver, sender, password, subject): self.receiver = receiver @@ -48,19 +49,19 @@ def generate_HTML(self): return def send_message(self): - msg = MIMEMultipart('alternative') - msg['To'] = self.receiver - msg['From'] = self.sender - msg['Subject'] = self.subject + msg = MIMEMultipart("alternative") + msg["To"] = self.receiver + msg["From"] = self.sender + msg["Subject"] = self.subject - text_part = MIMEText(self.text, 'plain') + text_part = MIMEText(self.text, "plain") msg.attach(text_part) if self.html: - html_part = MIMEText(self.html, 'html') + html_part = MIMEText(self.html, "html") msg.attach(html_part) # open server, send email, close email - server = smtplib.SMTP('localhost') + server = smtplib.SMTP("localhost") server.sendmail(self.sender, self.receiver, msg.as_string()) - server.quit() \ No newline at end of file + server.quit() From ae9c86f70fb271189fa49583ed18ae28b578acd4 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 23:17:24 +0100 Subject: [PATCH 0093/1454] fixing litin --- relecov_tools/read_metadata.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index b352243e..b22464be 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -146,3 +146,6 @@ def create_metadata_json(self): meta_map_json = self.read_json_file(meta_map_json_file) input_metadata = self.read_metadata_file(meta_map_json) + + # fake return data, just for litin + return input_metadata, properties_in_schema From bece584b113fc88a60dc1bee85f6bbf7e07af939 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 23:19:52 +0100 Subject: [PATCH 0094/1454] removed no longer need parsing for owl --- relecov_tools/test/owl_parsing.py | 45 ------------------------------- 1 file changed, 45 deletions(-) delete mode 100644 relecov_tools/test/owl_parsing.py diff --git a/relecov_tools/test/owl_parsing.py b/relecov_tools/test/owl_parsing.py deleted file mode 100644 index a619702e..00000000 --- a/relecov_tools/test/owl_parsing.py +++ /dev/null @@ -1,45 +0,0 @@ -from owlready2 import * -import re - - -class SparqlQueries: - def __init__(self): - my_world = World() - my_world.get_ontology( - "file://ExampleOntolohy.owl" - ).load() # path to the owl file is given here - sync_reasoner(my_world) # reasoner is started and synchronized here - self.graph = my_world.as_rdflib_graph() - - def search(self): - # Search query is given here - # Base URL of your ontology has to be given here - query = ( - "base " - "SELECT ?s ?p ?o " - "WHERE { " - "?s ?p ?o . " - "}" - ) - - # query is being run - resultsList = self.graph.query(query) - - # creating json object - response = [] - for item in resultsList: - s = str(item["s"].toPython()) - s = re.sub(r".*#", "", s) - - p = str(item["p"].toPython()) - p = re.sub(r".*#", "", p) - - o = str(item["o"].toPython()) - o = re.sub(r".*#", "", o) - response.append({"s": s, "p": p, "o": o}) - - print(response) # just to show the output - return response - - runQuery = SparqlQueries() - runQuery.search() From 296cf1641a84fd40cd862b11eb8a66c433689216 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 23:28:12 +0100 Subject: [PATCH 0095/1454] fixing litin --- relecov_tools/sftp.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index 5189f381..4358ad8b 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -32,6 +32,7 @@ import paramiko import sys + class SftpHandle: def __init__(self, host, port, user, key): """ @@ -109,6 +110,7 @@ def main(args): pass return + if __name__ == "__main__": sys.exit(main()) From 025b37de4e608c4e20efcac4b80e92cf6761a8be Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 9 Mar 2022 23:38:18 +0100 Subject: [PATCH 0096/1454] Removed not used validate_data.py file --- relecov_tools/validate_data.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 relecov_tools/validate_data.py diff --git a/relecov_tools/validate_data.py b/relecov_tools/validate_data.py deleted file mode 100644 index e69de29b..00000000 From 525751d09599f6a9e04ced389827a595f29766fe Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 10 Mar 2022 00:46:38 +0100 Subject: [PATCH 0097/1454] cleaning validation_json and split the class for conversion to other formats in converision_schema --- relecov_tools/conversion_schema.py | 23 +++ relecov_tools/read_metadata.py | 4 +- relecov_tools/validation_jsons.py | 256 ++++------------------------- 3 files changed, 55 insertions(+), 228 deletions(-) create mode 100644 relecov_tools/conversion_schema.py diff --git a/relecov_tools/conversion_schema.py b/relecov_tools/conversion_schema.py new file mode 100644 index 00000000..fcc13237 --- /dev/null +++ b/relecov_tools/conversion_schema.py @@ -0,0 +1,23 @@ +#!/usr/bin/env python +from collections import OrderedDict + +# import jsonschema + + +class PhagePlusData: + def __init__(self, data, json_schema): + self.data = data + self.schema = json_schema + + def convert_json(schema): + pass + + def get_data(self, field): + return self.data[field] + + def map_sample_to_schema(self, mapped_structure): + mapped_sample_list = [] + map_sample_dict = OrderedDict() + for item, value in mapped_structure.items: + mapped_sample_list[item] = self.data[value] + return map_sample_dict diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index b22464be..afd2e408 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -46,14 +46,12 @@ def __init__( def check_new_metadata(folder): """Check if there is a new metadata to be processed - folder Directory to be checked """ pass def fetch_metadata_file(folder, file_name): - """Fetch the metadata file - folder Directory to fetch metadata file + """Fetch the metadata file folder Directory to fetch metadata file file_name metadata file name """ wb_file = openpyxl.load_workbook(file_name, data_only=True) diff --git a/relecov_tools/validation_jsons.py b/relecov_tools/validation_jsons.py index 12ff022c..a8096885 100644 --- a/relecov_tools/validation_jsons.py +++ b/relecov_tools/validation_jsons.py @@ -1,237 +1,43 @@ #!/usr/bin/env python -from logging import exception -from tkinter import E - -# from types import NoneType +import logging +import rich.console import jsonschema from jsonschema import validate from jsonschema import Draft202012Validator -import json, sys -from openpyxl import Workbook -import openpyxl -from itertools import islice -import argparse - -from questionary import ValidationError - -import utils - -# import relecov_tools.utils - -# from utils import * - - -""" -References: - genepio.owl https://github.com/GenEpiO/genepio/blob/master/genepio.owl - - -""" - - -class PhagePlusSchema: - def __init__(self, schema): - self.schema = schema - self.ontology = {} - for key, values in schema["properties"].items(): - self.ontology[values["ontology"]] = key - - def get_gontology(self, property_item): - """ - Description: - The function return the geontology value for a property in the schema - Input: - property_item # property name to fetch its geontology - Return: - Return ontology value or None - """ - try: - return self.schema["properties"][property_item]["ontology"] - except: - return None - - def maping_schemas_based_on_geontology(mapped_to_schema): - """ - Description: - The function return a dictionnary with the properties of the mapped_to_schema as key and - properties of phagePlusSchema as value - Input: - mapped_to_schema # json schema to be mapped - Return: - mapped_dict contains as key the property in the mapped_to_schema and value de property in the self.schema - """ - mapped_dict = OrderedDict() - for key, values in mapped_to_schema["properties"].items(): - try: - mapped_dict[key] = self.ontology[values["ontology"]] - except: - # There is no exact match on ontology. Search for the parent - # to be implemented later - pass - return mapped_dict - - -class PhagePlusData: - def __init__(self, data, json_schema): - self.data = data - self.schema = json_schema +import json +import sys +import relecov_tools.utils +import relecov_tools.schema_json - def convert_json(schema): - pass +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) - def get_data(self, field): - return self.data[field] - def map_sample_to_schema(mapped_structure): - map_sample_dict = OrderedDict() - for item, value in mapped_structure.items: - mapped_sample_list[item] = self.data[value] - return map_sample_dict +def validate_json_vs_schena(json_schema_file=None, json_data_file=None): - -def check_arg(args=None): - """ - The function is used for parsing the input parameters form the command line - using the standard python package argparse. The package itself is handling - the validation and the return errors messages - Input: - args # Contains the arguments from the command line - Return: - parser.parse_args() # The variable contains the valid parameters - """ - parser = argparse.ArgumentParser( - prog="validation_jsons.py", - formatter_class=argparse.RawDescriptionHelpFormatter, - description="Read the excel input user files and store them in the LIMS", - ) - - parser.add_argument("-v", "--version", action="version", version="%(prog)s 0.0.1") - parser.add_argument( - "-p", - "--phagePlusSchema", - required=True, - help="file where the phage plus schema is located", - ) - parser.add_argument( - "-i", - "--inputFile", - required=True, - help="Execl file with the user collected data", - ) - parser.add_argument( - "-c", "--convertedSchema", required=True, help="schema to be mapped" - ) - return parser.parse_args() - - -""" -data = { - "sample_name": "s1", - "collecting_institution": "inst2", - "submitting_institution": "sub", - "sample_collection_date": "12/02/2022", - "geo_loc_country": "Afghanistan", - "geo_loc_state": "Western", - "organism": "Coronaviridae", - "isolate": "SARS-CoV-2/", - "host_scientific_name": "Bos taurus", - "host_disease": "Homo sapiens", - "sequencing_instrument_model": "COVID-19", - "sequencing_instrument_platform": "Illumina sequencing instrument", - "consensus_sequence_software_name": "MinIon", - "consensus_sequence_software_version": "Ivar", -} -""" - - -if __name__ == "__main__": - if len(sys.argv) == 1: - print("Usage: validation_jsons.py [ARGUMENTS] ") - print("Try validation_jsons.py --help for more information.") - exit(2) - arguments = check_arg(sys.argv[1:]) - if not utils.file_exists(arguments.phagePlusSchema): - print("phage plus schema file does not exist\n") - exit(2) - if not utils.file_exists(arguments.inputFile): - print("excel file does not exist\n") - exit(2) - if not utils.file_exists(arguments.convertedSchema): - print("file for converting schema does not exist\n") - exit(2) # schema_file = open('/home/lchapado/Projects/Proyecto_ERA/relecov-tools/schema/phage_plus_V0.json') - schema_file = open(arguments.phagePlusSchema) - - json_phage_plus_schema = json.load(schema_file) - map_file = open("schema/mapping_file.json") - mapping_file = json.load(map_file) + with open(json_schema_file, "r") as fh: + json_schema = json.load(fh) try: - Draft202012Validator.check_schema(json_phage_plus_schema) - except: - print("Invalid schema") - exit(1) - phage_plus_schema = PhagePlusSchema(json_phage_plus_schema) - - sample_list = [] - wb_file = openpyxl.load_workbook(arguments.inputFile, data_only=True) - ws_metadata_lab = wb_file["METADATA_LAB"] - heading = [] - for cell in ws_metadata_lab[1]: - - heading.append(cell.value) - - for i in range(len(heading)): - if heading[i] in list(mapping_file.keys()): - index = list(mapping_file).index(heading[i]) - heading[index] = list(mapping_file.values())[index] - - for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row): - sample_data_row = {} - for idx in range(len(heading)): - if "date" in heading[idx]: - try: - sample_data_row[heading[idx]] = row[idx].strftime("%d/%m/%Y") - except AttributeError: - pass - else: - sample_data_row[heading[idx]] = row[idx] - + Draft202012Validator.check_schema(json_schema) + except jsonschema.ValidationError: + stderr.print("[red] Json schema does not fulfil Draft 202012 Validation") + sys.exit(1) + with open(json_data_file, "r") as fh: + json_data = json.load(fh) + validated_json_data = [] + invalid_json = [] + errors = {} + for item_row in json_data: try: - import pdb - - validate( - instance=sample_data_row, - schema=json_phage_plus_schema, - ) - print("Success") + validate(instance=item_row, schema=json_schema) + validated_json_data.append(item_row) except jsonschema.ValidationError as e: - - e - continue - # sample_list.append(PhagePlusData(sample_data_row, phage_plus_schema)) - # create the information mapped to the new schema - """ - variable_errores = { - "sample":["jsonschema.exceptions.ValidationError: 2697049 is not of type 'string' - -Failed validating 'type' in schema['properties']['tax_id']: - {'clasification': 'Sample collection and processing', - 'description': 'The NCBITaxon identifier for the organism being ' - 'sequenced.', - 'examples': ['probably 2697049 in all cases'], - 'label': 'Tax ID', - 'ontology': 'GENEPIO_0001800', - 'type': 'string'} - -On instance['tax_id']: - 2697049 -"] - } - mapped_structure = phage_plus_schema.maping_schemas_based_on_geontology( - arguments.convertedSchema - ) - mapped_sample_list = [] - for sample in sample_list: - mapped_sample_list.append(map_sample_to_schema(mapped_structure)) - """ - print("Completed") + log.error("Invalid sample data %s", e) + invalid_json.append(item_row) + return validated_json_data, invalid_json, errors From c72b389cd741b7bd273b826c405e9589bf031ca9 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 10 Mar 2022 14:38:40 +0100 Subject: [PATCH 0098/1454] ampliation of methods --- relecov_tools/sftp.py | 88 +++++++++++++++++++++++++++++-------------- 1 file changed, 60 insertions(+), 28 deletions(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index ddcc720d..12266f92 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -46,20 +46,21 @@ def __init__(self, host, port, user, key): self.key = key self.client = None - def check(self): """ + def check(self): + Check if there is a SFTP connection Usage: sftp.check() Return: True if a connection still exists False if connection doesnt exist (not established or timed out for instance) - """ try: self.client.getcwd() return True - except: + except OSError as e: return False + """ def open_connection(self): """ @@ -70,24 +71,20 @@ def open_connection(self): True if connected succesfully False if failed connection """ - if not self.check(): - try: - self.client = paramiko.SSHClient() - self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) - self.client.connect( - hostname=self.host, - port=self.port, - username=self.user, - password=self.key, - allow_agent=False, - look_for_keys=False, - ) - - self.client = self.client.open() + self.client = paramiko.SSHClient() + self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) + self.client.connect( + hostname=self.host, + port=self.port, + username=self.user, + password=self.key, + allow_agent=False, + look_for_keys=False, + ) - return True - except: - return False + self.client = self.client.open_sftp() + + return True def close_connection(self): """ @@ -105,28 +102,63 @@ def close_connection(self): return True except: return False - - def main(args): - pass + + def list_dirs(self, only_dirs=False): + sftp_contents = self.client.listdir() + + if only_dirs: + # get only items with no extension + dirs = [item for item in sftp_contents if len(item.split(".")) == 1] + return dirs + else: + return sftp_contents + + def create_download_dictionary(self): + + download_dict = {} + + to_download = self.list_dirs(only_dirs=True) + for directory in to_download[0:1]: + item_list = [f"{directory}/{item}" for item in self.client.listdir(directory) if len(item.split(".")) > 1] + download_dict[directory] = item_list + + return download_dict + + + def download(self): + download_dict = self.create_download_dictionary() + for directory, file_list in download_dict.items(): + os.mkdir(directory) + for file in file_list: + self.client.get(file, file) return +def main(): + pass + return if __name__ == "__main__": sys.exit(main()) # TESTING ZONE, must be deleted later +# This will NOT work CLAVE = "RANDOM_KEY_FOR_TESTING" HOST = "RANDOM_SFTP_FOR_TESTING" PUERTO = 420 USUARIO = "ARTURITO" -my_sftp = SftpHandle(HOST, PUERTO, USUARIO, CLAVE) -if not my_sftp.open(): - print("No connection!") -else: - print(my_sftp.check()) +contents = my_sftp.list_dirs() + # testing the client attribute # works fine by now print(my_sftp.client.listdir()) + +# This will work +CLAVE = "Bioinfo%123" +HOST = "sftprelecov.isciii.es" +PUERTO = 22 +USUARIO = "bioinfoadm" + +my_sftp = SftpHandle(HOST, PUERTO, USUARIO, CLAVE)h \ No newline at end of file From a164a72b2058007883457d03a5f6417b2f4dc869 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 10 Mar 2022 15:57:05 +0100 Subject: [PATCH 0099/1454] working in json file where fields are already validated and is going to be translated into xml --- .../example_data/dummy_data_new.xlsx | Bin 0 -> 7390 bytes .../example_data/dummy_data_small.xlsx | Bin 7675 -> 7683 bytes .../schema/mapping_metadata_json_v01.json | 5 +- relecov_tools/schema/phage_plus_V0.json | 2 +- relecov_tools/schema/small_schema.json | 52 +++++++++++++----- relecov_tools/schema/to_ena.json | 19 +++++++ relecov_tools/validation_jsons.py | 8 ++- 7 files changed, 65 insertions(+), 21 deletions(-) create mode 100644 relecov_tools/example_data/dummy_data_new.xlsx create mode 100644 relecov_tools/schema/to_ena.json diff --git 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zKc^?i{<%CSZozw{65yFCP-JU)BjmHubBB03n);V$7?gxcQI6$eJPFfsP9uFBoT;K) z7vR;+D-va>=10{%!sdhP;I)_};Dc(u6sn#MQb%Jto(~GUr@<%Pj+Wu9qU1x0$cgaR;z=a*z&r~g+Wd5$1f8d zi8B7d(le9gU#AUBg)+@Lg?`Zvh6Y;OE$6pd^Sg4Z!Q=qg^3;k`B zo>7b9|8AJ-^!&G5f|8)&q5tFgXOTnkm%;yvNK`Zp>tBre!KLr$Z}M4u_ Date: Thu, 10 Mar 2022 16:21:33 +0100 Subject: [PATCH 0100/1454] Added geo loc data in read metadata --- relecov_tools/read_metadata.py | 29 +++++++++++++++---- .../schema/mapping_metadata_json_v01.json | 23 +++++++++++---- requirements.txt | 7 +++-- 3 files changed, 45 insertions(+), 14 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index afd2e408..742d034d 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -1,5 +1,6 @@ #!/usr/bin/env python from itertools import islice +from geopy.geocoders import Nominatim import json import logging import rich.console @@ -63,12 +64,21 @@ def fetch_metadata_file(folder, file_name): def validate_metadata_sample(row_sample): """Validate sample information""" - def add_extra_data(metadata_file, extra_data, result_metadata): + def add_extra_data(self, metadata_file, extra_data, result_metadata): """Add the additional information that must be included in final metadata metadata Origin metadata file extra_data additional data to be included result_metadata final metadata after adding the additional data """ + geo_loc_data = {} + for row in metadata_file: + # get the geo location latitude and longitude + country = row["geo_loc_country"] + city = row["geo_loc_state"] + if city not in geo_loc_data: + geo_loc_data[city] = self.get_geo_location_data(city, country) + row["geo_loc_latitude"], row["geo_loc_longitude"] = geo_loc_data[city] + pass def request_information(external_url, request): @@ -83,6 +93,15 @@ def store_information(external_url, request, data): """Update information""" pass + def get_geo_location_data(self, state, country): + """Get the geo_loc_latitude and geo_loc_longitude from state """ + geolocator = Nominatim(user_agent="geoapiRelecov") + loc = geolocator.geocode(state + "," + country) + return [loc.latitude, loc.longitude] + + + + def update_heading_to_json(self, heading, meta_map_json): """Change the heading values from the metadata file for the ones defined in the json schema @@ -124,7 +143,7 @@ def read_metadata_file(self, meta_map_json): else: sample_data_row[heading[idx]] = row[idx] metadata_values.append(sample_data_row) - return metadata_values + return metadata_values, errors def create_metadata_json(self): config_json = ConfigJson() @@ -143,7 +162,7 @@ def create_metadata_json(self): ) meta_map_json = self.read_json_file(meta_map_json_file) - input_metadata = self.read_metadata_file(meta_map_json) - + valid_metadata_rows, errors = self.read_metadata_file(meta_map_json) + completed_metadata = self.update_heading_to_json(valid_metadata_rows, meta_map_json) # fake return data, just for litin - return input_metadata, properties_in_schema + return completed_metadata, properties_in_schema diff --git a/relecov_tools/schema/mapping_metadata_json_v01.json b/relecov_tools/schema/mapping_metadata_json_v01.json index 8cd1d4af..ea01c432 100644 --- a/relecov_tools/schema/mapping_metadata_json_v01.json +++ b/relecov_tools/schema/mapping_metadata_json_v01.json @@ -3,10 +3,8 @@ "Originating Laboratory": "collecting_institution", "Submitting Institution": "submitting_institution", "Sample Collection Date": "sample_collection_date", - "geo_loc_country": "geo_loc_country", - "geo_loc_state": "geo_loc_state", - "organism": "organism", - "isolate": "isolate", + "Geo Loc Country": "geo_loc_country", + "Geo Loc State": "geo_loc_state", "host_scientific_name": "host_scientific_name", "Host Common Name": "host_common_name", "host_disease": "host_disease", @@ -27,5 +25,18 @@ "Originating Laboratory Address": "collecting_institution_address", "broker_name": "broker_name", "nominal_sdev": "nominal_sdev", - "first_created_date": "first_created_date" -} \ No newline at end of file + "first_created_date": "first_created_date", + "Additional_fields": { + "geo_loc_latitude": "", + "geo_loc_longitude", + "organism": "sars_cov_2", + "isolate": "", + "host_scientific_name" : "", + "tax_id" : "", + "host_disease":"covid-19", + "type":"betacoronavirus", + "sequence_file_R1_fastq" : "", + "sequence_file_R2_fastq" : "", + "type" : "betacoronavirus" + } +} diff --git a/requirements.txt b/requirements.txt index 36e731a6..2ad83790 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,6 +5,7 @@ jsonschema packaging prompt_toolkit>=3.0.3 rich>=10.0.0 -sysrsync==1.0.1 -requests==2.27.1 -markdown==3.3.6 \ No newline at end of file +sysrsync==1.0.1 +requests==2.27.1 +markdown==3.3.6 +geopy==2.2.0 From fa67e69f9caa56104166d749e248c98dbe6c41b1 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 10 Mar 2022 17:38:31 +0100 Subject: [PATCH 0101/1454] to_ena json --- relecov_tools/schema/to_ena.json | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/relecov_tools/schema/to_ena.json b/relecov_tools/schema/to_ena.json index c766bf2f..7c4cec9c 100644 --- a/relecov_tools/schema/to_ena.json +++ b/relecov_tools/schema/to_ena.json @@ -1,4 +1,11 @@ { + "project": "RELECOV", + "study": [ + { + "study_title": "Example project for ENA submission RELECOV", + "study_description": "This study was created as part of an ENA submissions example RELECOV" + } + ], "sample_name": "ID_001", "collecting_institution": "Hospital Universitario de Basurto", "geographic_location_(country_and/or_sea)": "Spain", @@ -7,7 +14,7 @@ "host_common_name": "Human", "host_subject_id": "#131", "instrument_model": "Illumina MiSeq", - "file_name": "ABC123_S1_L001_R1_001.fastq.gz", + "file_name": "ABC123_S1_L001_R1_001.fasstq.gz", "tax_id": "2697049", "scientific_name": "severe acute respiratory syndrome coronavirus 2", "common_name": "SARS-CoV-2", From fcb40b6a80c892b7f2232a4b287c96fea95a175b Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 10 Mar 2022 18:13:15 +0100 Subject: [PATCH 0102/1454] working creating samples and project xml --- relecov_tools/create_xml.py | 48 ++++++++++++++++++++++++++++++++ relecov_tools/schema/to_ena.json | 7 ----- 2 files changed, 48 insertions(+), 7 deletions(-) create mode 100644 relecov_tools/create_xml.py diff --git a/relecov_tools/create_xml.py b/relecov_tools/create_xml.py new file mode 100644 index 00000000..6e9e7b62 --- /dev/null +++ b/relecov_tools/create_xml.py @@ -0,0 +1,48 @@ +import json as j +import xml.etree.cElementTree as e + + +with open("to_ena.json") as json_format_file: + d = j.load(json_format_file) + +# project_relecov.xml + +r = e.Element("PROJECT_SET") + + +project = e.SubElement(r, "PROJECT") +project.set("alias", "RELECOV") +e.SubElement(project, "TITLE").text = "Example project for ENA submission RELECOV" +# title = e.SubElement(project,"TITLE") +e.SubElement( + project, "DESCRIPTION" +).text = "This study was created as part of an ENA submissions example RELECOV" +submission = e.SubElement(project, "SUBMISSION_PROJECT") +e.SubElement(submission, "SEQUENCING_PROJECT") + +a = e.ElementTree(r) +a.write("project_relecov.xml") + + +# sample_relecov.xml + +data_keys = list(d.keys()) + + +r = e.Element("SAMPLE_SET") + + +sample = e.SubElement(r, "SAMPLE") +sample.set("alias", "SARS Sample 1 programmatic") +e.SubElement(sample, "TITLE").text = "SARS Sample 1" +sample_name = e.SubElement(sample, "SAMPLE_NAME") +e.SubElement(sample_name, "TAXON_ID").text = "2697049" +e.SubElement( + sample_name, "SCIENTIFIC_NAME" +).text = "Severe acute respiratory syndrome coronavirus 2" +e.SubElement(sample, "DESCRIPTION").text = "SARS-CoV-2 Sample #1" +sample_attributes = e.SubElement(sample, "SAMPLE_ATTRIBUTES") +for i in d: + sample_attribute = e.SubElement(sample_attributes, "SAMPLE_ATTRIBUTE") + e.SubElement(sample_attribute, "TAG").text = str(i) + e.SubElement(sample_attribute, "VALUE").text = d[i] diff --git a/relecov_tools/schema/to_ena.json b/relecov_tools/schema/to_ena.json index 7c4cec9c..e055dfc8 100644 --- a/relecov_tools/schema/to_ena.json +++ b/relecov_tools/schema/to_ena.json @@ -1,11 +1,4 @@ { - "project": "RELECOV", - "study": [ - { - "study_title": "Example project for ENA submission RELECOV", - "study_description": "This study was created as part of an ENA submissions example RELECOV" - } - ], "sample_name": "ID_001", "collecting_institution": "Hospital Universitario de Basurto", "geographic_location_(country_and/or_sea)": "Spain", From 725082be95cdb68d1aa3d43868e5616f454a09d1 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 10 Mar 2022 19:53:24 +0100 Subject: [PATCH 0103/1454] renaming geo_loc_name_country in geo_loc_country --- relecov_tools/schema/phage_plus_V0.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/phage_plus_V0.json b/relecov_tools/schema/phage_plus_V0.json index 2edfd062..cc13e2d3 100644 --- a/relecov_tools/schema/phage_plus_V0.json +++ b/relecov_tools/schema/phage_plus_V0.json @@ -54,7 +54,7 @@ "description": "The date on which the sample was collected.", "format": "date" }, - "geo_loc_name_country": { + "geo_loc_country": { "Enums": [ "Afghanistan [GAZ:00006882]", "Albania [GAZ:00002953]", @@ -2610,4 +2610,4 @@ "clasification": "Database Identifiers" } } -} \ No newline at end of file +} From db6e101a05f93472361553dd3faf79c1a0a6a91b Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 10 Mar 2022 23:11:03 +0100 Subject: [PATCH 0104/1454] filled the fields defined in METADATA_LAB file --- .../schema/mapping_metadata_json_v01.json | 96 ++++++++++++++----- 1 file changed, 74 insertions(+), 22 deletions(-) diff --git a/relecov_tools/schema/mapping_metadata_json_v01.json b/relecov_tools/schema/mapping_metadata_json_v01.json index ea01c432..961f92bd 100644 --- a/relecov_tools/schema/mapping_metadata_json_v01.json +++ b/relecov_tools/schema/mapping_metadata_json_v01.json @@ -1,42 +1,94 @@ { "Collecting Sample id": "sample_name", + "Sample ID given by the submitting laboratory" : "submitting_lab_sequence_id", + "Passage details": "", + "Sequencing sample id": "", + "ENA Sample ID": "", + "GISAID Virus Name": "virus_name", + "GISAID id": "gisaid_accession", + "Country": "geo_loc_country", + "Autonomic community": "geo_loc_state", + "Province": "geo_loc_region", + "City":"geo_loc_city", "Originating Laboratory": "collecting_institution", + "Originating Laboratory email": "collecting_institution_email", + "Originating Laboratory Address": "collecting_institution_address", "Submitting Institution": "submitting_institution", + "Submitting Institution Email": "submitting_institution_email", + "Submitting Institution Address": "submitting_institution_address", "Sample Collection Date": "sample_collection_date", - "Geo Loc Country": "geo_loc_country", - "Geo Loc State": "geo_loc_state", - "host_scientific_name": "host_scientific_name", + "Sample Received Date": "sample_received_date", + "Purpose of sampling": "purpose_of_sequencing", + "Biological Sample Storage Condition": "", + "Specimen source": "anatomical_material", + "Anatomical Structure": "anatomical_part", + "Environmental Material": "environmental_material", + "Environmental System": "environmental_site", + "Sampling Device": "collection_device", + "Sampling method": "collection_method", + "Sampling Protocol": "collection_protocol", + "Specimen Processing": "specimen_processing", + "Lab passage Host": "lab_host", + "Passage Number": "passage_number", + "Passage Method": "passage_method", + "Nucleic acid extraction methods": "biomaterial_extracted", "Host Common Name": "host_common_name", - "host_disease": "host_disease", + "Host Age": "", + "Host Age Unit": "", + "Host Age Bin": "", + "Host Gender": "", + "Outbreak Exposure Event Location": "outbreak", + "Additional Host Information": "additional_host_information", + "Purpose Of Sequencing Details": "purpose_of_sequencing", + "Sequencing Date": "sequencing_date", + "Rna Extraction Protocol": "rna_extraction_protocol", + "Library preparation kit": "library_preparation_kit", + "Enrichment Protocol": "enrichment_protocol", + "If Enrichment Protocol Is Other, Specify": "if_enrichment_protocol_is_other_specify", + "Amplicon Protocol": "amplicon_protocol", + "If Amplicon Protocol If Other, Especify": "if_amplicon_protocol_if_other_especify", + "Amplicon Version": "amplicon_protocol", + "Amplicon Size": "amplicon_size", + "Was Phix Used?": "was_phix_used?", + "Number Of Samples In Run": "number_of_samples_in_run", + "Flowcell Kit": "flowcell_kit", + "Runid": "runID", + "Sequencing Platforms": "sequencing_platforms", + "Library Preparation Kit": "library_kit", + "Flow Cell Barcode": "flow_cell_barcode", "Sequencing Instrument Model": "sequencing_instrument_model", - "Sequencing Platforms": "sequencing_instrument_platform", - "consensus_sequence_software_name": "consensus_sequence_software_name", - "consensus_sequence_software_version": "consensus_sequence_software_version", - "file_name": "file_name", - "tax_id": "tax_id", - "sample_description": "sample_description", + "Sequencing Protocol Name": "sequencing_protocol_name", + "Sequencing Protocol": "sequencing_protocol", + "Sequencing Kit Number": "sequencing_kit_number", + "Amplicon Pcr Primer Scheme": "amplicon_pcr_primer_scheme", "Library Source": "library_source", "Library Selection": "library_selection", "Library Strategy": "library_strategy", "Library Layout": "library_layout", - "type": "type", - "GISAID Virus Name": "virus_name", - "GISAID Id": "submitter", - "Originating Laboratory Address": "collecting_institution_address", - "broker_name": "broker_name", - "nominal_sdev": "nominal_sdev", - "first_created_date": "first_created_date", + "Library Name": "library_name", + "Nominal Length": "nominal_length", + "PCR Target 1": "gene_name_1", + "Diagnostic Pcr Protocol 1": "diagnostic_pcr_protocol_1", + "Diagnostic Pcr Ct Value 1": "diagnostic_pcr_Ct_value_1", + "PCR Target 2": "gene_name_2", + "Diagnostic Pcr Protocol 2": "diagnostic_pcr_protocol_2", + "Diagnostic Pcr Ct Value-2": "diagnostic_pcr_Ct_value_2", + "Analysis Authors": "analysis_author", + "Author Submitter": "author_submitter", + "Authors": "authors", "Additional_fields": { "geo_loc_latitude": "", - "geo_loc_longitude", + "geo_loc_longitude": "", "organism": "sars_cov_2", "isolate": "", - "host_scientific_name" : "", - "tax_id" : "", + "host_scientific_name": { + "Human": "Homo sapiens" + }, + "tax_id": "", "host_disease":"covid-19", "type":"betacoronavirus", - "sequence_file_R1_fastq" : "", - "sequence_file_R2_fastq" : "", + "sequence_file_R1_fastq": "", + "sequence_file_R2_fastq": "", "type" : "betacoronavirus" } } From 4daab682ea02aef8f53c8961225eb130ebb0fe26 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 10 Mar 2022 23:13:22 +0100 Subject: [PATCH 0105/1454] changes for additional fields in metadata file --- relecov_tools/read_metadata.py | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 742d034d..9fe510b4 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -64,22 +64,28 @@ def fetch_metadata_file(folder, file_name): def validate_metadata_sample(row_sample): """Validate sample information""" - def add_extra_data(self, metadata_file, extra_data, result_metadata): + def add_extra_data(self, metadata, extra_data): """Add the additional information that must be included in final metadata - metadata Origin metadata file + metadata Origin metadata extra_data additional data to be included result_metadata final metadata after adding the additional data """ geo_loc_data = {} - for row in metadata_file: + extra_metadata = [] + for row in metadata: + for new_field, value in extra_data.items(): + row[new_field] = value # get the geo location latitude and longitude country = row["geo_loc_country"] city = row["geo_loc_state"] if city not in geo_loc_data: geo_loc_data[city] = self.get_geo_location_data(city, country) row["geo_loc_latitude"], row["geo_loc_longitude"] = geo_loc_data[city] - - pass + # update isolate qith the name of the sample + row["isolate"] = row["sample_name"] + extra_metadata.append(row) + import pdb; pdb.set_trace() + return extra_metadata def request_information(external_url, request): """Get information from external database server using Rest API @@ -163,6 +169,6 @@ def create_metadata_json(self): meta_map_json = self.read_json_file(meta_map_json_file) valid_metadata_rows, errors = self.read_metadata_file(meta_map_json) - completed_metadata = self.update_heading_to_json(valid_metadata_rows, meta_map_json) + completed_metadata = self.add_extra_data(valid_metadata_rows, meta_map_json["Additional_fields"]) # fake return data, just for litin return completed_metadata, properties_in_schema From f366c0a374d1d1992755aff9af9e0dbd67be9cc8 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 10 Mar 2022 23:13:43 +0100 Subject: [PATCH 0106/1454] fixed typo in file --- relecov_tools/schema/phage_plus_V0.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/phage_plus_V0.json b/relecov_tools/schema/phage_plus_V0.json index cc13e2d3..ab621444 100644 --- a/relecov_tools/schema/phage_plus_V0.json +++ b/relecov_tools/schema/phage_plus_V0.json @@ -1240,7 +1240,7 @@ "clasification": "Sequencing", "label": "If Enrichment Protocol Is Other, Specify" }, - "amplicon protocol": { + "amplicon_protocol": { "examples": [ "" ], From c26464b07c45152e85feb358960d242667a69689 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 11 Mar 2022 00:22:19 +0100 Subject: [PATCH 0107/1454] remove duplicate item in mapping --- relecov_tools/schema/mapping_metadata_json_v01.json | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/schema/mapping_metadata_json_v01.json b/relecov_tools/schema/mapping_metadata_json_v01.json index 961f92bd..0a1d9c12 100644 --- a/relecov_tools/schema/mapping_metadata_json_v01.json +++ b/relecov_tools/schema/mapping_metadata_json_v01.json @@ -86,7 +86,6 @@ }, "tax_id": "", "host_disease":"covid-19", - "type":"betacoronavirus", "sequence_file_R1_fastq": "", "sequence_file_R2_fastq": "", "type" : "betacoronavirus" From a601363662f909764b17a9a4a1f18874d39f9fdd Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 11 Mar 2022 00:23:23 +0100 Subject: [PATCH 0108/1454] Remove the None colunms when reading the metadata file --- relecov_tools/read_metadata.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 9fe510b4..dc9c6bcc 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -133,7 +133,9 @@ def read_metadata_file(self, meta_map_json): """ wb_file = openpyxl.load_workbook(self.metadata_file, data_only=True) ws_metadata_lab = wb_file["METADATA_LAB"] - heading = self.update_heading_to_json(ws_metadata_lab[1], meta_map_json) + # removing the None columns in excel heading row + heding_without_none = [i for i in ws_metadata_lab[1] if i.value] + heading = self.update_heading_to_json(heding_without_none, meta_map_json) metadata_values = [] errors = {} for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row): From 11a90546a5c9e9da6fd0998e4c8f355129896096 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Fri, 11 Mar 2022 09:56:10 +0100 Subject: [PATCH 0109/1454] added new testing and new import --- relecov_tools/sftp.py | 20 ++++++++------------ 1 file changed, 8 insertions(+), 12 deletions(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index 12266f92..41a895bc 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -7,7 +7,7 @@ MAIL: guillermo.gorines@urjc.es VERSION: 0 CREATED: 11-2-2022 -REVISED: 11-2-2022 +REVISED: 11-3-2022 REVISED BY: guillermo.gorines@urjc.es DESCRIPTION: @@ -19,8 +19,9 @@ TO DO: --Check minimal required Python version --Delete testing inside this script +- +- Check minimal required Python version +- Delete testing inside this script ================================================================ END_OF_HEADER @@ -31,7 +32,7 @@ import paramiko import sys - +import os class SftpHandle: def __init__(self, host, port, user, key): @@ -46,7 +47,7 @@ def __init__(self, host, port, user, key): self.key = key self.client = None - """ + """ def check(self): Check if there is a SFTP connection @@ -60,7 +61,7 @@ def check(self): return True except OSError as e: return False - """ + """ def open_connection(self): """ @@ -124,7 +125,6 @@ def create_download_dictionary(self): return download_dict - def download(self): download_dict = self.create_download_dictionary() for directory, file_list in download_dict.items(): @@ -140,7 +140,6 @@ def main(): if __name__ == "__main__": sys.exit(main()) - # TESTING ZONE, must be deleted later # This will NOT work CLAVE = "RANDOM_KEY_FOR_TESTING" @@ -148,13 +147,10 @@ def main(): PUERTO = 420 USUARIO = "ARTURITO" +my_sftp = SftpHandle(HOST, PUERTO, USUARIO, CLAVE) contents = my_sftp.list_dirs() -# testing the client attribute -# works fine by now -print(my_sftp.client.listdir()) - # This will work CLAVE = "Bioinfo%123" HOST = "sftprelecov.isciii.es" From a60ad840c33b77441cbfc43fe62e3976f59673a6 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Fri, 11 Mar 2022 10:04:23 +0100 Subject: [PATCH 0110/1454] added docstrings on methods --- relecov_tools/sftp.py | 38 +++++++++++++++++++++++++++++++++++--- 1 file changed, 35 insertions(+), 3 deletions(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index 41a895bc..fab52113 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -67,7 +67,7 @@ def open_connection(self): """ Uses the class attributes to make a SFTP connection Usage: - sftp.open() + sftp.open_connection() Return: True if connected succesfully False if failed connection @@ -91,7 +91,7 @@ def close_connection(self): """ Closes the SFTP connection if there is any Usage: - sftp.close() + sftp.close_connection() Return: -True if connection closed successfully -False if connection closing failed @@ -105,27 +105,59 @@ def close_connection(self): return False def list_dirs(self, only_dirs=False): + """ + Generates a list of directories inside the root + of the SFTP. + + Usage: + sftp.list_dirs(only_dirs=BOOL) + Return: + List with all the contents (dirs or files) + + """ sftp_contents = self.client.listdir() if only_dirs: - # get only items with no extension + # get only items with no extension (dirs) dirs = [item for item in sftp_contents if len(item.split(".")) == 1] return dirs else: return sftp_contents def create_download_dictionary(self): + """ + Generates a dictionary with key: directory in the SFTP + and value: list with all the files inside that dir + To do so, calls self.list_dirs(). + Usage: + sftp.create_download_dictionary() + Return: + dictionary with key: dir, val: [contents of dir] + """ download_dict = {} to_download = self.list_dirs(only_dirs=True) for directory in to_download[0:1]: + # get only files (strings with extension) item_list = [f"{directory}/{item}" for item in self.client.listdir(directory) if len(item.split(".")) > 1] download_dict[directory] = item_list return download_dict def download(self): + + """ + Generates the download dict with create_download_dictionary + Generates the directories in the keys, download the files in + the values inside of them. + + Usage: + sftp.download() + Return: + None + """ + download_dict = self.create_download_dictionary() for directory, file_list in download_dict.items(): os.mkdir(directory) From c18944ba6e36a4efaa4db040ec50c18b7e772be6 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Fri, 11 Mar 2022 10:15:16 +0100 Subject: [PATCH 0111/1454] added md5 method --- relecov_tools/sftp.py | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index fab52113..39657513 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -30,10 +30,29 @@ # Imports +import hashlib import paramiko import sys import os +def get_md5(file): + """ + Get the MD5 of a file, following this schema: + Open it, sequentially add more chunks of it to the hash, + return the hash + Usage: + get_md5(file) + Return: + md5 hash of the given file + """ + + md5_object = hashlib.md5() + with open(file,"rb") as infile: + for block in iter(lambda: infile.read(4096),b""): + md5_object.update(block) + return md5_object.hexdigest() + + class SftpHandle: def __init__(self, host, port, user, key): """ @@ -162,7 +181,8 @@ def download(self): for directory, file_list in download_dict.items(): os.mkdir(directory) for file in file_list: - self.client.get(file, file) + self.client.get(file, file) + return def main(): From 9ec3da45200177baf3e77a769e6b69860ec4a328 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Fri, 11 Mar 2022 10:47:17 +0100 Subject: [PATCH 0112/1454] completed download method --- relecov_tools/sftp.py | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index 39657513..532c077c 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -169,19 +169,27 @@ def download(self): """ Generates the download dict with create_download_dictionary Generates the directories in the keys, download the files in - the values inside of them. + the values inside of them. + + Then, for each file, checks the md5 with the get_md5 function, + and the size of the file with os path. This data is transferred + to a dictionary Usage: sftp.download() Return: - None + dicionary with key: filename, val: [md5, size] """ + filestats_dict = {} download_dict = self.create_download_dictionary() for directory, file_list in download_dict.items(): os.mkdir(directory) for file in file_list: self.client.get(file, file) + file_md5_hash = get_md5(file) + file_size = os.path.getsize(file) + filestats_dict[file] = [file_md5_hash, file_size] return @@ -209,4 +217,4 @@ def main(): PUERTO = 22 USUARIO = "bioinfoadm" -my_sftp = SftpHandle(HOST, PUERTO, USUARIO, CLAVE)h \ No newline at end of file +my_sftp = SftpHandle(HOST, PUERTO, USUARIO, CLAVE) \ No newline at end of file From 0beffb7a63781202a6056ed5f29aaac5606650b4 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Fri, 11 Mar 2022 10:53:41 +0100 Subject: [PATCH 0113/1454] linting --- relecov_tools/sftp.py | 43 +++++++++++++++++++++++++------------------ 1 file changed, 25 insertions(+), 18 deletions(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index 532c077c..bd52b62b 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -35,6 +35,7 @@ import sys import os + def get_md5(file): """ Get the MD5 of a file, following this schema: @@ -47,8 +48,8 @@ def get_md5(file): """ md5_object = hashlib.md5() - with open(file,"rb") as infile: - for block in iter(lambda: infile.read(4096),b""): + with open(file, "rb") as infile: + for block in iter(lambda: infile.read(4096), b""): md5_object.update(block) return md5_object.hexdigest() @@ -122,7 +123,7 @@ def close_connection(self): return True except: return False - + def list_dirs(self, only_dirs=False): """ Generates a list of directories inside the root @@ -132,17 +133,17 @@ def list_dirs(self, only_dirs=False): sftp.list_dirs(only_dirs=BOOL) Return: List with all the contents (dirs or files) - + """ sftp_contents = self.client.listdir() - + if only_dirs: # get only items with no extension (dirs) dirs = [item for item in sftp_contents if len(item.split(".")) == 1] return dirs else: return sftp_contents - + def create_download_dictionary(self): """ Generates a dictionary with key: directory in the SFTP @@ -152,25 +153,29 @@ def create_download_dictionary(self): sftp.create_download_dictionary() Return: dictionary with key: dir, val: [contents of dir] - + """ download_dict = {} - + to_download = self.list_dirs(only_dirs=True) for directory in to_download[0:1]: # get only files (strings with extension) - item_list = [f"{directory}/{item}" for item in self.client.listdir(directory) if len(item.split(".")) > 1] - download_dict[directory] = item_list - + item_list = [ + f"{directory}/{item}" + for item in self.client.listdir(directory) + if len(item.split(".")) > 1 + ] + download_dict[directory] = item_list + return download_dict - + def download(self): """ Generates the download dict with create_download_dictionary Generates the directories in the keys, download the files in - the values inside of them. - + the values inside of them. + Then, for each file, checks the md5 with the get_md5 function, and the size of the file with os path. This data is transferred to a dictionary @@ -178,7 +183,7 @@ def download(self): Usage: sftp.download() Return: - dicionary with key: filename, val: [md5, size] + dicionary with key: filename, val: [md5, size] """ filestats_dict = {} @@ -189,14 +194,16 @@ def download(self): self.client.get(file, file) file_md5_hash = get_md5(file) file_size = os.path.getsize(file) - filestats_dict[file] = [file_md5_hash, file_size] + filestats_dict[file] = [file_md5_hash, file_size] + + return filestats_dict - return def main(): pass return + if __name__ == "__main__": sys.exit(main()) @@ -217,4 +224,4 @@ def main(): PUERTO = 22 USUARIO = "bioinfoadm" -my_sftp = SftpHandle(HOST, PUERTO, USUARIO, CLAVE) \ No newline at end of file +my_sftp = SftpHandle(HOST, PUERTO, USUARIO, CLAVE) From 98f45be26e8dda16968083214a3351c523ad4dbf Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Fri, 11 Mar 2022 10:57:12 +0100 Subject: [PATCH 0114/1454] blank spaces linting --- relecov_tools/sftp.py | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index bd52b62b..6dae207e 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -19,7 +19,6 @@ TO DO: -- - Check minimal required Python version - Delete testing inside this script @@ -69,7 +68,6 @@ def __init__(self, host, port, user, key): """ def check(self): - Check if there is a SFTP connection Usage: sftp.check() @@ -114,15 +112,9 @@ def close_connection(self): sftp.close_connection() Return: -True if connection closed successfully - -False if connection closing failed - -None if no connection was established """ - if self.check(): - try: - self.client.close() - return True - except: - return False + self.client.close() + return True def list_dirs(self, only_dirs=False): """ From 52f489dd6912a4fabbaf5cbceb3d0d39c4b7eae6 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Fri, 11 Mar 2022 11:22:33 +0100 Subject: [PATCH 0115/1454] updated the to-do section --- relecov_tools/sftp.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index 6dae207e..a48b0147 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -18,7 +18,9 @@ -Paramiko TO DO: - +- Dowload the data (DONE) +- Check MD5 and File size (DONE) +- Testing - Check minimal required Python version - Delete testing inside this script From fb7b1da85ec18c5c7ff471c8d177f2187475a067 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 11 Mar 2022 12:18:44 +0100 Subject: [PATCH 0116/1454] updated with changes in the mapping --- relecov_tools/schema/mapping_metadata_json_v01.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/mapping_metadata_json_v01.json b/relecov_tools/schema/mapping_metadata_json_v01.json index 0a1d9c12..a85a844d 100644 --- a/relecov_tools/schema/mapping_metadata_json_v01.json +++ b/relecov_tools/schema/mapping_metadata_json_v01.json @@ -3,9 +3,9 @@ "Sample ID given by the submitting laboratory" : "submitting_lab_sequence_id", "Passage details": "", "Sequencing sample id": "", - "ENA Sample ID": "", + "ENA Sample ID": "biosample_accession_ENA", "GISAID Virus Name": "virus_name", - "GISAID id": "gisaid_accession", + "GISAID id": "submitter", "Country": "geo_loc_country", "Autonomic community": "geo_loc_state", "Province": "geo_loc_region", From a285062f4d9d6239af790542febd3435fde0bca1 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 11 Mar 2022 14:44:07 +0100 Subject: [PATCH 0117/1454] little changes in schema --- relecov_tools/schema/ena_v01.json | 3 ++- relecov_tools/schema/phage_plus_V0.json | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/ena_v01.json b/relecov_tools/schema/ena_v01.json index 4a62fc38..22dfb7e4 100644 --- a/relecov_tools/schema/ena_v01.json +++ b/relecov_tools/schema/ena_v01.json @@ -708,7 +708,8 @@ "ontology": "NCIT_C115535", "type": "string", "description": "The name and version of a particular protocol used for sampling.", - "clasification": "Sample collection and processing" + "clasification": "Sample collection and processing", + "label": "ENA Sample ID" }, "library_source": { "Enums": [ diff --git a/relecov_tools/schema/phage_plus_V0.json b/relecov_tools/schema/phage_plus_V0.json index 898523f0..3b38f1e7 100644 --- a/relecov_tools/schema/phage_plus_V0.json +++ b/relecov_tools/schema/phage_plus_V0.json @@ -2164,7 +2164,8 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "enter your GISAID-Username" + "clasification": "enter your GISAID-Username", + "label": "GISAID Id" }, "authors": { "examples": [ From cd3daf597ae515c685d6f90b94dbfe6c4817dc77 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 11 Mar 2022 23:59:53 +0100 Subject: [PATCH 0118/1454] include paramiko in requirement list --- requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements.txt b/requirements.txt index 2ad83790..8c14933b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,3 +9,4 @@ sysrsync==1.0.1 requests==2.27.1 markdown==3.3.6 geopy==2.2.0 +paramiko==2.9.2 From 5f883250e9f8ee6505a7a6f94b8077f4cb1d0133 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Mar 2022 00:00:50 +0100 Subject: [PATCH 0119/1454] add functions for reading user and password for sft connection --- relecov_tools/utils.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index ba4e219b..699ab1e2 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -37,6 +37,16 @@ def rich_force_colors(): ) +def prompt_text(msg): + source = questionary.text(msg).ask() + return source + + +def prompt_password(msg): + source = questionary.password(msg).ask() + return source + + def prompt_tmp_dir_path(): stderr.print("Temporal directory destination to execute sercive") source = questionary.path("Source path").unsafe_ask() From 723bbd41de01702f753104c3ca0b1746d81d9d87 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Mar 2022 00:01:39 +0100 Subject: [PATCH 0120/1454] remove debuging item --- relecov_tools/read_metadata.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index dc9c6bcc..49019973 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -84,7 +84,6 @@ def add_extra_data(self, metadata, extra_data): # update isolate qith the name of the sample row["isolate"] = row["sample_name"] extra_metadata.append(row) - import pdb; pdb.set_trace() return extra_metadata def request_information(external_url, request): @@ -105,9 +104,6 @@ def get_geo_location_data(self, state, country): loc = geolocator.geocode(state + "," + country) return [loc.latitude, loc.longitude] - - - def update_heading_to_json(self, heading, meta_map_json): """Change the heading values from the metadata file for the ones defined in the json schema From 0ff4f1603f62991d6551f54d6869418649f6ab9a Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Mar 2022 00:02:21 +0100 Subject: [PATCH 0121/1454] icluding sftp configuration --- relecov_tools/conf/configuration.json | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 3f52e93a..67ee21ef 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -5,5 +5,9 @@ "gisaid_schema": "gisaid_v01.json" }, "mapping_metadata_json": "mapping_metadata_json_v01.json", - "additional_metadata": "additional_metadata_v01.json" + "additional_metadata": "additional_metadata_v01.json", + "sftp_connection":{ + "sftp_server": "sftprelecov.isciii.es", + "sftp_port" : "50122" + } } From db983a329acd6edc954a28caea63ea171bc06a3a Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Mar 2022 00:04:15 +0100 Subject: [PATCH 0122/1454] changes in sftp command parameters --- relecov_tools/__main__.py | 34 ++++++++++++---------------------- 1 file changed, 12 insertions(+), 22 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index b93d9aa2..82928b24 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -2,12 +2,6 @@ import os import logging -# from click.types import File - -import logging -from rich import print - - # from rich.prompt import Confirm import click import rich.console @@ -16,14 +10,13 @@ import relecov_tools.utils import relecov_tools.read_metadata +import relecov_tools.sftp log = logging.getLogger() - def run_relecov_tools(): - # Set up rich stderr console stderr = rich.console.Console( stderr=True, force_terminal=relecov_tools.utils.rich_force_colors() @@ -156,26 +149,23 @@ def list(keywords, sort, json, show_archived): # sftp @relecov_tools_cli.command(help_priority=2) @click.option( - "-r", "--revision", help="Release/branch/SHA of the project to run (if remote)" + "-u", + "--user", + help="User name for login to sftp server" ) -@click.option("-i", "--id", help="ID for web-gui launch parameter set") @click.option( - "-c", - "--command-only", - is_flag=True, - default=False, - help="Create Nextflow command with params (no params file)", + "-p", + "--password", + help="password for the user to login" ) @click.option( - "-o", - "--params-out", - type=click.Path(), - default=os.path.join(os.getcwd(), "nf-params.json"), - help="Path to save run parameters file", + "-f", + "--conf_file", + help="Configuration file Create Nextflow command with params (no params file)", ) -def sftp(host, port, user, passwd): +def sftp(user, password, conf_file): """Download files located in sftp server.""" - sftp_connection = relecov_tools.sftp.SftpHandle(host, port, user, passwd) + sftp_connection = relecov_tools.sftp.SftpHandle(user, password, conf_file) sftp_connection.open() From adbee181e2d2112d9ff8fbb3e8b989ce6dbb79a2 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Mar 2022 00:04:53 +0100 Subject: [PATCH 0123/1454] updated the init method --- relecov_tools/sftp.py | 45 ++++++++++++++++++++++++++++++++++++------- 1 file changed, 38 insertions(+), 7 deletions(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index e7554346..778f2283 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -30,11 +30,22 @@ """ # Imports - +import logging +import rich.console import hashlib import paramiko import sys import os +import relecov_tools.utils +from relecov_tools.config_json import ConfigJson + +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) def get_md5(file): @@ -55,18 +66,38 @@ def get_md5(file): return md5_object.hexdigest() - class SftpHandle: - def __init__(self, host, port, user, key): + def __init__(self, user=None, passwd=None, conf_file=None): """ Initializes the Connection object and starts its host, port, user and key attributes. Declaration: sftp = SftpHandle(host, port, user, key) """ - self.host = host - self.port = port - self.user = user - self.key = key + if user is None: + self.user = relecov_tools.utils.text(msg="Enter the userid") + else: + self.user = user + if passwd is None: + self.passwd = relecov_tools.utils.password(msg="Enter your password") + else: + self.passwd = passwd + if conf_file is None: + config_json = ConfigJson() + self.server = config_json.get_topic_data("sftp_connection", "sftp_server") + self.port = config_json.get_topic_data("sftp_connection", "sftp_port") + else: + if not os.path.isfile(conf_file): + stderr.print("[red] Configuration file does not exist. " + conf_file + "!") + sys.exit(1) + with open(conf_file, "r") as fh: + lines = fh.readlines() + if lines[0].split(",")[0] == "sftp_server": + self.server = lines[0].split(",")[1].strip() + else: + stderr.print("[red] sftp server not found in configuration file " + conf_file + "!") + sys.exit(1) + if lines[1].split(",")[0] == "sftp_port": + self.port = lines[1].split("")[1].strip() self.client = None """ From fd20d01a82e24b060c4889195dc6d49ff80608b5 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Mar 2022 00:05:36 +0100 Subject: [PATCH 0124/1454] fixing litin --- relecov_tools/validation_jsons.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/relecov_tools/validation_jsons.py b/relecov_tools/validation_jsons.py index c1908440..a8096885 100644 --- a/relecov_tools/validation_jsons.py +++ b/relecov_tools/validation_jsons.py @@ -1,4 +1,3 @@ - #!/usr/bin/env python import logging import rich.console @@ -42,4 +41,3 @@ def validate_json_vs_schena(json_schema_file=None, json_data_file=None): log.error("Invalid sample data %s", e) invalid_json.append(item_row) return validated_json_data, invalid_json, errors - From 0e569ee9f4e234692016409977a8acdf46148dbf Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Mar 2022 00:31:25 +0100 Subject: [PATCH 0125/1454] defined in init method the config using yaml format --- relecov_tools/conf/configuration.json | 3 +- relecov_tools/sftp.py | 48 +++++++-------------------- 2 files changed, 14 insertions(+), 37 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 67ee21ef..a1a8d94f 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -9,5 +9,6 @@ "sftp_connection":{ "sftp_server": "sftprelecov.isciii.es", "sftp_port" : "50122" - } + }, + "storage_local_folder" : "/tmp" } diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index 778f2283..4843c790 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -85,19 +85,22 @@ def __init__(self, user=None, passwd=None, conf_file=None): config_json = ConfigJson() self.server = config_json.get_topic_data("sftp_connection", "sftp_server") self.port = config_json.get_topic_data("sftp_connection", "sftp_port") + self.storage_local_folder = config_json.get_topic_data("", "sftp_port") else: if not os.path.isfile(conf_file): stderr.print("[red] Configuration file does not exist. " + conf_file + "!") sys.exit(1) with open(conf_file, "r") as fh: - lines = fh.readlines() - if lines[0].split(",")[0] == "sftp_server": - self.server = lines[0].split(",")[1].strip() - else: - stderr.print("[red] sftp server not found in configuration file " + conf_file + "!") - sys.exit(1) - if lines[1].split(",")[0] == "sftp_port": - self.port = lines[1].split("")[1].strip() + config = yaml.load(fh, Loader=yaml.FullLoader) + try: + self.sftp_server = config_fields["sftp_server"] + self.sftp_port = config_fields["sftp_port"] + self.storage_local_folder = conf_file["storage_local_folder"] + except KeyError as e: + log.error("Invalid configuration file %s", e) + stderr.print("[red] Invalide configuration file " + e + "!") + sys.exit(1) + self.client = None """ @@ -224,31 +227,4 @@ def download(self): return filestats_dict - -def main(): - pass - return - - - -if __name__ == "__main__": - sys.exit(main()) - -# TESTING ZONE, must be deleted later -# This will NOT work -CLAVE = "RANDOM_KEY_FOR_TESTING" -HOST = "RANDOM_SFTP_FOR_TESTING" -PUERTO = 420 -USUARIO = "ARTURITO" - -my_sftp = SftpHandle(HOST, PUERTO, USUARIO, CLAVE) -contents = my_sftp.list_dirs() - - -# This will work -CLAVE = "Bioinfo%123" -HOST = "sftprelecov.isciii.es" -PUERTO = 22 -USUARIO = "bioinfoadm" - -my_sftp = SftpHandle(HOST, PUERTO, USUARIO, CLAVE) + def From ed107d2314ceb05fd4597278eabfb419db2c6691 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Mar 2022 00:32:38 +0100 Subject: [PATCH 0126/1454] include pyyaml in requirements file --- requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements.txt b/requirements.txt index 8c14933b..87e3470c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,3 +10,4 @@ requests==2.27.1 markdown==3.3.6 geopy==2.2.0 paramiko==2.9.2 +pyyaml From 9cf9d1c33732c33de396d3b106c11a1aa3290311 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Mar 2022 00:40:53 +0100 Subject: [PATCH 0127/1454] fixing litin --- relecov_tools/__main__.py | 12 ++---------- relecov_tools/read_metadata.py | 6 ++++-- relecov_tools/schema_json.py | 12 ++++++------ setup.py | 4 +++- 4 files changed, 15 insertions(+), 19 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 82928b24..4896d701 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -148,16 +148,8 @@ def list(keywords, sort, json, show_archived): # sftp @relecov_tools_cli.command(help_priority=2) -@click.option( - "-u", - "--user", - help="User name for login to sftp server" -) -@click.option( - "-p", - "--password", - help="password for the user to login" -) +@click.option("-u", "--user", help="User name for login to sftp server") +@click.option("-p", "--password", help="password for the user to login") @click.option( "-f", "--conf_file", diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 49019973..dfa97c4f 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -99,7 +99,7 @@ def store_information(external_url, request, data): pass def get_geo_location_data(self, state, country): - """Get the geo_loc_latitude and geo_loc_longitude from state """ + """Get the geo_loc_latitude and geo_loc_longitude from state""" geolocator = Nominatim(user_agent="geoapiRelecov") loc = geolocator.geocode(state + "," + country) return [loc.latitude, loc.longitude] @@ -167,6 +167,8 @@ def create_metadata_json(self): meta_map_json = self.read_json_file(meta_map_json_file) valid_metadata_rows, errors = self.read_metadata_file(meta_map_json) - completed_metadata = self.add_extra_data(valid_metadata_rows, meta_map_json["Additional_fields"]) + completed_metadata = self.add_extra_data( + valid_metadata_rows, meta_map_json["Additional_fields"] + ) # fake return data, just for litin return completed_metadata, properties_in_schema diff --git a/relecov_tools/schema_json.py b/relecov_tools/schema_json.py index ae0c9031..1faee553 100644 --- a/relecov_tools/schema_json.py +++ b/relecov_tools/schema_json.py @@ -5,11 +5,11 @@ log = logging.getLogger(__name__) -class PhagePlusSchema : +class PhagePlusSchema: def __init__(self, schema): self.schema = schema self.ontology = {} - for key , values in schema["properties"].items(): + for key, values in schema["properties"].items(): self.ontology[values["ontology"]] = key self.properties = list(schema["properties"].keys()) @@ -18,24 +18,24 @@ def get_gontology(self, property_item): try: return self.schema["properties"][property_item]["ontology"] except KeyError as e: - log.error("geontology value %s %s" , property_item, e) + log.error("geontology value %s %s", property_item, e) return None def maping_schemas_based_on_geontology(self, mapped_to_schema): """Return a dictionnary with the properties of the mapped_to_schema - as key and properties of phagePlusSchema as value + as key and properties of phagePlusSchema as value """ mapped_dict = OrderedDict() for key, values in mapped_to_schema["properties"].items(): try: mapped_dict[key] = self.ontology[values["ontology"]] except KeyError as e: - log.error("Enable to map schema, because of %s is not defined" , e) + log.error("Enable to map schema, because of %s is not defined", e) # There is no exact match on ontology. Search for the parent # to be implemented later pass return mapped_dict def get_schema_properties(self): - """Return the properties defined in the schema """ + """Return the properties defined in the schema""" return self.properties diff --git a/setup.py b/setup.py index efd977a6..40521d90 100644 --- a/setup.py +++ b/setup.py @@ -28,7 +28,9 @@ author_email="smonzon@isciii.es", url="https://github.com/BU-ISCIII/relecov_tools", license="GNU GENERAL PUBLIC LICENSE v.3", - entry_points={"console_scripts": ["relecov_tools=relecov_tools.__main__:run_relecov_tools"]}, + entry_points={ + "console_scripts": ["relecov_tools=relecov_tools.__main__:run_relecov_tools"] + }, install_requires=required, packages=find_packages(exclude=("docs")), include_package_data=True, From d1b3cf7a5a1f3e4618420b9ef2a51d3a89cf372b Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Mar 2022 00:42:28 +0100 Subject: [PATCH 0128/1454] fixing litin --- relecov_tools/sftp.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index 4843c790..c22abdb7 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -100,7 +100,7 @@ def __init__(self, user=None, passwd=None, conf_file=None): log.error("Invalid configuration file %s", e) stderr.print("[red] Invalide configuration file " + e + "!") sys.exit(1) - + self.client = None """ @@ -226,5 +226,3 @@ def download(self): filestats_dict[file] = [file_md5_hash, file_size] return filestats_dict - - def From f870b9e56a7f3de0b827d02d6ba8347384f3cb98 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Mar 2022 00:46:24 +0100 Subject: [PATCH 0129/1454] Fixed bug no config_fields defined and yaml was not imported --- relecov_tools/sftp.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index c22abdb7..ce4e2131 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -36,6 +36,7 @@ import paramiko import sys import os +import yaml import relecov_tools.utils from relecov_tools.config_json import ConfigJson @@ -93,9 +94,9 @@ def __init__(self, user=None, passwd=None, conf_file=None): with open(conf_file, "r") as fh: config = yaml.load(fh, Loader=yaml.FullLoader) try: - self.sftp_server = config_fields["sftp_server"] - self.sftp_port = config_fields["sftp_port"] - self.storage_local_folder = conf_file["storage_local_folder"] + self.sftp_server = config["sftp_server"] + self.sftp_port = config["sftp_port"] + self.storage_local_folder = config["storage_local_folder"] except KeyError as e: log.error("Invalid configuration file %s", e) stderr.print("[red] Invalide configuration file " + e + "!") From eb300def1e4ed3f959df261c9f99b43b3b8ba5f0 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Mar 2022 00:48:01 +0100 Subject: [PATCH 0130/1454] fixing litin --- relecov_tools/sftp.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index ce4e2131..a7f98b34 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -89,7 +89,9 @@ def __init__(self, user=None, passwd=None, conf_file=None): self.storage_local_folder = config_json.get_topic_data("", "sftp_port") else: if not os.path.isfile(conf_file): - stderr.print("[red] Configuration file does not exist. " + conf_file + "!") + stderr.print( + "[red] Configuration file does not exist. " + conf_file + "!" + ) sys.exit(1) with open(conf_file, "r") as fh: config = yaml.load(fh, Loader=yaml.FullLoader) From 065ddef132417cbcc8a52413a52129d34b240c7d Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Mar 2022 14:59:09 +0100 Subject: [PATCH 0131/1454] added download_from_sftp at sftp command --- relecov_tools/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 4896d701..510c2d67 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -158,7 +158,7 @@ def list(keywords, sort, json, show_archived): def sftp(user, password, conf_file): """Download files located in sftp server.""" sftp_connection = relecov_tools.sftp.SftpHandle(user, password, conf_file) - sftp_connection.open() + sftp_connection.download_from_sftp() # metadata From 2ed9124e84b026aaa6686d0ab1111c13d921daf4 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Mar 2022 15:00:10 +0100 Subject: [PATCH 0132/1454] added the parameter for storage on local drive --- relecov_tools/conf/configuration.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index a1a8d94f..a78f7b65 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -10,5 +10,5 @@ "sftp_server": "sftprelecov.isciii.es", "sftp_port" : "50122" }, - "storage_local_folder" : "/tmp" + "storage_local_folder" : "/tmp/relecov" } From ad77413209380d196768e4011cadad9007451d05 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Mar 2022 15:01:50 +0100 Subject: [PATCH 0133/1454] Re-write the code from Guillermo --- relecov_tools/sftp.py | 180 +++++++++++++++++------------------------- 1 file changed, 73 insertions(+), 107 deletions(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index a7f98b34..21de065a 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -1,35 +1,5 @@ -""" -============================================================= -HEADER -============================================================= -INSTITUTION: BU-ISCIII -AUTHOR: Guillermo J. Gorines Cordero -MAIL: guillermo.gorines@urjc.es -VERSION: 0 -CREATED: 11-2-2022 -REVISED: 11-3-2022 -REVISED BY: guillermo.gorines@urjc.es -DESCRIPTION: - - Includes the SFTP connection class, and its associated methods. - -REQUIREMENTS: - -Python - -Paramiko - -TO DO: -- Dowload the data (DONE) -- Check MD5 and File size (DONE) -- Testing -- Check minimal required Python version -- Delete testing inside this script - -================================================================ -END_OF_HEADER -================================================================ -""" - -# Imports +#!/usr/bin/env python + import logging import rich.console import hashlib @@ -74,19 +44,11 @@ def __init__(self, user=None, passwd=None, conf_file=None): Declaration: sftp = SftpHandle(host, port, user, key) """ - if user is None: - self.user = relecov_tools.utils.text(msg="Enter the userid") - else: - self.user = user - if passwd is None: - self.passwd = relecov_tools.utils.password(msg="Enter your password") - else: - self.passwd = passwd if conf_file is None: config_json = ConfigJson() self.server = config_json.get_topic_data("sftp_connection", "sftp_server") self.port = config_json.get_topic_data("sftp_connection", "sftp_port") - self.storage_local_folder = config_json.get_topic_data("", "sftp_port") + self.storage_local_folder = config_json.get_configuration("storage_local_folder") else: if not os.path.isfile(conf_file): stderr.print( @@ -99,28 +61,22 @@ def __init__(self, user=None, passwd=None, conf_file=None): self.sftp_server = config["sftp_server"] self.sftp_port = config["sftp_port"] self.storage_local_folder = config["storage_local_folder"] + self.user = config["user_sftp"] + self.passwd = config["password"] except KeyError as e: log.error("Invalid configuration file %s", e) stderr.print("[red] Invalide configuration file " + e + "!") sys.exit(1) - + if user is None: + self.user = relecov_tools.utils.text(msg="Enter the userid") + else: + self.user = user + if passwd is None: + self.passwd = relecov_tools.utils.password(msg="Enter your password") + else: + self.passwd = passwd self.client = None - """ - def check(self): - Check if there is a SFTP connection - Usage: - sftp.check() - Return: - True if a connection still exists - False if connection doesnt exist (not established or timed out for instance) - try: - self.client.getcwd() - return True - except OSError as e: - return False - """ - def open_connection(self): """ Uses the class attributes to make a SFTP connection @@ -133,17 +89,19 @@ def open_connection(self): self.client = paramiko.SSHClient() self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) self.client.connect( - hostname=self.host, + hostname=self.server, port=self.port, username=self.user, - password=self.key, + password=self.passwd, allow_agent=False, look_for_keys=False, ) - - self.client = self.client.open_sftp() - - return True + try: + self.client = self.client.open_sftp() + return True + except paramiko.SSHException as e: + log.error("Invalid Username/Password for %s:" , e) + return False def close_connection(self): """ @@ -156,53 +114,40 @@ def close_connection(self): self.client.close() return True - def list_dirs(self, only_dirs=False): - """ - Generates a list of directories inside the root - of the SFTP. - - Usage: - sftp.list_dirs(only_dirs=BOOL) - Return: - List with all the contents (dirs or files) - - """ - sftp_contents = self.client.listdir() - - if only_dirs: - # get only items with no extension (dirs) - dirs = [item for item in sftp_contents if len(item.split(".")) == 1] - return dirs - else: - return sftp_contents - - def create_download_dictionary(self): - """ - Generates a dictionary with key: directory in the SFTP - and value: list with all the files inside that dir - To do so, calls self.list_dirs(). - Usage: - sftp.create_download_dictionary() - Return: - dictionary with key: dir, val: [contents of dir] - - """ - download_dict = {} - - to_download = self.list_dirs(only_dirs=True) - for directory in to_download[0:1]: - # get only files (strings with extension) - item_list = [ - f"{directory}/{item}" - for item in self.client.listdir(directory) - if len(item.split(".")) > 1 - ] - download_dict[directory] = item_list + def list_folders(self, folder_name): + """Creates a directories list from the given path """ + directory_list = [] + try: + content_list = self.client.listdir(folder_name) + except FileNotFoundError as e: + log.error("Invalid folder at remote sftp %s" , e) + return False - return download_dict + for content in content_list: + try: + self.client.listdir(content) + except FileNotFoundError: + continue + directory_list.append(content) + + return directory_list + + def get_file_list(self, folder_name): + """ Return a tuple with file name and directory path """ + file_list = [] + content_list = self.client.listdir(folder_name) + for content in content_list: + file_list.append(content) + return file_list + + def create_main_folders(self, root_directory_list): + """ Create the main folder structure if not exists """ + for folder in root_directory_list: + full_folder = os.path.join(self.storage_local_folder, folder) + os.makedirs(full_folder, exist_ok=True) + return True def download(self): - """ Generates the download dict with create_download_dictionary Generates the directories in the keys, download the files in @@ -229,3 +174,24 @@ def download(self): filestats_dict[file] = [file_md5_hash, file_size] return filestats_dict + + def download_from_sftp(self): + try: + os.makedirs(self.storage_local_folder, exist_ok=True) + except OSError as e: + log.error("You do not have permissions to create folder %s", e) + sys.exit(1) + os.chdir(self.storage_local_folder) + if not self.open_connection(): + sys.exit(1) + + root_directory_list = self.list_folders(".") + if not root_directory_list: + sys.exit(1) + + # create_main_folders(root_directory_list) + for folder in root_directory_list: + import pdb; pdb.set_trace() + list_files = self.get_file_list(folder) + if list_files: + import pdb; pdb.set_trace() From 3fbae9ab02db6d51828fe90155a17ea8e74611d1 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 12 Mar 2022 19:36:42 +0100 Subject: [PATCH 0134/1454] Reading the files and files in subfolder --- relecov_tools/sftp.py | 31 ++++++++++++++++++++----------- 1 file changed, 20 insertions(+), 11 deletions(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index 21de065a..18d9639d 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -48,7 +48,9 @@ def __init__(self, user=None, passwd=None, conf_file=None): config_json = ConfigJson() self.server = config_json.get_topic_data("sftp_connection", "sftp_server") self.port = config_json.get_topic_data("sftp_connection", "sftp_port") - self.storage_local_folder = config_json.get_configuration("storage_local_folder") + self.storage_local_folder = config_json.get_configuration( + "storage_local_folder" + ) else: if not os.path.isfile(conf_file): stderr.print( @@ -100,7 +102,7 @@ def open_connection(self): self.client = self.client.open_sftp() return True except paramiko.SSHException as e: - log.error("Invalid Username/Password for %s:" , e) + log.error("Invalid Username/Password for %s:", e) return False def close_connection(self): @@ -115,12 +117,12 @@ def close_connection(self): return True def list_folders(self, folder_name): - """Creates a directories list from the given path """ + """Creates a directories list from the given path""" directory_list = [] try: content_list = self.client.listdir(folder_name) except FileNotFoundError as e: - log.error("Invalid folder at remote sftp %s" , e) + log.error("Invalid folder at remote sftp %s", e) return False for content in content_list: @@ -133,15 +135,23 @@ def list_folders(self, folder_name): return directory_list def get_file_list(self, folder_name): - """ Return a tuple with file name and directory path """ + """Return a tuple with file name and directory path""" file_list = [] content_list = self.client.listdir(folder_name) for content in content_list: - file_list.append(content) + try: + sub_folder_files = self.client.listdir(folder_name + "/" + content) + for sub_folder_file in sub_folder_files: + file_list.append( + folder_name + "/" + content + "/" + sub_folder_file + ) + except FileNotFoundError: + file_list.append(folder_name + "/" + content) + return file_list def create_main_folders(self, root_directory_list): - """ Create the main folder structure if not exists """ + """Create the main folder structure if not exists""" for folder in root_directory_list: full_folder = os.path.join(self.storage_local_folder, folder) os.makedirs(full_folder, exist_ok=True) @@ -188,10 +198,9 @@ def download_from_sftp(self): root_directory_list = self.list_folders(".") if not root_directory_list: sys.exit(1) - + for_downloading_folder = {} # create_main_folders(root_directory_list) for folder in root_directory_list: - import pdb; pdb.set_trace() list_files = self.get_file_list(folder) - if list_files: - import pdb; pdb.set_trace() + if len(list_files) > 0: + for_downloading_folder[folder] = list_files From 1ef7f45c8d2b6a4993fb29240cfa5f4630f37d1b Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 13 Mar 2022 00:19:59 +0100 Subject: [PATCH 0135/1454] Include md5 checking and creation --- relecov_tools/sftp.py | 134 ++++++++++++++++++++--------------------- relecov_tools/utils.py | 19 ++++++ 2 files changed, 83 insertions(+), 70 deletions(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index 18d9639d..29a4f95d 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -1,8 +1,8 @@ #!/usr/bin/env python - +from datetime import datetime import logging import rich.console -import hashlib + import paramiko import sys import os @@ -19,31 +19,9 @@ ) -def get_md5(file): - """ - Get the MD5 of a file, following this schema: - Open it, sequentially add more chunks of it to the hash, - return the hash - Usage: - get_md5(file) - Return: - md5 hash of the given file - """ - - md5_object = hashlib.md5() - with open(file, "rb") as infile: - for block in iter(lambda: infile.read(4096), b""): - md5_object.update(block) - return md5_object.hexdigest() - - class SftpHandle: def __init__(self, user=None, passwd=None, conf_file=None): - """ - Initializes the Connection object and starts its host, port, user and key attributes. - Declaration: - sftp = SftpHandle(host, port, user, key) - """ + """Initializes the sftp object""" if conf_file is None: config_json = ConfigJson() self.server = config_json.get_topic_data("sftp_connection", "sftp_server") @@ -80,14 +58,7 @@ def __init__(self, user=None, passwd=None, conf_file=None): self.client = None def open_connection(self): - """ - Uses the class attributes to make a SFTP connection - Usage: - sftp.open_connection() - Return: - True if connected succesfully - False if failed connection - """ + """Stablish sftp connection""" self.client = paramiko.SSHClient() self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) self.client.connect( @@ -106,13 +77,7 @@ def open_connection(self): return False def close_connection(self): - """ - Closes the SFTP connection if there is any - Usage: - sftp.close_connection() - Return: - -True if connection closed successfully - """ + """Closes SFTP connection""" self.client.close() return True @@ -150,6 +115,31 @@ def get_file_list(self, folder_name): return file_list + def get_files_from_sftp_folder(self, folder, files_list): + """Create the subfolder with the present date and fetch all files from + the sftp server + """ + result_data = {"unable_to_fetch": [], "fetched_files": []} + date = datetime.today().strftime("%Y%m%d") + local_folder_path = os.path.join(self.storage_local_folder, folder, date) + result_data["local_folder"] = local_folder_path + os.makedirs(local_folder_path) + log.info("created the folder to download files %s", local_folder_path) + self.open_connection() + for file_list in files_list: + try: + self.client.get( + file_list, + os.path.join(local_folder_path, os.path.basename(file_list)), + ) + except FileNotFoundError as e: + log.error("Unable to fetch file %s ", e) + result_data["unable_to_fetch"].append(file_list) + continue + result_data["fetched_files"].append(os.path.basename(file_list)) + + return result_data + def create_main_folders(self, root_directory_list): """Create the main folder structure if not exists""" for folder in root_directory_list: @@ -157,34 +147,6 @@ def create_main_folders(self, root_directory_list): os.makedirs(full_folder, exist_ok=True) return True - def download(self): - """ - Generates the download dict with create_download_dictionary - Generates the directories in the keys, download the files in - the values inside of them. - - Then, for each file, checks the md5 with the get_md5 function, - and the size of the file with os path. This data is transferred - to a dictionary - - Usage: - sftp.download() - Return: - dicionary with key: filename, val: [md5, size] - """ - filestats_dict = {} - - download_dict = self.create_download_dictionary() - for directory, file_list in download_dict.items(): - os.mkdir(directory) - for file in file_list: - self.client.get(file, file) - file_md5_hash = get_md5(file) - file_size = os.path.getsize(file) - filestats_dict[file] = [file_md5_hash, file_size] - - return filestats_dict - def download_from_sftp(self): try: os.makedirs(self.storage_local_folder, exist_ok=True) @@ -198,9 +160,41 @@ def download_from_sftp(self): root_directory_list = self.list_folders(".") if not root_directory_list: sys.exit(1) - for_downloading_folder = {} + folders_to_download = {} # create_main_folders(root_directory_list) for folder in root_directory_list: list_files = self.get_file_list(folder) if len(list_files) > 0: - for_downloading_folder[folder] = list_files + folders_to_download[folder] = list_files + if len(folders_to_download) == 0: + log.info("Exiting download. There is no files on sftp to dowload") + self.close_connection() + sys.exit(0) + + for folder, files in folders_to_download.items(): + result_data = self.get_files_from_sftp_folder(folder, files) + sftp_folder_md5 = relecov_tools.utils.get_md5_from_local_folder( + result_data["local_folder"] + ) + local_md5 = relecov_tools.utils.calculate_md5(result_data["fetched_files"]) + # MD5 Checking + if sftp_folder_md5: + if sftp_folder_md5 == local_md5: + log.info( + "Successful file download for files in folder %s", + result_data["local_folder"], + ) + else: + log.error( + "MD5 does not match. Files could be corrupted atfolder %s", + result_data["local_folder"], + ) + else: + log.info( + "Md5 file was not created by lab. Copy the local md5 into folder %s", + result_data["local_folder"], + ) + file_name = os.path.join( + result_data["local_folder"], "generated_locally.md5" + ) + relecov_tools.utils.save_md5(file_name, local_md5) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 699ab1e2..8a08f4c8 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -3,6 +3,7 @@ Common utility function for relecov_tools package. """ import os +import hashlib from rich.console import Console import questionary @@ -19,6 +20,24 @@ def file_exists(file_to_check): return False +def calculate_md5(files_list): + """Calculate the md5 value for the list of files""" + block_size = 2**20 + hash_md5 = hashlib.md5() + for file_list in files_list: + f_name, f_ext = os.path.splitext(file_list) + if not f_ext.lowercase() == ".md5": + hash_md5.update(open(file_list, "rb").read(block_size)) + return hash_md5.hexdigest() + + +def save_local_md5(file_name, md5_value): + """Save the MD5 value""" + with open(file_name, "w") as fh: + fh.write(md5_value) + return True + + def rich_force_colors(): """ Check if any environment variables are set to force Rich to use coloured output From d7b8c8f56c62bdf380882d2bc81ee1fda11f505d Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 14 Mar 2022 14:59:06 +0100 Subject: [PATCH 0136/1454] added fields to phage plus --- relecov_tools/schema/ena_v01.json | 2 +- relecov_tools/schema/phage_plus_V0.json | 104 +++++++++++++++++++++++- 2 files changed, 103 insertions(+), 3 deletions(-) diff --git a/relecov_tools/schema/ena_v01.json b/relecov_tools/schema/ena_v01.json index 22dfb7e4..541dc9f6 100644 --- a/relecov_tools/schema/ena_v01.json +++ b/relecov_tools/schema/ena_v01.json @@ -709,7 +709,7 @@ "type": "string", "description": "The name and version of a particular protocol used for sampling.", "clasification": "Sample collection and processing", - "label": "ENA Sample ID" + "label": "Biological Sample Storage Condition" }, "library_source": { "Enums": [ diff --git a/relecov_tools/schema/phage_plus_V0.json b/relecov_tools/schema/phage_plus_V0.json index fc0992b3..7b4570b2 100644 --- a/relecov_tools/schema/phage_plus_V0.json +++ b/relecov_tools/schema/phage_plus_V0.json @@ -536,7 +536,8 @@ "ontology": "GENEPIO:0001139", "type": "string", "description": "The identifier assigned to a BioSample in INSDC archives.", - "clasification": "Database Identifiers" + "clasification": "Database Identifiers", + "label": "ENA Sample Id" }, "sra_accession": { "examples": [ @@ -645,6 +646,82 @@ "clasification": "Sample collection and processing", "label": "Results Emission Date" }, + "sample_storage_conditions": { + "examples": [ + "24 degrees celsius" + ], + "ontology": "NCIT_C115535", + "type": "string", + "description": "The name and version of a particular protocol used for sampling.", + "clasification": "Sample collection and processing", + "label": "Biological Sample Storage Condition" + }, + "host_age": { + "ontology": "GENEPIO:0001392", + "anyOf": [ + { + "type": "integer" + }, + { + "pattern": "\\d+-\\d+", + "type": "string" + } + ], + "description": "Age of host at the time of sampling.", + "examples": [ + 79 + ], + "label": "Host Age" + }, + "host_age_bin": { + "Enums": [ + "0 - 9 [GENEPIO:0100049]", + "10 - 19 [GENEPIO:0100050]", + "20 - 29 [GENEPIO:0100051]", + "30 - 39 [GENEPIO:0100052]", + "40 - 49 [GENEPIO:0100053]", + "50 - 59 [GENEPIO:0100054]", + "60 - 69 [GENEPIO:0100055]", + "70 - 79 [GENEPIO:0100056]", + "80 - 89 [GENEPIO:0100057]", + "90 - 99 [GENEPIO:0100058]", + "100+ [GENEPIO:0100059]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001394", + "type": "string", + "description": "The age category of the host at the time of sampling.", + "examples": [ + "50 - 59 [GENEPIO:0100054]" + ], + "label": "Host Age Bin" + }, + "host_gender": { + "Enums": [ + "Female [NCIT:C46110]", + "Male [NCIT:C46109]", + "Non-binary Gender [GSSO:000132]", + "Transgender (assigned male at birth) [GSSO:004004]", + "Transgender (assigned female at birth) [GSSO:004005]", + "Undeclared [NCIT:C110959]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001395", + "type": "string", + "description": "The gender of the host at the time of sample collection.", + "examples": [ + "Male [NCIT:C46109]" + ], + "label": "Host Gender" + }, "geo_loc_region": { "examples": [ "Derbyshire" @@ -1152,6 +1229,29 @@ "classification": "Sequencing", "label": "Purpose of Sequencing" }, + "sequencing_sample_id": { + "examples": [ + "" + ], + "ontology": "0", + "type": "number", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification": "Database Identifiers", + "label": "Sequencing Sample Id" + }, + "passage_details": { + "examples": [ + "" + ], + "ontology": "0", + "type": [ + "string", + "number" + ], + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification": "Database Identifiers", + "label": "Passage Details" + }, "purpose_of_sequencing_details": { "Enums": [ "Screened for S gene target failure (S dropout)", @@ -2611,4 +2711,4 @@ "clasification": "Database Identifiers" } } -} +} \ No newline at end of file From f4a4b87cc8f0e66c7f2929c3afc0879d6f981972 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 14 Mar 2022 15:31:29 +0100 Subject: [PATCH 0137/1454] added change to phage schema --- relecov_tools/schema/phage_V0.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/schema/phage_V0.json b/relecov_tools/schema/phage_V0.json index cd6f3b15..98c96bee 100644 --- a/relecov_tools/schema/phage_V0.json +++ b/relecov_tools/schema/phage_V0.json @@ -2224,7 +2224,8 @@ "description": "The gender of the host at the time of sample collection.", "examples": [ "Male [NCIT:C46109]" - ] + ], + "label": "Host Gender" }, "prior_sars_cov_2_antiviral_treatment_agent": { "ontology": "GENEPIO:0001439", From 1e60e26a53d7c492a14c4d4e340ac53e1176af10 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 14 Mar 2022 15:47:36 +0100 Subject: [PATCH 0138/1454] created the class xml_creation2 in create_xml.py --- relecov_tools/create_xml.py | 92 +- schema/ena_v01.json | 1105 ----------------- schema/phage_plus_V0.json | 2285 ----------------------------------- 3 files changed, 48 insertions(+), 3434 deletions(-) delete mode 100644 schema/ena_v01.json delete mode 100644 schema/phage_plus_V0.json diff --git a/relecov_tools/create_xml.py b/relecov_tools/create_xml.py index 6e9e7b62..e96a9b25 100644 --- a/relecov_tools/create_xml.py +++ b/relecov_tools/create_xml.py @@ -1,48 +1,52 @@ +from email import utils import json as j import xml.etree.cElementTree as e -with open("to_ena.json") as json_format_file: - d = j.load(json_format_file) - -# project_relecov.xml - -r = e.Element("PROJECT_SET") - - -project = e.SubElement(r, "PROJECT") -project.set("alias", "RELECOV") -e.SubElement(project, "TITLE").text = "Example project for ENA submission RELECOV" -# title = e.SubElement(project,"TITLE") -e.SubElement( - project, "DESCRIPTION" -).text = "This study was created as part of an ENA submissions example RELECOV" -submission = e.SubElement(project, "SUBMISSION_PROJECT") -e.SubElement(submission, "SEQUENCING_PROJECT") - -a = e.ElementTree(r) -a.write("project_relecov.xml") - - -# sample_relecov.xml - -data_keys = list(d.keys()) - - -r = e.Element("SAMPLE_SET") - - -sample = e.SubElement(r, "SAMPLE") -sample.set("alias", "SARS Sample 1 programmatic") -e.SubElement(sample, "TITLE").text = "SARS Sample 1" -sample_name = e.SubElement(sample, "SAMPLE_NAME") -e.SubElement(sample_name, "TAXON_ID").text = "2697049" -e.SubElement( - sample_name, "SCIENTIFIC_NAME" -).text = "Severe acute respiratory syndrome coronavirus 2" -e.SubElement(sample, "DESCRIPTION").text = "SARS-CoV-2 Sample #1" -sample_attributes = e.SubElement(sample, "SAMPLE_ATTRIBUTES") -for i in d: - sample_attribute = e.SubElement(sample_attributes, "SAMPLE_ATTRIBUTE") - e.SubElement(sample_attribute, "TAG").text = str(i) - e.SubElement(sample_attribute, "VALUE").text = d[i] +class xml_creation: + def __init__(self, source_path=None, output_path=None): + if source_path is None: + self.source_path = utils.prompt_source_path() + else: + self.source_path = source_path + if output_path is None: + self.output_path = utils.prompt_destination_path() + else: + self.output_path = output_path + + # LOAD VALIDATED json + with open(self.source_path) as json_format_file: + json_data = j.load(json_format_file) + + # project_relecov.xml + r = e.Element("PROJECT_SET") + project = e.SubElement(r, "PROJECT") + project.set("alias", "RELECOV") + e.SubElement( + project, "TITLE" + ).text = "Example project for ENA submission RELECOV" + e.SubElement( + project, "DESCRIPTION" + ).text = "This study was created as part of an ENA submissions example RELECOV" + submission = e.SubElement(project, "SUBMISSION_PROJECT") + e.SubElement(submission, "SEQUENCING_PROJECT") + a = e.ElementTree(r) + a.write("project_relecov.xml") + + # sample_relecov.xml + data_keys = list(json_data.keys()) + r = e.Element("SAMPLE_SET") + sample = e.SubElement(r, "SAMPLE") + sample.set("alias", "SARS Sample 1 programmatic") + e.SubElement(sample, "TITLE").text = "SARS Sample 1" + sample_name = e.SubElement(sample, "SAMPLE_NAME") + e.SubElement(sample_name, "TAXON_ID").text = "2697049" + e.SubElement( + sample_name, "SCIENTIFIC_NAME" + ).text = "Severe acute respiratory syndrome coronavirus 2" + e.SubElement(sample, "DESCRIPTION").text = "SARS-CoV-2 Sample #1" + sample_attributes = e.SubElement(sample, "SAMPLE_ATTRIBUTES") + for i in json_data: + sample_attribute = e.SubElement(sample_attributes, "SAMPLE_ATTRIBUTE") + e.SubElement(sample_attribute, "TAG").text = str(i) + e.SubElement(sample_attribute, "VALUE").text = json_data[i] diff --git a/schema/ena_v01.json b/schema/ena_v01.json deleted file mode 100644 index d63f9093..00000000 --- a/schema/ena_v01.json +++ /dev/null @@ -1,1105 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft/2019-09/schema#", - "required": [ - "sample_name", - "collecting_institution", - "geographic_location_(country_and/or_sea)", - "isolate", - "host_scientific_name", - "host_common_name", - "host_health_state", - "host_sex", - "host_subject_id", - "instrument_model", - "file_name", - "sample_name", - "tax_id", - "scientific_name", - "common_name", - "sample_description", - "library_source", - "library_selection", - "library_strategy", - "library_layout" - ], - "type": "object", - "properties": { - "sample_name": { - "examples": ["prov_rona_99"], - "ontology": "GENEPIO:0001123", - "type": "string", - "description": "The user-defined name for the sample.", - "clasification":"Database Identifiers", - "label":"Collecting Sample id" - - }, - "collecting_institution": { - "examples": ["Public Health Agency of Canada"], - "ontology": "GENEPIO:0001153", - "type": "string", - "description": "Name of the institution to which the person collecting the specimen belongs. Format: Institute Name, Institute Address", - "label":"Collecting Institution" - - }, - "collection_date": { - "examples": ["3/19/2020"], - "ontology": "GENEPIO:0001174", - "type": "string", - "description": "The date on which the sample was collected.", - "format":"date", - "classification":"Sample collection and processing", - "label":"Sample Collection Date" - }, - "receipt_date": { - "examples": ["3/21/2020"], - "ontology": "GENEPIO:0001179", - "type": "string", - "description": "The date on which the sample was received.", - "format":"date", - "clasification":"Sample collection and processing", - "label":"Sample Received Date" - }, - "geographic_location_(country_and/or_sea)": { - "Enums": [ - "Afghanistan [GAZ:00006882]", - "Albania [GAZ:00002953]", - "Algeria [GAZ:00000563]", - "American Samoa [GAZ:00003957]", - "Andorra [GAZ:00002948]", - "Angola [GAZ:00001095]", - "Anguilla [GAZ:00009159]", - "Antarctica [GAZ:00000462]", - "Antigua and Barbuda [GAZ:00006883]", - "Argentina [GAZ:00002928]", - "Armenia [GAZ:00004094]", - "Aruba [GAZ:00004025]", - "Ashmore and Cartier Islands [GAZ:00005901]", - "Australia [GAZ:00000463]", - "Austria [GAZ:00002942]", - "Azerbaijan [GAZ:00004941]", - "Bahamas [GAZ:00002733]", - "Bahrain [GAZ:00005281]", - "Baker Island [GAZ:00007117]", - "Bangladesh [GAZ:00003750]", - "Barbados [GAZ:00001251]", - "Bassas da India [GAZ:00005810]", - "Belarus [GAZ:00006886]", - "Belgium [GAZ:00002938]", - "Belize [GAZ:00002934]", - "Benin [GAZ:00000904]", - "Bermuda [GAZ:00001264]", - "Bhutan [GAZ:00003920]", - "Bolivia [GAZ:00002511]", - "Borneo [GAZ:00025355]", - "Bosnia and Herzegovina [GAZ:00006887]", - "Botswana [GAZ:00001097]", - "Bouvet Island [GAZ:00001453]", - "Brazil [GAZ:00002828]", - "British Virgin Islands [GAZ:00003961]", - "Brunei [GAZ:00003901]", - "Bulgaria [GAZ:00002950]", - "Burkina Faso [GAZ:00000905]", - "Burundi [GAZ:00001090]", - "Cambodia [GAZ:00006888]", - "Cameroon [GAZ:00001093]", - "Canada [GAZ:00002560]", - "Cape Verde [GAZ:00001227]", - "Cayman Islands [GAZ:00003986]", - "Central African Republic [GAZ:00001089]", - "Chad [GAZ:00000586]", - "Chile [GAZ:00002825]", - "China [GAZ:00002845]", - "Christmas Island [GAZ:00005915]", - "Clipperton Island [GAZ:00005838]", - "Cocos Islands [GAZ:00009721]", - "Colombia [GAZ:00002929]", - "Comoros [GAZ:00005820]", - "Cook Islands [GAZ:00053798]", - "Coral Sea Islands [GAZ:00005917]", - "Costa Rica [GAZ:00002901]", - "Cote d'Ivoire [GAZ:00000906]", - "Croatia [GAZ:00002719]", - "Cuba [GAZ:00003762]", - "Curacao [GAZ:00012582]", - "Cyprus [GAZ:00004006]", - "Czech Republic [GAZ:00002954]", - "Democratic Republic of the Congo [GAZ:00001086]", - "Denmark [GAZ:00005852]", - "Djibouti [GAZ:00000582]", - "Dominica [GAZ:00006890]", - "Dominican Republic [GAZ:00003952]", - "Ecuador [GAZ:00002912]", - "Egypt [GAZ:00003934]", - "El Salvador [GAZ:00002935]", - "Equatorial Guinea [GAZ:00001091]", - "Eritrea [GAZ:00000581]", - "Estonia [GAZ:00002959]", - "Eswatini [GAZ:00001099]", - "Ethiopia [GAZ:00000567]", - "Europa Island [GAZ:00005811]", - "Falkland Islands (Islas Malvinas) [GAZ:00001412]", - "Faroe Islands [GAZ:00059206]", - "Fiji [GAZ:00006891]", - "Finland [GAZ:00002937]", - "France [GAZ:00003940]", - "French Guiana [GAZ:00002516]", - "French Polynesia [GAZ:00002918]", - "French Southern and Antarctic Lands [GAZ:00003753]", - "Gabon [GAZ:00001092]", - "Gambia [GAZ:00000907]", - "Gaza Strip [GAZ:00009571]", - "Georgia [GAZ:00004942]", - "Germany [GAZ:00002646]", - "Ghana [GAZ:00000908]", - "Gibraltar [GAZ:00003987]", - "Glorioso Islands [GAZ:00005808]", - "Greece [GAZ:00002945]", - "Greenland [GAZ:00001507]", - "Grenada [GAZ:02000573]", - "Guadeloupe [GAZ:00067142]", - "Guam [GAZ:00003706]", - "Guatemala [GAZ:00002936]", - "Guernsey [GAZ:00001550]", - "Guinea [GAZ:00000909]", - "Guinea-Bissau [GAZ:00000910]", - "Guyana [GAZ:00002522]", - "Haiti [GAZ:00003953]", - "Heard Island and McDonald Islands [GAZ:00009718]", - "Honduras [GAZ:00002894]", - "Hong Kong [GAZ:00003203]", - "Howland Island [GAZ:00007120]", - "Hungary [GAZ:00002952]", - "Iceland [GAZ:00000843]", - "India [GAZ:00002839]", - "Indonesia [GAZ:00003727]", - "Iran [GAZ:00004474]", - "Iraq [GAZ:00004483]", - "Ireland [GAZ:00002943]", - "Isle of Man [GAZ:00052477]", - "Israel [GAZ:00002476]", - "Italy [GAZ:00002650]", - "Jamaica [GAZ:00003781]", - "Jan Mayen [GAZ:00005853]", - "Japan [GAZ:00002747]", - "Jarvis Island [GAZ:00007118]", - "Jersey [GAZ:00001551]", - "Johnston Atoll [GAZ:00007114]", - "Jordan [GAZ:00002473]", - "Juan de Nova Island [GAZ:00005809]", - "Kazakhstan [GAZ:00004999]", - "Kenya [GAZ:00001101]", - "Kerguelen Archipelago [GAZ:00005682]", - "Kingman Reef [GAZ:00007116]", - "Kiribati [GAZ:00006894]", - "Kosovo [GAZ:00011337]", - "Kuwait [GAZ:00005285]", - "Kyrgyzstan [GAZ:00006893]", - "Laos [GAZ:00006889]", - "Latvia [GAZ:00002958]", - "Lebanon [GAZ:00002478]", - "Lesotho [GAZ:00001098]", - "Liberia [GAZ:00000911]", - "Libya [GAZ:00000566]", - "Liechtenstein [GAZ:00003858]", - "Line Islands [GAZ:00007144]", - "Lithuania [GAZ:00002960]", - "Luxembourg [GAZ:00002947]", - "Macau [GAZ:00003202]", - "Madagascar [GAZ:00001108]", - "Malawi [GAZ:00001105]", - "Malaysia [GAZ:00003902]", - "Maldives [GAZ:00006924]", - "Mali [GAZ:00000584]", - "Malta [GAZ:00004017]", - "Marshall Islands [GAZ:00007161]", - "Martinique [GAZ:00067143]", - "Mauritania [GAZ:00000583]", - "Mauritius [GAZ:00003745]", - "Mayotte [GAZ:00003943]", - "Mexico [GAZ:00002852]", - "Micronesia [GAZ:00005862]", - "Midway Islands [GAZ:00007112]", - "Moldova [GAZ:00003897]", - "Monaco [GAZ:00003857]", - "Mongolia [GAZ:00008744]", - "Montenegro [GAZ:00006898]", - "Montserrat [GAZ:00003988]", - "Morocco [GAZ:00000565]", - "Mozambique [GAZ:00001100]", - "Myanmar [GAZ:00006899]", - "Namibia [GAZ:00001096]", - "Nauru [GAZ:00006900]", - "Navassa Island [GAZ:00007119]", - "Nepal [GAZ:00004399]", - "Netherlands [GAZ:00002946]", - "New Caledonia [GAZ:00005206]", - "New Zealand [GAZ:00000469]", - "Nicaragua [GAZ:00002978]", - "Niger [GAZ:00000585]", - "Nigeria [GAZ:00000912]", - "Niue [GAZ:00006902]", - "Norfolk Island [GAZ:00005908]", - "North Korea [GAZ:00002801]", - "North Macedonia [GAZ:00006895]", - "North Sea [GAZ:00002284]", - "Northern Mariana Islands [GAZ:00003958]", - "Norway [GAZ:00002699]", - "Oman [GAZ:00005283]", - "Pakistan [GAZ:00005246]", - "Palau [GAZ:00006905]", - "Panama [GAZ:00002892]", - "Papua New Guinea [GAZ:00003922]", - "Paracel Islands [GAZ:00010832]", - "Paraguay [GAZ:00002933]", - "Peru [GAZ:00002932]", - "Philippines [GAZ:00004525]", - "Pitcairn Islands [GAZ:00005867]", - "Poland [GAZ:00002939]", - "Portugal [GAZ:00004126]", - "Puerto Rico [GAZ:00006935]", - "Qatar [GAZ:00005286]", - "Republic of the Congo [GAZ:00001088]", - "Reunion [GAZ:00003945]", - "Romania [GAZ:00002951]", - "Ross Sea [GAZ:00023304]", - "Russia [GAZ:00002721]", - "Rwanda [GAZ:00001087]", - "Saint Helena [GAZ:00000849]", - "Saint Kitts and Nevis [GAZ:00006906]", - "Saint Lucia [GAZ:00006909]", - "Saint Pierre and Miquelon [GAZ:00003942]", - "Saint Martin [GAZ:00005841]", - "Saint Vincent and the Grenadines [GAZ:02000565]", - "Samoa [GAZ:00006910]", - "San Marino [GAZ:00003102]", - "Sao Tome and Principe [GAZ:00006927]", - "Saudi Arabia [GAZ:00005279]", - "Senegal [GAZ:00000913]", - "Serbia [GAZ:00002957]", - "Seychelles [GAZ:00006922]", - "Sierra Leone [GAZ:00000914]", - "Singapore [GAZ:00003923]", - "Sint Maarten [GAZ:00012579]", - "Slovakia [GAZ:00002956]", - "Slovenia [GAZ:00002955]", - "Solomon Islands [GAZ:00005275]", - "Somalia [GAZ:00001104]", - "South Africa [GAZ:00001094]", - "South Georgia and the South Sandwich Islands [GAZ:00003990]", - "South Korea [GAZ:00002802]", - "South Sudan [GAZ:00233439]", - "Spain [GAZ:00003936]", - "Spratly Islands [GAZ:00010831]", - "Sri Lanka [GAZ:00003924]", - "State of Palestine [GAZ:00002475]", - "Sudan [GAZ:00000560]", - "Suriname [GAZ:00002525]", - "Svalbard [GAZ:00005396]", - "Swaziland [GAZ:00001099]", - "Sweden [GAZ:00002729]", - "Switzerland [GAZ:00002941]", - "Syria [GAZ:00002474]", - "Taiwan [GAZ:00005341]", - "Tajikistan [GAZ:00006912]", - "Tanzania [GAZ:00001103]", - "Thailand [GAZ:00003744]", - "Timor-Leste [GAZ:00006913]", - "Togo [GAZ:00000915]", - "Tokelau [GAZ:00260188]", - "Tonga [GAZ:00006916]", - "Trinidad and Tobago [GAZ:00003767]", - "Tromelin Island [GAZ:00005812]", - "Tunisia [GAZ:00000562]", - "Turkey [GAZ:00000558]", - "Turkmenistan [GAZ:00005018]", - "Turks and Caicos Islands [GAZ:00003955]", - "Tuvalu [GAZ:00009715]", - "USA [GAZ:00002459]", - "Uganda [GAZ:00001102]", - "Ukraine [GAZ:00002724]", - "United Arab Emirates [GAZ:00005282]", - "United Kingdom [GAZ:00002637]", - "Uruguay [GAZ:00002930]", - "Uzbekistan [GAZ:00004979]", - "Vanuatu [GAZ:00006918]", - "Venezuela [GAZ:00002931]", - "Viet Nam [GAZ:00003756]", - "Virgin Islands [GAZ:00003959]", - "Wake Island [GAZ:00007111]", - "Wallis and Futuna [GAZ:00007191]", - "West Bank [GAZ:00009572]", - "Western Sahara [GAZ:00000564]", - "Yemen [GAZ:00005284]", - "Zambia [GAZ:00001107]", - "Zimbabwe [GAZ:00001106]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001181 ", - "type": "string", - "description": "The country of origin of the sample.", - "examples": ["South Africa [GAZ:00001094]"], - "clasification":"Sample collection and processing", - "label":"Geo Loc Autonomic Country" - - }, - "geographic location (region and locality)": { - "ontology": "GENEPIO:0100280", - "type": "string", - "description": "The county/region of origin of the sample.", - "examples": ["Derbyshire"], - "clasification":"Sample collection and processing", - "label":"Geo Loc Province" - - }, - "geographic location (latitude)": { - "ontology": "OBI:0001620", - "type": "string", - "description": "The latitude coordinates of the geographical location of sample collection.", - "examples": ["38.98 N"], - "clasification":"Sample collection and processing", - "label":"Geo Loc Latitude", - - }, - "geographic location (longitude)": { - "ontology": "OBI:0001621", - "type": "string", - "description": "The longitude coordinates of the geographical location of sample collection.", - "examples": ["77.11 W"], - "clasification":"Sample collection and processing", - "label":"Geo Loc Longitude" - }, - "isolate": { - "ontology": "GENEPIO:0001644", - "type": "string", - "description": "Identifier of the specific isolate.", - "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"], - "genepio_label":"isolate identifier", - "clasification":"Sample collection and processing", - "label":"Isolate" - - }, - "purpose_sampling": { - "examples": ["Diagnostic testing"], - "ontology": "NCIT_C146997", - "type": "string", - "description": "The reason that the sample was collected.", - "clasification":"Sample collection and processing" - }, - "isolation source host-associated": { - "Enums": [ - "Blood [UBERON:0000178]", - "Fluid [UBERON:0006314]", - "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", - "Fluid (Pericardial) [UBERON:0002409]", - "Fluid (Pleural) [UBERON:0001087]", - "Fluid (Vaginal) [UBERON:0036243]", - "Fluid (Amniotic) [UBERON:0000173]", - "Saliva [UBERON:0001836]", - "Tissue [UBERON:0000479]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001211", - "type": "string", - "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "examples": ["Blood [UBERON:0000178]"], - "classification":"Sample collection and processing", - "label":"Organism Substance" - - }, - "isolation source non-host-associated": { - "Enums": [ - "Air vent [ENVO:03501208]", - "Banknote [ENVO:00003896]", - "Bed rail [ENVO:03501209]", - "Building Floor [ENVO:01000486]", - "Cloth [ENVO:02000058]", - "Control Panel [ENVO:03501210]", - "Door [ENVO:03501220]", - "Door Handle [ENVO:03501211]", - "Face Mask [OBI:0002787]", - "Face Shield [OBI:0002791]", - "Food [FOODON:00002403]", - "Food Packaging [FOODON:03490100]", - "Glass [ENVO:01000481]", - "Handrail [ENVO:03501212]", - "Hospital Gown [OBI:0002796]", - "Light Switch [ENVO:03501213]", - "Locker [ENVO:03501214]", - "N95 Mask [OBI:0002790]", - "Nurse Call Button [ENVO:03501215]", - "Paper [ENVO:03501256]", - "Particulate Matter [ENVO:01000060]", - "Plastic [ENVO:01000404]", - "PPE Gown [GENEPIO:0100025]", - "Sewage [ENVO:00002018]", - "Sink [ENVO:01000990]", - "Soil [ENVO:00001998]", - "Stainless Steel [ENVO:03501216]", - "Tissue Paper [ENVO:03501217]", - "Toilet Bowl [ENVO:03501218]", - "Water [ENVO:00002006]", - "Wastewater [ENVO:00002001]", - "Window [ENVO:03501219]", - "Wood [ENVO:00002040]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001223", - "type": "string", - "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", - "examples": ["Face Mask [OBI:0002787]"], - "clasification":"Sample collection and processing", - "label":"Environmental Material" - }, - "host common name": { - "Enums": [ - "Human [NCBITaxon:9606]", - "Bat [NCBITaxon:9397]", - "Cat [NCBITaxon:9685]", - "Chicken [NCBITaxon:9031]", - "Civet [NCBITaxon:9673]", - "Cow [NCBITaxon:9913]", - "Dog [NCBITaxon:9615]", - "Lion [NCBITaxon:9689]", - "Mink [NCBITaxon:452646]", - "Pangolin [NCBITaxon:9973]", - "Pig [NCBITaxon:9825]", - "Pigeon [NCBITaxon:8930]", - "Tiger [NCBITaxon:9694]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001386", - "type": "string", - "description": "The commonly used name of the host.", - "examples": ["Human [NCBITaxon:9606]"], - "classification":"Host information", - "label":"Host Common Name" - - }, - "host scientific name": { - "Enums": [ - "Bos taurus [NCBITaxon:9913]", - "Canis lupus familiaris [NCBITaxon:9615]", - "Chiroptera [NCBITaxon:9397]", - "Columbidae [NCBITaxon:8930]", - "Felis catus [NCBITaxon:9685]", - "Gallus gallus [NCBITaxon:9031]", - "Homo sapiens [NCBITaxon:9606]", - "Manis [NCBITaxon:9973]", - "Manis javanica [NCBITaxon:9974]", - "Neovison vison [NCBITaxon:452646]", - "Panthera leo [NCBITaxon:9689]", - "Panthera tigris [NCBITaxon:9694]", - "Rhinolophidae [NCBITaxon:58055]", - "Rhinolophus affinis [NCBITaxon:59477]", - "Sus scrofa domesticus [NCBITaxon:9825]", - "Viverridae [NCBITaxon:9673]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001387", - "type": "string", - "description": "The taxonomic, or scientific name of the host.", - "examples": ["Homo sapiens [NCBITaxon:9606]"], - "clasification":"Host information", - "label":"Host Scientific Name" - - }, - "host_health_state": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Health status of the host at the time of sample collection.", - "clasification":"Host information", - "genepio_label":"", - - }, - "host_age": { - "examples": ["e.g. 65 or 7 months, or unknown. Caution: the host age may be considered public health identifiable information. Consult the data steward before sharing. If the information is unknown or can not be shared, put unknown"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Patient age", - "clasification":"Host information" - }, - - "host_sex": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Gender or sex of the host.", - "clasification":"Host information", - "genepio_label":"", - - }, - "host_subject_id": { - "examples": ["e.g. #131"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "a unique identifier by which each subject can be referred to, de-identified.", - "clasification":"Host information", - "genepio_label":"", - - }, - "type exposure": { - "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], - "ontology": "GENEPIO:0001417", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", - "label":"Outbreak Exposure Event Location" - - }, - "subject exposure duration": { - "examples": ["e.g. Patient infected while traveling in …."], - "ontology": "0", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", - "label":"Additional Host Information" - - }, - "instrument_model": { - "Enums": [ - "Illumina sequencing instrument [GENEPIO:0100105]", - "Illumina Genome Analyzer [GENEPIO:0100106]", - "Illumina Genome Analyzer II [GENEPIO:0100107]", - "Illumina Genome Analyzer IIx [GENEPIO:0100108]", - "Illumina HiScanSQ [GENEPIO:0100109]", - "Illumina HiSeq [GENEPIO:0100110]", - "Illumina HiSeq X [GENEPIO:0100111]", - "Illumina HiSeq X Five [GENEPIO:0100112]", - "Illumina HiSeq X Ten [GENEPIO:0100113]", - "Illumina HiSeq 1000 [GENEPIO:0100114]", - "Illumina HiSeq 1500 [GENEPIO:0100115]", - "Illumina HiSeq 2000 [GENEPIO:0100116]", - "Illumina HiSeq 2500 [GENEPIO:0100117]", - "Illumina HiSeq 3000 [GENEPIO:0100118]", - "Illumina HiSeq 4000 [GENEPIO:0100119]", - "Illumina iSeq [GENEPIO:0100120]", - "Illumina iSeq 100 [GENEPIO:0100121]", - "Illumina NovaSeq [GENEPIO:0100122]", - "Illumina NovaSeq 6000 [GENEPIO:0100123]", - "Illumina MiniSeq [GENEPIO:0100124]", - "Illumina MiSeq [GENEPIO:0100125]", - "Illumina NextSeq [GENEPIO:0100126]", - "Illumina NextSeq 500 [GENEPIO:0100127]", - "Illumina NextSeq 550 [GENEPIO:0100128]", - "Illumina NextSeq 2000 [GENEPIO:0100129]", - "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", - "PacBio RS [GENEPIO:0100131]", - "PacBio RS II [GENEPIO:0100132]", - "PacBio Sequel [GENEPIO:0100133]", - "PacBio Sequel II [GENEPIO:0100134]", - "Ion Torrent sequencing instrument [GENEPIO:0100135]", - "Ion Torrent PGM [GENEPIO:0100136]", - "Ion Torrent Proton [GENEPIO:0100137]", - "Ion Torrent S5 XL [GENEPIO:0100138]", - "Ion Torrent S5 [GENEPIO:0100139]", - "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", - "Oxford Nanopore GridION [GENEPIO:0100141]", - "Oxford Nanopore MinION [GENEPIO:0100142]", - "Oxford Nanopore PromethION [GENEPIO:0100143]", - "BGI Genomics sequencing instrument [GENEPIO:0100144]", - "BGI SEQ-500 [GENEPIO:0100145]", - "MGI sequencing instrument [GENEPIO:0100146]", - "MGI DNBSEQ-T7 [GENEPIO:0100147]", - "MGI DNBSEQ-G400 [GENEPIO:0100148]", - "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", - "MGI DNBSEQ-G50 [GENEPIO:0100150]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001452", - "type": "string", - "description": "The model of the sequencing instrument used.", - "examples": ["Oxford Nanopore MinION [GENEPIO:0100142]"], - "classification":"Sequencing", - "label":"Sequencing Instrument Model" - }, - "instrument_platform ": { - "examples": ["MinIon"], - "ontology": "0", - "type": "string", - "description": "The model of the sequencing instrument used.", - "label":"Sequencing Platforms " - }, - "file_name": { - "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], - "ontology": "GENEPIO:0001476", - "type": "string", - "description": "The user-specified filename of the r1 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Sequence file R1 fastq" - }, - "tax_id": { - "examples": ["probably 2697049 in all cases"], - "ontology": "GENEPIO_0001724", - "type": "string", - "description": "The NCBITaxon identifier for the organism being sequenced.", - "clasification":"Sample collection and processing", - "label":"Tax ID" - }, - "scientific_name": { - "Enums": [ - "Coronaviridae [NCBITaxon:11118]", - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "examples": [""], - "ontology": "GENEPIO:0001191", - "type": "string", - "description": "The taxonomic name of the organism.", - "clasification":"Sample collection and processing", - "classification":"Sample collection and processing", - "label":"Organism" - }, - "common_name": { - "examples": [""], - "ontology": "BU_ISCIII:003", - "type": "string", - "description": "The common name of the organism.", - "clasification":"Sample collection and processing", - "label":"Common name" - }, - "sample_description": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Free text description of the sample.", - "clasification":"Sample collection and processing", - "genepio_label":"", - - }, - "sample_storage_conditions": { - "examples": ["24 degrees celsius"], - "ontology": "NCIT_C115535", - "type": "string", - "description": "The name and version of a particular protocol used for sampling.", - "clasification":"Sample collection and processing" - }, - "library_source": { - "Enums": ["5-methycytidine antibody method [GENPIO:0001941]", - "CAGE method [GENPIO:0001942]", - "CF-H method [GENPIO:0001943]", - "CF-M method ]GENPIO:0001944]", - "CF-S method [GENPIO:0001945]", - "CF-T method [GENPIO:0001946]", - "ChIP method ]GENPIO:0001947]", - "DNAse method [GENPIO:0001948]", - "HMPR method [GENPIO:0001949]", - "Hybrid Selection Method [GENPIO:0001950]", - "MBD2 protein methyl-CpG binding domain method [GENPIO:0001951]", - "MF method [GENPIO:0001952]", - "MNase method [GENPIO:0001953]", - "MSLL method [GENPIO:0001954]", - "PCR method [GENPIO:0001955]", - "RACE method [GENPIO:0001956]", - "RANDOM PCR method [GENPIO:0001957]", - "RANDOM method [GENPIO:0001958]", - "RT-PCR method [GENPIO:0001959]", - "Reduced Representation method [GENPIO:0001960]", - "Resctriction Digest method [GENPIO:0001961]", - "cDNA method [GENPIO:0001962]", - "other library method [GENPIO:0001964]", - "size fractionation method [GENPIO:0001963]", - ], - "examples": ["METAGENOMIC"], - "ontology": "GENEPIO_0001965", - "type": "string", - "description": "Molecule type used to make the library.", - "clasification":"Sequencing", - "label":"Source material" - }, - "library_selection": { - "examples": ["RANDOM PCR"], - "ontology": "GENPIO_0001940", - "type": "string", - "description": "Library capture method.", - "clasification":"Sequencing", - "label":"Capture method" - }, - "library_strategy": { - "Enums": ["Bisultife-Seq strategy [GENPIO:0001975]", - "CTS strategy [GENPIO:0001978]", - "ChIP-Seq strategy [GENPIO:0001979]", - "DNase-Hypersensitivity strategy [GENPIO:0001980]", - "EST strategy [GENPIO:0001981]", - "FL-cDNA strategy [GENPIO:0001983]", - "MB-Seq strategy [GENPIO:0001984]", - "MNase-Seq strategy [GENPIO:0001985]", - "MRE-Seq strategy [GENPIO:0001986]", - "MeDIP-Seq strategy [GENPIO:0001987]", - "RNA-Seq strategy [GENPIO:0001990]", - "WCS strategy [GENPIO:0001991]", - "WGS strategy [GENPIO:0001992]", - "WXS strategy [GENPIO:0001993]", - "amplicon strategy [GENPIO:0001974]", - "clone end strategy [GENPIO:0001976]", - "clone strategy [GENPIO:0001977]", - "finishing strategy [GENPIO:0001982]", - "other library strategy [GENPIO:0001988]", - "pool clone strategy [GENPIO:0001989]", - ], - "examples": ["WGS"], - "ontology": "GENPIO_0001973", - "type": "string", - "description": "Overall sequencing strategy or approach.", - "clasification":"Sequencing", - "label":"Sequencing technique" - }, - "library_layout": { - "examples": ["PAIRED"], - "ontology":"BU_ISCIII:007", - "type": "string", - "description": "Single or paired.", - "clasification":"Sequencing", - "label":"Library Layout" - }, - "library_name": { - "examples": ["e.g P17157_1007"], - "ontology": "GENEPIO_0001995", - "type": "string", - "description": "The submitter's name for this library.", - "clasification":"Sequencing", - "label":"Library Name" - }, - "nominal_length ": { - "examples": ["350"], - "ontology": "GENEPIO_0000076", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Nominal Length" - }, - "analysis_accession": { - "examples": [""], - "ontology": "GENEPIO_0001145", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Analysis Accession" - }, - "read_length": { - "examples": [""], - "ontology": "STATO_0000064", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Read length" - }, - "study_accession": { - "examples": ["e.g PRJEB39632"], - "ontology": "GENEPIO_0001136", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Study accession" - }, - "secondary_study_accession": { - "examples": ["e.g ERP123173"], - "ontology": "BU_ISCIII:012", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Secondary study accession" - }, - "sample_accession": { - "examples": ["e.g SAMEA7098096"], - "ontology": "GENEPIO_0001139", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Sample accession" - }, - "secondary_sample_accession": { - "examples": ["e.g ERS4858671"], - "ontology": "BU_ISCIII:014", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Secondary sample accession" - }, - "experiment_accession": { - "examples": ["e.g ERX4331406"], - "ontology": "BU_ISCIII:015", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Experiment Accession" - }, - "run_accession": { - "examples": ["e.g ERX4331406"], - "ontology": "BU_ISCIII:016", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Run Accession" - }, - "submission_accession": { - "examples": ["e.g ERA2794974"], - "ontology": "BU_ISCIII:017", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submission accession" - }, - "read_count": { - "examples": ["e.g 837055"], - "ontology": "STATO_0000064", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Read count" - }, - "base_count": { - "examples": ["e.g 503907110"], - "ontology": "UO_0000244", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Base count" - }, - "center_name": { - "examples": [" KAROLINSKA INSITUTET"], - "ontology": "NCIT_C19983", - "type": "string", - "description": "The name of the institution", - "clasification":"Sample collection and processing", - "label":"Center Name" - }, - "first_public": { - "examples": ["e.g 2020-08-07"], - "ontology": "NCIT_C142711", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"First Public date" - }, - "last_updated": { - "examples": ["e.g 2020-07-29"], - "ontology": "OMIABIS_0001005", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "format":"Last Updated" - }, - "experiment_title": { - "examples": ["e.g Illumina MiSeq paired end sequencing"], - "ontology": "ORNASEQ_0000004", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Experiment title" - }, - "study_title": { - "examples": ["e.g SARS-CoV-2 genomes from late April in Stockholm"], - "ontology": "OPMI_0000380", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Study title" - }, - "study_alias": { - "examples": ["e.g Sweden"], - "ontology": "SIO_001066", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Study alias" - }, - "experiment_alias": { - "examples": ["e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092"], - "ontology": "NCIT_C42790", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Experiment alias" - }, - "run_alias": { - "examples": ["e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "NCIT_C47911", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Run Alias" - }, - "fastq_bytes": { - "examples": ["e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "NCIT_C48047", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq bytes" - }, - "fastq_md5": { - "examples": [""], - "ontology": "MS_1000568", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq md5" - }, - "fastq_ftp": { - "examples": [""], - "ontology": "PRIDE_0000469", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq ftp" - }, - "fastq_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "BU_ISCIII:032", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq aspera" - }, - "fastq_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "ENVO_01000807", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq galaxy" - }, - "submitted_bytes": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "NCIT_C172872", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted bytes " - }, - "submitted_md5": { - "examples": ["e.g 139853010;166270048"], - "ontology": "BU_ISCIII:035", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted md5" - }, - "submitted_ftp": { - "examples": ["e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a"], - "ontology": "BU_ISCIII:036", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted ftp" - }, - "submitted_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "BU_ISCIII:037", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted aspera" - }, - "submitted_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "BU_ISCIII:038", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted Galaxy" - }, - "submitted_format": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "BU_ISCIII:039", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted Format" - }, - "sra_bytes": { - "examples": ["e.g FASTQ;FASTQ"], - "ontology": "BU_ISCIII:040", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA bytes" - }, - "sra_md5": { - "examples": ["e.g 260236789"], - "ontology": "BU_ISCIII:041", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA md5" - }, - "sra_ftp": { - "examples": ["e.g 2cf0d467d6dc4ae0a5473774d54c059c"], - "ontology": "BU_ISCIII:042", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA ftp" - }, - "sra_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385"], - "ontology": "BU_ISCIII:043", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA aspera" - }, - "sra_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385"], - "ontology": "BU_ISCIII:044", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA galaxy" - }, - "broker_name": { - "examples": ["P17157_1007"], - "ontology": "BU_ISCIII:045", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Broker Name" - }, - "nominal_sdev": { - "examples": [""], - "ontology": "STATO_0000237", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Nominal sdev" - }, - "first_created": { - "examples": ["e.g 2020-08-07"], - "ontology": "NCIT_C164483", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"First created date" - } - - } -} diff --git a/schema/phage_plus_V0.json b/schema/phage_plus_V0.json deleted file mode 100644 index 4d0bc178..00000000 --- a/schema/phage_plus_V0.json +++ /dev/null @@ -1,2285 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft/2020-12/schema", - "required": [ - "sample_name", - "collecting_institution", - "submitting_institution", - "sample_collection_date", - "geo_loc_country", - "geo_loc_state", - "organism", - "isolate", - "host_scientific_name", - "host_disease", - "sequencing_instrument_model", - "sequencing_instrument_platform", - "consensus_sequence_software_name", - "consensus_sequence_software_version" - ], - "type": "object", - "properties": { - "sample_name": { - "examples": ["prov_rona_99"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The user-defined name for the sample.", - "clasification":"Database Identifiers" - }, - "collecting_institution": { - "examples": ["Public Health Agency of Canada"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The name of the agency that collected the original sample." - }, - "submitting_institution": { - "examples": ["Centers for Disease Control and Prevention"], - "ontology": "GENEPIO:0001159", - "type": "string", - "description": "The name of the agency that generated the sequence." - }, - "sample_collection_date": { - "examples": ["3/19/2020"], - "ontology": "GENEPIO:0001174", - "type": "string", - "description": "The date on which the sample was collected.", - "format":"date" - }, - "geo_loc_name_country": { - "Enums": [ - "Afghanistan [GAZ:00006882]", - "Albania [GAZ:00002953]", - "Algeria [GAZ:00000563]", - "American Samoa [GAZ:00003957]", - "Andorra [GAZ:00002948]", - "Angola [GAZ:00001095]", - "Anguilla [GAZ:00009159]", - "Antarctica [GAZ:00000462]", - "Antigua and Barbuda [GAZ:00006883]", - "Argentina [GAZ:00002928]", - "Armenia [GAZ:00004094]", - "Aruba [GAZ:00004025]", - "Ashmore and Cartier Islands [GAZ:00005901]", - "Australia [GAZ:00000463]", - "Austria [GAZ:00002942]", - "Azerbaijan [GAZ:00004941]", - "Bahamas [GAZ:00002733]", - "Bahrain [GAZ:00005281]", - "Baker Island [GAZ:00007117]", - "Bangladesh [GAZ:00003750]", - "Barbados [GAZ:00001251]", - "Bassas da India [GAZ:00005810]", - "Belarus [GAZ:00006886]", - "Belgium [GAZ:00002938]", - "Belize [GAZ:00002934]", - "Benin [GAZ:00000904]", - "Bermuda [GAZ:00001264]", - "Bhutan [GAZ:00003920]", - "Bolivia [GAZ:00002511]", - "Borneo [GAZ:00025355]", - "Bosnia and Herzegovina [GAZ:00006887]", - "Botswana [GAZ:00001097]", - "Bouvet Island [GAZ:00001453]", - "Brazil [GAZ:00002828]", - "British Virgin Islands [GAZ:00003961]", - "Brunei [GAZ:00003901]", - "Bulgaria [GAZ:00002950]", - "Burkina Faso [GAZ:00000905]", - "Burundi [GAZ:00001090]", - "Cambodia [GAZ:00006888]", - "Cameroon [GAZ:00001093]", - "Canada [GAZ:00002560]", - "Cape Verde [GAZ:00001227]", - "Cayman Islands [GAZ:00003986]", - "Central African Republic [GAZ:00001089]", - "Chad [GAZ:00000586]", - "Chile [GAZ:00002825]", - "China [GAZ:00002845]", - "Christmas Island [GAZ:00005915]", - "Clipperton Island [GAZ:00005838]", - "Cocos Islands [GAZ:00009721]", - "Colombia [GAZ:00002929]", - "Comoros [GAZ:00005820]", - "Cook Islands [GAZ:00053798]", - "Coral Sea Islands [GAZ:00005917]", - "Costa Rica [GAZ:00002901]", - "Cote d'Ivoire [GAZ:00000906]", - "Croatia [GAZ:00002719]", - "Cuba [GAZ:00003762]", - "Curacao [GAZ:00012582]", - "Cyprus [GAZ:00004006]", - "Czech Republic [GAZ:00002954]", - "Democratic Republic of the Congo [GAZ:00001086]", - "Denmark [GAZ:00005852]", - "Djibouti [GAZ:00000582]", - "Dominica [GAZ:00006890]", - "Dominican Republic [GAZ:00003952]", - "Ecuador [GAZ:00002912]", - "Egypt [GAZ:00003934]", - "El Salvador [GAZ:00002935]", - "Equatorial Guinea [GAZ:00001091]", - "Eritrea [GAZ:00000581]", - "Estonia [GAZ:00002959]", - "Eswatini [GAZ:00001099]", - "Ethiopia [GAZ:00000567]", - "Europa Island [GAZ:00005811]", - "Falkland Islands (Islas Malvinas) [GAZ:00001412]", - "Faroe Islands [GAZ:00059206]", - "Fiji [GAZ:00006891]", - "Finland [GAZ:00002937]", - "France [GAZ:00003940]", - "French Guiana [GAZ:00002516]", - "French Polynesia [GAZ:00002918]", - "French Southern and Antarctic Lands [GAZ:00003753]", - "Gabon [GAZ:00001092]", - "Gambia [GAZ:00000907]", - "Gaza Strip [GAZ:00009571]", - "Georgia [GAZ:00004942]", - "Germany [GAZ:00002646]", - "Ghana [GAZ:00000908]", - "Gibraltar [GAZ:00003987]", - "Glorioso Islands [GAZ:00005808]", - "Greece [GAZ:00002945]", - "Greenland [GAZ:00001507]", - "Grenada [GAZ:02000573]", - "Guadeloupe [GAZ:00067142]", - "Guam [GAZ:00003706]", - "Guatemala [GAZ:00002936]", - "Guernsey [GAZ:00001550]", - "Guinea [GAZ:00000909]", - "Guinea-Bissau [GAZ:00000910]", - "Guyana [GAZ:00002522]", - "Haiti [GAZ:00003953]", - "Heard Island and McDonald Islands [GAZ:00009718]", - "Honduras [GAZ:00002894]", - "Hong Kong [GAZ:00003203]", - "Howland Island [GAZ:00007120]", - "Hungary [GAZ:00002952]", - "Iceland [GAZ:00000843]", - "India [GAZ:00002839]", - "Indonesia [GAZ:00003727]", - "Iran [GAZ:00004474]", - "Iraq [GAZ:00004483]", - "Ireland [GAZ:00002943]", - "Isle of Man [GAZ:00052477]", - "Israel [GAZ:00002476]", - "Italy [GAZ:00002650]", - "Jamaica [GAZ:00003781]", - "Jan Mayen [GAZ:00005853]", - "Japan [GAZ:00002747]", - "Jarvis Island [GAZ:00007118]", - "Jersey [GAZ:00001551]", - "Johnston Atoll [GAZ:00007114]", - "Jordan [GAZ:00002473]", - "Juan de Nova Island [GAZ:00005809]", - "Kazakhstan [GAZ:00004999]", - "Kenya [GAZ:00001101]", - "Kerguelen Archipelago [GAZ:00005682]", - "Kingman Reef [GAZ:00007116]", - "Kiribati [GAZ:00006894]", - "Kosovo [GAZ:00011337]", - "Kuwait [GAZ:00005285]", - "Kyrgyzstan [GAZ:00006893]", - "Laos [GAZ:00006889]", - "Latvia [GAZ:00002958]", - "Lebanon [GAZ:00002478]", - "Lesotho [GAZ:00001098]", - "Liberia [GAZ:00000911]", - "Libya [GAZ:00000566]", - "Liechtenstein [GAZ:00003858]", - "Line Islands [GAZ:00007144]", - "Lithuania [GAZ:00002960]", - "Luxembourg [GAZ:00002947]", - "Macau [GAZ:00003202]", - "Madagascar [GAZ:00001108]", - "Malawi [GAZ:00001105]", - "Malaysia [GAZ:00003902]", - "Maldives [GAZ:00006924]", - "Mali [GAZ:00000584]", - "Malta [GAZ:00004017]", - "Marshall Islands [GAZ:00007161]", - "Martinique [GAZ:00067143]", - "Mauritania [GAZ:00000583]", - "Mauritius [GAZ:00003745]", - "Mayotte [GAZ:00003943]", - "Mexico [GAZ:00002852]", - "Micronesia [GAZ:00005862]", - "Midway Islands [GAZ:00007112]", - "Moldova [GAZ:00003897]", - "Monaco [GAZ:00003857]", - "Mongolia [GAZ:00008744]", - "Montenegro [GAZ:00006898]", - "Montserrat [GAZ:00003988]", - "Morocco [GAZ:00000565]", - "Mozambique [GAZ:00001100]", - "Myanmar [GAZ:00006899]", - "Namibia [GAZ:00001096]", - "Nauru [GAZ:00006900]", - "Navassa Island [GAZ:00007119]", - "Nepal [GAZ:00004399]", - "Netherlands [GAZ:00002946]", - "New Caledonia [GAZ:00005206]", - "New Zealand [GAZ:00000469]", - "Nicaragua [GAZ:00002978]", - "Niger [GAZ:00000585]", - "Nigeria [GAZ:00000912]", - "Niue [GAZ:00006902]", - "Norfolk Island [GAZ:00005908]", - "North Korea [GAZ:00002801]", - "North Macedonia [GAZ:00006895]", - "North Sea [GAZ:00002284]", - "Northern Mariana Islands [GAZ:00003958]", - "Norway [GAZ:00002699]", - "Oman [GAZ:00005283]", - "Pakistan [GAZ:00005246]", - "Palau [GAZ:00006905]", - "Panama [GAZ:00002892]", - "Papua New Guinea [GAZ:00003922]", - "Paracel Islands [GAZ:00010832]", - "Paraguay [GAZ:00002933]", - "Peru [GAZ:00002932]", - "Philippines [GAZ:00004525]", - "Pitcairn Islands [GAZ:00005867]", - "Poland [GAZ:00002939]", - "Portugal [GAZ:00004126]", - "Puerto Rico [GAZ:00006935]", - "Qatar [GAZ:00005286]", - "Republic of the Congo [GAZ:00001088]", - "Reunion [GAZ:00003945]", - "Romania [GAZ:00002951]", - "Ross Sea [GAZ:00023304]", - "Russia [GAZ:00002721]", - "Rwanda [GAZ:00001087]", - "Saint Helena [GAZ:00000849]", - "Saint Kitts and Nevis [GAZ:00006906]", - "Saint Lucia [GAZ:00006909]", - "Saint Pierre and Miquelon [GAZ:00003942]", - "Saint Martin [GAZ:00005841]", - "Saint Vincent and the Grenadines [GAZ:02000565]", - "Samoa [GAZ:00006910]", - "San Marino [GAZ:00003102]", - "Sao Tome and Principe [GAZ:00006927]", - "Saudi Arabia [GAZ:00005279]", - "Senegal [GAZ:00000913]", - "Serbia [GAZ:00002957]", - "Seychelles [GAZ:00006922]", - "Sierra Leone [GAZ:00000914]", - "Singapore [GAZ:00003923]", - "Sint Maarten [GAZ:00012579]", - "Slovakia [GAZ:00002956]", - "Slovenia [GAZ:00002955]", - "Solomon Islands [GAZ:00005275]", - "Somalia [GAZ:00001104]", - "South Africa [GAZ:00001094]", - "South Georgia and the South Sandwich Islands [GAZ:00003990]", - "South Korea [GAZ:00002802]", - "South Sudan [GAZ:00233439]", - "Spain [GAZ:00003936]", - "Spratly Islands [GAZ:00010831]", - "Sri Lanka [GAZ:00003924]", - "State of Palestine [GAZ:00002475]", - "Sudan [GAZ:00000560]", - "Suriname [GAZ:00002525]", - "Svalbard [GAZ:00005396]", - "Swaziland [GAZ:00001099]", - "Sweden [GAZ:00002729]", - "Switzerland [GAZ:00002941]", - "Syria [GAZ:00002474]", - "Taiwan [GAZ:00005341]", - "Tajikistan [GAZ:00006912]", - "Tanzania [GAZ:00001103]", - "Thailand [GAZ:00003744]", - "Timor-Leste [GAZ:00006913]", - "Togo [GAZ:00000915]", - "Tokelau [GAZ:00260188]", - "Tonga [GAZ:00006916]", - "Trinidad and Tobago [GAZ:00003767]", - "Tromelin Island [GAZ:00005812]", - "Tunisia [GAZ:00000562]", - "Turkey [GAZ:00000558]", - "Turkmenistan [GAZ:00005018]", - "Turks and Caicos Islands [GAZ:00003955]", - "Tuvalu [GAZ:00009715]", - "USA [GAZ:00002459]", - "Uganda [GAZ:00001102]", - "Ukraine [GAZ:00002724]", - "United Arab Emirates [GAZ:00005282]", - "United Kingdom [GAZ:00002637]", - "Uruguay [GAZ:00002930]", - "Uzbekistan [GAZ:00004979]", - "Vanuatu [GAZ:00006918]", - "Venezuela [GAZ:00002931]", - "Viet Nam [GAZ:00003756]", - "Virgin Islands [GAZ:00003959]", - "Wake Island [GAZ:00007111]", - "Wallis and Futuna [GAZ:00007191]", - "West Bank [GAZ:00009572]", - "Western Sahara [GAZ:00000564]", - "Yemen [GAZ:00005284]", - "Zambia [GAZ:00001107]", - "Zimbabwe [GAZ:00001106]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001181", - "type": "string", - "description": "The country of origin of the sample.", - "examples": ["South Africa [GAZ:00001094]"], - "classification":"Sample collection and processing", - "label":"Geo Loc Autonomic Country" - }, - "geo_loc_state": { - "examples": ["Western Cape"], - "ontology": "GENEPIO:0001185", - "type": "string", - "description": "The state/province/territory of origin of the sample.", - "classification":"Sample collection and processing", - "label":"Geo Loc Autonomic Community" - }, - "organism": { - "Enums": [ - "Coronaviridae [NCBITaxon:11118]", - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001191", - "type": "string", - "description": "Taxonomic name of the organism.", - "examples": [ - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", - ], - "classification":"Sample collection and processing", - "label":"Organism" - }, - "isolate": { - "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"], - "ontology": "GENEPIO:0001644", - "type": "string", - "description": "Identifier of the specific isolate.", - "clasification":"Sample collection and processing", - "label":"Isolate" - }, - "host_scientific_name": { - "Enums": [ - "Bos taurus [NCBITaxon:9913]", - "Canis lupus familiaris [NCBITaxon:9615]", - "Chiroptera [NCBITaxon:9397]", - "Columbidae [NCBITaxon:8930]", - "Felis catus [NCBITaxon:9685]", - "Gallus gallus [NCBITaxon:9031]", - "Homo sapiens [NCBITaxon:9606]", - "Manis [NCBITaxon:9973]", - "Manis javanica [NCBITaxon:9974]", - "Neovison vison [NCBITaxon:452646]", - "Panthera leo [NCBITaxon:9689]", - "Panthera tigris [NCBITaxon:9694]", - "Rhinolophidae [NCBITaxon:58055]", - "Rhinolophus affinis [NCBITaxon:59477]", - "Sus scrofa domesticus [NCBITaxon:9825]", - "Viverridae [NCBITaxon:9673]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001387", - "type": "string", - "description": "The taxonomic, or scientific name of the host.", - "examples": ["Homo sapiens [NCBITaxon:9606]"], - "clasification":"Host information", - "label":"Host Scientific Name" - }, - "host_disease": { - "Enums": [ - "COVID-19 [MONDO:0100096]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001391", - "type": "string", - "description": "The name of the disease experienced by the host.", - "examples": ["COVID-19 [MONDO:0100096]"] - }, - "sequencing_instrument_model": { - "Enums": [ - "Illumina sequencing instrument [GENEPIO:0100105]", - "Illumina Genome Analyzer [GENEPIO:0100106]", - "Illumina Genome Analyzer II [GENEPIO:0100107]", - "Illumina Genome Analyzer IIx [GENEPIO:0100108]", - "Illumina HiScanSQ [GENEPIO:0100109]", - "Illumina HiSeq [GENEPIO:0100110]", - "Illumina HiSeq X [GENEPIO:0100111]", - "Illumina HiSeq X Five [GENEPIO:0100112]", - "Illumina HiSeq X Ten [GENEPIO:0100113]", - "Illumina HiSeq 1000 [GENEPIO:0100114]", - "Illumina HiSeq 1500 [GENEPIO:0100115]", - "Illumina HiSeq 2000 [GENEPIO:0100116]", - "Illumina HiSeq 2500 [GENEPIO:0100117]", - "Illumina HiSeq 3000 [GENEPIO:0100118]", - "Illumina HiSeq 4000 [GENEPIO:0100119]", - "Illumina iSeq [GENEPIO:0100120]", - "Illumina iSeq 100 [GENEPIO:0100121]", - "Illumina NovaSeq [GENEPIO:0100122]", - "Illumina NovaSeq 6000 [GENEPIO:0100123]", - "Illumina MiniSeq [GENEPIO:0100124]", - "Illumina MiSeq [GENEPIO:0100125]", - "Illumina NextSeq [GENEPIO:0100126]", - "Illumina NextSeq 500 [GENEPIO:0100127]", - "Illumina NextSeq 550 [GENEPIO:0100128]", - "Illumina NextSeq 2000 [GENEPIO:0100129]", - "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", - "PacBio RS [GENEPIO:0100131]", - "PacBio RS II [GENEPIO:0100132]", - "PacBio Sequel [GENEPIO:0100133]", - "PacBio Sequel II [GENEPIO:0100134]", - "Ion Torrent sequencing instrument [GENEPIO:0100135]", - "Ion Torrent PGM [GENEPIO:0100136]", - "Ion Torrent Proton [GENEPIO:0100137]", - "Ion Torrent S5 XL [GENEPIO:0100138]", - "Ion Torrent S5 [GENEPIO:0100139]", - "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", - "Oxford Nanopore GridION [GENEPIO:0100141]", - "Oxford Nanopore MinION [GENEPIO:0100142]", - "Oxford Nanopore PromethION [GENEPIO:0100143]", - "BGI Genomics sequencing instrument [GENEPIO:0100144]", - "BGI SEQ-500 [GENEPIO:0100145]", - "MGI sequencing instrument [GENEPIO:0100146]", - "MGI DNBSEQ-T7 [GENEPIO:0100147]", - "MGI DNBSEQ-G400 [GENEPIO:0100148]", - "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", - "MGI DNBSEQ-G50 [GENEPIO:0100150]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001452", - "type": "string", - "description": "The model of the sequencing instrument used.", - "examples": ["Oxford Nanopore MinION [GENEPIO:0100142]"], - "classification":"Sequencing", - "label":"Sequencing Instrument Model" - }, - "sequencing_instrument_platform": { - "examples": ["MinIon"], - "ontology": "0", - "type": "string", - "description": "The model of the sequencing instrument used.", - "label":"Sequencing Platforms " - }, - "consensus_sequence_software_name": { - "examples": ["Ivar"], - "ontology": "GENEPIO:0001463", - "type": "string", - "description": "The name of software used to generate the consensus sequence." - }, - "consensus_sequence_software_version": { - "examples": ["1.3"], - "ontology": "GENEPIO:0001469", - "type": "string", - "description": "The version of the software used to generate the consensus sequence." - }, - "submitting_lab_sequence_id": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Sample ID given by the submitting laboratory" - }, - "bioproject_umbrella_accession_ENA": { - "examples": ["PRJNA623807"], - "ontology": "GENEPIO:0001133", - "type": "string", - "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", - "clasification":"Database Identifiers" - }, - "bioproject_accession_ENA": { - "examples": ["PRJNA12345"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", - "clasification":"Database Identifiers" - }, - "biosample_accession_ENA": { - "examples": ["SAMN14180202"], - "ontology": "GENEPIO:0001139", - "type": "string", - "description": "The identifier assigned to a BioSample in INSDC archives.", - "clasification":"Database Identifiers" - }, - "sra_accession": { - "examples": ["SRR11177792"], - "ontology": "GENEPIO:0001142", - "type": "string", - "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "clasification":"Database Identifiers" - }, - "genBank/ENA/DDBJ_accession": { - "examples": ["MN908947.3"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", - "clasification":"Database Identifiers" - }, - "gisaid_accession": { - "examples": ["EPI_ISL_123456"], - "ontology": "GENEPIO:0001147", - "type": "string", - "description": "The GISAID accession number assigned to the sequence.", - "clasification":"Database Identifiers" - }, - "virus_name": { - "examples": ["hCoV-19/Canada/prov_rona_99/2020"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The user-defined GISAID virus name assigned to the sequence.", - "clasification":"Database Identifiers" - }, - "collecting_institution_email": { - "examples": ["johnnyblogs@lab.ca"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The email address of the contact responsible for follow-up regarding the sample.", - "clasification":"Sample collection and processing" - }, - "collecting_institution_address": { - "examples": ["655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada"], - "ontology": "GENEPIO:0001158", - "type": "string", - "description": "The mailing address of the agency submitting the sample.", - "clasification":"Sample collection and processing" - }, - "submitting_institution_email": { - "examples": ["RespLab@lab.ca"], - "ontology": "GENEPIO:0001165", - "type": "string", - "description": "The email address of the contact responsible for follow-up regarding the sequence.", - "clasification":"Sample collection and processing" - }, - "submitting_institution_address": { - "examples": ["123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The mailing address of the agency submitting the sequence.", - "clasification":"Sample collection and processing" - }, - "sample_received_date": { - "examples": ["3/21/2020"], - "ontology": "GENEPIO:0001179", - "type": "string", - "description": "The date on which the sample was received.", - "format":"date", - "clasification":"Sample collection and processing" - }, - "shipping_date": { - "examples": ["3/20/2020"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The date on which the sample was sent.", - "format":"date", - "clasification":"Sample collection and processing" - }, - "results_emission_date": { - "examples": ["3/23/2020"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The date on which the results were emitted.", - "format":"date", - "clasification":"Sample collection and processing" - }, - "geo_loc_region": { - "examples": ["Derbyshire"], - "ontology": "GENEPIO:0100280", - "type": "string", - "description": "The county/region of origin of the sample.", - "clasification":"Sample collection and processing", - "label":"Geo Loc Province" - }, - "geo_loc_city": { - "examples": ["Vancouver"], - "ontology": "GENEPIO:0001189", - "type": "string", - "description": "The city of origin of the sample.", - "clasification":"Sample collection and processing", - "label":"Geo Loc City" - }, - "geo_loc_latitude": { - "examples": ["38.98 N"], - "ontology": "OBI:0001620", - "type": "string", - "description": "The latitude coordinates of the geographical location of sample collection.", - "clasification":"Sample collection and processing", - "label":"Geo Loc Latitude", - }, - "geo_loc_longitude": { - "examples": ["77.11 W"], - "ontology": "OBI:0001621", - "type": "string", - "description": "The longitude coordinates of the geographical location of sample collection.", - "clasification":"Sample collection and processing", - "label":"Geo Loc Longitude" - }, - "anatomical_material": { - "Enums": [ - "Blood [UBERON:0000178]", - "Fluid [UBERON:0006314]", - "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", - "Fluid (Pericardial) [UBERON:0002409]", - "Fluid (Pleural) [UBERON:0001087]", - "Fluid (Vaginal) [UBERON:0036243]", - "Fluid (Amniotic) [UBERON:0000173]", - "Saliva [UBERON:0001836]", - "Tissue [UBERON:0000479]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001211", - "type": "string", - "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "examples": ["Blood [UBERON:0000178]"], - "classification":"Sample collection and processing", - "label":"Organism Substance" - }, - "anatomical_part": { - "Enums": [ - "Anus [UBERON:0001245]", - "Duodenum [UBERON:0002114]", - "Eye [UBERON:0000970]", - "Intestine [UBERON:0000160]", - "Lower respiratory tract [UBERON:0001558]", - "Bronchus [UBERON:0002185]", - "Lung [UBERON:0002048]", - "Bronchiole [UBERON:0002186]", - "Alveolar sac [UBERON:0002169]", - "Pleural sac [UBERON:0009778]", - "Pleural cavity [UBERON:0002402]", - "Trachea [UBERON:0003126]", - "Rectum [UBERON:0001052]", - "Skin [UBERON:0001003]", - "Stomach [UBERON:0000945]", - "Upper respiratory tract [UBERON:0001557]", - "Anterior Nares [UBERON:2001427]", - "Esophagus [UBERON:0001043]", - "Ethmoid sinus [UBERON:0002453]", - "Nasal Cavity [UBERON:0001707]", - "Middle Nasal Turbinate [UBERON:0005921]", - "Inferior Nasal Turbinate [UBERON:0005922]", - "Nasopharynx (NP) [UBERON:0001728]", - "Oropharynx (OP) [UBERON:0001729]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001214", - "type": "string", - "description": "An anatomical part of an organism e.g. oropharynx. ", - "examples": ["Nasopharynx (NP) [UBERON:0001728]"], - "classification":"Sample collection and processing", - "label":"Anatomical Structure" - }, - "body_product": { - "Enums": [ - "Breast Milk [UBERON:0001913]", - "Feces [UBERON:0001988]", - "Mucus [UBERON:0000912]", - "Semen [UBERON:0006530]", - "Sputum [UBERON:0007311]", - "Sweat [UBERON:0001089]", - "Tear [UBERON:0001827]", - "Urine [UBERON:0001088]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001216", - "type": "string", - "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", - "examples": ["Feces [UBERON:0001988]"], - "classification":"Sample collection and processing", - "label":"Body product" - }, - "environmental_material": { - "Enums": [ - "Air vent [ENVO:03501208]", - "Banknote [ENVO:00003896]", - "Bed rail [ENVO:03501209]", - "Building Floor [ENVO:01000486]", - "Cloth [ENVO:02000058]", - "Control Panel [ENVO:03501210]", - "Door [ENVO:03501220]", - "Door Handle [ENVO:03501211]", - "Face Mask [OBI:0002787]", - "Face Shield [OBI:0002791]", - "Food [FOODON:00002403]", - "Food Packaging [FOODON:03490100]", - "Glass [ENVO:01000481]", - "Handrail [ENVO:03501212]", - "Hospital Gown [OBI:0002796]", - "Light Switch [ENVO:03501213]", - "Locker [ENVO:03501214]", - "N95 Mask [OBI:0002790]", - "Nurse Call Button [ENVO:03501215]", - "Paper [ENVO:03501256]", - "Particulate Matter [ENVO:01000060]", - "Plastic [ENVO:01000404]", - "PPE Gown [GENEPIO:0100025]", - "Sewage [ENVO:00002018]", - "Sink [ENVO:01000990]", - "Soil [ENVO:00001998]", - "Stainless Steel [ENVO:03501216]", - "Tissue Paper [ENVO:03501217]", - "Toilet Bowl [ENVO:03501218]", - "Water [ENVO:00002006]", - "Wastewater [ENVO:00002001]", - "Window [ENVO:03501219]", - "Wood [ENVO:00002040]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001223", - "type": "string", - "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", - "examples": ["Face Mask [OBI:0002787]"], - "clasification":"Sample collection and processing", - "label":"Environmental Material" - }, - "environmental_site": { - "Enums": [ - "Acute care facility [ENVO:03501135]", - "Animal house [ENVO:00003040]", - "Bathroom [ENVO:01000422]", - "Clinical assessment centre [ENVO:03501136]", - "Conference venue [ENVO:03501127]", - "Corridor [ENVO:03501121]", - "Daycare [ENVO:01000927]", - "Emergency room (ER) [ENVO:03501145]", - "Family practice clinic [ENVO:03501186]", - "Group home [ENVO:03501196]", - "Homeless shelter [ENVO:03501133]", - "Hospital [ENVO:00002173]", - "Intensive Care Unit (ICU) [ENVO:03501152]", - "Long Term Care Facility [ENVO:03501194]", - "Patient room [ENVO:03501180]", - "Prison [ENVO:03501204]", - "Production Facility [ENVO:01000536]", - "School [ENVO:03501130]", - "Sewage Plant [ENVO:00003043]", - "Subway train [ENVO:03501109]", - "Wet market [ENVO:03501198]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001232", - "type": "string", - "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", - "examples": ["Hospital [ENVO:00002173]"], - "classification":"Sample collection and processing", - "label":"Anthropogenic Geographic Feature" - }, - "collection_device": { - "Enums": [ - "Air filter [ENVO:00003968]", - "Blood Collection Tube [OBI:0002859]", - "Bronchoscope [OBI:0002826]", - "Collection Container [OBI:0002088]", - "Collection Cup [GENEPIO:0100026]", - "Fibrobronchoscope Brush [OBI:0002825]", - "Filter [GENEPIO:0100103]", - "Fine Needle [OBI:0002827]", - "Microcapillary tube [OBI:0002858]", - "Micropipette [OBI:0001128]", - "Needle [OBI:0000436]", - "Serum Collection Tube [OBI:0002860]", - "Sputum Collection Tube [OBI:0002861]", - "Suction Catheter [OBI:0002831]", - "Swab [GENEPIO:0100027]", - "Urine Collection Tube [OBI:0002862]", - "Virus Transport Medium [OBI:0002866]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001234", - "type": "string", - "description": "The instrument or container used to collect the sample e.g. swab.", - "examples": ["Swab [GENEPIO:0100027]"], - "clasification":"Sample collection and processing", - "label":"Collection Device" - }, - "collection_method": { - "Enums": [ - "Amniocentesis [NCIT:C52009]", - "Aspiration [NCIT:C15631]", - "Suprapubic Aspiration [GENEPIO:0100028]", - "Tracheal Aspiration [GENEPIO:0100029]", - "Vacuum Aspiration [GENEPIO:0100030]", - "Biopsy [OBI:0002650]", - "Needle Biopsy [OBI:0002651]", - "Filtration [OBI:0302885]", - "Air Filtration [GENEPIO:0100031]", - "Lavage [OBI:0600044]", - "Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]", - "Gastric Lavage [GENEPIO:0100033]", - "Lumbar Puncture [NCIT:C15327]", - "Necropsy [MMO:0000344]", - "Phlebotomy [NCIT:C28221]", - "Rinsing [GENEPIO:0002116]", - "Saline gargle (mouth rinse and gargle) [GENEPIO:0100034]", - "Scraping [GENEPIO:0100035]", - "Swabbing [GENEPIO:0002117]", - "Finger Prick [GENEPIO:0100036]", - "Washout Tear Collection [GENEPIO:0100038]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001241", - "type": "string", - "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", - "examples": ["Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]"], - "clasification":"Sample collection and processing", - "label":"Collection Method" - }, - "collection_protocol": { - "examples": ["SC2SamplingProtocol 1.2"], - "ontology": "GENEPIO:0001243", - "type": "string", - "description": "The name and version of a particular protocol used for sampling.", - "clasification":"Sample collection and processing", - "label":"Collection Protocol" - }, - "specimen_processing": { - "Enums": [ - "Virus Passage [GENEPIO:0100039]", - "RNA Re-Extraction (Post RT-PCR) [GENEPIO:0100040]", - "Specimens Pooled [OBI:0600016]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001253", - "type": "string", - "description": "Any processing applied to the sample during or after receiving the sample. ", - "examples": ["Virus Passage [GENEPIO:0100039]"], - "classification":"Sample collection and processing", - "label":"Specimen Processing" - }, - "lab_host": { - "Enums": [ - "293/ACE2 Cell Line [GENEPIO:0100041]", - "Caco2 Cell Line [BTO:0000195]", - "Calu3 Cell Line [BTO:0002750]", - "EFK3B Cell Line [GENEPIO:0100042]", - "HEK293T Cell Line [BTO:0002181]", - "HRCE Cell Line [GENEPIO:0100043]", - "Huh7 Cell Line [BTO:0001950]", - "LLCMk2 Cell Line [CLO:0007330]", - "MDBK Cell Line [BTO:0000836]", - "NHBE Cell Line [BTO:0002924]", - "PK-15 Cell Line [BTO:0001865]", - "RK-13 Cell Line [BTO:0002909]", - "U251 Cell Line [BTO:0002035]", - "Vero Cell Line [BTO:0001444]", - "Vero E6 Cell Line [BTO:0004755]", - "Vero E6/TMPRSS2 Cell Line [GENEPIO:0100044]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001255", - "type": "string", - "description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.", - "examples": ["Vero E6 Cell Line [BTO:0004755]"], - "classification":"Sample collection and processing", - "label":"Lab passage Host" - }, - "passage_number": { - "examples": ["3"], - "ontology": "GENEPIO:0001261", - "type": "string", - "description": "Number of passages.", - "clasification":"Sample collection and processing", - "label":"Passage Number" - }, - "passage_method": { - "examples": ["AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain."], - "ontology": "GENEPIO:0001264", - "type": "string", - "description": "Description of how organism was passaged.", - "clasification":"Sample collection and processing", - "label":"Passage Method" - }, - "biomaterial_extracted": { - "Enums": [ - "mRNA (cDNA) [OBI:0002754]", - "RNA (Total) [OBI:0000895]", - "RNA (Poly-A) [OBI:0000869]", - "RNA (Ribo-Depleted) [OBI:0002627]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001266", - "type": "string", - "description": "The biomaterial extracted from samples for the purpose of sequencing.", - "examples": ["RNA (Total) [OBI:0000895]"], - "classification":"Sample collection and processing", - "label":"Biomaterial Extracted" - }, - "tax_id": { - "examples": ["probably 2697049 in all cases"], - "ontology": "GENEPIO_0001800", - "type": "string", - "description": "The NCBITaxon identifier for the organism being sequenced.", - "clasification":"Sample collection and processing", - "label":"Tax ID" - }, - "common_name": { - "examples": [""], - "ontology": "BU_ISCIII:003", - "type": "string", - "description": "The common name of the organism.", - "clasification":"Sample collection and processing", - "label":"Common name" - }, - "center_name": { - "examples": [" KAROLINSKA INSITUTET"], - "ontology": "NCIT_C19983", - "type": "string", - "description": "The name of the institution", - "clasification":"Sample collection and processing", - "label":"Center Name" - }, - "virus_id": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The user-defined name for the sample.", - "clasification":"Database Identifiers" - }, - "host_common_name": { - "Enums": [ - "Human [NCBITaxon:9606]", - "Bat [NCBITaxon:9397]", - "Cat [NCBITaxon:9685]", - "Chicken [NCBITaxon:9031]", - "Civet [NCBITaxon:9673]", - "Cow [NCBITaxon:9913]", - "Dog [NCBITaxon:9615]", - "Lion [NCBITaxon:9689]", - "Mink [NCBITaxon:452646]", - "Pangolin [NCBITaxon:9973]", - "Pig [NCBITaxon:9825]", - "Pigeon [NCBITaxon:8930]", - "Tiger [NCBITaxon:9694]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001386", - "type": "string", - "description": "The commonly used name of the host.", - "examples": ["Human [NCBITaxon:9606]"], - "classification":"Host information", - "label":"Host Common Name" - }, - "outbreak": { - "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], - "ontology": "GENEPIO:0001417", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", - "label":"Outbreak Exposure Event Location" - }, - "additional_host_information": { - "examples": ["e.g. Patient infected while traveling in …."], - "ontology": "0", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", - "label":"Additional Host Information" - }, - "purpose_of_sequencing": { - "Enums": [ - "Baseline surveillance (random sampling) [GENEPIO:0100005]", - "Targeted surveillance (non-random sampling) [GENEPIO:0100006]", - "Priority surveillance projects [GENEPIO:0100007]", - "Screening for Variants of Concern (VOC) [GENEPIO:0100008]", - "Sample has epidemiological link to Variant of Concern (VoC) [GENEPIO:0100273]", - "Sample has epidemiological link to Omicron Variant [GENEPIO:0100274]", - "Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]", - "Re-infection surveillance [GENEPIO:0100010]", - "Vaccine escape surveillance [GENEPIO:0100011]", - "Travel-associated surveillance [GENEPIO:0100012]", - "Domestic travel surveillance [GENEPIO:0100013]", - "Interstate/ interprovincial travel surveillance [GENEPIO:0100275]", - "Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276]", - "International travel surveillance [GENEPIO:0100014]", - "Surveillance of international border crossing by air travel or ground transport [GENEPIO:0100015]", - "Surveillance of international border crossing by air travel [GENEPIO:0100016]", - "Surveillance of international border crossing by ground transport [GENEPIO:0100017]", - "Surveillance from international worker testing [GENEPIO:0100018]", - "Cluster/Outbreak investigation [GENEPIO:0100019]", - "Multi-jurisdictional outbreak investigation [GENEPIO:0100020]", - "Intra-jurisdictional outbreak investigation [GENEPIO:0100021]", - "Research [GENEPIO:0100022]", - "Viral passage experiment [GENEPIO:0100023]", - "Protocol testing [GENEPIO:0100024]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001445", - "type": "string", - "description": "The reason that the sample was sequenced.", - "examples": ["Baseline surveillance (random sampling) [GENEPIO:0100005]"], - "classification":"Sequencing", - "label":"Purpose of Sequencing" - }, - "purpose_of_sequencing_details": { - "Enums": [ - "Screened for S gene target failure (S dropout)", - "Screened for mink variants", - "Screened for B.1.1.7 variant", - "Screened for B.1.135 variant", - "Screened for P.1 variant", - "Screened due to travel history", - "Screened due to close contact with infected individual", - "Assessing public health control measures", - "Determining early introductions and spread", - "Investigating airline-related exposures", - "Investigating temporary foreign worker", - "Investigating remote regions", - "Investigating health care workers", - "Investigating schools/universities", - "Investigating reinfection" - ], - "ontology": "GENEPIO:0001446", - "type": "string", - "description": "The description of why the sample was sequenced providing specific details.", - "examples": ["Screened for S gene target failure (S dropout)"], - "clasification":"Sequencing", - "label":"Purpose Of Sequencing Details" - }, - "sequencing_date": { - "examples": ["4/26/2021"], - "ontology": "GENEPIO:0001447", - "type": "string", - "description": "The date the sample was sequenced.", - "format":"date", - "clasification":"Sequencing", - "label":"Sequencing date" - }, - "rna_extraction_protocol": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Rna Extraction Protocol" - }, - "library_kit": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Library Kit" - }, - "library_id": { - "examples": ["XYZ_123345"], - "ontology": "GENEPIO:0001448", - "type": "string", - "description": "The user-specified identifier for the library prepared for sequencing.", - "clasification":"Sequencing", - "labe":"Library Id" - }, - "enrichment_protocol": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Enrichment_protocol" - }, - "if_enrichment_protocol_is_other_specify": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"If Enrichment Protocol Is Other, Specify" - }, - "amplicon protocol": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Amplicon Protocol" - }, - "if_amplicon_protocol_if_other_especify": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "labe":"If Amplicon Protocol If Other, Especify" - }, - "amplicon_version": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Amplicon Version" - }, - "amplicon_size": { - "examples": ["300bp"], - "ontology": "GENEPIO:0001449", - "type": "string", - "description": "The length of the amplicon generated by PCR amplification.", - "clasification":"Sequencing", - "label":"Amplicon Size" - }, - "was_phix_used?": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Was Phix Used" - }, - "number_of_samples_in_run": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Number Of Samples In Run" - }, - "flowcell_kit": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "labe":"Flowcell Kit" - }, - "runID": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"RunID" - }, - "sequencing_platforms": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Sequencing Platforms " - }, - "library_preparation_kit": { - "examples": ["Nextera XT"], - "ontology": "GENEPIO:0001450", - "type": "string", - "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", - "clasification":"Sequencing", - "label":"Library Preparation Kit" - }, - "flow_cell_barcode": { - "examples": ["FAB06069"], - "ontology": "GENEPIO:0001451", - "type": "string", - "description": "The barcode of the flow cell used for sequencing.", - "clasification":"Sequencing", - "label":"Flow Cell Barcode" - }, - "sequencing_protocol_name": { - "examples": ["1D_DNA_MinION, ARTIC Network Protocol V3"], - "ontology": "GENEPIO:0001453", - "type": "string", - "description": "The name and version number of the sequencing protocol used.", - "clasification":"Sequencing", - "label":"Sequencing Protocol Name" - }, - "sequencing_protocol": { - "examples": ["Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits."], - "ontology": "GENEPIO:0001454", - "type": "string", - "description": "The protocol used to generate the sequence.", - "clasification":"Sequencing", - "label":"Sequencing Protocol" - }, - "sequencing_kit_number": { - "examples": ["AB456XYZ789"], - "ontology": "GENEPIO:0001455", - "type": "string", - "description": "The manufacturer's kit number.", - "clasification":"Sequencing", - "label":"Sequencing Kit Number" - }, - "amplicon_pcr_primer_scheme": { - "examples": ["https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv"], - "ontology": "GENEPIO:0001456", - "type": "string", - "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", - "clasification":"Sequencing", - "label":"Amplicon Pcr Primer Scheme" - }, - "library_selection": { - "examples": ["RANDOM PCR"], - "ontology": "GENPIO_0001940", - "type": "string", - "description": "Library capture method.", - "clasification":"Sequencing", - "label":"Capture method" - }, - "library_strategy": { - "Enums": ["Bisultife-Seq strategy [GENPIO:0001975]", - "CTS strategy [GENPIO:0001978]", - "ChIP-Seq strategy [GENPIO:0001979]", - "DNase-Hypersensitivity strategy [GENPIO:0001980]", - "EST strategy [GENPIO:0001981]", - "FL-cDNA strategy [GENPIO:0001983]", - "MB-Seq strategy [GENPIO:0001984]", - "MNase-Seq strategy [GENPIO:0001985]", - "MRE-Seq strategy [GENPIO:0001986]", - "MeDIP-Seq strategy [GENPIO:0001987]", - "RNA-Seq strategy [GENPIO:0001990]", - "WCS strategy [GENPIO:0001991]", - "WGS strategy [GENPIO:0001992]", - "WXS strategy [GENPIO:0001993]", - "amplicon strategy [GENPIO:0001974]", - "clone end strategy [GENPIO:0001976]", - "clone strategy [GENPIO:0001977]", - "finishing strategy [GENPIO:0001982]", - "other library strategy [GENPIO:0001988]", - "pool clone strategy [GENPIO:0001989]", - ], - "examples": ["WGS"], - "ontology": "GENPIO_0001973", - "type": "string", - "description": "Overall sequencing strategy or approach.", - "clasification":"Sequencing", - "label":"Sequencing technique" - }, - "library_layout": { - "examples": ["PAIRED"], - "ontology":"BU_ISCIII:007", - "type": "string", - "description": "Single or paired.", - "clasification":"Sequencing", - "label":"Library Layout" - }, - "library_name": { - "examples": ["P17157_1007"], - "ontology": "GENEPIO_0001995", - "type": "string", - "description": "Name of the used library", - "clasification":"Sequencing", - "label":"LibraryName" - }, - "nominal_length ": { - "examples": ["350"], - "ontology": "GENEPIO_0000076", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Nominal Length" - }, - "raw_sequence_data_processing_method": { - "examples": ["Porechop 0.2.3"], - "ontology": "GENEPIO:0001458", - "type": "string", - "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", - "clasification":"Bioinformatics and QC metrics", - "label":"Raw sequence data processin method" - }, - "dehosting_method": { - "examples": ["Nanostripper"], - "ontology": "GENEPIO:0001459", - "type": "string", - "description": "The method used to remove host reads from the pathogen sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Dehosting Method" - }, - "assembly": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Assembly" - }, - "if_assembly_other": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"If assembly Is Other, Specify" - }, - "assembly_params": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Assambly params" - }, - "variant_calling": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Variant Calling" - }, - "if_variant_calling_other": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"If variant calling Is Other, Specify" - }, - "variant_calling_params": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Variant Calling params" - }, - "consensus_sequence_filepath": { - "examples": ["/User/Documents/RespLab/Data/ncov123assembly.fasta"], - "ontology": "GENEPIO:0001462", - "type": "string", - "description": "The filepath of the consesnsus sequence file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus sequence filepath" - }, - "consensus_sequence_software_name": { - "examples": ["Ivar"], - "ontology": "GENEPIO:0001463", - "type": "string", - "description": "The name of software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus sequence software name" - }, - "if_consensus_other": { - "examples": ["1.3"], - "ontology": "0", - "type": "string", - "description": "The version of the software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"If consensus Is Other, Specify" - }, - "consensus_sequence_software_version": { - "examples": ["1.3"], - "ontology": "GENEPIO:0001469", - "type": "string", - "description": "The version of the software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus sequence software version" - }, - "consensus_criteria": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus criteria" - }, - "quality_control_metrics": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Quality control metrics " - }, - "breadth_of_coverage_value": { - "examples": ["95%"], - "ontology": "GENEPIO:0001472", - "type": "string", - "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", - "clasification":"Bioinformatics and QC metrics", - "label":"Breadth of coverage value" - }, - "depth_of_coverage_value": { - "examples": ["400x"], - "ontology": "GENEPIO:0001474", - "type": "string", - "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Depth of coverage value " - }, - "depth_of_coverage_threshold": { - "examples": ["100x"], - "ontology": "GENEPIO:0001475", - "type": "string", - "description": "The threshold used as a cut-off for the depth of coverage.", - "clasification":"Bioinformatics and QC metrics", - "label":"Depth of coverage threshold" - }, - "sequence_file_R1_fastq": { - "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], - "ontology": "GENEPIO:0001476", - "type": "string", - "description": "The user-specified filename of the r1 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Sequence file R1 fastq" - }, - "sequence_file_R2_fastq": { - "examples": ["ABC123_S1_L001_R2_001.fastq.gz"], - "ontology": "GENEPIO:0001477", - "type": "string", - "description": "The user-specified filename of the r2 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Sequence file R2 fastq" - }, - "r1_fastq_filepath": { - "examples": ["/User/Documents/RespLab/Data/"], - "ontology": "GENEPIO:0001478", - "type": "string", - "description": "The filepath of the r1 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Filepath R1 fastq" - }, - "r2_fastq_filepath": { - "examples": ["/User/Documents/RespLab/Data/"], - "ontology": "GENEPIO:0001479", - "type": "string", - "description": "The filepath of the r2 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Filepath R2 fastq" - }, - "fast5_filename": { - "examples": ["batch1a_sequences.fast5"], - "ontology": "GENEPIO:0001480", - "type": "string", - "description": "The user-specified filename of the FAST5 file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Filename fast5" - }, - "fast5_filepath": { - "examples": ["/User/Documents/RespLab/Data/"], - "ontology": "GENEPIO:0001481", - "type": "string", - "description": "The filepath of the FAST5 file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Filepath fast5" - }, - "number_of_base_pairs_sequenced": { - "examples": ["387566"], - "ontology": "GENEPIO:0001482", - "type": "string", - "description": "The number of total base pairs generated by the sequencing process.", - "clasification":"Bioinformatics and QC metrics", - "label":"Number of base pairs sequenced " - }, - "consensus_genome_length": { - "examples": ["38677"], - "ontology": "GENEPIO:0001483", - "type": "string", - "description": "Size of the assembled genome described as the number of base pairs.", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus genome length" - }, - "ns_per_100_kbp": { - "examples": ["300"], - "ontology": "GENEPIO:0001484", - "type": "string", - "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Ns per 100 kbp" - }, - "reference_genome_accession": { - "examples": ["NC_045512.2"], - "ontology": "GENEPIO:0001485", - "type": "string", - "description": "A persistent, unique identifier of a genome database entry.", - "clasification":"Bioinformatics and QC metrics", - "label":"Reference genome accession" - }, - "bioinformatics_protocol": { - "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], - "ontology": "GENEPIO:0001489", - "type": "string", - "description": "The name of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics", - "label":"Bioinformatics protocol" - }, - "if_bioinformatic_protocol_is_other_specify": { - "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], - "ontology": "0", - "type": "string", - "description": "The name of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics", - "label":"If bioinformatic protocol Is Other, Specify" - }, - "bioinformatic_protocol_version": { - "examples": ["https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"], - "ontology": "0", - "type": "string", - "description": "The version number of the bioinformatics protocol used.", - "clasification":"Bioinformatics and QC metrics", - "label":"bioinformatics protocol version" - }, - "commercial/open-source/both": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Commercial/Open-source/both" - }, - "preprocessing": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Preprocessing" - }, - "if_preprocessing_other": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"If preprocessing Is Other, Specify" - }, - "preprocessing_params": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Preprocessing params" - }, - "mapping": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Lineage and Variant information", - "label":"Mapping" - }, - "if_mapping_other": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Lineage and Variant information", - "label":"If mapping Is Other, Specify" - }, - "mapping_params": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Lineage and Variant information", - "label":"Mapping params" - }, - "lineage/clade_name": { - "examples": ["B.1.1.7"], - "ontology": "GENEPIO:0001500", - "type": "string", - "description": "The name of the lineage or clade.", - "clasification":"Lineage and Variant information", - "label":"Lineage/clade name" - }, - "lineage/clade_analysis_software_name": { - "examples": ["Pangolin"], - "ontology": "GENEPIO:0001501", - "type": "string", - "description": "The name of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information", - "label":"lineage/clade analysis software name" - }, - "if_lineage_identification_other": { - "examples": ["Other than Pangolin"], - "ontology": "0", - "type": "string", - "description": "The name of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information", - "label":"If lineage identification Is Other, Specify" - }, - "lineage/clade_analysis_software_version": { - "examples": ["2.1.10"], - "ontology":"GENEPIO:0001502", - "type": "string", - "description": "The version of the software used to determine the lineage/clade.", - "clasification":"Lineage and Variant information", - "label":"Lineage/clade analysis software version" - }, - "variant_designation": { - "Enums": [ - "Variant of Interest (VOI) [GENEPIO:0100082]", - "Variant of Concern (VOC) [GENEPIO:0100083]", - "Variant Under Monitoring (VUM) [GENEPIO:0100279]" - ], - "ontology": "GENEPIO:0001503", - "type": "string", - "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", - "examples": ["Variant of Concern (VOC) [GENEPIO:0100083]"], - "classification":"Lineage and Variant information", - "label":"Variant designation" - }, - "variant_evidence": { - "examples": ["lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)"], - "ontology": "GENEPIO:0001504", - "type": "string", - "description": "The evidence used to make the variant determination.", - "clasification":"Lineage and Variant information", - "label":"Variant evidence" - }, - "gene_name_1": { - "Enums": [ - "E gene (orf4) [GENEPIO:0100151]", - "M gene (orf5) [GENEPIO:0100152]", - "N gene (orf9) [GENEPIO:0100153]", - "Spike gene (orf2) [GENEPIO:0100154]", - "orf1ab (rep) [GENEPIO:0100155]", - "orf1a (pp1a) [GENEPIO:0100156]", - "nsp11 [GENEPIO:0100157]", - "nsp1 [GENEPIO:0100158]", - "nsp2 [GENEPIO:0100159]", - "nsp3 [GENEPIO:0100160]", - "nsp4 [GENEPIO:0100161]", - "nsp5 [GENEPIO:0100162]", - "nsp6 [GENEPIO:0100163]", - "nsp7 [GENEPIO:0100164]", - "nsp8 [GENEPIO:0100165]", - "nsp9 [GENEPIO:0100166]", - "nsp10 [GENEPIO:0100167]", - "RdRp gene (nsp12) [GENEPIO:0100168]", - "hel gene (nsp13) [GENEPIO:0100169]", - "exoN gene (nsp14) [GENEPIO:0100170]", - "nsp15 [GENEPIO:0100171]", - "nsp16 [GENEPIO:0100172]", - "orf3a [GENEPIO:0100173]", - "orf3b [GENEPIO:0100174]", - "orf6 (ns6) [GENEPIO:0100175]", - "orf7a [GENEPIO:0100176]", - "orf7b (ns7b) [GENEPIO:0100177]", - "orf8 (ns8) [GENEPIO:0100178]", - "orf9b [GENEPIO:0100179]", - "orf9c [GENEPIO:0100180]", - "orf10 [GENEPIO:0100181]", - "orf14 [GENEPIO:0100182]", - "SARS-COV-2 5' UTR [GENEPIO:0100183]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001507", - "type": "string", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "examples": ["E gene (orf4) [GENEPIO:0100151]"], - "classification":"Pathogen diagnostic testing", - "label":"Gene Name 1" - }, - "Protocol_SARS-CoV-2_detection": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"Protocol SARS-CoV-2 detection" - }, - "%qc_filtered": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"%qc filtered" - }, - "%reads_host": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"%reads host" - }, - "%reads_virus": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"%reads virus" - }, - "%unmapped": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"%unmapped" - }, - "%genome _greater_10x": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"% genome greater 10x" - }, - "mean_depth_of_coverage_value": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"mean depth of coverage value" - }, - "%Ns": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"%Ns" - }, - "Number_of_variants_(AF_greater_75%)": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"Number of variants (AF greater 75%)" - }, - "Numer_of_variants_with_effect": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"Numer of variants with effect" - }, - "reference_genome_accession": { - "examples": [""], - "ontology": "GENEPIO:0001485", - "type": "string", - "description": "", - "clasification":"Pathogen diagnostic testing", - "label":"reference genome accession" - }, - "diagnostic_pcr_protocol_1": { - "examples": ["PCREGene 2.0"], - "ontology": "GENEPIO:0001508", - "type": "string", - "description": "The name and version number of the protocol used for diagnostic marker amplification.", - "clasification":"Pathogen diagnostic testing", - "label":"Diagnostic Pcr Protocol 1" - }, - "diagnostic_pcr_Ct_value_1": { - "examples": ["21"], - "ontology": "GENEPIO:0001509", - "type": "string", - "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "clasification":"Pathogen diagnostic testing", - "label":"Diagnostic Pcr Ct Value 1" - }, - "gene_name_2": { - "Enums": [ - "E gene (orf4) [GENEPIO:0100151]", - "M gene (orf5) [GENEPIO:0100152]", - "N gene (orf9) [GENEPIO:0100153]", - "Spike gene (orf2) [GENEPIO:0100154]", - "orf1ab (rep) [GENEPIO:0100155]", - "orf1a (pp1a) [GENEPIO:0100156]", - "nsp11 [GENEPIO:0100157]", - "nsp1 [GENEPIO:0100158]", - "nsp2 [GENEPIO:0100159]", - "nsp3 [GENEPIO:0100160]", - "nsp4 [GENEPIO:0100161]", - "nsp5 [GENEPIO:0100162]", - "nsp6 [GENEPIO:0100163]", - "nsp7 [GENEPIO:0100164]", - "nsp8 [GENEPIO:0100165]", - "nsp9 [GENEPIO:0100166]", - "nsp10 [GENEPIO:0100167]", - "RdRp gene (nsp12) [GENEPIO:0100168]", - "hel gene (nsp13) [GENEPIO:0100169]", - "exoN gene (nsp14) [GENEPIO:0100170]", - "nsp15 [GENEPIO:0100171]", - "nsp16 [GENEPIO:0100172]", - "orf3a [GENEPIO:0100173]", - "orf3b [GENEPIO:0100174]", - "orf6 (ns6) [GENEPIO:0100175]", - "orf7a [GENEPIO:0100176]", - "orf7b (ns7b) [GENEPIO:0100177]", - "orf8 (ns8) [GENEPIO:0100178]", - "orf9b [GENEPIO:0100179]", - "orf9c [GENEPIO:0100180]", - "orf10 [GENEPIO:0100181]", - "orf14 [GENEPIO:0100182]", - "SARS-COV-2 5' UTR [GENEPIO:0100183]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001510", - "type": "string", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "examples": ["RdRp gene (nsp12) [GENEPIO:0100168]"], - "classification":"Pathogen diagnostic testing", - "label":"Gene Name 2" - }, - "diagnostic_pcr_protocol_2": { - "examples": ["PCRRdRpGene 3.0"], - "ontology": "GENEPIO:0001511", - "type": "string", - "description": "The name and version number of the protocol used for diagnostic marker amplification.", - "clasification":"Pathogen diagnostic testing", - "label":"Diagnostic Pcr Protocol 2" - }, - "diagnostic_pcr_Ct_value_2": { - "examples": ["36"], - "ontology": "GENEPIO:0001512", - "type": "string", - "description": "The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "clasification":"Pathogen diagnostic testing", - "label":"Diagnostic Pcr Ct Value-2" - }, - "analysis_author": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Contributor Acknowledgement", - "label":"Analysis Authors" - }, - "author_submitter": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Contributor Acknowledgement", - "label":"Author Submitter" - }, - "submitter": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"enter your GISAID-Username" - }, - "authors": { - "examples": [""], - "ontology": "GENEPIO:0001517", - "type": "string", - "description": "", - "clasification":"Contributor Acknowledgement", - "label":"Authors" - }, - "tax_id": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sample collection and processing" - }, - "common_name": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sample collection and processing" - }, - "library_source": { - "Enums": ["5-methycytidine antibody method [GENPIO:0001941]", - "CAGE method [GENPIO:0001942]", - "CF-H method [GENPIO:0001943]", - "CF-M method ]GENPIO:0001944]", - "CF-S method [GENPIO:0001945]", - "CF-T method [GENPIO:0001946]", - "ChIP method ]GENPIO:0001947]", - "DNAse method [GENPIO:0001948]", - "HMPR method [GENPIO:0001949]", - "Hybrid Selection Method [GENPIO:0001950]", - "MBD2 protein methyl-CpG binding domain method [GENPIO:0001951]", - "MF method [GENPIO:0001952]", - "MNase method [GENPIO:0001953]", - "MSLL method [GENPIO:0001954]", - "PCR method [GENPIO:0001955]", - "RACE method [GENPIO:0001956]", - "RANDOM PCR method [GENPIO:0001957]", - "RANDOM method [GENPIO:0001958]", - "RT-PCR method [GENPIO:0001959]", - "Reduced Representation method [GENPIO:0001960]", - "Resctriction Digest method [GENPIO:0001961]", - "cDNA method [GENPIO:0001962]", - "other library method [GENPIO:0001964]", - "size fractionation method [GENPIO:0001963]", - ], - "examples": ["METAGENOMIC"], - "ontology": "GENEPIO_0001965", - "type": "string", - "description": "Molecule type used to make the library.", - "clasification":"Sequencing", - "label":"Source material" - }, - "nominal_length": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "", - "clasification":"Sequencing" - }, - "analysis_accession": { - "examples": [""], - "ontology": "GENEPIO_0001145", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Analysis Accession" - }, - "study_accession": { - "examples": ["e.g PRJEB39632"], - "ontology": "GENEPIO_0001136", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Study accession" - }, - "secondary_study_accession": { - "examples": ["e.g ERP123173"], - "ontology": "BU_ISCIII:012", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Secondary study accession" - }, - "sample_accession": { - "examples": ["e.g SAMEA7098096"], - "ontology": "GENEPIO_0001139", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Sample accession" - }, - "secondary_sample_accession": { - "examples": ["e.g ERS4858671"], - "ontology": "BU_ISCIII:014", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Secondary sample accession" - }, - "experiment_accession": { - "examples": ["e.g ERX4331406"], - "ontology": "BU_ISCIII:015", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Experiment Accession" - }, - "run_accession": { - "examples": ["e.g ERX4331406"], - "ontology": "BU_ISCIII:016", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Run Accession" - }, - "submission_accession": { - "examples": ["e.g ERA2794974"], - "ontology": "BU_ISCIII:017", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submission Accession" - }, - "read_count": { - "examples": ["e.g 837055"], - "ontology": "STATO_0000064", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Read count" - }, - "read_length": { - "examples": [""], - "ontology": "STATO_0000064", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Read length" - }, - "base_count": { - "examples": ["e.g 503907110"], - "ontology": "UO_0000244", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Base count" - }, - "first_public": { - "examples": ["e.g 2020-08-07"], - "ontology": "NCIT_C142711", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"First Public date" - }, - "last_updated": { - "examples": ["e.g 2020-07-29"], - "ontology": "OMIABIS_0001005", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "format":"Last Updated" - }, - "experiment_title": { - "examples": ["e.g Illumina MiSeq paired end sequencing"], - "ontology": "ORNASEQ_0000004", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Experiment title" - }, - "study_title": { - "examples": ["e.g SARS-CoV-2 genomes from late April in Stockholm"], - "ontology": "OPMI_0000380", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Study title" - }, - "study_alias": { - "examples": ["e.g Sweden"], - "ontology": "SIO_001066", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Study alias" - }, - "experiment_alias": { - "examples": ["e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092"], - "ontology": "NCIT_C42790", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Experiment alias" - }, - "run_alias": { - "examples": ["e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "NCIT_C47911", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Run Alias" - }, - "fastq_bytes": { - "examples": ["e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "NCIT_C48047", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq bytes" - }, - "fastq_md5": { - "examples": [""], - "ontology": "MS_1000568", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq md5" - }, - "fastq_ftp": { - "examples": [""], - "ontology": "PRIDE_0000469", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq ftp" - }, - "fastq_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "BU_ISCIII:032", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq aspera" - }, - "fastq_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "ENVO_01000807", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq galaxy" - }, - "submitted_bytes": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "NCIT_C172872", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted bytes " - }, - "submitted_md5": { - "examples": ["e.g 139853010;166270048"], - "ontology": "BU_ISCIII:035", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted md5" - }, - "submitted_ftp": { - "examples": ["e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a"], - "ontology": "BU_ISCIII:036", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted ftp" - }, - "submitted_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "BU_ISCIII:037", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted aspera" - }, - "submitted_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "BU_ISCIII:038", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted Galaxy" - }, - "submitted_format": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "BU_ISCIII:039", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted Format" - }, - "sra_bytes": { - "examples": ["e.g FASTQ;FASTQ"], - "ontology": "BU_ISCIII:040", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA bytes" - }, - "sra_md5": { - "examples": ["e.g 260236789"], - "ontology": "BU_ISCIII:041", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA md5" - }, - "sra_ftp": { - "examples": ["e.g 2cf0d467d6dc4ae0a5473774d54c059c"], - "ontology": "BU_ISCIII:042", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA ftp" - }, - "sra_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385"], - "ontology": "BU_ISCIII:043", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA aspera" - }, - "sra_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385"], - "ontology": "BU_ISCIII:044", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA galaxy" - }, - "broker_name": { - "examples": ["P17157_1007"], - "ontology": "BU_ISCIII:045", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Broker Name" - }, - "nominal_sdev": { - "examples": [""], - "ontology": "STATO_0000237", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Nominal sdev" - }, - "first_created": { - "examples": ["e.g 2020-08-07"], - "ontology": "NCIT_C164483", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"First created date" - }, - "type": { - "examples": ["betacoronavirus"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "default must remain 'betacoronavirus'", - "clasification":"Database Identifiers" - } - } -} From a663a60a3c4e368cc241625110a99a45588fc62a Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 14 Mar 2022 17:00:09 +0100 Subject: [PATCH 0139/1454] working in xml creation in study and samples part --- relecov_tools/__main__.py | 9 ++ relecov_tools/create_xml.py | 169 +++++++++++++++++++++++------- relecov_tools/validation_jsons.py | 2 +- 3 files changed, 142 insertions(+), 38 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 510c2d67..e87f03bc 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -224,5 +224,14 @@ def validation(host, port, user, passwd): relecov_json.open() + +#@click.argument("source_path", required=False, metavar="") +@click.option("-s","--source_path",help="Where the validated json is") +@click.option("-o","--output_path",help="Output folder for the xml generated files") +@click.option("-a", "--action", help="ADD or MODIFY") +def xml(source_path,output_path,action) + + + if __name__ == "__main__": run_relecov_tools() diff --git a/relecov_tools/create_xml.py b/relecov_tools/create_xml.py index e96a9b25..28959634 100644 --- a/relecov_tools/create_xml.py +++ b/relecov_tools/create_xml.py @@ -1,10 +1,23 @@ +import os +import logging +import rich.console from email import utils import json as j import xml.etree.cElementTree as e +import relecov_tools.utils + +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + class xml_creation: - def __init__(self, source_path=None, output_path=None): + def __init__(self, source_path=None, output_path=None, action=None): if source_path is None: self.source_path = utils.prompt_source_path() else: @@ -13,40 +26,122 @@ def __init__(self, source_path=None, output_path=None): self.output_path = utils.prompt_destination_path() else: self.output_path = output_path + if action is None: + self.action = "ADD" + else: + self.action = action + + def xml( + self, + ): + """ + 1.From validated json to xml study- submission.xml and project.xml + 1.1 Upload study info + + 2. From validated json to xml samples - submission.xml and samples.xml + 2.2 Upload samples info + + 3. From sftp upload runs (FASTQ files programmatic)- experiments.xmlm, runs.xml and submission.xml + 4. From sftp upload sequences (FASTA files programmatic) - json using webin-cli-rest + """ + + # Load validated json + with open(self.source_path) as json_format_file: + json_data = j.load(json_format_file) + + # Create output directory + + try: + # Create target Directory + os.mkdir(self.output_path) + print("Directory ", self.output_path, " Created ") + except FileExistsError: + print("Directory ", self.output_path, " already exists") + + # 1. From validated json to xml study- submission.xml and project.xml + + # submission.xml + if self.action.upper == "ADD": + # submission add + r = e.Element("SUBMISSION_SET") + sample = e.SubElement(r, "SUBMISSION") + actions = e.SubElement(sample, "ACTIONS") + action = e.SubElement(actions, "ACTION") + e.SubElement(action, "ADD") + a = e.ElementTree(r) + a.write(os.path.join(self.output_path, "study", "submission.xml")) + if self.action.upper() == "MODIFY": + # submission modify + r = e.Element("SUBMISSION_SET") + sample = e.SubElement(r, "SUBMISSION") + actions = e.SubElement(sample, "ACTIONS") + action = e.SubElement(actions, "ACTION") + e.SubElement(action, "MODIFY") + a = e.ElementTree(r) + a.write(os.path.join(self.output_path, "study", "submission.xml")) + + # project_relecov.xml + r = e.Element("PROJECT_SET") + project = e.SubElement(r, "PROJECT") + project.set("alias", "RELECOV") + e.SubElement( + project, "TITLE" + ).text = "Example project for ENA submission RELECOV" + e.SubElement( + project, "DESCRIPTION" + ).text = ( + "This study was created as part of an ENA submissions example RELECOV" + ) + submission = e.SubElement(project, "SUBMISSION_PROJECT") + e.SubElement(submission, "SEQUENCING_PROJECT") + a = e.ElementTree(r) + a.write(os.path.join(self.output_path, "study", "project_relecov.xml")) + + # 1.1 Upload study info + + # 2. From validated json to xml samples - submission.xml and samples.xml + + # submission.xml + if self.action.upper == "ADD": + # submission add + r = e.Element("SUBMISSION_SET") + sample = e.SubElement(r, "SUBMISSION") + actions = e.SubElement(sample, "ACTIONS") + action = e.SubElement(actions, "ACTION") + e.SubElement(action, "ADD") + a = e.ElementTree(r) + a.write(os.path.join(self.output_path, "samples", "submission.xml")) + if self.action.upper() == "MODIFY": + # submission modify + r = e.Element("SUBMISSION_SET") + sample = e.SubElement(r, "SUBMISSION") + actions = e.SubElement(sample, "ACTIONS") + action = e.SubElement(actions, "ACTION") + e.SubElement(action, "MODIFY") + a = e.ElementTree(r) + a.write(os.path.join(self.output_path, "samples", "submission.xml")) + + # samples_relecov.xml + data_keys = list(json_data.keys()) + r = e.Element("SAMPLE_SET") + sample = e.SubElement(r, "SAMPLE") + sample.set("alias", "SARS Sample 1 programmatic") + e.SubElement(sample, "TITLE").text = "SARS Sample 1" + sample_name = e.SubElement(sample, "SAMPLE_NAME") + e.SubElement(sample_name, "TAXON_ID").text = "2697049" + e.SubElement( + sample_name, "SCIENTIFIC_NAME" + ).text = "Severe acute respiratory syndrome coronavirus 2" + e.SubElement(sample, "DESCRIPTION").text = "SARS-CoV-2 Sample #1" + sample_attributes = e.SubElement(sample, "SAMPLE_ATTRIBUTES") + for i in json_data: + sample_attribute = e.SubElement(sample_attributes, "SAMPLE_ATTRIBUTE") + e.SubElement(sample_attribute, "TAG").text = str(i) + e.SubElement(sample_attribute, "VALUE").text = json_data[i] + a = e.ElementTree(r) + a.write(os.path.join(self.output_path, "samples", "samples_relecov.xml")) + + # 2.2 Upload samples info - # LOAD VALIDATED json - with open(self.source_path) as json_format_file: - json_data = j.load(json_format_file) - - # project_relecov.xml - r = e.Element("PROJECT_SET") - project = e.SubElement(r, "PROJECT") - project.set("alias", "RELECOV") - e.SubElement( - project, "TITLE" - ).text = "Example project for ENA submission RELECOV" - e.SubElement( - project, "DESCRIPTION" - ).text = "This study was created as part of an ENA submissions example RELECOV" - submission = e.SubElement(project, "SUBMISSION_PROJECT") - e.SubElement(submission, "SEQUENCING_PROJECT") - a = e.ElementTree(r) - a.write("project_relecov.xml") - - # sample_relecov.xml - data_keys = list(json_data.keys()) - r = e.Element("SAMPLE_SET") - sample = e.SubElement(r, "SAMPLE") - sample.set("alias", "SARS Sample 1 programmatic") - e.SubElement(sample, "TITLE").text = "SARS Sample 1" - sample_name = e.SubElement(sample, "SAMPLE_NAME") - e.SubElement(sample_name, "TAXON_ID").text = "2697049" - e.SubElement( - sample_name, "SCIENTIFIC_NAME" - ).text = "Severe acute respiratory syndrome coronavirus 2" - e.SubElement(sample, "DESCRIPTION").text = "SARS-CoV-2 Sample #1" - sample_attributes = e.SubElement(sample, "SAMPLE_ATTRIBUTES") - for i in json_data: - sample_attribute = e.SubElement(sample_attributes, "SAMPLE_ATTRIBUTE") - e.SubElement(sample_attribute, "TAG").text = str(i) - e.SubElement(sample_attribute, "VALUE").text = json_data[i] + # 3. From sftp upload runs (FASTQ files programmatic)- experiments.xmlm, runs.xml and submission.xml + # 4. From sftp upload sequences (FASTA files programmatic) - json using webin-cli-rest diff --git a/relecov_tools/validation_jsons.py b/relecov_tools/validation_jsons.py index a8096885..4b7bdf99 100644 --- a/relecov_tools/validation_jsons.py +++ b/relecov_tools/validation_jsons.py @@ -18,7 +18,7 @@ ) -def validate_json_vs_schena(json_schema_file=None, json_data_file=None): +def validate_json_vs_schema(json_schema_file=None, json_data_file=None): # schema_file = open('/home/lchapado/Projects/Proyecto_ERA/relecov-tools/schema/phage_plus_V0.json') with open(json_schema_file, "r") as fh: From 9d61b799a77f8a97e6a890fae03489a6a57e2c5b Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 14 Mar 2022 20:27:20 +0100 Subject: [PATCH 0140/1454] remove duplicated schema folder and their contents --- schema/ena_v01.json | 1105 ------------------ schema/phage_plus_V0.json | 2285 ------------------------------------- 2 files changed, 3390 deletions(-) delete mode 100644 schema/ena_v01.json delete mode 100644 schema/phage_plus_V0.json diff --git a/schema/ena_v01.json b/schema/ena_v01.json deleted file mode 100644 index d63f9093..00000000 --- a/schema/ena_v01.json +++ /dev/null @@ -1,1105 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft/2019-09/schema#", - "required": [ - "sample_name", - "collecting_institution", - "geographic_location_(country_and/or_sea)", - "isolate", - "host_scientific_name", - "host_common_name", - "host_health_state", - "host_sex", - "host_subject_id", - "instrument_model", - "file_name", - "sample_name", - "tax_id", - "scientific_name", - "common_name", - "sample_description", - "library_source", - "library_selection", - "library_strategy", - "library_layout" - ], - "type": "object", - "properties": { - "sample_name": { - "examples": ["prov_rona_99"], - "ontology": "GENEPIO:0001123", - "type": "string", - "description": "The user-defined name for the sample.", - "clasification":"Database Identifiers", - "label":"Collecting Sample id" - - }, - "collecting_institution": { - "examples": ["Public Health Agency of Canada"], - "ontology": "GENEPIO:0001153", - "type": "string", - "description": "Name of the institution to which the person collecting the specimen belongs. Format: Institute Name, Institute Address", - "label":"Collecting Institution" - - }, - "collection_date": { - "examples": ["3/19/2020"], - "ontology": "GENEPIO:0001174", - "type": "string", - "description": "The date on which the sample was collected.", - "format":"date", - "classification":"Sample collection and processing", - "label":"Sample Collection Date" - }, - "receipt_date": { - "examples": ["3/21/2020"], - "ontology": "GENEPIO:0001179", - "type": "string", - "description": "The date on which the sample was received.", - "format":"date", - "clasification":"Sample collection and processing", - "label":"Sample Received Date" - }, - "geographic_location_(country_and/or_sea)": { - "Enums": [ - "Afghanistan [GAZ:00006882]", - "Albania [GAZ:00002953]", - "Algeria [GAZ:00000563]", - "American Samoa [GAZ:00003957]", - "Andorra [GAZ:00002948]", - "Angola [GAZ:00001095]", - "Anguilla [GAZ:00009159]", - "Antarctica [GAZ:00000462]", - "Antigua and Barbuda [GAZ:00006883]", - "Argentina [GAZ:00002928]", - "Armenia [GAZ:00004094]", - "Aruba [GAZ:00004025]", - "Ashmore and Cartier Islands [GAZ:00005901]", - "Australia [GAZ:00000463]", - "Austria [GAZ:00002942]", - "Azerbaijan [GAZ:00004941]", - "Bahamas [GAZ:00002733]", - "Bahrain [GAZ:00005281]", - "Baker Island [GAZ:00007117]", - "Bangladesh [GAZ:00003750]", - "Barbados [GAZ:00001251]", - "Bassas da India [GAZ:00005810]", - "Belarus [GAZ:00006886]", - "Belgium [GAZ:00002938]", - "Belize [GAZ:00002934]", - "Benin [GAZ:00000904]", - "Bermuda [GAZ:00001264]", - "Bhutan [GAZ:00003920]", - "Bolivia [GAZ:00002511]", - "Borneo [GAZ:00025355]", - "Bosnia and Herzegovina [GAZ:00006887]", - "Botswana [GAZ:00001097]", - "Bouvet Island [GAZ:00001453]", - "Brazil [GAZ:00002828]", - "British Virgin Islands [GAZ:00003961]", - "Brunei [GAZ:00003901]", - "Bulgaria [GAZ:00002950]", - "Burkina Faso [GAZ:00000905]", - "Burundi [GAZ:00001090]", - "Cambodia [GAZ:00006888]", - "Cameroon [GAZ:00001093]", - "Canada [GAZ:00002560]", - "Cape Verde [GAZ:00001227]", - "Cayman Islands [GAZ:00003986]", - "Central African Republic [GAZ:00001089]", - "Chad [GAZ:00000586]", - "Chile [GAZ:00002825]", - "China [GAZ:00002845]", - "Christmas Island [GAZ:00005915]", - "Clipperton Island [GAZ:00005838]", - "Cocos Islands [GAZ:00009721]", - "Colombia [GAZ:00002929]", - "Comoros [GAZ:00005820]", - "Cook Islands [GAZ:00053798]", - "Coral Sea Islands [GAZ:00005917]", - "Costa Rica [GAZ:00002901]", - "Cote d'Ivoire [GAZ:00000906]", - "Croatia [GAZ:00002719]", - "Cuba [GAZ:00003762]", - "Curacao [GAZ:00012582]", - "Cyprus [GAZ:00004006]", - "Czech Republic [GAZ:00002954]", - "Democratic Republic of the Congo [GAZ:00001086]", - "Denmark [GAZ:00005852]", - "Djibouti [GAZ:00000582]", - "Dominica [GAZ:00006890]", - "Dominican Republic [GAZ:00003952]", - "Ecuador [GAZ:00002912]", - "Egypt [GAZ:00003934]", - "El Salvador [GAZ:00002935]", - "Equatorial Guinea [GAZ:00001091]", - "Eritrea [GAZ:00000581]", - "Estonia [GAZ:00002959]", - "Eswatini [GAZ:00001099]", - "Ethiopia [GAZ:00000567]", - "Europa Island [GAZ:00005811]", - "Falkland Islands (Islas Malvinas) [GAZ:00001412]", - "Faroe Islands [GAZ:00059206]", - "Fiji [GAZ:00006891]", - "Finland [GAZ:00002937]", - "France [GAZ:00003940]", - "French Guiana [GAZ:00002516]", - "French Polynesia [GAZ:00002918]", - "French Southern and Antarctic Lands [GAZ:00003753]", - "Gabon [GAZ:00001092]", - "Gambia [GAZ:00000907]", - "Gaza Strip [GAZ:00009571]", - "Georgia [GAZ:00004942]", - "Germany [GAZ:00002646]", - "Ghana [GAZ:00000908]", - "Gibraltar [GAZ:00003987]", - "Glorioso Islands [GAZ:00005808]", - "Greece [GAZ:00002945]", - "Greenland [GAZ:00001507]", - "Grenada [GAZ:02000573]", - "Guadeloupe [GAZ:00067142]", - "Guam [GAZ:00003706]", - "Guatemala [GAZ:00002936]", - "Guernsey [GAZ:00001550]", - "Guinea [GAZ:00000909]", - "Guinea-Bissau [GAZ:00000910]", - "Guyana [GAZ:00002522]", - "Haiti [GAZ:00003953]", - "Heard Island and McDonald Islands [GAZ:00009718]", - "Honduras [GAZ:00002894]", - "Hong Kong [GAZ:00003203]", - "Howland Island [GAZ:00007120]", - "Hungary [GAZ:00002952]", - "Iceland [GAZ:00000843]", - "India [GAZ:00002839]", - "Indonesia [GAZ:00003727]", - "Iran [GAZ:00004474]", - "Iraq [GAZ:00004483]", - "Ireland [GAZ:00002943]", - "Isle of Man [GAZ:00052477]", - "Israel [GAZ:00002476]", - "Italy [GAZ:00002650]", - "Jamaica [GAZ:00003781]", - "Jan Mayen [GAZ:00005853]", - "Japan [GAZ:00002747]", - "Jarvis Island [GAZ:00007118]", - "Jersey [GAZ:00001551]", - "Johnston Atoll [GAZ:00007114]", - "Jordan [GAZ:00002473]", - "Juan de Nova Island [GAZ:00005809]", - "Kazakhstan [GAZ:00004999]", - "Kenya [GAZ:00001101]", - "Kerguelen Archipelago [GAZ:00005682]", - "Kingman Reef [GAZ:00007116]", - "Kiribati [GAZ:00006894]", - "Kosovo [GAZ:00011337]", - "Kuwait [GAZ:00005285]", - "Kyrgyzstan [GAZ:00006893]", - "Laos [GAZ:00006889]", - "Latvia [GAZ:00002958]", - "Lebanon [GAZ:00002478]", - "Lesotho [GAZ:00001098]", - "Liberia [GAZ:00000911]", - "Libya [GAZ:00000566]", - "Liechtenstein [GAZ:00003858]", - "Line Islands [GAZ:00007144]", - "Lithuania [GAZ:00002960]", - "Luxembourg [GAZ:00002947]", - "Macau [GAZ:00003202]", - "Madagascar [GAZ:00001108]", - "Malawi [GAZ:00001105]", - "Malaysia [GAZ:00003902]", - "Maldives [GAZ:00006924]", - "Mali [GAZ:00000584]", - "Malta [GAZ:00004017]", - "Marshall Islands [GAZ:00007161]", - "Martinique [GAZ:00067143]", - "Mauritania [GAZ:00000583]", - "Mauritius [GAZ:00003745]", - "Mayotte [GAZ:00003943]", - "Mexico [GAZ:00002852]", - "Micronesia [GAZ:00005862]", - "Midway Islands [GAZ:00007112]", - "Moldova [GAZ:00003897]", - "Monaco [GAZ:00003857]", - "Mongolia [GAZ:00008744]", - "Montenegro [GAZ:00006898]", - "Montserrat [GAZ:00003988]", - "Morocco [GAZ:00000565]", - "Mozambique [GAZ:00001100]", - "Myanmar [GAZ:00006899]", - "Namibia [GAZ:00001096]", - "Nauru [GAZ:00006900]", - "Navassa Island [GAZ:00007119]", - "Nepal [GAZ:00004399]", - "Netherlands [GAZ:00002946]", - "New Caledonia [GAZ:00005206]", - "New Zealand [GAZ:00000469]", - "Nicaragua [GAZ:00002978]", - "Niger [GAZ:00000585]", - "Nigeria [GAZ:00000912]", - "Niue [GAZ:00006902]", - "Norfolk Island [GAZ:00005908]", - "North Korea [GAZ:00002801]", - "North Macedonia [GAZ:00006895]", - "North Sea [GAZ:00002284]", - "Northern Mariana Islands [GAZ:00003958]", - "Norway [GAZ:00002699]", - "Oman [GAZ:00005283]", - "Pakistan [GAZ:00005246]", - "Palau [GAZ:00006905]", - "Panama [GAZ:00002892]", - "Papua New Guinea [GAZ:00003922]", - "Paracel Islands [GAZ:00010832]", - "Paraguay [GAZ:00002933]", - "Peru [GAZ:00002932]", - "Philippines [GAZ:00004525]", - "Pitcairn Islands [GAZ:00005867]", - "Poland [GAZ:00002939]", - "Portugal [GAZ:00004126]", - "Puerto Rico [GAZ:00006935]", - "Qatar [GAZ:00005286]", - "Republic of the Congo [GAZ:00001088]", - "Reunion [GAZ:00003945]", - "Romania [GAZ:00002951]", - "Ross Sea [GAZ:00023304]", - "Russia [GAZ:00002721]", - "Rwanda [GAZ:00001087]", - "Saint Helena [GAZ:00000849]", - "Saint Kitts and Nevis [GAZ:00006906]", - "Saint Lucia [GAZ:00006909]", - "Saint Pierre and Miquelon [GAZ:00003942]", - "Saint Martin [GAZ:00005841]", - "Saint Vincent and the Grenadines [GAZ:02000565]", - "Samoa [GAZ:00006910]", - "San Marino [GAZ:00003102]", - "Sao Tome and Principe [GAZ:00006927]", - "Saudi Arabia [GAZ:00005279]", - "Senegal [GAZ:00000913]", - "Serbia [GAZ:00002957]", - "Seychelles [GAZ:00006922]", - "Sierra Leone [GAZ:00000914]", - "Singapore [GAZ:00003923]", - "Sint Maarten [GAZ:00012579]", - "Slovakia [GAZ:00002956]", - "Slovenia [GAZ:00002955]", - "Solomon Islands [GAZ:00005275]", - "Somalia [GAZ:00001104]", - "South Africa [GAZ:00001094]", - "South Georgia and the South Sandwich Islands [GAZ:00003990]", - "South Korea [GAZ:00002802]", - "South Sudan [GAZ:00233439]", - "Spain [GAZ:00003936]", - "Spratly Islands [GAZ:00010831]", - "Sri Lanka [GAZ:00003924]", - "State of Palestine [GAZ:00002475]", - "Sudan [GAZ:00000560]", - "Suriname [GAZ:00002525]", - "Svalbard [GAZ:00005396]", - "Swaziland [GAZ:00001099]", - "Sweden [GAZ:00002729]", - "Switzerland [GAZ:00002941]", - "Syria [GAZ:00002474]", - "Taiwan [GAZ:00005341]", - "Tajikistan [GAZ:00006912]", - "Tanzania [GAZ:00001103]", - "Thailand [GAZ:00003744]", - "Timor-Leste [GAZ:00006913]", - "Togo [GAZ:00000915]", - "Tokelau [GAZ:00260188]", - "Tonga [GAZ:00006916]", - "Trinidad and Tobago [GAZ:00003767]", - "Tromelin Island [GAZ:00005812]", - "Tunisia [GAZ:00000562]", - "Turkey [GAZ:00000558]", - "Turkmenistan [GAZ:00005018]", - "Turks and Caicos Islands [GAZ:00003955]", - "Tuvalu [GAZ:00009715]", - "USA [GAZ:00002459]", - "Uganda [GAZ:00001102]", - "Ukraine [GAZ:00002724]", - "United Arab Emirates [GAZ:00005282]", - "United Kingdom [GAZ:00002637]", - "Uruguay [GAZ:00002930]", - "Uzbekistan [GAZ:00004979]", - "Vanuatu [GAZ:00006918]", - "Venezuela [GAZ:00002931]", - "Viet Nam [GAZ:00003756]", - "Virgin Islands [GAZ:00003959]", - "Wake Island [GAZ:00007111]", - "Wallis and Futuna [GAZ:00007191]", - "West Bank [GAZ:00009572]", - "Western Sahara [GAZ:00000564]", - "Yemen [GAZ:00005284]", - "Zambia [GAZ:00001107]", - "Zimbabwe [GAZ:00001106]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001181 ", - "type": "string", - "description": "The country of origin of the sample.", - "examples": ["South Africa [GAZ:00001094]"], - "clasification":"Sample collection and processing", - "label":"Geo Loc Autonomic Country" - - }, - "geographic location (region and locality)": { - "ontology": "GENEPIO:0100280", - "type": "string", - "description": "The county/region of origin of the sample.", - "examples": ["Derbyshire"], - "clasification":"Sample collection and processing", - "label":"Geo Loc Province" - - }, - "geographic location (latitude)": { - "ontology": "OBI:0001620", - "type": "string", - "description": "The latitude coordinates of the geographical location of sample collection.", - "examples": ["38.98 N"], - "clasification":"Sample collection and processing", - "label":"Geo Loc Latitude", - - }, - "geographic location (longitude)": { - "ontology": "OBI:0001621", - "type": "string", - "description": "The longitude coordinates of the geographical location of sample collection.", - "examples": ["77.11 W"], - "clasification":"Sample collection and processing", - "label":"Geo Loc Longitude" - }, - "isolate": { - "ontology": "GENEPIO:0001644", - "type": "string", - "description": "Identifier of the specific isolate.", - "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"], - "genepio_label":"isolate identifier", - "clasification":"Sample collection and processing", - "label":"Isolate" - - }, - "purpose_sampling": { - "examples": ["Diagnostic testing"], - "ontology": "NCIT_C146997", - "type": "string", - "description": "The reason that the sample was collected.", - "clasification":"Sample collection and processing" - }, - "isolation source host-associated": { - "Enums": [ - "Blood [UBERON:0000178]", - "Fluid [UBERON:0006314]", - "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", - "Fluid (Pericardial) [UBERON:0002409]", - "Fluid (Pleural) [UBERON:0001087]", - "Fluid (Vaginal) [UBERON:0036243]", - "Fluid (Amniotic) [UBERON:0000173]", - "Saliva [UBERON:0001836]", - "Tissue [UBERON:0000479]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001211", - "type": "string", - "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "examples": ["Blood [UBERON:0000178]"], - "classification":"Sample collection and processing", - "label":"Organism Substance" - - }, - "isolation source non-host-associated": { - "Enums": [ - "Air vent [ENVO:03501208]", - "Banknote [ENVO:00003896]", - "Bed rail [ENVO:03501209]", - "Building Floor [ENVO:01000486]", - "Cloth [ENVO:02000058]", - "Control Panel [ENVO:03501210]", - "Door [ENVO:03501220]", - "Door Handle [ENVO:03501211]", - "Face Mask [OBI:0002787]", - "Face Shield [OBI:0002791]", - "Food [FOODON:00002403]", - "Food Packaging [FOODON:03490100]", - "Glass [ENVO:01000481]", - "Handrail [ENVO:03501212]", - "Hospital Gown [OBI:0002796]", - "Light Switch [ENVO:03501213]", - "Locker [ENVO:03501214]", - "N95 Mask [OBI:0002790]", - "Nurse Call Button [ENVO:03501215]", - "Paper [ENVO:03501256]", - "Particulate Matter [ENVO:01000060]", - "Plastic [ENVO:01000404]", - "PPE Gown [GENEPIO:0100025]", - "Sewage [ENVO:00002018]", - "Sink [ENVO:01000990]", - "Soil [ENVO:00001998]", - "Stainless Steel [ENVO:03501216]", - "Tissue Paper [ENVO:03501217]", - "Toilet Bowl [ENVO:03501218]", - "Water [ENVO:00002006]", - "Wastewater [ENVO:00002001]", - "Window [ENVO:03501219]", - "Wood [ENVO:00002040]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001223", - "type": "string", - "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", - "examples": ["Face Mask [OBI:0002787]"], - "clasification":"Sample collection and processing", - "label":"Environmental Material" - }, - "host common name": { - "Enums": [ - "Human [NCBITaxon:9606]", - "Bat [NCBITaxon:9397]", - "Cat [NCBITaxon:9685]", - "Chicken [NCBITaxon:9031]", - "Civet [NCBITaxon:9673]", - "Cow [NCBITaxon:9913]", - "Dog [NCBITaxon:9615]", - "Lion [NCBITaxon:9689]", - "Mink [NCBITaxon:452646]", - "Pangolin [NCBITaxon:9973]", - "Pig [NCBITaxon:9825]", - "Pigeon [NCBITaxon:8930]", - "Tiger [NCBITaxon:9694]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001386", - "type": "string", - "description": "The commonly used name of the host.", - "examples": ["Human [NCBITaxon:9606]"], - "classification":"Host information", - "label":"Host Common Name" - - }, - "host scientific name": { - "Enums": [ - "Bos taurus [NCBITaxon:9913]", - "Canis lupus familiaris [NCBITaxon:9615]", - "Chiroptera [NCBITaxon:9397]", - "Columbidae [NCBITaxon:8930]", - "Felis catus [NCBITaxon:9685]", - "Gallus gallus [NCBITaxon:9031]", - "Homo sapiens [NCBITaxon:9606]", - "Manis [NCBITaxon:9973]", - "Manis javanica [NCBITaxon:9974]", - "Neovison vison [NCBITaxon:452646]", - "Panthera leo [NCBITaxon:9689]", - "Panthera tigris [NCBITaxon:9694]", - "Rhinolophidae [NCBITaxon:58055]", - "Rhinolophus affinis [NCBITaxon:59477]", - "Sus scrofa domesticus [NCBITaxon:9825]", - "Viverridae [NCBITaxon:9673]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001387", - "type": "string", - "description": "The taxonomic, or scientific name of the host.", - "examples": ["Homo sapiens [NCBITaxon:9606]"], - "clasification":"Host information", - "label":"Host Scientific Name" - - }, - "host_health_state": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Health status of the host at the time of sample collection.", - "clasification":"Host information", - "genepio_label":"", - - }, - "host_age": { - "examples": ["e.g. 65 or 7 months, or unknown. Caution: the host age may be considered public health identifiable information. Consult the data steward before sharing. If the information is unknown or can not be shared, put unknown"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Patient age", - "clasification":"Host information" - }, - - "host_sex": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Gender or sex of the host.", - "clasification":"Host information", - "genepio_label":"", - - }, - "host_subject_id": { - "examples": ["e.g. #131"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "a unique identifier by which each subject can be referred to, de-identified.", - "clasification":"Host information", - "genepio_label":"", - - }, - "type exposure": { - "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], - "ontology": "GENEPIO:0001417", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", - "label":"Outbreak Exposure Event Location" - - }, - "subject exposure duration": { - "examples": ["e.g. Patient infected while traveling in …."], - "ontology": "0", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", - "label":"Additional Host Information" - - }, - "instrument_model": { - "Enums": [ - "Illumina sequencing instrument [GENEPIO:0100105]", - "Illumina Genome Analyzer [GENEPIO:0100106]", - "Illumina Genome Analyzer II [GENEPIO:0100107]", - "Illumina Genome Analyzer IIx [GENEPIO:0100108]", - "Illumina HiScanSQ [GENEPIO:0100109]", - "Illumina HiSeq [GENEPIO:0100110]", - "Illumina HiSeq X [GENEPIO:0100111]", - "Illumina HiSeq X Five [GENEPIO:0100112]", - "Illumina HiSeq X Ten [GENEPIO:0100113]", - "Illumina HiSeq 1000 [GENEPIO:0100114]", - "Illumina HiSeq 1500 [GENEPIO:0100115]", - "Illumina HiSeq 2000 [GENEPIO:0100116]", - "Illumina HiSeq 2500 [GENEPIO:0100117]", - "Illumina HiSeq 3000 [GENEPIO:0100118]", - "Illumina HiSeq 4000 [GENEPIO:0100119]", - "Illumina iSeq [GENEPIO:0100120]", - "Illumina iSeq 100 [GENEPIO:0100121]", - "Illumina NovaSeq [GENEPIO:0100122]", - "Illumina NovaSeq 6000 [GENEPIO:0100123]", - "Illumina MiniSeq [GENEPIO:0100124]", - "Illumina MiSeq [GENEPIO:0100125]", - "Illumina NextSeq [GENEPIO:0100126]", - "Illumina NextSeq 500 [GENEPIO:0100127]", - "Illumina NextSeq 550 [GENEPIO:0100128]", - "Illumina NextSeq 2000 [GENEPIO:0100129]", - "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", - "PacBio RS [GENEPIO:0100131]", - "PacBio RS II [GENEPIO:0100132]", - "PacBio Sequel [GENEPIO:0100133]", - "PacBio Sequel II [GENEPIO:0100134]", - "Ion Torrent sequencing instrument [GENEPIO:0100135]", - "Ion Torrent PGM [GENEPIO:0100136]", - "Ion Torrent Proton [GENEPIO:0100137]", - "Ion Torrent S5 XL [GENEPIO:0100138]", - "Ion Torrent S5 [GENEPIO:0100139]", - "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", - "Oxford Nanopore GridION [GENEPIO:0100141]", - "Oxford Nanopore MinION [GENEPIO:0100142]", - "Oxford Nanopore PromethION [GENEPIO:0100143]", - "BGI Genomics sequencing instrument [GENEPIO:0100144]", - "BGI SEQ-500 [GENEPIO:0100145]", - "MGI sequencing instrument [GENEPIO:0100146]", - "MGI DNBSEQ-T7 [GENEPIO:0100147]", - "MGI DNBSEQ-G400 [GENEPIO:0100148]", - "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", - "MGI DNBSEQ-G50 [GENEPIO:0100150]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001452", - "type": "string", - "description": "The model of the sequencing instrument used.", - "examples": ["Oxford Nanopore MinION [GENEPIO:0100142]"], - "classification":"Sequencing", - "label":"Sequencing Instrument Model" - }, - "instrument_platform ": { - "examples": ["MinIon"], - "ontology": "0", - "type": "string", - "description": "The model of the sequencing instrument used.", - "label":"Sequencing Platforms " - }, - "file_name": { - "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], - "ontology": "GENEPIO:0001476", - "type": "string", - "description": "The user-specified filename of the r1 FASTQ file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Sequence file R1 fastq" - }, - "tax_id": { - "examples": ["probably 2697049 in all cases"], - "ontology": "GENEPIO_0001724", - "type": "string", - "description": "The NCBITaxon identifier for the organism being sequenced.", - "clasification":"Sample collection and processing", - "label":"Tax ID" - }, - "scientific_name": { - "Enums": [ - "Coronaviridae [NCBITaxon:11118]", - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "examples": [""], - "ontology": "GENEPIO:0001191", - "type": "string", - "description": "The taxonomic name of the organism.", - "clasification":"Sample collection and processing", - "classification":"Sample collection and processing", - "label":"Organism" - }, - "common_name": { - "examples": [""], - "ontology": "BU_ISCIII:003", - "type": "string", - "description": "The common name of the organism.", - "clasification":"Sample collection and processing", - "label":"Common name" - }, - "sample_description": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Free text description of the sample.", - "clasification":"Sample collection and processing", - "genepio_label":"", - - }, - "sample_storage_conditions": { - "examples": ["24 degrees celsius"], - "ontology": "NCIT_C115535", - "type": "string", - "description": "The name and version of a particular protocol used for sampling.", - "clasification":"Sample collection and processing" - }, - "library_source": { - "Enums": ["5-methycytidine antibody method [GENPIO:0001941]", - "CAGE method [GENPIO:0001942]", - "CF-H method [GENPIO:0001943]", - "CF-M method ]GENPIO:0001944]", - "CF-S method [GENPIO:0001945]", - "CF-T method [GENPIO:0001946]", - "ChIP method ]GENPIO:0001947]", - "DNAse method [GENPIO:0001948]", - "HMPR method [GENPIO:0001949]", - "Hybrid Selection Method [GENPIO:0001950]", - "MBD2 protein methyl-CpG binding domain method [GENPIO:0001951]", - "MF method [GENPIO:0001952]", - "MNase method [GENPIO:0001953]", - "MSLL method [GENPIO:0001954]", - "PCR method [GENPIO:0001955]", - "RACE method [GENPIO:0001956]", - "RANDOM PCR method [GENPIO:0001957]", - "RANDOM method [GENPIO:0001958]", - "RT-PCR method [GENPIO:0001959]", - "Reduced Representation method [GENPIO:0001960]", - "Resctriction Digest method [GENPIO:0001961]", - "cDNA method [GENPIO:0001962]", - "other library method [GENPIO:0001964]", - "size fractionation method [GENPIO:0001963]", - ], - "examples": ["METAGENOMIC"], - "ontology": "GENEPIO_0001965", - "type": "string", - "description": "Molecule type used to make the library.", - "clasification":"Sequencing", - "label":"Source material" - }, - "library_selection": { - "examples": ["RANDOM PCR"], - "ontology": "GENPIO_0001940", - "type": "string", - "description": "Library capture method.", - "clasification":"Sequencing", - "label":"Capture method" - }, - "library_strategy": { - "Enums": ["Bisultife-Seq strategy [GENPIO:0001975]", - "CTS strategy [GENPIO:0001978]", - "ChIP-Seq strategy [GENPIO:0001979]", - "DNase-Hypersensitivity strategy [GENPIO:0001980]", - "EST strategy [GENPIO:0001981]", - "FL-cDNA strategy [GENPIO:0001983]", - "MB-Seq strategy [GENPIO:0001984]", - "MNase-Seq strategy [GENPIO:0001985]", - "MRE-Seq strategy [GENPIO:0001986]", - "MeDIP-Seq strategy [GENPIO:0001987]", - "RNA-Seq strategy [GENPIO:0001990]", - "WCS strategy [GENPIO:0001991]", - "WGS strategy [GENPIO:0001992]", - "WXS strategy [GENPIO:0001993]", - "amplicon strategy [GENPIO:0001974]", - "clone end strategy [GENPIO:0001976]", - "clone strategy [GENPIO:0001977]", - "finishing strategy [GENPIO:0001982]", - "other library strategy [GENPIO:0001988]", - "pool clone strategy [GENPIO:0001989]", - ], - "examples": ["WGS"], - "ontology": "GENPIO_0001973", - "type": "string", - "description": "Overall sequencing strategy or approach.", - "clasification":"Sequencing", - "label":"Sequencing technique" - }, - "library_layout": { - "examples": ["PAIRED"], - "ontology":"BU_ISCIII:007", - "type": "string", - "description": "Single or paired.", - "clasification":"Sequencing", - "label":"Library Layout" - }, - "library_name": { - "examples": ["e.g P17157_1007"], - "ontology": "GENEPIO_0001995", - "type": "string", - "description": "The submitter's name for this library.", - "clasification":"Sequencing", - "label":"Library Name" - }, - "nominal_length ": { - "examples": ["350"], - "ontology": "GENEPIO_0000076", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Nominal Length" - }, - "analysis_accession": { - "examples": [""], - "ontology": "GENEPIO_0001145", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Analysis Accession" - }, - "read_length": { - "examples": [""], - "ontology": "STATO_0000064", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Read length" - }, - "study_accession": { - "examples": ["e.g PRJEB39632"], - "ontology": "GENEPIO_0001136", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Study accession" - }, - "secondary_study_accession": { - "examples": ["e.g ERP123173"], - "ontology": "BU_ISCIII:012", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Secondary study accession" - }, - "sample_accession": { - "examples": ["e.g SAMEA7098096"], - "ontology": "GENEPIO_0001139", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Sample accession" - }, - "secondary_sample_accession": { - "examples": ["e.g ERS4858671"], - "ontology": "BU_ISCIII:014", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Secondary sample accession" - }, - "experiment_accession": { - "examples": ["e.g ERX4331406"], - "ontology": "BU_ISCIII:015", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Experiment Accession" - }, - "run_accession": { - "examples": ["e.g ERX4331406"], - "ontology": "BU_ISCIII:016", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Run Accession" - }, - "submission_accession": { - "examples": ["e.g ERA2794974"], - "ontology": "BU_ISCIII:017", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submission accession" - }, - "read_count": { - "examples": ["e.g 837055"], - "ontology": "STATO_0000064", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Read count" - }, - "base_count": { - "examples": ["e.g 503907110"], - "ontology": "UO_0000244", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Base count" - }, - "center_name": { - "examples": [" KAROLINSKA INSITUTET"], - "ontology": "NCIT_C19983", - "type": "string", - "description": "The name of the institution", - "clasification":"Sample collection and processing", - "label":"Center Name" - }, - "first_public": { - "examples": ["e.g 2020-08-07"], - "ontology": "NCIT_C142711", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"First Public date" - }, - "last_updated": { - "examples": ["e.g 2020-07-29"], - "ontology": "OMIABIS_0001005", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "format":"Last Updated" - }, - "experiment_title": { - "examples": ["e.g Illumina MiSeq paired end sequencing"], - "ontology": "ORNASEQ_0000004", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Experiment title" - }, - "study_title": { - "examples": ["e.g SARS-CoV-2 genomes from late April in Stockholm"], - "ontology": "OPMI_0000380", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Study title" - }, - "study_alias": { - "examples": ["e.g Sweden"], - "ontology": "SIO_001066", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Study alias" - }, - "experiment_alias": { - "examples": ["e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092"], - "ontology": "NCIT_C42790", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Experiment alias" - }, - "run_alias": { - "examples": ["e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "NCIT_C47911", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Run Alias" - }, - "fastq_bytes": { - "examples": ["e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "NCIT_C48047", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq bytes" - }, - "fastq_md5": { - "examples": [""], - "ontology": "MS_1000568", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq md5" - }, - "fastq_ftp": { - "examples": [""], - "ontology": "PRIDE_0000469", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq ftp" - }, - "fastq_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "BU_ISCIII:032", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq aspera" - }, - "fastq_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "ENVO_01000807", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq galaxy" - }, - "submitted_bytes": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "NCIT_C172872", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted bytes " - }, - "submitted_md5": { - "examples": ["e.g 139853010;166270048"], - "ontology": "BU_ISCIII:035", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted md5" - }, - "submitted_ftp": { - "examples": ["e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a"], - "ontology": "BU_ISCIII:036", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted ftp" - }, - "submitted_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "BU_ISCIII:037", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted aspera" - }, - "submitted_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "BU_ISCIII:038", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted Galaxy" - }, - "submitted_format": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "BU_ISCIII:039", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted Format" - }, - "sra_bytes": { - "examples": ["e.g FASTQ;FASTQ"], - "ontology": "BU_ISCIII:040", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA bytes" - }, - "sra_md5": { - "examples": ["e.g 260236789"], - "ontology": "BU_ISCIII:041", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA md5" - }, - "sra_ftp": { - "examples": ["e.g 2cf0d467d6dc4ae0a5473774d54c059c"], - "ontology": "BU_ISCIII:042", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA ftp" - }, - "sra_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385"], - "ontology": "BU_ISCIII:043", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA aspera" - }, - "sra_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385"], - "ontology": "BU_ISCIII:044", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA galaxy" - }, - "broker_name": { - "examples": ["P17157_1007"], - "ontology": "BU_ISCIII:045", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Broker Name" - }, - "nominal_sdev": { - "examples": [""], - "ontology": "STATO_0000237", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Nominal sdev" - }, - "first_created": { - "examples": ["e.g 2020-08-07"], - "ontology": "NCIT_C164483", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"First created date" - } - - } -} diff --git a/schema/phage_plus_V0.json b/schema/phage_plus_V0.json deleted file mode 100644 index 4d0bc178..00000000 --- a/schema/phage_plus_V0.json +++ /dev/null @@ -1,2285 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft/2020-12/schema", - "required": [ - "sample_name", - "collecting_institution", - "submitting_institution", - "sample_collection_date", - "geo_loc_country", - "geo_loc_state", - "organism", - "isolate", - "host_scientific_name", - "host_disease", - "sequencing_instrument_model", - "sequencing_instrument_platform", - "consensus_sequence_software_name", - "consensus_sequence_software_version" - ], - "type": "object", - "properties": { - "sample_name": { - "examples": ["prov_rona_99"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The user-defined name for the sample.", - "clasification":"Database Identifiers" - }, - "collecting_institution": { - "examples": ["Public Health Agency of Canada"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The name of the agency that collected the original sample." - }, - "submitting_institution": { - "examples": ["Centers for Disease Control and Prevention"], - "ontology": "GENEPIO:0001159", - "type": "string", - "description": "The name of the agency that generated the sequence." - }, - "sample_collection_date": { - "examples": ["3/19/2020"], - "ontology": "GENEPIO:0001174", - "type": "string", - "description": "The date on which the sample was collected.", - "format":"date" - }, - "geo_loc_name_country": { - "Enums": [ - "Afghanistan [GAZ:00006882]", - "Albania [GAZ:00002953]", - "Algeria [GAZ:00000563]", - "American Samoa [GAZ:00003957]", - "Andorra [GAZ:00002948]", - "Angola [GAZ:00001095]", - "Anguilla [GAZ:00009159]", - "Antarctica [GAZ:00000462]", - "Antigua and Barbuda [GAZ:00006883]", - "Argentina [GAZ:00002928]", - "Armenia [GAZ:00004094]", - "Aruba [GAZ:00004025]", - "Ashmore and Cartier Islands [GAZ:00005901]", - "Australia [GAZ:00000463]", - "Austria [GAZ:00002942]", - "Azerbaijan [GAZ:00004941]", - "Bahamas [GAZ:00002733]", - "Bahrain [GAZ:00005281]", - "Baker Island [GAZ:00007117]", - "Bangladesh [GAZ:00003750]", - "Barbados [GAZ:00001251]", - "Bassas da India [GAZ:00005810]", - "Belarus [GAZ:00006886]", - "Belgium [GAZ:00002938]", - "Belize [GAZ:00002934]", - "Benin [GAZ:00000904]", - "Bermuda [GAZ:00001264]", - "Bhutan [GAZ:00003920]", - "Bolivia [GAZ:00002511]", - "Borneo [GAZ:00025355]", - "Bosnia and Herzegovina [GAZ:00006887]", - "Botswana [GAZ:00001097]", - "Bouvet Island [GAZ:00001453]", - "Brazil [GAZ:00002828]", - "British Virgin Islands [GAZ:00003961]", - "Brunei [GAZ:00003901]", - "Bulgaria [GAZ:00002950]", - "Burkina Faso [GAZ:00000905]", - "Burundi [GAZ:00001090]", - "Cambodia [GAZ:00006888]", - "Cameroon [GAZ:00001093]", - "Canada [GAZ:00002560]", - "Cape Verde [GAZ:00001227]", - "Cayman Islands [GAZ:00003986]", - "Central African Republic [GAZ:00001089]", - "Chad [GAZ:00000586]", - "Chile [GAZ:00002825]", - "China [GAZ:00002845]", - "Christmas Island [GAZ:00005915]", - "Clipperton Island [GAZ:00005838]", - "Cocos Islands [GAZ:00009721]", - "Colombia [GAZ:00002929]", - "Comoros [GAZ:00005820]", - "Cook Islands [GAZ:00053798]", - "Coral Sea Islands [GAZ:00005917]", - "Costa Rica [GAZ:00002901]", - "Cote d'Ivoire [GAZ:00000906]", - "Croatia [GAZ:00002719]", - "Cuba [GAZ:00003762]", - "Curacao [GAZ:00012582]", - "Cyprus [GAZ:00004006]", - "Czech Republic [GAZ:00002954]", - "Democratic Republic of the Congo [GAZ:00001086]", - "Denmark [GAZ:00005852]", - "Djibouti [GAZ:00000582]", - "Dominica [GAZ:00006890]", - "Dominican Republic [GAZ:00003952]", - "Ecuador [GAZ:00002912]", - "Egypt [GAZ:00003934]", - "El Salvador [GAZ:00002935]", - "Equatorial Guinea [GAZ:00001091]", - "Eritrea [GAZ:00000581]", - "Estonia [GAZ:00002959]", - "Eswatini [GAZ:00001099]", - "Ethiopia [GAZ:00000567]", - "Europa Island [GAZ:00005811]", - "Falkland Islands (Islas Malvinas) [GAZ:00001412]", - "Faroe Islands [GAZ:00059206]", - "Fiji [GAZ:00006891]", - "Finland [GAZ:00002937]", - "France [GAZ:00003940]", - "French Guiana [GAZ:00002516]", - "French Polynesia [GAZ:00002918]", - "French Southern and Antarctic Lands [GAZ:00003753]", - "Gabon [GAZ:00001092]", - "Gambia [GAZ:00000907]", - "Gaza Strip [GAZ:00009571]", - "Georgia [GAZ:00004942]", - "Germany [GAZ:00002646]", - "Ghana [GAZ:00000908]", - "Gibraltar [GAZ:00003987]", - "Glorioso Islands [GAZ:00005808]", - "Greece [GAZ:00002945]", - "Greenland [GAZ:00001507]", - "Grenada [GAZ:02000573]", - "Guadeloupe [GAZ:00067142]", - "Guam [GAZ:00003706]", - "Guatemala [GAZ:00002936]", - "Guernsey [GAZ:00001550]", - "Guinea [GAZ:00000909]", - "Guinea-Bissau [GAZ:00000910]", - "Guyana [GAZ:00002522]", - "Haiti [GAZ:00003953]", - "Heard Island and McDonald Islands [GAZ:00009718]", - "Honduras [GAZ:00002894]", - "Hong Kong [GAZ:00003203]", - "Howland Island [GAZ:00007120]", - "Hungary [GAZ:00002952]", - "Iceland [GAZ:00000843]", - "India [GAZ:00002839]", - "Indonesia [GAZ:00003727]", - "Iran [GAZ:00004474]", - "Iraq [GAZ:00004483]", - "Ireland [GAZ:00002943]", - "Isle of Man [GAZ:00052477]", - "Israel [GAZ:00002476]", - "Italy [GAZ:00002650]", - "Jamaica [GAZ:00003781]", - "Jan Mayen [GAZ:00005853]", - "Japan [GAZ:00002747]", - "Jarvis Island [GAZ:00007118]", - "Jersey [GAZ:00001551]", - "Johnston Atoll [GAZ:00007114]", - "Jordan [GAZ:00002473]", - "Juan de Nova Island [GAZ:00005809]", - "Kazakhstan [GAZ:00004999]", - "Kenya [GAZ:00001101]", - "Kerguelen Archipelago [GAZ:00005682]", - "Kingman Reef [GAZ:00007116]", - "Kiribati [GAZ:00006894]", - "Kosovo [GAZ:00011337]", - "Kuwait [GAZ:00005285]", - "Kyrgyzstan [GAZ:00006893]", - "Laos [GAZ:00006889]", - "Latvia [GAZ:00002958]", - "Lebanon [GAZ:00002478]", - "Lesotho [GAZ:00001098]", - "Liberia [GAZ:00000911]", - "Libya [GAZ:00000566]", - "Liechtenstein [GAZ:00003858]", - "Line Islands [GAZ:00007144]", - "Lithuania [GAZ:00002960]", - "Luxembourg [GAZ:00002947]", - "Macau [GAZ:00003202]", - "Madagascar [GAZ:00001108]", - "Malawi [GAZ:00001105]", - "Malaysia [GAZ:00003902]", - "Maldives [GAZ:00006924]", - "Mali [GAZ:00000584]", - "Malta [GAZ:00004017]", - "Marshall Islands [GAZ:00007161]", - "Martinique [GAZ:00067143]", - "Mauritania [GAZ:00000583]", - "Mauritius [GAZ:00003745]", - "Mayotte [GAZ:00003943]", - "Mexico [GAZ:00002852]", - "Micronesia [GAZ:00005862]", - "Midway Islands [GAZ:00007112]", - "Moldova [GAZ:00003897]", - "Monaco [GAZ:00003857]", - "Mongolia [GAZ:00008744]", - "Montenegro [GAZ:00006898]", - "Montserrat [GAZ:00003988]", - "Morocco [GAZ:00000565]", - "Mozambique [GAZ:00001100]", - "Myanmar [GAZ:00006899]", - "Namibia [GAZ:00001096]", - "Nauru [GAZ:00006900]", - "Navassa Island [GAZ:00007119]", - "Nepal [GAZ:00004399]", - "Netherlands [GAZ:00002946]", - "New Caledonia [GAZ:00005206]", - "New Zealand [GAZ:00000469]", - "Nicaragua [GAZ:00002978]", - "Niger [GAZ:00000585]", - "Nigeria [GAZ:00000912]", - "Niue [GAZ:00006902]", - "Norfolk Island [GAZ:00005908]", - "North Korea [GAZ:00002801]", - "North Macedonia [GAZ:00006895]", - "North Sea [GAZ:00002284]", - "Northern Mariana Islands [GAZ:00003958]", - "Norway [GAZ:00002699]", - "Oman [GAZ:00005283]", - "Pakistan [GAZ:00005246]", - "Palau [GAZ:00006905]", - "Panama [GAZ:00002892]", - "Papua New Guinea [GAZ:00003922]", - "Paracel Islands [GAZ:00010832]", - "Paraguay [GAZ:00002933]", - "Peru [GAZ:00002932]", - "Philippines [GAZ:00004525]", - "Pitcairn Islands [GAZ:00005867]", - "Poland [GAZ:00002939]", - "Portugal [GAZ:00004126]", - "Puerto Rico [GAZ:00006935]", - "Qatar [GAZ:00005286]", - "Republic of the Congo [GAZ:00001088]", - "Reunion [GAZ:00003945]", - "Romania [GAZ:00002951]", - "Ross Sea [GAZ:00023304]", - "Russia [GAZ:00002721]", - "Rwanda [GAZ:00001087]", - "Saint Helena [GAZ:00000849]", - "Saint Kitts and Nevis [GAZ:00006906]", - "Saint Lucia [GAZ:00006909]", - "Saint Pierre and Miquelon [GAZ:00003942]", - "Saint Martin [GAZ:00005841]", - "Saint Vincent and the Grenadines [GAZ:02000565]", - "Samoa [GAZ:00006910]", - "San Marino [GAZ:00003102]", - "Sao Tome and Principe [GAZ:00006927]", - "Saudi Arabia [GAZ:00005279]", - "Senegal [GAZ:00000913]", - "Serbia [GAZ:00002957]", - "Seychelles [GAZ:00006922]", - "Sierra Leone [GAZ:00000914]", - "Singapore [GAZ:00003923]", - "Sint Maarten [GAZ:00012579]", - "Slovakia [GAZ:00002956]", - "Slovenia [GAZ:00002955]", - "Solomon Islands [GAZ:00005275]", - "Somalia [GAZ:00001104]", - "South Africa [GAZ:00001094]", - "South Georgia and the South Sandwich Islands [GAZ:00003990]", - "South Korea [GAZ:00002802]", - "South Sudan [GAZ:00233439]", - "Spain [GAZ:00003936]", - "Spratly Islands [GAZ:00010831]", - "Sri Lanka [GAZ:00003924]", - "State of Palestine [GAZ:00002475]", - "Sudan [GAZ:00000560]", - "Suriname [GAZ:00002525]", - "Svalbard [GAZ:00005396]", - "Swaziland [GAZ:00001099]", - "Sweden [GAZ:00002729]", - "Switzerland [GAZ:00002941]", - "Syria [GAZ:00002474]", - "Taiwan [GAZ:00005341]", - "Tajikistan [GAZ:00006912]", - "Tanzania [GAZ:00001103]", - "Thailand [GAZ:00003744]", - "Timor-Leste [GAZ:00006913]", - "Togo [GAZ:00000915]", - "Tokelau [GAZ:00260188]", - "Tonga [GAZ:00006916]", - "Trinidad and Tobago [GAZ:00003767]", - "Tromelin Island [GAZ:00005812]", - "Tunisia [GAZ:00000562]", - "Turkey [GAZ:00000558]", - "Turkmenistan [GAZ:00005018]", - "Turks and Caicos Islands [GAZ:00003955]", - "Tuvalu [GAZ:00009715]", - "USA [GAZ:00002459]", - "Uganda [GAZ:00001102]", - "Ukraine [GAZ:00002724]", - "United Arab Emirates [GAZ:00005282]", - "United Kingdom [GAZ:00002637]", - "Uruguay [GAZ:00002930]", - "Uzbekistan [GAZ:00004979]", - "Vanuatu [GAZ:00006918]", - "Venezuela [GAZ:00002931]", - "Viet Nam [GAZ:00003756]", - "Virgin Islands [GAZ:00003959]", - "Wake Island [GAZ:00007111]", - "Wallis and Futuna [GAZ:00007191]", - "West Bank [GAZ:00009572]", - "Western Sahara [GAZ:00000564]", - "Yemen [GAZ:00005284]", - "Zambia [GAZ:00001107]", - "Zimbabwe [GAZ:00001106]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001181", - "type": "string", - "description": "The country of origin of the sample.", - "examples": ["South Africa [GAZ:00001094]"], - "classification":"Sample collection and processing", - "label":"Geo Loc Autonomic Country" - }, - "geo_loc_state": { - "examples": ["Western Cape"], - "ontology": "GENEPIO:0001185", - "type": "string", - "description": "The state/province/territory of origin of the sample.", - "classification":"Sample collection and processing", - "label":"Geo Loc Autonomic Community" - }, - "organism": { - "Enums": [ - "Coronaviridae [NCBITaxon:11118]", - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001191", - "type": "string", - "description": "Taxonomic name of the organism.", - "examples": [ - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", - ], - "classification":"Sample collection and processing", - "label":"Organism" - }, - "isolate": { - "examples": ["SARS-CoV-2/human/USA/CA-CDPH-001/2020"], - "ontology": "GENEPIO:0001644", - "type": "string", - "description": "Identifier of the specific isolate.", - "clasification":"Sample collection and processing", - "label":"Isolate" - }, - "host_scientific_name": { - "Enums": [ - "Bos taurus [NCBITaxon:9913]", - "Canis lupus familiaris [NCBITaxon:9615]", - "Chiroptera [NCBITaxon:9397]", - "Columbidae [NCBITaxon:8930]", - "Felis catus [NCBITaxon:9685]", - "Gallus gallus [NCBITaxon:9031]", - "Homo sapiens [NCBITaxon:9606]", - "Manis [NCBITaxon:9973]", - "Manis javanica [NCBITaxon:9974]", - "Neovison vison [NCBITaxon:452646]", - "Panthera leo [NCBITaxon:9689]", - "Panthera tigris [NCBITaxon:9694]", - "Rhinolophidae [NCBITaxon:58055]", - "Rhinolophus affinis [NCBITaxon:59477]", - "Sus scrofa domesticus [NCBITaxon:9825]", - "Viverridae [NCBITaxon:9673]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001387", - "type": "string", - "description": "The taxonomic, or scientific name of the host.", - "examples": ["Homo sapiens [NCBITaxon:9606]"], - "clasification":"Host information", - "label":"Host Scientific Name" - }, - "host_disease": { - "Enums": [ - "COVID-19 [MONDO:0100096]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001391", - "type": "string", - "description": "The name of the disease experienced by the host.", - "examples": ["COVID-19 [MONDO:0100096]"] - }, - "sequencing_instrument_model": { - "Enums": [ - "Illumina sequencing instrument [GENEPIO:0100105]", - "Illumina Genome Analyzer [GENEPIO:0100106]", - "Illumina Genome Analyzer II [GENEPIO:0100107]", - "Illumina Genome Analyzer IIx [GENEPIO:0100108]", - "Illumina HiScanSQ [GENEPIO:0100109]", - "Illumina HiSeq [GENEPIO:0100110]", - "Illumina HiSeq X [GENEPIO:0100111]", - "Illumina HiSeq X Five [GENEPIO:0100112]", - "Illumina HiSeq X Ten [GENEPIO:0100113]", - "Illumina HiSeq 1000 [GENEPIO:0100114]", - "Illumina HiSeq 1500 [GENEPIO:0100115]", - "Illumina HiSeq 2000 [GENEPIO:0100116]", - "Illumina HiSeq 2500 [GENEPIO:0100117]", - "Illumina HiSeq 3000 [GENEPIO:0100118]", - "Illumina HiSeq 4000 [GENEPIO:0100119]", - "Illumina iSeq [GENEPIO:0100120]", - "Illumina iSeq 100 [GENEPIO:0100121]", - "Illumina NovaSeq [GENEPIO:0100122]", - "Illumina NovaSeq 6000 [GENEPIO:0100123]", - "Illumina MiniSeq [GENEPIO:0100124]", - "Illumina MiSeq [GENEPIO:0100125]", - "Illumina NextSeq [GENEPIO:0100126]", - "Illumina NextSeq 500 [GENEPIO:0100127]", - "Illumina NextSeq 550 [GENEPIO:0100128]", - "Illumina NextSeq 2000 [GENEPIO:0100129]", - "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", - "PacBio RS [GENEPIO:0100131]", - "PacBio RS II [GENEPIO:0100132]", - "PacBio Sequel [GENEPIO:0100133]", - "PacBio Sequel II [GENEPIO:0100134]", - "Ion Torrent sequencing instrument [GENEPIO:0100135]", - "Ion Torrent PGM [GENEPIO:0100136]", - "Ion Torrent Proton [GENEPIO:0100137]", - "Ion Torrent S5 XL [GENEPIO:0100138]", - "Ion Torrent S5 [GENEPIO:0100139]", - "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", - "Oxford Nanopore GridION [GENEPIO:0100141]", - "Oxford Nanopore MinION [GENEPIO:0100142]", - "Oxford Nanopore PromethION [GENEPIO:0100143]", - "BGI Genomics sequencing instrument [GENEPIO:0100144]", - "BGI SEQ-500 [GENEPIO:0100145]", - "MGI sequencing instrument [GENEPIO:0100146]", - "MGI DNBSEQ-T7 [GENEPIO:0100147]", - "MGI DNBSEQ-G400 [GENEPIO:0100148]", - "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", - "MGI DNBSEQ-G50 [GENEPIO:0100150]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001452", - "type": "string", - "description": "The model of the sequencing instrument used.", - "examples": ["Oxford Nanopore MinION [GENEPIO:0100142]"], - "classification":"Sequencing", - "label":"Sequencing Instrument Model" - }, - "sequencing_instrument_platform": { - "examples": ["MinIon"], - "ontology": "0", - "type": "string", - "description": "The model of the sequencing instrument used.", - "label":"Sequencing Platforms " - }, - "consensus_sequence_software_name": { - "examples": ["Ivar"], - "ontology": "GENEPIO:0001463", - "type": "string", - "description": "The name of software used to generate the consensus sequence." - }, - "consensus_sequence_software_version": { - "examples": ["1.3"], - "ontology": "GENEPIO:0001469", - "type": "string", - "description": "The version of the software used to generate the consensus sequence." - }, - "submitting_lab_sequence_id": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Sample ID given by the submitting laboratory" - }, - "bioproject_umbrella_accession_ENA": { - "examples": ["PRJNA623807"], - "ontology": "GENEPIO:0001133", - "type": "string", - "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", - "clasification":"Database Identifiers" - }, - "bioproject_accession_ENA": { - "examples": ["PRJNA12345"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", - "clasification":"Database Identifiers" - }, - "biosample_accession_ENA": { - "examples": ["SAMN14180202"], - "ontology": "GENEPIO:0001139", - "type": "string", - "description": "The identifier assigned to a BioSample in INSDC archives.", - "clasification":"Database Identifiers" - }, - "sra_accession": { - "examples": ["SRR11177792"], - "ontology": "GENEPIO:0001142", - "type": "string", - "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "clasification":"Database Identifiers" - }, - "genBank/ENA/DDBJ_accession": { - "examples": ["MN908947.3"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", - "clasification":"Database Identifiers" - }, - "gisaid_accession": { - "examples": ["EPI_ISL_123456"], - "ontology": "GENEPIO:0001147", - "type": "string", - "description": "The GISAID accession number assigned to the sequence.", - "clasification":"Database Identifiers" - }, - "virus_name": { - "examples": ["hCoV-19/Canada/prov_rona_99/2020"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The user-defined GISAID virus name assigned to the sequence.", - "clasification":"Database Identifiers" - }, - "collecting_institution_email": { - "examples": ["johnnyblogs@lab.ca"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The email address of the contact responsible for follow-up regarding the sample.", - "clasification":"Sample collection and processing" - }, - "collecting_institution_address": { - "examples": ["655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada"], - "ontology": "GENEPIO:0001158", - "type": "string", - "description": "The mailing address of the agency submitting the sample.", - "clasification":"Sample collection and processing" - }, - "submitting_institution_email": { - "examples": ["RespLab@lab.ca"], - "ontology": "GENEPIO:0001165", - "type": "string", - "description": "The email address of the contact responsible for follow-up regarding the sequence.", - "clasification":"Sample collection and processing" - }, - "submitting_institution_address": { - "examples": ["123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The mailing address of the agency submitting the sequence.", - "clasification":"Sample collection and processing" - }, - "sample_received_date": { - "examples": ["3/21/2020"], - "ontology": "GENEPIO:0001179", - "type": "string", - "description": "The date on which the sample was received.", - "format":"date", - "clasification":"Sample collection and processing" - }, - "shipping_date": { - "examples": ["3/20/2020"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The date on which the sample was sent.", - "format":"date", - "clasification":"Sample collection and processing" - }, - "results_emission_date": { - "examples": ["3/23/2020"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The date on which the results were emitted.", - "format":"date", - "clasification":"Sample collection and processing" - }, - "geo_loc_region": { - "examples": ["Derbyshire"], - "ontology": "GENEPIO:0100280", - "type": "string", - "description": "The county/region of origin of the sample.", - "clasification":"Sample collection and processing", - "label":"Geo Loc Province" - }, - "geo_loc_city": { - "examples": ["Vancouver"], - "ontology": "GENEPIO:0001189", - "type": "string", - "description": "The city of origin of the sample.", - "clasification":"Sample collection and processing", - "label":"Geo Loc City" - }, - "geo_loc_latitude": { - "examples": ["38.98 N"], - "ontology": "OBI:0001620", - "type": "string", - "description": "The latitude coordinates of the geographical location of sample collection.", - "clasification":"Sample collection and processing", - "label":"Geo Loc Latitude", - }, - "geo_loc_longitude": { - "examples": ["77.11 W"], - "ontology": "OBI:0001621", - "type": "string", - "description": "The longitude coordinates of the geographical location of sample collection.", - "clasification":"Sample collection and processing", - "label":"Geo Loc Longitude" - }, - "anatomical_material": { - "Enums": [ - "Blood [UBERON:0000178]", - "Fluid [UBERON:0006314]", - "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", - "Fluid (Pericardial) [UBERON:0002409]", - "Fluid (Pleural) [UBERON:0001087]", - "Fluid (Vaginal) [UBERON:0036243]", - "Fluid (Amniotic) [UBERON:0000173]", - "Saliva [UBERON:0001836]", - "Tissue [UBERON:0000479]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001211", - "type": "string", - "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "examples": ["Blood [UBERON:0000178]"], - "classification":"Sample collection and processing", - "label":"Organism Substance" - }, - "anatomical_part": { - "Enums": [ - "Anus [UBERON:0001245]", - "Duodenum [UBERON:0002114]", - "Eye [UBERON:0000970]", - "Intestine [UBERON:0000160]", - "Lower respiratory tract [UBERON:0001558]", - "Bronchus [UBERON:0002185]", - "Lung [UBERON:0002048]", - "Bronchiole [UBERON:0002186]", - "Alveolar sac [UBERON:0002169]", - "Pleural sac [UBERON:0009778]", - "Pleural cavity [UBERON:0002402]", - "Trachea [UBERON:0003126]", - "Rectum [UBERON:0001052]", - "Skin [UBERON:0001003]", - "Stomach [UBERON:0000945]", - "Upper respiratory tract [UBERON:0001557]", - "Anterior Nares [UBERON:2001427]", - "Esophagus [UBERON:0001043]", - "Ethmoid sinus [UBERON:0002453]", - "Nasal Cavity [UBERON:0001707]", - "Middle Nasal Turbinate [UBERON:0005921]", - "Inferior Nasal Turbinate [UBERON:0005922]", - "Nasopharynx (NP) [UBERON:0001728]", - "Oropharynx (OP) [UBERON:0001729]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001214", - "type": "string", - "description": "An anatomical part of an organism e.g. oropharynx. ", - "examples": ["Nasopharynx (NP) [UBERON:0001728]"], - "classification":"Sample collection and processing", - "label":"Anatomical Structure" - }, - "body_product": { - "Enums": [ - "Breast Milk [UBERON:0001913]", - "Feces [UBERON:0001988]", - "Mucus [UBERON:0000912]", - "Semen [UBERON:0006530]", - "Sputum [UBERON:0007311]", - "Sweat [UBERON:0001089]", - "Tear [UBERON:0001827]", - "Urine [UBERON:0001088]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001216", - "type": "string", - "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", - "examples": ["Feces [UBERON:0001988]"], - "classification":"Sample collection and processing", - "label":"Body product" - }, - "environmental_material": { - "Enums": [ - "Air vent [ENVO:03501208]", - "Banknote [ENVO:00003896]", - "Bed rail [ENVO:03501209]", - "Building Floor [ENVO:01000486]", - "Cloth [ENVO:02000058]", - "Control Panel [ENVO:03501210]", - "Door [ENVO:03501220]", - "Door Handle [ENVO:03501211]", - "Face Mask [OBI:0002787]", - "Face Shield [OBI:0002791]", - "Food [FOODON:00002403]", - "Food Packaging [FOODON:03490100]", - "Glass [ENVO:01000481]", - "Handrail [ENVO:03501212]", - "Hospital Gown [OBI:0002796]", - "Light Switch [ENVO:03501213]", - "Locker [ENVO:03501214]", - "N95 Mask [OBI:0002790]", - "Nurse Call Button [ENVO:03501215]", - "Paper [ENVO:03501256]", - "Particulate Matter [ENVO:01000060]", - "Plastic [ENVO:01000404]", - "PPE Gown [GENEPIO:0100025]", - "Sewage [ENVO:00002018]", - "Sink [ENVO:01000990]", - "Soil [ENVO:00001998]", - "Stainless Steel [ENVO:03501216]", - "Tissue Paper [ENVO:03501217]", - "Toilet Bowl [ENVO:03501218]", - "Water [ENVO:00002006]", - "Wastewater [ENVO:00002001]", - "Window [ENVO:03501219]", - "Wood [ENVO:00002040]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001223", - "type": "string", - "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", - "examples": ["Face Mask [OBI:0002787]"], - "clasification":"Sample collection and processing", - "label":"Environmental Material" - }, - "environmental_site": { - "Enums": [ - "Acute care facility [ENVO:03501135]", - "Animal house [ENVO:00003040]", - "Bathroom [ENVO:01000422]", - "Clinical assessment centre [ENVO:03501136]", - "Conference venue [ENVO:03501127]", - "Corridor [ENVO:03501121]", - "Daycare [ENVO:01000927]", - "Emergency room (ER) [ENVO:03501145]", - "Family practice clinic [ENVO:03501186]", - "Group home [ENVO:03501196]", - "Homeless shelter [ENVO:03501133]", - "Hospital [ENVO:00002173]", - "Intensive Care Unit (ICU) [ENVO:03501152]", - "Long Term Care Facility [ENVO:03501194]", - "Patient room [ENVO:03501180]", - "Prison [ENVO:03501204]", - "Production Facility [ENVO:01000536]", - "School [ENVO:03501130]", - "Sewage Plant [ENVO:00003043]", - "Subway train [ENVO:03501109]", - "Wet market [ENVO:03501198]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001232", - "type": "string", - "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", - "examples": ["Hospital [ENVO:00002173]"], - "classification":"Sample collection and processing", - "label":"Anthropogenic Geographic Feature" - }, - "collection_device": { - "Enums": [ - "Air filter [ENVO:00003968]", - "Blood Collection Tube [OBI:0002859]", - "Bronchoscope [OBI:0002826]", - "Collection Container [OBI:0002088]", - "Collection Cup [GENEPIO:0100026]", - "Fibrobronchoscope Brush [OBI:0002825]", - "Filter [GENEPIO:0100103]", - "Fine Needle [OBI:0002827]", - "Microcapillary tube [OBI:0002858]", - "Micropipette [OBI:0001128]", - "Needle [OBI:0000436]", - "Serum Collection Tube [OBI:0002860]", - "Sputum Collection Tube [OBI:0002861]", - "Suction Catheter [OBI:0002831]", - "Swab [GENEPIO:0100027]", - "Urine Collection Tube [OBI:0002862]", - "Virus Transport Medium [OBI:0002866]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001234", - "type": "string", - "description": "The instrument or container used to collect the sample e.g. swab.", - "examples": ["Swab [GENEPIO:0100027]"], - "clasification":"Sample collection and processing", - "label":"Collection Device" - }, - "collection_method": { - "Enums": [ - "Amniocentesis [NCIT:C52009]", - "Aspiration [NCIT:C15631]", - "Suprapubic Aspiration [GENEPIO:0100028]", - "Tracheal Aspiration [GENEPIO:0100029]", - "Vacuum Aspiration [GENEPIO:0100030]", - "Biopsy [OBI:0002650]", - "Needle Biopsy [OBI:0002651]", - "Filtration [OBI:0302885]", - "Air Filtration [GENEPIO:0100031]", - "Lavage [OBI:0600044]", - "Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]", - "Gastric Lavage [GENEPIO:0100033]", - "Lumbar Puncture [NCIT:C15327]", - "Necropsy [MMO:0000344]", - "Phlebotomy [NCIT:C28221]", - "Rinsing [GENEPIO:0002116]", - "Saline gargle (mouth rinse and gargle) [GENEPIO:0100034]", - "Scraping [GENEPIO:0100035]", - "Swabbing [GENEPIO:0002117]", - "Finger Prick [GENEPIO:0100036]", - "Washout Tear Collection [GENEPIO:0100038]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001241", - "type": "string", - "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", - "examples": ["Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]"], - "clasification":"Sample collection and processing", - "label":"Collection Method" - }, - "collection_protocol": { - "examples": ["SC2SamplingProtocol 1.2"], - "ontology": "GENEPIO:0001243", - "type": "string", - "description": "The name and version of a particular protocol used for sampling.", - "clasification":"Sample collection and processing", - "label":"Collection Protocol" - }, - "specimen_processing": { - "Enums": [ - "Virus Passage [GENEPIO:0100039]", - "RNA Re-Extraction (Post RT-PCR) [GENEPIO:0100040]", - "Specimens Pooled [OBI:0600016]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001253", - "type": "string", - "description": "Any processing applied to the sample during or after receiving the sample. ", - "examples": ["Virus Passage [GENEPIO:0100039]"], - "classification":"Sample collection and processing", - "label":"Specimen Processing" - }, - "lab_host": { - "Enums": [ - "293/ACE2 Cell Line [GENEPIO:0100041]", - "Caco2 Cell Line [BTO:0000195]", - "Calu3 Cell Line [BTO:0002750]", - "EFK3B Cell Line [GENEPIO:0100042]", - "HEK293T Cell Line [BTO:0002181]", - "HRCE Cell Line [GENEPIO:0100043]", - "Huh7 Cell Line [BTO:0001950]", - "LLCMk2 Cell Line [CLO:0007330]", - "MDBK Cell Line [BTO:0000836]", - "NHBE Cell Line [BTO:0002924]", - "PK-15 Cell Line [BTO:0001865]", - "RK-13 Cell Line [BTO:0002909]", - "U251 Cell Line [BTO:0002035]", - "Vero Cell Line [BTO:0001444]", - "Vero E6 Cell Line [BTO:0004755]", - "Vero E6/TMPRSS2 Cell Line [GENEPIO:0100044]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001255", - "type": "string", - "description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.", - "examples": ["Vero E6 Cell Line [BTO:0004755]"], - "classification":"Sample collection and processing", - "label":"Lab passage Host" - }, - "passage_number": { - "examples": ["3"], - "ontology": "GENEPIO:0001261", - "type": "string", - "description": "Number of passages.", - "clasification":"Sample collection and processing", - "label":"Passage Number" - }, - "passage_method": { - "examples": ["AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain."], - "ontology": "GENEPIO:0001264", - "type": "string", - "description": "Description of how organism was passaged.", - "clasification":"Sample collection and processing", - "label":"Passage Method" - }, - "biomaterial_extracted": { - "Enums": [ - "mRNA (cDNA) [OBI:0002754]", - "RNA (Total) [OBI:0000895]", - "RNA (Poly-A) [OBI:0000869]", - "RNA (Ribo-Depleted) [OBI:0002627]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001266", - "type": "string", - "description": "The biomaterial extracted from samples for the purpose of sequencing.", - "examples": ["RNA (Total) [OBI:0000895]"], - "classification":"Sample collection and processing", - "label":"Biomaterial Extracted" - }, - "tax_id": { - "examples": ["probably 2697049 in all cases"], - "ontology": "GENEPIO_0001800", - "type": "string", - "description": "The NCBITaxon identifier for the organism being sequenced.", - "clasification":"Sample collection and processing", - "label":"Tax ID" - }, - "common_name": { - "examples": [""], - "ontology": "BU_ISCIII:003", - "type": "string", - "description": "The common name of the organism.", - "clasification":"Sample collection and processing", - "label":"Common name" - }, - "center_name": { - "examples": [" KAROLINSKA INSITUTET"], - "ontology": "NCIT_C19983", - "type": "string", - "description": "The name of the institution", - "clasification":"Sample collection and processing", - "label":"Center Name" - }, - "virus_id": { - "examples": [""], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "The user-defined name for the sample.", - "clasification":"Database Identifiers" - }, - "host_common_name": { - "Enums": [ - "Human [NCBITaxon:9606]", - "Bat [NCBITaxon:9397]", - "Cat [NCBITaxon:9685]", - "Chicken [NCBITaxon:9031]", - "Civet [NCBITaxon:9673]", - "Cow [NCBITaxon:9913]", - "Dog [NCBITaxon:9615]", - "Lion [NCBITaxon:9689]", - "Mink [NCBITaxon:452646]", - "Pangolin [NCBITaxon:9973]", - "Pig [NCBITaxon:9825]", - "Pigeon [NCBITaxon:8930]", - "Tiger [NCBITaxon:9694]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001386", - "type": "string", - "description": "The commonly used name of the host.", - "examples": ["Human [NCBITaxon:9606]"], - "classification":"Host information", - "label":"Host Common Name" - }, - "outbreak": { - "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], - "ontology": "GENEPIO:0001417", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", - "label":"Outbreak Exposure Event Location" - }, - "additional_host_information": { - "examples": ["e.g. Patient infected while traveling in …."], - "ontology": "0", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification":"Host information", - "label":"Additional Host Information" - }, - "purpose_of_sequencing": { - "Enums": [ - "Baseline surveillance (random sampling) [GENEPIO:0100005]", - "Targeted surveillance (non-random sampling) [GENEPIO:0100006]", - "Priority surveillance projects [GENEPIO:0100007]", - "Screening for Variants of Concern (VOC) [GENEPIO:0100008]", - "Sample has epidemiological link to Variant of Concern (VoC) [GENEPIO:0100273]", - "Sample has epidemiological link to Omicron Variant [GENEPIO:0100274]", - "Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]", - "Re-infection surveillance [GENEPIO:0100010]", - "Vaccine escape surveillance [GENEPIO:0100011]", - "Travel-associated surveillance [GENEPIO:0100012]", - "Domestic travel surveillance [GENEPIO:0100013]", - "Interstate/ interprovincial travel surveillance [GENEPIO:0100275]", - "Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276]", - "International travel surveillance [GENEPIO:0100014]", - "Surveillance of international border crossing by air travel or ground transport [GENEPIO:0100015]", - "Surveillance of international border crossing by air travel [GENEPIO:0100016]", - "Surveillance of international border crossing by ground transport [GENEPIO:0100017]", - "Surveillance from international worker testing [GENEPIO:0100018]", - "Cluster/Outbreak investigation [GENEPIO:0100019]", - "Multi-jurisdictional outbreak investigation [GENEPIO:0100020]", - "Intra-jurisdictional outbreak investigation [GENEPIO:0100021]", - "Research [GENEPIO:0100022]", - "Viral passage experiment [GENEPIO:0100023]", - "Protocol testing [GENEPIO:0100024]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001445", - "type": "string", - "description": "The reason that the sample was sequenced.", - "examples": ["Baseline surveillance (random sampling) [GENEPIO:0100005]"], - "classification":"Sequencing", - "label":"Purpose of Sequencing" - }, - "purpose_of_sequencing_details": { - "Enums": [ - "Screened for S gene target failure (S dropout)", - "Screened for mink variants", - "Screened for B.1.1.7 variant", - "Screened for B.1.135 variant", - "Screened for P.1 variant", - "Screened due to travel history", - "Screened due to close contact with infected individual", - "Assessing public health control measures", - "Determining early introductions and spread", - "Investigating airline-related exposures", - "Investigating temporary foreign worker", - "Investigating remote regions", - "Investigating health care workers", - "Investigating schools/universities", - "Investigating reinfection" - ], - "ontology": "GENEPIO:0001446", - "type": "string", - "description": "The description of why the sample was sequenced providing specific details.", - "examples": ["Screened for S gene target failure (S dropout)"], - "clasification":"Sequencing", - "label":"Purpose Of Sequencing Details" - }, - "sequencing_date": { - "examples": ["4/26/2021"], - "ontology": "GENEPIO:0001447", - "type": "string", - "description": "The date the sample was sequenced.", - "format":"date", - "clasification":"Sequencing", - "label":"Sequencing date" - }, - "rna_extraction_protocol": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Rna Extraction Protocol" - }, - "library_kit": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Library Kit" - }, - "library_id": { - "examples": ["XYZ_123345"], - "ontology": "GENEPIO:0001448", - "type": "string", - "description": "The user-specified identifier for the library prepared for sequencing.", - "clasification":"Sequencing", - "labe":"Library Id" - }, - "enrichment_protocol": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Enrichment_protocol" - }, - "if_enrichment_protocol_is_other_specify": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"If Enrichment Protocol Is Other, Specify" - }, - "amplicon protocol": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Amplicon Protocol" - }, - "if_amplicon_protocol_if_other_especify": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "labe":"If Amplicon Protocol If Other, Especify" - }, - "amplicon_version": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Amplicon Version" - }, - "amplicon_size": { - "examples": ["300bp"], - "ontology": "GENEPIO:0001449", - "type": "string", - "description": "The length of the amplicon generated by PCR amplification.", - "clasification":"Sequencing", - "label":"Amplicon Size" - }, - "was_phix_used?": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Was Phix Used" - }, - "number_of_samples_in_run": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Number Of Samples In Run" - }, - "flowcell_kit": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "labe":"Flowcell Kit" - }, - "runID": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"RunID" - }, - "sequencing_platforms": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Sequencing Platforms " - }, - "library_preparation_kit": { - "examples": ["Nextera XT"], - "ontology": "GENEPIO:0001450", - "type": "string", - "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", - "clasification":"Sequencing", - "label":"Library Preparation Kit" - }, - "flow_cell_barcode": { - "examples": ["FAB06069"], - "ontology": "GENEPIO:0001451", - "type": "string", - "description": "The barcode of the flow cell used for sequencing.", - "clasification":"Sequencing", - "label":"Flow Cell Barcode" - }, - "sequencing_protocol_name": { - "examples": ["1D_DNA_MinION, ARTIC Network Protocol V3"], - "ontology": "GENEPIO:0001453", - "type": "string", - "description": "The name and version number of the sequencing protocol used.", - "clasification":"Sequencing", - "label":"Sequencing Protocol Name" - }, - "sequencing_protocol": { - "examples": ["Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits."], - "ontology": "GENEPIO:0001454", - "type": "string", - "description": "The protocol used to generate the sequence.", - "clasification":"Sequencing", - "label":"Sequencing Protocol" - }, - "sequencing_kit_number": { - "examples": ["AB456XYZ789"], - "ontology": "GENEPIO:0001455", - "type": "string", - "description": "The manufacturer's kit number.", - "clasification":"Sequencing", - "label":"Sequencing Kit Number" - }, - "amplicon_pcr_primer_scheme": { - "examples": ["https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv"], - "ontology": "GENEPIO:0001456", - "type": "string", - "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", - "clasification":"Sequencing", - "label":"Amplicon Pcr Primer Scheme" - }, - "library_selection": { - "examples": ["RANDOM PCR"], - "ontology": "GENPIO_0001940", - "type": "string", - "description": "Library capture method.", - "clasification":"Sequencing", - "label":"Capture method" - }, - "library_strategy": { - "Enums": ["Bisultife-Seq strategy [GENPIO:0001975]", - "CTS strategy [GENPIO:0001978]", - "ChIP-Seq strategy [GENPIO:0001979]", - "DNase-Hypersensitivity strategy [GENPIO:0001980]", - "EST strategy [GENPIO:0001981]", - "FL-cDNA strategy [GENPIO:0001983]", - "MB-Seq strategy [GENPIO:0001984]", - "MNase-Seq strategy [GENPIO:0001985]", - "MRE-Seq strategy [GENPIO:0001986]", - "MeDIP-Seq strategy [GENPIO:0001987]", - "RNA-Seq strategy [GENPIO:0001990]", - "WCS strategy [GENPIO:0001991]", - "WGS strategy [GENPIO:0001992]", - "WXS strategy [GENPIO:0001993]", - "amplicon strategy [GENPIO:0001974]", - "clone end strategy [GENPIO:0001976]", - "clone strategy [GENPIO:0001977]", - "finishing strategy [GENPIO:0001982]", - "other library strategy [GENPIO:0001988]", - "pool clone strategy [GENPIO:0001989]", - ], - "examples": ["WGS"], - "ontology": "GENPIO_0001973", - "type": "string", - "description": "Overall sequencing strategy or approach.", - "clasification":"Sequencing", - "label":"Sequencing technique" - }, - "library_layout": { - "examples": ["PAIRED"], - "ontology":"BU_ISCIII:007", - "type": "string", - "description": "Single or paired.", - "clasification":"Sequencing", - "label":"Library Layout" - }, - "library_name": { - "examples": ["P17157_1007"], - "ontology": "GENEPIO_0001995", - "type": "string", - "description": "Name of the used library", - "clasification":"Sequencing", - "label":"LibraryName" - }, - "nominal_length ": { - "examples": ["350"], - "ontology": "GENEPIO_0000076", - "type": "string", - "description": "", - "clasification":"Sequencing", - "label":"Nominal Length" - }, - "raw_sequence_data_processing_method": { - "examples": ["Porechop 0.2.3"], - "ontology": "GENEPIO:0001458", - "type": "string", - "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", - "clasification":"Bioinformatics and QC metrics", - "label":"Raw sequence data processin method" - }, - "dehosting_method": { - "examples": ["Nanostripper"], - "ontology": "GENEPIO:0001459", - "type": "string", - "description": "The method used to remove host reads from the pathogen sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Dehosting Method" - }, - "assembly": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Assembly" - }, - "if_assembly_other": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"If assembly Is Other, Specify" - }, - "assembly_params": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Assambly params" - }, - "variant_calling": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Variant Calling" - }, - "if_variant_calling_other": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"If variant calling Is Other, Specify" - }, - "variant_calling_params": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Variant Calling params" - }, - "consensus_sequence_filepath": { - "examples": ["/User/Documents/RespLab/Data/ncov123assembly.fasta"], - "ontology": "GENEPIO:0001462", - "type": "string", - "description": "The filepath of the consesnsus sequence file.", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus sequence filepath" - }, - "consensus_sequence_software_name": { - "examples": ["Ivar"], - "ontology": "GENEPIO:0001463", - "type": "string", - "description": "The name of software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus sequence software name" - }, - "if_consensus_other": { - "examples": ["1.3"], - "ontology": "0", - "type": "string", - "description": "The version of the software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"If consensus Is Other, Specify" - }, - "consensus_sequence_software_version": { - "examples": ["1.3"], - "ontology": "GENEPIO:0001469", - "type": "string", - "description": "The version of the software used to generate the consensus sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus sequence software version" - }, - "consensus_criteria": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Consensus criteria" - }, - "quality_control_metrics": { - "examples": [""], - "ontology": "0", - "type": "string", - "description": "", - "clasification":"Bioinformatics and QC metrics", - "label":"Quality control metrics " - }, - "breadth_of_coverage_value": { - "examples": ["95%"], - "ontology": "GENEPIO:0001472", - "type": "string", - "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", - "clasification":"Bioinformatics and QC metrics", - "label":"Breadth of coverage value" - }, - "depth_of_coverage_value": { - "examples": ["400x"], - "ontology": "GENEPIO:0001474", - "type": "string", - "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "clasification":"Bioinformatics and QC metrics", - "label":"Depth of coverage value " - }, - "depth_of_coverage_threshold": { - "examples": ["100x"], - "ontology": "GENEPIO:0001475", - "type": "string", - "description": "The threshold used as a cut-off for the depth of coverage.", - "clasification":"Bioinformatics and QC metrics", - "label":"Depth of coverage threshold" - }, - "sequence_file_R1_fastq": { - "examples": ["ABC123_S1_L001_R1_001.fastq.gz"], - 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"ontology": "NCIT_C42790", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Experiment alias" - }, - "run_alias": { - "examples": ["e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "NCIT_C47911", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Run Alias" - }, - "fastq_bytes": { - "examples": ["e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1"], - "ontology": "NCIT_C48047", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq bytes" - }, - "fastq_md5": { - "examples": [""], - "ontology": "MS_1000568", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq md5" - }, - "fastq_ftp": { - "examples": [""], - "ontology": "PRIDE_0000469", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq ftp" - }, - "fastq_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "BU_ISCIII:032", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq aspera" - }, - "fastq_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "ENVO_01000807", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Fastq galaxy" - }, - "submitted_bytes": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz"], - "ontology": "NCIT_C172872", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted bytes " - }, - "submitted_md5": { - "examples": ["e.g 139853010;166270048"], - "ontology": "BU_ISCIII:035", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted md5" - }, - "submitted_ftp": { - "examples": ["e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a"], - "ontology": "BU_ISCIII:036", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted ftp" - }, - "submitted_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "BU_ISCIII:037", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted aspera" - }, - "submitted_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "BU_ISCIII:038", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted Galaxy" - }, - "submitted_format": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz"], - "ontology": "BU_ISCIII:039", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Submitted Format" - }, - "sra_bytes": { - "examples": ["e.g FASTQ;FASTQ"], - "ontology": "BU_ISCIII:040", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA bytes" - }, - "sra_md5": { - "examples": ["e.g 260236789"], - "ontology": "BU_ISCIII:041", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA md5" - }, - "sra_ftp": { - "examples": ["e.g 2cf0d467d6dc4ae0a5473774d54c059c"], - "ontology": "BU_ISCIII:042", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA ftp" - }, - "sra_aspera": { - "examples": ["e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385"], - "ontology": "BU_ISCIII:043", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA aspera" - }, - "sra_galaxy": { - "examples": ["e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385"], - "ontology": "BU_ISCIII:044", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"SRA galaxy" - }, - "broker_name": { - "examples": ["P17157_1007"], - "ontology": "BU_ISCIII:045", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Broker Name" - }, - "nominal_sdev": { - "examples": [""], - "ontology": "STATO_0000237", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"Nominal sdev" - }, - "first_created": { - "examples": ["e.g 2020-08-07"], - "ontology": "NCIT_C164483", - "type": "string", - "description": "", - "clasification":"Submission ENA", - "label":"First created date" - }, - "type": { - "examples": ["betacoronavirus"], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "default must remain 'betacoronavirus'", - "clasification":"Database Identifiers" - } - } -} From ad1afca573bb21ee990087c8e9c9e9daf38cc5c2 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 14 Mar 2022 22:52:07 +0100 Subject: [PATCH 0141/1454] added allowed_sample_extensions in config.json --- relecov_tools/conf/configuration.json | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index a78f7b65..a9648381 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -10,5 +10,7 @@ "sftp_server": "sftprelecov.isciii.es", "sftp_port" : "50122" }, - "storage_local_folder" : "/tmp/relecov" + "storage_local_folder" : "/tmp/relecov", + "tmp_folder_for_metadata": "/tmp/relecov/tmp", + "allowed_sample_extensions": ["fastq.gz", "fasta"] } From eb1de83deab6aada7c1406ae9c7201c65f0b42d1 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 14 Mar 2022 22:53:10 +0100 Subject: [PATCH 0142/1454] md5 is moved to a function, and create function to save metadata info in tmp folder --- relecov_tools/sftp.py | 117 ++++++++++++++++++++++++++++++++---------- 1 file changed, 89 insertions(+), 28 deletions(-) diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp.py index 29a4f95d..8c590847 100644 --- a/relecov_tools/sftp.py +++ b/relecov_tools/sftp.py @@ -2,10 +2,11 @@ from datetime import datetime import logging import rich.console - +import re import paramiko import sys import os +import shutil import yaml import relecov_tools.utils from relecov_tools.config_json import ConfigJson @@ -22,13 +23,13 @@ class SftpHandle: def __init__(self, user=None, passwd=None, conf_file=None): """Initializes the sftp object""" + config_json = ConfigJson() + self.allowed_sample_ext = config_json.get_configuration( + "allowed_sample_extensions" + ) if conf_file is None: - config_json = ConfigJson() self.server = config_json.get_topic_data("sftp_connection", "sftp_server") self.port = config_json.get_topic_data("sftp_connection", "sftp_port") - self.storage_local_folder = config_json.get_configuration( - "storage_local_folder" - ) else: if not os.path.isfile(conf_file): stderr.print( @@ -40,7 +41,18 @@ def __init__(self, user=None, passwd=None, conf_file=None): try: self.sftp_server = config["sftp_server"] self.sftp_port = config["sftp_port"] - self.storage_local_folder = config["storage_local_folder"] + try: + self.storage_local_folder = config["storage_local_folder"] + except KeyError: + self.storage_local_folder = config_json.get_configuration( + "storage_local_folder" + ) + try: + self.metadata_tmp_folder = config["tmp_metadata_folder"] + except KeyError: + self.metadata_tmp_folder = config_json.get_configuration( + "tmp_folder_for_metadata" + ) self.user = config["user_sftp"] self.passwd = config["password"] except KeyError as e: @@ -140,6 +152,64 @@ def get_files_from_sftp_folder(self, folder, files_list): return result_data + def verify_md5_checksum(self, local_folder, file_list): + """Get the md5 value from sftp match with the generated at local + folder + """ + # fetch the md5 file if exists + sftp_md5 = relecov_tools.utils.get_md5_from_local_folder(local_folder) + local_md5 = relecov_tools.utils.calculate_md5(file_list) + # MD5 Checking + if sftp_md5: + if sftp_md5 == local_md5: + log.info( + "Successful file download for files in folder %s", + local_folder, + ) + return True + else: + log.error( + "MD5 does not match. Files could be corrupted atfolder %s", + local_folder, + ) + return False + else: + log.info( + "Md5 file was not created by lab. Copy the local md5 into folder %s", + local_folder, + ) + file_name = os.path.join(local_folder, "generated_locally.md5") + relecov_tools.utils.save_md5(file_name, local_md5) + return True + + def create_tmp_files_with_metadata_info(self, local_folder, file_list): + """Copy metadata file from folder and create a file with the sample + names + """ + out_folder = self.metadata_tmp_folder + os.makedirs(out_folder, exist_ok=True) + metadata_file = "_".join(local_folder.split("/")[-2:]) + "_metadata_lab.xlsx" + shutil.copy( + os.path.join(local_folder, "Metadata_lab.xlsx"), + os.path.join(out_folder, metadata_file), + ) + for ext in self.allowed_sample_ext: + sample_names = [] + for file_name in os.listdir(local_folder): + if file_name.endswith("*." + ext): + m = re.search(r"(.*)_R[1,2].*", file_name) + if m.group(1) not in metadata_file: + sample_names.append(m.group(1)) + if len(sample_names) > 0: + break + if len(sample_names) == 0: + log.error("There is no samples in folder %s", local_folder) + file_with_samples = metadata_file.split("_")[0] + "samples.txt" + with open(file_with_samples, "w") as fh: + for sample_name in sample_names: + fh.write(sample_name + "\n") + return + def create_main_folders(self, root_directory_list): """Create the main folder structure if not exists""" for folder in root_directory_list: @@ -172,29 +242,20 @@ def download_from_sftp(self): sys.exit(0) for folder, files in folders_to_download.items(): + # get the files in each folder result_data = self.get_files_from_sftp_folder(folder, files) - sftp_folder_md5 = relecov_tools.utils.get_md5_from_local_folder( - result_data["local_folder"] - ) - local_md5 = relecov_tools.utils.calculate_md5(result_data["fetched_files"]) - # MD5 Checking - if sftp_folder_md5: - if sftp_folder_md5 == local_md5: - log.info( - "Successful file download for files in folder %s", - result_data["local_folder"], - ) - else: + if not self.verify_md5_checksum( + result_data["local_folder"], result_data["fetched_files"] + ): + # retrasmision of files in folder + result_data = self.get_files_from_sftp_folder(folder, files) + if not self.verify_md5_checksum( + result_data["local_folder"], result_data["fetched_files"] + ): log.error( - "MD5 does not match. Files could be corrupted atfolder %s", + "Second retransmision of files on folder %s", result_data["local_folder"], ) - else: - log.info( - "Md5 file was not created by lab. Copy the local md5 into folder %s", - result_data["local_folder"], - ) - file_name = os.path.join( - result_data["local_folder"], "generated_locally.md5" - ) - relecov_tools.utils.save_md5(file_name, local_md5) + self.create_tmp_files_with_metadata_info( + result_data["local_folder"], result_data["fetched_files"] + ) From c362d7ca5bf647c9d4808d2e524dd644d596006c Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 14 Mar 2022 23:13:58 +0100 Subject: [PATCH 0143/1454] Fixing litin --- relecov_tools/__main__.py | 15 +++++++++------ relecov_tools/create_xml.py | 14 ++++++++------ 2 files changed, 17 insertions(+), 12 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index e87f03bc..f98d65c3 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -11,6 +11,7 @@ import relecov_tools.utils import relecov_tools.read_metadata import relecov_tools.sftp +import relecov_tools.create_xml log = logging.getLogger() @@ -224,13 +225,15 @@ def validation(host, port, user, passwd): relecov_json.open() - -#@click.argument("source_path", required=False, metavar="") -@click.option("-s","--source_path",help="Where the validated json is") -@click.option("-o","--output_path",help="Output folder for the xml generated files") +@click.option("-s", "--source_json", help="Where the validated json is") +@click.option("-o", "--output_path", help="Output folder for the xml generated files") @click.option("-a", "--action", help="ADD or MODIFY") -def xml(source_path,output_path,action) - +def xml(source_json, output_path, action): + """Parsed data to create xml files to upload to ENA""" + xml_creation = relecov_tools.create_xml.XmlCreation( + source_json, output_path, action + ) + xml_creation.generate_xml() if __name__ == "__main__": diff --git a/relecov_tools/create_xml.py b/relecov_tools/create_xml.py index 28959634..1a02717a 100644 --- a/relecov_tools/create_xml.py +++ b/relecov_tools/create_xml.py @@ -16,12 +16,12 @@ ) -class xml_creation: - def __init__(self, source_path=None, output_path=None, action=None): - if source_path is None: - self.source_path = utils.prompt_source_path() +class XmlCreation: + def __init__(self, source_json=None, output_path=None, action=None): + if source_json is None: + self.source_json = utils.prompt_source_path() else: - self.source_path = source_path + self.source_json = source_json if output_path is None: self.output_path = utils.prompt_destination_path() else: @@ -46,7 +46,7 @@ def xml( """ # Load validated json - with open(self.source_path) as json_format_file: + with open(self.source_json) as json_format_file: json_data = j.load(json_format_file) # Create output directory @@ -123,6 +123,8 @@ def xml( # samples_relecov.xml data_keys = list(json_data.keys()) + # just for fix litin + print(data_keys) r = e.Element("SAMPLE_SET") sample = e.SubElement(r, "SAMPLE") sample.set("alias", "SARS Sample 1 programmatic") From 5fb931565fa34d9ed196b761d134309e74a41f52 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 14 Mar 2022 23:49:05 +0100 Subject: [PATCH 0144/1454] Change the input from additional metadata to file which contains samples --- relecov_tools/__main__.py | 8 ++++---- relecov_tools/read_metadata.py | 13 +++++++------ 2 files changed, 11 insertions(+), 10 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index f98d65c3..6a9c9d4e 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -172,8 +172,8 @@ def sftp(user, password, conf_file): help="file containing metadata", ) @click.option( - "-a", - "--add_metadata", + "-s", + "--sample_list_file", type=click.Path(), default=os.path.join( os.path.dirname(os.path.realpath(__file__)), @@ -185,12 +185,12 @@ def sftp(user, password, conf_file): @click.option( "-o", "--metadata-out", type=click.Path(), help="Path to save output metadata file" ) -def read_metadata(metadata_file, add_metadata, metadata_out): +def read_metadata(metadata_file, sample_list_file, metadata_out): """ Create the json complaining the relecov schema from the Metadata file. """ new_metadata = relecov_tools.read_metadata.RelecovMetadata( - metadata_file, add_metadata, metadata_out + metadata_file, sample_list_file, metadata_out ) relecov_json = new_metadata.create_metadata_json() return relecov_json diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index dfa97c4f..2f9c6c7e 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -23,9 +23,7 @@ class RelecovMetadata: - def __init__( - self, metadata_file=None, additional_metadata_file=None, output_folder=None - ): + def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None): if metadata_file is None: self.metadata_file = relecov_tools.utils.prompt_path( msg="Select the excel file which contains metadata" @@ -35,15 +33,18 @@ def __init__( if not os.path.exists(self.metadata_file): log.error("Metadata file %s does not exist ", self.metadata_file) sys.exit(1) + if sample_list_file is None: + self.sample_list_file = relecov_tools.utils.prompt_path( + msg="Select the file which contains the sample list" + ) + else: + self.sample_list_file = sample_list_file if output_folder is None: self.output_folder = relecov_tools.utils.prompt_path( msg="Select the output folder" ) else: self.output_folder = output_folder - self.additional_metadata_file = additional_metadata_file - - # Perform workflow details def check_new_metadata(folder): """Check if there is a new metadata to be processed From c2f815c2748e462b681702814474235d13fc9c5d Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 15 Mar 2022 13:36:37 +0100 Subject: [PATCH 0145/1454] Metadata file with the additional info is saved to json file --- relecov_tools/read_metadata.py | 39 ++++++++++++++++++++++++++++++++-- 1 file changed, 37 insertions(+), 2 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 2f9c6c7e..96ac7727 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -87,6 +87,23 @@ def add_extra_data(self, metadata, extra_data): extra_metadata.append(row) return extra_metadata + def compare_sample_in_metadata(self, completed_metadata): + """Compare te samples defined in metadata file and the ones in the + sample file + """ + not_found_samples = [] + if not os.path.exists(self.sample_list_file): + return False + # get the smaples defined in json + with open(self.sample_list_file, "r") as fh: + samples = fh.read().split("\n") + for line_metadata in completed_metadata: + if line_metadata["sample_name"] not in samples: + not_found_samples.append(line_metadata["sample_name"]) + if len(not_found_samples) > 0: + return not_found_samples + return True + def request_information(external_url, request): """Get information from external database server using Rest API @@ -150,8 +167,17 @@ def read_metadata_file(self, meta_map_json): metadata_values.append(sample_data_row) return metadata_values, errors + def write_json_fo_file(self, completed_metadata, file_name): + """Write metadata to json file""" + os.makedirs(self.output_folder, exist_ok=True) + json_file = os.path.join(self.output_folder, file_name) + with open(json_file, "w") as fh: + fh.write(json.dumps(completed_metadata)) + return True + def create_metadata_json(self): config_json = ConfigJson() + """ schema_location = config_json.get_topic_data( "json_schemas", "phage_plus_schema" ) @@ -161,6 +187,7 @@ def create_metadata_json(self): schema_json = self.read_json_file(schema_location_file) phage_plus_schema = relecov_tools.schema_json.PhagePlusSchema(schema_json) properties_in_schema = phage_plus_schema.get_schema_properties() + """ metadata_mapping_json = config_json.get_configuration("mapping_metadata_json") meta_map_json_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", metadata_mapping_json @@ -171,5 +198,13 @@ def create_metadata_json(self): completed_metadata = self.add_extra_data( valid_metadata_rows, meta_map_json["Additional_fields"] ) - # fake return data, just for litin - return completed_metadata, properties_in_schema + comp_result = self.compare_sample_in_metadata(completed_metadata) + if isinstance(comp_result, list): + missing_samples = ",".join(comp_result) + log.error("Missing samples %s", missing_samples) + elif comp_result: + log.info("Samples in metadata matches with the ones uploaded") + else: + log.error("There is missing samples in metadata and/or uploaded") + self.write_json_fo_file(completed_metadata, "completed_metadata.json") + return True From bc8b789c2db9883b0ddcb24f910a89bd2c5ecd86 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 16 Mar 2022 10:52:59 +0100 Subject: [PATCH 0146/1454] created xml_files folder and added subimissions_add and modfiy --- relecov_tools/xml_files/submission_add.xml | 10 ++++++++++ relecov_tools/xml_files/submission_modify.xml | 10 ++++++++++ 2 files changed, 20 insertions(+) create mode 100644 relecov_tools/xml_files/submission_add.xml create mode 100644 relecov_tools/xml_files/submission_modify.xml diff --git a/relecov_tools/xml_files/submission_add.xml b/relecov_tools/xml_files/submission_add.xml new file mode 100644 index 00000000..8edfc2ad --- /dev/null +++ b/relecov_tools/xml_files/submission_add.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/relecov_tools/xml_files/submission_modify.xml b/relecov_tools/xml_files/submission_modify.xml new file mode 100644 index 00000000..d9bc1a3a --- /dev/null +++ b/relecov_tools/xml_files/submission_modify.xml @@ -0,0 +1,10 @@ + + + + + + + + + + From abecdcf70b1b8402561b555741a71c282add5651 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 16 Mar 2022 11:21:04 +0100 Subject: [PATCH 0147/1454] added relecov project example data to conf json --- relecov_tools/conf/configuration.json | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index a9648381..e3a7cce3 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -6,11 +6,19 @@ }, "mapping_metadata_json": "mapping_metadata_json_v01.json", "additional_metadata": "additional_metadata_v01.json", - "sftp_connection":{ + "sftp_connection": { "sftp_server": "sftprelecov.isciii.es", - "sftp_port" : "50122" + "sftp_port": "50122" }, - "storage_local_folder" : "/tmp/relecov", + "storage_local_folder": "/tmp/relecov", "tmp_folder_for_metadata": "/tmp/relecov/tmp", - "allowed_sample_extensions": ["fastq.gz", "fasta"] -} + "allowed_sample_extensions": [ + "fastq.gz", + "fasta" + ], + "project_relecov_xml": { + "alias": "RELECOV", + "TITLE": "Example project for ENA submission RELECOV", + "DESCRIPTION": "This study was created as part of an ENA submissions example RELECOV" + } +} \ No newline at end of file From 2ee626721dfbd9fb9f3599e713005b6e700b7329 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 16 Mar 2022 17:11:19 +0100 Subject: [PATCH 0148/1454] changes on schema phage plus --- relecov_tools/__main__.py | 1 + relecov_tools/conf/configuration.json | 4 + relecov_tools/create_xml.py | 119 +++++++++++------- relecov_tools/schema/phage_plus_V0.json | 21 +++- relecov_tools/schema/to_ena.json | 19 --- relecov_tools/xml_files/submission_add.xml | 10 -- relecov_tools/xml_files/submission_modify.xml | 10 -- 7 files changed, 95 insertions(+), 89 deletions(-) delete mode 100644 relecov_tools/schema/to_ena.json delete mode 100644 relecov_tools/xml_files/submission_add.xml delete mode 100644 relecov_tools/xml_files/submission_modify.xml diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 6a9c9d4e..52814902 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -224,6 +224,7 @@ def validation(host, port, user, passwd): ) relecov_json.open() +#mapeo a ena @click.option("-s", "--source_json", help="Where the validated json is") @click.option("-o", "--output_path", help="Output folder for the xml generated files") diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index e3a7cce3..59da123a 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -20,5 +20,9 @@ "alias": "RELECOV", "TITLE": "Example project for ENA submission RELECOV", "DESCRIPTION": "This study was created as part of an ENA submissions example RELECOV" + }, + "fixed_data": { + "tax_id": "2697049", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2" } } \ No newline at end of file diff --git a/relecov_tools/create_xml.py b/relecov_tools/create_xml.py index 1a02717a..226f04a3 100644 --- a/relecov_tools/create_xml.py +++ b/relecov_tools/create_xml.py @@ -31,7 +31,7 @@ def __init__(self, source_json=None, output_path=None, action=None): else: self.action = action - def xml( + def xml_study( self, ): """ @@ -61,80 +61,88 @@ def xml( # 1. From validated json to xml study- submission.xml and project.xml # submission.xml + os.chdir("xml_files/") if self.action.upper == "ADD": # submission add - r = e.Element("SUBMISSION_SET") - sample = e.SubElement(r, "SUBMISSION") - actions = e.SubElement(sample, "ACTIONS") - action = e.SubElement(actions, "ACTION") - e.SubElement(action, "ADD") - a = e.ElementTree(r) - a.write(os.path.join(self.output_path, "study", "submission.xml")) + submission_file = "submission_add.xml" if self.action.upper() == "MODIFY": # submission modify - r = e.Element("SUBMISSION_SET") - sample = e.SubElement(r, "SUBMISSION") - actions = e.SubElement(sample, "ACTIONS") - action = e.SubElement(actions, "ACTION") - e.SubElement(action, "MODIFY") - a = e.ElementTree(r) - a.write(os.path.join(self.output_path, "study", "submission.xml")) + submission_file = "submission_modify.xml" # project_relecov.xml + os.chdir("../conf") + dict_conf = j.loads("configuration.json") r = e.Element("PROJECT_SET") project = e.SubElement(r, "PROJECT") - project.set("alias", "RELECOV") - e.SubElement( - project, "TITLE" - ).text = "Example project for ENA submission RELECOV" - e.SubElement( - project, "DESCRIPTION" - ).text = ( - "This study was created as part of an ENA submissions example RELECOV" - ) + project.set("alias", dict_conf["project_relecov_xml"]["alias"]) + e.SubElement(project, "TITLE").text = dict_conf["project_relecov_xml"][ + "TITLE" + ] + e.SubElement(project, "DESCRIPTION").text = dict_conf[ + "project_relecov_xml" + ]["DESCRIPTION"] submission = e.SubElement(project, "SUBMISSION_PROJECT") e.SubElement(submission, "SEQUENCING_PROJECT") a = e.ElementTree(r) a.write(os.path.join(self.output_path, "study", "project_relecov.xml")) # 1.1 Upload study info + """ + import requests + from requests.structures import CaseInsensitiveDict + + url = "https://reqbin.com/echo/post/json" + + headers = CaseInsensitiveDict() + headers["Content-Type"] = "application/json" + headers["Authorization"] = "Basic bG9naW46cGFzc3dvcmQ=" + + data = '{"login":"my_login","password":"my_password"}' + + + resp = requests.post(url, headers=headers, data=data) + + print(resp.status_code) + """ # 2. From validated json to xml samples - submission.xml and samples.xml + def xml_samples(): # submission.xml + os.chdir("../xml_files/") if self.action.upper == "ADD": # submission add - r = e.Element("SUBMISSION_SET") - sample = e.SubElement(r, "SUBMISSION") - actions = e.SubElement(sample, "ACTIONS") - action = e.SubElement(actions, "ACTION") - e.SubElement(action, "ADD") - a = e.ElementTree(r) - a.write(os.path.join(self.output_path, "samples", "submission.xml")) + submission_file = "submission_add.xml" if self.action.upper() == "MODIFY": # submission modify - r = e.Element("SUBMISSION_SET") - sample = e.SubElement(r, "SUBMISSION") - actions = e.SubElement(sample, "ACTIONS") - action = e.SubElement(actions, "ACTION") - e.SubElement(action, "MODIFY") - a = e.ElementTree(r) - a.write(os.path.join(self.output_path, "samples", "submission.xml")) + submission_file = "submission_modify.xml" # samples_relecov.xml + os.chdir("../schema/") + json_data = j.loads("to_ena.json") + os.chdir("../conf") + dict_conf = j.loads("configuration.json") + data_keys = list(json_data.keys()) - # just for fix litin - print(data_keys) r = e.Element("SAMPLE_SET") sample = e.SubElement(r, "SAMPLE") - sample.set("alias", "SARS Sample 1 programmatic") - e.SubElement(sample, "TITLE").text = "SARS Sample 1" + sample.set( + "alias", + "Programmatic Test SARS-CoV-2 Sample" + str(json_data["sample_name"]), + ) + e.SubElement(sample, "TITLE").text = "SARS-CoV-2 Sample" + str( + json_data["sample_name"] + ) sample_name = e.SubElement(sample, "SAMPLE_NAME") - e.SubElement(sample_name, "TAXON_ID").text = "2697049" - e.SubElement( - sample_name, "SCIENTIFIC_NAME" - ).text = "Severe acute respiratory syndrome coronavirus 2" - e.SubElement(sample, "DESCRIPTION").text = "SARS-CoV-2 Sample #1" + e.SubElement(sample_name, "TAXON_ID").text = dict_conf["fixed_data"][ + "tax_id" + ] + e.SubElement(sample_name, "SCIENTIFIC_NAME").text = dict_conf["fixed_data"][ + "scientific_name" + ] + e.SubElement(sample, "DESCRIPTION").text = "SARS-CoV-2 Sample" + str( + json_data["sample_name"] + ) sample_attributes = e.SubElement(sample, "SAMPLE_ATTRIBUTES") for i in json_data: sample_attribute = e.SubElement(sample_attributes, "SAMPLE_ATTRIBUTE") @@ -144,6 +152,23 @@ def xml( a.write(os.path.join(self.output_path, "samples", "samples_relecov.xml")) # 2.2 Upload samples info + """ + import requests + from requests.structures import CaseInsensitiveDict + + url = "https://reqbin.com/echo/post/json" + + headers = CaseInsensitiveDict() + headers["Content-Type"] = "application/json" + headers["Authorization"] = "Basic bG9naW46cGFzc3dvcmQ=" + + data = '{"login":"my_login","password":"my_password"}' + + + resp = requests.post(url, headers=headers, data=data) + + print(resp.status_code) + """ # 3. From sftp upload runs (FASTQ files programmatic)- experiments.xmlm, runs.xml and submission.xml # 4. From sftp upload sequences (FASTA files programmatic) - json using webin-cli-rest diff --git a/relecov_tools/schema/phage_plus_V0.json b/relecov_tools/schema/phage_plus_V0.json index 7b4570b2..616544e3 100644 --- a/relecov_tools/schema/phage_plus_V0.json +++ b/relecov_tools/schema/phage_plus_V0.json @@ -12,9 +12,7 @@ "host_scientific_name", "host_disease", "sequencing_instrument_model", - "sequencing_instrument_platform", - "consensus_sequence_software_name", - "consensus_sequence_software_version" + "sequencing_instrument_platform" ], "type": "object", "properties": { @@ -673,6 +671,23 @@ ], "label": "Host Age" }, + "host_age_unit": { + "Enums": [ + "months [UO:0000035]", + "years [UO:0000036]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001393", + "type": "string", + "description": "The units used to measure the host's age.", + "examples": [ + "years [UO:0000036]" + ] + }, "host_age_bin": { "Enums": [ "0 - 9 [GENEPIO:0100049]", diff --git a/relecov_tools/schema/to_ena.json b/relecov_tools/schema/to_ena.json deleted file mode 100644 index e055dfc8..00000000 --- a/relecov_tools/schema/to_ena.json +++ /dev/null @@ -1,19 +0,0 @@ -{ - "sample_name": "ID_001", - "collecting_institution": "Hospital Universitario de Basurto", - "geographic_location_(country_and/or_sea)": "Spain", - "isolate": "ID_001", - "host_scientific_name": "Homo sapiens", - "host_common_name": "Human", - "host_subject_id": "#131", - "instrument_model": "Illumina MiSeq", - "file_name": "ABC123_S1_L001_R1_001.fasstq.gz", - "tax_id": "2697049", - "scientific_name": "severe acute respiratory syndrome coronavirus 2", - "common_name": "SARS-CoV-2", - "sample_description": "SARS-CoV-2 Sample #1", - "library_source": "METAGENOMIC", - "library_selection": "RANDOM PCR", - "library_strategy": "WGS", - "library_layout": "PAIRED" -} \ No newline at end of file diff --git a/relecov_tools/xml_files/submission_add.xml b/relecov_tools/xml_files/submission_add.xml deleted file mode 100644 index 8edfc2ad..00000000 --- a/relecov_tools/xml_files/submission_add.xml +++ /dev/null @@ -1,10 +0,0 @@ - - - - - - - - - - diff --git a/relecov_tools/xml_files/submission_modify.xml b/relecov_tools/xml_files/submission_modify.xml deleted file mode 100644 index d9bc1a3a..00000000 --- a/relecov_tools/xml_files/submission_modify.xml +++ /dev/null @@ -1,10 +0,0 @@ - - - - - - - - - - From 052360a48a1f2672209eb6b941ab8ee4ca0f5d9d Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 16 Mar 2022 17:17:38 +0100 Subject: [PATCH 0149/1454] Changes in validation step --- relecov_tools/__main__.py | 36 +++++++------------ relecov_tools/read_metadata.py | 5 +-- .../schema/mapping_metadata_json_v01.json | 14 ++++---- ...validation_jsons.py => validation_json.py} | 22 ++++++++++-- 4 files changed, 41 insertions(+), 36 deletions(-) rename relecov_tools/{validation_jsons.py => validation_json.py} (61%) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 6a9c9d4e..17737d40 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -12,6 +12,7 @@ import relecov_tools.read_metadata import relecov_tools.sftp import relecov_tools.create_xml +import relecov_tools.validation_json log = logging.getLogger() @@ -198,31 +199,18 @@ def read_metadata(metadata_file, sample_list_file, metadata_out): # validation @relecov_tools_cli.command(help_priority=4) -@click.argument("pipeline", required=False, metavar="") -@click.option( - "-r", "--revision", help="Release/branch/SHA of the project to run (if remote)" -) -@click.option("-i", "--id", help="ID for web-gui launch parameter set") -@click.option( - "-c", - "--command-only", - is_flag=True, - default=False, - help="Create Nextflow command with params (no params file)", -) -@click.option( - "-o", - "--params-out", - type=click.Path(), - default=os.path.join(os.getcwd(), "nf-params.json"), - help="Path to save run parameters file", -) -def validation(host, port, user, passwd): - """Download files located in sftp server.""" - relecov_json = relecov_tools.validation_jsons.ValidationJson( - host, port, user, passwd +@click.option("-j", "--json_file", help="Json file to validate") +@click.option("-s", "--json_schema", help="Json schema") +@click.option("-o", "--out_folder", help="Path to save validate json file") +def validation(json_file, json_schema, out_folder): + """Validate json file against schema.""" + validation_result = relecov_tools.validation_json.validate_json_vs_schema( + json_file, json_schema, out_folder ) - relecov_json.open() + if validation_result is not True: + log.error("Some of the samples in json metadata were not validated") + else: + log.info("All data in json were validated") @click.option("-s", "--source_json", help="Where the validated json is") diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 96ac7727..a88d376b 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -148,8 +148,9 @@ def read_metadata_file(self, meta_map_json): wb_file = openpyxl.load_workbook(self.metadata_file, data_only=True) ws_metadata_lab = wb_file["METADATA_LAB"] # removing the None columns in excel heading row - heding_without_none = [i for i in ws_metadata_lab[1] if i.value] - heading = self.update_heading_to_json(heding_without_none, meta_map_json) + heading_without_none = [i for i in ws_metadata_lab[1] if i.value] + import pdb; pdb.set_trace() + heading = self.update_heading_to_json(heading_without_none, meta_map_json) metadata_values = [] errors = {} for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row): diff --git a/relecov_tools/schema/mapping_metadata_json_v01.json b/relecov_tools/schema/mapping_metadata_json_v01.json index a85a844d..692d5b6e 100644 --- a/relecov_tools/schema/mapping_metadata_json_v01.json +++ b/relecov_tools/schema/mapping_metadata_json_v01.json @@ -1,8 +1,8 @@ { "Collecting Sample id": "sample_name", "Sample ID given by the submitting laboratory" : "submitting_lab_sequence_id", - "Passage details": "", - "Sequencing sample id": "", + "Passage details": "passage_details", + "Sequencing sample id": "sequencing_sample_id", "ENA Sample ID": "biosample_accession_ENA", "GISAID Virus Name": "virus_name", "GISAID id": "submitter", @@ -19,7 +19,7 @@ "Sample Collection Date": "sample_collection_date", "Sample Received Date": "sample_received_date", "Purpose of sampling": "purpose_of_sequencing", - "Biological Sample Storage Condition": "", + "Biological Sample Storage Condition": "sample_storage_conditions", "Specimen source": "anatomical_material", "Anatomical Structure": "anatomical_part", "Environmental Material": "environmental_material", @@ -33,10 +33,10 @@ "Passage Method": "passage_method", "Nucleic acid extraction methods": "biomaterial_extracted", "Host Common Name": "host_common_name", - "Host Age": "", - "Host Age Unit": "", - "Host Age Bin": "", - "Host Gender": "", + "Host Age": "host_age", + "Host Age Unit": "host_age_unit", + "Host Age Bin": "host_age_bin", + "Host Gender": "host_gender", "Outbreak Exposure Event Location": "outbreak", "Additional Host Information": "additional_host_information", "Purpose Of Sequencing Details": "purpose_of_sequencing", diff --git a/relecov_tools/validation_jsons.py b/relecov_tools/validation_json.py similarity index 61% rename from relecov_tools/validation_jsons.py rename to relecov_tools/validation_json.py index 4b7bdf99..3c811bdf 100644 --- a/relecov_tools/validation_jsons.py +++ b/relecov_tools/validation_json.py @@ -4,10 +4,12 @@ import jsonschema from jsonschema import validate from jsonschema import Draft202012Validator + import json import sys +import os import relecov_tools.utils -import relecov_tools.schema_json +from relecov_tools.config_json import ConfigJson log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -18,8 +20,18 @@ ) -def validate_json_vs_schema(json_schema_file=None, json_data_file=None): - +def validate_json_vs_schema(json_data_file=None, json_schema_file=None, out_folder=None): + """Validate json file against the schema""" + if json_data_file is None: + json_data_file = relecov_tools.utils.prompt_path( + msg="Select the json file to validate" + ) + if json_schema_file is None: + config_json = ConfigJson() + schema_name = config_json.get_topic_data("json_schemas", "phage_plus_schema") + json_schema_file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), "schema", schema_name + ) # schema_file = open('/home/lchapado/Projects/Proyecto_ERA/relecov-tools/schema/phage_plus_V0.json') with open(json_schema_file, "r") as fh: json_schema = json.load(fh) @@ -28,6 +40,9 @@ def validate_json_vs_schema(json_schema_file=None, json_data_file=None): except jsonschema.ValidationError: stderr.print("[red] Json schema does not fulfil Draft 202012 Validation") sys.exit(1) + if not os.path.isfile(json_data_file): + stderr.print("[red] Json file does not exists") + sys.exit(1) with open(json_data_file, "r") as fh: json_data = json.load(fh) validated_json_data = [] @@ -35,6 +50,7 @@ def validate_json_vs_schema(json_schema_file=None, json_data_file=None): errors = {} for item_row in json_data: try: + import pdb; pdb.set_trace() validate(instance=item_row, schema=json_schema) validated_json_data.append(item_row) except jsonschema.ValidationError as e: From 4a505af634888f6df9252711e0b058a839dd7f04 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 16 Mar 2022 17:37:50 +0100 Subject: [PATCH 0150/1454] built ena_upload json schema --- relecov_tools/example_data/ena_upload.json | 178 +++++++++++++++++++++ 1 file changed, 178 insertions(+) create mode 100644 relecov_tools/example_data/ena_upload.json diff --git a/relecov_tools/example_data/ena_upload.json b/relecov_tools/example_data/ena_upload.json new file mode 100644 index 00000000..e6689ca8 --- /dev/null +++ b/relecov_tools/example_data/ena_upload.json @@ -0,0 +1,178 @@ +{ + "study": { + "alias": [ + "study_alias_4", + "study_alias_5" + ], + "title": [ + "study_title_1", + "study_title_2" + ], + "study_type": [ + "Transcriptome Analysis", + "RNASeq" + ], + "study_abstract": [ + "study_abstract_1", + "study_abstract_2" + ], + "pubmed_id": [None, + "pubmed_id_2" + ] + }, + "samples": { + "alias": [ + "sample_alias_4", + "sample_alias_5" + ], + "title": [ + "sample_title_2", + "sample_title_3" + ], + "taxon_id": [ + "2697049", + "2697049" + ], + "sample_description": [ + "sample_description_1", + "sample_description_2" + ], + "collection date": [ + "2020-10-11", + "2008-01-24" + ], + "geographic location (country and/or sea)": [ + "Argentina", + "Belgium" + ], + "host common name": [ + "host_common_name_1", + "host_common_name_2" + ], + "host subject id": [ + "host_subject_id_1", + "host_subject_id_2" + ], + "host health state": [ + "diseased", + "restricted access" + ], + "host sex": [ + "male", + "female" + ], + "host scientific name": [ + "host_scientific_name_1", + "host_scientific_name_2" + ], + "collector name": [ + "collector_name_1", + "collector_name_2" + ], + "collecting institution": [ + "collecting_institution_1", + "collecting_institution_2" + ], + "isolate": [ + "isolate_1", + "isolate_2" + ] + }, + "runs": { + "alias": [ + "run_alias_1a", + "run_alias_1a", + "run_alias_3c" + ], + "experiment_alias": [ + "experiment_alias_7a", + "experiment_alias_7a", + "experiment_alias_9c" + ], + "file_name": [ + "ENA_TEST2.R1.fastq.gz", + "ENA_TEST2.R2.fastq.gz", + "ENA_TEST1.R1.fastq.gz" + ], + "file_type": [ + "fastq", + "fastq", + "fastq" + ], + "file_checksum": [ + "3e69af1f875fab020aed82f5edbc1f03", + "3e69af1f875fab020aed82f5edbc1f03", + "3e69af1f875fab020aed82f5edbc1f03" + ] + }, + "experiments": { + "alias": [ + "experiment_alias_7a", + "experiment_alias_8b", + "experiment_alias_9c" + ], + "title": [ + "experiment_title_1", + "experiment_title_2", + "experiment_title_3" + ], + "study_alias": [ + "study_alias_4", + "study_alias_5", + "study_alias_5" + ], + "sample_alias": [ + "study_alias_4", + "study_alias_5", + "study_alias_5" + ], + "design_description": [ + "design_description_1", + "design_description_2", + "design_description_3" + ], + "library_name": [ + "library_name_1", + "library_name_2", + "library_name_3" + ], + "library_strategy": [ + "WGA", + "RNA-Seq", + "RNA-Seq" + ], + "library_source": [ + "GENOMIC", + "TRANSCRIPTOMIC", + "TRANSCRIPTOMIC" + ], + "library_selection": [ + "RANDOM", + "repeat fractionation", + "repeat fractionation" + ], + "library_layout": [ + "paired", + "single", + "single" + ], + "insert_size": [ + "250",None,None + ], + "library_construction_protocol": [ + "library_construction_protocol_1", + "library_construction_protocol_2", + "library_construction_protocol_2" + ], + "platform": [ + "LS454", + "illumina", + "illumina" + ], + "instrument_model": [ + "454 GS 20", + "Illumina Genome Analyzer", + "Illumina Genome Analyzer" + ] + } +} \ No newline at end of file From 70fcc5a324964d339a94f8841e452f1abbb7afc7 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 17 Mar 2022 11:40:41 +0100 Subject: [PATCH 0151/1454] remove wrong format value at Last update property --- relecov_tools/schema/phage_plus_V0.json | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/phage_plus_V0.json b/relecov_tools/schema/phage_plus_V0.json index 616544e3..4b909000 100644 --- a/relecov_tools/schema/phage_plus_V0.json +++ b/relecov_tools/schema/phage_plus_V0.json @@ -2474,7 +2474,8 @@ "type": "string", "description": "", "clasification": "Submission ENA", - "format": "Last Updated" + "format": "date", + "label": "Last Updated" }, "experiment_title": { "examples": [ @@ -2726,4 +2727,4 @@ "clasification": "Database Identifiers" } } -} \ No newline at end of file +} From 4a08b529e39319c0c200423669d5e9a36f39c104 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 17 Mar 2022 11:41:47 +0100 Subject: [PATCH 0152/1454] set to caps leters COVID-19 --- relecov_tools/schema/mapping_metadata_json_v01.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/mapping_metadata_json_v01.json b/relecov_tools/schema/mapping_metadata_json_v01.json index 692d5b6e..301e0967 100644 --- a/relecov_tools/schema/mapping_metadata_json_v01.json +++ b/relecov_tools/schema/mapping_metadata_json_v01.json @@ -85,7 +85,7 @@ "Human": "Homo sapiens" }, "tax_id": "", - "host_disease":"covid-19", + "host_disease":"COVID-19", "sequence_file_R1_fastq": "", "sequence_file_R2_fastq": "", "type" : "betacoronavirus" From f196243f77f1ff88938adde9a006ab45bcfced29 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 17 Mar 2022 11:42:40 +0100 Subject: [PATCH 0153/1454] fixing mapping errors --- relecov_tools/read_metadata.py | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index a88d376b..7a475d9e 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -84,7 +84,10 @@ def add_extra_data(self, metadata, extra_data): row["geo_loc_latitude"], row["geo_loc_longitude"] = geo_loc_data[city] # update isolate qith the name of the sample row["isolate"] = row["sample_name"] + row["host_scientific_name"] = extra_data["host_scientific_name"][row["host_common_name"]] + row["sequencing_instrument_platform"] = "To change" extra_metadata.append(row) + import pdb; pdb.set_trace() return extra_metadata def compare_sample_in_metadata(self, completed_metadata): @@ -120,7 +123,7 @@ def get_geo_location_data(self, state, country): """Get the geo_loc_latitude and geo_loc_longitude from state""" geolocator = Nominatim(user_agent="geoapiRelecov") loc = geolocator.geocode(state + "," + country) - return [loc.latitude, loc.longitude] + return [str(loc.latitude), str(loc.longitude)] def update_heading_to_json(self, heading, meta_map_json): """Change the heading values from the metadata file for the ones defined @@ -128,10 +131,10 @@ def update_heading_to_json(self, heading, meta_map_json): """ mapped_heading = [] for cell in heading: - if cell.value in meta_map_json: - mapped_heading.append(meta_map_json[cell.value]) + if cell in meta_map_json: + mapped_heading.append(meta_map_json[cell]) else: - mapped_heading.append(cell.value) + mapped_heading.append(cell) return mapped_heading def read_json_file(self, j_file): @@ -148,8 +151,7 @@ def read_metadata_file(self, meta_map_json): wb_file = openpyxl.load_workbook(self.metadata_file, data_only=True) ws_metadata_lab = wb_file["METADATA_LAB"] # removing the None columns in excel heading row - heading_without_none = [i for i in ws_metadata_lab[1] if i.value] - import pdb; pdb.set_trace() + heading_without_none = [i.value.strip() for i in ws_metadata_lab[1] if i.value] heading = self.update_heading_to_json(heading_without_none, meta_map_json) metadata_values = [] errors = {} @@ -158,13 +160,15 @@ def read_metadata_file(self, meta_map_json): for idx in range(len(heading)): if "date" in heading[idx]: try: - sample_data_row[heading[idx]] = row[idx].strftime("%d/%m/%Y") + sample_data_row[heading[idx]] = row[idx].strftime("%Y/%m/%d") except AttributeError: if row[0] not in errors: errors[row[0]] = {} errors[row[0]][heading[idx]] = "Invalid date format" else: - sample_data_row[heading[idx]] = row[idx] + if heading[idx] == 'host_age': + import pdb; pdb.set_trace() + sample_data_row[heading[idx]] = row[idx] if row[idx] else "" metadata_values.append(sample_data_row) return metadata_values, errors From 2ca32360cb4785973b42fc180e88d0b186bf5fe6 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 17 Mar 2022 11:43:52 +0100 Subject: [PATCH 0154/1454] Modify the return values after calling validation function --- relecov_tools/__main__.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index fb02d7ba..bee727ff 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -204,15 +204,15 @@ def read_metadata(metadata_file, sample_list_file, metadata_out): @click.option("-o", "--out_folder", help="Path to save validate json file") def validation(json_file, json_schema, out_folder): """Validate json file against schema.""" - validation_result = relecov_tools.validation_json.validate_json_vs_schema( + validated_json_data, invalid_json, errors = relecov_tools.validation_json.validate_json_vs_schema( json_file, json_schema, out_folder ) - if validation_result is not True: + if len(invalid_json) > 0: log.error("Some of the samples in json metadata were not validated") else: log.info("All data in json were validated") -#mapeo a ena +#mapeo a ena @click.option("-s", "--source_json", help="Where the validated json is") @click.option("-o", "--output_path", help="Output folder for the xml generated files") From 6c055ca71f43913c060cc77c3b7711714bd9c2ea Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 17 Mar 2022 11:48:44 +0100 Subject: [PATCH 0155/1454] fixing litin --- relecov_tools/__main__.py | 7 +++++-- relecov_tools/read_metadata.py | 10 +++++----- relecov_tools/validation_json.py | 5 +++-- 3 files changed, 13 insertions(+), 9 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index bee727ff..f31a4ecf 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -204,7 +204,11 @@ def read_metadata(metadata_file, sample_list_file, metadata_out): @click.option("-o", "--out_folder", help="Path to save validate json file") def validation(json_file, json_schema, out_folder): """Validate json file against schema.""" - validated_json_data, invalid_json, errors = relecov_tools.validation_json.validate_json_vs_schema( + ( + validated_json_data, + invalid_json, + errors, + ) = relecov_tools.validation_json.validate_json_vs_schema( json_file, json_schema, out_folder ) if len(invalid_json) > 0: @@ -212,7 +216,6 @@ def validation(json_file, json_schema, out_folder): else: log.info("All data in json were validated") -#mapeo a ena @click.option("-s", "--source_json", help="Where the validated json is") @click.option("-o", "--output_path", help="Output folder for the xml generated files") diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 7a475d9e..beffcf89 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -84,10 +84,11 @@ def add_extra_data(self, metadata, extra_data): row["geo_loc_latitude"], row["geo_loc_longitude"] = geo_loc_data[city] # update isolate qith the name of the sample row["isolate"] = row["sample_name"] - row["host_scientific_name"] = extra_data["host_scientific_name"][row["host_common_name"]] + row["host_scientific_name"] = extra_data["host_scientific_name"][ + row["host_common_name"] + ] row["sequencing_instrument_platform"] = "To change" extra_metadata.append(row) - import pdb; pdb.set_trace() return extra_metadata def compare_sample_in_metadata(self, completed_metadata): @@ -166,9 +167,8 @@ def read_metadata_file(self, meta_map_json): errors[row[0]] = {} errors[row[0]][heading[idx]] = "Invalid date format" else: - if heading[idx] == 'host_age': - import pdb; pdb.set_trace() - sample_data_row[heading[idx]] = row[idx] if row[idx] else "" + if heading[idx] == "host_age": + sample_data_row[heading[idx]] = row[idx] if row[idx] else "" metadata_values.append(sample_data_row) return metadata_values, errors diff --git a/relecov_tools/validation_json.py b/relecov_tools/validation_json.py index 3c811bdf..1206d34f 100644 --- a/relecov_tools/validation_json.py +++ b/relecov_tools/validation_json.py @@ -20,7 +20,9 @@ ) -def validate_json_vs_schema(json_data_file=None, json_schema_file=None, out_folder=None): +def validate_json_vs_schema( + json_data_file=None, json_schema_file=None, out_folder=None +): """Validate json file against the schema""" if json_data_file is None: json_data_file = relecov_tools.utils.prompt_path( @@ -50,7 +52,6 @@ def validate_json_vs_schema(json_data_file=None, json_schema_file=None, out_fold errors = {} for item_row in json_data: try: - import pdb; pdb.set_trace() validate(instance=item_row, schema=json_schema) validated_json_data.append(item_row) except jsonschema.ValidationError as e: From bc5dc39837a7145cde5a6642fe19a0f28a3c74ca Mon Sep 17 00:00:00 2001 From: ErikaKvalem Date: Thu, 17 Mar 2022 13:00:09 +0100 Subject: [PATCH 0156/1454] added sequencing instrument platformto schema phage plus --- relecov_tools/schema/phage_plus_V0.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/phage_plus_V0.json b/relecov_tools/schema/phage_plus_V0.json index 4b909000..c669b5b5 100644 --- a/relecov_tools/schema/phage_plus_V0.json +++ b/relecov_tools/schema/phage_plus_V0.json @@ -498,7 +498,7 @@ "ontology": "GENEPIO_0000071", "type": "string", "description": "The model of the sequencing instrument used.", - "label": "Sequencing Platforms " + "label": "Sequencing Instrument Platform" }, "submitting_lab_sequence_id": { "examples": [ From 9ebd5107451b945e92bd1645d8203bc626056641 Mon Sep 17 00:00:00 2001 From: ErikaKvalem Date: Thu, 17 Mar 2022 16:02:27 +0100 Subject: [PATCH 0157/1454] from json to dataframe --- relecov_tools/example_data/ena_upload.json | 4 +- relecov_tools/test/try_01.ipynb | 261 +++++++++++++++++++++ 2 files changed, 263 insertions(+), 2 deletions(-) create mode 100644 relecov_tools/test/try_01.ipynb diff --git a/relecov_tools/example_data/ena_upload.json b/relecov_tools/example_data/ena_upload.json index e6689ca8..92aaefb9 100644 --- a/relecov_tools/example_data/ena_upload.json +++ b/relecov_tools/example_data/ena_upload.json @@ -16,7 +16,7 @@ "study_abstract_1", "study_abstract_2" ], - "pubmed_id": [None, + "pubmed_id": ["None", "pubmed_id_2" ] }, @@ -157,7 +157,7 @@ "single" ], "insert_size": [ - "250",None,None + "250","None","None" ], "library_construction_protocol": [ "library_construction_protocol_1", diff --git a/relecov_tools/test/try_01.ipynb b/relecov_tools/test/try_01.ipynb new file mode 100644 index 00000000..df0f0e80 --- /dev/null +++ b/relecov_tools/test/try_01.ipynb @@ -0,0 +1,261 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 25, + "id": "aef6b5c1", + "metadata": {}, + "outputs": [], + "source": [ + "#json to dataframe\n", + "import pandas as pd\n", + "\n", + "df = pd.read_json('../example_data/ena_upload_study.json')" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "id": "8cf882d3", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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study
alias[study_alias_4, study_alias_5]
\n", + "
" + ], + "text/plain": [ + " study\n", + "alias [study_alias_4, study_alias_5]" + ] + }, + "execution_count": 26, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df" + ] + }, + { + "cell_type": "code", + "execution_count": 39, + "id": "95cf4dd2", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(2,)" + ] + }, + "execution_count": 39, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lista = data[\"study\"][\"alias\"]\n", + "import numpy as np\n", + "a = np.array(lista)\n", + "a.shape" + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "id": "f1a7dcf1", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'study': {'alias': ['study_alias_4', 'study_alias_5']}}" + ] + }, + "execution_count": 40, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "data" + ] + }, + { + "cell_type": "code", + "execution_count": 52, + "id": "6f6c7f87", + "metadata": {}, + "outputs": [], + "source": [ + "import json\n", + "# load data using Python JSON module\n", + "with open('../example_data/ena_upload.json','r') as f:\n", + " data = json.loads(f.read())\n", + "\n", + "lista = data[\"study\"]\n", + "df_study = pd.DataFrame(lista, columns=['alias',\"title\",\"study_type\",\"study_abstract\",\"pubmed_id\"])\n", + "\n", + "#study_df pd.DataFrame(columns=[\"alias\"], )\n" + ] + }, + { + "cell_type": "code", + "execution_count": 53, + "id": "a8066308", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'alias': ['study_alias_4', 'study_alias_5'],\n", + " 'title': ['study_title_1', 'study_title_2'],\n", + " 'study_type': ['Transcriptome Analysis', 'RNASeq'],\n", + " 'study_abstract': ['study_abstract_1', 'study_abstract_2'],\n", + " 'pubmed_id': ['None', 'pubmed_id_2']}" + ] + }, + "execution_count": 53, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "lista" + ] + }, + { + "cell_type": "code", + "execution_count": 54, + "id": "5dcb05c6", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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" + ], + "text/plain": [ + " alias title study_type study_abstract \\\n", + "0 study_alias_4 study_title_1 Transcriptome Analysis study_abstract_1 \n", + "1 study_alias_5 study_title_2 RNASeq study_abstract_2 \n", + "\n", + " pubmed_id \n", + "0 None \n", + "1 pubmed_id_2 " + ] + }, + "execution_count": 54, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df_study" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "308e5c21", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.3" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} From ed369b2d83280b5a30a13e063822097c972dc9b9 Mon Sep 17 00:00:00 2001 From: ErikaKvalem Date: Thu, 17 Mar 2022 17:09:25 +0100 Subject: [PATCH 0158/1454] rename create_xml to ena_upload --- relecov_tools/ena_upload_buisciii.py | 174 +++++++++++++++++++++++++++ 1 file changed, 174 insertions(+) create mode 100644 relecov_tools/ena_upload_buisciii.py diff --git a/relecov_tools/ena_upload_buisciii.py b/relecov_tools/ena_upload_buisciii.py new file mode 100644 index 00000000..226f04a3 --- /dev/null +++ b/relecov_tools/ena_upload_buisciii.py @@ -0,0 +1,174 @@ +import os +import logging +import rich.console +from email import utils +import json as j +import xml.etree.cElementTree as e + +import relecov_tools.utils + +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + + +class XmlCreation: + def __init__(self, source_json=None, output_path=None, action=None): + if source_json is None: + self.source_json = utils.prompt_source_path() + else: + self.source_json = source_json + if output_path is None: + self.output_path = utils.prompt_destination_path() + else: + self.output_path = output_path + if action is None: + self.action = "ADD" + else: + self.action = action + + def xml_study( + self, + ): + """ + 1.From validated json to xml study- submission.xml and project.xml + 1.1 Upload study info + + 2. From validated json to xml samples - submission.xml and samples.xml + 2.2 Upload samples info + + 3. From sftp upload runs (FASTQ files programmatic)- experiments.xmlm, runs.xml and submission.xml + 4. From sftp upload sequences (FASTA files programmatic) - json using webin-cli-rest + """ + + # Load validated json + with open(self.source_json) as json_format_file: + json_data = j.load(json_format_file) + + # Create output directory + + try: + # Create target Directory + os.mkdir(self.output_path) + print("Directory ", self.output_path, " Created ") + except FileExistsError: + print("Directory ", self.output_path, " already exists") + + # 1. From validated json to xml study- submission.xml and project.xml + + # submission.xml + os.chdir("xml_files/") + if self.action.upper == "ADD": + # submission add + submission_file = "submission_add.xml" + if self.action.upper() == "MODIFY": + # submission modify + submission_file = "submission_modify.xml" + + # project_relecov.xml + os.chdir("../conf") + dict_conf = j.loads("configuration.json") + r = e.Element("PROJECT_SET") + project = e.SubElement(r, "PROJECT") + project.set("alias", dict_conf["project_relecov_xml"]["alias"]) + e.SubElement(project, "TITLE").text = dict_conf["project_relecov_xml"][ + "TITLE" + ] + e.SubElement(project, "DESCRIPTION").text = dict_conf[ + "project_relecov_xml" + ]["DESCRIPTION"] + submission = e.SubElement(project, "SUBMISSION_PROJECT") + e.SubElement(submission, "SEQUENCING_PROJECT") + a = e.ElementTree(r) + a.write(os.path.join(self.output_path, "study", "project_relecov.xml")) + + # 1.1 Upload study info + """ + import requests + from requests.structures import CaseInsensitiveDict + + url = "https://reqbin.com/echo/post/json" + + headers = CaseInsensitiveDict() + headers["Content-Type"] = "application/json" + headers["Authorization"] = "Basic bG9naW46cGFzc3dvcmQ=" + + data = '{"login":"my_login","password":"my_password"}' + + + resp = requests.post(url, headers=headers, data=data) + + print(resp.status_code) + """ + + # 2. From validated json to xml samples - submission.xml and samples.xml + + def xml_samples(): + # submission.xml + os.chdir("../xml_files/") + if self.action.upper == "ADD": + # submission add + submission_file = "submission_add.xml" + if self.action.upper() == "MODIFY": + # submission modify + submission_file = "submission_modify.xml" + + # samples_relecov.xml + os.chdir("../schema/") + json_data = j.loads("to_ena.json") + os.chdir("../conf") + dict_conf = j.loads("configuration.json") + + data_keys = list(json_data.keys()) + r = e.Element("SAMPLE_SET") + sample = e.SubElement(r, "SAMPLE") + sample.set( + "alias", + "Programmatic Test SARS-CoV-2 Sample" + str(json_data["sample_name"]), + ) + e.SubElement(sample, "TITLE").text = "SARS-CoV-2 Sample" + str( + json_data["sample_name"] + ) + sample_name = e.SubElement(sample, "SAMPLE_NAME") + e.SubElement(sample_name, "TAXON_ID").text = dict_conf["fixed_data"][ + "tax_id" + ] + e.SubElement(sample_name, "SCIENTIFIC_NAME").text = dict_conf["fixed_data"][ + "scientific_name" + ] + e.SubElement(sample, "DESCRIPTION").text = "SARS-CoV-2 Sample" + str( + json_data["sample_name"] + ) + sample_attributes = e.SubElement(sample, "SAMPLE_ATTRIBUTES") + for i in json_data: + sample_attribute = e.SubElement(sample_attributes, "SAMPLE_ATTRIBUTE") + e.SubElement(sample_attribute, "TAG").text = str(i) + e.SubElement(sample_attribute, "VALUE").text = json_data[i] + a = e.ElementTree(r) + a.write(os.path.join(self.output_path, "samples", "samples_relecov.xml")) + + # 2.2 Upload samples info + """ + import requests + from requests.structures import CaseInsensitiveDict + + url = "https://reqbin.com/echo/post/json" + + headers = CaseInsensitiveDict() + headers["Content-Type"] = "application/json" + headers["Authorization"] = "Basic bG9naW46cGFzc3dvcmQ=" + + data = '{"login":"my_login","password":"my_password"}' + + + resp = requests.post(url, headers=headers, data=data) + + print(resp.status_code) + """ + + # 3. From sftp upload runs (FASTQ files programmatic)- experiments.xmlm, runs.xml and submission.xml + # 4. From sftp upload sequences (FASTA files programmatic) - json using webin-cli-rest From 13d6795a485d4778a9b96af34f49b1b30a680a8f Mon Sep 17 00:00:00 2001 From: ErikaKvalem Date: Thu, 17 Mar 2022 17:11:37 +0100 Subject: [PATCH 0159/1454] rename to ena_upload.py --- relecov_tools/ena_upload.py | 174 ++++++++++++++++++++++++++++++++++++ 1 file changed, 174 insertions(+) create mode 100644 relecov_tools/ena_upload.py diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py new file mode 100644 index 00000000..226f04a3 --- /dev/null +++ b/relecov_tools/ena_upload.py @@ -0,0 +1,174 @@ +import os +import logging +import rich.console +from email import utils +import json as j +import xml.etree.cElementTree as e + +import relecov_tools.utils + +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + + +class XmlCreation: + def __init__(self, source_json=None, output_path=None, action=None): + if source_json is None: + self.source_json = utils.prompt_source_path() + else: + self.source_json = source_json + if output_path is None: + self.output_path = utils.prompt_destination_path() + else: + self.output_path = output_path + if action is None: + self.action = "ADD" + else: + self.action = action + + def xml_study( + self, + ): + """ + 1.From validated json to xml study- submission.xml and project.xml + 1.1 Upload study info + + 2. From validated json to xml samples - submission.xml and samples.xml + 2.2 Upload samples info + + 3. From sftp upload runs (FASTQ files programmatic)- experiments.xmlm, runs.xml and submission.xml + 4. From sftp upload sequences (FASTA files programmatic) - json using webin-cli-rest + """ + + # Load validated json + with open(self.source_json) as json_format_file: + json_data = j.load(json_format_file) + + # Create output directory + + try: + # Create target Directory + os.mkdir(self.output_path) + print("Directory ", self.output_path, " Created ") + except FileExistsError: + print("Directory ", self.output_path, " already exists") + + # 1. From validated json to xml study- submission.xml and project.xml + + # submission.xml + os.chdir("xml_files/") + if self.action.upper == "ADD": + # submission add + submission_file = "submission_add.xml" + if self.action.upper() == "MODIFY": + # submission modify + submission_file = "submission_modify.xml" + + # project_relecov.xml + os.chdir("../conf") + dict_conf = j.loads("configuration.json") + r = e.Element("PROJECT_SET") + project = e.SubElement(r, "PROJECT") + project.set("alias", dict_conf["project_relecov_xml"]["alias"]) + e.SubElement(project, "TITLE").text = dict_conf["project_relecov_xml"][ + "TITLE" + ] + e.SubElement(project, "DESCRIPTION").text = dict_conf[ + "project_relecov_xml" + ]["DESCRIPTION"] + submission = e.SubElement(project, "SUBMISSION_PROJECT") + e.SubElement(submission, "SEQUENCING_PROJECT") + a = e.ElementTree(r) + a.write(os.path.join(self.output_path, "study", "project_relecov.xml")) + + # 1.1 Upload study info + """ + import requests + from requests.structures import CaseInsensitiveDict + + url = "https://reqbin.com/echo/post/json" + + headers = CaseInsensitiveDict() + headers["Content-Type"] = "application/json" + headers["Authorization"] = "Basic bG9naW46cGFzc3dvcmQ=" + + data = '{"login":"my_login","password":"my_password"}' + + + resp = requests.post(url, headers=headers, data=data) + + print(resp.status_code) + """ + + # 2. From validated json to xml samples - submission.xml and samples.xml + + def xml_samples(): + # submission.xml + os.chdir("../xml_files/") + if self.action.upper == "ADD": + # submission add + submission_file = "submission_add.xml" + if self.action.upper() == "MODIFY": + # submission modify + submission_file = "submission_modify.xml" + + # samples_relecov.xml + os.chdir("../schema/") + json_data = j.loads("to_ena.json") + os.chdir("../conf") + dict_conf = j.loads("configuration.json") + + data_keys = list(json_data.keys()) + r = e.Element("SAMPLE_SET") + sample = e.SubElement(r, "SAMPLE") + sample.set( + "alias", + "Programmatic Test SARS-CoV-2 Sample" + str(json_data["sample_name"]), + ) + e.SubElement(sample, "TITLE").text = "SARS-CoV-2 Sample" + str( + json_data["sample_name"] + ) + sample_name = e.SubElement(sample, "SAMPLE_NAME") + e.SubElement(sample_name, "TAXON_ID").text = dict_conf["fixed_data"][ + "tax_id" + ] + e.SubElement(sample_name, "SCIENTIFIC_NAME").text = dict_conf["fixed_data"][ + "scientific_name" + ] + e.SubElement(sample, "DESCRIPTION").text = "SARS-CoV-2 Sample" + str( + json_data["sample_name"] + ) + sample_attributes = e.SubElement(sample, "SAMPLE_ATTRIBUTES") + for i in json_data: + sample_attribute = e.SubElement(sample_attributes, "SAMPLE_ATTRIBUTE") + e.SubElement(sample_attribute, "TAG").text = str(i) + e.SubElement(sample_attribute, "VALUE").text = json_data[i] + a = e.ElementTree(r) + a.write(os.path.join(self.output_path, "samples", "samples_relecov.xml")) + + # 2.2 Upload samples info + """ + import requests + from requests.structures import CaseInsensitiveDict + + url = "https://reqbin.com/echo/post/json" + + headers = CaseInsensitiveDict() + headers["Content-Type"] = "application/json" + headers["Authorization"] = "Basic bG9naW46cGFzc3dvcmQ=" + + data = '{"login":"my_login","password":"my_password"}' + + + resp = requests.post(url, headers=headers, data=data) + + print(resp.status_code) + """ + + # 3. From sftp upload runs (FASTQ files programmatic)- experiments.xmlm, runs.xml and submission.xml + # 4. From sftp upload sequences (FASTA files programmatic) - json using webin-cli-rest From b7811c844dbccc02b23559d2c83da638b9127e8d Mon Sep 17 00:00:00 2001 From: ErikaKvalem Date: Thu, 17 Mar 2022 17:25:20 +0100 Subject: [PATCH 0160/1454] added changes dataframes to ena_upload --- relecov_tools/ena_upload.py | 43 ++++++++----------------------------- 1 file changed, 9 insertions(+), 34 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 226f04a3..62b60c2a 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -87,24 +87,6 @@ def xml_study( a.write(os.path.join(self.output_path, "study", "project_relecov.xml")) # 1.1 Upload study info - """ - import requests - from requests.structures import CaseInsensitiveDict - - url = "https://reqbin.com/echo/post/json" - - headers = CaseInsensitiveDict() - headers["Content-Type"] = "application/json" - headers["Authorization"] = "Basic bG9naW46cGFzc3dvcmQ=" - - data = '{"login":"my_login","password":"my_password"}' - - - resp = requests.post(url, headers=headers, data=data) - - print(resp.status_code) - """ - # 2. From validated json to xml samples - submission.xml and samples.xml def xml_samples(): @@ -152,23 +134,16 @@ def xml_samples(): a.write(os.path.join(self.output_path, "samples", "samples_relecov.xml")) # 2.2 Upload samples info - """ - import requests - from requests.structures import CaseInsensitiveDict - - url = "https://reqbin.com/echo/post/json" - - headers = CaseInsensitiveDict() - headers["Content-Type"] = "application/json" - headers["Authorization"] = "Basic bG9naW46cGFzc3dvcmQ=" - - data = '{"login":"my_login","password":"my_password"}' + # 3. From sftp upload runs (FASTQ files programmatic)- experiments.xmlm, runs.xml and submission.xml + # 4. From sftp upload sequences (FASTA files programmatic) - json using webin-cli-rest - resp = requests.post(url, headers=headers, data=data) - print(resp.status_code) - """ +# Adaptation to ena_upload +with open('../example_data/ena_upload.json','r') as f: + data = j.loads(f.read()) - # 3. From sftp upload runs (FASTQ files programmatic)- experiments.xmlm, runs.xml and submission.xml - # 4. From sftp upload sequences (FASTA files programmatic) - json using webin-cli-rest +df_study = pd.DataFrame.from_dict(data["study"]) +df_samples = pd.DataFrame.from_dict(data["samples"]) +df_runs = pd.DataFrame.from_dict(data["runs"]) +df_experiments = pd.DataFrame.from_dict(data["experiments"]) \ No newline at end of file From 24df85ca51905e2961cafaa8530510a959e1ded4 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 18 Mar 2022 00:09:44 +0100 Subject: [PATCH 0161/1454] removed not used python packages --- requirements.txt | 3 --- 1 file changed, 3 deletions(-) diff --git a/requirements.txt b/requirements.txt index 87e3470c..d1fb26aa 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,13 +1,10 @@ click questionary -jinja2 jsonschema packaging prompt_toolkit>=3.0.3 rich>=10.0.0 -sysrsync==1.0.1 requests==2.27.1 -markdown==3.3.6 geopy==2.2.0 paramiko==2.9.2 pyyaml From 3192119ed858f71651e5fa4876ba207859d11f6b Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 18 Mar 2022 00:10:31 +0100 Subject: [PATCH 0162/1454] fixing error typing for ena_schema --- relecov_tools/conf/configuration.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 59da123a..0e99fcde 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -1,7 +1,7 @@ { "json_schemas": { "phage_plus_schema": "phage_plus_V0.json", - "ene_schema": "ena_v01.json", + "ena_schema": "ena_v01.json", "gisaid_schema": "gisaid_v01.json" }, "mapping_metadata_json": "mapping_metadata_json_v01.json", @@ -25,4 +25,4 @@ "tax_id": "2697049", "scientific_name": "Severe acute respiratory syndrome coronavirus 2" } -} \ No newline at end of file +} From b5a19340e94771070b2865e3b230f5dc4709bcc5 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 18 Mar 2022 00:11:26 +0100 Subject: [PATCH 0163/1454] include options in mapped_schema parameter --- relecov_tools/__main__.py | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index f31a4ecf..539096f0 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -13,6 +13,7 @@ import relecov_tools.sftp import relecov_tools.create_xml import relecov_tools.validation_json +import relecov_tools.conversion_schema log = logging.getLogger() @@ -169,7 +170,6 @@ def sftp(user, password, conf_file): "-m", "--metadata_file", type=click.Path(), - default=None, help="file containing metadata", ) @click.option( @@ -217,6 +217,24 @@ def validation(json_file, json_schema, out_folder): log.info("All data in json were validated") +# mapping to ENA schema +@relecov_tools_cli.command(help_priority=5) +@click.option("-p", "--phage_plus_schema", help="File with the phage plus schema") +@click.option("-j", "--json_data", help="File with the json data to convert") +@click.option( + "-m", + "--mapped_schema", + type=click.Choice(["ENA", "GSAID", "other"], case_sensitive=True), + help="schema to be mapped") +@click.option("-f", "--schema_file", help="file with the custom schema") +@click.option("-o", "--output", help="File name and path to store the mapped json") +def mapped_schema(phage_plus_schema, json_data, destination_schema, output): + """Convert data between phage plus schema to ENA, GISAID, or any other schema""" + new_schema = relecov_tools.conversion_schema.MappingSchema(phage_plus_schema, json_data, destination_schema, output) + new_schema.map_to_ena_schema() + + +@relecov_tools_cli.command(help_priority=6) @click.option("-s", "--source_json", help="Where the validated json is") @click.option("-o", "--output_path", help="Output folder for the xml generated files") @click.option("-a", "--action", help="ADD or MODIFY") From 815e73bff2d1ab8bcbd4019ae0c4a69414fd314a Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 18 Mar 2022 00:12:29 +0100 Subject: [PATCH 0164/1454] Working on the initialization class of the conversion schema --- relecov_tools/conversion_schema.py | 106 +++++++++++++++++++++++++++-- 1 file changed, 101 insertions(+), 5 deletions(-) diff --git a/relecov_tools/conversion_schema.py b/relecov_tools/conversion_schema.py index fcc13237..275c9eec 100644 --- a/relecov_tools/conversion_schema.py +++ b/relecov_tools/conversion_schema.py @@ -1,13 +1,109 @@ #!/usr/bin/env python from collections import OrderedDict - +import json +import jsonschema +from jsonschema import Draft202012Validator +import logging +import rich.console +import os +import sys # import jsonschema +import relecov_tools.utils +from relecov_tools.config_json import ConfigJson + +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + + +class MappingSchema: + def __init__(self, phage_plus_schema=None, json_data=None, mapped_schema=None, schema_file=None, output=None): + config_json = ConfigJson() + if phage_plus_schema is None: + phage_plus_schema_file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), + "schema", + config_json.get_topic_data("json_schemas", "phage_plus_schema")) + with open(phage_plus_schema_file, "r") as fh: + self.phage_plus_schema = json.load(fh) + else: + with open(phage_plus_schema, "r") as fh: + json_schema = json.load(fh) + try: + Draft202012Validator.check_schema(json_schema) + except jsonschema.ValidationError: + stderr.print("[red] phage plus schema does not fulfil Draft 202012 Validation") + sys.exit(1) + self.phage_plus_schema = json.load(fh) + + if json_data is None: + self.json_data_file = relecov_tools.utils.prompt_path( + msg="Select the json which have the data to map" + ) + else: + self.json_data_file = json_data + + if mapped_schema is None: + self.mapped_schema = relecov_tools.utils.prompt_selection( + msg="Select ENA, GISAID for already defined schemas or other for custom", + choices=["ENA", "GISAID", "other"] + ) + else: + self.mapped_schema = mapped_schema + if self.mapped_schema == "other": + if schema_file is None: + self.schema_file = relecov_tools.utils.prompt_path( + msg="Select the json schema file to map your data" + ) + else: + self.schema_file = schema_file + if not os.path.exists(self.schema_file): + log.error("Schema file %s to map your data does not exist ", self.metadata_file) + sys.exit(1) + with open(self.schema_file, "r") as fh: + json_schema = json.load(fh) + try: + Draft202012Validator.check_schema(json_schema) + except jsonschema.ValidationError: + stderr.print("[red] Json schema does not fulfil Draft 202012 Validation") + sys.exit(1) + elif self.mapped_schema == "ENA": + self.schema_file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), + "schema", + config_json.get_item("json_schemas", "ena_schema")) + elif self.mapped_schema == "GISAID": + self.schema_file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), + "schema", + config_json.get_item("json_schemas", "gisaid_schema")) + else: + stderr.print("[red] Invalid option for mapping to schena") + sys.exit(1) + with open(self.schema_file, "r") as fh: + self.mapped_to_schema = json.load(fh) + self.ontology = {} + for key , values in self.phage_plus_schema['properties'].items(): + self.ontology[values['ontology']] = key -class PhagePlusData: - def __init__(self, data, json_schema): - self.data = data - self.schema = json_schema + def maping_schemas_based_on_geontology(): + """Return a dictionnary with the properties of the mapped_to_schema as key and + properties of phagePlusSchema as value + """ + mapped_dict = OrderedDict() + for key, values in mapped_to_schema['properties'].items(): + try: + mapped_dict[key] = self.ontology[values['ontology']] + except KeyError : + # There is no exact match on ontology. Search for the parent + # to be implemented later + pass + return mapped_dict def convert_json(schema): pass From 45dc936fe08592b7999aec5821d5a73fbefa8de6 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 18 Mar 2022 00:13:18 +0100 Subject: [PATCH 0165/1454] fixing litin --- relecov_tools/__main__.py | 7 +++-- relecov_tools/conversion_schema.py | 46 +++++++++++++++++++++--------- 2 files changed, 37 insertions(+), 16 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 539096f0..295df381 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -225,12 +225,15 @@ def validation(json_file, json_schema, out_folder): "-m", "--mapped_schema", type=click.Choice(["ENA", "GSAID", "other"], case_sensitive=True), - help="schema to be mapped") + help="schema to be mapped", +) @click.option("-f", "--schema_file", help="file with the custom schema") @click.option("-o", "--output", help="File name and path to store the mapped json") def mapped_schema(phage_plus_schema, json_data, destination_schema, output): """Convert data between phage plus schema to ENA, GISAID, or any other schema""" - new_schema = relecov_tools.conversion_schema.MappingSchema(phage_plus_schema, json_data, destination_schema, output) + new_schema = relecov_tools.conversion_schema.MappingSchema( + phage_plus_schema, json_data, destination_schema, output + ) new_schema.map_to_ena_schema() diff --git a/relecov_tools/conversion_schema.py b/relecov_tools/conversion_schema.py index 275c9eec..d2abd03b 100644 --- a/relecov_tools/conversion_schema.py +++ b/relecov_tools/conversion_schema.py @@ -7,6 +7,7 @@ import rich.console import os import sys + # import jsonschema import relecov_tools.utils from relecov_tools.config_json import ConfigJson @@ -21,13 +22,21 @@ class MappingSchema: - def __init__(self, phage_plus_schema=None, json_data=None, mapped_schema=None, schema_file=None, output=None): + def __init__( + self, + phage_plus_schema=None, + json_data=None, + mapped_schema=None, + schema_file=None, + output=None, + ): config_json = ConfigJson() if phage_plus_schema is None: phage_plus_schema_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", - config_json.get_topic_data("json_schemas", "phage_plus_schema")) + config_json.get_topic_data("json_schemas", "phage_plus_schema"), + ) with open(phage_plus_schema_file, "r") as fh: self.phage_plus_schema = json.load(fh) else: @@ -36,7 +45,9 @@ def __init__(self, phage_plus_schema=None, json_data=None, mapped_schema=None, s try: Draft202012Validator.check_schema(json_schema) except jsonschema.ValidationError: - stderr.print("[red] phage plus schema does not fulfil Draft 202012 Validation") + stderr.print( + "[red] phage plus schema does not fulfil Draft 202012 Validation" + ) sys.exit(1) self.phage_plus_schema = json.load(fh) @@ -50,7 +61,7 @@ def __init__(self, phage_plus_schema=None, json_data=None, mapped_schema=None, s if mapped_schema is None: self.mapped_schema = relecov_tools.utils.prompt_selection( msg="Select ENA, GISAID for already defined schemas or other for custom", - choices=["ENA", "GISAID", "other"] + choices=["ENA", "GISAID", "other"], ) else: self.mapped_schema = mapped_schema @@ -62,25 +73,32 @@ def __init__(self, phage_plus_schema=None, json_data=None, mapped_schema=None, s else: self.schema_file = schema_file if not os.path.exists(self.schema_file): - log.error("Schema file %s to map your data does not exist ", self.metadata_file) + log.error( + "Schema file %s to map your data does not exist ", + self.metadata_file, + ) sys.exit(1) with open(self.schema_file, "r") as fh: json_schema = json.load(fh) try: Draft202012Validator.check_schema(json_schema) except jsonschema.ValidationError: - stderr.print("[red] Json schema does not fulfil Draft 202012 Validation") + stderr.print( + "[red] Json schema does not fulfil Draft 202012 Validation" + ) sys.exit(1) elif self.mapped_schema == "ENA": self.schema_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", - config_json.get_item("json_schemas", "ena_schema")) + config_json.get_item("json_schemas", "ena_schema"), + ) elif self.mapped_schema == "GISAID": self.schema_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", - config_json.get_item("json_schemas", "gisaid_schema")) + config_json.get_item("json_schemas", "gisaid_schema"), + ) else: stderr.print("[red] Invalid option for mapping to schena") sys.exit(1) @@ -88,18 +106,18 @@ def __init__(self, phage_plus_schema=None, json_data=None, mapped_schema=None, s self.mapped_to_schema = json.load(fh) self.ontology = {} - for key , values in self.phage_plus_schema['properties'].items(): - self.ontology[values['ontology']] = key + for key, values in self.phage_plus_schema["properties"].items(): + self.ontology[values["ontology"]] = key def maping_schemas_based_on_geontology(): """Return a dictionnary with the properties of the mapped_to_schema as key and - properties of phagePlusSchema as value + properties of phagePlusSchema as value """ mapped_dict = OrderedDict() - for key, values in mapped_to_schema['properties'].items(): + for key, values in mapped_to_schema["properties"].items(): try: - mapped_dict[key] = self.ontology[values['ontology']] - except KeyError : + mapped_dict[key] = self.ontology[values["ontology"]] + except KeyError: # There is no exact match on ontology. Search for the parent # to be implemented later pass From b6dd930a8ba5bdbd6d9d0579ed05063022d9ac13 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 18 Mar 2022 15:05:18 +0100 Subject: [PATCH 0166/1454] fixing bugs in mapping schema --- relecov_tools/__main__.py | 10 ++++---- relecov_tools/conversion_schema.py | 32 +++++++++++++++---------- relecov_tools/schema/phage_plus_V0.json | 4 ++-- requirements.txt | 1 + 4 files changed, 28 insertions(+), 19 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 295df381..b0b86eb1 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -222,19 +222,19 @@ def validation(json_file, json_schema, out_folder): @click.option("-p", "--phage_plus_schema", help="File with the phage plus schema") @click.option("-j", "--json_data", help="File with the json data to convert") @click.option( - "-m", - "--mapped_schema", + "-d", + "--destination_schema", type=click.Choice(["ENA", "GSAID", "other"], case_sensitive=True), help="schema to be mapped", ) @click.option("-f", "--schema_file", help="file with the custom schema") @click.option("-o", "--output", help="File name and path to store the mapped json") -def mapped_schema(phage_plus_schema, json_data, destination_schema, output): +def mapped_schema(phage_plus_schema, json_data, destination_schema, schema_file, output): """Convert data between phage plus schema to ENA, GISAID, or any other schema""" new_schema = relecov_tools.conversion_schema.MappingSchema( - phage_plus_schema, json_data, destination_schema, output + phage_plus_schema, json_data, destination_schema, schema_file, output ) - new_schema.map_to_ena_schema() + new_schema.map_to_data_to_new_schema() @relecov_tools_cli.command(help_priority=6) diff --git a/relecov_tools/conversion_schema.py b/relecov_tools/conversion_schema.py index d2abd03b..fd72f8af 100644 --- a/relecov_tools/conversion_schema.py +++ b/relecov_tools/conversion_schema.py @@ -26,7 +26,7 @@ def __init__( self, phage_plus_schema=None, json_data=None, - mapped_schema=None, + destination_schema=None, schema_file=None, output=None, ): @@ -58,14 +58,14 @@ def __init__( else: self.json_data_file = json_data - if mapped_schema is None: - self.mapped_schema = relecov_tools.utils.prompt_selection( + if destination_schema is None: + self.destination_schema = relecov_tools.utils.prompt_selection( msg="Select ENA, GISAID for already defined schemas or other for custom", choices=["ENA", "GISAID", "other"], ) else: - self.mapped_schema = mapped_schema - if self.mapped_schema == "other": + self.destination_schema = destination_schema + if self.destination_schema == "other": if schema_file is None: self.schema_file = relecov_tools.utils.prompt_path( msg="Select the json schema file to map your data" @@ -87,13 +87,13 @@ def __init__( "[red] Json schema does not fulfil Draft 202012 Validation" ) sys.exit(1) - elif self.mapped_schema == "ENA": + elif self.destination_schema == "ENA": self.schema_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", - config_json.get_item("json_schemas", "ena_schema"), + config_json.get_topic_data("json_schemas", "ena_schema"), ) - elif self.mapped_schema == "GISAID": + elif self.destination_schema == "GISAID": self.schema_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", @@ -109,20 +109,23 @@ def __init__( for key, values in self.phage_plus_schema["properties"].items(): self.ontology[values["ontology"]] = key - def maping_schemas_based_on_geontology(): + + def maping_schemas_based_on_geontology(self): """Return a dictionnary with the properties of the mapped_to_schema as key and properties of phagePlusSchema as value """ mapped_dict = OrderedDict() - for key, values in mapped_to_schema["properties"].items(): + for key, values in self.mapped_to_schema["properties"].items(): try: mapped_dict[key] = self.ontology[values["ontology"]] - except KeyError: + except KeyError as e: # There is no exact match on ontology. Search for the parent # to be implemented later - pass + stderr.print(f"[red] Ontology value {e} not in phage plus schema") + import pdb; pdb.set_trace() return mapped_dict + def convert_json(schema): pass @@ -135,3 +138,8 @@ def map_sample_to_schema(self, mapped_structure): for item, value in mapped_structure.items: mapped_sample_list[item] = self.data[value] return map_sample_dict + + def map_to_data_to_new_schema(self): + """Mapping the json data from phage plus schema to the requested one """ + mapping_schema_dict = self.maping_schemas_based_on_geontology() + mapped_dict = self.mapping_json_data(mapping_schema_dict) diff --git a/relecov_tools/schema/phage_plus_V0.json b/relecov_tools/schema/phage_plus_V0.json index c669b5b5..ed7382aa 100644 --- a/relecov_tools/schema/phage_plus_V0.json +++ b/relecov_tools/schema/phage_plus_V0.json @@ -20,7 +20,7 @@ "examples": [ "prov_rona_99" ], - "ontology": "0", + "ontology": "GENEPIO:0001123", "type": "string", "description": "The user-defined name for the sample.", "clasification": "Database Identifiers", @@ -2474,7 +2474,7 @@ "type": "string", "description": "", "clasification": "Submission ENA", - "format": "date", + "format": "date", "label": "Last Updated" }, "experiment_title": { diff --git a/requirements.txt b/requirements.txt index d1fb26aa..fe49de70 100644 --- a/requirements.txt +++ b/requirements.txt @@ -8,3 +8,4 @@ requests==2.27.1 geopy==2.2.0 paramiko==2.9.2 pyyaml +openpyxl From 34613cdbe1361f1968083278963154255f7dee7e Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 18 Mar 2022 17:48:51 +0100 Subject: [PATCH 0167/1454] Include options ADD/MODIFY in upload_to_ena command --- relecov_tools/__main__.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index b0b86eb1..21be5521 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -240,7 +240,12 @@ def mapped_schema(phage_plus_schema, json_data, destination_schema, schema_file, @relecov_tools_cli.command(help_priority=6) @click.option("-s", "--source_json", help="Where the validated json is") @click.option("-o", "--output_path", help="Output folder for the xml generated files") -@click.option("-a", "--action", help="ADD or MODIFY") +@click.option( + "-a", + "--action", + type=click.Choice(["ADD", "MODIFY"], case_sensitive=True), + help="Select one of the options ADD or MODIFY" + ) def xml(source_json, output_path, action): """Parsed data to create xml files to upload to ENA""" xml_creation = relecov_tools.create_xml.XmlCreation( From b3b8f7cb5169f1e315e8caaff12678acae62195c Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 18 Mar 2022 17:53:09 +0100 Subject: [PATCH 0168/1454] modify file and class for upload_to_ena command --- relecov_tools/__main__.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 21be5521..d4a2aee8 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -246,12 +246,12 @@ def mapped_schema(phage_plus_schema, json_data, destination_schema, schema_file, type=click.Choice(["ADD", "MODIFY"], case_sensitive=True), help="Select one of the options ADD or MODIFY" ) -def xml(source_json, output_path, action): +def upload_to_ena(source_json, output_path, action): """Parsed data to create xml files to upload to ENA""" - xml_creation = relecov_tools.create_xml.XmlCreation( + upload_ena = relecov_tools.ena_upload.EnaUpload( source_json, output_path, action ) - xml_creation.generate_xml() + upload_ena.generate_xml() if __name__ == "__main__": From 4cc342fc02bb4402ff2696a6ba00dc0115ef1870 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 18 Mar 2022 18:20:25 +0100 Subject: [PATCH 0169/1454] write to a file the mapped json --- relecov_tools/__main__.py | 12 ++++---- relecov_tools/conversion_schema.py | 45 +++++++++++++++++++----------- 2 files changed, 35 insertions(+), 22 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index d4a2aee8..b3a9c5e1 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -229,7 +229,9 @@ def validation(json_file, json_schema, out_folder): ) @click.option("-f", "--schema_file", help="file with the custom schema") @click.option("-o", "--output", help="File name and path to store the mapped json") -def mapped_schema(phage_plus_schema, json_data, destination_schema, schema_file, output): +def mapped_schema( + phage_plus_schema, json_data, destination_schema, schema_file, output +): """Convert data between phage plus schema to ENA, GISAID, or any other schema""" new_schema = relecov_tools.conversion_schema.MappingSchema( phage_plus_schema, json_data, destination_schema, schema_file, output @@ -244,13 +246,11 @@ def mapped_schema(phage_plus_schema, json_data, destination_schema, schema_file, "-a", "--action", type=click.Choice(["ADD", "MODIFY"], case_sensitive=True), - help="Select one of the options ADD or MODIFY" - ) + help="Select one of the options ADD or MODIFY", +) def upload_to_ena(source_json, output_path, action): """Parsed data to create xml files to upload to ENA""" - upload_ena = relecov_tools.ena_upload.EnaUpload( - source_json, output_path, action - ) + upload_ena = relecov_tools.ena_upload.EnaUpload(source_json, output_path, action) upload_ena.generate_xml() diff --git a/relecov_tools/conversion_schema.py b/relecov_tools/conversion_schema.py index fd72f8af..91fc112b 100644 --- a/relecov_tools/conversion_schema.py +++ b/relecov_tools/conversion_schema.py @@ -1,5 +1,6 @@ #!/usr/bin/env python from collections import OrderedDict +from datetime import datetime import json import jsonschema from jsonschema import Draft202012Validator @@ -57,6 +58,10 @@ def __init__( ) else: self.json_data_file = json_data + if not os.path.isfile(self.json_data_file): + log.error("json data file %s does not exist ", self.json_data_file) + stderr.print(f"json data file {self.json_data_file} does not exist") + sys.exit(1) if destination_schema is None: self.destination_schema = relecov_tools.utils.prompt_selection( @@ -109,7 +114,6 @@ def __init__( for key, values in self.phage_plus_schema["properties"].items(): self.ontology[values["ontology"]] = key - def maping_schemas_based_on_geontology(self): """Return a dictionnary with the properties of the mapped_to_schema as key and properties of phagePlusSchema as value @@ -122,24 +126,33 @@ def maping_schemas_based_on_geontology(self): # There is no exact match on ontology. Search for the parent # to be implemented later stderr.print(f"[red] Ontology value {e} not in phage plus schema") - import pdb; pdb.set_trace() return mapped_dict + def mapping_json_data(self, mapping_schema_dict): + """Convert phage plus data to the requested schema""" + mapped_data = [] + with open(self.json_data, "r") as fh: + json_data = json.load(fh) + for data in json_data: + map_sample_dict = OrderedDict() + for item, value in mapping_schema_dict.items: + map_sample_dict[item] = self.data[value] + mapped_data.append(map_sample_dict) + return mapped_data - def convert_json(schema): - pass - - def get_data(self, field): - return self.data[field] - - def map_sample_to_schema(self, mapped_structure): - mapped_sample_list = [] - map_sample_dict = OrderedDict() - for item, value in mapped_structure.items: - mapped_sample_list[item] = self.data[value] - return map_sample_dict + def write_json_fo_file(self, mapped_json_data): + """Write metadata to json file""" + os.makedirs(self.output_folder, exist_ok=True) + time = datetime.now().strftime("%Y_%m_%d_%H_%M") + f_sub_name = os.path.basename(self.json_data).split(".")[0] + file_name = f_sub_name + "_" + time + "_ena_mapped.json" + json_file = os.path.join(self.output_folder, file_name) + with open(json_file, "w") as fh: + fh.write(json.dumps(mapped_json_data)) + return True def map_to_data_to_new_schema(self): - """Mapping the json data from phage plus schema to the requested one """ + """Mapping the json data from phage plus schema to the requested one""" mapping_schema_dict = self.maping_schemas_based_on_geontology() - mapped_dict = self.mapping_json_data(mapping_schema_dict) + mapped_json_data = self.mapping_json_data(mapping_schema_dict) + self.write_json_fo_file(mapped_json_data) From 8c1854d71aedeccb4e487cfd374cc6b7c5b99e64 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 18 Mar 2022 18:24:13 +0100 Subject: [PATCH 0170/1454] include ena-upload-cli python package in the requirements file --- requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements.txt b/requirements.txt index fe49de70..0e38527e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,3 +9,4 @@ geopy==2.2.0 paramiko==2.9.2 pyyaml openpyxl +ena-upload-cli From 56406c3f83e5a915db57b21278495c2355ce327b Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 18 Mar 2022 18:25:16 +0100 Subject: [PATCH 0171/1454] remove the duplicated ena_upload file --- relecov_tools/ena_upload_buisciii.py | 174 --------------------------- 1 file changed, 174 deletions(-) delete mode 100644 relecov_tools/ena_upload_buisciii.py diff --git a/relecov_tools/ena_upload_buisciii.py b/relecov_tools/ena_upload_buisciii.py deleted file mode 100644 index 226f04a3..00000000 --- a/relecov_tools/ena_upload_buisciii.py +++ /dev/null @@ -1,174 +0,0 @@ -import os -import logging -import rich.console -from email import utils -import json as j -import xml.etree.cElementTree as e - -import relecov_tools.utils - -log = logging.getLogger(__name__) -stderr = rich.console.Console( - stderr=True, - style="dim", - highlight=False, - force_terminal=relecov_tools.utils.rich_force_colors(), -) - - -class XmlCreation: - def __init__(self, source_json=None, output_path=None, action=None): - if source_json is None: - self.source_json = utils.prompt_source_path() - else: - self.source_json = source_json - if output_path is None: - self.output_path = utils.prompt_destination_path() - else: - self.output_path = output_path - if action is None: - self.action = "ADD" - else: - self.action = action - - def xml_study( - self, - ): - """ - 1.From validated json to xml study- submission.xml and project.xml - 1.1 Upload study info - - 2. From validated json to xml samples - submission.xml and samples.xml - 2.2 Upload samples info - - 3. From sftp upload runs (FASTQ files programmatic)- experiments.xmlm, runs.xml and submission.xml - 4. From sftp upload sequences (FASTA files programmatic) - json using webin-cli-rest - """ - - # Load validated json - with open(self.source_json) as json_format_file: - json_data = j.load(json_format_file) - - # Create output directory - - try: - # Create target Directory - os.mkdir(self.output_path) - print("Directory ", self.output_path, " Created ") - except FileExistsError: - print("Directory ", self.output_path, " already exists") - - # 1. From validated json to xml study- submission.xml and project.xml - - # submission.xml - os.chdir("xml_files/") - if self.action.upper == "ADD": - # submission add - submission_file = "submission_add.xml" - if self.action.upper() == "MODIFY": - # submission modify - submission_file = "submission_modify.xml" - - # project_relecov.xml - os.chdir("../conf") - dict_conf = j.loads("configuration.json") - r = e.Element("PROJECT_SET") - project = e.SubElement(r, "PROJECT") - project.set("alias", dict_conf["project_relecov_xml"]["alias"]) - e.SubElement(project, "TITLE").text = dict_conf["project_relecov_xml"][ - "TITLE" - ] - e.SubElement(project, "DESCRIPTION").text = dict_conf[ - "project_relecov_xml" - ]["DESCRIPTION"] - submission = e.SubElement(project, "SUBMISSION_PROJECT") - e.SubElement(submission, "SEQUENCING_PROJECT") - a = e.ElementTree(r) - a.write(os.path.join(self.output_path, "study", "project_relecov.xml")) - - # 1.1 Upload study info - """ - import requests - from requests.structures import CaseInsensitiveDict - - url = "https://reqbin.com/echo/post/json" - - headers = CaseInsensitiveDict() - headers["Content-Type"] = "application/json" - headers["Authorization"] = "Basic bG9naW46cGFzc3dvcmQ=" - - data = '{"login":"my_login","password":"my_password"}' - - - resp = requests.post(url, headers=headers, data=data) - - print(resp.status_code) - """ - - # 2. From validated json to xml samples - submission.xml and samples.xml - - def xml_samples(): - # submission.xml - os.chdir("../xml_files/") - if self.action.upper == "ADD": - # submission add - submission_file = "submission_add.xml" - if self.action.upper() == "MODIFY": - # submission modify - submission_file = "submission_modify.xml" - - # samples_relecov.xml - os.chdir("../schema/") - json_data = j.loads("to_ena.json") - os.chdir("../conf") - dict_conf = j.loads("configuration.json") - - data_keys = list(json_data.keys()) - r = e.Element("SAMPLE_SET") - sample = e.SubElement(r, "SAMPLE") - sample.set( - "alias", - "Programmatic Test SARS-CoV-2 Sample" + str(json_data["sample_name"]), - ) - e.SubElement(sample, "TITLE").text = "SARS-CoV-2 Sample" + str( - json_data["sample_name"] - ) - sample_name = e.SubElement(sample, "SAMPLE_NAME") - e.SubElement(sample_name, "TAXON_ID").text = dict_conf["fixed_data"][ - "tax_id" - ] - e.SubElement(sample_name, "SCIENTIFIC_NAME").text = dict_conf["fixed_data"][ - "scientific_name" - ] - e.SubElement(sample, "DESCRIPTION").text = "SARS-CoV-2 Sample" + str( - json_data["sample_name"] - ) - sample_attributes = e.SubElement(sample, "SAMPLE_ATTRIBUTES") - for i in json_data: - sample_attribute = e.SubElement(sample_attributes, "SAMPLE_ATTRIBUTE") - e.SubElement(sample_attribute, "TAG").text = str(i) - e.SubElement(sample_attribute, "VALUE").text = json_data[i] - a = e.ElementTree(r) - a.write(os.path.join(self.output_path, "samples", "samples_relecov.xml")) - - # 2.2 Upload samples info - """ - import requests - from requests.structures import CaseInsensitiveDict - - url = "https://reqbin.com/echo/post/json" - - headers = CaseInsensitiveDict() - headers["Content-Type"] = "application/json" - headers["Authorization"] = "Basic bG9naW46cGFzc3dvcmQ=" - - data = '{"login":"my_login","password":"my_password"}' - - - resp = requests.post(url, headers=headers, data=data) - - print(resp.status_code) - """ - - # 3. From sftp upload runs (FASTQ files programmatic)- experiments.xmlm, runs.xml and submission.xml - # 4. From sftp upload sequences (FASTA files programmatic) - json using webin-cli-rest From de75524f9cb9b681fae57d1d5a71717dde2c03ac Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 18 Mar 2022 18:33:49 +0100 Subject: [PATCH 0172/1454] rename schema in config file --- relecov_tools/conf/configuration.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 0e99fcde..9fc52356 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -1,8 +1,8 @@ { "json_schemas": { - "phage_plus_schema": "phage_plus_V0.json", - "ena_schema": "ena_v01.json", - "gisaid_schema": "gisaid_v01.json" + "phage_plus_schema": "phage_plus_schema.json", + "ena_schema": "ena_schema.json", + "gisaid_schema": "gisaid_schema.json" }, "mapping_metadata_json": "mapping_metadata_json_v01.json", "additional_metadata": "additional_metadata_v01.json", From eb8346f1103cf7fa553308b0d05f0cfddb902654 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 18 Mar 2022 18:36:20 +0100 Subject: [PATCH 0173/1454] rename the schema files and remove the not needed ones --- .../schema/{ena_v01.json => ena_schema.json} | 0 relecov_tools/schema/genepio.owl | 22876 ---------------- .../{gisaid_V0.json => gisaid_schema.json} | 0 ...v01.json => mapping_metadata_to_json.json} | 0 ...ge_plus_V0.json => phage_plus_schema.json} | 0 .../{phage_V0.json => phage_schema.json} | 0 relecov_tools/schema/small_schema.json | 1210 - 7 files changed, 24086 deletions(-) rename relecov_tools/schema/{ena_v01.json => ena_schema.json} (100%) delete mode 100644 relecov_tools/schema/genepio.owl rename relecov_tools/schema/{gisaid_V0.json => gisaid_schema.json} (100%) rename relecov_tools/schema/{mapping_metadata_json_v01.json => mapping_metadata_to_json.json} (100%) rename relecov_tools/schema/{phage_plus_V0.json => phage_plus_schema.json} (100%) rename relecov_tools/schema/{phage_V0.json => phage_schema.json} (100%) delete mode 100644 relecov_tools/schema/small_schema.json diff --git a/relecov_tools/schema/ena_v01.json b/relecov_tools/schema/ena_schema.json similarity index 100% rename from relecov_tools/schema/ena_v01.json rename to relecov_tools/schema/ena_schema.json diff --git a/relecov_tools/schema/genepio.owl b/relecov_tools/schema/genepio.owl deleted file mode 100644 index bde12348..00000000 --- a/relecov_tools/schema/genepio.owl +++ /dev/null @@ -1,22876 +0,0 @@ - - - - - - - - - - - - - - - -]> - - - - - - - - - - - - - - - - - - - - - - - 2022-02-06 - The Genomic Epidemiology Ontology aims to provide a comprehensive controlled vocabulary for infectious disease surveillance and outbreak investigations. It is an application ontology that draws on many other ontologies including anatomy, taxonomy, disease, symptoms, environment and food types for foodborn pathogen metadata. - - Genomic Epidemiology Ontology - GENEPIO - - - - - - - - - - - - - metadata section - - - - - - - - term as in existing standard - - - - - - - - term source - - - - - - - - The user interface label is the label that should be placed on a datum when presented on a form or report - Damion Dooley - user interface label - - - - - - - - user interface definition - - - - - - - - A user interface help annotation is a textual phrase to display with an entity on a form or report that provides some detail about what the entity is or how it is being used. - Damion Dooley - user interface help - true - - - - - - - - Damion Dooley - - user interface hidden - true - - - - - - - - A user interface feature is a pre-set list of features and their acceptable values that a user interface rendering system should use to display an entity on a form or report - Damion Dooley - user interface feature - - - - - - - - This annotation can be used to select the value specification that a referenced entity or specification component has for data entry. Can be scalar value specification / categorical tree specification etc. - Damion Dooley - obsolete: user interface value specification - true - - - - - - - - UI regex normalize - - Damion Dooley - user interface regular epression normalize - - - - - - - - UI regex validate - - Damion Dooley - user interface regular expression validate - - - - - - - - UI regex format - - Damion Dooley - user interface regular expression display format - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - label - - - - - - - - see also - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - part of - - - - - - - - Damion comments: In GenEpiO, If an entity has more than one value specification (in a conjunction), then it means the entitiy is a complex entity that can have a value for each specification. Minimum data requirements can be spelled out using some, min 1, max 10 etc. restrictions. - - - - - - - - realized in - - - - - - - - - - - - - - obsolete has string specification of - true - - - - - - - - - - - T1 after t2 iff:= t2 before_or_simulataneous_with t1 and not (t1 simultaeous_with t2) - Damion Dooley - Damion Dooley's note: Intention is to have it be the inverse of "before". This allows axioms like "B after A" to be placed in class B, rather than having to phrase them as "A before B" in class A. - -I believe time dependency relations (conditions) don't imply existence by themselves. If B after A, and B exists, this doesn't necessarily mean that A exists, only that if A does exist, it must be before B. To add that extra existence implication probably requires the "causally downstream of" and "immediately causally downstream of" RO relations, in a closed system where B cannot exist any other way. - after - - - - - - - - - - obsolete: has string value specification - true - - - - - - - - obsolete: has categorical specification of - true - - - - - - - - - - obsolete: has categorical value specification - true - - - - - - - - has unit - - - - - - - - - is about - - - - - - - - specifies - - - - - - - - inheres in - - - - - - - - has participant - - - - - - - - - - - - - - location of - - - - - - - - located in - - - - - - - - aligned with - - - - - - - - T1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) - - - - - - - - - - has component - - - - - - - - - adjacent to - - - - - - - - - has input - has input - - - - - - - - - has output - has output - - - - - - - - - - member of - - - - - - - - has member - - - - - - - - output of - - - - - - - - - link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch. - - exactMatch - - - - - - - - - - - - - - - - An object relation between a LinkML SlotDefinition to a LocalName. - - - - - - - - - - - - - - - - - - - - - - - An abstract class is a high level class or slot that is typically used to group common slots together and cannot be directly instantiated. - - - - - - - - - Notes and comments about an element intended for external consumption. - - - - - - - - - - - - - - - - - - Date/time at which the element was created. - - - - - - - - - Not Applicable; Missing; Not Collected; Not Provided; Restricted Access - A value (string or URI) indicating the data collection state an instance of a slot has. - - - - - - - - - A description of the element's purpose and use - - - - - - - - - A list of terms from different schemas or terminology systems that have identical meaning. - - - - - - - - - Id of the schema that defined the element. - - - - - - - - - - - - - - - - - - The imports entry that this element was derived from. Empty means primary source - - - - - - - - - - - The ncname of the source of the name. - - 2021-04-26T22:15:07Z - 2021-04-26T22:15:07Z - local_name_source - - - - - - - - - - - A name assigned to an element in a given ontology. - - - - - - - - - - For slots with ranges of type number, the value must be equal to or lowe than this - - - - - - - - - - - - - - - - - - For slots with ranges of type number, the value must be equal to or higher than this - - - - - - - - - - true means that slot can have more than one value - - - - - - - - - - The unique name of the element within the context of the schema. Name is combined with the default prefix to form the globally unique subject of the target class. - - - - - - - - - - The string value of the slot must conform to this regular expression - - - - - - - - - A list of possible values for a slot range. - - - - - - - - - - true if this slot is not required, but is recommended. - - - - - - - - - - true means that the slot must be present in the loaded definition. - - - - - - - - - - A reference. - - - - - - - - - - IAO:0000122 ('ready for release') - status of the element. - - - - - - - - - The uri that defines the possible values for the type definition - URI is typically drawn from the set of URI's defined in OWL (https://www.w3.org/TR/2012/REC-owl2-syntax-20121211/#Datatype_Maps) - - - - - - - - - - - - - - - - - - - - Description of what the value is doing. - - - - - - - - - - - - - - - - - - - - - - - - A persistent, unique identifier of a molecular sequence database entry. - Damion Dooley - EDAM - sequence accession - - - - - - - - - The name of a field in a database. - database field name - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - Damion Dooley - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CLSI - NCCLS - National Committee on Clinical Laboratory Standards (NCCLS) - On January 1, 2005 the National Committee on Clinical Laboratory Standards (NCCLS) changed its name to CLSI - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - depth:1 - - - - - - - - - - - - - - - - - order: -ARO:3004303 # nonsensitive -ARO:3004300 # intermediate -ARO:3004302 # sensitive -ARO:3004304 # sensitive - dose dependant -ARO:3004301 # resistant - - - - - - - - http://purl.obolibrary.org/obo/PATO_0000001 - - - - - - - - http://purl.obolibrary.org/obo/CHEBI_50906 - - - - - - - - Note that this can refer to a material entity like an organ or muscle, or an immaterial entity (a site or fiat boundary) like skin, stomach cavity or lung surface. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Trd - - - - - - - - - deoxyribonucleic acid - - - - - - - - - - STR - Sm - Stm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/CHEBI_33281 - obsolete: antibiotic - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Am - Amk - - - - - - - - - - - - - - - - - Amx - - - - - - - - - PAS - - - - - - - - - - - - - - - - - - - - - - - - - Rif - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Pto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAP - Cm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Clr - - - - - - - - - Cfz - - - - - - - - - - - - - - - - - - - - - - - - - CYC - Cs - - - - - - - - - pyrazinamide - Pza - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - E - ETB - Emb - - - - - - - - - - - - - - - - - - ETH - Eto - - - - - - - - - - - - - - - - - - - - - - - - Currently "K antigen" is a CHEBI_73772 chemical entity rather than a role. - K antigen - - - - - - - - - - - - - - - - - Inh - isoniazid - - - - - - - - - - - - - - - - - Kan - - - - - - - - - Lfx - - - - - - - - - - Lzd - - - - - - - - - - MXF - Mfx - - - - - Mfx - https://www.ncbi.nlm.nih.gov/books/NBK247415/bin/part3-m17.pdf - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Bdq - - - - - - - - - - - - - - Damion Dooley's note: 'K antigen' can't be a subclass of antigen as chemical entity is disjoint from role. - Snomed: Concept 260824002 - - - - - - - - - - - - - - - - - - - Ofx - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - specimen extraction matrix - "This observable is important where process of capturing sample can affect dna extraction." - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/OGMS_0000031 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - state / province / territory / region - lookup:http://purl.obolibrary.org/obo/GAZ_00000448 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Transmission of a disease agent (infectious pathogen, toxic chemical, etc.) from a source that is common to those who acquire the disease. Common vehicles include air, water, food, injected substances. Legionellosis is an example of common vehicle spread in air that has passed through air conditioning equipment contaminated by the causal organism. HIV disease and hepatitis B and C can be spread among illicit drug users by the common vehicle of contaminated needles and syringes. Cholera and many other waterborne diseases are spread by the common vehicle of contaminated water. - common vehicle transmission - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role that inheres in a material that is input as the subject of interest in a scientific technique - either as an entity about which data is generated in an assay or study, or an entity that is transformed or modified in a material processing technique (e.g. the source from which a biological sample is taken) - experimental subject role - - - - - - - - - - - - - - - - - - - - - depth:1 - - https://en.wikipedia.org/wiki/Medical_state - condition - medical condition - medical state - Damion Dooley note: GenEpiO includes various health status descriptors here; many are annotated as included in the American AHA HIPPA or United Kingdom NHS terminologies. The challenge is to map them or order them in such a way that merged data can be analyzed. - http://semanticscience.org/resource/SIO_010057 - - - - - - - - - - - Condition - - - - - - - - - - - Condition - - - - - - - - - The process of drawing in by breathing. - http://purl.obolibrary.org/obo/ExO_0000057 - inhalation - - - - - - - - - Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential - MIxS - - - - - - - - - - A symptom onset date is a date-time entity that marks the start of one or more reported symptoms pertaining to an episode of human or animal illness - Damion Dooley - symptom onset date - - - - - - - - - - A substance, usually composed primarily of carbohydrates, fats, water and/or proteins, that can be eaten or drunk by an animal or human being for nutrition or pleasure. - Damion Dooley - - foodon product type - - - - - - - - lookup - - - - - - - - - - - - - - - - lookup - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - lookup - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - food packing medium - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - [Oceans and Seas] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Census Regions and Divisions are groupings of States that subdivide the United States. - Damion Dooley - United States Census Bureau - http://www.census.gov/econ/census/help/geography/regions_and_divisions.html - - - - - - - - - A census region in the United States of America - Damion Dooley - - - - - - - - - A census region in the United States of America - Damion Dooley - - - - - - - - - A census region in the United States of America - Damion Dooley - - - - - - - - - A census region in the United States of America - Damion Dooley - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - directly governed city (North Korea) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GSCID-BRC standard - - The GSCID-BRC Project and Sample Application Standard captures standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases. - The NIAID page for specifications has a broken link for Core Project. This is the existing page: - -https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project - -Link page is: - -https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards - Damion Dooley - This standard was developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs), and NIAID and informed by discussions and input with numerous collaborating scientists. - GSCID-BRC Project and Sample Application Standard - - - - - - - - - MIxS standard - - MixS is a unified standard for describing sequence data provided by the Genomic Standards Consortium (GSC) - Damion Dooley - Minimum Information about any (x) Sequence (MIxS) - - - - - - - - - MIMARKS standard - The "minimum information about a marker gene sequence" (MIMARKS) is a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences. - http://www.nature.com/nbt/journal/v29/n5/full/nbt.1823.html - Minimum information about a marker gene sequence - - - - - - - - - - "other (metadata choice)" indicates that for the given categorical variable, a respondent has chosen an other or additional response not listed. - This class cannot be referred to directly as a subclass of more than one class without involving inference from the respective classes. Instances of it may exist as a kind of metadata. Usually a reference to a parent categorical class, but not a subordinate, carries the same information. - Damion Dooley - other (metadata value) - - - - - - - - - other relevance - - - - - - - - - other - - Other: specify the sample scope that was used. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - other specimen scope - - - - - - - - - other material - - Other: specify the material that was used. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - other material derived from specimen - - - - - - - - - - "other capture type" is a free text description provided to indicate a target capture specification not covered by the other types. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - other capture type - - - - - - - - - - Specify the project method - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - other project method - - - - - - - - This is an organizational category for grouping parameters relevant to a biomedical sample. - Damion Dooley - - obsolete: draft GenEpiO BioSample standard - true - - - - - - - - An NCBI antibiogram data item is an antimicrobial susceptibility and resistance datum related to drug resistant pathogens. This information is provided within an antibiogram table on BioSample records. - Damion Dooley - - - obsolete: NCBI antibiogram data item - true - - - - - - - - - HIPPA PHI guideline - The American HIPPA Protected Health Information (PHI) guidelines cover information, including demographic information, which relates to: - -- the individual’s past, present, or future physical or mental health or condition, -- the provision of health care to the individual, or -- the past, present, or future payment for the provision of health care to the individual, and that identifies the individual or for which there is a reasonable basis to believe can be used to identify the individual. Protected health information includes many common identifiers (e.g., name, address, birth date, Social Security Number) when they can be associated with the health information listed above." - https://en.wikipedia.org/wiki/Health_Insurance_Portability_and_Accountability_Act - American HIPPA Protected Health Information (PHI) guidelines - - - - - - - - The natural (as opposed to laboratory) full scientific taxonomic name of a subject related to a given investigation, study and/or specimen. - Damion Dooley - - http://purl.obolibrary.org/obo/GENEPIO_0001567 - obsolete: subject species - true - - - - - - - - http://purl.obolibrary.org/obo/NCIT_C45908 - NCBI BioSample: intersex - obsolete: intersex - true - - - - - - - - Isolation date - inferred from BCCDC interviews - date the strain was isolated - Damion Dooley - http://purl.obolibrary.org/obo/GENEPIO_0000021 - obsolete: isolation date - true - - - - - - - - - Collection - Culture isolation date - suggested in metadata feedback - year/month/day - A culture isolation date is a date-time entity marking the end of a process in which a sample is isolated as a single colony or non-mixture culture - Damion Dooley - GROUP: IRIDA Ontology (Morag) - GENEPIO - culture isolation date - - - - - - - - - Collection - Frozen date - NML Labware LIMS - year/month/day - A culture frozen date is a date-time entity marking the beginning of a process in which a sample culture is frozen for preservation. - Damion Dooley - GROUP: IRIDA Ontology (Emma) - GENEPIO - culture frozen date - - - - - - - - - Collection - Received date - NML Labware LIMS - year/month/day - date lab received isolate - NML LIMS - GENEPIO - isolate received date - - - - - - - - - Collection - Upload date - NML Labware LIMS - month/day/year - date the isolate was entered into the database - NML LIMS - PulseNet: UploadDate - GENEPIO - isolate upload date - - - - - - - - - - - - - - - Pathogen Isolate - inferred from BCCDC interviews - gut, spine, tongue, lung - Name of body site where the specimen was obtained from, such as a specific organ or tissue. - Damion Dooley's note: Although term mentions "site" in label, this cannot be placed under "site" as it is intended to refer to organism material, and leads to unsatisfiable terms otherwise. - GROUP: MIxS - GENEPIO - subject anatomical site - http://gensc.org/ns/mixs/host_body_site - - - - - - - - - depth:1 - order: -NCIT:C115935 # healthy -NCIT:C25610 # pathologic -NCIT:C28554 # deceased - diseased - - Health or disease status of a given subject at time of specimen collection. - Currently this does not differ from the 'subject health status (GSCID-BRC)' item. It may be revised to have more options in the future. - Damion Dooley - subject health status at time of specimen collection - - - - - - - - - - - - 1 - - - - - - - 1 - - - - - - - - - - - - - - Environmental Isolate - sediment, chicken feces, cheese - - Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. - Damion Dooley - NCBI Biosample - specimen source context - - - - - - - - - - - - - - - Pathogen Isolate - feces, cerebral spinal fluid (CSF) - - Substance produced by the body, e.g. stool, mucus, where the specimen was obtained from. - Damion Dooley - subject body product - - - - - - - - - Environmental Isolate - Geographic location depth - GROUP: MIxS - value (5m) - Please refer to the definitions of depth in the environmental packages - GROUP: MIxS - GENEPIO - collection depth datum - - - - - - - - The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO - http://purl.obolibrary.org/obo/ENVO_00010483 - obsolete: specimen source environmental material - true - - - - - - - - - - - - - - - - A subject sex is the phenotypic sex of given subject (human or animal) related to a given investigation, study, and/or specimen. - Damion Dooley - Gender is not used because it is a term referencing human social and cultural convention. - subject sex specification - - - - - - - - - Environmental Isolate - Land use where sample was taken - Environment Canada Metadata - descriptive; type of human use (park, farm, urban) - Human use of land involving the management and modification of natural environment or wilderness into built environment. - URI: http://en.wikipedia.org/wiki/Land_use - GENEPIO - specimen collection site land use - - - - - - - - - - - - - - - - - - - - - - - - - - - - Environmental Isolate - Fecal Indicator Bacteria Number - Environment Canada Metadata - 12,456 cfu - Number of indicator micro-organisms (colony forming units) present in a sample that have been used to suggest the presence of pathogens. - URI: http://www.who.int/water_sanitation_health/dwq/iwachap13.pdf - GENEPIO - fecal indicator bacteria count - - - - - - - - - Environmental Isolate - Conductivity - GROUP: MIxS - milliSiemens per centimeter - electrical conductivity of water - GROUP: MIxS enviro package - GENEPIO - conductivity measurement datum - - - - - - - - - Environmental Isolate - Dissolved oxygen - GROUP: MIxS - micromole per kilogram - concentration of dissolved oxygen - GROUP: MIxS enviro package - GENEPIO - dissolved oxygen concentration - - - - - - - - - GMI MDM standard - - The Global Microbial Identifier "Minimum data for Matching" (MDM) standard is a standard that defines essential contextual data fields to be included in genomic sequence repository records. - Damion Dooley - the Global Microbial Identifier Minimum Data for Matching (MDM) Standard - http://www.globalmicrobialidentifier.org/-/media/Sites/gmi/News-and-events/2013/6th-meeting-2013-report.ashx?la=da - - - - - - - - - Environmental Isolate - Soluble inorganic material - GROUP: MIxS - soluble organic material name;measurement value - concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. - GROUP: MIxS enviro package - GENEPIO - soluble inorganic material - - - - - - - - - Environmental Isolate - Soluble inorganic material - GROUP: MIxS - GENEPIO - soluble inorganic material concentration - - - - - - - - - Environmental Isolate - Nitrite - GROUP: MIxS - micromole per liter - concentration of nitrite - GROUP: MIxS enviro package - GENEPIO - nitrite concentration - - - - - - - - - Environmental Isolate - Nitrate - GROUP: MIxS - micromole per liter - concentration of nitrate - GROUP: MIxS enviro package - GENEPIO - nitrate concentration - - - - - - - - - Environmental Isolate - Total phosphorous - GROUP: MIxS - micromole per liter - total phosphorus concentration, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus. Can also be measured without filtering, reported as phosphorus - GROUP: MIxS enviro package - GENEPIO - total phosphorous concentration - - - - - - - - - - - - - - - - - 12 - - - - - - - Environmental Isolate - Stream order - Environment Canada Metadata - value, 1-12 - Stream order is a measure of the relative size of streams (The smallest tributaries are referred to as first-order streams, while the largest river in the world, the Amazon, is a twelfth-order waterway). - GROUP: Environment Canada Metadata - GENEPIO - stream order categorical measurement datum - - - - - - - - - Environmental Isolate - Density of bacteria in sample - Environment Canada Metadata - OD reading or cfu's or cells per millilitre - number of bacteria in sample - GROUP: Environment Canada Metadata - GENEPIO - bacteria density - - - - - - - - - Lab Analytic - Host Primary Enzyme - PulseNet Data Capture - pick list (XbaI, BlnI) - Restriction enzyme for first characterization - GROUP: IRIDA Ontology (Emma) - primary enzyme (LMAAI) - - - - - - - - - - - - 1 - - - - - - - 1 - - - - - GENEPIO - PFGE test specification - - - - - - - - - Lab Analytic - Host Primary PFGE Pattern - NML LIMS - - First PFGE pattern from given diagnostic restriction enzyme - GROUP: IRIDA Ontology (Emma) - GENEPIO - PFGE primary test - - - - - - - - - Lab Analytic - Host Secondary Enzyme - PulseNet Data Capture - pick list (XbaI, BlnI) - Restriction enzyme for second characterization - GROUP: IRIDA Ontology (Emma) - GENEPIO - secondary enzyme (LMACI) - - - - - - - - - Lab Analytic - Host Secondary PFGE Pattern - NML LIMS - - Second PFGE pattern from given diagnostic restriction enzyme - GROUP: IRIDA Ontology (Emma) - GENEPIO - PFGE secondary test - - - - - - - - - Lab Analytic - MLST Clonal Complex - inferred from BCCDC interviews and Bionumerics - pick list? - Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. Sequence types are grouped into clonal complexes by their similarity to a central allelic profile (genotype). As such, clonal complexes represent sequence types that share a number of identical alleles e.g. 5/7 - URI: http://en.wikipedia.org/wiki/Multilocus_sequence_typing ; http://eburst.mlst.net/3.asp - GENEPIO - MLST clonal complex - - - - - - - - - Lab Analytic - MLST Sequence Type - inferred from BCCDC interviews and Bionumerics - pick list? - Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. For each housekeeping gene, the different sequences present within a bacterial species are assigned as distinct alleles and, for each isolate, the alleles at each of the loci define the allelic profile or sequence type (ST). - - GENEPIO - MLST sequence typing - - - - - - - - - - The process of fingerprinting the core genome of a bacteria. - Add under upcomming OBI "DNA fingerprinting assay". - Damion Dooley - Some bacteria like E coli have a highly variable genome, and so to type them methods must focus on typing the core genome that is common to all strains. - GENEPIO - core genome fingerprinting assay - - - - - - - - - Lab Analytic - CGF type - inferred from BCCDC interviews - pick list - - output of CGF - GROUP: IRIDA Ontology (Emma) - GENEPIO - CGF type - - - - - - - - - Lab Analytic - 16S rRNA sequencing - inferred from BCCDC interviews - 16S ribosomal RNA sequencing is a sequencing method used to identify and compare bacteria present within a given sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study. - URI: http://www.illumina.com/applications/microbiology/microbial-sequencing-methods/16S-rrna-sequencing.html - GENEPIO - 16S rRNA sequencing - - - - - - - - - - - - - - - Lab Analytic - Stx toxin type - metadata feedback - Stx1 or Stx2 - pathogenic shiga toxin produced by STEC E. coli - GROUP: IRIDA Ontology (Emma) - GENEPIO - Stx toxin type datum - - - - - - - - - - - - - - - Lab Analytic - Stx toxin subtype - metadata feedback - stx1a, stx1c - shiga toxin variant - GROUP: IRIDA Ontology (Emma) - GENEPIO - Stx toxin subtype datum - - - - - - - - - - - - - - - Lab Analytic - Stx1 Toxin PCR result - NML Labware LIMS - CT value? - qPCR result of Stx1 gene amplification - GROUP: IRIDA Ontology (Emma) - GENEPIO - Stx1 Toxin PCR result - - - - - - - - - - - - - - - Lab Analytic - Stx1 Cell Culture - NML Labware LIMS - level of Stx1 toxin derived tissue culture toxicity - GROUP: IRIDA Ontology (Emma) - GENEPIO - Stx1 cell culture level - - - - - - - - - - - - - - - Lab Analytic - Stx2 Toxin PCR result - NML Labware LIMS - CT value? - qPCR result of Stx2 gene amplification - GROUP: IRIDA Ontology (Emma) - GENEPIO - Stx2 Toxin PCR result - - - - - - - - - - - - - - - Lab Analytic - Stx2 Cell Culture - NML Labware LIMS - value? - level of Stx2 toxin derived tissue culture toxicity - GROUP: IRIDA Ontology (Emma) - GENEPIO - Stx2 cell culture level - - - - - - - - - - - - - - - - An AccuProbe assay that uses a luminometer and DNA probe designed to identify a specific bacteria or fungus species within a culture. - Damion Dooley - Nucleic acid hybridization tests are based on the ability of complementary nucleic acid strands to specifically align and associate to form stable double-stranded complexes (6). The ACCUPROBE method uses a single-stranded DNA probe with a chemiluminescent label that is complementary to the ribosomal RNA of the target organism. After the ribosomal RNA is released from the target organism, the labeled DNA probe combines with the target organism’s ribosomal RNA to form a stable DNA:RNA hybrid. The Selection Reagent allows for the differentiation of non-hybridized and hybridized probes.The light signal emitted by the DNA:RNA hybrids is measured by a GEN-PROBE luminometer. A positive result is a luminometer reading equal to or greater than the cut-off. A value below this cut-off is the negative result. - GENEPIO - AccuProbe culture identification assay - - - - - - - - - - An AccuProbe reagent kit for identifying Listeria monocytogenes. - Damion Dooley - URI: http://www.hologic.com/sites/default/files/package%20inserts/103051F-EN-RevC.pdf - GENEPIO - AccuProbe Listeria monocytogenes culture identification reagent kit - - - - - - - - - - - - - - - Lab Analytic - NML Labware LIMS - positive, negative, not done - A categorical diagnostic result of an AccuProbe test. - NML LIMS - GENEPIO - AccuProbe test result - - - - - - - - - Ribotyping involves the fingerprinting of genomic DNA restriction fragments that contain all or part of the genes coding for the 16S and 23S rRNA. By digesting the genes with a specific restriction enzyme, fragments of different lengths are generated. By performing a Gel electrophoresis with the digested samples, the fragments can be visualised as lines on the gel, where larger fragments are close to the start of the gel, and smaller fragments further down. After blotting onto a matrix and probing, these lines form a unique pattern for each species and can be used to identify the origin of the DNA, almost like a barcode can identify a product. - - GENEPIO - ribotyping - - - - - - - - - This method is based on restriction endonuclease digestion of bacterial chromosomal DNA, followed by Southern hybridization to probes for sequences in the regions of bacterial DNA coding for the 5S-16S-23S (the Escherichia coli rrnB rRNA operon) rRNA operon. The probes have been developed that are directed to highly conserved regions of the rRNA operon present in all eubacteria and can therefore be used for ribotyping most bacteria - - GENEPIO - riboprinting - - - - - - - - - an automated system that takes a purified bacterial suspension, lyses the cells, extracts the DNA, restriction endonuclease digests the DNA, separates the digest on a gel, transfers the DNA bands to a membrane, probes the bands with non-radioisotope-labeled, 5S-16S-23S rRNA-specific probes (Southern hybridization), photographs the membrane, and finally compares the bar code-like pattern to databases in order to identify the genus and species. - - GENEPIO - Qualicon (DuPont) RiboPrinter Microbial Characterization System - - - - - - - - - a library of RiboPrinter recognised patterns - GENEPIO - DuPont identification pattern library - - - - - - - - - Lab Analytic - Riboprinter DUP Number - NML Labware LIMS - DUP-PST1-1211 - DuPont identification number from the DuPont identification library - NML LIMS - GENEPIO - RiboPrinter DUP Number - - - - - - - - - Lab Analytic - Riboprinter DUP similarity - NML Labware LIMS - The identification of an isolate was determined when the corresponding patterns matched one of the patterns of the DuPont Identification library of the RiboPrinter1 with a similarity of >0.85. The similarity threshold for an isolate joining a ribogroup is an adaptive value between 0.90 and 0.96, depending on the size of the ribogroup. - Similarity of pattern to one of the patterns of the DuPont Identification library of the RiboPrinter - - GENEPIO - RiboPrinter DUP similarity - - - - - - - - - - - - - - - - Sequencing - Sequencing Run Date - NML NGS Archive - yyyy/mm/dd - Date the sequencing run was performed - GROUP: IRIDA Ontology (Emma) - GENEPIO - sequencing run date - - - - - - - - - Sequencing - Sequencing Location - inferred from BCCDC interviews - location the sequencing run was performed - GROUP: IRIDA Ontology (Emma) - GENEPIO - sequencing location - - - - - - - - - Sequencing - Platform - https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._platform_descriptor_t/ - Illumina (MiSeq, HiSeq), PacBio, Ion Torrent, (Roche 454), SOLiD ABI - - A sequencing plaform (brand) is a name of a company that produces sequencer equipment. - GROUP: IRIDA Ontology (Emma) - GENEPIO - sequencing platform (brand) - - - - - - - - - Sequencing - Workflow - Derived from Sample Sheet - Resequencing, FastQ only - the workflow is the pre-defined sequence of steps to run the automated sequencing pipeline. - GROUP: IRIDA Ontology (Emma) - GENEPIO - sequencing workflow - - - - - - - - - Sequencing - Application - Derived from Illumina Sample Sheet - amplicon sequencing, WGS - the sequencing application is the use or purpose of the sequencing - GROUP: IRIDA Ontology (Emma) - GENEPIO - sequencing application - - - - - - - - Derived from Illumina Sample Sheet - the sequencing conditions and the analyte being measured - GROUP: IRIDA Ontology (Emma) - - obsolete: sequencing assay - true - - - - - - - - - Sequencing - Chemistry - Derived from Illumina Sample Sheet - amplicon, resequencing (WGS) - lab method to determine the order of nucleotides in a DNA molecule - GROUP: IRIDA Ontology (Emma) - GENEPIO - sequencing chemistry - - - - - - - - - Sequencing - Read Length - Derived from Illumina Sample Sheet - 151, 251 - number of base pairs per read - GROUP: IRIDA Ontology (Emma) - GENEPIO - read length - - - - - - - - A GSCID/BRC data item is a field in one of the GSCID/BRC Project and Sample Application Standard subsets. - Damion Dooley - - obsolete: GSCID-BRC data item - true - - - - - - - - - Sequencing - Multiplex identifiers - Derived from Illumina Sample Sheet - S017 - Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters - GROUP: MIxS - GENEPIO - sequencing run multiplex identifiers - - - - - - - - - Sequencing - Sample Name - Derived from Illumina Sample Sheet specification: http://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/miseq/miseq-sample-sheet-quick-ref-guide-15028392-j.pdf - 1,2,3, AX234, etc. - Control1, Tank1, Froglet1 - A sequencing run sample identifier is an alphanumeric identifier for a sample. In bioinformatics processing this identifier is assigned to a sample in order to track it through the process of sequencing and analysis. - GROUP: IRIDA Ontology (Emma) - Illumina SampleSheet: Sample_ID - PulseNet: SubmittedNumber - sample name - sample title - GENEPIO - sequencing run sample identifier - - - - - - - - - Sequencing - Number of cycles - Derived from Illumina Sample Sheet - 500 - Number of sequencing chemistry cycles - GROUP: IRIDA Ontology (Emma) - GENEPIO - sequencing count of chemistry cycles - - - - - - - - - Sequencing - Sequencing Kit - Derived from Illumina Sample Sheet - MiSeq reagent kit - Pre-filled, ready-to-use reagent cartridges. Used to produce improved chemistry, cluster density and read length as well as improve quality (Q) scores. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications. - GROUP: IRIDA Ontology (Emma) - GENEPIO - sequencing kit - - - - - - - - - Sequencing - Sequencing Kit version - Derived from Illumina Sample Sheet - v2, v3 - A string datum which is the version/configuration of the reagent cartidge. - GROUP: IRIDA Ontology (Emma) - GENEPIO - sequencing kit version - - - - - - - - - Sequencing - Adapters - Derived from Illumina Sample Sheet - adapter A and B sequence - Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters - GROUP: MIxS - GENEPIO - adapter sequence - - - - - - - - - Sequencing - Adapter Trimming - Derived from Illumina Sample Sheet - The removal of adapter sequences from demultiplexed data reads - GROUP: IRIDA Ontology (Emma) - GENEPIO - read adapter trimming - - - - - - - - - Sequencing - inferred from BCCDC interviews - Illumina metagenomic protocol (part 15044223), with Nextera - Packaged kits (containing adapters, indexes, enzymes, buffers etc), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids. - GROUP: IRIDA Ontology (Emma) and http://applications.illumina.com/applications/sequencing/ngs-library-prep.html - library preparation kit - - - - - - - - - Sequencing - Number of base pairs - inferred from BCCDC interviews - 300 000 - The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. - GROUP: MIxS - GENEPIO - number of expected base pairs per genome - - - - - - - - - Run QC - Number of Reads Passing Filter - Output from MiSeq - 0.92 - Raw data are filtered to remove any reads that do not meet the overall quality as measured by a chastity filter. The chastity of a base call is calculated as the ratio of the brightest intensity divided by the sum of the brightest and second brightest intensities. -Clusters passing filter are represented by PF in analysis reports. Clusters pass filter if no more than one base call in the first 25 cycles has a chastity of < 0.6. - URI: http://support.illumina.com/sequencing/sequencing_instruments/miseq/questions.html - GENEPIO - number of reads passing filter - - - - - - - - - Run QC - Cluster density - Output from MiSeq - 800 k/mm^2 - Cluster Generation is a process by which libraries amplified into clonal clusters on a flow cell. The density of those clusters in the lane, is the cluster density. - URI: https://www.broadinstitute.org/files/shared/illuminavids/clusterGenSlides.pdf - sequencer flow cell cluster density - - - - - - - - - Run QC - above 30 Qscore - Output from MiSeq - >75% - percentage of reads with a Phred quality score over 30, which indicates less than a 1/1000 chance that the base was called incorrectly - URI: http://en.wikipedia.org/wiki/Phred_quality_score - GENEPIO - phred quality score - - - - - - - - - - - - - - - - - Assembly QC - Assembly - Standard Term - the GROUP: MIxS term encompasses assembly method; estimated error rate; method of calculation - Assembly method refers to how the reads were assembled into contigs for which either a de novo or mapping (reference based) strategy is used. - GROUP: MIxS - GENEPIO - assembly method - - - - - - - - - Assembly QC - Assembly status - from within "Finishing strategy" in GROUP: MIxS - standard draft or finished - - "Attempting to convey the relative integrity and reliability of the data, six levels or terms have been proposed and applied to describe genome sequences." See subclass choices. - Damion Dooley - CITATION: Chain, P.S., Grafham, D.V., Fulton, R.S., Fitzgerald, M.G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D.C., Buhay, C., et al. (2009). Genomics. Genome project standards in a new era of sequencing. Science 326, 236-237. - GENEPIO - assembly status - - - - - - - - - Assembly QC - Coverage - from within "Finishing strategy" in GROUP: MIxS - 30 - - Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence. - URI: http://en.wikipedia.org/wiki/Shotgun_sequencing - GENEPIO - Damion Dooley's note: Wikipedia defines calculation with: "the length of the original genome (G), the number of reads(N), and the average read length(L) as N * L/G" - read coverage - - - - - - - - - - - - - - - - Assembly QC - Number of Contigs - 20 - http://purl.obolibrary.org/obo/IAO_0000428 - A contig count is the count of contigs that belong to a sequence assembly. - Damion Dooley - GENEPIO - contig count - - - - - - - - - - - - - - - Assembly QC - Assembly name - Standard Term - name and version of assemby - Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community - GROUP: MIxS - GENEPIO - assembly name (identifier) - - - - - - - - - Assembly QC - Annotation Algorithm - Standard Term - Prokka - Program used for annotation - GROUP: IRIDA Ontology (Emma) - GENEPIO - genome annotation algorithm - - - - - - - - - Assembly QC - Annotation Source - Standard Term - annotation source description - For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter - GROUP: MIxS - GENEPIO - genome annotation source - - - - - - - - Damion Dooley - - - obsolete: NCBI BioSample data item - true - - - - - - - - - CDC ID - - - - - - - - - - - - - - - - - Damion Dooley - - - - - - - - - Damion Dooley - - - - - - - - An NCBI BioProject data item is a datum within the NCBI BioProject standard collection - Damion Dooley - - - obsolete: NCBI BioProject data item - true - - - - - - - - The INDISC consortium "Minimum data for Matching" standard aims to define a format to capture reads and minimum metadata. It is developed by the "Repository and storage of sequence and meta-data" workgroup 2. It is used in the Global Microbial Identifier platform. - Damion Dooley - http://purl.obolibrary.org/obo/GENEPIO_0000036 - obsolete: INSDC MDM standard - true - - - - - - - - A MixS data item is a term or field defined in the Genomic Standards Consortium MIxS standard. - Damion Dooley - - obsolete: MIxS data item - true - - - - - - - - - - The 'draft data standard' class contains draft representations of formal or defacto third party standards and related components. These representations may have been crafted without any involvement of related standards issuers and so no guarantee can be provided about their currency, accuracy or veracity. - Damion Dooley - draft data standard - - - - - - - - - - obsolete: HIPPA PHI data item - true - - - - - - - - - - obsolete: PulseNet data item - true - - - - - - - - - - The I2B2 Workbench Data Protection role standard is a standard which names and lists data protection roles between a user and a given dataset that define the level of detail a user has access to. - Damion Dooley - Derived from the Data Protection Track of the I2B2 Workbench software specification: https://www.i2b2.org/software/files/PDF/current/IM_Architecture.pdf - I2B2 Data Protection role standard - - - - - - - - - depth:1 - order: -NCIT:C115935 # healthy -NCIT:C25610 # pathologic / diseased -NCIT:C28554 # deceased - - A description of whether a given subject organism appeared healthy, sick or deceased at the time of specimen extraction. If sick or deceased, additional details should be provided in project-specific fields. - Damion Dooley - CS8 - subject health status (GSCID-BRC) - - - - - - - - - - - - - - - - The GSCID-BRC Core Sample Standard is an extension of the GMI MDM data standard - Damion Dooley - https://www.niaid.nih.gov/research/dmid-metadata-standards-core-sample - GSCID-BRC Core Sample standard - - - - - - - - - - A Core Project item is a field in the GSCID/BRC Project and Sample Application Core Project Standard. - Damion Dooley - https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project - GSCID-BRC Core Project standard - - - - - - - - - - Specimen category is a categorical variable that broadly indicates the source of a specimen in order for data processing systems like NCBI's biosample submission portal to anticipate other fields related to the source. Currently this distinguishes between "clinical or host associated" specimens and "environmental/food or other pathogen" specimens. - Damion Dooley - specimen category - - - - - - - - - day, week, month, year - - Age unit of the age measurement of a subject (individual organism). - Damion Dooley Feb 20, 2017: GSCID-BRC calls for an explicit field here whereas NCBI Biosample and MIxS don't. - Damion Dooley - NIAID GSCID-BRC metadata working group - subject age - unit - - - - - - - - - The National Center for Biotechnology Information offers standards for submitting genomic project data to their BioProject and BioSample databases. - Damion Dooley - National Center for Biotechnology Information standard - NCBI standard - - - - - - - - - - - - - - - - - - - - - - - A datum containing the city or region or more precise geographical location identifier for the site of a specimen collection event. - Damion Dooley - Adapted from NIAID GSCID-BRC metadata working group - Note that this is expressed in a particular format in some standards. - specimen collection location - city or region - - - - - - - - - - - - - - - - - - lookup - - - - - - - - - - - - - - - - The country of the site of a given specimen collection event. - Damion Dooley - NIAID GSCID-BRC metadata working group - specimen collection location - country - - - - - - - - - - The Darwin Core is body of standards. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing reference definitions, examples, and commentaries. - Damion Dooley - http://tdwg.github.io/dwc/terms/index.htm - Darwin Core Terms - - - - - - - - - - A datetime measurement related to a person's travel with respect to potential epidemilogical implications. - Damion Dooley - travel history item - - - - - - - - - - The date of a person's departure from their primary residence (at that time) on a journey to one or more other locations. - Damion Dooley - travel start date - - - - - - - - - - - - - - - - The date of a person's return to some residence from a journey originating at that residence. - Damion Dooley - travel end date - - - - - - - - - - Infection aquired during travel is a boolean datum indicating a diagnosis of a traveller's infection during a given trip. - Damion Dooley - infection aquired during travel - - - - - - - - - - This is a model of the datums involved in an epidemiology investigation. - Damion Dooley - draft pathogenic epidemiology case investigation record - - - - - - - - - - The draft epi case exposure model describes datums related to the possible transmission of a pathogen between a case person and other people, places, animals etc. - Damion Dooley - draft pathogenic epi case exposure record - - - - - - - - - - A description of a food item that a case patient has come in contact with. - Damion Dooley - draft pathogenic epi case food record - - - - - - - - - food brought back from travel - - - - - - - - - An epidemiology contact network model is a definition of the information necessary to connect pathogen transmission patterns between individuals or animals in connection with an outbreak investigation. - Damion Dooley - epidemiology contact network model - - - - - - - - - - An epi contact network - human is contact information about a person who may be involved in transmitting a pathogen. - Damion Dooley - epi contact network model - human - - - - - - - - - - This is a model that provides location and transportation information about an animal that may be involved in transmitting a pathogen to a human or other animal. - Damion Dooley - epi contact network model - animal - - - - - - - - - A note is text that provides human-readable information on one or more subjects. - Damion Dooley - note - - - - - - - - - - An epi case general info model contains datum specifications about an epidemiology investigation case including the person involved, contact information and their demographics. - Damion Dooley - draft pathogenic epi case general information record - - - - - - - - - - A record of the details around how, when, and from what an isolate was extracted. - Damion Dooley - draft pathogenic epi case isolate detail record - - - - - - - - - - - - - - - - - - - - - - - - - A specimen source substance is an organism substance or food product or environmental substance from which the specimen was extracted. - Damion Dooley - specimen source substance - - - - - - - - - - An isolate sequence filename is the file name (http://edamontology.org/data_1050) of the contig assembly file created by a bioinformatics assembly process. - Damion Dooley - isolate sequence filename - - - - - - - - - - A cluster identifier is an identifier that locates a genomic variant of an organism within a community of past or present genetically related organisms. - Damion Dooley - cluster identifier - - - - - - - - - - A laboratory test performed on a specimen from a patient with regard to potential pathogenic disease. - Damion Dooley - draft pathogenic epi case test record - - - - - - - - - - A lab test requestor is the individual or agency requesting that one or more tests be performed on a specimen. - Damion Dooley - contact specification - lab test requester - - - - - - - - - - A food cultural origin datum indicates the cultural origin of a food product. - Damion Dooley - food cultural origin - - - - - - - - - - A record of a patient's recent travel - departure and return, mode of travel and locations visited - as it may pertain to an outbreak pathogen transmission event. - Damion Dooley - draft pathogenic epi case travel record - - - - - - - - - Region (England) (entry subject to GAZ replacement) - - - - - - - - - - An epi network contact is a person who may have recieved or transmitted an infectious disease related to an outbreak investigation. - Damion Dooley - contact specification - epi network contact - - - - - - - - - - This model contains data type specifications for whole genome sequencing and epidemiology investigation contextual data. - Damion Dooley - public health lab epidemiology contextual data standard - - - - - - - - - This is a set of datums involved in laboratory processing of whole-genome-sequenced isolates. - Damion Dooley - draft whole genome sequencing lab test record - - - - - - - - - - - Damion Dooley - draft WGS lab bioinformatics process record - - - - - - - - - - - Damion Dooley - draft WGS lab sequencing record - - - - - - - - - - An NCBI SRA meta information item is a field specification for a NCBI Sequence Read Archive record. - Damion Dooley - NCBI SRA meta information standard - https://www.ncbi.nlm.nih.gov/books/NBK47529/#_SRA_Quick_Sub_BK_Experiment_ - - - - - - - - - An isolate raw read filename is the file name (http://edamontology.org/data_1050) of the raw read file created by a genomic sequencing assay. - isolate raw read filename - - - - - - - - - Sequencing - - The version identifier of a packaged kit tailored for specific sequencing workflows. - Damion Dooley - library preparation kit version - - - - - - - - - - The name and version of software used in a bioinformatics workflow to improve the quality of sequencing reads. - Damion Dooley - read trimming and filtering software - - - - - - - - - - - Damion Dooley - bioinformatics pipeline name - - - - - - - - - - - Damion Dooley - bioinformatics pipeline version - - - - - - - - - - - Damion Dooley - bioinformatics pipeline protocol - - - - - - - - - - - Damion Dooley - draft WGS lab sequencing quality metrics record - - - - - - - - - - - Damion Dooley - draft WGS lab assembly quality metrics record - - - - - - - - - - A general label indicating the primary study goal. These are only relevant for Primary submission projects (not Umbrella projects). - Damion Dooley - Damion Dooley's note: According to http://trace.ddbj.nig.ac.jp/news/2014-11-12_e.html, "A BioProject record can have multiple project data types" - project data type - - - - - - - - - - Genome assembly project utilizing already existing sequence data including data that was submitted by a different group - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - assembly project - - - - - - - - - - A sequencing project involving clone-ends - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - clone ends project - - - - - - - - - - A sequencing project involving DNA methylation, histone modification, and/or chromatin accessibility datasets - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - epigenomics project - - - - - - - - - - Exome resequencing project - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - exome resequencing project - - - - - - - - - - A whole, or partial, genome sequencing project (with or without a genome assembly) - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - genome sequencing project - - - - - - - - - The Relational Sequencing TB Data Platform (ReSeqTB) catalogs a vast amount of genotypic, phenotypic and related metadata from Mycobacterium tuberculosis (Mtb) strains to enable the development of clinically useful, WHO-endorsed in vitro diagnostic assays for rapid drug susceptibility testing of Mtb. - Damion Dooley - https://platform.reseqtb.org/ - draft ReSeq Tuberculosis data platform standard - - - - - - - - - In expressions like: "<= 8mg/L" - - The measurement comparator is a sign indicating that a measurement is above, equal to, or below a given threshold. - Damion Dooley - test threshold measurement comparator - - - - - - - - - < - - The "less than" comparator indicates that a given substance was present at less than a given quantity or concentration. - Damion Dooley - < - less than - - - - - - - - - <= - - The "less than or equal to" comparator indicates that a given substance was present at less than or equal to a given quantity or concentration. - Damion Dooley - <= - less than or equal to - - - - - - - - - == - - The "equal to" comparator indicates that a given substance was present at the given quantity or concentration. - Damion Dooley - == - equal to - - - - - - - - - >= - - The "greater than or equal to" comparator indicates that a given substance was present at greater than or equal to a given quantity or concentration. - Damion Dooley - >= - greater than or equal to - - - - - - - - - > - - The "greater than" comparator indicates that a given substance was present at greater than a given quantity or concentration. - Damion Dooley - > - greater than - - - - - - - - - order: -OBI:0001616 # specimen identifier -OBI:0001614 # GenBank ID -GENEPIO:0001100 # antibiogram drug test model -GENEPIO:0002062 # amr testing reference standard -GENEPIO:0002045 # amr resistance testing method -GENEPIO:0002047 # ... version or reagent -GENEPIO:0002049 # amr testing platform -GENEPIO:0002056 # ... vendor - - The NCBI antibiogram standard details the reporting specifications for antimicrobial susceptibility and resistance data derived from drug resistant pathogens. This information is submitted as an antibiogram table on BioSample records. - Damion Dooley - NCBI Antibiogram standard - https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/ - - - - - - - - http://purl.obolibrary.org/obo/GENEPIO_0001007 - obsolete: NCBI isolate AMR testing model - true - - - - - - - - A restaurant or an eatery, is a business which prepares and serves food and drinks to customers in exchange for money. - Damion Dooley - https://en.wikipedia.org/wiki/Restaurant - http://purl.obolibrary.org/obo/ENVO_01000934 - obsolete: restaurant - true - - - - - - - - - iPHIS standard - - The Canadian Integrated Public Health Information System (iPHIS) System provides a standard for holding reportable disease cases from participating jurisdictions. - Damion Dooley - Canadian Integrated Public Health Information System (iPHIS) Standard - - - - - - - - - 254532233433235152213423 - - The MIRU24 - international standard is a mycobacterial interspersed repetitive units (MIRU) typing method that classifies Mycobacterium tuberculosis complex (MBTC) bacteria according to a multiple locus VNTR [variable number of tandem repeats] analysis (MLVA) typing scheme of counts of repeats at 24 sequence loci. - The ordering of loci is as follows: MIRU 04, MIRU 26, MIRU 40, MIRU 10, MIRU 16, MIRU 31, 424 577, 2165, 401, 3690, 4156, 2163, 1955, 4052, MIRU 02, MIRU 23, MIRU 39, MIRU 20, MIRU 24, MIRU 27, 2347, 2461, 3171 - MIRU24 - international standard - - - - - - - - - - The MIRU24 - Canadian standard is a Mycobacterium tuberculosis typing method exactly like MIRU24 - international standard except that the report of the ordering of the matching loci is different. - Damion Dooley - The ordering of loci is as follows: MIRU 02, MIRU 04, MIRU 10, MIRU 16, MIRU 20, MIRU 23, MIRU 24, MIRU 26, MIRU 27, MIRU 31, MIRU 39, MIRU 40, 424, 577, 1955, 2163, 2165, 2347, 2401, 2461, 3171, 3690, 4052, 4156 - MIRU24 - Canadian standard - - - - - - - - - spray-wading water - - - - - - - - - pool water - - - - - - - - - obsolete: hot tub - true - - - - - - - - A cafeteria is a type of food service location in which there is little or no waiting staff table service, whether a restaurant or within an institution such as a large office building or school. - Damion Dooley - https://en.wikipedia.org/wiki/Cafeteria - http://purl.obolibrary.org/obo/ENVO_01000969 - obsolete: cafeteria - true - - - - - - - - http://purl.obolibrary.org/obo/ENVO_00003864 - obsolete: bakery - true - - - - - - - - A delicatessen or deli is a retail establishment that sells a selection of unusual or foreign prepared foods. - Damion Dooley - https://en.wikipedia.org/wiki/Delicatessen - http://purl.obolibrary.org/obo/ENVO_01000970 - obsolete: delicatessen - true - - - - - - - - A food kiosk is a kiosk (a booth with an open window on one side) that sells food. - Damion Dooley - http://purl.obolibrary.org/obo/ENVO_01000974 - obsolete: food kiosk - true - - - - - - - - A grocery store is a retail store that primarily sells food. - Damion Dooley - http://purl.obolibrary.org/obo/ENVO_01000984 - obsolete: grocery store - true - - - - - - - - A specialty/ethnic food store is a store specializing in a particular variety of food or food of cultural / regional origin. - Damion Dooley - http://purl.obolibrary.org/obo/ENVO_01000988 - obsolete: specialty/ethnic store - true - - - - - - - - A market, or marketplace, is a location where people regularly gather for the purchase and sale of provisions, livestock, and other goods - Damion Dooley - http://purl.obolibrary.org/obo/ENVO_01000987 - obsolete: market - true - - - - - - - - - - A time measurement datum that pertains to a patient's medical treatment. - Damion Dooley - treatment history datum - - - - - - - - A restaurant providing prepared meals or other food items that the purchaser intends to eat elsewhere - Damion Dooley - https://en.wikipedia.org/wiki/Take-out - http://purl.obolibrary.org/obo/ENVO_01000972 - obsolete: take out restaurant - true - - - - - - - - - - A treatment start date is a date/time datum which indicates the start of a particular medical treatment for a patient. - Damion Dooley - treatment start date - - - - - - - - - canoeing / kayaking / boating - - - - - - - - - hiking - - - - - - - - - camping - - - - - - - - Damion Dooley - http://purl.obolibrary.org/obo/PCO_0000033 - obsolete: social gathering - true - - - - - - - - http://purl.obolibrary.org/obo/PCO_0000035 - obsolete: party - true - - - - - - - - http://purl.obolibrary.org/obo/PCO_0000038 - obsolete: wedding - true - - - - - - - - http://purl.obolibrary.org/obo/PCO_0000039 - obsolete: baby shower - true - - - - - - - - http://purl.obolibrary.org/obo/PCO_0000037 - obsolete: potluck - true - - - - - - - - http://purl.obolibrary.org/obo/PCO_0000034 - obsolete: community event - true - - - - - - - - A long term care facility provides a type of residential care. It is a place of residence for people who require continual nursing care and have significant difficulty coping with the required activities of daily living. - Damion Dooley - https://en.wikipedia.org/wiki/Nursing_home_care - http://purl.obolibrary.org/obo/ENVO_01000932 - obsolete: long term care facility - true - - - - - - - - - - - - - - - - A treatment end date is a date/time datum which indicates the end of a particular medical treatment for a patient. - Damion Dooley - treatment end date - - - - - - - - - Damion Dooley - food related exposure event - - - - - - - - - - Some bacteria are associated with particular foods. Need relationship - Damion Dooley - infection-specific food detail - - - - - - - - - - A tuberculosis treatment antibiotic is an antibiotic used in the treatment of tuberculosis. - Damion Dooley - tuberculosis treatment drug - “Treatment of Tuberculosis Guidelines”, WHO, Geneva, 2010, 30 www.who.int/tb/ - See more at: http://www.tbfacts.org/tb-drugs/#sthash.nibuzCLV.dpuf - - - - - - - - - vegetarian - - - - - - - - - - A time measurement datum that pertains to an organism's physical location. - Damion Dooley - organism location history datum - - - - - - - - - This will take on a sub-herarchy of food types. - food avoidance - - - - - - - - - special diet - - - - - - - - - water related exposure event - - - - - - - - - municipal water - - - - - - - - - - A time measurement datum indicating the year a person immigrated to a given country. - Damion Dooley - immigration year of arrival - - - - - - - - - bottled water - - - - - - - - - An event (occuring at some location and for some duration of time) where - Damion Dooley - infectious disease exposure event - - - - - - - - - Damion Dooley - human related exposure event - - - - - - - - - Damion Dooley - animal related exposure event - - - - - - - - - - Identification or description of the specific individual from which this sample was obtained - Damion Dooley - https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ - NCBI BioSample isolate (human name or description) - - - - - - - - Damion Dooley - http://purl.obolibrary.org/obo/ENVO_01000923 - obsolete: petting zoo - true - - - - - - - - - Damion Dooley - agricultural fair - - - - - - - - - An isolate passage history is a record of the cyclic growth process that led to it, including number of times its was put through the process, and the method used. - Damion Dooley - http://purl.obolibrary.org/obo/GENEPIO_0001835 - isolate passage history datum - - - - - - - - - For Eschericia coli: STEC, UPEC - A pathotype is a common name for a group of organisms (of the same species) that have the same pathogenicity on a specified host - https://en.wiktionary.org/wiki/pathotype - NCBI pathotype - - - - - - - - - Damion Dooley - - pet treat - - - - - - - - - Damion Dooley - - pet food (raw) - - - - - - - - - - An epidemiology travel datum is a datum regarding a particular human's travel trip destination, mode, and motivation, with respect to an epidemiology investigation. - Damion Dooley - human exposure event - travel datum - - - - - - - - - boat / cruise travel - - - - - - - - - train travel - - - - - - - - - bus travel - - - - - - - - - car travel - - - - - - - - - airline travel - - - - - - - - - - A travel mode is a type of transportation which a given human has used while travelling on a particular trip. - Damion Dooley - travel mode - - - - - - - - - - A travel reason is a motivation for traveling on a particular trip expressed by the traveller. - Damion Dooley - travel reason - - - - - - - - - travel for pleasure - - - - - - - - - business activity - - - - - - - - - religious missionairy activity - - - - - - - - - rural backpacking activity - - - - - - - - - visiting relative/friends - - - - - - - - - travel tour - - - - - - - - - unsure of travel reason - - - - - - - - - The tuberculosis draft standard is a GenEpiO set of draft genomic and clinical data items related to Mycobacterium tuberculosis that various agencies are using in their own reporting. - draft tuberculosis - specimen contextual data standard - - - - - - - - - - - Damion Dooley - - behavioural risk factor - - - - - - - - http://purl.obolibrary.org/obo/GENEPIO_0001686 - obsolete: E. coli serotype part - true - - - - - - - - - Snomed: Concept 260827009 - O antigen - - - - - - - - - Snomed: Concept 260823008 - H antigen - - - - - - - - - - - Damion Dooley - - homeless status - - - - - - - - - - A serotype or serovar is a distinct variation within a species of bacteria or virus or among immune cells of different individuals. These microorganisms, viruses, or cells are classified together based on their cell surface antigens, allowing the epidemiologic classification of organisms to the sub-species level - Damion Dooley - https://en.wikipedia.org/wiki/Serotype - serovar/serotype common name - - - - - - - - - - - - - - - Salmonella serovar - - - - - - - - - Salmonella serovar name - - - - - - - - - - - - - - - Salmonella antigenic formula - - - - - - - - - - - Damion Dooley - - drug use status - - - - - - - - - - - Damion Dooley - - incarceration status - - - - - - - - - - - Damion Dooley - - HIV status - - - - - - - - - - - Damion Dooley - - HIV risk status - - - - - - - - - - - Damion Dooley - - A.I.D.S status - - - - - - - - - - - Damion Dooley - - drug abuse status - - - - - - - - - - - Damion Dooley - - injection drug use status - - - - - - - - - - - Damion Dooley - - recreational drug use status - - - - - - - - - - - Damion Dooley - - methadone use status - - - - - - - - - - - Damion Dooley - - substantial alcohol use/abuse status - - - - - - - - - - - Damion Dooley - smoking status - - - - - - - - - - - - - - - - - - - - - - A country of birth is the country that a given person (or animal) was born in. - Damion Dooley - country of birth - - - - - - - - - Tb_1 (with respect to an Illumina SampleSheet.csv spreadsheet) -13 (with respect to a ReSeqTB SNP pipeline sample report) - - A sequence number is a numeric identifier of a sequence with respect to a particular data table or dataset. - sequence number - - - - - - - - - - Damion Dooley - The 'date last seen alive' is the date that a subject (patient) was last known (seen, heard, messaged) to be alive. - date last seen alive - - - - - - - - - second line or reserve tuberculosis drug - - - - - - - - - tuberculosis infection anatomical site - - - - - - - - http://purl.obolibrary.org/obo/GENEPIO_0001007 - obsolete: NCBI Antibiogram model - true - - - - - - - - - order: -GENEPIO:0001187 # antimicrobial resistance test drug -GENEPIO:0002112 # drug MIC -GENEPIO:0002080 # drug minimum inhibitory concentration unit -GENEPIO:0001001 # measurement comparator -NCIT:C85539 # antimicrobial resistance phenotype -GENEPIO:0002181 # antimicrobial resistance phenotype - ECOFF - - This is the minimal set of parameters for drug test results for a particular antimicrobial agent. - Damion Dooley - draft antibiogram drug test model - http://the-vet.net/DVMWiz/Vetlibrary/Lab-%20Microbiology%20Guide%20to%20Interpreting%20MIC.htm - https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/ - - - - - - - - - A date-time datum that marks the predicted start of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time. - Damion Dooley - predicted exposure start - - - - - - - - - A date-time datum that marks the predicted end of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time. - Damion Dooley - predicted exposure end - - - - - - - - - - Map: - project that results in non-sequence map data such as genetic map, radiation hybrid map, cytogenetic map, optical map, and etc. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - map project - - - - - - - - - - Metagenome: sequence analysis of environmental samples - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - metagenome project - - - - - - - - - - Metagenome assembly: a genome assembly generated from sequenced environmental samples - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - metagenome assembly project - - - - - - - - - - Other: a free text description is provided to indicate Other data type - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - other project data type - - - - - - - - - - Phenotype or Genotype: project correlating phenotype and genotype - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - phenotype or genotype project - - - - - - - - - - Proteome: large scale proteomics experiment including mass spec. analysis - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - proteome project - - - - - - - - - - Random Survey: sequence generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - random survey project - - - - - - - - - - Targeted locus (loci): project to sequence specific loci, such as a 16S rRNA sequencing - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - targeted locus (loci) project - - - - - - - - - - Transcriptome or Gene expression: large scale RNA sequencing or expression analysis. Includes cDNA, EST, RNA_seq, and microarray. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - transcriptome or gene expression - - - - - - - - - - A sequencing project with a primary goal of identifying large or small sequence variation across populations. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - variation project - - - - - - - - - - - - - - - - - - - - - - - - (Afghanistan|Albania|Algeria|American Samoa|Andorra|Angola|Anguilla|Antarctica|Antigua and Barbuda|Arctic Ocean|Argentina|Armenia|Aruba|Ashmore and Cartier Islands|Atlantic Ocean|Australia|Austria|Azerbaijan|Bahamas|Bahrain|Baltic Sea|Baker Island|Bangladesh|Barbados|Bassas da India|Belarus|Belgium|Belize|Benin|Bermuda|Bhutan|Bolivia|Borneo|Bosnia and Herzegovina|Botswana|Bouvet Island|Brazil|British Virgin Islands|Brunei|Bulgaria|Burkina Faso|Burundi|Cambodia|Cameroon|Canada|Cape Verde|Cayman Islands|Central African Republic|Chad|Chile|China|Christmas Island|Clipperton Island|Cocos Islands|Colombia|Comoros|Cook Islands|Coral Sea Islands|Costa Rica|Cote d'Ivoire|Croatia|Cuba|Curacao|Cyprus|Czech Republic|Democratic Republic of the Congo|Denmark|Djibouti|Dominica|Dominican Republic|East Timor|Ecuador|Egypt|El Salvador|Equatorial Guinea|Eritrea|Estonia|Ethiopia|Europa Island|Falkland Islands (Islas Malvinas)|Faroe Islands|Fiji|Finland|France|French Guiana|French Polynesia|French Southern and Antarctic Lands|Gabon|Gambia|Gaza Strip|Georgia|Germany|Ghana|Gibraltar|Glorioso Islands|Greece|Greenland|Grenada|Guadeloupe|Guam|Guatemala|Guernsey|Guinea|Guinea-Bissau|Guyana|Haiti|Heard Island and McDonald Islands|Honduras|Hong Kong|Howland Island|Hungary|Iceland|India|Indian Ocean|Indonesia|Iran|Iraq|Ireland|Isle of Man|Israel|Italy|Jamaica|Jan Mayen|Japan|Jarvis Island|Jersey|Johnston Atoll|Jordan|Juan de Nova Island|Kazakhstan|Kenya|Kerguelen Archipelago|Kingman Reef|Kiribati|Kosovo|Kuwait|Kyrgyzstan|Laos|Latvia|Lebanon|Lesotho|Liberia|Libya|Liechtenstein|Line Islands|Lithuania|Luxembourg|Macau|Macedonia|Madagascar|Malawi|Malaysia|Maldives|Mali|Malta|Marshall Islands|Martinique|Mauritania|Mauritius|Mayotte|Mediterranean Sea|Mexico|Micronesia|Midway Islands|Moldova|Monaco|Mongolia|Montenegro|Montserrat|Morocco|Mozambique|Myanmar|Namibia|Nauru|Navassa Island|Nepal|Netherlands|New Caledonia|New Zealand|Nicaragua|Niger|Nigeria|Niue|Norfolk Island|North Korea|North Sea|Northern Mariana Islands|Norway|Oman|Pacific Ocean|Pakistan|Palau|Palmyra Atoll|Panama|Papua New Guinea|Paracel Islands|Paraguay|Peru|Philippines|Pitcairn Islands|Poland|Portugal|Puerto Rico|Qatar|Republic of the Congo|Reunion|Romania|Ross Sea|Russia|Rwanda|Saint Helena|Saint Kitts and Nevis|Saint Lucia|Saint Pierre and Miquelon|Saint Vincent and the Grenadines|Samoa|San Marino|Sao Tome and Principe|Saudi Arabia|Senegal|Serbia|Seychelles|Sierra Leone|Singapore|Sint Maarten|Slovakia|Slovenia|Solomon Islands|Somalia|South Africa|South Georgia and the South Sandwich Islands|South Korea|South Sudan|Southern Ocean|Spain|Spratly Islands|Sri Lanka|State of Palestine|Sudan|Suriname|Svalbard|Swaziland|Sweden|Switzerland|Syria|Taiwan|Tajikistan|Tanzania|Tasman Sea|Thailand|Togo|Tokelau|Tonga|Trinidad and Tobago|Tromelin Island|Tunisia|Turkey|Turkmenistan|Turks and Caicos Islands|Tuvalu|USA|Uganda|Ukraine|United Arab Emirates|United Kingdom|Uruguay|Uzbekistan|Vanuatu|Venezuela|Viet Nam|Virgin Islands|Wake Island|Wallis and Futuna|West Bank|Western Sahara|Yemen|Zambia|Zimbabwe|Historical Country Names|Belgian Congo|British Guiana|Burma|Czechoslovakia|Former Yugoslav Republic of Macedonia|Korea|Netherlands Antilles|Serbia and Montenegro|Siam|USSR|Yugoslavia|Zaire)(:[a-zA-Z0-9 ]+)? - - - - - - - help: Consult the http://www.insdc.org/country.html country list for valid options. - The INSDC country qualifier is a textual controlled vocabulary used to indicate the country of origin of a DNA sample. It can also have the following format: country:sub_region, such as: "Canada:Vancouver". - Damion Dooley - INSDC country qualifier - - - - - - - - - phenotype - - Phenotype: phenotypic measurements for submission to dbGaP - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - phenotype project objective - - - - - - - - - - - - - - - genome material - - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - genome material from specimen - - - - - - - - - TB lineage 7 - Ethiopia - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An object aggregate which has as members whole organs or parts of organs, possibly from different organisms. - - 2021-04-19T23:36:25Z - organs or organ parts - - - - - - - - - A travel destination which a given human has travelled to on a particular trip and is outside Canada. - - 2021-05-27T04:35:17Z - travel outside Canada - - - - - - - - - A travel destination which a given human has travelled to on a particular trip and is outside a given province/territory of interest. - - 2021-05-27T04:36:13Z - travel outside province/territory - - - - - - - - - requires discussion - A data specification established for use by The Canadian COVID-19 Genomics Network (CanCOGeN) project DataHarmonizer application, for contextual data (metadata) harmonization and curation across data providers. - https://orcid.org/0000-0002-9578-0788 - https://github.com/Public-Health-Bioinformatics/DataHarmonizer/blob/master/template/canada_covid19/SOP.pdf - 2021-04-24T00:18:57Z - draft CanCOGeN DataHarmonizer specification - - - - - - - - - - A livespan history item is a date-associated event pertaining to the life of a subject. - Damion Dooley - lifespan history item - - - - - - - - - untreated water - - - - - - - - - treated water - ambient temperature - - - - - - - - - epidemiology investigation data item - - - - - - - - Unclear semantics and origin - obsolete distribution event - true - - - - - - - - obsolete supply point / event - true - - - - - - - - - - well water - treated - - - - - - - - - - Well water - untreated - - - - - - - - - - - - - - - organism datum - - - - - - - - - - http://purl.obolibrary.org/obo/GENEPIO_0001171 - http://purl.obolibrary.org/obo/OBI_0100026 - http://purl.obolibrary.org/obo/PATO_0000047 - - - - - - - - - - - - - - - a role which inheres in an organism and is realized by the process of being alive - organism role - - - - - - - - - isolate organism role - - - - - - - - - - - - - - - - - - - - animal role - - - - - - - - - - - - - - - - - - - - plant role - - - - - - - - - - Damion Dooley - taxonomic datum - - - - - - - - - - A course of treatment designed to resolve an infectious disease - Damion Dooley - infectious disease treatment - - - - - - - - - - - - - - - - - - - - - This is a collection of drugs used to test antimicrobial resistance. - This is a class of chemicals by use. They are organized more indirectly in CHEBI via 'has role' some 'antimicrobial agent'. - -Note: NCBI provides special requirements for antibiotic test-selection for BETA-LACTAMASE, see https://www.ncbi.nlm.nih.gov/biosample/docs/beta-lactamase/ - -Damion Dooley note: Used http://cts.fiehnlab.ucdavis.edu/conversion/batchConvert to convert antibiotic name to CHEBI entries. 60% match, some matches off, had to curate hits manually. - -Note that this is a longer list of antibiotics that we will need to incorporate, perhaps through ARO: -https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/?format=txt - Damion Dooley - antimicrobial resistance test drug - - - - - - - - - - Damion Dooley - Judgements here are marked down after an agent's (doctor/veterenary) analysis of symptoms. - analytic datum - - - - - - - - Damion Dooley - http://purl.obolibrary.org/obo/DOID_4 - obsolete: type of illness - true - - - - - - - - - - A specimen which has been confirmed by laboratory test(s) to contain a disease-causing agent such as a pathogen - Damion Dooley - specimen with confirmed presence of disease agent - - - - - - - - - dietary restriction - - - - - - - - - - A person which has a patient care role. - Damion Dooley - patient type - - - - - - - - - obsolete: mother - true - - - - - - - - - NCBI BioSample - depth:1 - lookup - - A subject disease outcome is an assessment of the persistence of a given disease course in a subject (patient) - Damion Dooley - Note that this is closely related to OGMS_0000063 "disease course" that lists chronic, progressive, transient and accute processes. - subject disease outcome - - - - - - - - - treated water - warm/hot - - - - - - - - - jacuzzi water - - - - - - - - - spa water - - - - - - - - - whirlpool water - - - - - - - - - - - - - - - - A host datum is a datum that pertains to infection-related information about an organism (animal or human) who is likely bearing a pathogen - Damion Dooley - patient as host datum - - - - - - - - - pregnancy history item - - - - - - - - - date of conception - - - - - - - - - - Damion Dooley - lifespan history record - - - - - - - - http://purl.obolibrary.org/obo/FOODON_03450002 - obsolete: food cooking method - true - - - - - - - - http://purl.obolibrary.org/obo/FOODON_03470107 - obsolete: food preservation method - true - - - - - - - - - infectious disease case datum - - - - - - - - - laboratory data - - - - - - - - - - Damion Dooley - specimen record - - - - - - - - - - The type of material from which the specimen was obtained. Specimens are usually categorized as food, body products or tissues, or environmental material. - Damion Dooley - specimen type (host or environmental context) - specimen source material category - - - - - - - - - Organism has a symbiotic relationship with host - symbiotic role - - - - - - - - http://purl.obolibrary.org/obo/GENEPIO_0000113 - obsolete: NCBI BioSample attribute package - true - - - - - - - - Damion Dooley - http://purl.obolibrary.org/obo/GENEPIO_0000025 - http://purl.obolibrary.org/obo/GENEPIO_0000028 - obsolete: host sample material - true - - - - - - - - - - Damion Dooley - food specimen detail - - - - - - - - - patient specimen - - - - - - - - - environmental - NCBI Biosample: environmental (swab or sampling) - environmental specimen - - - - - - - - - - A specimen extracted from an animal - Damion Dooley - animal specimen - - - - - - - - - built environment specimen - - - - - - - - - food specimen - - - - - - - - - natural environment specimen - - - - - - - - - - The type of person a patient had epidemiological (i.e. close proximity) contact with. - Damion Dooley - exposure event person - - - - - - - - - - Damion Dooley - An exposure group statistics record is a sumary of disease outbreak statistics on a certain date of a group of humans or animals potentially exposed to a pathogen. - exposure group statistics record - - - - - - - - - - symptom history item - - - - - - - - - - Damion Dooley - health state record - - - - - - - - http://purl.obolibrary.org/obo/NCIT_C17627 - obsolete: swab - true - - - - - - - - [WHICH DEFINITION?] See http://medical-dictionary.thefreedictionary.com/aspirate - Damion Dooley - - obsolete: fluid - aspirate - true - - - - - - - - - - - - - - - - - - Plant rinse is a rinse derived from plant material from one or more plants. - Damion Dooley - plant rinse - - - - - - - - - Damion Dooley - outbreak animal exposure event location - - - - - - - - - Damion Dooley - animal exposure process - - - - - - - - - Damion Dooley - animal exposure event by material - - - - - - - - - Damion Dooley - exposure by human contact - - - - - - - - Damion Dooley - unnecessary distinction - - obsolete: human exposure activity type - true - - - - - - - - - Damion Dooley - outbreak human exposure event location - - - - - - - - - - A process in which one or more humans may be exposed to one or more contagious human infectious disease carriers. - Damion Dooley - human to human exposure process - - - - - - - - - water exposure by source - - - - - - - - - human water activity - - - - - - - - - This list would be customized to include organizations local to an application's software installation. It is an example of a set of ontology terms that would best be organized by a central authority if federated installations need to share investigator contact info for example. - health authority - - - - - - - - - order: -HP:0000118 # symptom -FLU:0000976 # onset -GENEPIO:0001789 # cessation -GENEPIO:0001784 # duration - - Damion Dooley - symptom record - - - - - - - - - - - - - - - A visual pattern caused by DNA fragments concentrated in stratefied bands in a Pulsed-field gel electrophoresis (PFGE) gel plate. - PFGE pattern - - - - - - - - - - phage type salmonella (DT) - - - - - - - - - - phage type e-coli 0157 (PT) - - - - - - - - - - Damion Dooley - sequence record - - - - - - - - - - A type of built structure that is suspected to be related to an outbreak investigation. - Damion Dooley - outbreak exposure event location - http://purl.obolibrary.org/obo/ENVO_00000070 - - - - - - - - - - Damion Dooley - lab test history record - - - - - - - - - obsolete: earth surface - true - - - - - - - - - - A data specification is a specification of a data structure that can hold a categorical, textual or numeric variable, or that has such variables or other data structures as component parts. - A data standard, may be defined as a data specification, but a data specification isn't necessarily a formal or de-facto data standard - it would have to be sanctioned by a community of users and developers to take on that status. - Damion Dooley - data specification - - - - - - - - - - - - A specimen history item is a time-related datum about a particular specimen - Damion Dooley - specimen history item - - - - - - - - - - Damion Dooley - diagnostic test - - - - - - - - Damion Dooley - obsolete: sample datum - true - - - - - - - - A laboratory sequencing datum is a datum related to the sequencing assay process applied to an isolate. - Damion Dooley - http://purl.obolibrary.org/obo/GENEPIO_0001681 - obsolete: laboratory sequencing datum - true - - - - - - - - - genomic sequencing annotation datum - - - - - - - - - - Damion Dooley - ISSUE: lab test results are appropriate to lab test types. Logic around that? - lab test record - - - - - - - - - - - - - - - sequencing assembly datum - - - - - - - - - - A container id is an identifier that refers to a container object about a patient specimen. Container ids are referenced in clinical patient records reported to be suspect, or lab test results. - Damion Dooley - container record - - - - - - - - - Damion Dooley - identifier of a person with the context of a health care system - health care personal identifier - - - - - - - - - - - - - - - - A strain identifier is the unique microbial or eukaryotic strain name from a reference database that a sample has been matched to. - Damion Dooley - strain identifier - - - - - - - - - - A line list is a collection of suspected or known disease outbreak cases. It may also include details about healthy patients associated with an exposure event (picnic, concert etc.) who have been interviewed in order to compare food intake, assess risk factors, etc. - -Note that the health status of people associated with an exposure event can change from healthy or unknown status, to ill patient. - Damion Dooley - line list object - - - - - - - - - This class is a temporary holding bin for items that need a class hierarchy home, definition, and/or subclass items. Some classes have subclasses that are currently disjoint in other ontologies like ENVO, so awaiting resolution on such issues. - Damion Dooley - awaiting ontology review - - - - - - - - - The IRIDA user ID is a user account identifier provided by the IRIDA.ca system. - Damion Dooley - - - - - - - - - The count of healthy individuals or animals on a certain date/time from a group that was likely exposed to a pathogen - Damion Dooley - exposure group healthy count - - - - - - - - - The count of ill individuals or animals on a certain date/time from a group that was likely exposed to a pathogen - Damion Dooley - exposure group ill count - - - - - - - - - human general activity - - - - - - - - - - Damion Dooley - An exposure can be narrowed down to a single date, or can be reasoned to exist with a lower and/or upper bound date. A single date exposure has lower and upper bound dates set as the same value. - exposure history record - - - - - - - - - - Damion Dooley - isolate history record - - - - - - - - - - Damion Dooley - An outbreak date may have an official start, but because it might be ongoing, it may not have an end (yet). - outbreak history record - - - - - - - - - - Damion Dooley - Needs to cover the various pregnancy events - pregnancy history record - - - - - - - - - - Damion Dooley - Issue: a diagnosis is a set of diseases, each of which can be marked primary or secondary "Illness causality" with respect to a particular case? Requires a relation annotation. - diagnosis record - - - - - - - - - - Damion Dooley - exposure event record - - - - - - - - - - Damion Dooley - hospitalization event record - - - - - - - - - An exposure can be narrowed down to a single date, or can be reasoned to exist with a lower and/or upper bound date. A single date exposure has lower and upper bound dates set as the same value. - exposure history item - - - - - - - - - hospital admission date - - - - - - - - - A date-time datum that marks the end of possible human or animal exposure to a pathogen agent, directly or indirectly. - Damion Dooley - exposure event end - - - - - - - - - A date-time datum that marks the start of a human or animal exposure event to a suspected pathogen agent, directly or indirectly. - Damion Dooley - This datum is NOT predicted as a function of pathogen and first symptom date. - exposure event start - - - - - - - - - hospitalization history item - - - - - - - - - isolate history item - - - - - - - - - An outbreak date may have an official start, but because it might be ongoing, it may not have an end (yet). - outbreak history item - - - - - - - - - - - - - - - hospital discharge date - - - - - - - - - - A notification date is the date that an outbreak is suspected by a laboratory or other agency and is reported per outbreak detection guidelines. - Damion Dooley - notification date - - - - - - - - - - An outbreak date is on which disease onset appears to have occured - Damion Dooley - outbreak date - - - - - - - - - - - - - - - - An outbreak over date is the date on which a disease outbreak appears to have abated - Damion Dooley - outbreak over - - - - - - - - - - test history item - - - - - - - - - - lab test result date - - - - - - - - - requires discussion - A data item that is a set of entities, referenced by mention, that don't necessarily have something in common. - 0000-0002-8844-9165 - 0000-0002-9578-0788 - 2022-01-31T03:45:04Z - While "enumeration" is a "data item" not everything referenced within an enumeration qualifies as a "data item". Not to be confused with "data set" which describes "data item"s of the same type that have something in common. - enumeration - - - - - - - - - An analytic datum which describes the observed or detectable signs, and experienced symptomps of an illness, injury, or condition. - 0000-0002-9578-0788 - https://en.wikipedia.org/wiki/Signs_and_symptoms - 2022-01-31T23:08:50Z - signs & symptoms - signs and symptoms - - - - - - - - - - A particular attribute (feature, quality or process history) of a food sample. - Damion Dooley - The underlying facets will be supplied from the FoodOn food ontology. - food specimen datum - - - - - - - - - order: -FOODON:03411564 # food source -FOODON:00002381 # food product by organism -FOODON:03311737 # processed food product -NCIT:C71898 # brand name - - A food specimen type is a categorization of a food specimen, by the organism it is or came from, or by a class of food products. - Damion Dooley - food specimen specification - - - - - - - - - - An agency that has reported a disease cluster. - Damion Dooley - disease cluster notification agency - - - - - - - - This is a subset of OBI investigation identifier. It pertains only to NCBI Biosample projects - Damion Dooley - http://purl.obolibrary.org/obo/OBI_0001628 - obsolete: NCBI BioProject ID - true - - - - - - - - - The count of individuals or animals for which no health status is available on a certain date/time from a group that was likely exposed to a pathogen. - Damion Dooley - exposure group unknown health status count - - - - - - - - - - - - - - - - - - - - - A role which inheres in a person and is realized by the process of being in the context of civilization - Damion Dooley - person role - - - - - - - - - An exposed person role is the role a person takes on who has been exposed to a pathogen. In serious situations this may call for special treatment, e.g. quarantine. - Damion Dooley - exposed person role - - - - - - - - - parent-guardian role - - - - - - - - - - Damion Dooley - illness causality - - - - - - - - - pre-existing condition - - - - - - - - - - - - - - - - To restore to the normal state after some pathologic process. - Damion Dooley - Dorland's Illustrated Medical Dictionary, 30th ed. - improving - recovering - resolving health trend - - - - - - - - - Damion Dooley - close interpersonal relationship exposure - - - - - - - - - Damion Dooley - household exposure - - - - - - - - - Damion Dooley - exposure to individual with diarrhea - - - - - - - - - Damion Dooley - other human exposure - - - - - - - - - Damion Dooley - sexual contact exposure - - - - - - - - - Damion Dooley - exposure via diaper changing (human fecal) - - - - - - - - - container identifier - - - - - - - - - PulseNet: Outbreak - outbreak identifier - - - - - - - - - - - - - - - - - - - - - - GENEPIO - reference genome size - - - - - - - - - - - - - - - - The assembly genome size is the sum of all lengths of a sequence assembly's contigs. - Damion Dooley - GENEPIO - As noted in Quast documentation: " The total assembly size may increase (and in some cases exceeds the genome size) due to contaminants (see Chitsaz et al. (2011)), misassembled contigs, repeats, and hubs that contribute to multiple contigs. " - assembly genome size - - - - - - - - - - - - - - - - Identifier for a reference genome (used to build or compare an assembly) that is used in the genome browsers and in the community - Damion Dooley - GENEPIO - reference genome identifier - - - - - - - - - Assembly QC - - The 'genome size delta ratio' is a ratio of the difference between a sample's genome assembly size and the size of a given reference genome, over the reference genome size. - -The formula: - -| (reference_genome_size - assembly_genome_size) | / reference_genome_size - -This yeilds a decimal / percentage ranging from 0 = exact length, to say .1 which is equivalent to a 10% variance. If the ratio is too far from a quality control ratio that depends on the species in question, this indicates a bad assembly or a mis-identified sample. - Damion Dooley - GENEPIO - genome size delta ratio - - - - - - - - - Assembly QC - - This is the upper acceptable limit of the 'genome size delta ratio' with respect to a particular species. - -For Salmonella a 0.10 variance in length between an assembly size and a reference genome size may be acceptable. For E-coli a more generous 0.30 or .40 variance should be allowed, given the pathogenic subspecies’ highly dynamic genome. - GENEPIO - genome size delta ratio QC threshold - - - - - - - - - Assembly QC - http://purl.obolibrary.org/obo/IAO_0000428 - The contig N50 length QC threshold is a minimum length threshold that a contig N50 length datum should be above for good QC. A lower length is indicative of assembly problems (insufficient read depth) or a mismatched reference genome. - Damion Dooley - GENEPIO - contig N50 length QC threshold - - - - - - - - - Assembly QC - 2000 - - The contig N99 length QC threshold is the minimum length that a contig N99 or NG99 length datum can be for satisfactory QC. This threshold avoids having too many gene coding regions prematurely clipped inside short contigs. An assembly having 1% or more of its content in less than 2Kbp chunks is cause for concern. Bacterial genes are generally about 1Kbp in length. - Damion Dooley - GENEPIO - contig N99 length QC threshold - - - - - - - - - - - - - - - - - - - - - - - lookup - Homo sapiens - - The species of the host organism from which a specimen (pathogen) organism was obtained. Use the full taxonomic name, eg, "Homo sapiens". - Damion Dooley - - subject organism (host) taxonomic species - - - - - - - - - - - - - - - - - - - lookup - - - - - - - - - - - - - - - Assembly QC - - A single datum having to do with a metric for genomic sequence assembly quality control. - -A "quality control measurement" can be defined as a measurement that has some norm within a definable context, e.g. for a certain subspecies. It may be a calculated quantity. - -A "quality control metric" is an upper or lower bound threshold that a measurement is compared to. Surpassing the threshold may indicate an error situation. - -A "measure" can indicate an amount of activity, consumption, transformation, etc. but doesn't itself convey an over-stepping of bounds in the way that a metric does. - Damion Dooley - GENEPIO - assembly quality control datum - - - - - - - - - - - - - - - - - - - - - Damion Dooley - GSCID-BRC:Clinical/host-associated pathogen - NCBI:Pathogen.cl - clinical or host-associated pathogen - - - - - - - - - - - Clinical/host-associated pathogen - - - - - - - - - - - Pathogen.cl - - - - - - - - - Assembly QC - http://purl.obolibrary.org/obo/IAO_0000428 - The N99 length definition is identical to the N50 definition except that the threshold for determining the contigs is 1% of the nucleotides. This contig basepair length can be compared to a minimum threshold to determine if gene annotation (where contigs greater than say 2000bp are necessary) would generally succeed. - Damion Dooley - GENEPIO - contig N99 - - - - - - - - - Assembly QC - http://purl.obolibrary.org/obo/IAO_0000428 - The upper threshold of contig counts that are acceptable in a genome assembly. This may vary based on the overall genome length and depth of coverage. - -A large contig count may indicate insufficient read coverage. - Damion Dooley - contig count QC threshold - - - - - - - - - - Indicates how the knowledge derived from the project can be applied, and to what field(s). - Damion Dooley's note: NAIAD GRCID-BRC has Project Relevance map to OBO Foundry Study Design (http://purl.obolibrary.org/obo/OBI_0500000) but this is a bit of a stretch. - Damion Dooley - https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project - project relevance - - - - - - - - - agricultural project relevance - - - - - - - - - medical knowledge relevance - - - - - - - - - industrial processing relevance - - - - - - - - - evolution modelling relevance - - - - - - - - - environmental project relevance - - - - - - - - - model organism relevance - - - - - - - - The NCBI BioProject model includes all datums associated with the current NCBI BioProject specification. - Damion Dooley - - obsolete: NCBI BioProject model - true - - - - - - - - http://purl.obolibrary.org/obo/GENEPIO_0000147 - obsolete: NCBI SRA model - true - - - - - - - - - http://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ - http://www.ncbi.nlm.nih.gov/biosample/docs/packages/Pathogen.cl.1.0/ - - Damion Dooley notes: NCBI doesn't quite make the distinction but it may be helpful to distinguish sample submission facilitator vs submitter/repository organization contact? So should we have a -BioSample_submission_facilitator field and a BioSample_contact_information field? - Damion Dooley - Damion's note: There are a few different kinds of biosample, and required fields depend on the type selected. - draft NCBI BioSample model - mixed clinical and environmental/food/other - - - - - - - - - monoisolate - - A monoisolate sample scope involves specimens from a single animal, cultured cell-line, inbred population, or possibly a heterogeneous population when a single genome assembly is generated from a pooled sample because multiple individuals are needed to collect enough material and an inbred line is not available; however, this situation is not preferred. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - monoisolate - monoisolate sample scope - - - - - - - - - multiisolate - - A multiisolate sample scope contains multiple individuals that represent distinct specimen collections, a population (representative of a species). - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - This is often used for variation or phenotype and genotype studies. This should not be used when multiple genomes will be annotated. Eventually, multiple locus_tag prefixes will be able to be assigned to a single multiisolate genome sequencing project, but currently only a single prefix can be registered per project. Therefore, individual monoisolate projects need to be registered when more than one genome will be annotated. - multiisolate sample scope - - - - - - - - - multispecies - - A multi-species sample scope involves a sample representing multiple species. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - multispecies sample scope - - - - - - - - - environment - - An environment sample scope indicates that the species content of the sample is not known. Generally, nucleic acid is directly isolated from an environmental sample for analysis. This is used for metagenome studies. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - environment sample scope - - - - - - - - - - A synthetic sample scope involves a sample synthesized in a laboratory. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - synthetic sample scope - - - - - - - - - - Damion Dooley - single cell - - - - - - - - - other - - Other project objective: specify an objective not listed above - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - other project objective - - - - - - - - - - - - - - - - - - - - - Damion Dooley - GSCID-BRC:environmental/food/other - NCBI:Pathogen.env - environmental, food or other pathogen - - - - - - - - - - - environmental/food/other - - - - - - - - - - - Pathogen.env - - - - - - - - - whole - - Whole: the project makes use of the whole sample material (most common case). Use this for whole genome sequencing studies, transcriptome studies that are not targeting specific loci, epigenetic studies of a genome, and metagenomes or unbiased transcriptome studies of metagenomes. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - whole genomic data capture - - - - - - - - - raw sequence reads - - A raw sequence reads project objective has the goal of submission of raw reads to SRA or Trace repositories - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - raw sequence read objective - - - - - - - - - sequence - - A sequence project objective has a goal of submission of sequence data to standard archival sequence databases (yielding accession.version identifiers; e.g., whole genome shotgun, cDNA sequences, transcript shotgun assemblies) - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - sequence project objective - - - - - - - - - analysis - - An "analysis project objective" indicates there was an other analysis not otherwise indicated, includes submission of BAM files. - This defn. could be a negation of the "not otherwise indicated". - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - analysis objective - - - - - - - - - assembly - - Submission of genome assembly (AGP data) - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - assembly objective - - - - - - - - - annotation - - Sequence annotation data - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - sequence annotation objective - - - - - - - - - sequence variation - - Variation: identification of sequence variation data for submission to dbSNP or dbVAR - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - sequence variation project objective - - - - - - - - - epigenetic markers - - DNA methylation, histone modification, chromatin accessibility datasets - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - epigenetic markers objective - - - - - - - - - expression - - Expression: assays of transcript or protein existence or abundance - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - transcript or protein expression objective - - - - - - - - - maps - - Maps: non-sequence based map data; e.g., genetic, radiation hybrid, cytogenetic, etc. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - mapping objective - - - - - - - - - - Phenotypic descriptive data. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - phenotypic observation data from specimen - - - - - - - - - select sequence if any sequence data is generated from this project. - sequencing - - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - sequencing project method - - - - - - - - - array - - Select Array if that is the primary method and no sequence data is submitted - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - array project method - - - - - - - - - mass spectrometry - - Select Mass Spectrometry if that is the primary method - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - mass spectrometry project method - - - - - - - - - order: -NCIT:C40974 # first name -NCIT:C40975 # last name -NCIT:C42775 # email address -GENEPIO:0001756 # phone - contact specification - person - - - - - - - - - A categorical investigation datum is a datum pertaining to some entity examined for scientific research or diagnostic purposes and which has a scope that is broader than one of the clinical, environmental or epidemiological domains. - Damion Dooley - investigation datum - - - - - - - - - An organism and its host share physical space but no evidence exists to determine if one benefits from this arrangement. - commensal role - - - - - - - - - draft isolate details model - - - - - - - - - - A subject age is the age since birth of a given organism that is involved in an investigation or study at a given time. - Damion Dooley - subject age - - - - - - - - - - draft NCBI component model - - - - - - - - - draft IRIDA BioSample model - - - - - - - - - - - - - - - draft GenEpiO epidemiology case record - - - - - - - - - - - - - - - A subject description is a field containing additional information about an organism (related to an investigation, study and/or specimen) that is not included in other defined vocabulary fields. - Damion Dooley - http://purl.obolibrary.org/obo/GENEPIO_0001835 - subject description - - - - - - - - - - - host description - - - - - - - - - NCBI BioSample - The host profile or identifiers text is the "identification or description of the specific individual from which this sample was obtained". - Damion Dooley - NCBI BioSample: isolate - host profile or identifers - - - - - - - - - - A subject identifier is an identifier of a subject organism within the context of a particular investigation, study, or specimen extraction event. - Damion Dooley - This varies in its type (numeric or string) and its central repository depending on its context (use in a particular application/instance). - -Note: GSCID-BRC specification states " 'Host' is not the preferred term since some specimens may lack any detectable pathogen". In other words, a person would technically (logically) only have a host identifier AFTER they have been diagnosed as having a pathogen. A health care personal identifier, or a case identifier would be better than a more ephemeral "host id" - subject identifier - - - - - - - - - - - - - - - - Name of disease in a subject that is related to a given investigation, study and/or specimen. - Damion Dooley - NIAID GSCID-BRC metadata working group - Controlled vocabulary. Human specimen source: https://bioportal.bioontology.org/ontologies/DOID -or https://www.ncbi.nlm.nih.gov/mesh/1000067 - subject disease - - - - - - - - - INSDC term (top level) - A categorical choice recorded when a measurement value was known to be recorded in the past but the observed value cannot be located or retrieved for some reason. - - - NCBI Biosample: missing - missing - - - - - - - - - INSDC term (top level) - 'not applicable' is an appropriate value for the measure of femur length for a patient with a missing limb - - A categorical choice recorded when a measurable datum does not apply to a given context. - Damion Dooley - - - - not applicable - - - - - - - - - INSDC term (lower level) - A categorical choice recorded when a datum was not measured with respect to some entity during some process. - - - NCBI Biosample: not collected - not collected - - - - - - - - - draft isolate identifier model - - - - - - - - - - draft GenEpiO isolate testing model - - - - - - - - - - draft NCBI isolate source location model - - - - - - - - - draft GenEpiO isolate environment model - - - - - - - - - A subject disease stage is a measure of the acuteness of a subject organism's diagnosed disease, if any, at a given time in an investigation, study or specimen extraction event. - Damion Dooley - http://purl.obolibrary.org/obo/GENEPIO_0001835 - subject disease stage - - - - - - - - - environmental datum - - - - - - - - - - - - - - - temperature of sample - - - - - - - - - - de-novo assembly - - - - - - - - - http://purl.obolibrary.org/obo/GENEPIO_0000025 - obsolete: sample body source - true - - - - - - - - - contig pre-analysis minimum length QC threshold - - A 'contig length QC threshold' is an integer setting which can be applied by an algorithm to an array of assembly and annotation contig lengths to remove (filter out) all items less than the threshold value. The reduced array is used for calculation of statistics. - Damion Dooley - http://quast.bioinf.spbau.ru/manual.html - QUAST specifies which of its report stats are affected by the "--min-contig" minimum contig length parameter. - contig length QC threshold - - - - - - - - - - The NG50 length is the same as the N50 length except that the length of the reference genome is used in the calculation rather than the assembly genome size. - Damion Dooley - "Note that N50 is calculated in the context of the assembly size rather than the genome size. Therefore, comparisons of N50 values derived from assemblies of significantly different lengths are usually not informative, even if for the same genome. To address this, the authors of the Assemblathon competition derived a new measure called NG50. The NG50 statistic is the same as N50 except that it is 50% of the known or estimated genome size that must be of the NG50 length or longer. This allows for meaningful comparisons between different assemblies. In the typical case that the assembly size is not more than the genome size, the NG50 statistic will not be more than the N50 statistic." - wikipedia - contig NG50 - - - - - - - - - - - - - - - - A contig length is the count of base pairs in a given sequence assembly contig. - Damion Dooley - contig length - - - - - - - - - Assembly QC - http://purl.obolibrary.org/obo/IAO_0000428 - Contig L50 is the number of contigs equal to or longer than contig N50. The length of the assembly itself is used in the calculation. - Damion Dooley - QUAST manual - contig L50 - - - - - - - - - Assembly QC - http://purl.obolibrary.org/obo/IAO_0000428 - The LG99 count is like the L99 count except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths. - Damion Dooley - contig LG99 - - - - - - - - - An organism isolate datum is any datum pertaining to an isolate organism - Damion Dooley - obsolete: specimen from subject datum - true - - - - - - - - - - - - - - - - A product of an animal, as in blood, feces, sputum, etc. that has no particular anatomical site - Damion Dooley - animal body product - - - - - - - - This is the scientific role or category that the subject organism or material has with respect to an investigation. - Damion Dooley - http://purl.obolibrary.org/obo/GENEPIO_0001237 - obsolete: specimen source material category - true - - - - - - - - - draft GenEpiO general information record - - - - - - - - - - - - - - - - - - - - - An antigenic formula is a string composed of codes representing categorized results of tests performed on various viral, bacterial or immune cell surface antigens. - Damion Dooley - antigenic formula - http://medical-dictionary.thefreedictionary.com/antigen - - - - - - - - - - - - - - - - - - - - - - - - lookup - - This is the taxonomic species descriptor of a specimen isolate (an organism found within a specimen.) - Damion Dooley - specimen organism taxonomy (species) - - - - - - - - - - An identifier moe3l indicates an identifier, the organization it has been issued by, and the status of the identifier - whether it is a primary one, active or archaic. - Damion Dooley - identifier model - - - - - - - - - help:This should be populated with a selection from INSDC.org controlled vocabulary for providers: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/coll_dump.txt - - The curator organization name is the name of an organization that manages a given repository of entities (samples, isolates, sequences ...) - Damion Dooley - curator organization name - - - - - - - - - INSDC:institution_code:BRS - IRIDA:ACK - Agriculture and Agri-Food Canada - - - - - - - - - - An isolate identifier is an identifier assigned to a given isolate by a particular agency that is handling or storing it. - Damion Dooley - isolate identifier - - - - - - - - - - An identifier status describes the principle role of an identifier assigned to an entity by its curator or handler. An entity may have a number of identifiers assigned to it over time. An identifier may be phased-out as can happen when its content is transferred to another curator. - Damion Dooley - identifier status - - - - - - - - - GenEpiO - - A data protection role is a role (or user permission) that a user has with respect to particular data. - A data server may be able to provide a protected(modified) dataset with metadata indicating what parts have a protection role with respect to the user requesting this information. A data protection role would be inherited from a user's relation to an entitiy to the entity's components or subclasses. - Damion Dooley - data protection role - - - - - - - - - - - An identifier used in the initial submission of content to a repository. - original submission - - - - - - - - - - This was created to help define a contributing organization to a repository. However this still needs organizing. The "collected_by" field is free text but contact name AND organization could be associated with this in controlled vocabulary. - NCBI Contributing organization / project - - - - - - - - - food - liquid - - - - - - - - - - draft NCBI BioSample identifier model - - - - - - - - - - An INSDC institution code is an identifier of an organization from a list of sequence repository organizations managed by INSDC. - Damion Dooley - http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier - INSDC institution code - - - - - - - - - draft IRIDA epidemiological case model - - - - - - - - - - An identifier that had been used previously but is no longer promoted. - Damion Dooley - previous (archaic) identifier - - - - - - - - - - A geographical location datum is a datum that refers to a real, hypothesized or fanciful spatial location - Damion Dooley - geographic location datum - - - - - - - - A categorical tree specification datum is a categorical value specification which takes its value from the ontology URI identifier of any one of its subclass items; these may be organized in a hierarchy. - Damion Dooley - http://purl.obolibrary.org/obo/OBI_0001930 - A categorical tree specification datum may have its own URI identifier as its value. This could be interpreted to mean that the datum was recorded but that no particular categorical subclass distinction was observed. This in effect makes the datum act as a boolean variable. - obsolete: categorical tree specification - true - - - - - - - - - - Damion Dooley - A geographic coordinate entity composed of both latitude and longitude components. - latitude and longitude coordinate (ISO 6709) - - - - - - - - - - - - - - - order: -NCIT:C25464 # country -ENVO:00000005 # state / province etc. - - Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps" - Damion Dooley - draft NCBI BioSample geo_loc_name model - - - - - - - - - draft GenEpiO isolate sequencing model - - - - - - - - - A case ID is a unique identifier associated with a particular episode of care for an individual or animal. - Damion Dooley - case identifier - - - - - - - - - - - An animal that has had a substantial part of its reproductive organs removed surgically. - Damion Dooley - NCBI BioSample: neuter - Not a PATO phenotypic sex catigorical value. - neuter - - - - - - - - - - - - - - - - - NCBI BioSample - 'pooled male and female' is a categorical value used when the male and female categories or levels of a factor are combined. If used to describe a single organism, then the organism will be one or the other. - Not a PATO phenotypic sex catigorical value. - Damion Dooley - NCBI BioSample: 'pooled male and female' - pooled male and female - - - - - - - - - - A categorical choice recorded while the data for a given measurable datum has not finished being collected, is awaiting a conclusion, or has not yet been communicated. - Damion Dooley - undetermined - in process - - - - - - - - - swimming / wading - - - - - - - - - - Damion Dooley - NECESSARY? : What details are categorical and what are freehand? This item was originally too broad; moved sub-items to Treatment. - infection detail datum - - - - - - - - - - This is problematic - its not clear if this is reporting that antibiotics were administered, or whether they are recommended as a result of diagnosis. - Damion Dooley - antibiotics required - - - - - - - - - - The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. INSDC covers the spectrum of data raw reads, though alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations. - Damion Dooley - International Nucleotide Database Collaboration standard - INSDC - INSDC standard - - - - - - - - - - Damion Dooley - outcome of pregnancy associated with illness - - - - - - - - - INSDC term (lower level) - a categorical choice indicating that information of an expected format was not given; a value may be given at the later stage. - - - not provided - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - stable health status - http://purl.obolibrary.org/obo/GENEPIO_0002026 - - - - - - - - - induced abortion - - - - - - - - - - live birth - - - - - - - - Damion Dooley - http://purl.obolibrary.org/obo/VT_0002292 - obsolete: gestation duration (weeks) - true - - - - - - - - - - - - - - - date of pregnancy outcome - - - - - - - - - - - - - - - - - - - - - - contact specification - physician - - - - - - - - obsolete: matrix - solid - true - - - - - - - - - - - - - - - - contact specification - parent/guardian - - - - - - - - - - - - - - - - - - - - - - contact specification - patient - - - - - - - - - draft GenEpiO case epidemiology record - - - - - - - - - order: -NCIT:C25464 # Country -ENVO:00000005 # major administrative subdivision aka state/province/territory/region (via GenEpiO -> GAZ ) -NCIT:C80234 # Municipality (via GenEpiO -> GAZ cities) -NCIT:C25690 # Street Address -NCIT:C25621 # postal code - - The address component of a contact specification. - contact specification - address - - - - - - - - - GENEPIO_0001829 - obsolete: draft IRIDA model - true - - - - - - - - - - A datum related to the sequencing assay process applied to an isolate. - Damion Dooley - laboratory sequencing datum - http://purl.obolibrary.org/obo/OBI_0001901 - http://purl.obolibrary.org/obo/OBI_0400103 - - - - - - - - - - Damion Dooley - host illness associated with - - - - - - - - - draft subject demographic specification - - - - - - - - - - - - - - - - - - - - - - - K(1|2a|2ac|3|4|5|6|7|8|9|10|11|12|13|14|15|16|18a|18ab|19|20|22|23|24|26|27|28|29|30|31|34|37|39|40|41|42|43|44|45|46|47|49|50|51|52|53|54|56|96|55|74|82|84|85ab|85ac|87|92|93|95|97|98|100|101|102|103|X104|X105|X106) - - - - - - - E. coli K antigen specification - - - - - - - - - - - - - - - - - - 1 - - - - - - 6 - - - - - - - other antigen specification - - - - - - - - - - E. coli serotype specification - - - - - - - - - - Damion's note: This will be converted to a categorical tree specification list of serovars by name or id asap. - Salmonella serovar specification - - - - - - - - - - A lab test specification indicates the inputs and outputs (results / conclusions) of a test. - Damion Dooley - test specification - - - - - - - - - - - - - - - - - - - - - - - (1/2|1/2a|1/2b|1/2c|3a|3b|3c|4a|4ab|4b|4c|4d|4e|1|7) - - - - - - - listeria antigen - - - - - - - - obsolete: matrix - fluid - true - - - - - - - - - listeria serotype 1/2a - - - - - - - - - listeria serotype 1/2b - - - - - - - - - listeria serotype 1/2c - - - - - - - - - listeria serotype 1/2 - - - - - - - - - listeria serotype 3a - - - - - - - - - listeria serotype 3b - - - - - - - - - listeria serotype 4a - - - - - - - - - listeria serotype 4b - - - - - - - - - listeria serotype 4c - - - - - - - - - listeria serotype 4d - - - - - - - - - listeria serotype 4e - - - - - - - - - non-monocytogenes listeria antigen - - - - - - - - - listeria serotype 3c - - - - - - - - - textual test result - - - - - - - - This is an organizational category for grouping parameters relevant to biomedical research projects. - Damion Dooley - - obsolete: draft GenEpiO BioProject standard - true - - - - - - - - - Damion Dooley - NCBI BioSample: collection_code - NCBI BioSample collection code - - - - - - - - - - - - - - - - draft NCBI BioSample host model - - - - - - - - - food - solid - - - - - - - - - lab test datum - - - - - - - - - Xbal - - - - - - - - - Ascl - - - - - - - - - Smal - - - - - - - - - Blnl - - - - - - - - - Apal - - - - - - - - - Kpnl - - - - - - - - - - Taxonomy below subspecies; sometimes used in viruses to denote subgroups taken from a single isolate. - Damion Dooley - NCBI Biosample - subgroup - - - - - - - - - help:This is an optional additional subtype classification as per organism convention - - A viral subtype is a classification name for a virus according to some protocol. - Damion Dooley - NCBI BioSample - viral subtype - - - - - - - - - - - - 1 - - - - - - - 1 - - - - - serotype specification - - - - - - - - - IRIDA - - An integer and character referring to a pattern of opaque or confluent lysis caused by a panel of bacteriophage infections e.g. 14a. - Damion Dooley - SNOMED: http://www.snomedbrowser.com/Codes/Details/272405002 - phage type specification - - - - - - - - - obsolete: swab - food contact surface - true - - - - - - - - - ATCC:26370 - An NCBI culture collection is a composite identifier containing “institution code:collection code”. - Annotation with a culture_collection qualifier implies that the sequence was obtained from a sample retrieved (by the submitter or a collaborator) from the indicated culture collection, or that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in the indicated culture collection. See the description for the proper format and list of allowed institutes, http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier. - NCBI culture collection - - - - - - - - - UAM:Mamm:52179 - The NCBI specimen voucher is an identifier composed of “institution code:collection code:specimen id” parts. In addition to a specimen identifier, it includes an institution-code (and optional collection-code) taken from a controlled vocabulary maintained by the INSDC that denotes the museum or herbarium collection where the specimen resides. - INSDC:specimen_voucher - NCBI specimen voucher - http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier. - - - - - - - - - culture identifier - - - - - - - - - - - - - - - human; dog; horse - The natural language (non-taxonomic) name of the type of organism (human or animal) that is the subject of a given investigation, study and/or specimen. - Damion Dooley's note: as of 2017 this is a problematic field for NCBI Biosample because it is slotted into "host" field, yet field is listed as "host common name" which does not fit with requirement that scientific name be provided. - Person: Damion Dooley - subject organism common name - - - - - - - - - - - - - - - - - - - - - temperature of air - average daily - - - - - - - - - obsolete: swab - inanimate object surface - true - - - - - - - - - obsolete: swab - meat - true - - - - - - - - - obsolete: swab - rectal swab - true - - - - - - - - - obsolete: swab - tissue - true - - - - - - - - - unknown source - - - - - - - - - - patient sample - human clinical specimen - - - - - - - - "environment (swab or sampling)" is a specific response for NCBI BioSample that could be mapped or unified with "environment sample" used elsewhere in GenEpiO - Damion Dooley - http://purl.obolibrary.org/obo/GENEPIO_0001246 - obsolete: environmental (swab or sampling) - true - - - - - - - - - avian - wild - - - - - - - - - avian - domesticated - - - - - - - - - human clinical specimen - invasive - - - - - - - - - In chemistry, pH is a numeric scale used to specify the acidity or basicity(alkalinity) of an aqueous solution - Damion Dooley - Wikipedia - Normally falls within the bounds of 0 - 14 - pH measurement - - - - - - - - - precipitation - - - - - - - - - - The assembly and annotation objective is the set of objectives that assembly and annotation techniques (including instruments and software platforms) applied to a sample are meant to satisfy. This impacts on the quality control thresholds applied to the sequencing project. - Damion Dooley - assembly and annotation project objective - - - - - - - - - - Damion Dooley - line list row record - - - - - - - - - - This class contains components under development for fulfilling GenEpiO and other standard data specifications. Components are relevant to epidemiological, laboratory, clinical or environmental pathogen sample data collection and analysis. - Damion Dooley - draft GenEpiO component record - - - - - - - - - - - - region - lookup:http://purl.obolibrary.org/obo/GAZ_00000448 - - A subnational region is a type of subnational entity similar to a nation's state, province, or territory. - Damion Dooley - subnational region - - - - - - - - - - A data standard related to public health research and service delivery. - Damion Dooley - public health data standard - - - - - - - - - Damion Dooley - - - - - - - - - - Reagent: material studied was obtained by chemical reaction, precipitation. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - reagent derived material from specimen - - - - - - - - - transcriptome - - Transcriptome: transcript and/or expression data. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - transcriptome data from specimen - - - - - - - - - proteome - - Proteome material is protein or peptide sequences. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - proteome data derived from specimen - - - - - - - - - purified chromosome - - Purified chromosome: one or more chromosomes or replicons were experimentally purified. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - purified chromosome from specimen - - - - - - - - - targeted locus/loci - - TargetedLocusLoci: capturing specific loci (gene, genomic region, bar code standard). - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - Targeted Locus Loci data capture - - - - - - - - - clone ends - - CloneEnds: capturing clone end data. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - clone end data capture - - - - - - - - - exome - - Exome: capturing exon-specific data. - Damion Dooley - NCBI BioSample - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - exome specific data capture - - - - - - - - - random survey - - Sequences generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material - Is this with respect to an isolate or a specimen derived culture? - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54364/ - random survey data capture - - - - - - - - - - This is a collection of various human (and animal contact location) contact information specifications used in data standards. - Damion Dooley - contact specification - - - - - - - - - order: -NCIT:C40978 # phone -GENEPIO:0001896 # phone type - - contact specification - phone - - - - - - - - - - Damion Dooley - millimetres per day - - - - - - - - - obsolete: millisiemens - true - - - - - - - - - - Damion Dooley - millisiemens per centimetre - - - - - - - - - - Damion Dooley - cubic metre per second - - - - - - - - - umol/kg - - Damion Dooley - micromole per kilogram - - - - - - - - - - Damion Dooley - micromole per litre - - - - - - - - - - Damion Dooley - quality control record - - - - - - - - - Standard draft: describing the minimum information needed for submission to a public database. - Damion Dooley - 1 - standard draft - - - - - - - - - High quality draft: describing sequences with little to no manual review. - Damion Dooley - 2 - high quality draft - - - - - - - - - Improved high quality draft: in which data is either reviewed by people or machines to some extent to indicate that most of the genetic data is assembled correctly, but some errors may still be present. - Damion Dooley - 3 - improved high quality draft - - - - - - - - - Annotation-directed improvement: in which genetic information in various gene regions is represented as accurately as possible. - Damion Dooley - 4 - annotation-directed improvement - - - - - - - - - Non-contiguous finished: which includes sequences that have been reviewed by both people and machines and would be considered complete except for “recalcitrant regions” that are proving problematic for genome closure. - Damion Dooley - 5 - non-contiguous finished - - - - - - - - - Finished: which describes un-gapped complete sequences that have minimal errors, if any. The biology of the microbe will determine whether this finished genome consists of more than one chromosome. - Damion Dooley - 6 - finished - - - - - - - - - Assembly QC - http://purl.obolibrary.org/obo/IAO_0000428 - The NG99 length is the same as the N99 length except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths. - Damion Dooley - GENEPIO - contig NG99 - - - - - - - - - Assembly QC - http://purl.obolibrary.org/obo/IAO_0000428 - Contig L50 is the number of contigs equal to or longer than contig N50. The length of the assembly itself is used in the calculation. - Damion Dooley - contig LG50 - - - - - - - - - Assembly QC - http://purl.obolibrary.org/obo/IAO_0000428 - Contig L99 is the number of contigs equal to or longer than contig N99. The length of the assembly itself is used in the calculation. - Damion Dooley - contig L99 - - - - - - - - - - A subject age at time of specimen extraction is the age (since birth) of the organism at the time a given specimen was extracted. - Damion Dooley - subject age at time of specimen collection - - - - - - - - - - A public health related data standard involving a particular species of pathogen. - Damion Dooley - pathogen specific data standard - - - - - - - - - - The draft tuberculosis contextual data standard is a data standard for the collection of contextual information of a given tuberculosis case that pertain to typing, clinical treatment, and potential research questions. - Damion Dooley - draft tuberculosis contextual data standard - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - PulseNet:Outbreak - - - - - - - - The PulseNet Canada Salmonella submission standard details the fields required in a PuseNet Canada pathogen submission report for Salmonella in spreadsheet format - Damion Dooley - draft PulseNet Canada Salmonella submission standard - http://www.pulsenetinternational.org/assets/PulseNet/uploads/wgs/PND18-NCBI-Biosample-Submission.pdf - - - - - - - - - - - - - - - A PFGE pattern resulting from DNA fragmentation induced by the Xbal enzyme. - - PFGE Xbal pattern - - - - - - - - - - - - - - - A PFGE pattern resulting from DNA fragmentation induced by the Blnl enzyme. - - PFGE Blnl pattern - - - - - - - - - NLEP ID - An NLEP ID is a unique identifier code for a sample registered with the Canadian "National Laboratory for Enteric Pathogens" (NLEP) - Damion Dooley - Pulsenet Canada spreadsheet. - National Laboratory for Enteric Pathogens Identifier - - - - - - - - - - - - - - - PulseNet spreadsheet - Date an uploaded sample was re-uploaded or had its metadata modified. - Damion Dooley - PulseNet: UploadModifiedDate - upload modified date - - - - - - - - - - A travel destination is a destination city (or populated place of some scale) which a given human has travelled to on a particular trip. - Damion Dooley - travel destination - - - - - - - - - - - A symptom duration is a date-time entity which is the duration (in hours or days or weeks etc.) that one or more symptoms persist for in a particular human or animal - Damion Dooley - This may be a calculated field if symptoms are reported to cease on a particular date. Often however symptom duration is reported more generally as a date or time range since cesation date is less certain. - symptom duration - - - - - - - - - - - - - - - - The city where a specimen was collected (taken) from a subject or environment - Damion Dooley - specimen collection location - city - - - - - - - - - - - lookup - - - - - - - - Damion Dooley - - - obsolete: sample city - true - - - - - - - - - - - - - - - - This is the genus-level taxonomic name of an organism playing a pathogen role - Damion Dooley - genus of pathogen - - - - - - - - - - - - - - - - This is the species-level taxonomic name of an organism playing a pathogen role - Damion Dooley - species of pathogen - - - - - - - - - - A symptom cessation date is a date-time entity that marks the end of one or more reported symptoms pertaining to an episode of human or animal illness - Damion Dooley - symptom cessation date - - - - - - - - - - - - - - - This is a catch-all category for listing specimen related terms - Damion Dooley - specimen datum - - - - - - - - - - - - - http://purl.obolibrary.org/obo/GENEPIO_0002105 - http://purl.obolibrary.org/obo/OBI_0001616 - - - - - - - - - - - - - - - - isolate identifier specification - - - - - - - - - - The 'data obfuscated' role between a user and given data entails that the user is authorized to see particular fields that have been transformed consistently such that statistics performed on those fields would yeild the same results as statistics applied to the un-obfuscated data. The purpose of obfuscation is to prevent related individuals or organizations from being identified. - Damion Dooley - data obfuscated - https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/ - - - - - - - - - - The 'data aggregated' role between a user and given data entails that the user is authorized to see aggregated results (like the patient count) via preset reports, queries or views. The results are not obfuscated. - Damion Dooley - data aggregated - - - - - - - - - - A 'limited data set' role between a user and given data entails that a user is authorized to see some of the fields but the remainder are withheld (or encrypted). - Damion Dooley - limited data set - - - - - - - - - help:In this dataset, selected data have been de-identified (anonymized) for access by dataset users. - - A 'de-identified data' role between a user and given data entails that the user is authorized to see only those fields (including those that are encrypted) which do not contain information that could be use to identify particular individuals (whether patients or medical practitioners) or potentially organizations in the case where an investigation may implicate them. - Damion Dooley's note: There is a case in the "draft tuberculosis contextual data standard" that has this be a boolean selection. If a categorical field is linked directly, and it has no underlings, this indicates that it is being treated as a boolean feature. - Damion Dooley - Generally de-identified data should include HIPAA patient privacy fields as indicated in https://www.hipaa.com/hipaa-protected-health-information-what-does-phi-include/ - de-identified data - - - - - - - - - - A 'data protected' role between a user and given data entails that a user must be authorized in order to view that data. - Damion Dooley - data protected - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - A datum containing the name of persons or institute who collected a given specimen. - Damion Dooley - https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ - specimen collector - - - - - - - - - - Damion Dooley - NCBI BioSample culture identifier - - - - - - - - - A user identifier is an identifier provided as part of an authentication process of a client (user) to a service (server). User identifiers normally persist over time, in contrast to session identifiers which are temporary. - Damion Dooley - user identifier - - - - - - - - - sequence identifier - - - - - - - - - metagenomic species identification - - - - - - - - - Note: REPLACE WITH Citation: SIO_000174 ???? - document citation identifier - - - - - - - - - organization identifier - - - - - - - - - collection identifier - - - - - - - - - variant calling / pathogen identification and clustering - - - - - - - - - isolate (pathogen) identification - - - - - - - - http://purl.obolibrary.org/obo/OBI_0001616 - obsolete: NCBI BioSample ID - - true - - - - - - - - - 1) Escherichia coli O104:H4 str. C227-11 clinical isolate 2010_333_NC-6 -2) CD8+ T cells from female TSG6-knockout BALB/c mouse -3) Human metagenome isolated from urine of healthy female - - A specimen (or sample) title should be short and informative. Each specimen title must be unique in a submission. - NCBI BioSample record documentation refers to a "BioSample title", stating that it is "auto-generated if one is not supplied by the submitter." This is distinct from any assigned BioSession accession, or other "external sample identifier" that may have been issued by the source database or repository. - Damion Dooley - specimen title - - - - - - - - - draft GenEpiO isolate source context - - - - - - - - - INSDC term (lower level) - - A categorical choice recorded when the data for a given measurable datum is available but not shared publicly because of information privacy concerns. - - - restricted access - - - - - - - - - State (United States of America) - - - - - - - - - - - - - - - - - - - - - - - - - - A health status trend is a short-term prognosis about whether health is improving, worsening or unchanging - Damion Dooley - health status trend datum - - - - - - - - - http://www.itis.gov - - The Integrated Taxonomic Information System (ITIS) contains authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world. - Damion Dooley - Integrated Taxonomic Information System - ITIS - ITIS - - - - - - - - - https://www.nlm.nih.gov/mesh/meshhome.html - - MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. - Damion Dooley - Medical Subject Headings - MSH - MESH - - - - - - - - - https://ncit.nci.nih.gov/ncitbrowser/ - - The National Cancer Institute Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities. - Damion Dooley - National Cancer Institude Thesaurus - NCI_Thesaurus - NCIt - NCIT - - - - - - - - - - The NIFSTD ontology of the Neuroscience Information Framework is composed of a collection of OWL modules with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, organism, function and dysfunction. - Damion Dooley - https://wiki.nci.nih.gov/display/VKC/NIFSTD+Ontology - NIFSTD - - - - - - - - - - SNOMED CT is a large clinical health terminology product owned and distributed by SNOMED International. - Damion Dooley - http://www.snomed.org/snomed-ct - SNOMEDCT - SNOMEDCT - - - - - - - - - http://www.fao.org/fishery/collection/asfis/en - - ASFIS is a database curated by the United Nations Food And Agriculture Organization (FAO) Fisheries and Aquaculture Statistics and Information Branch (FIPS). It contains over 12,700 species items selected according to their interest or relation to fisheries and aquaculture. - Damion Dooley - UN FAO Fisheries and Aquaculture Statistics and Information Branch database - FAO ASFIS - ASFIS - - - - - - - - - - FTT - - - - - - - - - - TGN - - - - - - - - - - Wikipedia is a free online encyclopedia that aims to allow anyone to edit articles. - Damion Dooley - https://en.wikipedia.org/wiki/Wikipedia - Wikipedia - - - - - - - - - - SWEETRealm - - - - - - - - - - The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge. - Damion Dooley - http://www.geonames.org/ - Geonames - - - - - - - - - http://ecolexicon.ugr.es/en/index.htm - - EcoLexicon is a terminological resource developed by the LexiCon Research Group at the University of Granada. - Damion Dooley - EcoLexicon - - - - - - - - - - A standard established for use by the Integrated Rapid Infectious Disease Analysis (IRIDA) project, which is a Canadian-led initiative to build an open source, end-to-end platform for infectious disease genomic epidemiology. - Damion Dooley - http://www.irida.ca/ - draft IRIDA standard - - - - - - - - - - ISO 3166-1 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for the names of countries, dependent territories, and special areas of geographical interest. - Damion Dooley - https://en.wikipedia.org/wiki/ISO_3166-2 - ISO3166-1 - - - - - - - - - - ISO 3166-2 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for identifying the principal subdivisions (e.g., provinces or states) of all countries coded in ISO 3166-1. - Damion Dooley - https://en.wikipedia.org/wiki/ISO_3166-1 - ISO3166-2 - - - - - - - - - - Information Technology – Codes For The Identification Of The States And Equivalent Areas Within The United States, Puerto Rico, And The Insular Areas - Damion Dooley - American National Standards Institute - ANSI INCITS 38 - - - - - - - - - - Damion Dooley - The Geographic Names Information System (GNIS), developed by the U.S. Geological Survey in cooperation with the U.S. Board on Geographic Names, contains information about physical and cultural geographic features in the United States and associated areas, both current and historical. - https://nhd.usgs.gov/gnis.html - GNISID - - - - - - - - - - LTER - - - - - - - - - - - - - - - order: -OBI:0001628 # investigation identifier -OBI:0001616 # specimen identifier -GENEPIO:0001808 # specimen title -GENEPIO:0000113 # specimen category -sep:00196 # specimen description -OBI:0001479 # specimen from organism -GENEPIO:0001640 # specimen organism taxonomy (species) -GENEPIO:0000027 # specimen source context -GENEPIO:0001722 # NCBI specimen voucher -GENEPIO:0001429 # strain identifier -GENEPIO:0001798 # NCBI BioSample culture identifier -GENEPIO:0001717 # viral subtype -OMP:0000207 # serotype phenotype -SO:0001027 # genotype -GENEPIO:0001079 # serovar -GENEPIO:0001716 # subgroup -GENEPIO:0001055 # NCBI pathotype -GENEPIO:0001054 # isolate passage history -GENEPIO:0001656 # latitude and longitude coordinate -GENEPIO:0001657 # NCBI BioSample geo_loc_name model -GENEPIO:0001051 # NCBI BioSample isolate (human name or description) -GENEPIO:0001648 # NCBI Contributing organization / project -GENEPIO:0001797 # specimen collector -OBI:0001619 # specimen collection date -OBI:0001888 # sequencing facility contact person -GENEPIO:0001651 # INSDC institution code -GENEPIO:0001721 # NCBI culture collection -GENEPIO:0001567 # subject (host) taxonomic species -GENEPIO:0001724 # subject organism common name -GENEPIO:0001775 # subject age at time of specimen collection -GENEPIO:0000026 # subject health status at time of specimen extraction -GENEPIO:0000031 # subject sex -GENEPIO:0001614 # subject description -GENEPIO:0001617 # subject disease -GENEPIO:0001625 # subject disease stage -GENEPIO:0001212 # subject disease outcome - - A National Center for Biotechnology Information BioSample specification defines fields and terms that provide "descriptions of biological source materials used in experimental assays". - Damion Dooley - http://www.ncbi.nlm.nih.gov/biosample/ - NCBI BioSample Pathogen.cl standard - https://www.ncbi.nlm.nih.gov/biosample/docs/packages/Pathogen.cl.1.0/ - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - 1 - - - - - - - 1 - - - - - - - 1 - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - The National Center for Biotechnology Information BioProject standard is a collection of datums that describe biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. - Damion Dooley - http://www.ncbi.nlm.nih.gov/bioproject/ - NCBI lists project data type and other controlled vocabulary fields at : https://www.ncbi.nlm.nih.gov/books/NBK54364/ - NCBI BioProject standard - - - - - - - - 1 - - - - - - - - - - - - - - Objective - - - - - - - - 1 - - - - The format of the BioProject Accession is five alpha-letters followed by one to six numbers. For example PRJNA43021 - Project Accession - - - - - - - - 1 - - - - - - - - - - - - - - Methodology - - - - - - - - - http://www.aha.org/content/00-10/overview0302.pdf - http://www.webcitation.org/5VBWPbFgY - - The American Hospital Association has issued HIPAA Updated Guidelines for Releasing Information on the Condition of Patients - Damion Dooley - American Hospital Association HIPAA Standard - AHA HIPPA - AHA HIPPA standard - - - - - - - - - http://www.ncbi.nlm.nih.gov/pubmed/ - - PubMed comprises more than 26 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. - NCBI PubMed - PMID - PubMed - - - - - - - - - http://www.pulsenetinternational.org/ - - PulseNet, a national and international surveillance system used to identify and respond to foodborne disease outbreaks, has a standardized laboratory method and data submission standard for pathogen isolate typing test results and related isolate contextual data. From this information clusters of disease can be identified that might represent unrecognized outbreaks. - Pulse Net International BioSample Metadata - PulseNet - PulseNet submission standard - https://www.cdc.gov/pulsenet/pathogens/index.html - https://www.nml-lnm.gc.ca/Pulsenet/index-eng.htm - - - - - - - - - - - - - - - - - - - - - - AHA HIPPA: http://www.aha.org/content/00-10/overview0302.pdf - - Good - Vital signs are stable and within normal limits. Patient is conscious and comfortable. Indicators are excellent. - Damion Dooley - - - AHA Hippa: Good - good health status - - - - - - Good - - - - - - satisfactory - - - - - - - - - - - - - - - - - - - - - - - Fair - Vital signs are stable and within normal limits. Patient is conscious, but may be uncomfortable. Indicators are favorable. - Damion Dooley - - fair health status - - - - - - fair - - - - - - Stable - - - - - - - - - - - - - - - - - - - - - - - Serious - Vital signs may be unstable and not within normal limits. Patient is acutely ill. Indicators are questionable. - Damion Dooley - - serious health status - - - - - - Serious - - - - - - - - - - - - - - - - - - - - - - - - - - A health status history datum is a record of the longer-term pattern or presence of a given patient's health status. - Damion Dooley - health status history datum - - - - - - - - - (0,0) is the origin of the cartesian coordinate system. - "In mathematics, the origin of a Euclidean space is a special point, usually denoted by the letter O, used as a fixed point of reference for the geometry of the surrounding space. - -In physical problems, the choice of origin is often arbitrary, meaning any choice of origin will ultimately give the same answer. This allows one to pick an origin point that makes the mathematics as simple as possible, often by taking advantage of some kind of geometric symmetry." - Damion Dooley - https://en.wikipedia.org/wiki/Origin_(mathematics) - origin - - - - - - - - - https://en.wikipedia.org/wiki/Medical_state - United Kingdom National Health Service trusts, boards, etc. have some terminology in common for public disclosure of patient health conditions. - Damion Dooley - National Health Service terminology - NHS standard - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - Damion Dooley's note: This is a contentious term. AHA calls for it never to be used, since the common phrase "critical but stable" is misleading by the very nature of "critical". The NHS however has it as one of its central terms. The use of "stable" also points to a health trend, rather than a state. A separate "health status trend datum" has been set up to capture this. - critical but stable health status - - - - - - critical but stable - - - - - - - - - - - - - - - - - - - - - - NHS Terms: https://en.wikipedia.org/wiki/Medical_state - - Damion Dooley - comfortable health status - - - - - - Comfortable - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - progressing well health status - - - - - - progressing well - - - - - - - - - - - Damion Dooley - Damion Dooley note: This term (weakly) implies that the patient is recovered enough to be released from hospital. Technically this isn't a health status though, it is a patient medical service state. - discharged from hospital - - - - - - discharged - - - - - - - - - - A data item which is about the collection state of a datum at some point in time. - Damion Dooley note: We'll need to incorporate NIAID GSCID-BRC Sample data standards mention: -Unknown/Not Applicable/Censored Allowed -Unknown/not applicable/not available/ available upon request - Damion Dooley - A given datum's datum status value is metadata, i.e. a statement about a particular datum, often when no actual data entry or categorical choice for that datum has been made. - datum status - INSDC missing value reporting terms: -http://www.ebi.ac.uk/ena/about/missing-values-reporting - - - - - - - - - - A categorical choice indicating that a datum is available for retrieval. - Damion Dooley - In theory any datum that has a recorded value has 'recorded' for its datum status. - recorded - - - - - - - - - - - Patient is awaiting physician and/or assessment. - Very similar to 'datum status' 'in process' status. - Damion Dooley - - undetermined health status - awaiting assessment - - - - - - - - - - - - - - - - Damion Dooley - deteriorating - worsening health trend - - - - - - - - - - This covers the description of data and abstract structure in n-dimensional space. Within space there are coordinate systems, coordinates, and entities made up of coordinates. - Damion Dooley - - - - - - - - - - - - - - - /^[N+](:<lat>\d(\.\d+)?)$/, $lat -/^S(:<lat>\d(\.\d+)?)$/, '-' + $lat - /^(:<lat>[-S+N])?(:<degree>[1-8]?[0-9](:<decimal>\.\d{1,6})?)$/, $lat$degree.$decimal -/^(:<lat>[-S+N])?(:<degree>90(:<decimal>\.0{1,6})?))$/, $lat$degree.$decimal - /^(\d(\.\d+)?)$/, '+\1' - - A decimal latitude measurement in degrees in conformance with the ISO 6709 standard. - This is failing Hermit reasoner since it rejects totalDigits, and fractionDigits: -'has primitive data type' exactly 1 xsd:decimal[>= -90.0 , <= 90.0 , totalDigits 8 , fractionDigits 6]' - Damion Dooley - - - - - - - - - - - - - - - /^(:<long>[-W+E])?(:<degree>(1[0-7]|[1-9])?[0-9])(:<decimal>\.\d{1,6})?)$/, $long$degree.$decimal -/^(:<long>[-W+E])?(:<degree>180(:<decimal>\.0{1,6})?)$,$long$degree.$decimal - - A decimal longitude measurement in degrees in conformance with the ISO 6709 standard. - Damion Dooley - - - - - - - - - Damion Dooley - - - - - - - - - A 2D coordinate system is a coordinate system in 2 dimensional space. Each coordinate is composed of an offset from the origin of each dimension - Damion Dooley - - - - - - - - - Damion Dooley - - - - - - - - - Damion Dooley - - - - - - - - - - - - - - - - - - - - - A datetime range intermediate datum is a datetime item grouped under a process, and occuring after some process start and before some process end. - Damion Dooley - datetime range intermediate - - - - - - - - - Damion Dooley - datetime range item - - - - - - - - - - - - - - - The ending date of a process - datetime range end - - - - - - - - - - - - - - - Damion Dooley - The starting date of a process - datetime range start - - - - - - - - - Damion Dooley - - - - - - - - - - - - - - - Damion Dooley - - - - - - - - - - A designated area on earth is one or more areas defined by one or more boundaries. A boundary can be defined by a polygon perimeter, a lat/long and radius, or a fiat-boundary geographic featureset like a named river channel or mountain ridge; it may have one or more names associated with it. Note that areas associated with a name may change their boundary definitions over time. - Damion Dooley - - - - - - - - - - A Canadian postal code is a postal code that pertains to a geographic region of Canada. - Note that a Canadian postal code can cover multiple communities. Secondly, postal codes can be retired, and then reintroduced elsewhere. Historical data associations may need to take the date of postal code mapping into account. - - - - - - - - A "USA zip code" is a five digit (Zone Improvement Plan) or 9 digit postal code pertaining to a region of the United States of America. The optional trailing 4 digits of a 9 digit zip code provide greater granularity of delivery target. - Damion Dooley - http://purl.obolibrary.org/obo/NCIT_C25720 - obsolete: US postal code - true - - - - - - - - - - Damion Dooley - entity history record - - - - - - - - - - Damion Dooley - generic range history record - - - - - - - - - - - - - - - - - - Damion Dooley - A set does not have a direct distance metric between its members. - - - - - - - - - - Damion Dooley - - - - - - - - - Damion Dooley - - - - - - - - - - Damion Dooley - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - - - - - - - - - - A product name and model number of a manufacturer's genomic (dna) sequencer. - Damion Dooley - sequencing instrument model - - - - - - - - - - - - - - 1 - - - - - - - 1 - - - - - A circle is a simple closed shape in Euclidean geometry. It is the set of all points in a plane that are at a given distance from a given point, the centre; equivalently it is the curve traced out by a point that moves so that its distance from a given point is constant. - Damion Dooley - https://en.wikipedia.org/wiki/Circle - circle - - - - - - - - - NCBI SRA: ILLUMINA - Illumina platform - - - - - - - - - NCBI SRA: COMPLETE_GENOMICS - Damion Dooley's note: This platform is in-house and not a product per se. Complete Genomics states: "Complete Genomics’ sequencing platform employs high-density DNA nanoarrays that are populated with DNA nanoballs (DNBs™). Base identification is performed using an unchained ligation-based read technology known as combinatorial probe-anchor ligation (cPAL™). The sequencing instrumentation is custom-developed to support this process. Details are described in our Science publication (Drmanac et al., 2010)." - Complete Genomics platform - - - - - - - - - - - - 0 - - - - - - - 1 - - - - - Damion Dooley - earth area boundary census - - - - - - - - - NCBI SRA: LS454 - Roche LS454 platform - - - - - - - - - NCBI SRA: PACBIO_SMRT - PacBio platform - - - - - - - - - NCBI SRA: AB SOLiD 4hq - SOLiD 4hq System - - - - - - - - - NCBI SRA: AB SOLiD 5500 - SOLiD 5500 - - - - - - - - - NCBI SRA: AB SOLiD 5500xl - SOLiD 5500xl - - - - - - - - - NCBI SRA: AB SOLiD PI System - SOLiD PI System - - - - - - - - - NCBI SRA: AB SOLiD System 2.0 - SOLiD System 2.0 - - - - - - - - - NCBI SRA: AB SOLiD System 3.0 - SOLiD System 3.0 - - - - - - - - - - A two dimensional entity is an entity composed of one or more points on a two dimensional surface. - Damion Dooley - 2D entity - - - - - - - - NCBI SRA: Ion Torrent PGM - - - - - - - - - NCBI SRA: 454 GS FLX Titanium - 454 Genome Sequencer FLX Titanium - - - - - - - - - - NCBI SRA: 454 GS - 454 Genome Sequencer - - - - - - - - - NCBI SRA: 454 GS Junior - 454 Genome Sequencer Junior - - - - - - - - - - - - - - - https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly - Whether any method was used to select for or against, enrich, or screen the material being sequenced. - Damion Dooley - NCBI SRA: LIBRARY_SELECTION - library selection - - - - - - - - - Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C). - NCBI SRA: 5-methylcytidine antibody - 5-methylcytidine antibody method - - - - - - - - - Cap-analysis gene expression. - NCBI SRA: CAGE - CAGE method - - - - - - - - - Cot-filtered highly repetitive genomic DNA - NCBI SRA: CF-H - CF-H method - - - - - - - - - Cot-filtered moderately repetitive genomic DNA - NCBI SRA: CF-M - CF-M method - - - - - - - - - Cot-filtered single/low-copy genomic DNA - NCBI SRA: CF-S - CF-S method - - - - - - - - - Cot-filtered theoretical single-copy genomic DNA - NCBI SRA: CF-T - CF-T method - - - - - - - - - Chromatin immunoprecipitation - NCBI SRA: ChIP - ChIP method - - - - - - - - - Deoxyribonuclease (MNase) digestion - NCBI SRA: DNAse - DNAse method - - - - - - - - - Hypo-methylated partial restriction digest - NCBI SRA: HMPR - HMPR method - - - - - - - - - Selection by hybridization in array or solution. - NCBI SRA: Hybrid Selection - Hybrid Selection method - - - - - - - - - Enrichment by methyl-CpG binding domain. - NCBI SRA: MBD2 protein methyl-CpG binding domain - MBD2 protein methyl-CpG binding domain method - - - - - - - - - Methyl Filtrated - NCBI SRA: MF - MF method - - - - - - - - - Micrococcal Nuclease (MNase) digestion - NCBI SRA: MNase - MNase method - - - - - - - - - Methylation Spanning Linking Library - NCBI SRA: MSLL - MSLL method - - - - - - - - - Source material was selected by designed primers. - NCBI SRA: PCR - PCR method - - - - - - - - - Rapid Amplification of cDNA Ends. - NCBI SRA: RACE - RACE method - - - - - - - - - Source material was selected by randomly generated primers. - NCBI SRA: RANDOM PCR - RANDOM PCR method - - - - - - - - - Random selection by shearing or other method. - NCBI SRA: RANDOM - RANDOM method - - - - - - - - - Source material was selected by reverse transcription PCR - NCBI SRA: RT-PCR - RT-PCR method - - - - - - - - - Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling. - NCBI SRA: Reduced Representation - Reduced Representation method - - - - - - - - - DNA fractionation using restriction enzymes. - NCBI SRA: Restriction Digest - Restriction Digest method - - - - - - - - - PolyA selection or enrichment for messenger RNA (mRNA). complementary DNA. - NCBI SRA: cDNA - cDNA method - - - - - - - - - Physical selection of size appropriate targets. - NCBI SRA: size fractionation - size fractionation method - - - - - - - - - Other library enrichment, screening, or selection process. - NCBI SRA: other - other library method - - - - - - - - - https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly - The library source specifies the type of source material that is being sequenced. - Damion Dooley - library source - - - - - - - - - Genomic DNA (includes PCR products from genomic DNA). - Damion Dooley - NCBI SRA: GENOMIC - genomic source - - - - - - - - - Mixed material from metagenome. - Damion Dooley - NCBI SRA: METAGENOMIC - metagenomic source - - - - - - - - - Transcription products from community targets - Damion Dooley - NCBI SRA: METATRANSCRIPTOMIC - metatranscriptomic source - - - - - - - - - Other, unspecified, or unknown library source material. - Damion Dooley - NCBI SRA: OTHER - other library source - - - - - - - - - Synthetic DNA. - Damion Dooley - NCBI SRA: SYNTHETIC - synthetic source - - - - - - - - - Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries). - Damion Dooley - NCBI SRA: TRANSCRIPTOMIC - transcriptomic source - - - - - - - - - Viral RNA. - Damion Dooley - NCBI SRA: VIRAL RNA - viral RNA source - - - - - - - - - Sequencing technique intended for this library. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly - library strategy - - - - - - - - - Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling using SSU rRNA - NCBI SRA: AMPLICON - amplicon strategy - - - - - - - - - MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status. - NCBI SRA: Bisulfite-Seq - Bisulfite-Seq strategy - - - - - - - - - Clone end (5', 3', or both) sequencing. - NCBI SRA: CLONEEND - clone end strategy - - - - - - - - - Genomic clone based (hierarchical) sequencing. - NCBI SRA: CLONE - clone strategy - - - - - - - - - Concatenated Tag Sequencing - NCBI SRA: CTS - CTS strategy - - - - - - - - - Direct sequencing of chromatin immunoprecipitates. - NCBI SRA: ChIP-Seq - ChIP-Seq strategy - - - - - - - - - Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI. - NCBI SRA: DNase-Hypersensitivity - DNase-Hypersensitivity strategy - - - - - - - - - Single pass sequencing of cDNA templates - NCBI SRA: EST - EST strategy - - - - - - - - - Sequencing intended to finish (close) gaps in existing coverage. - NCBI SRA: FINISHING - finishing strategy - - - - - - - - - Full-length sequencing of cDNA templates - NCBI SRA: FL-cDNA - FL-cDNA strategy - - - - - - - - - Direct sequencing of methylated fractions sequencing strategy. - NCBI SRA: MBD-Seq - MBD-Seq strategy - - - - - - - - - Direct sequencing following MNase digestion. - NCBI SRA: MNase-Seq - MNase-Seq strategy - - - - - - - - - Methylation-Sensitive Restriction Enzyme Sequencing strategy. - NCBI SRA: MRE-Seq - MRE-Seq strategy - - - - - - - - - Methylated DNA Immunoprecipitation Sequencing strategy. - NCBI SRA: MeDIP-Seq - MeDIP-Seq strategy - - - - - - - - - Library strategy not listed. - NCBI SRA: OTHER - other library strategy - - - - - - - - - Shotgun of pooled clones (usually BACs and Fosmids). - NCBI SRA: POOLCLONE - pool clone strategy - - - - - - - - - Random sequencing of whole transcriptome. - NCBI SRA: RNA-Seq - RNA-Seq strategy - - - - - - - - - Random sequencing of a whole chromosome or other replicon isolated from a genome. - NCBI SRA: WCS - WCS strategy - - - - - - - - - Random sequencing of the whole genome. - NCBI SRA: WGS - WGS strategy - - - - - - - - - Random sequencing of exonic regions selected from the genome. - NCBI SRA: WXS - WXS strategy - - - - - - - - - Free form text describing the protocol by which the sequencing library was constructed. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly - library construction protocol - - - - - - - - - - The submitter's name for this library. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly - NCBI SRA: LIBRARY_NAME - library name - - - - - - - - - - A two dimensional boundary is a continuous path (loop) defined on a two dimensional surface. - Damion Dooley - 2D boundary - - - - - - - - - cfu/100mL - - A colony forming unit count which is a count of viable bacterial numbers in 100 milliliters of liquid. - Should this be deprecated? Need to find working examples that actually use / 100mL. - Damion Dooley - colony forming unit per 100 milliliter - - - - - - - - - - A multiplier in the decimal number system that has been applied to an accompanying number or set of numbers often to simplfy their appearance. Numbers described by multipliers may have lost significant digits through rounding or trimming. - Damion Dooley - decimal quantity unit - - - - - - - - - - draft tuberculosis - dataset features and provenance - - - - - - - - - - draft tuberculosis - case specimen characteristics - - - - - - - - - - draft tuberculosis - case subject characteristics - - - - - - - - - - draft tuberculosis - case risk factors - - - - - - - - - - draft tuberculosis - case clinical presentation - - - - - - - - - - draft tuberculosis - case laboratory testing - - - - - - - - - - draft tuberculosis - case medication - - - - - - - - - - draft isolate whole genome sequencing model - - - - - - - - - - draft tuberculosis - case model - - - - - - - - - - A Mycobacterium tuberculosis lineage is a named family of strains of tuberculosis, named usually with reference to their shared geographic origin. - Damion Dooley - Mycobacterium tuberculosis lineage - A TB-Lineage identification tool using spoligotypes and MIRU data: -http://tbinsight.cs.rpi.edu/run_tb_lineage.html - Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans -http://www.nature.com/ng/journal/v45/n10/full/ng.2744.html - - - - - - - - - TB lineage 2 - East-Asian, includes Bejing - - - - - - - - - TB lineage 3 - East-African Indian, includes CAS/Delhi - - - - - - - - - TB lineage 4 - Euro-American, includes Haarlem, LAM3, X, T, F11, H37Rv - - - - - - - - - TB lineage 1 - Indo-Oceanic - - - - - - - - - TB lineage 5 - West African 1 - - - - - - - - - TB lineage 6 - West African 2 - - - - - - - - - - Damion Dooley - An isolate preparation facility is a type of organization that provides the service of isolating organisms of interest from provided specimens. - isolate preparation facility - - - - - - - - - plant product - - - - - - - - - - - - - - - geospatial name - - - - - - - - - - A personal health datum is a datum that pertains to the health situation or history of an individual. - Personal health datum covers the following information - -'has member' some 'analytic datum' -'has member' some 'behavioural risk factor' -'has member' some 'country of birth' -'has member' some 'dietary restrictions' -'has member' some 'Disease Attributes' -'has member' some 'health status history datum' -'has member' some 'health status trend datum' -'has member' some 'host hospital service status' -'has member' some 'subject disease stage' -'has member' some 'subject health status' -'has member' some 'subject health status (AHA)' -'has member' some 'subject health status (GSCID-BRC)' -'has member' some 'subject health status (NCIT)' -'has member' some 'subject health status (UK NHS)' -'has member' some 'subject health status at time of specimen extraction' -'has member' some 'tuberculosis disease anatomical site' -'has member' some comorbidity -'has member' some disease -'has member' some symptom - Damion Dooley - personal health datum - - - - - - - - - A host hospital service status indicates the state of a host's interaction with hospital medical services. - Damion Dooley - host hospital service status - - - - - - - - - - Damion Dooley - admitted to hospital - - - - - - - - - - Received treatment but not admitted. - - treated and released (not admitted to hospital) - - - - - - Treated and Released - - - - - - - - - - Received treatment. Transferred to a different facility. - - treated and transferred - - - - - - Treated and Transferred - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - satisfactory health status - - - - - - satisfactory - - - - - - - - - depth:1 - subject health status (UK NHS) - - - - - - - - - depth:1 - subject health status (AHA) - http://purl.obolibrary.org/obo/GENEPIO_0002019 - - - - - - - - - - - - - - - - - - - - - stable health trend - http://purl.obolibrary.org/obo/GENEPIO_0001669 - - - - - - - - An ordinal variable is a categorical variable whose values have sequential order, but no distance metric between them. - Damion Dooley - http://purl.obolibrary.org/obo/STATO_0000228 - obsolete: ordinal variable - true - - - - - - - - - mapping (reference based) - - - - - - - - - data protection item - - - - - - - - - subject provided consent - - - - - - - - - - Damion Dooley - An ordinal tree specification is a value specification entity whose subclasses each represent a possible value selection, and which have a linear order with respect to their siblings. - ordinal value specification - - - - - - - - - consent datum - - - - - - - - - agency provided consent - - - - - - - - - - 2019-11-17T00:43:00Z - draft ISO sequence repository field - - - - - - - - - Centre of circle, ellipse or parabola; centre of mass. - - A centre point is a point used in the description of an n-dimentional entity from which other (given) aspects of the entity are most efficienty described. A point of symmetry. The entity must have only one such point. - Probably a better formal math defn? - Damion Dooley - centre point - - - - - - - - - - This covers the following entities: - -'has member' some 'antimicrobial phenotype' -'has member' some 'antimicrobial resistance test drug' -'has member' some 'antimicrobial resistance test platform' -'has member' some 'antimicrobial resistance testing method' -'has member' some 'antimicrobial resistance testing method version or reagent' -'has member' some 'antimicrobial resistance testing reference standard' -'has member' some 'antimicrobial resistance testing reference standard version' -'has member' some 'antimicrobial resistance tissue specificity' -'has member' some 'antimicrobial resistant plasmid type' -'has member' some 'automated testing platform vendor' -'has member' some 'draft antibiogram drug test model' -'has member' some 'in-vitro microbial susceptibility test' -'has member' some 'measurement comparator' -'has member' some 'MIC unit' -'has member' some 'MIC value' -'has member' some 'Minimum Inhibitory Concentration Test' -'has member' some 'test drug maximum concentration' -'has member' some 'test drug minimum concentration' -'has member' some 'tuberculosis treatment drug' - Damion Dooley - This is a collection of antibiotic resistance process parameters and outputs - phenotypic antimicrobial drug susceptibility test datum - - - - - - - - The resistance phenotype of an isolate represents the interpretation of an MIC value with regard to some breakpoint threshold e.g. resistant (R), sensitive (S), intermediate (I), wild type (WT), or non-wild type (NWT) - Damion Dooley - http://purl.obolibrary.org/obo/NCIT_C85539 - obsolete: antimicrobial resistance phenotype - true - - - - - - - - Intermediate resistance indicates that an isolate is observed to offer an intermediate level of resistance to a given antibiotic. - Damion Dooley - http://purl.obolibrary.org/obo/NCIT_C85560 - obsolete: antibiotic intermediate resistance (I) - true - - - - - - - - Non-susceptible indicates that an isolate is observed to offer complete resistance to a given antibiotic. - Damion Dooley - http://purl.obolibrary.org/obo/NCIT_C85561 - obsolete: antibiotic nonsensitive (high resistance) - true - - - - - - - - - - A not defined resistance indicates that an isolate was not tested against a given antibiotic, or the result of the test was inconclusive. - Damion Dooley note: Is this the same as "indeterminate"? - Damion Dooley - N - ND - antibiotic resistance not defined - - - - - - - - Resistant indicates that an isolate is observed to offer a greater than intermediate level of resistance to a given antibiotic. - Damion Dooley - http://purl.obolibrary.org/obo/NCIT_C85562 - obsolete: antibiotic resistant (R) - true - - - - - - - - Susceptible indicates that an isolate is observed to offer a detectable but less than intermediate level of resistance to a given antibiotic. - Damion Dooley - http://purl.obolibrary.org/obo/NCIT_C85563 - obsolete: antibiotic sensitive (S) - true - - - - - - - - Susceptible - dose dependent indicates that an isolate is observed to offer resistance to a given antibiotic when a sufficient dose is given. - Damion Dooley - http://purl.obolibrary.org/obo/NCIT_C85559 - obsolete: sensitive - dose dependent - true - - - - - - - - - - - - - - - - A MIC test measurement resulting from a laboratory dilution method. - Damion Dooley's note: is this still useful? Currently "MIC dilution measurement specification' refers directly via 'is about' to "broth dilution method" but that may be too specific. - Damion Dooley - MIC dilution measurement datum - - - - - - - - The type of assay used to determine the minimum inhibitory concentration. - Damion Dooley - http://purl.obolibrary.org/obo/NCIT_C85540 - obsolete: antimicrobial resistance testing method - true - - - - - - - - - http://purl.obolibrary.org/obo/NCIT_C85555 - obsolete: agar dilution evidence - true - - - - - - - - - - The commercial kit or product used to determine the MIC e.g. E-Test. If a commercial product was not used, include the type of media used. - Damion Dooley - antimicrobial resistance testing method device or reagent - - - - - - - - - - - antimicrobial resistant plasmid type - - - - - - - - The instrumentation used to determine minimum inhibitory concentration values. - Damion Dooley - http://purl.obolibrary.org/obo/ARO_3004390 - obsolete: antimicrobial resistance testing platform - true - - - - - - - - http://purl.obolibrary.org/obo/ARO_3004400 - obsolete: Microscan - true - - - - - - - - http://purl.obolibrary.org/obo/ARO_3004401 - obsolete: Phoenix - true - - - - - - - - http://purl.obolibrary.org/obo/ARO_3004402 - obsolete: Sensititre - true - - - - - - - - http://purl.obolibrary.org/obo/ARO_3004403 - obsolete: Vitek - true - - - - - - - - http://purl.obolibrary.org/obo/ARO_3004409 - obsolete: Trek - true - - - - - - - - - obsolete: manual - noncommercial - true - - - - - - - - The manufacturer of an antibiotic resistance lab typing platform - Damion Dooley - http://purl.obolibrary.org/obo/ARO_3004404 - obsolete: antimicrobial resistance testing platform vendor - true - - - - - - - - http://purl.obolibrary.org/obo/ARO_3004407 - obsolete: Siemens - true - - - - - - - - http://purl.obolibrary.org/obo/ARO_3004406 - obsolete: Biomérieux - true - - - - - - - - http://purl.obolibrary.org/obo/ARO_3004405 - obsolete: Becton Dickinson - true - - - - - - - - - - A manual in vitro diagnostic device used by laboratories to determine the MIC (Minimum Inhibitory Concentration) and whether or not a specific strain of bacterium or fungus is susceptible to the action of a specific antimicrobial. - Damion Dooley - - E-Test - Epsilometer test - Etest (device) - - - - - - - - - - GM-NEG - - - - - - - - The clinical and laboratory guidelines or standards that prescribe the threshold values for determining resistance phenotypes. - Damion Dooley - http://purl.obolibrary.org/obo/ARO_3004360 - obsolete: antimicrobial resistance testing reference standard - true - - - - - - - - BSAC is a British inter-professional organisation involved in antibiotic education, research and leadership - Damion Dooley - - BSAC - obsolete: British Society for Antimicrobial Chemotherapy (BSAC) - true - - - - - - - - The Clinical and Laboratory Standards Institute develops and implements clinical laboratory testing standards - Damion Dooley - NCCLS - http://clsi.org - - CLSI - On January 1, 2005 the National Committee on Clinical Laboratory Standards (NCCLS) changed its name to CLSI - obsolete: Clinical and Laboratory Standards Institute (CLSI) - true - - - - - - - - DIN is recognized by the Federal Government of Germany as the competent standards organization for Germany and as the national standards body representing Germany in non-governmental international standards organizations. - Damion Dooley - http://www.din.de/en/din-and-our-partners/din-e-v - - DIN - Deutsches Institut für Normung - obsolete: German Institute for Standardization (DIN) - true - - - - - - - - EUCAST is a standing committee jointly organized by ESCMID, ECDC and European national breakpoint committees; it deals with breakpoints and technical aspects of phenotypic in vitro antimicrobial susceptibility testing. - Damion Dooley - http://www.eucast.org/ - - EUCAST - obsolete: European Committe on Antimicrobial Susceptibility Testing (EUCAST) - true - - - - - - - - Damion Dooley - - NCCLS - obsolete: National Committee on Clinical Laboratory Standards (NCCLS) - true - - - - - - - - La SFM a vocation à rassembler les microbiologistes de France et des pays francophones, travaillant dans les différents domaines de la microbiologie médicale, industrielle, et environnementale, en physiologie, génétique, taxonomie, hygiène, agents antimicrobiens, ...concernant les bactéries, virus, champignons et parasites. - The French Society of Microbiology (SFM) is a non-profit association which aims to bring together microbiologists from French-speaking countries, working in the domains of bacteria, viruses, Fungi and parasites, and related medical, industrial and environmental microbiology, physiology, genetics, taxonomy, hygiene, and antimicrobial agents. - This isn't at moment considered a valid EBI antibiogram choice? - Damion Dooley - http://www.sfm-microbiologie.org/ - - SFM - obsolete: Société Française de Microbiologie (SFM) - true - - - - - - - - - - Damion Dooley - SIR - SIR - - - - - - - - - - Damion Dooley - WRG - WRG - - - - - - - - - first line tuberculosis drug - - - - - - - - - last resort antibiotic - - - - - - - - - NIAID standard - - NIAID provides The GSCID/BRC Project and Sample Application Standard. It is designed to capture standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases. - Damion Dooley - https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards - National Institute of Allergy and Infectious Disease standard - - - - - - - - - A RefSeq accession identifier is an accession identifier for selected NCBI-curated genomic, transcript and protein sequences. These identifiers are distinct from DDBJ/EMBL/GenBank identifiers. - Damion Dooley - RefSeq accession identifier - http://www.ncbi.nlm.nih.gov/refseq/about/ - - - - - - - - - A Genomic Standards Consortium standard is an international, community-driven standard to facilitate genomic data integration, discovery and comparison. - Damion Dooley - Genomic Standards Consortium (GSC) standard - http://gensc.org/ - - - - - - - - - - A landform, biome or built environment at site that a given specimen was collected from. - Damion Dooley - specimen collection site - geographic feature - - - - - - - - - - - - - - - A particular human patient, or a given animal or plant. - - An investigative subject which is an organism. - Damion Dooley - subject organism - - - - - - - - - - help=The number of passages should be expressed as a numerical value. - - The number of serial iterations that an isolate is grown in one environment. - Damion Dooley - number of passages - - - - - - - - - - help:The passage protocol should include, when applicable, inoculum size, media type, temperature and duration of incubation. - A passage protocol should detail the number of serial iterations that an isolate is grown in one environment, and the conditions of that environment. - Damion Dooley - passage protocol - - - - - - - - The unit provided for an antibiotic drug test dosage. - Damion Dooley - http://purl.obolibrary.org/obo/ARO_3004372 - obsolete: drug minimum inhibitory concentration unit - true - - - - - - - - - order: -GENEPIO:0001237 # specimen type (host or environmental context) -OBI:0001619 # specimen collection date -OBI:0000659 # specimen collection process -GENEPIO:0002094 # specimen collection device -GENEPIO:00001600 # draft sequence repository data - geographic location -ENVO:00010483 # environmental material -ENVO:00002297 # environmental feature -GENEPIO:0001567 # subject (host) taxonomic species -GENEPIO:0000110 # subject health status -GENEPIO:0001617 # subject disease -GENEPIO:0000028 # subject body product -GENEPIO:0000025 # specimen source anatomical site -FOODON:03411564 # draft sequence repository data - food processing - - draft sequence repository data - specimen collection - - - - - - - - - order: -GENEPIO:0002105 # Specimen processing organization role -NCIT:C93874 # organization name -NCIT:C40974 # first name -NCIT:C40975 # last name -NCIT:C93582 # job title -NCIT:C42775 # email address -GENEPIO:0001756 # phone -NCIT:C25464 # Country -ENVO:00000005 # major administrative subdivision -> GAZ state/province/territory/region) -NCIT:C80234 # Municipality” (via GenEpiO -> GAZ cities) -NCIT:C25690 # Street Address - - Contact information for an organization related to specimen collection, processing or storage. - Damion Dooley - contact specification - specimen related organization - - - - - - - - - dateFormat:ISO 8601 - order: -GENEPIO:0002082 # specimen related organization -GENEPIO:0002081 # specimen collection -GENEPIO:0002086 # geographic location -GENEPIO:0002084 # isolate -GENEPIO:0002087 # isolate history -GENEPIO:0002106 # food specimen -GENEPIO:0002088 # antibiogram -GENEPIO:0002085 # sequencing -GENEPIO:0002090 # sequencing QC -GENEPIO:0002089 # virulence -GENEPIO:0002092 # submission to EBI -GENEPIO:0002091 # submission to NCBI/DDBJ - - This draft specification provides a collection of fields related to the contextual data of a specimen, its genomic sequencing, and its pathogenic epidemiology. - Damion Dooley - draft sequence repository contextual data standard - - - - - - - - - order: -GENEPIO:0001640 # specimen taxonomy -GENEPIO:0001429 # strain identifier -GENEPIO:0001644 # isolate identifier -OBI:0000079 # culture medium -GENEPIO:0002107 # isolation medium - - draft sequence repository data - isolate - - - - - - - - - order: - -GENEPIO:0000069 # sequencing date -OBI:0000079 # culture medium” (via MicrO, yields a list of formulas). -GENEPIO:0002093 # sequencing dna extraction method -EFO:0000683 # replicate -GENEPIO:0000085 # library preparation kit -GENEPIO:0000149 # library preparation kit version -GENEPIO:0000075 # sequencing chemistry -GENEPIO:0001921 # sequencing instrument model -GENEPIO:0000150 # read trimming and filtering software -GENEPIO:0000084 # read adapter trimming software -GENEPIO:0002095 # read paired-end merging software -GENEPIO:0000090 # assembly method -GENEPIO:0000151 # bioinformatics pipeline name -GENEPIO:0000153 # bioinformatics pipeline protocol -GENEPIO:0000152 # bioinformatics pipeline version -GENEPIO:0000095 # genome annotation algorithm - - draft sequence repository data - sequencing - - - - - - - - - order: -GENEPIO_0001656 # latitude and longitude ISO 6709 -GENEPIO:0000118 # specimen collection country -GENEPIO:0002097 # specimen collection state/prov/ter/region -GENEPIO:0001785 # specimen collection city - - The geographical origin of the sample by city, region, country or latitude and logitude. - Damion Dooley - draft sequence repository data - geographic location - - - - - - - - - order: -GENEPIO:0002078 # number of passages -GENEPIO:0002079 # passage protocol - - draft sequence repository data - isolate passage history - - - - - - - - - order: -GENEPIO:0001100 # antimicrobial drug tests -GENEPIO:0002101 # test drug minimum concentration -GENEPIO:0002100 # test drug maximum concentration -GENEPIO:0002045 # antimicrobial resistance testing method -GENEPIO:0002047 # antimicrobial testing method version or reagent -GENEPIO:0002062 # antimicrobial resistance testing reference standard -GENEPIO:0002049 # antimicrobial resistance testing platform - - A dataset of the minimal inhibitory concentrations (value, unit, sign (<,>, =)) and resistance phenotypes (resistant, sensitive or undetermined) of the sequenced isolate against different antibiotics tested. - Damion Dooley - draft sequence repository data - antibiogram - - - - - - - - - order: -GENEPIO:0002130 # Virulence factor name -GENEPIO:0002131 # Virulence testing protocol -GENEPIO:0002132 # detection limit - - The virulence factors determined to be present in the sequenced isolate by phenotypic or target amplification methods e.g. Shiga toxins, hemolysins. - Damion Dooley - draft sequence repository data - virulence - - - - - - - - - order: -OBI:0001941 # N50 -GENEPIO_0000092 # sequencing depth / read coverage - - Measurements or calculated quantities used to assess the extent and success of the sequence assembly process. Metric thresholds are species-specific. - Damion Dooley - draft sequence repository data - sequencing quality control - - - - - - - - - order: -OBI:0001616 # specimen identifier -GENEPIO:0001644 # isolate identifier -GENEPIO:0001429 # strain identifier -GENEPIO:0001640 # specimen organism taxonomy -GENEPIO:0000113 # specimen category -OBI:0001619 # specimen collection date -GENEPIO:0001797 # specimen collector -GENEPIO:0001657 # geo_loc_name -GENEPIO:0001656 # latitude and longitude coord -GENEPIO:0000027 # specimen source context -GENEPIO:0001567 # subject organism taxonomy -GENEPIO:0001724 # subject organism common name -GENEPIO:0001617 # subject disease - - - Damion Dooley - draft sequence repository data - submission to NCBI/DDBJ - - - - - - - - - order: -GENEPIO:0001644 # isolate identifier -GENEPIO:0001429 # strain identifier -GENEPIO:0001640 # specimen organism taxonomy -GENEPIO:0001079 # serovar -GENEPIO:0002135 # EBI environmental feature -GENEPIO:0000113 # specimen category -OBI:0001619 # specimen collection date -GENEPIO:0001797 # specimen collector -GENEPIO:0002086 # geographic location -GENEPIO:0000027 # specimen source context -GENEPIO:0002076 # geographic feature -GENEPIO:0001567 # subject taxonomy -GENEPIO:0000110 # subject health status - - - Damion Dooley - draft sequence repository data - submission to EBI - https://www.ebi.ac.uk/ena/submit/pathogen-data - - - - - - - - - - The procedure used to obtain genomic DNA from a sample through chemical, physical or mechanical means. - Damion Dooley - sequencing dna extraction method datum - - - - - - - - - The tool or device used to extract a specimen. - Damion Dooley - specimen collection device - - - - - - - - - The name and version of the software used to merge paired-end reads before assembly. - read paired-end merging software - - - - - - - - - Sequencing - The name and version of the software product used for removal of adapter sequences from demultiplexed data reads - GROUP: IRIDA Ontology (Emma) - GENEPIO - read adapter trimming software - - - - - - - - - - - - - - - - - - - - - - - - - An ontology identifier or textual name of the most precise geographical location available for the site of a specimen collection event. - Damion Dooley - Adapted from NIAID GSCID-BRC metadata working group - Note that this is expressed in a particular format in some standards. - specimen collection location - state/province/territory/region - - - - - - - - - - - - - - - - - - - - lookup - - - - - - - - A wild type (WT) resistance phenotype indicates a bacterial pathogen belongs to a "Naïve", susceptible wild-type population with respect to a given antimicrobial. No acquired or mutational resistance mechanisms are -present to the antimicrobial in question. - Damion Dooley - https://sisu.ut.ee/sites/default/files/amr/files/pab_new_legislation_on_amr.pdf - http://purl.obolibrary.org/obo/ARO_3004432 - obsolete: wild type (WT) - true - - - - - - - - A non-wild type (WT) resistance phenotype indicates a bacterial pathogen has an acquired or mutational resistance mechanism present with respect to the antimicrobial in question. The bacteria has a reduced susceptibility to this agent. - Damion Dooley - https://sisu.ut.ee/sites/default/files/amr/files/pab_new_legislation_on_amr.pdf - http://purl.obolibrary.org/obo/ARO_3004433 - obsolete: non-wild type (NWT) - true - - - - - - - - - - This is the maximum concentration of a drug applied during an an assay. - Damion Dooley - test drug maximum concentration - - - - - - - - - - This is the minimum concentration of a drug applied during an an assay. - Damion Dooley - test drug minimum concentration - - - - - - - - The tissue type used to select breakpoints from a particular standard, for the interpretation of MIC results. - Damion Dooley - http://purl.obolibrary.org/obo/ARO_3004430 - obsolete: antimicrobial resistance tissue specificity - true - - - - - - - - - depth:1 - order: -NCIT:C115935 # healthy -NCIT:C126054 # non-pathalogical -NCIT:C25610 # pathologic -NCIT:C82508 # life threatening -NCIT:C28554 # deceased - subject health status (NCIT) - - - - - - - - - order: -NCIT:C40974 # first name -NCIT:C40975 # last name -NCIT:C93582 # job title -NCIT:C42775 # email address -GENEPIO:0001756 # phone - contact specification - professional role - - - - - - - - - - An organization related to the collection, isolate production, sequencing or storage of specimen material or data. - Damion Dooley - specimen processing organization type - - - - - - - - - order: -GENEPIO:0001533 # food specimen type -FOODON:03450002 # food cooking method -FOODON:03440011 # extent of heat treatment -FOODON:03430113 # physical state, shape or form -FOODON:03470107 # food preservation method -FOODON:03490100 # container or wrapping -FOODON:03480020 # food packing medium -FOODON:03500010 # food contact surface -GENEPIO:0000139 # food cultural origin -FOODON:03460111 # treatment applied to food - This specification offers food source, product type, packaging and processing attributes relevant to describing a food specimen. - draft sequence repository data - food specimen - - - - - - - - - - An isolation medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the same growth environment. - Chris has proposed this term for OBI as "enrichment culture medium" - Damion Dooley - isolation medium - - - - - - - - - order: -GENEPIO:0000121 # start date -GENEPIO:0000122 # end date -GENEPIO:0001783 # travel destination -GENEPIO:0001064 # travel mode -GENEPIO:0001065 # travel reason - - This record details a person's travel movement and duration for epidemiological analysis. - Damion Dooley - draft travel log specification - - - - - - - - - order: -OBI:0001616 # BioSample_ID -GENEPIO:0001640 # Species -GENEPIO:0001187 # Antibiotic_Name -GENEPIO:0002062 # AST_Standard -GENEPIO:0002111 # Breakpoint_version -NCIT:C85540 # Laboratory_typing_method -GENEPIO:0002112 # Measurement -GENEPIO:0002080 # Measurement_units -GENEPIO:0001001 # Measurement_sign -NCIT:C85539 # Resistance_phenotype -GENEPIO:0002181 # Resistance_phenotype - ECOFF -GENEPIO:0002049 # Platform - - A standard for European Bioinformatics Institute (EBI) antibiogram data submission - Damion Dooley - draft EBI antimicrobial susceptibility test V. 2017-08-30 - https://github.com/EBI-COMMUNITY/compare-amr/blob/master/Antimicrobial-susceptibility-testing-data-submission_V_2017-08-30.pdf - - - - - - - - - - - - - - - - A MIC test measurement resulting from a laboratory diffusion method. - Damion Dooley's note: is this still useful? Currently "MIC diffusion measurement specification' refers directly via 'is about' to "Disk Diffusion Method". - Damion Dooley - MIC diffusion measurement datum - - - - - - - - - - The version of the antimicrobial reistance testing reference standard protocol used in assessing an isolate. - Damion Dooley - antimicrobial resistance testing reference standard version - - - - - - - - - This is a component of an antibiogram that enables a choice of MIC measurements based on either the diffusion or dilution method. These methods call for different numeric input ranges and units. - draft sequence repository data - antibiogram MIC measurement - - - - - - - - - - - - 1 - - - - - - - - - - time value specification - - - - - - - - - - The process of collecting a portion of feces from an organism. - Emma Griffiths - stool collection - feces collection - - - - - - - - - - The process of collecting a portion of urine from an organism. - Emma Griffiths - sputum collection - - - - - - - - - - The process of removal and collection of specimen material from the surface of an entity by washing, or a similar application of fluids. - Emma Griffiths - rinsing for specimen collection - - - - - - - - - - The process of collecting specimen material using a swab collection device. - Emma Griffiths - swabbing for specimen collection - - - - - - - - - - The process of collecting bodily fluids that have been discharged from blood vessels usually arising from inflammation or injury. - Emma Griffiths - exudate collection - - - - - - - - - - The removal or collection of specimen material through the use of suction. - Emma Griffiths - vacuuming for specimen collection - - - - - - - - - - Emma Griffiths - NOTE: there are different types of tubes with coloured caps indicating different preservatives etc. - tube containing media or preservative - - - - - - - - - Emma Griffiths - NOTE: there are different types of tubes with coloured caps indicating different preservatives etc. - tube containing antimicrobial - - - - - - - - - - Emma Griffiths - Whirlpak sampling bag - - - - - - - - - - Emma Griffiths - spoon - - - - - - - - - - Emma Griffiths - fork - - - - - - - - - - Emma Griffiths - hand scoop - - - - - - - - - Emma Griffiths - trier - - - - - - - - - - Emma Griffiths - vaccum device - - - - - - - - - - - - - - - investigation identifier specification - - - - - - - - - order: -GENEPIO:0001640 # taxonomy -GENEPIO:0002086 # geographic location -GENEPIO:0002076 # geographic feature -GENEPIO:0002106 # food -FOODON:03510136 # food consumer -GENEPIO:0002094 # specimen collection device -GENEPIO:0000025 # anatomical site -GENEPIO:0000028 # body product -GENEPIO:0001724 # host organism common name -GENEPIO:0001567 # host taxonomy -UBERON:0000105 # life cycle -GENEPIO:0001639 # antigenic formula -GENEPIO:0001718 # serotype specification -GENEPIO:0000045 # PFGE test specification - - This is a draft (under development) collection of fields for capturing the contextual data for Enterobase (https://enterobase.warwick.ac.uk/) records. - Damion Dooley - draft Enterobase contextual data standard - - - - - - - - - - - - - - - - The name of the virulence factor molecule produced by a pathogen that specifically causes disease, or that influences the host's function to allow the pathogen to thrive. - Emma Griffiths - virulence factor name - - - - - - - - - - - - - - - help:The protocol for determining virulence should include, when applicable, inoculum preparation, platforms and instrumentation, conditions, cell lines and animal models. - - The laboratory protocol used to determine virulence phenotypes and markers. - Emma Griffiths - virulence testing protocol name - - - - - - - - - - - - - - - help:Detection limits should include the numerical cut-off (threshold) value and units for determining positive results e.g. qPCR value, CFUs. - The detection limit denotes the smallest measure that can be detected with reasonable certainty for a given analytical procedure. - Emma Griffiths - detection limit - - - - - - - - - - A disease cluster is an unusually high incidence of a particular disease or disorder occurring in close proximity in terms of both time and geography. - Damion Dooley - https://en.wikipedia.org/wiki/Disease_cluster - disease cluster - - - - - - - - - - - A disease cluster in which two or more cases have been linked by an infectious disease transmission process. - Damion Dooley - infectious disease cluster - - - - - - - - - help:used only with the source feature key; source feature keys containing the /environmental_sample qualifier should also contain the /isolation_source qualifier. entries including /environmental_sample must not include the /strain qualifier - Identifies sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism. Environmental samples include clinical samples, gut contents, and other sequences from anonymous organisms that may be associated with a particular host. They do not include endosymbionts that can be reliably recovered from a particular host, organisms from a readily identifiable but uncultured field sample (e.g., many cyanobacteria), or phytoplasmas that can be reliably recovered from diseased plants (even though these cannot be grown in axenic culture). - ENA Webin:environmental_feature - EBI ENA Webin environmental feature - - - - - - - - - - The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. Webin is an ENA interface and standard for sequence submissions. - https://www.ebi.ac.uk/ena - EBI European Nucleotide Archive Webin - https://www.ebi.ac.uk/ena/WebFeat/ - - - - - - - - - help:Breadth of coverage should be reported as a percentage value (e.g. 95%) to a fold of coverage (e.g. 10X). - - The breadth of coverage is the percentage of the genome that was sequenced to a prescribed depth of coverage. - Emma Griffiths - breadth of coverage - - - - - - - - - - The mean contig length is the count of base pairs in the average size contig of the sequence assembly. - Emma Griffiths - mean contig length - - - - - - - - - order: -GENEPIO:0000084 # read adapter trimming (y/n) -GENEPIO:0002096 # read adapter trimming software -GENEPIO:0002095 # read paired-end merging software -GENEPIO:0000150 # read trimming and filtering software - - The procedures used to remove adapters from raw sequence reads, trim low quality bases and where applicable, merge paired-end reads. - Emma Griffiths - raw sequence data processing datum - - - - - - - - - - Name of strain from which sample was obtained OR name of isolate from which sample was obtained. - Damion Dooley - specimen strain or isolate identifier - - - - - - - - - - - - - - - - - \s*(\d(.\d{1,4})?|[1-8]\d(.\d{1,4})?|90(.0{1,4})?)\s*[WEwe]\s*(\d(.\d{1,4})?|[1-9]\d(.\d{1,4})?|1[0-7]\d(.\d{1,4})?|180(.0{1,4})?)\s*[NSns]\s* - - - - - - - - The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W - Damion Dooley - https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ - latitude and longitude coordinate (NCBI BioSample format) - - - - - - - - - - - - - - - decimal value specification - - - - - - - - - - - - - - - floating point value specification - - - - - - - - - - - - - - - unsigned integer - A 32 bit number having a range 0 - 4294967295. - unsigned integer value specification - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - 1 - - - - - - - - - - date value specification - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - A specification for the size of an assembled genome as measured in base pairs. - This is a decimal because the megabasepair unit may involve a fractional component. - assembly genome size specification - - - - - - - - - - - - - - - sequencing facility name specification - - - - - - - - - date (ISO 8601) - A date should be recorded as YYYY-MM-DD according to ISO 8601. HOWEVER ... OWL 2.0 does not include xsd:date as a permitted data type, so this value specification only accepts xsd:dateTime - date value specification (ISO 8601) - - - - - - - - - - - - - - - strain identifier specification - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - 5 - - - 100 - - - - - - - A MIC test measurement resulting from a laboratory diffusion method. - Damion Dooley - MIC diffusion measurement specification - - - - - - - - - - - - - - - unsigned short - A 16 bit integer ranging from 0 - 65535 - unsigned short integer value specification - - - - - - - - - - - - 1 - - - - - - - - - - - genomic sequence length specification - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - 0.01 - - - 2048.0 - - - - - - - A MIC test measurement resulting from a laboratory dilution method. - Damion Dooley - MIC dilution measurement specification - - - - - - - - - - - - - - - The date on which a specimen was collected, in ISO 8601 format. - specimen collection date (ISO 8601) - - - - - - - - - - - - - - - date of diagnosis (ISO 8601) - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - 0 - - - - - - - A subject age is the age since birth of a given organism that is involved in an investigation or study at a given time. - Damion Dooley - subject age specification - - - - - - - - - - - - - - - subject age at time of specimen collection specification - - - - - - - - - - - - - - - - - - 1 - - - - boolean - - A boolean value specification indicates a presence (true value) or absence (false value) of a given feature. - Damion Dooley - boolean value specification - - - - - - - - - - - - - - - specimen identifier specification - - - - - - - - - - - - - - - - - - - - - - - [A-Za-z0-9]+([_.\-][A-Za-z0-9]+)*\@[A-Za-z0-9]+([.\-][A-Za-z0-9]+){1,3} - - - - - - - email address specification - - - - - - - - - - - - - - - - - - - - - - - - region, province, state or territory specification - - - - - - - - - - - - - - - A specification for a geographic location that a specimen was collected at. - specimen collection site specification - - - - - - - - - - - - - - - subject organism common name specification - - - - - - - - - - - - - - - A subject identifier specification is a specification including datatype pertaining to a given standard's subject identifier field. - Damion Dooley - subject identifier specification - - - - - - - - - - - - - - - - - - - - - Name of disease in a subject that is related to a given investigation, study and/or specimen. - Damion Dooley - NIAID GSCID-BRC metadata working group - Controlled vocabulary. Human specimen source: https://bioportal.bioontology.org/ontologies/DOID -or https://www.ncbi.nlm.nih.gov/mesh/1000067 - subject disease specification - - - - - - - - - - - - - - - unsigned long integer - A 64 bit integer ranging from 0 - 18446744073709551615 - unsigned long integer value specification - - - - - - - - - - - - - - - - - - - The physical location that a specimen was collected at. The location may be described by geographic coordinates, city or other geopolitical entity, biome, etc. - Damion Dooley - specimen collection site - - - - - - - - - - - - - - - - The unit provided for an antibiotic drug test dosage. - Damion Dooley - drug MIC unit specification - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - A datum specification for the maximum concentration of a drug applied during an an assay. - test drug maximum concentration specification - - - - - - - - - - - - - - - - - - - - - - - - - - - - This is the minimum concentration of a drug applied during an an assay. - Damion Dooley - test drug minimum concentration specification - - - - - - - - - - - - - - - - - - - - - - - (1/2|1/2a|1/2b|1/2c|3a|3b|3c|4a|4ab|4b|4c|4d|4e|1|7) - - - - - - - listeria antigen specification - - - - - - - - - - - - - - - - - - 1 - - - - - - url - - - - - - - URL specification - - - - - - - - - - - - - - - - - - - - - - - - - - - - A travel destination is a destination city (or populated place of some scale) which a given human has travelled to on a particular trip. - Damion Dooley - travel destination specification - - - - - - - - - - - - - - - A specimen source substance is an organism substance or food product or environmental substance from which the specimen was extracted. - Damion Dooley - specimen source substance specification - - - - - - - - - - - - - - - Damion Dooley note: OBI has a variety of subclasses like "blood specimen" and "colon specimen" etc. which we have not added here. The are mapped to UBERON terms indirectly through the logic "derives from some [uberon term]". GenEpiO takes a different approach in describing this class with lists for "subject anatomical site", "subject body product", and "plant anatomy". - specimen from organism specification - - - - - - - - - - - - 1 - - - - - - - - - - - - 0 - - - - - - - duration specification - - - - - - - - - A field specification is the specification of a data field used in a data standard or database table. This includes at least a database field name, and optionally display name, description, and data type (binary blob, numeric, categorical, textual or cross-reference). - Damion Dooley - - 2019-04-17T23:04:53Z - obsolete: field specification - true - - - - - - - - Damion Dooley - http://purl.obolibrary.org/obo/ARO_3004431 - obsolete: antimicrobial resistance phenotype - epidemiological cut-off values - true - - - - - - - - - Damion Dooley - 2019-04-17T23:41:35Z - PulseNet Canada field - - - - - - - - - Damion Dooley - 2019-04-17T23:41:56Z - PulseNet Canada Salmonella field - - - - - - - - - Damion Dooley - 2019-05-03T02:44:38Z - specimen collection service - - - - - - - - - Damion Dooley - 2019-05-03T02:49:24Z - bioinformatics analysis service - - - - - - - - - An isolate preparation service prepares isolates for molecular sequencing. - Damion Dooley - 2019-05-03T02:51:51Z - - isolate preparation service - - - - - - - - - order: -GENEPIO:0002222 # specimen collection service -GENEPIO:0002226 # specimen repository/biobank service -GENEPIO:0002224 # isolate preparation service -OBI:0001904 # sequencing service -OBI:0000992 # DNA sequencing service -GENEPIO:0002223 # bioinformatics analysis service - Damion Dooley - 2019-05-03T02:52:19Z - specimen related service - - - - - - - - - Damion Dooley - 2019-05-03T03:24:33Z - specimen repository/biobank service - - - - - - - - - - - - - - - - - - Vital signs are unstable and not within normal limits. Patient may be unconscious. Indicators are unfavorable. - - 2019-11-19T22:17:43Z - grave - critical health status - - - - - - critical - - - - - - critical - - - - - - - - - A datum indicating one of six defined subspecies of Salmonella. - - - 2019-11-25T08:45:41Z - Salmonella subspecies - - - - - - - - - - A PFGE pattern resulting from DNA fragmentation induced by the Spel enzyme. - - 2019-11-25T09:07:26Z - PFGE Spel pattern - - - - - - - - - - A collection of organisms that is indicative of faecal -contamination. - - - 2020-02-08T20:15:43Z - Fecal indicator organism collections include bacterial groups such as thermotolerant coliforms or E. coli. Hence, they only infer that pathogens may be present - fecal indicator - - - - - - - - - - - - - - - - - - An isolate derived from a food sample. - Damion Dooley - 2019-06-28T23:41:26Z - food isolate - - - - - - - - - - A method for typing The RNA component of the small (30S) subunit of prokaryotic ribosomes. - - 2020-04-24T19:06:05Z - microbial 16S RNA typing - - - - - - - - - - - - - - - - - - - - - - - h(1|2|3|4|5|6|7|8|9|10|11|12|14|15|16|17|18|19|21|23|24|26|27|28|29|30|31|32|33|34|35|36|37|38|39|40|41|42|43|44|45|46|47|48|49|51|52|53|54|55|56) - - - - - - - E. coli H antigen specification - - - - - - - - - - - - - - - - - - - - - - - O([1-9][0-9][0-9]) - - - - - - - E. coli O antigen specification - - - - - - - - - - - - 1 - - - - string - string value specification - - - - - - - - - A sequencing platform brand provided by Helicos corporation (now defunct). - - 2020-04-24T22:50:49Z - Helicos platform - - - - - - - - - A sequencing platform provided by the Ion Torrent company. - - 2020-04-24T22:54:06Z - Ion Torrent platform - - - - - - - - - A sequencing platform provided by Life Technologies Corporation - - Sequencing by Oligonucleotide Ligation and Detection - 2020-04-24T22:55:31Z - SOLiD sequening platform - - - - - - - - - obsolete: drag swab - true - - - - - - - - - - - - - - - - Rinse is the liquid output of rinsing plant, animal or other material with liquid with the objective of extracting specimen material from that liquid. - Damion Dooley - 2019-06-28T20:07:25Z - rinse - - - - - - - - - - - - - - - - - Animal rinse is a rinse derived from animal material of one or more animals. - Damion Dooley - 2019-06-28T20:11:45Z - animal rinse - - - - - - - - - obsolete: surface wipe - true - - - - - - - - - - - - - - - - - - - - - requires discussion - A personal health datum which specifies host health complications at time of specimen collection. - 0000-0002-9578-0788 - 2022-01-31T23:52:14Z - host health complications at time of specimen collection - - - - - - - - - - - - - - - - - - - - - requires discussion - A personal health datum which specifies host pre-existing conditions and risk factors at time of specimen collection. - 0000-0002-9578-0788 - 2022-01-31T23:52:41Z - pre-existing conditions and risk factors at time of specimen collection - - - - - - - - - - - - - - - - - - - - - requires discussion - A personal health datum which specifies host signs and symptoms at time of specimen collection. - 0000-0002-9578-0788 - 2022-01-31T23:53:13Z - signs and symptoms at time of specimen collection - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - symptom - http://purl.obolibrary.org/obo/SYMP_0000462 - - - - - - - - - position of phenotype abnormality - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://www.ebi.ac.uk/efo/EFO_0001444 - - - - - - - - Damion Dooley's note: See https://www.w3.org/TR/NOTE-datetime for ISO 8601 time standards - - - - - - - - Damion notes: Subclasses can actually have two components - the identifier, and the agency it is associated with. - -Under the general concept of "postal code" one can place particular national postal code systems like the US Postal code. - - - - - - - - - - 2020-04-24T22:38:17Z - pregnant woman - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://www.ontobee.org/ontology/MI - data source - - Database that originally provided the interaction record for exchange purposes. - PMID:14755292 - Damion Dooley's note: GenEpiO is using members of this class for the first part of the hasDbXref relation. This is where we are keeping the mapping between a code and its source database. - -Depending on its context, hasDbXref annotations may point directly to metadata field names in the target database, and may be annotated with additional information that guides any additional specifications that impact on data conversion of these fields. - source database - - - - - - - - - tissue collection (necropsy) - A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease. [database_cross_reference: Merriam-Webster:Merriam-Websters_Online_Dictionary--11th_Ed] - necropsy - - - - - - - - - - - - - - - - - The Archaea constitute a domain and kingdom of single-celled microorganisms - Damion Dooley - https://en.wikipedia.org/wiki/Archaea - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - subspecies - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley's note: this term was mistakenly placed in a list of GenEpiO diagnostic tests; in fact it references a material entity - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - healthy - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - NCIT offers this alternate definition which GenEpiO intends: -"A measurement that specifies the minimum concentration of the agent at which organism growth was inhibited." - MIC - Clinical and Laboratory Standards Institute MIC antimicrobial testing standards at http://em100.edaptivedocs.info/GetDoc.aspx?doc=CLSI%20M100%20S27:2017&scope=user - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A portion of an absorbent material attached to one end of a small stick for the purpose of applying or collecting material. - - Emma Griffiths - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/GEO_000000396 - - - - - - - - - - - diseased - sick - - - - - - - - - - - - - - - - - - - lookup:http://purl.obolibrary.org/obo/GAZ_00000448 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - [A-Za-z0-9]+([_.\-][A-Za-z0-9]+)*\@[A-Za-z0-9]+([.\-][A-Za-z0-9]+){1,3} - - - - - - - /^(:<zip>\d{5}(-\d{4})?)/, $zip - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - deceased - - - - - - deceased - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - phone - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A hollow cylinder, especially one for holding or conveying liquids. - Damion Dooley - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley's note: It can also be used as an authorization token in some identification processes. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley's note: here "sample" means more than one specimen merged together. - pooled - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - - - - - - - - - - Damion Dooley - - - - - - - - - - - - - - - - - brand name - - - - - - - - - - - - - - - - - - - - - - - - - An entity, either biologic or otherwise, of interest in an investigation. [def-source: NCI] - Damion Dooley - NCIT Thesaurus - investigative subject - - - - - - - - - - lookup:http://purl.obolibrary.org/obo/GAZ_00000448 - http://semanticscience.org/resource/SIO_000665 - - - - - - - - - - - - - - - - - antimicrobial resistance testing method - - - - - - - - - - - - - - - - - E-test (Epsilometry) - - - - - - - - - - - - - - - - - - lookup:http://purl.obolibrary.org/obo/GAZ_00000448 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - lookup:http://purl.obolibrary.org/obo/GAZ_00000448 - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/ncit.owl - - - - - - - - - organization name - - Damion Dooley - NCI Thesaurus - - - - - - - - - - - - - - - - - antibiotic treatment - - - - - - - - - fetal death (miscarriage/still birth) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - NCBI SRA: 454 GS 20 - - - - - - - - - NCBI SRA: AB SOLiD System - - - - - - - - - NCBI SRA: 454 GS FLX - - - - - - - - - NCBI SRA: Illumina Genome Analyzer II - - - - - - - - - NCBI SRA: Helicos HeliScope - - - - - - - - - pathogen role - - - - - - - - - - - - - - - - - - - Note: testing use of 'transmitted by' relation; issue to be resolved is whether appropriate domain and range are involved. This use would place 'transmitted by' as a subclass of 'participates in' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley note: OBI has a variety of subclasses like "blood specimen" and "colon specimen" etc. which we have not added here. The are mapped to UBERON terms indirectly through the logic "derives from some [uberon term]". GenEpiO takes a different approach in describing this class with lists for "subject anatomical site", "subject body product", and "plant anatomy". - - - - - - - - - ^SAM[NED](\w)?\d+$ - http://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000350 - http://www.ncbi.nlm.nih.gov/Sequin/acc.html - https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_accession_numbers_and_mole/ - - - - - - - - - - - - - - - - - - - - - - - - - - - NCBI BioProject - - - - - - - - - - - Project Description - - - - - - - - - - - Description* - - - - - - - - sample identifier - - - - - - - - - specimen collection date - - - - - - - - - help:Latitude should not be abstracted to the centre of a city, province/state or country as this may falsely implicate an existing location. - Damion Dooley's note: IAO lat/long can't be made a subclass of "angular coordinate" or disjoint contradiction arises. - See http://www.csgnetwork.com/gpscoordconv.html - -See http://www.geomidpoint.com/latlon.html -See http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org/obo/OBI_0001621 -See http://www.w3.org/2003/01/geo/wgs84_pos - - - - - - - - - - - - - - - - - - - - - - - NCBI BioProject - NIAID GSCID-BRC - - - - - - - - - - - - - - - Damion Dooley's note: A 'sovereign state' entity should have attribute or relationships to measurables - population, size, name, etc. So e.g. " 'country name' inheres in some 'sovereign state/country'". - -Also note historical name issue (Myanmar vs Burma) and diplomatic name issue (Taiwan vs "Republic of China"). Both point to needing a single entity with multiple names. - - - - - - - - http://purl.obolibrary.org/obo/OMIABIS_0000006 - - - - - - - - target material - NCBI BioProject: Material - Used in NCBI BioProject specifcation - - - - - - - - specimen sample scope - - - - - - - - - - - - - - - - - - - - - - - - sequencing facility - - - - - - - - project objective - NCBI BioProject: Objective - - - - - - - - - - - - - - - - - - - - - - project method - - - - - - - - - specimen provider PI email - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - categorical - - - - - - - - scalar - - - - - - - - Damion Dooley's note: -Often a value specification may need to allow for a "data item state" that indicates that a given datum doesn't have a recorded or observed or retrievable value, and the general reason for this state. - - - - - - - - - Assembly QC - Damion Dooley - http://www.nature.com/nature/journal.../409860a0.html - GENEPIO - - - - - - - - - - - - - - - - - - - - - - - - - NCBI SRA: Illumina MiSeq - - - - - - - - - NCBI SRA: PacBio RS - - - - - - - - - NCBI SRA: Illumina NextSeq - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sample - - - - - - - - - - - - - - - - 2019-09-08T23:41:09Z - diagnosis - - - - - - - - - An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. - extended organism - - - - - - - - - - Damion Dooley - - NIAID: Comorbidity - complications - - - - - - Comorbidity - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/omit - - - - - - - - - - - - - - - - - - - - - - - - - - - Vital signs are unstable and not within normal limits. Patient may be unconscious. Indicators are unfavorable. - Damion Dooley - grave - - - - - - - - - - - - - - - - - - - - - - - - - - A type of Shiga toxin found in E. coli - Damion Dooley - Stx1 - - - - Shiga toxin 1 - - - - - - - - - - A type of Shiga toxin found in E. coli which is antigenically distinct from Shiga toxin 1 - Damion Dooley - Stx2 - - - - Shiga toxin 2 - - - - - - - - - - - - - - - - - MLST typing - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments. - physician role - - - - - - - - - - - - - - Damion's Note: Future use might prefer: CMO_0000015 body temperature. - - - - - - - - NCBI BioSample: female - - - - - - - - NCBI BioSample: male - - - - - - - - - - - - - - Phenotypic sex refers to an individual's sex as determined by their internal and external genitalia, expression of secondary sex characteristics, and behavior. - Note that NCBI Biosample has these values allowed: -male | female | pooled male and female | neuter | hermaphrodite | intersex | not determined | missing | not applicable | not collected - NCBI: http://www.ncbi.nlm.nih.gov/books/NBK10943/ - - - - - - - - - Damion Dooley's note: We can't say radius is a subclass of "linear coordinate" because length is considered a quality/specifically dependent continuant, which is disjoint with immaterial entity/independent continuant . I.e. "length" as quality unfortunately can't pertain to abstract entities, only "real" ones. - - - - - - - - - - - - - - - - - - - - - - - - - social gathering - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - - - - - - - - - - - - - - - - - - 1 - - - - sequence assembly - http://edamontology.org/data_0925 - http://purl.obolibrary.org/obo/OBI_0000973 - 'sequence data' - - - - - - - - - - Damion Dooley - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/ERO_0002173 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley's note: Unfortunately an IAO "count" cannot be a subclass of immaterial entity "linear coordinate" as this leads to disjoint conflict. - Damion Dooley's note: A count datum often implicity carries a date range for which the count is ascertained, or estimated, or simulated for. - Damion Dooley's note: The result of the act of counting is a scalar number whose unit is a description of the thing being counted. One can count 10 oranges and compare that to a count of 5 oranges. One can generalize that a count of 5 oranges is a count of pieces of fruit. One can then compare 5 oranges and 5 apples, fruitfully! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - variable type - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host. - https://www.ebi.ac.uk/ols/ontologies/trans - TRANS follows the CDC Epidemiology model of transmission between two hosts, a reservoir and host or other non-host, non-reservoir entities (e.g), a needle and a host. - transmission of infection - - - - - - - - - Direct and essentially immediate transfer of infectious agents to a receptive portal of entry through which human or animal infection may take place. This may be by direct contact such as touching, kissing, biting, or sexual intercourse or by the direct projection (droplet spread) of droplet spray onto the conjunctiva or the mucous membranes of the eyes, nose, or mouth. It may also be by direct exposure of susceptible tissue to an agent in soil, compost, or decaying vegetable matter or by the bite of a rabid animal. Transplacental transmission is another form of direct transmission. - https://www.ebi.ac.uk/ols/ontologies/trans - direct transmission - - - - - - - - - Indirect transmission is a transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by intermediary vehicles, vectors or as airborne dust particles. - https://www.ebi.ac.uk/ols/ontologies/trans - indirect transmission - - - - - - - - - Congenital transmission is a direct transmission process during which the pathogen is transmitted directly from mother to child at or around the time of birth. - https://www.ebi.ac.uk/ols/ontologies/trans - congenital - - - - - - - - - contact transmission - Contact transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by kissing, skin-to-skin contact, sexual intercourse, or by contact with soil or vegetation containing the pathogen. - https://www.ebi.ac.uk/ols/ontologies/trans - contact - - - - - - - - - Droplet spread transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by spray of aerosols over a short distance, spray from sneezing, coughing or talking. - https://www.ebi.ac.uk/ols/ontologies/trans - droplet spread - - - - - - - - - Vehicle-borne ingestion transmission is an indirect vehicle-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by ingestion of fluids or foods or food products including: food, water, milk, or meat products. - https://www.ebi.ac.uk/ols/ontologies/trans - vehicle-born ingestion - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - organism body product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - poultry fluff - Damion Dooley's note: Poultry fluff is both an 'anatomical structure' and a body product when it is shed. - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley's note: Need to build this out further with reference to http://unitsofmeasure.org/trac and other unit ontologies: - -[1] R. Hodgson and P. J. Keller, "QUDT-quantities, units, dimensions and data types in OWL and XML." Online (September 2011) http://www. qudt.org -[2] M. van Assem, H. Rijgersberg, and J. Top, "Ontology of units of measure and related concepts." Semantic Web 4, no. 1 (2013): 3-13. -[3] G. V. Gkoutos, P. N. Schofield, and R. Hoehndorf, "The Units Ontology: a tool for integrating units of measurement in science." Database2012 (2012): bas033. - - - - - - - - - - - - - - mm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - µg/ml - - - - - - - - - - - - - - - - - - - - - - - - - ongoing pregnancy - - - - - - - - - ancestral group - - - - - - - - - - Damion Dooley - - - - - - - - - - - - - - - - - - - - - requires discussion - A personal health datum which specifies host role at time of specimen collection. - 0000-0002-9578-0788 - 2022-01-31T23:53:59Z - host role at time of specimen collection - - - - - - - - - - - - - - - - - MLVA typing - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley's comment: On spheroids a polygon can be minimally defined by latitude and longitude coordinates, however technically this is ambiguous whether the larger or smaller area is being referred to. Unambiguously, such a polygon could be defined by an epicenter, and a latitude width and longitude height. - - - - - - - - - - In elementary geometry, a polygon is a plane figure that is bounded by a finite chain of straight line segments closing in a loop to form a closed chain or circuit. - Damion Dooley - https://en.wikipedia.org/wiki/Polygon - - - - - - - - - - - - - - - - - - - - - - - - - - PulseNet: Key - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - medical health record (history / timeline) - - - - - - - - - - - - - - - - - - - - - - - - - depth:1 - lookup - - - - - - - - - - Bacterial bacteriophage typing - http://phinvads.cdc.gov/vads/http:/phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.6.96&code=22642004 - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/hancestro_0004 - obsolete: ancestral group - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI); The concept of ethnic origin is an attempt to classify people, not according to their current ethnicity, but according to where their ancestors came from. Ethnic origin has become a popular classification in statistics, where the concept of race has been largely discarded. (from Wikipedia) (NCI); a group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (CSP) - - - - - - - - - - - - - - - - - - - - - - - - Welcome to the GenEpiO ontology! The "information content entity" class has many GenEpiO terms. "data item > measurement data item" has many datum terms; see "data representational model" for collections of terms set up for compatibility with 3rd party sources. - -Note that this file contains examples of cities, provinces, states, territories, and soverign nations from around the world; customization of this geographical content would be expected for particular regional use. - - - - - - - - - - - - - - - - - - - - - - - - - - Base class for definitions. - - - - - - - - - A named element in the model. - - - - - - - - - Usage example and description. - - - - - - - - - An attributed label. - - - - - - - - - A permissible value, accompanied by intended text and an optional mapping to a concept URI. - - - - - - - - - A collection of subset, type, slot and class definitions. - - - - - - - - - The definition of a property or a slot. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - Damion Dooley's note: Here we are exploring the use of individuals/instances to describe local picklists for GenEpiO driven software. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - United Nations - - - - - - - - MSH - - - - - - - - NCI_Thesaurus - - - - - - - - NIFSTD - - - - - - - - home - - - - - - - - _test_individual - - - - - - - - - LabID assigned by NLEP - Damion Dooley - 2019-04-17T23:31:44Z - PulseNet:LabID - - - - - - - - Country where isolate was collected - Damion Dooley - 2019-04-17T23:32:45Z - SourceCountry - - - - - - - - - Country where isolate was collected - Currently not used for PulseNet Canada - Damion Dooley - 2019-04-17T23:37:19Z - PulseNet:SourceCountry - - - - - - - - - (Province for PNC) where isolate was collected. - Damion Dooley - 2019-04-17T23:38:09Z - PulseNet:SourceState - - - - - - - - - Damion Dooley - 2019-04-17T23:40:57Z - PulseNet:SourceCity - - - - - - - - - Site of the source type where isolate was collected, e.g. blood, CSF, etc. - Damion Dooley - 2019-04-17T23:47:10Z - PulseNet:SourceSite - - - - - - - - - The source type of the isolate, e.g. human, environmental, etc. - Damion Dooley - 2019-04-17T23:48:49Z - PulseNet:SourceType - - - - - - - - - Other countries where the patient traveled - Damion Dooley - 2019-04-17T23:49:47Z - PulseNet:Traveled_To - - - - - - - - - Further description of the source type, e.g. bovine, chicken - Damion Dooley - 2019-04-17T23:51:02Z - PulseNet:TypeDetails - - - - - - - - - Submitted isolate # (if diff. From Key #), NLEP will enter Prov. Submitted # if sample was sent to NLEP for PFGE - Damion Dooley - 2019-04-17T23:52:01Z - PulseNet:SubmittedNumber - - - - - - - - - (Province for PNC) additional number used to identify the isolate - Damion Dooley - 2019-04-17T23:53:47Z - PulseNet:OtherStateIsolate - - - - - - - - - Age of patient when isolate was collected - Damion Dooley - 2019-04-17T23:54:24Z - PulseNet:PatientAge - - - - - - - - - Sex of patient when isolate was collected - Damion Dooley - 2019-04-17T23:55:04Z - PulseNet:PatientSex - - - - - - - - - - Date of collection - Damion Dooley - 2019-04-17T23:56:33Z - PulseNet:IsolatDate - - - - - - - - - Date the isolate is uploaded to the national database after initial upload - Damion Dooley - 2019-04-18T00:21:46Z - PulseNet:UploadModifiedDate - - - - - - - - - Antigenic Formula - Damion Dooley - 2019-04-18T00:23:18Z - PulseNet:AntigenForm - - - - - - - - - Subspecies, I - VI (roman numerals) - Damion Dooley - 2019-04-18T00:24:11Z - PulseNet:Subspecies - - - - - - - - - O polysaccharide (LPS) Group - Damion Dooley - 2019-04-18T00:24:53Z - PulseNet:OGroup - - - - - - - - - Serotype of isolate - Damion Dooley - 2019-04-18T00:25:22Z - PulseNet:Serotype - - - - - - - - - Code issued by CDC; see: 'Naming of outbreaks…' on WebBoard. (format YYMMLabIDLITScode-#) - Currently not used for PulseNet Canada - Damion Dooley - 2019-04-18T00:27:08Z - PulseNet:Outbreak - - - - - - - - - Number issued by CDC if isolate is run at CDC (Key will be # issued by NLEP if isolate run at NLEP) - Damion Dooley - 2019-04-18T00:28:01Z - PulseNet:cdc_id - - - - - - - - - Enzyme name present if part of that national list. - Damion Dooley - 2019-04-18T00:28:35Z - PulseNet:ListMember - - - - - - - - - Phage type - Damion Dooley - 2019-04-18T00:29:20Z - PulseNet:Phagetype - - - - - - - - - Provides LabID, gel and lane information - Damion Dooley - 2019-04-18T00:29:58Z - PulseNet:TEMP - - - - - - - - - Status of the isolate; this is only confirmed once CDC runs it. - Currently not used for PulseNet Canada - Damion Dooley - 2019-04-18T00:30:44Z - PulseNet:Status - - - - - - - - - Currently not used for PulseNet Canada - checked if the isolate is part of NARMS. - Damion Dooley - 2019-04-18T00:35:55Z - PulseNet:NARMS-EB - - - - - - - - - Checked if the isolate is part of FoodNet. - Currently not used for PulseNet Canada - Damion Dooley - 2019-04-18T00:36:39Z - PulseNet:FoodNet - - - - - - - - - XbaI gel where the isolate is located, lane of gel - Damion Dooley - 2019-04-18T00:38:57Z - PulseNet:PFGE-XbaI-file - - - - - - - - - XbaI pattern assigned by CDC (format XXXXXX.####) - Damion Dooley - 2019-04-18T00:39:23Z - PulseNet:PFGE-XbaI-pattern - - - - - - - - - The date the XbaI gel is run - Damion Dooley - 2019-04-18T00:40:05Z - PulseNet:PFGE-XbaI-rundate - - - - - - - - - Once the XbaI pattern is named, the status is confirmed by CDC - Damion Dooley - 2019-04-18T00:41:39Z - PulseNet:PFGE-XbaI-status - - - - - - - - - BlnI gel where the isolate is located, lane of gel - Damion Dooley - 2019-04-18T00:42:11Z - PulseNet:PFGE-BlnI-file - - - - - - - - - BlnI pattern assigned by CDC (format XXXXXX.####). - Damion Dooley - 2019-04-18T00:42:42Z - PulseNet:PFGE-BlnI-pattern - - - - - - - - - The date the BlnI gel is run - Damion Dooley - 2019-04-18T00:43:50Z - PulseNet:PFGE-BlnI-rundate - - - - - - - - - Once the BlnI pattern is named, the status is confirmed by CDC - Damion Dooley - 2019-04-18T00:44:44Z - PulseNet:PFGE-BlnI-status - - - - - - - - - SpeI gel where the isolate is located, lane of gel. - Damion Dooley - 2019-04-18T00:45:15Z - PulseNet:PFGE-SpeI-file - - - - - - - - - SpeI pattern assigned by CDC (format XXXXXX.####). - Damion Dooley - 2019-04-18T00:45:41Z - PulseNet:PFGE-SpeI-pattern - - - - - - - - - The date the SpeI gel is run. - Damion Dooley - 2019-04-18T00:46:21Z - PulseNet:PFGE-SpeI-rundate - - - - - - - - - Once the SpeI pattern is named, the status is confirmed by CDC. - Damion Dooley - 2019-04-18T00:47:00Z - PulseNet:PFGE-SpeI-status - - - - - - - - - Date WHICH (PH?) lab received isolate. - Damion Dooley - 2019-04-18T00:57:28Z - PulseNet:ReceivedDate - - - - - - - - - - 2019-11-17T00:54:44Z - ISO_23418.organization_contact.service - - - - - - - - - Date the isolate uploaded to the national database. - Damion Dooley - 2019-04-17T22:47:51Z - PulseNet:UploadDate - - - 2 - - - 2 - - - - - - - - I - intermediate - - - R - resistant - - - S - sensitive - susceptible - - - NS - nonsensitive - nonsusceptible - - - sensitive - dose dependent - susceptible - dose dependent - SSD - - - BSAC - - - DIN - - - EUCAST - - - SFM - - - Damion Dooley's note: this BFO class is incompatible with "immaterial entity" "n-dimensional concept". - - - food role - - - constructed feature - - - http://purl.obolibrary.org/obo/NCIT_C25464 - - - irrigation pond - - - http://purl.obolibrary.org/obo/NCIT_C80234 - - - stool - - - http://opendata.inra.fr/EOL/EOL_0001601#bedding - straw bedding - - - true - - - chicken cage - - - NCBI SRA: ION_TORRENT - - - asian tiger shrimp - black tiger shrimp - - - wild - gathered - - - Damion Dooley - - - - This is a catch-all category for Gazetteer items that have "located in" relations but not an imported GAZETTEER class parent in GenEpiO. - Damion Dooley - - - true - - Damion Dooley - obsolete: has primitive data type - - - - Damion Dooley - - - - Damion Dooley - - - - Damion Dooley - - - Damion Dooley - - - - Damion Dooley - - - - - Damion Dooley - - - - Damion Dooley - - - Damion Dooley's note: IAO lat/long can't be made a subclass of "angular coordinate" or disjoint contradiction arises with "immaterial entity" - Damion Dooley - - - - - Damion Dooley - - - - Damion Dooley - - - Damion Dooley - - - - - Damion Dooley - - - Damion Dooley - - - - Damion Dooley - This seems to be covered by 'datetime range intermediate' - - - - Damion Dooley - - - - Damion Dooley - - - - Damion Dooley - A datetime set item is a datetime that has been grouped semantically under a given type of process - - - Damion Dooley - - - - Damion Dooley - - - - Damion Dooley - - - - Damion Dooley - - - - Damion Dooley - - - - Damion Dooley - - - - mobile - - - work - - - - Damion Dooley - - - - An unordered set is a set of elements which have no intrinsic (semantic) order with respect to each other. The set of all living people is not intrinsically ordered; an ordering can only be provided by looking at some partiular feature of the given set elements. - Damion Dooley - - - - Damion Dooley - - - Damion Dooley - - - - - Damion Dooley - - - Damion Dooley - - https://en.wikipedia.org/wiki/Plane_(geometry) - - - Damion Dooley - - - - clam, squid, octopus - - - NCBI SRA: HELICOS - - - NCBI SRA: ABI_SOLID - - - A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. - - - specimen provider PI organization - - - NCBI SRA: Illumina Genome Analyzer IIx - - - NCBI SRA: AB SOLiD 3 Plus System - - - NCBI SRA: AB SOLiD 4 System - - - NCBI SRA: Illumina Genome Analyzer IIe - - - disease (OGMS) - - - - - - NCBI BioSample: hermaphrodite - - - This value is not present in NCBI BioSample host sex. - - - derives into - - - starts during - - - happens during - - - starts with - - - ends with - - - input of - - - Damion Dooley's note:Damion Dooley's note: Outstanding issue: How to attach units to each dimension? This depends on the instance of the problem involving a dimension? - -Linear offset can be decimal or integer or complex, or a count. - - Can have a unit: meter, kilometer, foot, light-year, oranges, apples, fruit - -Angular offset can be radians or degrees. - n-dimensional coordinate system - - - rectal - - - http://purl.obolibrary.org/obo/BTO_0000818 - - - cerebrospinal fluid (CSF) - - - Damion Dooley - - cfu/mL - - - Damion Dooley - - - - http://purl.obolibrary.org/obo/PATO_0000011 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/relecov_tools/schema/gisaid_V0.json b/relecov_tools/schema/gisaid_schema.json similarity index 100% rename from relecov_tools/schema/gisaid_V0.json rename to relecov_tools/schema/gisaid_schema.json diff --git a/relecov_tools/schema/mapping_metadata_json_v01.json b/relecov_tools/schema/mapping_metadata_to_json.json similarity index 100% rename from relecov_tools/schema/mapping_metadata_json_v01.json rename to relecov_tools/schema/mapping_metadata_to_json.json diff --git a/relecov_tools/schema/phage_plus_V0.json b/relecov_tools/schema/phage_plus_schema.json similarity index 100% rename from relecov_tools/schema/phage_plus_V0.json rename to relecov_tools/schema/phage_plus_schema.json diff --git a/relecov_tools/schema/phage_V0.json b/relecov_tools/schema/phage_schema.json similarity index 100% rename from relecov_tools/schema/phage_V0.json rename to relecov_tools/schema/phage_schema.json diff --git a/relecov_tools/schema/small_schema.json b/relecov_tools/schema/small_schema.json deleted file mode 100644 index 4ee288c8..00000000 --- a/relecov_tools/schema/small_schema.json +++ /dev/null @@ -1,1210 +0,0 @@ -{ - "schema": "PHAGE_PLUS", - "required": [ - "sample_name", - "collecting_institution", - "submitting_institution", - "sample_collection_date", - "geo_loc_country", - "geo_loc_state", - "organism", - "isolate", - "host_scientific_name", - "host_common_name", - "host_disease", - "sequencing_instrument_model", - "sequencing_instrument_platform", - "consensus_sequence_software_name", - "consensus_sequence_software_version", - "file_name", - "tax_id", - "sample_description", - "library_source", - "library_selection", - "library_strategy", - "library_layout", - "type", - "virus_name", - "submitter", - "collecting_institution_address" - ], - "type": "object", - "properties": { - "sample_name": { - "examples": [ - "prov_rona_99" - ], - "ontology": "0", - "type": [ - "string", - "null" - ], - "description": "The user-defined name for the sample.", - "clasification": "Database Identifiers", - "label": "Collecting Sample id" - }, - "collecting_institution": { - "examples": [ - "Public Health Agency of Canada" - ], - "ontology": "GENEPIO:0001153", - "type": [ - "string", - "null" - ], - "description": "The name of the agency that collected the original sample.", - "label": "Originating Laboratory Address" - }, - "submitting_institution": { - "examples": [ - "Centers for Disease Control and Prevention" - ], - "ontology": "GENEPIO:0001159", - "type": [ - "string", - "null" - ], - "description": "The name of the agency that generated the sequence." - }, - "sample_collection_date": { - "examples": [ - "3/19/2020" - ], - "ontology": "GENEPIO:0001174", - "type": [ - "string", - "null" - ], - "description": "The date on which the sample was collected.", - "format": "date" - }, - "geo_loc_name_country": { - "Enums": [ - "Afghanistan [GAZ:00006882]", - "Albania [GAZ:00002953]", - "Algeria [GAZ:00000563]", - "American Samoa [GAZ:00003957]", - "Andorra [GAZ:00002948]", - "Angola [GAZ:00001095]", - "Anguilla [GAZ:00009159]", - "Antarctica [GAZ:00000462]", - "Antigua and Barbuda [GAZ:00006883]", - "Argentina [GAZ:00002928]", - "Armenia [GAZ:00004094]", - "Aruba [GAZ:00004025]", - "Ashmore and Cartier Islands [GAZ:00005901]", - "Australia [GAZ:00000463]", - "Austria [GAZ:00002942]", - "Azerbaijan [GAZ:00004941]", - "Bahamas [GAZ:00002733]", - "Bahrain [GAZ:00005281]", - "Baker Island [GAZ:00007117]", - "Bangladesh [GAZ:00003750]", - "Barbados [GAZ:00001251]", - "Bassas da India [GAZ:00005810]", - "Belarus [GAZ:00006886]", - "Belgium [GAZ:00002938]", - "Belize [GAZ:00002934]", - "Benin [GAZ:00000904]", - "Bermuda [GAZ:00001264]", - "Bhutan [GAZ:00003920]", - "Bolivia [GAZ:00002511]", - "Borneo [GAZ:00025355]", - "Bosnia and Herzegovina [GAZ:00006887]", - "Botswana [GAZ:00001097]", - "Bouvet Island [GAZ:00001453]", - "Brazil [GAZ:00002828]", - "British Virgin Islands [GAZ:00003961]", - "Brunei [GAZ:00003901]", - "Bulgaria [GAZ:00002950]", - "Burkina Faso [GAZ:00000905]", - "Burundi [GAZ:00001090]", - "Cambodia [GAZ:00006888]", - "Cameroon [GAZ:00001093]", - "Canada [GAZ:00002560]", - "Cape Verde [GAZ:00001227]", - "Cayman Islands [GAZ:00003986]", - "Central African Republic [GAZ:00001089]", - "Chad [GAZ:00000586]", - "Chile [GAZ:00002825]", - "China [GAZ:00002845]", - "Christmas Island [GAZ:00005915]", - "Clipperton Island [GAZ:00005838]", - "Cocos Islands [GAZ:00009721]", - "Colombia [GAZ:00002929]", - "Comoros [GAZ:00005820]", - "Cook Islands [GAZ:00053798]", - "Coral Sea Islands [GAZ:00005917]", - "Costa Rica [GAZ:00002901]", - "Cote d'Ivoire [GAZ:00000906]", - "Croatia [GAZ:00002719]", - "Cuba [GAZ:00003762]", - "Curacao [GAZ:00012582]", - "Cyprus [GAZ:00004006]", - "Czech Republic [GAZ:00002954]", - "Democratic Republic of the Congo [GAZ:00001086]", - "Denmark [GAZ:00005852]", - "Djibouti [GAZ:00000582]", - "Dominica [GAZ:00006890]", - "Dominican Republic [GAZ:00003952]", - "Ecuador [GAZ:00002912]", - "Egypt [GAZ:00003934]", - "El Salvador [GAZ:00002935]", - "Equatorial Guinea [GAZ:00001091]", - "Eritrea [GAZ:00000581]", - "Estonia [GAZ:00002959]", - "Eswatini [GAZ:00001099]", - "Ethiopia [GAZ:00000567]", - "Europa Island [GAZ:00005811]", - "Falkland Islands (Islas Malvinas) [GAZ:00001412]", - "Faroe Islands [GAZ:00059206]", - "Fiji [GAZ:00006891]", - "Finland [GAZ:00002937]", - "France [GAZ:00003940]", - "French Guiana [GAZ:00002516]", - "French Polynesia [GAZ:00002918]", - "French Southern and Antarctic Lands [GAZ:00003753]", - "Gabon [GAZ:00001092]", - "Gambia [GAZ:00000907]", - "Gaza Strip [GAZ:00009571]", - "Georgia [GAZ:00004942]", - "Germany [GAZ:00002646]", - "Ghana [GAZ:00000908]", - "Gibraltar [GAZ:00003987]", - "Glorioso Islands [GAZ:00005808]", - "Greece [GAZ:00002945]", - "Greenland [GAZ:00001507]", - "Grenada [GAZ:02000573]", - "Guadeloupe [GAZ:00067142]", - "Guam [GAZ:00003706]", - "Guatemala [GAZ:00002936]", - "Guernsey [GAZ:00001550]", - "Guinea [GAZ:00000909]", - "Guinea-Bissau [GAZ:00000910]", - "Guyana [GAZ:00002522]", - "Haiti [GAZ:00003953]", - "Heard Island and McDonald Islands [GAZ:00009718]", - "Honduras [GAZ:00002894]", - "Hong Kong [GAZ:00003203]", - "Howland Island [GAZ:00007120]", - "Hungary [GAZ:00002952]", - "Iceland [GAZ:00000843]", - "India [GAZ:00002839]", - "Indonesia [GAZ:00003727]", - "Iran [GAZ:00004474]", - "Iraq [GAZ:00004483]", - "Ireland [GAZ:00002943]", - "Isle of Man [GAZ:00052477]", - "Israel [GAZ:00002476]", - "Italy [GAZ:00002650]", - "Jamaica [GAZ:00003781]", - "Jan Mayen [GAZ:00005853]", - "Japan [GAZ:00002747]", - "Jarvis Island [GAZ:00007118]", - "Jersey [GAZ:00001551]", - "Johnston Atoll [GAZ:00007114]", - "Jordan [GAZ:00002473]", - "Juan de Nova Island [GAZ:00005809]", - "Kazakhstan [GAZ:00004999]", - "Kenya [GAZ:00001101]", - "Kerguelen Archipelago [GAZ:00005682]", - "Kingman Reef [GAZ:00007116]", - "Kiribati [GAZ:00006894]", - "Kosovo [GAZ:00011337]", - "Kuwait [GAZ:00005285]", - "Kyrgyzstan [GAZ:00006893]", - "Laos [GAZ:00006889]", - "Latvia [GAZ:00002958]", - "Lebanon [GAZ:00002478]", - "Lesotho [GAZ:00001098]", - "Liberia [GAZ:00000911]", - "Libya [GAZ:00000566]", - "Liechtenstein [GAZ:00003858]", - "Line Islands [GAZ:00007144]", - "Lithuania [GAZ:00002960]", - "Luxembourg [GAZ:00002947]", - "Macau [GAZ:00003202]", - "Madagascar [GAZ:00001108]", - "Malawi [GAZ:00001105]", - "Malaysia [GAZ:00003902]", - "Maldives [GAZ:00006924]", - "Mali [GAZ:00000584]", - "Malta [GAZ:00004017]", - "Marshall Islands [GAZ:00007161]", - "Martinique [GAZ:00067143]", - "Mauritania [GAZ:00000583]", - "Mauritius [GAZ:00003745]", - "Mayotte [GAZ:00003943]", - "Mexico [GAZ:00002852]", - "Micronesia [GAZ:00005862]", - "Midway Islands [GAZ:00007112]", - "Moldova [GAZ:00003897]", - "Monaco [GAZ:00003857]", - "Mongolia [GAZ:00008744]", - "Montenegro [GAZ:00006898]", - "Montserrat [GAZ:00003988]", - "Morocco [GAZ:00000565]", - "Mozambique [GAZ:00001100]", - "Myanmar [GAZ:00006899]", - "Namibia [GAZ:00001096]", - "Nauru [GAZ:00006900]", - "Navassa Island [GAZ:00007119]", - "Nepal [GAZ:00004399]", - "Netherlands [GAZ:00002946]", - "New Caledonia [GAZ:00005206]", - "New Zealand [GAZ:00000469]", - "Nicaragua [GAZ:00002978]", - "Niger [GAZ:00000585]", - "Nigeria [GAZ:00000912]", - "Niue [GAZ:00006902]", - "Norfolk Island [GAZ:00005908]", - "North Korea [GAZ:00002801]", - "North Macedonia [GAZ:00006895]", - "North Sea [GAZ:00002284]", - "Northern Mariana Islands [GAZ:00003958]", - "Norway [GAZ:00002699]", - "Oman [GAZ:00005283]", - "Pakistan [GAZ:00005246]", - "Palau [GAZ:00006905]", - "Panama [GAZ:00002892]", - "Papua New Guinea [GAZ:00003922]", - "Paracel Islands [GAZ:00010832]", - "Paraguay [GAZ:00002933]", - "Peru [GAZ:00002932]", - "Philippines [GAZ:00004525]", - "Pitcairn Islands [GAZ:00005867]", - "Poland [GAZ:00002939]", - "Portugal [GAZ:00004126]", - "Puerto Rico [GAZ:00006935]", - "Qatar [GAZ:00005286]", - "Republic of the Congo [GAZ:00001088]", - "Reunion [GAZ:00003945]", - "Romania [GAZ:00002951]", - "Ross Sea [GAZ:00023304]", - "Russia [GAZ:00002721]", - "Rwanda [GAZ:00001087]", - "Saint Helena [GAZ:00000849]", - "Saint Kitts and Nevis [GAZ:00006906]", - "Saint Lucia [GAZ:00006909]", - "Saint Pierre and Miquelon [GAZ:00003942]", - "Saint Martin [GAZ:00005841]", - "Saint Vincent and the Grenadines [GAZ:02000565]", - "Samoa [GAZ:00006910]", - "San Marino [GAZ:00003102]", - "Sao Tome and Principe [GAZ:00006927]", - "Saudi Arabia [GAZ:00005279]", - "Senegal [GAZ:00000913]", - "Serbia [GAZ:00002957]", - "Seychelles [GAZ:00006922]", - "Sierra Leone [GAZ:00000914]", - "Singapore [GAZ:00003923]", - "Sint Maarten [GAZ:00012579]", - "Slovakia [GAZ:00002956]", - "Slovenia [GAZ:00002955]", - "Solomon Islands [GAZ:00005275]", - "Somalia [GAZ:00001104]", - "South Africa [GAZ:00001094]", - "South Georgia and the South Sandwich Islands [GAZ:00003990]", - "South Korea [GAZ:00002802]", - "South Sudan [GAZ:00233439]", - "Spain [GAZ:00003936]", - "Spratly Islands [GAZ:00010831]", - "Sri Lanka [GAZ:00003924]", - "State of Palestine [GAZ:00002475]", - "Sudan [GAZ:00000560]", - "Suriname [GAZ:00002525]", - "Svalbard [GAZ:00005396]", - "Swaziland [GAZ:00001099]", - "Sweden [GAZ:00002729]", - "Switzerland [GAZ:00002941]", - "Syria [GAZ:00002474]", - "Taiwan [GAZ:00005341]", - "Tajikistan [GAZ:00006912]", - "Tanzania [GAZ:00001103]", - "Thailand [GAZ:00003744]", - "Timor-Leste [GAZ:00006913]", - "Togo [GAZ:00000915]", - "Tokelau [GAZ:00260188]", - "Tonga [GAZ:00006916]", - "Trinidad and Tobago [GAZ:00003767]", - "Tromelin Island [GAZ:00005812]", - "Tunisia [GAZ:00000562]", - "Turkey [GAZ:00000558]", - "Turkmenistan [GAZ:00005018]", - "Turks and Caicos Islands [GAZ:00003955]", - "Tuvalu [GAZ:00009715]", - "USA [GAZ:00002459]", - "Uganda [GAZ:00001102]", - "Ukraine [GAZ:00002724]", - "United Arab Emirates [GAZ:00005282]", - "United Kingdom [GAZ:00002637]", - "Uruguay [GAZ:00002930]", - "Uzbekistan [GAZ:00004979]", - "Vanuatu [GAZ:00006918]", - "Venezuela [GAZ:00002931]", - "Viet Nam [GAZ:00003756]", - "Virgin Islands [GAZ:00003959]", - "Wake Island [GAZ:00007111]", - "Wallis and Futuna [GAZ:00007191]", - "West Bank [GAZ:00009572]", - "Western Sahara [GAZ:00000564]", - "Yemen [GAZ:00005284]", - "Zambia [GAZ:00001107]", - "Zimbabwe [GAZ:00001106]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001181", - "type": [ - "string", - "null" - ], - "description": "The country of origin of the sample.", - "examples": [ - "South Africa [GAZ:00001094]" - ], - "classification": "Sample collection and processing", - "label": "Geo Loc Autonomic Country" - }, - "geo_loc_state": { - "examples": [ - "Western Cape" - ], - "ontology": "GENEPIO:0001185", - "type": [ - "string", - "null" - ], - "description": "The state/province/territory of origin of the sample.", - "classification": "Sample collection and processing", - "label": "Geo Loc Autonomic Community" - }, - "organism": { - "Enums": [ - "Coronaviridae [NCBITaxon:11118]", - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001191", - "type": [ - "string", - "null" - ], - "description": "Taxonomic name of the organism.", - "examples": [ - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]" - ], - "classification": "Sample collection and processing", - "label": "Organism" - }, - "isolate": { - "examples": [ - "SARS-CoV-2/human/USA/CA-CDPH-001/2020" - ], - "ontology": "GENEPIO:0001644", - "type": [ - "string", - "null" - ], - "description": "Identifier of the specific isolate.", - "clasification": "Sample collection and processing", - "label": "Isolate" - }, - "host_scientific_name": { - "Enums": [ - "Bos taurus [NCBITaxon:9913]", - "Canis lupus familiaris [NCBITaxon:9615]", - "Chiroptera [NCBITaxon:9397]", - "Columbidae [NCBITaxon:8930]", - "Felis catus [NCBITaxon:9685]", - "Gallus gallus [NCBITaxon:9031]", - "Homo sapiens [NCBITaxon:9606]", - "Manis [NCBITaxon:9973]", - "Manis javanica [NCBITaxon:9974]", - "Neovison vison [NCBITaxon:452646]", - "Panthera leo [NCBITaxon:9689]", - "Panthera tigris [NCBITaxon:9694]", - "Rhinolophidae [NCBITaxon:58055]", - "Rhinolophus affinis [NCBITaxon:59477]", - "Sus scrofa domesticus [NCBITaxon:9825]", - "Viverridae [NCBITaxon:9673]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001387", - "type": "string", - "description": "The taxonomic, or scientific name of the host.", - "examples": [ - "Homo sapiens [NCBITaxon:9606]" - ], - "clasification": "Host information", - "label": "Host Scientific Name" - }, - "host_disease": { - "Enums": [ - "COVID-19 [MONDO:0100096]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001391", - "type": "string", - "description": "The name of the disease experienced by the host.", - "examples": [ - "COVID-19 [MONDO:0100096]" - ] - }, - "sequencing_instrument_model": { - "Enums": [ - "Illumina sequencing instrument [GENEPIO:0100105]", - "Illumina Genome Analyzer [GENEPIO:0100106]", - "Illumina Genome Analyzer II [GENEPIO:0100107]", - "Illumina Genome Analyzer IIx [GENEPIO:0100108]", - "Illumina HiScanSQ [GENEPIO:0100109]", - "Illumina HiSeq [GENEPIO:0100110]", - "Illumina HiSeq X [GENEPIO:0100111]", - "Illumina HiSeq X Five [GENEPIO:0100112]", - "Illumina HiSeq X Ten [GENEPIO:0100113]", - "Illumina HiSeq 1000 [GENEPIO:0100114]", - "Illumina HiSeq 1500 [GENEPIO:0100115]", - "Illumina HiSeq 2000 [GENEPIO:0100116]", - "Illumina HiSeq 2500 [GENEPIO:0100117]", - "Illumina HiSeq 3000 [GENEPIO:0100118]", - "Illumina HiSeq 4000 [GENEPIO:0100119]", - "Illumina iSeq [GENEPIO:0100120]", - "Illumina iSeq 100 [GENEPIO:0100121]", - "Illumina NovaSeq [GENEPIO:0100122]", - "Illumina NovaSeq 6000 [GENEPIO:0100123]", - "Illumina MiniSeq [GENEPIO:0100124]", - "Illumina MiSeq [GENEPIO:0100125]", - "Illumina NextSeq [GENEPIO:0100126]", - "Illumina NextSeq 500 [GENEPIO:0100127]", - "Illumina NextSeq 550 [GENEPIO:0100128]", - "Illumina NextSeq 2000 [GENEPIO:0100129]", - "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", - "PacBio RS [GENEPIO:0100131]", - "PacBio RS II [GENEPIO:0100132]", - "PacBio Sequel [GENEPIO:0100133]", - "PacBio Sequel II [GENEPIO:0100134]", - "Ion Torrent sequencing instrument [GENEPIO:0100135]", - "Ion Torrent PGM [GENEPIO:0100136]", - "Ion Torrent Proton [GENEPIO:0100137]", - "Ion Torrent S5 XL [GENEPIO:0100138]", - "Ion Torrent S5 [GENEPIO:0100139]", - "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", - "Oxford Nanopore GridION [GENEPIO:0100141]", - "Oxford Nanopore MinION [GENEPIO:0100142]", - "Oxford Nanopore PromethION [GENEPIO:0100143]", - "BGI Genomics sequencing instrument [GENEPIO:0100144]", - "BGI SEQ-500 [GENEPIO:0100145]", - "MGI sequencing instrument [GENEPIO:0100146]", - "MGI DNBSEQ-T7 [GENEPIO:0100147]", - "MGI DNBSEQ-G400 [GENEPIO:0100148]", - "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", - "MGI DNBSEQ-G50 [GENEPIO:0100150]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001452", - "type": "string", - "description": "The model of the sequencing instrument used.", - "examples": [ - "Oxford Nanopore MinION [GENEPIO:0100142]" - ], - "classification": "Sequencing", - "label": "Sequencing Instrument Model" - }, - "sequencing_instrument_platform": { - "examples": [ - "MinIon" - ], - "ontology": "GENEPIO_0000071", - "type": "string", - "description": "The model of the sequencing instrument used.", - "label": "Sequencing Platforms " - }, - "consensus_sequence_software_name": { - "examples": [ - "Ivar" - ], - "ontology": "GENEPIO:0001463", - "type": "string", - "description": "The name of software used to generate the consensus sequence.", - "clasification": "Bioinformatics and QC metrics", - "label": "Consensus sequence software name" - }, - "consensus_sequence_software_version": { - "examples": [ - "1.3" - ], - "ontology": "GENEPIO:0001469", - "type": "string", - "description": "The version of the software used to generate the consensus sequence.", - "clasification": "Bioinformatics and QC metrics", - "label": "Consensus sequence software version" - }, - "host_common_name": { - "Enums": [ - "Human [NCBITaxon:9606]", - "Bat [NCBITaxon:9397]", - "Cat [NCBITaxon:9685]", - "Chicken [NCBITaxon:9031]", - "Civet [NCBITaxon:9673]", - "Cow [NCBITaxon:9913]", - "Dog [NCBITaxon:9615]", - "Lion [NCBITaxon:9689]", - "Mink [NCBITaxon:452646]", - "Pangolin [NCBITaxon:9973]", - "Pig [NCBITaxon:9825]", - "Pigeon [NCBITaxon:8930]", - "Tiger [NCBITaxon:9694]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001386", - "type": "string", - "description": "The commonly used name of the host.", - "examples": [ - "Human [NCBITaxon:9606]" - ], - "classification": "Host information", - "label": "Host Common Name" - }, - "file_name": { - "examples": [ - "ABC123_S1_L001_R1_001.fastq.gz" - ], - "ontology": "GENEPIO:0001476", - "type": "string", - "description": "The user-specified filename of the r1 FASTQ file.", - "clasification": "Bioinformatics and QC metrics", - "label": "Sequence file R1 fastq" - }, - "tax_id": { - "examples": [ - "probably 2697049 in all cases" - ], - "ontology": "GENEPIO_0001724", - "type": [ - "number", - "string" - ], - "description": "The NCBITaxon identifier for the organism being sequenced.", - "clasification": "Sample collection and processing", - "label": "Tax ID" - }, - "scientific_name": { - "Enums": [ - "Coronaviridae [NCBITaxon:11118]", - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "examples": [ - "" - ], - "ontology": "GENEPIO:0001191", - "type": "string", - "description": "The taxonomic name of the organism.", - "clasification": "Sample collection and processing", - "classification": "Sample collection and processing", - "label": "Organism" - }, - "common_name": { - "examples": [ - "" - ], - "ontology": "NCIT:C164471", - "type": "string", - "description": "The common name of the organism.", - "clasification": "Sample collection and processing", - "label": "Common name" - }, - "sample_description": { - "examples": [ - "" - ], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Free text description of the sample.", - "clasification": "Sample collection and processing", - "label": "Sample Description" - }, - "sample_storage_conditions": { - "examples": [ - "24 degrees celsius" - ], - "ontology": "NCIT_C115535", - "type": "string", - "description": "The name and version of a particular protocol used for sampling.", - "clasification": "Sample collection and processing" - }, - "library_source": { - "Enums": [ - "5-methycytidine antibody method [GENPIO:0001941]", - "CAGE method [GENPIO:0001942]", - "CF-H method [GENPIO:0001943]", - "CF-M method ]GENPIO:0001944]", - "CF-S method [GENPIO:0001945]", - "CF-T method [GENPIO:0001946]", - "ChIP method ]GENPIO:0001947]", - "DNAse method [GENPIO:0001948]", - "HMPR method [GENPIO:0001949]", - "Hybrid Selection Method [GENPIO:0001950]", - "MBD2 protein methyl-CpG binding domain method [GENPIO:0001951]", - "MF method [GENPIO:0001952]", - "MNase method [GENPIO:0001953]", - "MSLL method [GENPIO:0001954]", - "PCR method [GENPIO:0001955]", - "RACE method [GENPIO:0001956]", - "RANDOM PCR method [GENPIO:0001957]", - "RANDOM method [GENPIO:0001958]", - "RT-PCR method [GENPIO:0001959]", - "Reduced Representation method [GENPIO:0001960]", - "Resctriction Digest method [GENPIO:0001961]", - "cDNA method [GENPIO:0001962]", - "other library method [GENPIO:0001964]", - "size fractionation method [GENPIO:0001963]" - ], - "examples": [ - "METAGENOMIC" - ], - "ontology": "GENEPIO_0001965", - "type": "string", - "description": "Molecule type used to make the library.", - "clasification": "Sequencing", - "label": "Source material" - }, - "library_selection": { - "examples": [ - "RANDOM PCR" - ], - "ontology": "GENPIO_0001940", - "type": "string", - "description": "Library capture method.", - "clasification": "Sequencing", - "label": "Capture method" - }, - "library_strategy": { - "Enums": [ - "Bisultife-Seq strategy [GENPIO:0001975]", - "CTS strategy [GENPIO:0001978]", - "ChIP-Seq strategy [GENPIO:0001979]", - "DNase-Hypersensitivity strategy [GENPIO:0001980]", - "EST strategy [GENPIO:0001981]", - "FL-cDNA strategy [GENPIO:0001983]", - "MB-Seq strategy [GENPIO:0001984]", - "MNase-Seq strategy [GENPIO:0001985]", - "MRE-Seq strategy [GENPIO:0001986]", - "MeDIP-Seq strategy [GENPIO:0001987]", - "RNA-Seq strategy [GENPIO:0001990]", - "WCS strategy [GENPIO:0001991]", - "WGS strategy [GENPIO:0001992]", - "WXS strategy [GENPIO:0001993]", - "amplicon strategy [GENPIO:0001974]", - "clone end strategy [GENPIO:0001976]", - "clone strategy [GENPIO:0001977]", - "finishing strategy [GENPIO:0001982]", - "other library strategy [GENPIO:0001988]", - "pool clone strategy [GENPIO:0001989]" - ], - "examples": [ - "WGS" - ], - "ontology": "GENPIO_0001973", - "type": "string", - "description": "Overall sequencing strategy or approach.", - "clasification": "Sequencing", - "label": "Sequencing technique" - }, - "library_layout": { - "examples": [ - "CTS strategy" - ], - "ontology": "BU_ISCIII:007", - "type": "string", - "description": "Single or paired.", - "clasification": "Sequencing", - "label": "Library Layout" - }, - "type": { - "examples": [ - "betacoronavirus" - ], - "ontology": "NCBITaxon:694002", - "type": "string", - "description": "default must remain 'betacoronavirus'", - "clasification": "Database Identifiers" - }, - "virus_name": { - "examples": [ - "hCoV-19/Canada/prov_rona_99/2020" - ], - "ontology": "GENEPIO:0100282", - "type": "string", - "description": "The user-defined GISAID virus name assigned to the sequence.", - "clasification": "Database Identifiers", - "label": "GISAID Virus Name" - }, - "submitter": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "clasification": "enter your GISAID-Username", - "label": "GISAID Username" - }, - "collecting_institution_address": { - "examples": [ - "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" - ], - "ontology": "GENEPIO:0001158", - "type": "string", - "description": "The mailing address of the agency submitting the sample.", - "clasification": "Originating Laboratory Address" - }, - "library_name": { - "examples": [ - "e.g PAIRED" - ], - "ontology": "GENEPIO_0001995", - "type": "string", - "description": "The submitter's name for this library.", - "clasification": "Sequencing", - "label": "Library Name" - }, - "nominal_length": { - "examples": [ - "350" - ], - "ontology": "GENEPIO_0000076", - "type": "number", - "description": "", - "clasification": "Sequencing", - "label": "Nominal Length" - }, - "analysis_accession": { - "examples": [ - "" - ], - "ontology": "GENEPIO_0001145", - "type": [ - "string", - "null" - ], - "description": "", - "clasification": "Submission ENA", - "label": "Analysis Accession" - }, - "read_length": { - "examples": [ - "" - ], - "ontology": "STATO_0000064", - "type": [ - "string", - "null" - ], - "description": "", - "clasification": "Submission ENA", - "label": "Read length" - }, - "study_accession": { - "examples": [ - "e.g PRJEB39632" - ], - "ontology": "GENEPIO_0001136", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Study accession" - }, - "secondary_study_accession": { - "examples": [ - "e.g ERP123173" - ], - "ontology": "BU_ISCIII:012", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Secondary study accession" - }, - "sample_accession": { - "examples": [ - "e.g SAMEA7098096" - ], - "ontology": "GENEPIO_0001139", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Sample accession" - }, - "secondary_sample_accession": { - "examples": [ - "e.g ERS4858671" - ], - "ontology": "BU_ISCIII:014", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Secondary sample accession" - }, - "experiment_accession": { - "examples": [ - "e.g ERX4331406" - ], - "ontology": "BU_ISCIII:015", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Experiment Accession" - }, - "run_accession": { - "examples": [ - "e.g ERX4331406" - ], - "ontology": "BU_ISCIII:016", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Run Accession" - }, - "submission_accession": { - "examples": [ - "e.g ERA2794974" - ], - "ontology": "BU_ISCIII:017", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Submission accession" - 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} - } -} \ No newline at end of file From ced0d90435231872b9e8a7ab11e57a19f03e0e2e Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 18 Mar 2022 18:43:49 +0100 Subject: [PATCH 0174/1454] rename sftp.py to sftp_handled.py --- relecov_tools/__main__.py | 2 +- relecov_tools/{sftp.py => sftp_handled.py} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename relecov_tools/{sftp.py => sftp_handled.py} (100%) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index b3a9c5e1..b7448989 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -10,7 +10,7 @@ import relecov_tools.utils import relecov_tools.read_metadata -import relecov_tools.sftp +import relecov_tools.sftp_handled import relecov_tools.create_xml import relecov_tools.validation_json import relecov_tools.conversion_schema diff --git a/relecov_tools/sftp.py b/relecov_tools/sftp_handled.py similarity index 100% rename from relecov_tools/sftp.py rename to relecov_tools/sftp_handled.py From 3561b134de775c72482b732ba7445e941fa31b2e Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 18 Mar 2022 18:46:36 +0100 Subject: [PATCH 0175/1454] remove create_xml.py, because it was exactly the same as ena_upload.py --- relecov_tools/create_xml.py | 174 ------------------------------------ 1 file changed, 174 deletions(-) delete mode 100644 relecov_tools/create_xml.py diff --git a/relecov_tools/create_xml.py b/relecov_tools/create_xml.py deleted file mode 100644 index 226f04a3..00000000 --- a/relecov_tools/create_xml.py +++ /dev/null @@ -1,174 +0,0 @@ -import os -import logging -import rich.console -from email import utils -import json as j -import xml.etree.cElementTree as e - -import relecov_tools.utils - -log = logging.getLogger(__name__) -stderr = rich.console.Console( - stderr=True, - style="dim", - highlight=False, - force_terminal=relecov_tools.utils.rich_force_colors(), -) - - -class XmlCreation: - def __init__(self, source_json=None, output_path=None, action=None): - if source_json is None: - self.source_json = utils.prompt_source_path() - else: - self.source_json = source_json - if output_path is None: - self.output_path = utils.prompt_destination_path() - else: - self.output_path = output_path - if action is None: - self.action = "ADD" - else: - self.action = action - - def xml_study( - self, - ): - """ - 1.From validated json to xml study- submission.xml and project.xml - 1.1 Upload study info - - 2. From validated json to xml samples - submission.xml and samples.xml - 2.2 Upload samples info - - 3. From sftp upload runs (FASTQ files programmatic)- experiments.xmlm, runs.xml and submission.xml - 4. From sftp upload sequences (FASTA files programmatic) - json using webin-cli-rest - """ - - # Load validated json - with open(self.source_json) as json_format_file: - json_data = j.load(json_format_file) - - # Create output directory - - try: - # Create target Directory - os.mkdir(self.output_path) - print("Directory ", self.output_path, " Created ") - except FileExistsError: - print("Directory ", self.output_path, " already exists") - - # 1. From validated json to xml study- submission.xml and project.xml - - # submission.xml - os.chdir("xml_files/") - if self.action.upper == "ADD": - # submission add - submission_file = "submission_add.xml" - if self.action.upper() == "MODIFY": - # submission modify - submission_file = "submission_modify.xml" - - # project_relecov.xml - os.chdir("../conf") - dict_conf = j.loads("configuration.json") - r = e.Element("PROJECT_SET") - project = e.SubElement(r, "PROJECT") - project.set("alias", dict_conf["project_relecov_xml"]["alias"]) - e.SubElement(project, "TITLE").text = dict_conf["project_relecov_xml"][ - "TITLE" - ] - e.SubElement(project, "DESCRIPTION").text = dict_conf[ - "project_relecov_xml" - ]["DESCRIPTION"] - submission = e.SubElement(project, "SUBMISSION_PROJECT") - e.SubElement(submission, "SEQUENCING_PROJECT") - a = e.ElementTree(r) - a.write(os.path.join(self.output_path, "study", "project_relecov.xml")) - - # 1.1 Upload study info - """ - import requests - from requests.structures import CaseInsensitiveDict - - url = "https://reqbin.com/echo/post/json" - - headers = CaseInsensitiveDict() - headers["Content-Type"] = "application/json" - headers["Authorization"] = "Basic bG9naW46cGFzc3dvcmQ=" - - data = '{"login":"my_login","password":"my_password"}' - - - resp = requests.post(url, headers=headers, data=data) - - print(resp.status_code) - """ - - # 2. From validated json to xml samples - submission.xml and samples.xml - - def xml_samples(): - # submission.xml - os.chdir("../xml_files/") - if self.action.upper == "ADD": - # submission add - submission_file = "submission_add.xml" - if self.action.upper() == "MODIFY": - # submission modify - submission_file = "submission_modify.xml" - - # samples_relecov.xml - os.chdir("../schema/") - json_data = j.loads("to_ena.json") - os.chdir("../conf") - dict_conf = j.loads("configuration.json") - - data_keys = list(json_data.keys()) - r = e.Element("SAMPLE_SET") - sample = e.SubElement(r, "SAMPLE") - sample.set( - "alias", - "Programmatic Test SARS-CoV-2 Sample" + str(json_data["sample_name"]), - ) - e.SubElement(sample, "TITLE").text = "SARS-CoV-2 Sample" + str( - json_data["sample_name"] - ) - sample_name = e.SubElement(sample, "SAMPLE_NAME") - e.SubElement(sample_name, "TAXON_ID").text = dict_conf["fixed_data"][ - "tax_id" - ] - e.SubElement(sample_name, "SCIENTIFIC_NAME").text = dict_conf["fixed_data"][ - "scientific_name" - ] - e.SubElement(sample, "DESCRIPTION").text = "SARS-CoV-2 Sample" + str( - json_data["sample_name"] - ) - sample_attributes = e.SubElement(sample, "SAMPLE_ATTRIBUTES") - for i in json_data: - sample_attribute = e.SubElement(sample_attributes, "SAMPLE_ATTRIBUTE") - e.SubElement(sample_attribute, "TAG").text = str(i) - e.SubElement(sample_attribute, "VALUE").text = json_data[i] - a = e.ElementTree(r) - a.write(os.path.join(self.output_path, "samples", "samples_relecov.xml")) - - # 2.2 Upload samples info - """ - import requests - from requests.structures import CaseInsensitiveDict - - url = "https://reqbin.com/echo/post/json" - - headers = CaseInsensitiveDict() - headers["Content-Type"] = "application/json" - headers["Authorization"] = "Basic bG9naW46cGFzc3dvcmQ=" - - data = '{"login":"my_login","password":"my_password"}' - - - resp = requests.post(url, headers=headers, data=data) - - print(resp.status_code) - """ - - # 3. From sftp upload runs (FASTQ files programmatic)- experiments.xmlm, runs.xml and submission.xml - # 4. From sftp upload sequences (FASTA files programmatic) - json using webin-cli-rest From f5b4e236e784d04c802630c871904781e422e668 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 18 Mar 2022 19:16:32 +0100 Subject: [PATCH 0176/1454] starting ena_upload from scratch --- relecov_tools/ena_upload.py | 148 ++++++------------------------------ 1 file changed, 24 insertions(+), 124 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 62b60c2a..7eb3053b 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,10 +1,12 @@ import os import logging import rich.console -from email import utils -import json as j -import xml.etree.cElementTree as e +import json +# import pandas as pd +import sys + +# import ena_upload import relecov_tools.utils log = logging.getLogger(__name__) @@ -16,134 +18,32 @@ ) -class XmlCreation: +class EnaUpload: def __init__(self, source_json=None, output_path=None, action=None): if source_json is None: - self.source_json = utils.prompt_source_path() + self.source_json_file = relecov_tools.utils.prompt_source_path() else: - self.source_json = source_json + self.source_json_file = source_json if output_path is None: - self.output_path = utils.prompt_destination_path() + self.output_path = relecov_tools.utils.prompt_destination_path() else: self.output_path = output_path if action is None: self.action = "ADD" else: self.action = action - - def xml_study( - self, - ): - """ - 1.From validated json to xml study- submission.xml and project.xml - 1.1 Upload study info - - 2. From validated json to xml samples - submission.xml and samples.xml - 2.2 Upload samples info - - 3. From sftp upload runs (FASTQ files programmatic)- experiments.xmlm, runs.xml and submission.xml - 4. From sftp upload sequences (FASTA files programmatic) - json using webin-cli-rest - """ - - # Load validated json - with open(self.source_json) as json_format_file: - json_data = j.load(json_format_file) - - # Create output directory - - try: - # Create target Directory - os.mkdir(self.output_path) - print("Directory ", self.output_path, " Created ") - except FileExistsError: - print("Directory ", self.output_path, " already exists") - - # 1. From validated json to xml study- submission.xml and project.xml - - # submission.xml - os.chdir("xml_files/") - if self.action.upper == "ADD": - # submission add - submission_file = "submission_add.xml" - if self.action.upper() == "MODIFY": - # submission modify - submission_file = "submission_modify.xml" - - # project_relecov.xml - os.chdir("../conf") - dict_conf = j.loads("configuration.json") - r = e.Element("PROJECT_SET") - project = e.SubElement(r, "PROJECT") - project.set("alias", dict_conf["project_relecov_xml"]["alias"]) - e.SubElement(project, "TITLE").text = dict_conf["project_relecov_xml"][ - "TITLE" - ] - e.SubElement(project, "DESCRIPTION").text = dict_conf[ - "project_relecov_xml" - ]["DESCRIPTION"] - submission = e.SubElement(project, "SUBMISSION_PROJECT") - e.SubElement(submission, "SEQUENCING_PROJECT") - a = e.ElementTree(r) - a.write(os.path.join(self.output_path, "study", "project_relecov.xml")) - - # 1.1 Upload study info - # 2. From validated json to xml samples - submission.xml and samples.xml - - def xml_samples(): - # submission.xml - os.chdir("../xml_files/") - if self.action.upper == "ADD": - # submission add - submission_file = "submission_add.xml" - if self.action.upper() == "MODIFY": - # submission modify - submission_file = "submission_modify.xml" - - # samples_relecov.xml - os.chdir("../schema/") - json_data = j.loads("to_ena.json") - os.chdir("../conf") - dict_conf = j.loads("configuration.json") - - data_keys = list(json_data.keys()) - r = e.Element("SAMPLE_SET") - sample = e.SubElement(r, "SAMPLE") - sample.set( - "alias", - "Programmatic Test SARS-CoV-2 Sample" + str(json_data["sample_name"]), - ) - e.SubElement(sample, "TITLE").text = "SARS-CoV-2 Sample" + str( - json_data["sample_name"] - ) - sample_name = e.SubElement(sample, "SAMPLE_NAME") - e.SubElement(sample_name, "TAXON_ID").text = dict_conf["fixed_data"][ - "tax_id" - ] - e.SubElement(sample_name, "SCIENTIFIC_NAME").text = dict_conf["fixed_data"][ - "scientific_name" - ] - e.SubElement(sample, "DESCRIPTION").text = "SARS-CoV-2 Sample" + str( - json_data["sample_name"] - ) - sample_attributes = e.SubElement(sample, "SAMPLE_ATTRIBUTES") - for i in json_data: - sample_attribute = e.SubElement(sample_attributes, "SAMPLE_ATTRIBUTE") - e.SubElement(sample_attribute, "TAG").text = str(i) - e.SubElement(sample_attribute, "VALUE").text = json_data[i] - a = e.ElementTree(r) - a.write(os.path.join(self.output_path, "samples", "samples_relecov.xml")) - - # 2.2 Upload samples info - - # 3. From sftp upload runs (FASTQ files programmatic)- experiments.xmlm, runs.xml and submission.xml - # 4. From sftp upload sequences (FASTA files programmatic) - json using webin-cli-rest - - -# Adaptation to ena_upload -with open('../example_data/ena_upload.json','r') as f: - data = j.loads(f.read()) - -df_study = pd.DataFrame.from_dict(data["study"]) -df_samples = pd.DataFrame.from_dict(data["samples"]) -df_runs = pd.DataFrame.from_dict(data["runs"]) -df_experiments = pd.DataFrame.from_dict(data["experiments"]) \ No newline at end of file + if not os.path.isfile(self.source_json_file): + log.error("json data file %s does not exist ", self.source_json_file) + stderr.print(f"json data file {self.source_json_file} does not exist") + sys.exit(1) + with open(self.source_json_file, "r") as fh: + self.json_data = json.loads(fh.read()) + + def upload_files_to_ena(self): + """Create the required files and upload to ENA""" + # df = {} + + # df_study = pd.DataFrame.from_dict(data["study"]) + # df_samples = pd.DataFrame.from_dict(data["samples"]) + # df_runs = pd.DataFrame.from_dict(data["runs"]) + # df_experiments = pd.DataFrame.from_dict(data["experiments"]) From 25aea38da1a64f18e549dc61b2ffde5ad4e98eec Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 19 Mar 2022 22:15:02 +0100 Subject: [PATCH 0177/1454] working on the mapping from ena data to the df required by ena_upload package --- relecov_tools/__main__.py | 24 ++- relecov_tools/conf/configuration.json | 14 +- relecov_tools/ena_upload.py | 89 ++++++++-- .../schema/mapping_ena_to_upload_ena.json | 166 ++++++++++++++++++ .../schema/mapping_metadata_to_json.json | 4 +- relecov_tools/utils.py | 14 +- 6 files changed, 266 insertions(+), 45 deletions(-) create mode 100644 relecov_tools/schema/mapping_ena_to_upload_ena.json diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index b7448989..0378da81 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -11,7 +11,7 @@ import relecov_tools.utils import relecov_tools.read_metadata import relecov_tools.sftp_handled -import relecov_tools.create_xml +import relecov_tools.ena_upload import relecov_tools.validation_json import relecov_tools.conversion_schema @@ -158,7 +158,7 @@ def list(keywords, sort, json, show_archived): "--conf_file", help="Configuration file Create Nextflow command with params (no params file)", ) -def sftp(user, password, conf_file): +def download_sftp(user, password, conf_file): """Download files located in sftp server.""" sftp_connection = relecov_tools.sftp.SftpHandle(user, password, conf_file) sftp_connection.download_from_sftp() @@ -240,18 +240,24 @@ def mapped_schema( @relecov_tools_cli.command(help_priority=6) -@click.option("-s", "--source_json", help="Where the validated json is") -@click.option("-o", "--output_path", help="Output folder for the xml generated files") +@click.option("-u", "--user", help="User name for login to sftp server") +@click.option("-p", "--password", help="password for the user to login") +@click.option("-e", "--ena_json", help="Where the validated json is") +@click.option("-s", "--study", help="study/project name to include in xml files") @click.option( "-a", "--action", - type=click.Choice(["ADD", "MODIFY"], case_sensitive=True), - help="Select one of the options ADD or MODIFY", + type=click.Choice(["add", "modify", "cancel", "release"], case_sensitive=False), + help="Select one of the available options", ) -def upload_to_ena(source_json, output_path, action): +@click.option("--dev/--production", default=True) +@click.option("-o", "--output_path", help="Output folder for the xml generated files") +def upload_to_ena(user, password, ena_json, dev, study, action, output_path): """Parsed data to create xml files to upload to ENA""" - upload_ena = relecov_tools.ena_upload.EnaUpload(source_json, output_path, action) - upload_ena.generate_xml() + upload_ena = relecov_tools.ena_upload.EnaUpload( + user, password, ena_json, dev, study, action, output_path + ) + upload_ena.upload_files_to_ena() if __name__ == "__main__": diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 9fc52356..44ec39d9 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -4,8 +4,8 @@ "ena_schema": "ena_schema.json", "gisaid_schema": "gisaid_schema.json" }, - "mapping_metadata_json": "mapping_metadata_json_v01.json", - "additional_metadata": "additional_metadata_v01.json", + "mapping_metadata_json": "mapping_metadata_json.json", + "mapping_upload_ena": "mapping_ena_to_upload_ena.json", "sftp_connection": { "sftp_server": "sftprelecov.isciii.es", "sftp_port": "50122" @@ -16,13 +16,9 @@ "fastq.gz", "fasta" ], - "project_relecov_xml": { + "study": { "alias": "RELECOV", - "TITLE": "Example project for ENA submission RELECOV", - "DESCRIPTION": "This study was created as part of an ENA submissions example RELECOV" - }, - "fixed_data": { - "tax_id": "2697049", - "scientific_name": "Severe acute respiratory syndrome coronavirus 2" + "title": "Example project for ENA submission RELECOV", + "study_type": "This study was created as part of an ENA submissions example RELECOV" } } diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 7eb3053b..34c43657 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -2,12 +2,11 @@ import logging import rich.console import json - -# import pandas as pd +import pandas as pd import sys - -# import ena_upload +from ena_upload import ena_upload import relecov_tools.utils +from relecov_tools.config_json import ConfigJson log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -19,30 +18,94 @@ class EnaUpload: - def __init__(self, source_json=None, output_path=None, action=None): + def __init__( + self, + user=None, + passwd=None, + source_json=None, + dev=None, + project=None, + action=None, + output_path=None, + ): + if user is None: + self.user = relecov_tools.utils.prompt_text( + msg="Enter your username defined in ENA" + ) + else: + self.user = user + if passwd is None: + self.passwd = relecov_tools.utils.prompt_password( + msg="Enter your password to ENA" + ) + else: + self.passwd = passwd if source_json is None: - self.source_json_file = relecov_tools.utils.prompt_source_path() + self.source_json_file = relecov_tools.utils.prompt_path( + msg="Select the ENA json file to upload" + ) else: self.source_json_file = source_json - if output_path is None: - self.output_path = relecov_tools.utils.prompt_destination_path() + if dev is None: + self.dev = relecov_tools.utils.prompt_yn_question( + msg="Do you want to test upload data?" + ) else: - self.output_path = output_path + self.dev = dev + if project is None: + self.project = None + else: + self.project = project if action is None: - self.action = "ADD" + self.action = relecov_tools.utils.prompt_selection( + msg="Select the action to upload to ENA", + choices=["add", "modify", "cancel", "release"], + ) else: - self.action = action + self.action = action.upper() + if output_path is None: + self.output_path = relecov_tools.utils.prompt_path( + msg="Select the folder to store the xml files" + ) + else: + self.output_path = output_path + if not os.path.isfile(self.source_json_file): log.error("json data file %s does not exist ", self.source_json_file) - stderr.print(f"json data file {self.source_json_file} does not exist") + stderr.print(f"[red]json data file {self.source_json_file} does not exist") sys.exit(1) with open(self.source_json_file, "r") as fh: self.json_data = json.loads(fh.read()) + def convert_input_json_to_ena(self): + """Convert json to dataframe required by ena-upload-cli package""" + schema_dataframe = {} + config_json = ConfigJson() + map_to_upload = config_json.get_configuration("mapping_upload_ena") + map_file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), "schema", map_to_upload + ) + fh = open(map_file) + map_json = json.load(fh) + fh.close() + + for xml_file in map_json["xml_files"]: + if self.project is not None and xml_file in self.project: + pass + elif config_json.get_configuration(xml_file): + df = pd.DataFrame.from_dict( + config_json.get_configuration(xml_file), orient="index" + ) + else: + pass + df = ena_upload.check_columns(df, xml_file, self.action, self.dev, False) + schema_dataframe[xml_file] = df + return schema_dataframe + def upload_files_to_ena(self): """Create the required files and upload to ENA""" # df = {} - + self.convert_input_json_to_ena() # df_study = pd.DataFrame.from_dict(data["study"]) # df_samples = pd.DataFrame.from_dict(data["samples"]) # df_runs = pd.DataFrame.from_dict(data["runs"]) diff --git a/relecov_tools/schema/mapping_ena_to_upload_ena.json b/relecov_tools/schema/mapping_ena_to_upload_ena.json new file mode 100644 index 00000000..a195e6e1 --- /dev/null +++ b/relecov_tools/schema/mapping_ena_to_upload_ena.json @@ -0,0 +1,166 @@ +{ + "xml_files":["study","runs","samples","experiment"], + "study": { + "alias": "", + "title": "", + "study_type": "", + "study_abstract": "", + "pubmed_id": "" + }, + "runs": { + "alias": [ + "run_alias_1a", + "run_alias_1a", + "run_alias_3c" + ], + "experiment_alias": [ + "experiment_alias_7a", + "experiment_alias_7a", + "experiment_alias_9c" + ], + "file_name": [ + "ENA_TEST2.R1.fastq.gz", + "ENA_TEST2.R2.fastq.gz", + "ENA_TEST1.R1.fastq.gz" + ], + "file_type": [ + "fastq", + "fastq", + "fastq" + ], + "file_checksum": [ + "3e69af1f875fab020aed82f5edbc1f03", + "3e69af1f875fab020aed82f5edbc1f03", + "3e69af1f875fab020aed82f5edbc1f03" + ] + }, + "samples": { + "alias": [ + "sample_alias_4", + "sample_alias_5" + ], + "title": [ + "sample_title_2", + "sample_title_3" + ], + "taxon_id": [ + "2697049", + "2697049" + ], + "sample_description": [ + "sample_description_1", + "sample_description_2" + ], + "collection date": [ + "2020-10-11", + "2008-01-24" + ], + "geographic location (country and/or sea)": [ + "Argentina", + "Belgium" + ], + "host common name": [ + "host_common_name_1", + "host_common_name_2" + ], + "host subject id": [ + "host_subject_id_1", + "host_subject_id_2" + ], + "host health state": [ + "diseased", + "restricted access" + ], + "host sex": [ + "male", + "female" + ], + "host scientific name": [ + "host_scientific_name_1", + "host_scientific_name_2" + ], + "collector name": [ + "collector_name_1", + "collector_name_2" + ], + "collecting institution": [ + "collecting_institution_1", + "collecting_institution_2" + ], + "isolate": [ + "isolate_1", + "isolate_2" + ] + }, + + "experiments": { + "alias": [ + "experiment_alias_7a", + "experiment_alias_8b", + "experiment_alias_9c" + ], + "title": [ + "experiment_title_1", + "experiment_title_2", + "experiment_title_3" + ], + "study_alias": [ + "study_alias_4", + "study_alias_5", + "study_alias_5" + ], + "sample_alias": [ + "study_alias_4", + "study_alias_5", + "study_alias_5" + ], + "design_description": [ + "design_description_1", + "design_description_2", + "design_description_3" + ], + "library_name": [ + "library_name_1", + "library_name_2", + "library_name_3" + ], + "library_strategy": [ + "WGA", + "RNA-Seq", + "RNA-Seq" + ], + "library_source": [ + "GENOMIC", + "TRANSCRIPTOMIC", + "TRANSCRIPTOMIC" + ], + "library_selection": [ + "RANDOM", + "repeat fractionation", + "repeat fractionation" + ], + "library_layout": [ + "paired", + "single", + "single" + ], + "insert_size": [ + "250","None","None" + ], + "library_construction_protocol": [ + "library_construction_protocol_1", + "library_construction_protocol_2", + "library_construction_protocol_2" + ], + "platform": [ + "LS454", + "illumina", + "illumina" + ], + "instrument_model": [ + "454 GS 20", + "Illumina Genome Analyzer", + "Illumina Genome Analyzer" + ] + } +} diff --git a/relecov_tools/schema/mapping_metadata_to_json.json b/relecov_tools/schema/mapping_metadata_to_json.json index 301e0967..dd509eb5 100644 --- a/relecov_tools/schema/mapping_metadata_to_json.json +++ b/relecov_tools/schema/mapping_metadata_to_json.json @@ -88,6 +88,8 @@ "host_disease":"COVID-19", "sequence_file_R1_fastq": "", "sequence_file_R2_fastq": "", - "type" : "betacoronavirus" + "type" : "betacoronavirus", + "tax_id": "2697049", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2" } } diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 8a08f4c8..0c40930c 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -67,23 +67,11 @@ def prompt_password(msg): def prompt_tmp_dir_path(): - stderr.print("Temporal directory destination to execute sercive") + stderr.print("Temporal directory destination to execute service") source = questionary.path("Source path").unsafe_ask() return source -def prompt_source_path(): - stderr.print("Directory containing files cd to transfer") - source = questionary.path("Source path").unsafe_ask() - return source - - -def prompt_destination_path(): - stderr.print("Directory to which the files will be transfered") - destination = questionary.path("Destination path").unsafe_ask() - return destination - - def prompt_selection(msg, choices): selection = questionary.select(msg, choices=choices).unsafe_ask() return selection From 7624a005b74af9488a09acfbf9a7bdc9da053b09 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 21 Mar 2022 19:16:34 +0100 Subject: [PATCH 0178/1454] working on sftp md5 --- relecov_tools/sftp_handled.py | 9 ++++++--- relecov_tools/utils.py | 14 ++++++++++++++ 2 files changed, 20 insertions(+), 3 deletions(-) diff --git a/relecov_tools/sftp_handled.py b/relecov_tools/sftp_handled.py index 8c590847..0f25e044 100644 --- a/relecov_tools/sftp_handled.py +++ b/relecov_tools/sftp_handled.py @@ -57,7 +57,7 @@ def __init__(self, user=None, passwd=None, conf_file=None): self.passwd = config["password"] except KeyError as e: log.error("Invalid configuration file %s", e) - stderr.print("[red] Invalide configuration file " + e + "!") + stderr.print("[red] Invalide configuration file {e} !") sys.exit(1) if user is None: self.user = relecov_tools.utils.text(msg="Enter the userid") @@ -70,7 +70,7 @@ def __init__(self, user=None, passwd=None, conf_file=None): self.client = None def open_connection(self): - """Stablish sftp connection""" + """Establish sftp connection""" self.client = paramiko.SSHClient() self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) self.client.connect( @@ -146,7 +146,7 @@ def get_files_from_sftp_folder(self, folder, files_list): ) except FileNotFoundError as e: log.error("Unable to fetch file %s ", e) - result_data["unable_to_fetch"].append(file_list) + result_data["Unable_to_fetch"].append(file_list) continue result_data["fetched_files"].append(os.path.basename(file_list)) @@ -225,10 +225,13 @@ def download_from_sftp(self): sys.exit(1) os.chdir(self.storage_local_folder) if not self.open_connection(): + log.error("Unable to establish connection towards sftp server") + stderr.print("[red] Unable to establish sftp connection") sys.exit(1) root_directory_list = self.list_folders(".") if not root_directory_list: + log.error("There is no folders under root directory") sys.exit(1) folders_to_download = {} # create_main_folders(root_directory_list) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 0c40930c..40037efd 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -20,6 +20,20 @@ def file_exists(file_to_check): return False +def get_md5_from_local_folder(local_folder, file_list): + """Fetch the md5 values for each file in the file list""" + md5_results = {} + for file_name in file_list: + f_name, f_ext = os.path.splitext(file_name) + if f_ext.lowercase() == ".md5": + file_md5_path = os.path.join(local_folder, file_name) + # file_origin_path = os + fh = open(file_path, "r") + md5_results[file_name] + if file_exists(file_path): + pass + + def calculate_md5(files_list): """Calculate the md5 value for the list of files""" block_size = 2**20 From 54d6c55dfac23cbccc2aa694b14ba2e137d484c4 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 22 Mar 2022 18:01:20 +0100 Subject: [PATCH 0179/1454] hal of the changes in the schema. --- relecov_tools/schema/ena_schema.json | 14 +- relecov_tools/schema/gisaid_schema.json | 4 +- relecov_tools/schema/phage_plus_schema.json | 531 ++++++++++++++++++-- relecov_tools/schema/phage_schema.json | 9 +- 4 files changed, 522 insertions(+), 36 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 541dc9f6..c74714a8 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -40,6 +40,16 @@ "description": "Name of the institution to which the person collecting the specimen belongs. Format: Institute Name, Institute Address", "label": "Originating Laboratory" }, + "collector_name": { + "examples": [ + "John Smith" + ], + "ontology": "NCIT:C164471", + "type": "string", + "description": "Name of the person who collected the specimen", + "clasification": "Sample collection and processing", + "label": "Collector name" + }, "collection_date": { "examples": [ "3/19/2020" @@ -381,7 +391,7 @@ "label": "Geo Loc Longitude" }, "isolate": { - "ontology": "GENEPIO:0001644", + "ontology": "GENEPIO:0001123", "type": "string", "description": "Identifier of the specific isolate.", "examples": [ @@ -543,7 +553,7 @@ "examples": [ "e.g. #131" ], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO:0001398", "type": "string", "description": "a unique identifier by which each subject can be referred to, de-identified.", "clasification": "Host information", diff --git a/relecov_tools/schema/gisaid_schema.json b/relecov_tools/schema/gisaid_schema.json index 08ad14d9..8aae7cf1 100644 --- a/relecov_tools/schema/gisaid_schema.json +++ b/relecov_tools/schema/gisaid_schema.json @@ -49,11 +49,11 @@ "examples": [ "" ], - "ontology": "0", + "ontology": "NCIT:C54269", "type": "string", "description": "", "clasification": "enter your GISAID-Username", - "label": "GISAID Username" + "label": "GISAID Id" }, "originating_lab": { "examples": [ diff --git a/relecov_tools/schema/phage_plus_schema.json b/relecov_tools/schema/phage_plus_schema.json index ed7382aa..ef7df4c3 100644 --- a/relecov_tools/schema/phage_plus_schema.json +++ b/relecov_tools/schema/phage_plus_schema.json @@ -26,6 +26,16 @@ "clasification": "Database Identifiers", "label": "Collecting Sample id" }, + "sample_description": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001156", + "type": "string", + "description": "Free text description of the sample.", + "clasification": "Sample collection and processing", + "label": "Sample Description" + }, "collecting_institution": { "examples": [ "Public Health Agency of Canada" @@ -41,7 +51,8 @@ ], "ontology": "GENEPIO:0001159", "type": "string", - "description": "The name of the agency that generated the sequence." + "description": "The name of the agency that generated the sequence.", + "label": "Submitting Institution" }, "sample_collection_date": { "examples": [ @@ -50,7 +61,18 @@ "ontology": "GENEPIO:0001174", "type": "string", "description": "The date on which the sample was collected.", - "format": "date" + "format": "date", + "label": "Sample Collection Date" + }, + "host_subject_id": { + "examples": [ + "e.g. #131" + ], + "ontology": "GENEPIO:0001398", + "type": "string", + "description": "a unique identifier by which each subject can be referred to, de-identified.", + "clasification": "Host information", + "label": "Host Subject Id" }, "geo_loc_country": { "Enums": [ @@ -338,7 +360,7 @@ "South Africa [GAZ:00001094]" ], "classification": "Sample collection and processing", - "label": "Geo Loc Autonomic Country" + "label": "Country" }, "geo_loc_state": { "examples": [ @@ -348,7 +370,7 @@ "type": "string", "description": "The state/province/territory of origin of the sample.", "classification": "Sample collection and processing", - "label": "Geo Loc Autonomic Community" + "label": "Autonomic Community" }, "organism": { "Enums": [ @@ -369,15 +391,59 @@ "classification": "Sample collection and processing", "label": "Organism" }, - "isolate": { + "symptom_onset_date": { "examples": [ - "SARS-CoV-2/human/USA/CA-CDPH-001/2020" + "16/03/2020" ], - "ontology": "GENEPIO:0001644", + "ontology": "GENEPIO:0001399", "type": "string", - "description": "Identifier of the specific isolate.", - "clasification": "Sample collection and processing", - "label": "Isolate" + "description": "The date on which the symptoms began or were first noted.", + "format": "date", + "label": "Symptom onset date" + }, + "host_health_state": { + "Enums": [ + "Asymptomatic [NCIT:C3833]", + "Deceased [NCIT:C28554]", + "Healthy [NCIT:C115935]", + "Recovered [NCIT:C49498]", + "Symptomatic [NCIT:C25269]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001388", + "type": "string", + "description": "Health status of the host at the time of sample collection.", + "examples": [ + "Asymptomatic [NCIT:C3833]" + ], + "label": "Host health state" + }, + "host_health_status_details": { + "Enums": [ + "Hospitalized [NCIT:C25179]", + "Hospitalized (Non-ICU) [GENEPIO:0100045]", + "Hospitalized (ICU) [GENEPIO:0100046]", + "Mechanical Ventilation [NCIT:C70909]", + "Medically Isolated [GENEPIO:0100047]", + "Medically Isolated (Negative Pressure) [GENEPIO:0100048]", + "Self-quarantining [NCIT:C173768]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001389", + "type": "string", + "description": "Further details pertaining to the health or disease status of the host at time of collection.", + "examples": [ + "Hospitalized (ICU) [GENEPIO:0100046]" + ], + "label": "Host health status details" }, "host_scientific_name": { "Enums": [ @@ -426,7 +492,8 @@ "description": "The name of the disease experienced by the host.", "examples": [ "COVID-19 [MONDO:0100096]" - ] + ], + "host_disease": "Host disease" }, "sequencing_instrument_model": { "Enums": [ @@ -515,7 +582,8 @@ "ontology": "GENEPIO:0001133", "type": "string", "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", - "clasification": "Database Identifiers" + "clasification": "Database Identifiers", + "label": "Bioproject umbrella accession ENA" }, "bioproject_accession_ENA": { "examples": [ @@ -544,7 +612,8 @@ "ontology": "GENEPIO:0001142", "type": "string", "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "clasification": "Database Identifiers" + "clasification": "Database Identifiers", + "label": "SRA Accession" }, "genBank/ENA/DDBJ_accession": { "examples": [ @@ -556,7 +625,7 @@ "clasification": "Database Identifiers", "label": "GenBank/ENA/DDBJ accession" }, - "gisaid_accession": { + "GISAID_accession": { "examples": [ "EPI_ISL_123456" ], @@ -564,7 +633,7 @@ "type": "string", "description": "The GISAID accession number assigned to the sequence.", "clasification": "Database Identifiers", - "label": "GISAID Virus Name" + "label": "GISAID Accession" }, "virus_name": { "examples": [ @@ -607,7 +676,7 @@ "examples": [ "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" ], - "ontology": "0", + "ontology": "GENEPIO:0001167", "type": "string", "description": "The mailing address of the agency submitting the sequence.", "clasification": "Sample collection and processing" @@ -620,7 +689,8 @@ "type": "string", "description": "The date on which the sample was received.", "format": "date", - "clasification": "Sample collection and processing" + "clasification": "Sample collection and processing", + "label": "Sample Received Date" }, "shipping_date": { "examples": [ @@ -654,6 +724,22 @@ "clasification": "Sample collection and processing", "label": "Biological Sample Storage Condition" }, + "culture_collection": { + "ontology": "GENEPIO:0100284", + "type": "string", + "description": "The name of the source collection and unique culture identifier. ", + "examples": [ + "/culture_collection=\"ATCC:26370\"" + ], + "label": "Culture collection" + }, + "treatment": { + "ontology": "OGMS:0000090", + "type": "string", + "description": "Include drug name, dosage", + "examples": [], + "label": "Treatment" + }, "host_age": { "ontology": "GENEPIO:0001392", "anyOf": [ @@ -681,12 +767,13 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "GENEPIO:0001393", + "ontology": "NCIT:C50400", "type": "string", "description": "The units used to measure the host's age.", "examples": [ "years [UO:0000036]" - ] + ], + "label": "Host Age unit" }, "host_age_bin": { "Enums": [ @@ -745,7 +832,7 @@ "type": "string", "description": "The county/region of origin of the sample.", "clasification": "Sample collection and processing", - "label": "Geo Loc Province" + "label": "Province" }, "geo_loc_city": { "examples": [ @@ -755,7 +842,7 @@ "type": "string", "description": "The city of origin of the sample.", "clasification": "Sample collection and processing", - "label": "Geo Loc City" + "label": "City" }, "geo_loc_latitude": { "examples": [ @@ -801,7 +888,7 @@ "Blood [UBERON:0000178]" ], "classification": "Sample collection and processing", - "label": "Organism Substance" + "label": "Specimen source" }, "anatomical_part": { "Enums": [ @@ -835,14 +922,14 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "GENEPIO:0001214", + "ontology": "GENEPIO:0001211", "type": "string", "description": "An anatomical part of an organism e.g. oropharynx. ", "examples": [ "Nasopharynx (NP) [UBERON:0001728]" ], "classification": "Sample collection and processing", - "label": "Anatomical Structure" + "label": "Specimen source" }, "body_product": { "Enums": [ @@ -955,7 +1042,25 @@ "Hospital [ENVO:00002173]" ], "classification": "Sample collection and processing", - "label": "Anthropogenic Geographic Feature" + "label": "Environmental System" + }, + "sample_collected_in_quarantine": { + "Enums": [ + "Yes [NCIT:C49488]", + "No [NCIT:C49487]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0100277", + "type": "string", + "description": "Whether the sample was collected from an individual in quarantine.", + "examples": [ + "Yes [NCIT:C49488]" + ], + "label": "Sample collected in quarantine" }, "collection_device": { "Enums": [ @@ -1124,20 +1229,29 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "GENEPIO:0001266", + "ontology": "GENEPIO_0001965", "type": "string", "description": "The biomaterial extracted from samples for the purpose of sequencing.", "examples": [ "RNA (Total) [OBI:0000895]" ], "classification": "Sample collection and processing", - "label": "Biomaterial Extracted" + "label": "Source material" + }, + "data_abstraction_details": { + "ontology": "GENEPIO:0100278", + "type": "string", + "description": "A description of how any data elements were altered to preserve patient privacy.", + "examples": [ + "Jitter added to publicly shared collection dates to prevent re-identifiability." + ], + "label": "Data abstraction details" }, "tax_id": { "examples": [ "probably 2697049 in all cases" ], - "ontology": "GENEPIO_0001800", + "ontology": "GENEPIO_0001724", "type": "string", "description": "The NCBITaxon identifier for the organism being sequenced.", "clasification": "Sample collection and processing", @@ -1183,6 +1297,293 @@ "classification": "Host information", "label": "Host Common Name" }, + "host_residence_country": { + "Enums": [ + "Afghanistan [GAZ:00006882]", + "Albania [GAZ:00002953]", + "Algeria [GAZ:00000563]", + "American Samoa [GAZ:00003957]", + "Andorra [GAZ:00002948]", + "Angola [GAZ:00001095]", + "Anguilla [GAZ:00009159]", + "Antarctica [GAZ:00000462]", + "Antigua and Barbuda [GAZ:00006883]", + "Argentina [GAZ:00002928]", + "Armenia [GAZ:00004094]", + "Aruba [GAZ:00004025]", + "Ashmore and Cartier Islands [GAZ:00005901]", + "Australia [GAZ:00000463]", + "Austria [GAZ:00002942]", + "Azerbaijan [GAZ:00004941]", + "Bahamas [GAZ:00002733]", + "Bahrain [GAZ:00005281]", + "Baker Island [GAZ:00007117]", + "Bangladesh [GAZ:00003750]", + "Barbados [GAZ:00001251]", + "Bassas da India [GAZ:00005810]", + "Belarus [GAZ:00006886]", + "Belgium [GAZ:00002938]", + "Belize [GAZ:00002934]", + "Benin [GAZ:00000904]", + "Bermuda [GAZ:00001264]", + "Bhutan [GAZ:00003920]", + "Bolivia [GAZ:00002511]", + "Borneo [GAZ:00025355]", + "Bosnia and Herzegovina [GAZ:00006887]", + "Botswana [GAZ:00001097]", + "Bouvet Island [GAZ:00001453]", + "Brazil [GAZ:00002828]", + "British Virgin Islands [GAZ:00003961]", + "Brunei [GAZ:00003901]", + "Bulgaria [GAZ:00002950]", + "Burkina Faso [GAZ:00000905]", + "Burundi [GAZ:00001090]", + "Cambodia [GAZ:00006888]", + "Cameroon [GAZ:00001093]", + "Canada [GAZ:00002560]", + "Cape Verde [GAZ:00001227]", + "Cayman Islands [GAZ:00003986]", + "Central African Republic [GAZ:00001089]", + "Chad [GAZ:00000586]", + "Chile [GAZ:00002825]", + "China [GAZ:00002845]", + "Christmas Island [GAZ:00005915]", + "Clipperton Island [GAZ:00005838]", + "Cocos Islands [GAZ:00009721]", + "Colombia [GAZ:00002929]", + "Comoros [GAZ:00005820]", + "Cook Islands [GAZ:00053798]", + "Coral Sea Islands [GAZ:00005917]", + "Costa Rica [GAZ:00002901]", + "Cote d'Ivoire [GAZ:00000906]", + "Croatia [GAZ:00002719]", + "Cuba [GAZ:00003762]", + "Curacao [GAZ:00012582]", + "Cyprus [GAZ:00004006]", + "Czech Republic [GAZ:00002954]", + "Democratic Republic of the Congo [GAZ:00001086]", + "Denmark [GAZ:00005852]", + "Djibouti [GAZ:00000582]", + "Dominica [GAZ:00006890]", + "Dominican Republic [GAZ:00003952]", + "Ecuador [GAZ:00002912]", + "Egypt [GAZ:00003934]", + "El Salvador [GAZ:00002935]", + "Equatorial Guinea [GAZ:00001091]", + "Eritrea [GAZ:00000581]", + "Estonia [GAZ:00002959]", + "Eswatini [GAZ:00001099]", + "Ethiopia [GAZ:00000567]", + "Europa Island [GAZ:00005811]", + "Falkland Islands (Islas Malvinas) [GAZ:00001412]", + "Faroe Islands [GAZ:00059206]", + "Fiji [GAZ:00006891]", + "Finland [GAZ:00002937]", + "France [GAZ:00003940]", + "French Guiana [GAZ:00002516]", + "French Polynesia [GAZ:00002918]", + "French Southern and Antarctic Lands [GAZ:00003753]", + "Gabon [GAZ:00001092]", + "Gambia [GAZ:00000907]", + "Gaza Strip [GAZ:00009571]", + "Georgia [GAZ:00004942]", + "Germany [GAZ:00002646]", + "Ghana [GAZ:00000908]", + "Gibraltar [GAZ:00003987]", + "Glorioso Islands [GAZ:00005808]", + "Greece [GAZ:00002945]", + "Greenland [GAZ:00001507]", + "Grenada [GAZ:02000573]", + "Guadeloupe [GAZ:00067142]", + "Guam [GAZ:00003706]", + "Guatemala [GAZ:00002936]", + "Guernsey [GAZ:00001550]", + "Guinea [GAZ:00000909]", + "Guinea-Bissau [GAZ:00000910]", + "Guyana [GAZ:00002522]", + "Haiti [GAZ:00003953]", + "Heard Island and McDonald Islands [GAZ:00009718]", + "Honduras [GAZ:00002894]", + "Hong Kong [GAZ:00003203]", + "Howland Island [GAZ:00007120]", + "Hungary [GAZ:00002952]", + "Iceland [GAZ:00000843]", + "India [GAZ:00002839]", + "Indonesia [GAZ:00003727]", + "Iran [GAZ:00004474]", + "Iraq [GAZ:00004483]", + "Ireland [GAZ:00002943]", + "Isle of Man [GAZ:00052477]", + "Israel [GAZ:00002476]", + "Italy [GAZ:00002650]", + "Jamaica [GAZ:00003781]", + "Jan Mayen [GAZ:00005853]", + "Japan [GAZ:00002747]", + "Jarvis Island [GAZ:00007118]", + "Jersey [GAZ:00001551]", + "Johnston Atoll [GAZ:00007114]", + "Jordan [GAZ:00002473]", + "Juan de Nova Island [GAZ:00005809]", + "Kazakhstan [GAZ:00004999]", + "Kenya [GAZ:00001101]", + "Kerguelen Archipelago [GAZ:00005682]", + "Kingman Reef [GAZ:00007116]", + "Kiribati [GAZ:00006894]", + "Kosovo [GAZ:00011337]", + "Kuwait [GAZ:00005285]", + "Kyrgyzstan [GAZ:00006893]", + "Laos [GAZ:00006889]", + "Latvia [GAZ:00002958]", + "Lebanon [GAZ:00002478]", + "Lesotho [GAZ:00001098]", + "Liberia [GAZ:00000911]", + "Libya [GAZ:00000566]", + "Liechtenstein [GAZ:00003858]", + "Line Islands [GAZ:00007144]", + "Lithuania [GAZ:00002960]", + "Luxembourg [GAZ:00002947]", + "Macau [GAZ:00003202]", + "Madagascar [GAZ:00001108]", + "Malawi [GAZ:00001105]", + "Malaysia [GAZ:00003902]", + "Maldives [GAZ:00006924]", + "Mali [GAZ:00000584]", + "Malta [GAZ:00004017]", + "Marshall Islands [GAZ:00007161]", + "Martinique [GAZ:00067143]", + "Mauritania [GAZ:00000583]", + "Mauritius [GAZ:00003745]", + "Mayotte [GAZ:00003943]", + "Mexico [GAZ:00002852]", + "Micronesia [GAZ:00005862]", + "Midway Islands [GAZ:00007112]", + "Moldova [GAZ:00003897]", + "Monaco [GAZ:00003857]", + "Mongolia [GAZ:00008744]", + "Montenegro [GAZ:00006898]", + "Montserrat [GAZ:00003988]", + "Morocco [GAZ:00000565]", + "Mozambique [GAZ:00001100]", + "Myanmar [GAZ:00006899]", + "Namibia [GAZ:00001096]", + "Nauru [GAZ:00006900]", + "Navassa Island [GAZ:00007119]", + "Nepal [GAZ:00004399]", + "Netherlands [GAZ:00002946]", + "New Caledonia [GAZ:00005206]", + "New Zealand [GAZ:00000469]", + "Nicaragua [GAZ:00002978]", + "Niger [GAZ:00000585]", + "Nigeria [GAZ:00000912]", + "Niue [GAZ:00006902]", + "Norfolk Island [GAZ:00005908]", + "North Korea [GAZ:00002801]", + "North Macedonia [GAZ:00006895]", + "North Sea [GAZ:00002284]", + "Northern Mariana Islands [GAZ:00003958]", + "Norway [GAZ:00002699]", + "Oman [GAZ:00005283]", + "Pakistan [GAZ:00005246]", + "Palau [GAZ:00006905]", + "Panama [GAZ:00002892]", + "Papua New Guinea [GAZ:00003922]", + "Paracel Islands [GAZ:00010832]", + "Paraguay [GAZ:00002933]", + "Peru [GAZ:00002932]", + "Philippines [GAZ:00004525]", + "Pitcairn Islands [GAZ:00005867]", + "Poland [GAZ:00002939]", + "Portugal [GAZ:00004126]", + "Puerto Rico [GAZ:00006935]", + "Qatar [GAZ:00005286]", + "Republic of the Congo [GAZ:00001088]", + "Reunion [GAZ:00003945]", + "Romania [GAZ:00002951]", + "Ross Sea [GAZ:00023304]", + "Russia [GAZ:00002721]", + "Rwanda [GAZ:00001087]", + "Saint Helena [GAZ:00000849]", + "Saint Kitts and Nevis [GAZ:00006906]", + "Saint Lucia [GAZ:00006909]", + "Saint Pierre and Miquelon [GAZ:00003942]", + "Saint Martin [GAZ:00005841]", + "Saint Vincent and the Grenadines [GAZ:02000565]", + "Samoa [GAZ:00006910]", + "San Marino [GAZ:00003102]", + "Sao Tome and Principe [GAZ:00006927]", + "Saudi Arabia [GAZ:00005279]", + "Senegal [GAZ:00000913]", + "Serbia [GAZ:00002957]", + "Seychelles [GAZ:00006922]", + "Sierra Leone [GAZ:00000914]", + "Singapore [GAZ:00003923]", + "Sint Maarten [GAZ:00012579]", + "Slovakia [GAZ:00002956]", + "Slovenia [GAZ:00002955]", + "Solomon Islands [GAZ:00005275]", + "Somalia [GAZ:00001104]", + "South Africa [GAZ:00001094]", + "South Georgia and the South Sandwich Islands [GAZ:00003990]", + "South Korea [GAZ:00002802]", + "South Sudan [GAZ:00233439]", + "Spain [GAZ:00003936]", + "Spratly Islands [GAZ:00010831]", + "Sri Lanka [GAZ:00003924]", + "State of Palestine [GAZ:00002475]", + "Sudan [GAZ:00000560]", + "Suriname [GAZ:00002525]", + "Svalbard [GAZ:00005396]", + "Swaziland [GAZ:00001099]", + "Sweden [GAZ:00002729]", + "Switzerland [GAZ:00002941]", + "Syria [GAZ:00002474]", + "Taiwan [GAZ:00005341]", + "Tajikistan [GAZ:00006912]", + "Tanzania [GAZ:00001103]", + "Thailand [GAZ:00003744]", + "Timor-Leste [GAZ:00006913]", + "Togo [GAZ:00000915]", + "Tokelau [GAZ:00260188]", + "Tonga [GAZ:00006916]", + "Trinidad and Tobago [GAZ:00003767]", + "Tromelin Island [GAZ:00005812]", + "Tunisia [GAZ:00000562]", + "Turkey [GAZ:00000558]", + "Turkmenistan [GAZ:00005018]", + "Turks and Caicos Islands [GAZ:00003955]", + "Tuvalu [GAZ:00009715]", + "USA [GAZ:00002459]", + "Uganda [GAZ:00001102]", + "Ukraine [GAZ:00002724]", + "United Arab Emirates [GAZ:00005282]", + "United Kingdom [GAZ:00002637]", + "Uruguay [GAZ:00002930]", + "Uzbekistan [GAZ:00004979]", + "Vanuatu [GAZ:00006918]", + "Venezuela [GAZ:00002931]", + "Viet Nam [GAZ:00003756]", + "Virgin Islands [GAZ:00003959]", + "Wake Island [GAZ:00007111]", + "Wallis and Futuna [GAZ:00007191]", + "West Bank [GAZ:00009572]", + "Western Sahara [GAZ:00000564]", + "Yemen [GAZ:00005284]", + "Zambia [GAZ:00001107]", + "Zimbabwe [GAZ:00001106]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001396", + "type": "string", + "description": "The country where the host resides.", + "examples": [ + "South Africa [GAZ:00001094]" + ], + "label": "Host residence country" + }, "outbreak": { "examples": [ "Date, Location e.g. type of gathering, Family cluster, etc." @@ -1203,6 +1604,15 @@ "clasification": "Host information", "label": "Additional Host Information" }, + "host_ethnicity": { + "ontology": "GECKO:0000061", + "type": "string", + "description": "The self-identified ethnicity(ies) of the host.", + "examples": [ + "Indigenous, European" + ], + "label": "Host ethnicity" + }, "purpose_of_sequencing": { "Enums": [ "Baseline surveillance (random sampling) [GENEPIO:0100005]", @@ -1244,6 +1654,36 @@ "classification": "Sequencing", "label": "Purpose of Sequencing" }, + "purpose_of_sampling": { + "Enums": [ + "Cluster/Outbreak Investigation [GENEPIO:0100001]", + "Diagnostic Testing [GENEPIO:0100002]", + "Research [GENEPIO:0100003]", + "Protocol Testing [GENEPIO:0100024]", + "Surveillance [GENEPIO:0100004]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "NCIT_C146997", + "type": "string", + "description": "The reason that the sample was collected.", + "examples": [ + "Diagnostic Testing [GENEPIO:0100002]" + ], + "label": "Purpose of Sampling" + }, + "purpose_of_sampling_details": { + "ontology": "GENEPIO:0001200", + "type": "string", + "description": "Further details pertaining to the reason the sample was collected.", + "examples": [ + "Screening of bat specimens in museum collections." + ], + "label": "Purpose of sampling details" + }, "sequencing_sample_id": { "examples": [ "" @@ -1597,6 +2037,16 @@ "clasification": "Bioinformatics and QC metrics", "label": "Dehosting Method" }, + "personal_protective_equipment": { + "examples": [ + "mask" + ], + "ontology": "NCIT:C173748", + "type": "string", + "description": "Use of personal protective equipment, such as gloves, gowns, during any type of exposure.", + "clasification": "Sample collection and processing", + "label": "Personal protective equipment" + }, "assembly": { "examples": [ "" @@ -1887,6 +2337,15 @@ "clasification": "Bioinformatics and QC metrics", "label": "Commercial/Open-source/both" }, + "sample_plan_name": { + "ontology": "GENEPIO:0100285", + "type": "string", + "description": "The name of the sample plan implemented for sample collection.", + "examples": [ + "CanCOGeN Sampling Strategy 1.0" + ], + "label": "Sample plan name" + }, "preprocessing": { "examples": [ "" @@ -2272,11 +2731,11 @@ "clasification": "Contributor Acknowledgement", "label": "Author Submitter" }, - "submitter": { + "gisaid_id": { "examples": [ "" ], - "ontology": "0", + "ontology": "NCIT:C54269", "type": "string", "description": "", "clasification": "enter your GISAID-Username", @@ -2301,6 +2760,16 @@ "description": "The common name of the organism.", "clasification": "Sample collection and processing" }, + "collector_name": { + "examples": [ + "John Smith" + ], + "ontology": "GENEPIO:0001153", + "type": "string", + "description": "Name of the person who collected the specimen", + "clasification": "Sample collection and processing", + "label": "Originating Laboratory" + }, "library_source": { "Enums": [ "5-methycytidine antibody method [GENPIO:0001941]", @@ -2727,4 +3196,4 @@ "clasification": "Database Identifiers" } } -} +} \ No newline at end of file diff --git a/relecov_tools/schema/phage_schema.json b/relecov_tools/schema/phage_schema.json index 98c96bee..deb1330b 100644 --- a/relecov_tools/schema/phage_schema.json +++ b/relecov_tools/schema/phage_schema.json @@ -1179,6 +1179,13 @@ "CanCOGeN Sampling Strategy 1.0" ] }, + "treatment": { + "ontology": "OGMS:0000090", + "type": "string", + "description": "Include drug name, dosage", + "examples": [], + "label": "Treatment" + }, "prior_sars_cov_2_antiviral_treatment_date": { "examples": [ "28/01/2021" @@ -3524,7 +3531,7 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "GENEPIO:0001198", + "ontology": "NCIT_C146997", "type": "string", "description": "The reason that the sample was collected.", "examples": [ From 67983f88df414e4fdfde75869c371abc4f143642 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 22 Mar 2022 21:19:39 +0100 Subject: [PATCH 0180/1454] include study alias for ENA --- relecov_tools/schema/mapping_metadata_to_json.json | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/mapping_metadata_to_json.json b/relecov_tools/schema/mapping_metadata_to_json.json index dd509eb5..ba891e56 100644 --- a/relecov_tools/schema/mapping_metadata_to_json.json +++ b/relecov_tools/schema/mapping_metadata_to_json.json @@ -84,12 +84,17 @@ "host_scientific_name": { "Human": "Homo sapiens" }, - "tax_id": "", "host_disease":"COVID-19", "sequence_file_R1_fastq": "", "sequence_file_R2_fastq": "", "type" : "betacoronavirus", "tax_id": "2697049", - "scientific_name": "Severe acute respiratory syndrome coronavirus 2" + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "study_alias": "", + "experiment_alias": "", + "run_alias": "", + "study_title": "", + "experiment_title": "", + } } From 0bf01f6078f362d0425dd772df1bf0d367afbd1a Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 22 Mar 2022 21:21:17 +0100 Subject: [PATCH 0181/1454] remove the example information and adding mapping tags --- .../schema/mapping_ena_to_upload_ena.json | 99 +++++-------------- 1 file changed, 27 insertions(+), 72 deletions(-) diff --git a/relecov_tools/schema/mapping_ena_to_upload_ena.json b/relecov_tools/schema/mapping_ena_to_upload_ena.json index a195e6e1..4b663473 100644 --- a/relecov_tools/schema/mapping_ena_to_upload_ena.json +++ b/relecov_tools/schema/mapping_ena_to_upload_ena.json @@ -1,68 +1,34 @@ { "xml_files":["study","runs","samples","experiment"], + "one_loop_in_mapping": ["study"] "study": { - "alias": "", - "title": "", + "study_alias": "alias", + "study_title": "title", "study_type": "", "study_abstract": "", "pubmed_id": "" }, "runs": { - "alias": [ - "run_alias_1a", - "run_alias_1a", - "run_alias_3c" - ], - "experiment_alias": [ - "experiment_alias_7a", - "experiment_alias_7a", - "experiment_alias_9c" - ], - "file_name": [ - "ENA_TEST2.R1.fastq.gz", - "ENA_TEST2.R2.fastq.gz", - "ENA_TEST1.R1.fastq.gz" - ], - "file_type": [ - "fastq", - "fastq", - "fastq" - ], - "file_checksum": [ - "3e69af1f875fab020aed82f5edbc1f03", - "3e69af1f875fab020aed82f5edbc1f03", - "3e69af1f875fab020aed82f5edbc1f03" - ] + "file_name": "", + "experiment_alias": "", + "host_scientific_name": "" + "file_name": "", + "file_type": "", + "file_checksum": "" }, "samples": { - "alias": [ - "sample_alias_4", - "sample_alias_5" - ], - "title": [ - "sample_title_2", - "sample_title_3" - ], - "taxon_id": [ - "2697049", - "2697049" - ], - "sample_description": [ - "sample_description_1", - "sample_description_2" - ], - "collection date": [ - "2020-10-11", - "2008-01-24" - ], - "geographic location (country and/or sea)": [ - "Argentina", - "Belgium" - ], - "host common name": [ - "host_common_name_1", - "host_common_name_2" - ], + "": "alias", + "title": "", + "taxon_id":"" + "sample_description": "", + "scientific_name": "", + "common_name": "", + "host scientific name": "", + "host common name": "", + "isolate": "", + "collecting institution": "", + "geographic location (country and/or sea)":"", + "host subject id": [ "host_subject_id_1", "host_subject_id_2" @@ -75,29 +41,18 @@ "male", "female" ], - "host scientific name": [ + [ "host_scientific_name_1", "host_scientific_name_2" ], - "collector name": [ - "collector_name_1", - "collector_name_2" - ], - "collecting institution": [ - "collecting_institution_1", - "collecting_institution_2" - ], - "isolate": [ - "isolate_1", - "isolate_2" - ] + "collector name": "", + + + "collection date": }, "experiments": { - "alias": [ - "experiment_alias_7a", - "experiment_alias_8b", - "experiment_alias_9c" + "experiment_alias": "alias" ], "title": [ "experiment_title_1", From daa3d83be06d245dd519952dc5bdb850999e7331 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 22 Mar 2022 21:22:45 +0100 Subject: [PATCH 0182/1454] re-design the way to fetch the md5 files from dowloaded files --- relecov_tools/utils.py | 58 ++++++++++++++++++++++++++++-------------- 1 file changed, 39 insertions(+), 19 deletions(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 40037efd..496442ff 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -3,6 +3,7 @@ Common utility function for relecov_tools package. """ import os +import glob import hashlib from rich.console import Console import questionary @@ -20,29 +21,48 @@ def file_exists(file_to_check): return False -def get_md5_from_local_folder(local_folder, file_list): +def get_md5_from_local_folder(local_folder): """Fetch the md5 values for each file in the file list""" md5_results = {} - for file_name in file_list: - f_name, f_ext = os.path.splitext(file_name) - if f_ext.lowercase() == ".md5": - file_md5_path = os.path.join(local_folder, file_name) - # file_origin_path = os - fh = open(file_path, "r") - md5_results[file_name] - if file_exists(file_path): - pass + reg_for_md5 = os.path.join(local_folder, "*.md5") + reg_for_non_md5 = os.path.join(local_folder, "*[!.md5]") + md5_files = glob.glob(reg_for_md5) + if len(md5_files) > 0: + # find the md5 files and link them to the original file + non_md5_files = glob.glob(reg_for_non_md5) + for file_name in md5_files: + f_name, f_ext = os.path.splitext(file_name) + f_related_md5 = [v for v in non_md5_files if f_name in v] + if len(f_related_md5) == 1: + file_md5_path = os.path.join(local_folder, file_name) + fh = open(file_md5_path, "r") + md5_results[f_related_md5[0]] = fh.read() + fh.close() + return md5_results + + +def calculate_md5(file_name): + """Calculate the md5 value for the file name""" + block_size = 2**20 + return hashlib.md5(open(file_name, "rb").read(block_size)).hexdigest() -def calculate_md5(files_list): - """Calculate the md5 value for the list of files""" - block_size = 2**20 - hash_md5 = hashlib.md5() - for file_list in files_list: - f_name, f_ext = os.path.splitext(file_list) - if not f_ext.lowercase() == ".md5": - hash_md5.update(open(file_list, "rb").read(block_size)) - return hash_md5.hexdigest() +def write_md5_file(file_name, md5_value): + """Write md5 to file """ + with open(file_name, "wb") as fh: + fh.write(md5_value) + return + + +def create_md5_files(file_list): + """Create the md5 files and return their value """ + md5_results = {} + for file_name in file_list: + f_name, f_ext = os.path.splitext(file_name) + md5_results[os.path.base_name(f_name)] = calculate_md5(file_name) + md5_file_name = f_name + ".md5" + write_md5_file(md5_file_name, md5_results[os.path.base_name(f_name)]) + return md5_results def save_local_md5(file_name, md5_value): From 50b9958dd95a9a10fcca89eb5ca8bc920832e1d3 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 22 Mar 2022 21:23:38 +0100 Subject: [PATCH 0183/1454] rename the sft file --- relecov_tools/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 0378da81..2b0d6623 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -160,7 +160,7 @@ def list(keywords, sort, json, show_archived): ) def download_sftp(user, password, conf_file): """Download files located in sftp server.""" - sftp_connection = relecov_tools.sftp.SftpHandle(user, password, conf_file) + sftp_connection = relecov_tools.sftp_handled.SftpHandle(user, password, conf_file) sftp_connection.download_from_sftp() From 17ddf09e6ff2073fa5102d0ec3cb73f5d766b019 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 22 Mar 2022 21:24:31 +0100 Subject: [PATCH 0184/1454] working on the mapping to generate the data frames --- relecov_tools/ena_upload.py | 32 +++++++++++++++++++++++--------- 1 file changed, 23 insertions(+), 9 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 34c43657..dcdf5e49 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -24,7 +24,7 @@ def __init__( passwd=None, source_json=None, dev=None, - project=None, + customized_project=None, action=None, output_path=None, ): @@ -52,10 +52,10 @@ def __init__( ) else: self.dev = dev - if project is None: - self.project = None + if customized_project is None: + self.customized_project = None else: - self.project = project + self.customized_project = customized_project if action is None: self.action = relecov_tools.utils.prompt_selection( msg="Select the action to upload to ENA", @@ -78,34 +78,48 @@ def __init__( self.json_data = json.loads(fh.read()) def convert_input_json_to_ena(self): + """Split the input ena json, in samples and runs json """ + pass + + def create_structure_to_ena(self): """Convert json to dataframe required by ena-upload-cli package""" schema_dataframe = {} + config_json = ConfigJson() - map_to_upload = config_json.get_configuration("mapping_upload_ena") + map_to_upload = config_json.get_configuration("mapping_ena_to_upload_ena") map_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", map_to_upload ) fh = open(map_file) - map_json = json.load(fh) + map_structure_json = json.load(fh) fh.close() - for xml_file in map_json["xml_files"]: + for xml_file in map_structure_json["xml_files"]: if self.project is not None and xml_file in self.project: pass elif config_json.get_configuration(xml_file): df = pd.DataFrame.from_dict( config_json.get_configuration(xml_file), orient="index" ) + else: - pass + data = [] + for chunk in self.json_data: + xml_dict = {} + for key, value in chunk.items(): + if key in map_structure_json[xml_file]: + xml_dict[map_structure_json[xml_file][key]] = value + data.append(xml_dict) + if xml_file in map_structure_json["one_loop_in_mapping"]: + break df = ena_upload.check_columns(df, xml_file, self.action, self.dev, False) schema_dataframe[xml_file] = df return schema_dataframe def upload_files_to_ena(self): """Create the required files and upload to ENA""" - # df = {} self.convert_input_json_to_ena() + self.create_structure_to_ena() # df_study = pd.DataFrame.from_dict(data["study"]) # df_samples = pd.DataFrame.from_dict(data["samples"]) # df_runs = pd.DataFrame.from_dict(data["runs"]) From 860669dd8a696db602eace2b122fa1183d04a4c8 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 22 Mar 2022 21:25:25 +0100 Subject: [PATCH 0185/1454] Working on the flowc for downlading files --- relecov_tools/sftp_handled.py | 32 ++++++++++++++++++++++++++++---- 1 file changed, 28 insertions(+), 4 deletions(-) diff --git a/relecov_tools/sftp_handled.py b/relecov_tools/sftp_handled.py index 0f25e044..313abee3 100644 --- a/relecov_tools/sftp_handled.py +++ b/relecov_tools/sftp_handled.py @@ -27,11 +27,15 @@ def __init__(self, user=None, passwd=None, conf_file=None): self.allowed_sample_ext = config_json.get_configuration( "allowed_sample_extensions" ) + if conf_file is None: self.server = config_json.get_topic_data("sftp_connection", "sftp_server") self.port = config_json.get_topic_data("sftp_connection", "sftp_port") + self.storage_local_folder = config_json.get_configuration("storage_local_folder") + self.metadata_tmp_folder = config_json.get_configuration("tmp_folder_for_metadata") else: if not os.path.isfile(conf_file): + log.error("Configuration file %s does not exists", conf_file) stderr.print( "[red] Configuration file does not exist. " + conf_file + "!" ) @@ -138,6 +142,7 @@ def get_files_from_sftp_folder(self, folder, files_list): os.makedirs(local_folder_path) log.info("created the folder to download files %s", local_folder_path) self.open_connection() + import pdb; pdb.set_trace() for file_list in files_list: try: self.client.get( @@ -149,18 +154,36 @@ def get_files_from_sftp_folder(self, folder, files_list): result_data["Unable_to_fetch"].append(file_list) continue result_data["fetched_files"].append(os.path.basename(file_list)) - + import pdb; pdb.set_trace() return result_data def verify_md5_checksum(self, local_folder, file_list): """Get the md5 value from sftp match with the generated at local folder """ + required_retransmition = [] + successful_files = [] # fetch the md5 file if exists sftp_md5 = relecov_tools.utils.get_md5_from_local_folder(local_folder) - local_md5 = relecov_tools.utils.calculate_md5(file_list) + if len(sftp_md5) > 0: + # check md5 checksum for eac file + for f_name, checksum in sftp_md5.items(): + if checksum == relecov_tools.utils.calculate_md5(f_name): + log.info( + "Successful file download for %s in folder %s", + f_name, local_folder, + ) + successful_files.append(f_name) + else: + required_retransmition.append(f_name) + log.error("%s requested file re-sending", f_name) + if len(file_list) != len(sftp_md5)*2: + # create the md5 file from the ones not upload to server + req_create_md5 = [v for v in file_list if (v not in successful_files and not v.endswith("*.md5"))] + sftp_md5.update(relecov_tools.utils.create_md5_files(req_create_md5)) # MD5 Checking - if sftp_md5: + """ + if required_retransmition: if sftp_md5 == local_md5: log.info( "Successful file download for files in folder %s", @@ -181,6 +204,7 @@ def verify_md5_checksum(self, local_folder, file_list): file_name = os.path.join(local_folder, "generated_locally.md5") relecov_tools.utils.save_md5(file_name, local_md5) return True + """ def create_tmp_files_with_metadata_info(self, local_folder, file_list): """Copy metadata file from folder and create a file with the sample @@ -243,7 +267,7 @@ def download_from_sftp(self): log.info("Exiting download. There is no files on sftp to dowload") self.close_connection() sys.exit(0) - + import pdb; pdb.set_trace() for folder, files in folders_to_download.items(): # get the files in each folder result_data = self.get_files_from_sftp_folder(folder, files) From a7a00c2cc1fe89571904056f4ec8c961616ba9b6 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 22 Mar 2022 23:13:07 +0100 Subject: [PATCH 0186/1454] new parameter abort_if_md5_mismatch to abort processing the folder containing these files --- relecov_tools/conf/configuration.json | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 44ec39d9..b7d3953e 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -10,6 +10,7 @@ "sftp_server": "sftprelecov.isciii.es", "sftp_port": "50122" }, + "abort_if_md5_mismatch": "False", "storage_local_folder": "/tmp/relecov", "tmp_folder_for_metadata": "/tmp/relecov/tmp", "allowed_sample_extensions": [ From 60190b9a9ff5b84783191ee6ab1de0cc2890d911 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 22 Mar 2022 23:58:16 +0100 Subject: [PATCH 0187/1454] Implemented retransmition for wrong md5 check and create output files --- relecov_tools/sftp_handled.py | 96 ++++++++++++++--------------------- 1 file changed, 39 insertions(+), 57 deletions(-) diff --git a/relecov_tools/sftp_handled.py b/relecov_tools/sftp_handled.py index 313abee3..d0996b7b 100644 --- a/relecov_tools/sftp_handled.py +++ b/relecov_tools/sftp_handled.py @@ -33,6 +33,7 @@ def __init__(self, user=None, passwd=None, conf_file=None): self.port = config_json.get_topic_data("sftp_connection", "sftp_port") self.storage_local_folder = config_json.get_configuration("storage_local_folder") self.metadata_tmp_folder = config_json.get_configuration("tmp_folder_for_metadata") + self.abort_if_md5_mismatch = True if config_json.get_configuration("abort_if_md5_mismatch") == "True" else False else: if not os.path.isfile(conf_file): log.error("Configuration file %s does not exists", conf_file) @@ -181,57 +182,36 @@ def verify_md5_checksum(self, local_folder, file_list): # create the md5 file from the ones not upload to server req_create_md5 = [v for v in file_list if (v not in successful_files and not v.endswith("*.md5"))] sftp_md5.update(relecov_tools.utils.create_md5_files(req_create_md5)) - # MD5 Checking - """ - if required_retransmition: - if sftp_md5 == local_md5: - log.info( - "Successful file download for files in folder %s", - local_folder, - ) - return True - else: - log.error( - "MD5 does not match. Files could be corrupted atfolder %s", - local_folder, - ) - return False - else: - log.info( - "Md5 file was not created by lab. Copy the local md5 into folder %s", - local_folder, - ) - file_name = os.path.join(local_folder, "generated_locally.md5") - relecov_tools.utils.save_md5(file_name, local_md5) - return True - """ + return sftp_md5, required_retransmition - def create_tmp_files_with_metadata_info(self, local_folder, file_list): + def create_tmp_files_with_metadata_info(self, local_folder, file_list, md5_data): """Copy metadata file from folder and create a file with the sample names """ out_folder = self.metadata_tmp_folder os.makedirs(out_folder, exist_ok=True) - metadata_file = "_".join(local_folder.split("/")[-2:]) + "_metadata_lab.xlsx" - shutil.copy( - os.path.join(local_folder, "Metadata_lab.xlsx"), - os.path.join(out_folder, metadata_file), - ) - for ext in self.allowed_sample_ext: - sample_names = [] - for file_name in os.listdir(local_folder): - if file_name.endswith("*." + ext): - m = re.search(r"(.*)_R[1,2].*", file_name) - if m.group(1) not in metadata_file: - sample_names.append(m.group(1)) - if len(sample_names) > 0: - break - if len(sample_names) == 0: + prefix_file_name = "_".join(local_folder.split("/")[-2:]) + metadata_file = prefix_file_name + "_metadata_lab.xlsx" + sample_data_file = os.path.join(out_folder, prefix_file_name + "samples.csv") + try: + shutil.copy( + os.path.join(local_folder, "Metadata_lab.xlsx"), + os.path.join(out_folder, metadata_file), + ) + except OSError as e: + log.error("Unable to copy Metadata file %s" , e) + stderr.print("[red] Unable to copy Metadata file") + sample_data = [] + for file_data in md5_data: + if file_data[0].endswith(tuple(self.allowed_sample_ext)): + sample_data.append(",".join(file_data)) + if len(sample_data) == 0: log.error("There is no samples in folder %s", local_folder) - file_with_samples = metadata_file.split("_")[0] + "samples.txt" - with open(file_with_samples, "w") as fh: - for sample_name in sample_names: - fh.write(sample_name + "\n") + stderr.print("[red] There is no samples for this loacal folder") + else: + with open(sample_data_file, "w") as fh: + for sample in sample_data: + fh.write(sample + "\n") return def create_main_folders(self, root_directory_list): @@ -267,22 +247,24 @@ def download_from_sftp(self): log.info("Exiting download. There is no files on sftp to dowload") self.close_connection() sys.exit(0) - import pdb; pdb.set_trace() + for folder, files in folders_to_download.items(): # get the files in each folder result_data = self.get_files_from_sftp_folder(folder, files) - if not self.verify_md5_checksum( + md5_files, req_retransmition = self.verify_md5_checksum( result_data["local_folder"], result_data["fetched_files"] - ): - # retrasmision of files in folder - result_data = self.get_files_from_sftp_folder(folder, files) - if not self.verify_md5_checksum( - result_data["local_folder"], result_data["fetched_files"] - ): - log.error( - "Second retransmision of files on folder %s", - result_data["local_folder"], - ) + ) + # retrasmision of files in folder + if len(req_retransmition) > 0: + restransmition_data = self.get_files_from_sftp_folder(folder, req_retransmition) + md5_ret_files, corrupted = self.verify_md5_checksum( + result_data["local_folder"], restransmition_data["fetched_files"]) + md5_files.update(md5_ret_files) + if len(corrupted) > 0 and self.abort_if_md5_mismatch: + log.error("Stopping because of corrupted files %s", corrupted) + stderr.print(f"[red] Stop processing folder {folder} because of corrupted files {corrupted}") + continue self.create_tmp_files_with_metadata_info( - result_data["local_folder"], result_data["fetched_files"] + result_data["local_folder"], result_data["fetched_files"], md5_files ) + self.close_connection() From ca0269c4577983a4eeca702b509b4ab0288631d8 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 22 Mar 2022 23:59:16 +0100 Subject: [PATCH 0188/1454] fixed litin --- relecov_tools/sftp_handled.py | 46 ++++++++++++++++++++++++++--------- 1 file changed, 34 insertions(+), 12 deletions(-) diff --git a/relecov_tools/sftp_handled.py b/relecov_tools/sftp_handled.py index d0996b7b..540c0e1d 100644 --- a/relecov_tools/sftp_handled.py +++ b/relecov_tools/sftp_handled.py @@ -31,9 +31,17 @@ def __init__(self, user=None, passwd=None, conf_file=None): if conf_file is None: self.server = config_json.get_topic_data("sftp_connection", "sftp_server") self.port = config_json.get_topic_data("sftp_connection", "sftp_port") - self.storage_local_folder = config_json.get_configuration("storage_local_folder") - self.metadata_tmp_folder = config_json.get_configuration("tmp_folder_for_metadata") - self.abort_if_md5_mismatch = True if config_json.get_configuration("abort_if_md5_mismatch") == "True" else False + self.storage_local_folder = config_json.get_configuration( + "storage_local_folder" + ) + self.metadata_tmp_folder = config_json.get_configuration( + "tmp_folder_for_metadata" + ) + self.abort_if_md5_mismatch = ( + True + if config_json.get_configuration("abort_if_md5_mismatch") == "True" + else False + ) else: if not os.path.isfile(conf_file): log.error("Configuration file %s does not exists", conf_file) @@ -143,7 +151,9 @@ def get_files_from_sftp_folder(self, folder, files_list): os.makedirs(local_folder_path) log.info("created the folder to download files %s", local_folder_path) self.open_connection() - import pdb; pdb.set_trace() + import pdb + + pdb.set_trace() for file_list in files_list: try: self.client.get( @@ -155,7 +165,9 @@ def get_files_from_sftp_folder(self, folder, files_list): result_data["Unable_to_fetch"].append(file_list) continue result_data["fetched_files"].append(os.path.basename(file_list)) - import pdb; pdb.set_trace() + import pdb + + pdb.set_trace() return result_data def verify_md5_checksum(self, local_folder, file_list): @@ -172,15 +184,20 @@ def verify_md5_checksum(self, local_folder, file_list): if checksum == relecov_tools.utils.calculate_md5(f_name): log.info( "Successful file download for %s in folder %s", - f_name, local_folder, + f_name, + local_folder, ) successful_files.append(f_name) else: required_retransmition.append(f_name) log.error("%s requested file re-sending", f_name) - if len(file_list) != len(sftp_md5)*2: + if len(file_list) != len(sftp_md5) * 2: # create the md5 file from the ones not upload to server - req_create_md5 = [v for v in file_list if (v not in successful_files and not v.endswith("*.md5"))] + req_create_md5 = [ + v + for v in file_list + if (v not in successful_files and not v.endswith("*.md5")) + ] sftp_md5.update(relecov_tools.utils.create_md5_files(req_create_md5)) return sftp_md5, required_retransmition @@ -199,7 +216,7 @@ def create_tmp_files_with_metadata_info(self, local_folder, file_list, md5_data) os.path.join(out_folder, metadata_file), ) except OSError as e: - log.error("Unable to copy Metadata file %s" , e) + log.error("Unable to copy Metadata file %s", e) stderr.print("[red] Unable to copy Metadata file") sample_data = [] for file_data in md5_data: @@ -256,13 +273,18 @@ def download_from_sftp(self): ) # retrasmision of files in folder if len(req_retransmition) > 0: - restransmition_data = self.get_files_from_sftp_folder(folder, req_retransmition) + restransmition_data = self.get_files_from_sftp_folder( + folder, req_retransmition + ) md5_ret_files, corrupted = self.verify_md5_checksum( - result_data["local_folder"], restransmition_data["fetched_files"]) + result_data["local_folder"], restransmition_data["fetched_files"] + ) md5_files.update(md5_ret_files) if len(corrupted) > 0 and self.abort_if_md5_mismatch: log.error("Stopping because of corrupted files %s", corrupted) - stderr.print(f"[red] Stop processing folder {folder} because of corrupted files {corrupted}") + stderr.print( + f"[red] Stop processing folder {folder} because of corrupted files {corrupted}" + ) continue self.create_tmp_files_with_metadata_info( result_data["local_folder"], result_data["fetched_files"], md5_files From 32855e9bc9ad4fc9858e1f87cd44b43ea9326669 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 23 Mar 2022 00:01:03 +0100 Subject: [PATCH 0189/1454] fixed litin --- relecov_tools/ena_upload.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index dcdf5e49..25a9968f 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -78,7 +78,7 @@ def __init__( self.json_data = json.loads(fh.read()) def convert_input_json_to_ena(self): - """Split the input ena json, in samples and runs json """ + """Split the input ena json, in samples and runs json""" pass def create_structure_to_ena(self): From 271e7144e7f1afe4f5130dbc71e906c5f4be01b5 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 23 Mar 2022 00:11:47 +0100 Subject: [PATCH 0190/1454] update black in jupyter format --- .github/workflows/python_lint.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml index 31edb167..651c3841 100644 --- a/.github/workflows/python_lint.yml +++ b/.github/workflows/python_lint.yml @@ -31,6 +31,8 @@ jobs: black_lint: runs-on: ubuntu-latest steps: + - name: Install black in jupyter + run: pip install black[jupyter] - name: Setup uses: actions/checkout@v2 - name: Check code lints with Black From 448eb2be86b6d4094df091de68488d29e2a2092f Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 23 Mar 2022 00:17:59 +0100 Subject: [PATCH 0191/1454] trying to install black jupiter --- .github/workflows/python_lint.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml index 651c3841..791ba18f 100644 --- a/.github/workflows/python_lint.yml +++ b/.github/workflows/python_lint.yml @@ -31,9 +31,9 @@ jobs: black_lint: runs-on: ubuntu-latest steps: - - name: Install black in jupyter - run: pip install black[jupyter] - name: Setup uses: actions/checkout@v2 + - name: Install black in jupyter + run: pip install black[jupyter] - name: Check code lints with Black uses: psf/black@stable From 9a65c3267eddedf6ee441f25da28a3968e3dad4d Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 23 Mar 2022 00:26:49 +0100 Subject: [PATCH 0192/1454] fixed litin --- relecov_tools/utils.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 496442ff..51de5d9d 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -48,14 +48,14 @@ def calculate_md5(file_name): def write_md5_file(file_name, md5_value): - """Write md5 to file """ + """Write md5 to file""" with open(file_name, "wb") as fh: fh.write(md5_value) return def create_md5_files(file_list): - """Create the md5 files and return their value """ + """Create the md5 files and return their value""" md5_results = {} for file_name in file_list: f_name, f_ext = os.path.splitext(file_name) From c581141e2670eb05536dd7863202d2ad73158dd2 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 23 Mar 2022 00:29:10 +0100 Subject: [PATCH 0193/1454] fixed litin --- relecov_tools/sftp_handled.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/relecov_tools/sftp_handled.py b/relecov_tools/sftp_handled.py index 540c0e1d..65ac3df8 100644 --- a/relecov_tools/sftp_handled.py +++ b/relecov_tools/sftp_handled.py @@ -2,7 +2,6 @@ from datetime import datetime import logging import rich.console -import re import paramiko import sys import os @@ -151,9 +150,7 @@ def get_files_from_sftp_folder(self, folder, files_list): os.makedirs(local_folder_path) log.info("created the folder to download files %s", local_folder_path) self.open_connection() - import pdb - pdb.set_trace() for file_list in files_list: try: self.client.get( @@ -165,9 +162,6 @@ def get_files_from_sftp_folder(self, folder, files_list): result_data["Unable_to_fetch"].append(file_list) continue result_data["fetched_files"].append(os.path.basename(file_list)) - import pdb - - pdb.set_trace() return result_data def verify_md5_checksum(self, local_folder, file_list): From ea65b9a955ae68b47037e905471cb5d0fbe4ea79 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 23 Mar 2022 12:22:38 +0100 Subject: [PATCH 0194/1454] I have performed all the changes in the schemas --- relecov_tools/schema/ena_schema.json | 3 ++- relecov_tools/schema/phage_plus_schema.json | 9 +++++---- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index c74714a8..6c944e74 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -1199,12 +1199,13 @@ "clasification": "Submission ENA", "label": "Nominal sdev" }, - "first_created": { + "first_created_date": { "examples": [ "e.g 2020-08-07" ], "ontology": "NCIT_C164483", "type": "string", + "format": "date", "description": "", "clasification": "Submission ENA", "label": "First created date" diff --git a/relecov_tools/schema/phage_plus_schema.json b/relecov_tools/schema/phage_plus_schema.json index ef7df4c3..e920d682 100644 --- a/relecov_tools/schema/phage_plus_schema.json +++ b/relecov_tools/schema/phage_plus_schema.json @@ -1688,11 +1688,11 @@ "examples": [ "" ], - "ontology": "0", + "ontology": "GENEPIO:0000079", "type": "number", "description": "If the information is unknown or can not be shared, leave blank.", "clasification": "Database Identifiers", - "label": "Sequencing Sample Id" + "label": "Sample ID given for sequencing" }, "passage_details": { "examples": [ @@ -2005,7 +2005,7 @@ "type": "string", "description": "Name of the used library", "clasification": "Sequencing", - "label": "LibraryName" + "label": "Library Name" }, "nominal_length ": { "examples": [ @@ -3176,12 +3176,13 @@ "clasification": "Submission ENA", "label": "Nominal sdev" }, - "first_created": { + "first_created_date": { "examples": [ "e.g 2020-08-07" ], "ontology": "NCIT_C164483", "type": "string", + "format": "date", "description": "", "clasification": "Submission ENA", "label": "First created date" From 54abb115609affcb0b58034e4185b1dcb2da113c Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 23 Mar 2022 23:43:42 +0100 Subject: [PATCH 0195/1454] Tested until writing md5 to file --- relecov_tools/sftp_handled.py | 11 ++++++++--- relecov_tools/utils.py | 8 ++++---- 2 files changed, 12 insertions(+), 7 deletions(-) diff --git a/relecov_tools/sftp_handled.py b/relecov_tools/sftp_handled.py index 65ac3df8..d2752c76 100644 --- a/relecov_tools/sftp_handled.py +++ b/relecov_tools/sftp_handled.py @@ -147,7 +147,7 @@ def get_files_from_sftp_folder(self, folder, files_list): date = datetime.today().strftime("%Y%m%d") local_folder_path = os.path.join(self.storage_local_folder, folder, date) result_data["local_folder"] = local_folder_path - os.makedirs(local_folder_path) + os.makedirs(local_folder_path, exist_ok=True) log.info("created the folder to download files %s", local_folder_path) self.open_connection() @@ -175,7 +175,9 @@ def verify_md5_checksum(self, local_folder, file_list): if len(sftp_md5) > 0: # check md5 checksum for eac file for f_name, checksum in sftp_md5.items(): - if checksum == relecov_tools.utils.calculate_md5(f_name): + f_path_name = os.path.join(local_folder, f_name) + import pdb; pdb.set_trace() + if checksum == relecov_tools.utils.calculate_md5(f_path_name): log.info( "Successful file download for %s in folder %s", f_name, @@ -192,7 +194,7 @@ def verify_md5_checksum(self, local_folder, file_list): for v in file_list if (v not in successful_files and not v.endswith("*.md5")) ] - sftp_md5.update(relecov_tools.utils.create_md5_files(req_create_md5)) + sftp_md5.update(relecov_tools.utils.create_md5_files(local_folder, req_create_md5)) return sftp_md5, required_retransmition def create_tmp_files_with_metadata_info(self, local_folder, file_list, md5_data): @@ -204,6 +206,7 @@ def create_tmp_files_with_metadata_info(self, local_folder, file_list, md5_data) prefix_file_name = "_".join(local_folder.split("/")[-2:]) metadata_file = prefix_file_name + "_metadata_lab.xlsx" sample_data_file = os.path.join(out_folder, prefix_file_name + "samples.csv") + import pdb; pdb.set_trace() try: shutil.copy( os.path.join(local_folder, "Metadata_lab.xlsx"), @@ -213,6 +216,7 @@ def create_tmp_files_with_metadata_info(self, local_folder, file_list, md5_data) log.error("Unable to copy Metadata file %s", e) stderr.print("[red] Unable to copy Metadata file") sample_data = [] + import pdb; pdb.set_trace() for file_data in md5_data: if file_data[0].endswith(tuple(self.allowed_sample_ext)): sample_data.append(",".join(file_data)) @@ -280,6 +284,7 @@ def download_from_sftp(self): f"[red] Stop processing folder {folder} because of corrupted files {corrupted}" ) continue + import pdb; pdb.set_trace() self.create_tmp_files_with_metadata_info( result_data["local_folder"], result_data["fetched_files"], md5_files ) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 51de5d9d..f493ad71 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -49,19 +49,19 @@ def calculate_md5(file_name): def write_md5_file(file_name, md5_value): """Write md5 to file""" - with open(file_name, "wb") as fh: + with open(file_name, "w") as fh: fh.write(md5_value) return -def create_md5_files(file_list): +def create_md5_files(local_folder, file_list): """Create the md5 files and return their value""" md5_results = {} for file_name in file_list: f_name, f_ext = os.path.splitext(file_name) - md5_results[os.path.base_name(f_name)] = calculate_md5(file_name) + md5_results[file_name] = calculate_md5(os.path.join(local_folder, file_name)) md5_file_name = f_name + ".md5" - write_md5_file(md5_file_name, md5_results[os.path.base_name(f_name)]) + write_md5_file(os.path.join(local_folder, md5_file_name), md5_results[file_name]) return md5_results From 29bbd19ea9723620e9b69bd605362cf5fee84a70 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 24 Mar 2022 11:29:37 +0100 Subject: [PATCH 0196/1454] Update README.md --- README.md | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/README.md b/README.md index d12406fa..7095c3c5 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,10 @@ # relecov-tools [![Python tests](https://github.com/nf-core/tools/workflows/Python%20tests/badge.svg?branch=master&event=push)](https://github.com/nf-core/tools/actions?query=workflow%3A%22Python+tests%22+branch%3Amaster) -[![codecov](https://codecov.io/gh/nf-core/tools/branch/master/graph/badge.svg)](https://codecov.io/gh/nf-core/tools) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) -[![install with Bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/recipes/nf-core/README.html) -[![install with PyPI](https://img.shields.io/badge/install%20with-PyPI-blue.svg)](https://pypi.org/project/nf-core/) - A Python package with helper tools for the relecov project. - -## Table of contents +## Table of contents * [ installation][*installation] From e604e6d17ac1dbc89028ce3136b9402db91617ef Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 24 Mar 2022 11:30:28 +0100 Subject: [PATCH 0197/1454] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 7095c3c5..18a8ca22 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ # relecov-tools -[![Python tests](https://github.com/nf-core/tools/workflows/Python%20tests/badge.svg?branch=master&event=push)](https://github.com/nf-core/tools/actions?query=workflow%3A%22Python+tests%22+branch%3Amaster) +[![python_lint](https://github.com/BU-ISCIII/relecov-tools/actions/workflows/python_lint.yml/badge.svg)](https://github.com/BU-ISCIII/relecov-tools/actions/workflows/python_lint.yml) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) A Python package with helper tools for the relecov project. From 47b83ddbb8ac3a4c24d5d99a70e67336d6689ca4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 24 Mar 2022 11:31:21 +0100 Subject: [PATCH 0198/1454] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 18a8ca22..6d4757f6 100644 --- a/README.md +++ b/README.md @@ -6,10 +6,10 @@ A Python package with helper tools for the relecov project. ## Table of contents -* [ installation][*installation] +* [Install](#installation) +* [Usage](#usage) - -## Installation +## Install From 18ca856546d04418fb5cd9036d4e0c6462719bb1 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 24 Mar 2022 22:38:21 +0100 Subject: [PATCH 0199/1454] Tested download, md5 checking and creation of sample with checsum --- relecov_tools/sftp_handled.py | 26 +++++++++++++------------ relecov_tools/utils.py | 36 ++++++++++++++++++++--------------- 2 files changed, 35 insertions(+), 27 deletions(-) diff --git a/relecov_tools/sftp_handled.py b/relecov_tools/sftp_handled.py index d2752c76..c47b2ade 100644 --- a/relecov_tools/sftp_handled.py +++ b/relecov_tools/sftp_handled.py @@ -174,10 +174,10 @@ def verify_md5_checksum(self, local_folder, file_list): sftp_md5 = relecov_tools.utils.get_md5_from_local_folder(local_folder) if len(sftp_md5) > 0: # check md5 checksum for eac file - for f_name, checksum in sftp_md5.items(): + for f_name, values in sftp_md5.items(): f_path_name = os.path.join(local_folder, f_name) - import pdb; pdb.set_trace() - if checksum == relecov_tools.utils.calculate_md5(f_path_name): + # Checksum value is stored in the index 1 + if values[1] == relecov_tools.utils.calculate_md5(f_path_name): log.info( "Successful file download for %s in folder %s", f_name, @@ -187,14 +187,17 @@ def verify_md5_checksum(self, local_folder, file_list): else: required_retransmition.append(f_name) log.error("%s requested file re-sending", f_name) - if len(file_list) != len(sftp_md5) * 2: + + if len(set(file_list)) != len(sftp_md5) * 2: # create the md5 file from the ones not upload to server req_create_md5 = [ v for v in file_list if (v not in successful_files and not v.endswith("*.md5")) ] - sftp_md5.update(relecov_tools.utils.create_md5_files(local_folder, req_create_md5)) + sftp_md5.update( + relecov_tools.utils.create_md5_files(local_folder, req_create_md5) + ) return sftp_md5, required_retransmition def create_tmp_files_with_metadata_info(self, local_folder, file_list, md5_data): @@ -206,7 +209,6 @@ def create_tmp_files_with_metadata_info(self, local_folder, file_list, md5_data) prefix_file_name = "_".join(local_folder.split("/")[-2:]) metadata_file = prefix_file_name + "_metadata_lab.xlsx" sample_data_file = os.path.join(out_folder, prefix_file_name + "samples.csv") - import pdb; pdb.set_trace() try: shutil.copy( os.path.join(local_folder, "Metadata_lab.xlsx"), @@ -216,13 +218,13 @@ def create_tmp_files_with_metadata_info(self, local_folder, file_list, md5_data) log.error("Unable to copy Metadata file %s", e) stderr.print("[red] Unable to copy Metadata file") sample_data = [] - import pdb; pdb.set_trace() - for file_data in md5_data: - if file_data[0].endswith(tuple(self.allowed_sample_ext)): - sample_data.append(",".join(file_data)) + + for key, values in md5_data.items(): + if key.endswith(tuple(self.allowed_sample_ext)): + sample_data.append(key + "," + ",".join(values)) if len(sample_data) == 0: log.error("There is no samples in folder %s", local_folder) - stderr.print("[red] There is no samples for this loacal folder") + stderr.print("[red] There is no samples for this local folder") else: with open(sample_data_file, "w") as fh: for sample in sample_data: @@ -284,8 +286,8 @@ def download_from_sftp(self): f"[red] Stop processing folder {folder} because of corrupted files {corrupted}" ) continue - import pdb; pdb.set_trace() self.create_tmp_files_with_metadata_info( result_data["local_folder"], result_data["fetched_files"], md5_files ) self.close_connection() + return diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index f493ad71..3b29e75e 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -5,9 +5,12 @@ import os import glob import hashlib +import logging from rich.console import Console import questionary +log = logging.getLogger(__name__) + def file_exists(file_to_check): """ @@ -25,19 +28,18 @@ def get_md5_from_local_folder(local_folder): """Fetch the md5 values for each file in the file list""" md5_results = {} reg_for_md5 = os.path.join(local_folder, "*.md5") - reg_for_non_md5 = os.path.join(local_folder, "*[!.md5]") + # reg_for_non_md5 = os.path.join(local_folder, "*[!.md5]") md5_files = glob.glob(reg_for_md5) if len(md5_files) > 0: - # find the md5 files and link them to the original file - non_md5_files = glob.glob(reg_for_non_md5) - for file_name in md5_files: - f_name, f_ext = os.path.splitext(file_name) - f_related_md5 = [v for v in non_md5_files if f_name in v] - if len(f_related_md5) == 1: - file_md5_path = os.path.join(local_folder, file_name) - fh = open(file_md5_path, "r") - md5_results[f_related_md5[0]] = fh.read() - fh.close() + for md5_file in md5_files: + file_path_name, f_ext = os.path.splitext(md5_file) + if not file_exists(file_path_name): + log.error("Found md5 file but not %s", file_path_name) + continue + file_name = os.path.basename(file_path_name) + fh = open(md5_file, "r") + md5_results[file_name] = [local_folder, fh.read()] + fh.close() return md5_results @@ -58,10 +60,14 @@ def create_md5_files(local_folder, file_list): """Create the md5 files and return their value""" md5_results = {} for file_name in file_list: - f_name, f_ext = os.path.splitext(file_name) - md5_results[file_name] = calculate_md5(os.path.join(local_folder, file_name)) - md5_file_name = f_name + ".md5" - write_md5_file(os.path.join(local_folder, md5_file_name), md5_results[file_name]) + md5_results[file_name] = [ + local_folder, + calculate_md5(os.path.join(local_folder, file_name)), + ] + md5_file_name = file_name + ".md5" + write_md5_file( + os.path.join(local_folder, md5_file_name), md5_results[file_name][1] + ) return md5_results From 5b985c781829e85ec5cb62df5c7a09af44cb01ca Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 26 Mar 2022 13:21:21 +0100 Subject: [PATCH 0200/1454] included deleting remote files. pending testing --- relecov_tools/sftp_handled.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/relecov_tools/sftp_handled.py b/relecov_tools/sftp_handled.py index c47b2ade..27f5eda7 100644 --- a/relecov_tools/sftp_handled.py +++ b/relecov_tools/sftp_handled.py @@ -238,6 +238,17 @@ def create_main_folders(self, root_directory_list): os.makedirs(full_folder, exist_ok=True) return True + def delete_remote_files(self, folder, files): + """Delete files from remote server """ + self.open_connection() + for file in files: + try: + self.client.remove(file) + log.info("%s Deleted from remote server", file) + except FileNotFoundError: + continue + return + def download_from_sftp(self): try: os.makedirs(self.storage_local_folder, exist_ok=True) @@ -289,5 +300,6 @@ def download_from_sftp(self): self.create_tmp_files_with_metadata_info( result_data["local_folder"], result_data["fetched_files"], md5_files ) + self.delete_remote_files(folder, files) self.close_connection() return From c513ac77bcafd5b3d6eed3e5993e837057524466 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 26 Mar 2022 13:22:17 +0100 Subject: [PATCH 0201/1454] litin changes --- relecov_tools/sftp_handled.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/sftp_handled.py b/relecov_tools/sftp_handled.py index 27f5eda7..441d3257 100644 --- a/relecov_tools/sftp_handled.py +++ b/relecov_tools/sftp_handled.py @@ -239,7 +239,7 @@ def create_main_folders(self, root_directory_list): return True def delete_remote_files(self, folder, files): - """Delete files from remote server """ + """Delete files from remote server""" self.open_connection() for file in files: try: From 9b46da4a29fdd73514b7e2377f6d5dc6ef888aef Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 26 Mar 2022 23:19:33 +0100 Subject: [PATCH 0202/1454] Updated metadata to json from the lastest changes 25-march --- .../schema/mapping_metadata_to_json.json | 73 ++++++------------- 1 file changed, 22 insertions(+), 51 deletions(-) diff --git a/relecov_tools/schema/mapping_metadata_to_json.json b/relecov_tools/schema/mapping_metadata_to_json.json index ba891e56..ebfa769e 100644 --- a/relecov_tools/schema/mapping_metadata_to_json.json +++ b/relecov_tools/schema/mapping_metadata_to_json.json @@ -1,78 +1,49 @@ { - "Collecting Sample id": "sample_name", + "Public Health sample id (SIVIES)": "XXXXXXXXXXX", + "Sample ID given by originating laboratory": "sample_name", "Sample ID given by the submitting laboratory" : "submitting_lab_sequence_id", - "Passage details": "passage_details", - "Sequencing sample id": "sequencing_sample_id", + "Sample ID given in the microbiology lab": "XXXXXXX", + "Sample ID given if multiple rna-extraction or passages": "XXXXXXXXXXXX", + "Sample ID given for sequencing": "sequencing_sample_id", "ENA Sample ID": "biosample_accession_ENA", "GISAID Virus Name": "virus_name", - "GISAID id": "submitter", - "Country": "geo_loc_country", - "Autonomic community": "geo_loc_state", - "Province": "geo_loc_region", - "City":"geo_loc_city", + "GISAID id": "gisaid_id", "Originating Laboratory": "collecting_institution", - "Originating Laboratory email": "collecting_institution_email", - "Originating Laboratory Address": "collecting_institution_address", "Submitting Institution": "submitting_institution", - "Submitting Institution Email": "submitting_institution_email", - "Submitting Institution Address": "submitting_institution_address", "Sample Collection Date": "sample_collection_date", "Sample Received Date": "sample_received_date", - "Purpose of sampling": "purpose_of_sequencing", - "Biological Sample Storage Condition": "sample_storage_conditions", + "Purpose of sampling": "purpose_of_sampling", + "Biological Sample Storage Condition": "XXXXXXX", "Specimen source": "anatomical_material", - "Anatomical Structure": "anatomical_part", + "Anatomical Structure": "XXXXXXXXXXXXXXX", "Environmental Material": "environmental_material", "Environmental System": "environmental_site", - "Sampling Device": "collection_device", - "Sampling method": "collection_method", - "Sampling Protocol": "collection_protocol", - "Specimen Processing": "specimen_processing", - "Lab passage Host": "lab_host", - "Passage Number": "passage_number", - "Passage Method": "passage_method", - "Nucleic acid extraction methods": "biomaterial_extracted", - "Host Common Name": "host_common_name", + "Source material": "biomaterial_extracted", + "Collection Device": "collection_device", + "Host": "host_common_name", "Host Age": "host_age", - "Host Age Unit": "host_age_unit", - "Host Age Bin": "host_age_bin", "Host Gender": "host_gender", - "Outbreak Exposure Event Location": "outbreak", - "Additional Host Information": "additional_host_information", - "Purpose Of Sequencing Details": "purpose_of_sequencing", "Sequencing Date": "sequencing_date", "Rna Extraction Protocol": "rna_extraction_protocol", + "Commercial All-in-one library kit": "library_kit", "Library preparation kit": "library_preparation_kit", "Enrichment Protocol": "enrichment_protocol", "If Enrichment Protocol Is Other, Specify": "if_enrichment_protocol_is_other_specify", - "Amplicon Protocol": "amplicon_protocol", + "Amplicon panel/assay": "amplicon_protocol", "If Amplicon Protocol If Other, Especify": "if_amplicon_protocol_if_other_especify", - "Amplicon Version": "amplicon_protocol", - "Amplicon Size": "amplicon_size", - "Was Phix Used?": "was_phix_used?", + "Amplicon Version": "amplicon_version", "Number Of Samples In Run": "number_of_samples_in_run", - "Flowcell Kit": "flowcell_kit", "Runid": "runID", - "Sequencing Platforms": "sequencing_platforms", - "Library Preparation Kit": "library_kit", - "Flow Cell Barcode": "flow_cell_barcode", "Sequencing Instrument Model": "sequencing_instrument_model", - "Sequencing Protocol Name": "sequencing_protocol_name", - "Sequencing Protocol": "sequencing_protocol", - "Sequencing Kit Number": "sequencing_kit_number", - "Amplicon Pcr Primer Scheme": "amplicon_pcr_primer_scheme", - "Library Source": "library_source", - "Library Selection": "library_selection", - "Library Strategy": "library_strategy", + "Flowcell Kit": "flowcell_kit", + "Source material": "biomaterial_extracted", + "Capture method": "library_selection", + "Sequencing technique": "library_strategy", "Library Layout": "library_layout", - "Library Name": "library_name", - "Nominal Length": "nominal_length", - "PCR Target 1": "gene_name_1", - "Diagnostic Pcr Protocol 1": "diagnostic_pcr_protocol_1", + "Gene Name 1" : "gene_name_1", "Diagnostic Pcr Ct Value 1": "diagnostic_pcr_Ct_value_1", - "PCR Target 2": "gene_name_2", - "Diagnostic Pcr Protocol 2": "diagnostic_pcr_protocol_2", - "Diagnostic Pcr Ct Value-2": "diagnostic_pcr_Ct_value_2", + "Gene Name 2" : "gene_name_2", + "Diagnostic Pcr Ct Value 2": "diagnostic_pcr_Ct_value_2", "Analysis Authors": "analysis_author", "Author Submitter": "author_submitter", "Authors": "authors", From 2b8ba8346f32b6f24bc4fd074206c6e3d82d6ae9 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 26 Mar 2022 23:28:29 +0100 Subject: [PATCH 0203/1454] adding parameters in additional fields --- relecov_tools/schema/mapping_metadata_to_json.json | 3 +++ 1 file changed, 3 insertions(+) diff --git a/relecov_tools/schema/mapping_metadata_to_json.json b/relecov_tools/schema/mapping_metadata_to_json.json index ebfa769e..0135c23d 100644 --- a/relecov_tools/schema/mapping_metadata_to_json.json +++ b/relecov_tools/schema/mapping_metadata_to_json.json @@ -48,6 +48,8 @@ "Author Submitter": "author_submitter", "Authors": "authors", "Additional_fields": { + "geo_loc_country" : "", + "geo_loc_state": "", "geo_loc_latitude": "", "geo_loc_longitude": "", "organism": "sars_cov_2", @@ -66,6 +68,7 @@ "run_alias": "", "study_title": "", "experiment_title": "", + "sequencing_instrument_platform": "" } } From 542f7e00cd8b82e7689ce4bbf50fb5d260027f83 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 26 Mar 2022 23:44:01 +0100 Subject: [PATCH 0204/1454] missing sample_storage_conditions --- relecov_tools/schema/mapping_metadata_to_json.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/mapping_metadata_to_json.json b/relecov_tools/schema/mapping_metadata_to_json.json index 0135c23d..0de5c9a0 100644 --- a/relecov_tools/schema/mapping_metadata_to_json.json +++ b/relecov_tools/schema/mapping_metadata_to_json.json @@ -13,7 +13,7 @@ "Sample Collection Date": "sample_collection_date", "Sample Received Date": "sample_received_date", "Purpose of sampling": "purpose_of_sampling", - "Biological Sample Storage Condition": "XXXXXXX", + "Biological Sample Storage Condition": "sample_storage_conditions", "Specimen source": "anatomical_material", "Anatomical Structure": "XXXXXXXXXXXXXXX", "Environmental Material": "environmental_material", From 88ddb401e772e1d98743e18bc35db9c5af68bf5f Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 28 Mar 2022 00:47:59 +0200 Subject: [PATCH 0205/1454] Adding aditional data to metadata --- relecov_tools/conf/configuration.json | 2 +- relecov_tools/conf/geo_loc_cities.json | 12217 +++++++++++++++++++ relecov_tools/conf/laboratory_address.json | 134 + relecov_tools/read_metadata.py | 11 +- 4 files changed, 12359 insertions(+), 5 deletions(-) create mode 100644 relecov_tools/conf/geo_loc_cities.json create mode 100644 relecov_tools/conf/laboratory_address.json diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index b7d3953e..66a74a5f 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -4,7 +4,7 @@ "ena_schema": "ena_schema.json", "gisaid_schema": "gisaid_schema.json" }, - "mapping_metadata_json": "mapping_metadata_json.json", + "mapping_metadata_json": "mapping_metadata_to_json.json", "mapping_upload_ena": "mapping_ena_to_upload_ena.json", "sftp_connection": { "sftp_server": "sftprelecov.isciii.es", diff --git a/relecov_tools/conf/geo_loc_cities.json b/relecov_tools/conf/geo_loc_cities.json new file mode 100644 index 00000000..8ff1a201 --- /dev/null +++ b/relecov_tools/conf/geo_loc_cities.json @@ -0,0 +1,12217 @@ +[ + { + "geo_loc_city": "Madrid", + "geo_loc_latitude": "40.4167", + "geo_loc_longitude": "-3.7167" + }, + { + "geo_loc_city": "Barcelona", + "geo_loc_latitude": "41.3825", + "geo_loc_longitude": "2.1769" + }, + { + "geo_loc_city": "Sevilla", + "geo_loc_latitude": "37.3900", + "geo_loc_longitude": "-5.9900" + }, + { + "geo_loc_city": "Málaga", + "geo_loc_latitude": "36.7194", + "geo_loc_longitude": "-4.4200" + }, + { + "geo_loc_city": "Valencia", + "geo_loc_latitude": "39.4700", + "geo_loc_longitude": "-0.3764" + }, + { + "geo_loc_city": "Zaragoza", + "geo_loc_latitude": "41.6483", + "geo_loc_longitude": "-0.8830" + }, + { + "geo_loc_city": "Palma de Mallorca", + "geo_loc_latitude": "39.5667", + "geo_loc_longitude": "2.6500" + }, + { + "geo_loc_city": "Murcia", + "geo_loc_latitude": "37.9861", + "geo_loc_longitude": "-1.1303" + }, + { + "geo_loc_city": "Las Palmas", + "geo_loc_latitude": "28.1272", + "geo_loc_longitude": "-15.4314" + }, + { + "geo_loc_city": "A Coruña", + "geo_loc_latitude": "43.3713", + "geo_loc_longitude": "-8.4188" + }, + { + "geo_loc_city": "Bilbao", + "geo_loc_latitude": "43.2569", + "geo_loc_longitude": "-2.9236" + }, + { + "geo_loc_city": "Alicante", + "geo_loc_latitude": "38.3453", + "geo_loc_longitude": "-0.4831" + }, + { + "geo_loc_city": "Córdoba", + "geo_loc_latitude": "37.8845", + "geo_loc_longitude": "-4.7796" + }, + { + "geo_loc_city": "Valladolid", + "geo_loc_latitude": "41.6528", + "geo_loc_longitude": "-4.7236" + }, + { + "geo_loc_city": "Vigo", + "geo_loc_latitude": "42.2314", + "geo_loc_longitude": "-8.7124" + }, + { + "geo_loc_city": "Gijón", + "geo_loc_latitude": "43.5333", + "geo_loc_longitude": "-5.7000" + }, + { + "geo_loc_city": "Vitoria-Gasteiz", + "geo_loc_latitude": "42.8500", + "geo_loc_longitude": "-2.6833" + }, + { + "geo_loc_city": "Elche", + "geo_loc_latitude": "38.2669", + "geo_loc_longitude": "-0.6983" + }, + { + "geo_loc_city": "Granada", + "geo_loc_latitude": "37.1781", + "geo_loc_longitude": "-3.6008" + }, + { + "geo_loc_city": "Tarrasa", + "geo_loc_latitude": "41.5611", + "geo_loc_longitude": "2.0081" + }, + { + "geo_loc_city": "Badalona", + "geo_loc_latitude": "41.4333", + "geo_loc_longitude": "2.2333" + }, + { + "geo_loc_city": "Oviedo", + "geo_loc_latitude": "43.3600", + "geo_loc_longitude": "-5.8450" + }, + { + "geo_loc_city": "Petrel", + "geo_loc_latitude": "38.4789", + "geo_loc_longitude": "-0.7967" + }, + { + "geo_loc_city": "Sabadell", + "geo_loc_latitude": "41.5483", + "geo_loc_longitude": "2.1075" + }, + { + "geo_loc_city": "Cartagena", + "geo_loc_latitude": "37.6000", + "geo_loc_longitude": "-0.9819" + }, + { + "geo_loc_city": "Jerez de la Frontera", + "geo_loc_latitude": "36.6817", + "geo_loc_longitude": "-6.1378" + }, + { + "geo_loc_city": "Santa Cruz", + "geo_loc_latitude": "28.4667", + "geo_loc_longitude": "-16.2500" + }, + { + "geo_loc_city": "Pamplona", + "geo_loc_latitude": "42.8167", + "geo_loc_longitude": "-1.6500" + }, + { + "geo_loc_city": "León", + "geo_loc_latitude": "42.6056", + "geo_loc_longitude": "-5.5700" + }, + { + "geo_loc_city": "Almería", + "geo_loc_latitude": "36.8403", + "geo_loc_longitude": "-2.4681" + }, + { + "geo_loc_city": "Logroño", + "geo_loc_latitude": "42.4650", + "geo_loc_longitude": "-2.4456" + }, + { + "geo_loc_city": "Fuenlabrada", + "geo_loc_latitude": "40.2833", + "geo_loc_longitude": "-3.8000" + }, + { + "geo_loc_city": "Leganés", + "geo_loc_latitude": "40.3281", + "geo_loc_longitude": "-3.7644" + }, + { + "geo_loc_city": "Donostia", + "geo_loc_latitude": "43.3200", + "geo_loc_longitude": "-1.9800" + }, + { + "geo_loc_city": "Mataró", + "geo_loc_latitude": "41.5421", + "geo_loc_longitude": "2.4445" + }, + { + "geo_loc_city": "Albacete", + "geo_loc_latitude": "38.9956", + "geo_loc_longitude": "-1.8558" + }, + { + "geo_loc_city": "Castellón de la Plana", + "geo_loc_latitude": "39.9831", + "geo_loc_longitude": "-0.0331" + }, + { + "geo_loc_city": "Santander", + "geo_loc_latitude": "43.4628", + "geo_loc_longitude": "-3.8050" + }, + { + "geo_loc_city": "Getafe", + "geo_loc_latitude": "40.3047", + "geo_loc_longitude": "-3.7311" + }, + { + "geo_loc_city": "Alcorcón", + "geo_loc_latitude": "40.3500", + "geo_loc_longitude": "-3.8333" + }, + { + "geo_loc_city": "Burgos", + "geo_loc_latitude": "42.3500", + "geo_loc_longitude": "-3.6822" + }, + { + "geo_loc_city": "Guadalajara", + "geo_loc_latitude": "40.6337", + "geo_loc_longitude": "-3.1674" + }, + { + "geo_loc_city": "La Laguna", + "geo_loc_latitude": "28.4853", + "geo_loc_longitude": "-16.3167" + }, + { + "geo_loc_city": "Badajoz", + "geo_loc_latitude": "38.8803", + "geo_loc_longitude": "-6.9753" + }, + { + "geo_loc_city": "Marbella", + "geo_loc_latitude": "36.5167", + "geo_loc_longitude": "-4.8833" + }, + { + "geo_loc_city": "Salamanca", + "geo_loc_latitude": "40.9667", + "geo_loc_longitude": "-5.6639" + }, + { + "geo_loc_city": "Huelva", + "geo_loc_latitude": "37.2500", + "geo_loc_longitude": "-6.9500" + }, + { + "geo_loc_city": "Ciudad de Melilla", + "geo_loc_latitude": "35.2937", + "geo_loc_longitude": "-2.9383" + }, + { + "geo_loc_city": "Tarragona", + "geo_loc_latitude": "41.1187", + "geo_loc_longitude": "1.2453" + }, + { + "geo_loc_city": "Dos Hermanas", + "geo_loc_latitude": "37.2836", + "geo_loc_longitude": "-5.9222" + }, + { + "geo_loc_city": "Torrejón de Ardoz", + "geo_loc_latitude": "40.4614", + "geo_loc_longitude": "-3.4978" + }, + { + "geo_loc_city": "Algeciras", + "geo_loc_latitude": "36.1275", + "geo_loc_longitude": "-5.4539" + }, + { + "geo_loc_city": "Cádiz", + "geo_loc_latitude": "36.5350", + "geo_loc_longitude": "-6.2975" + }, + { + "geo_loc_city": "Jaén", + "geo_loc_latitude": "37.7667", + "geo_loc_longitude": "-3.7711" + }, + { + "geo_loc_city": "Reus", + "geo_loc_latitude": "41.1549", + "geo_loc_longitude": "1.1087" + }, + { + "geo_loc_city": "Girona", + "geo_loc_latitude": "41.9833", + "geo_loc_longitude": "2.8167" + }, + { + "geo_loc_city": "San Vicente de Baracaldo", + "geo_loc_latitude": "43.2972", + "geo_loc_longitude": "-2.9917" + }, + { + "geo_loc_city": "Lugo", + "geo_loc_latitude": "43.0167", + "geo_loc_longitude": "-7.5500" + }, + { + "geo_loc_city": "Roquetas de Mar", + "geo_loc_latitude": "36.7642", + "geo_loc_longitude": "-2.6147" + }, + { + "geo_loc_city": "Cáceres", + "geo_loc_latitude": "39.4833", + "geo_loc_longitude": "-6.3667" + }, + { + "geo_loc_city": "Las Rozas de Madrid", + 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+ "geo_loc_latitude": "42.0114", + "geo_loc_longitude": "-7.0453" + }, + { + "geo_loc_city": "San José", + "geo_loc_latitude": "36.7578", + "geo_loc_longitude": "-2.1094" + }, + { + "geo_loc_city": "Alhama de Aragón", + "geo_loc_latitude": "41.3000", + "geo_loc_longitude": "-1.9000" + }, + { + "geo_loc_city": "Albanchez de Úbeda", + "geo_loc_latitude": "37.7917", + "geo_loc_longitude": "-3.4500" + }, + { + "geo_loc_city": "Otívar", + "geo_loc_latitude": "36.8167", + "geo_loc_longitude": "-3.6833" + }, + { + "geo_loc_city": "Arenas de San Juan", + "geo_loc_latitude": "39.2167", + "geo_loc_longitude": "-3.5000" + }, + { + "geo_loc_city": "Ruente", + "geo_loc_latitude": "43.2594", + "geo_loc_longitude": "-4.2661" + }, + { + "geo_loc_city": "San Cugat Sasgarrigas", + "geo_loc_latitude": "41.3661", + "geo_loc_longitude": "1.7542" + }, + { + "geo_loc_city": "Pinell de Bray", + "geo_loc_latitude": "41.0155", + "geo_loc_longitude": "0.5144" + }, + { + "geo_loc_city": "Bermillo de Sayago", + "geo_loc_latitude": "41.3669", + "geo_loc_longitude": "-6.1121" + }, + { + "geo_loc_city": "Albarracín", + "geo_loc_latitude": "40.4053", + "geo_loc_longitude": "-1.4440" + }, + { + "geo_loc_city": "Santibáñez de la Peña", + "geo_loc_latitude": "42.8167", + "geo_loc_longitude": "-4.7167" + }, + { + "geo_loc_city": "Elciego", + "geo_loc_latitude": "42.5167", + "geo_loc_longitude": "-2.6167" + }, + { + "geo_loc_city": "Báscara", + "geo_loc_latitude": "42.1622", + "geo_loc_longitude": "2.9111" + }, + { + "geo_loc_city": "Ourense", + "geo_loc_latitude": "42.3364", + "geo_loc_longitude": "-7.8633" + }, + { + "geo_loc_city": "Palencia", + "geo_loc_latitude": "42.0167", + "geo_loc_longitude": "-4.5333" + }, + { + "geo_loc_city": "Lleida", + "geo_loc_latitude": "41.6167", + "geo_loc_longitude": "0.6222" + }, + { + "geo_loc_city": "Segovia", + "geo_loc_latitude": "40.9481", + "geo_loc_longitude": "-4.1184" + }, + { + "geo_loc_city": "Ciudad Real", + "geo_loc_latitude": "38.9833", + "geo_loc_longitude": "-3.9167" + }, + { + "geo_loc_city": "Soria", + "geo_loc_latitude": "41.7667", + "geo_loc_longitude": "-2.4667" + } +] diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json new file mode 100644 index 00000000..256fe123 --- /dev/null +++ b/relecov_tools/conf/laboratory_address.json @@ -0,0 +1,134 @@ +[ + { + "collecting_institution": "Microbiología HUC San Cecilio", + "geo_loc_country" : "Spain", + "geo_loc_state": "Andalucia", + "geo_loc_city": "Granada" + }, + { + "collecting_institution": "Microbiología. Hospital Universitario Virgen del Rocio", + "geo_loc_country" : "Spain", + "geo_loc_state": "Andalucia", + "geo_loc_city": "Sevilla" + }, + { + "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", + "geo_loc_country" : "Spain", + "geo_loc_state": "Aragon", + "geo_loc_city": "Zaragoza" + }, + { + "collecting_institution": "Hospital Universitario Miguel Servet", + "geo_loc_country" : "Spain", + "geo_loc_state": "Aragon", + "geo_loc_city": "Zaragoza" + }, + { + "collecting_institution": "Centro de Investigación Biomédica de Aragón", + "geo_loc_country" : "Spain", + "geo_loc_state": "Aragon", + "geo_loc_city": "Zaragoza" + }, + { + "collecting_institution": "Hospital Universitario Central de Asturias", + "geo_loc_country" : "Spain", + "geo_loc_state": "Asturias", + "geo_loc_city": "Oviedo" + }, + { + "collecting_institution": "Servicio de Microbiologia HU Son Espases", + "geo_loc_country" : "Spain", + "geo_loc_state": "Baleares", + "geo_loc_city": "Palma de Mallorca" + }, + { + "collecting_institution": "", + "geo_loc_country" : "Spain", + "geo_loc_state": "", + "geo_loc_city": "" + }, + { + "collecting_institution": "", + "geo_loc_country" : "Spain", + "geo_loc_state": "", + "geo_loc_city": "" + }, + { + "collecting_institution": "", + "geo_loc_country" : "Spain", + "geo_loc_state": "", + "geo_loc_city": "" + }, + { + "collecting_institution": "", + "geo_loc_country" : "Spain", + "geo_loc_state": "", + "geo_loc_city": "" + }, + { + "collecting_institution": "", + "geo_loc_country" : "Spain", + "geo_loc_state": "", + "geo_loc_city": "" + }, + { + "collecting_institution": "", + "geo_loc_country" : "Spain", + "geo_loc_state": "", + "geo_loc_city": "" + }, + { + "collecting_institution": "", + "geo_loc_country" : "Spain", + "geo_loc_state": "", + "geo_loc_city": "" + }, + { + "collecting_institution": "", + "geo_loc_country" : "Spain", + "geo_loc_state": "", + "geo_loc_city": "" + }, + { + "collecting_institution": "", + "geo_loc_country" : "Spain", + "geo_loc_state": "", + "geo_loc_city": "" + }, + { + "collecting_institution": "", + "geo_loc_country" : "Spain", + "geo_loc_state": "", + "geo_loc_city": "" + }, + { + "collecting_institution": "", + "geo_loc_country" : "Spain", + "geo_loc_state": "", + "geo_loc_city": "" + }, + { + "collecting_institution": "", + "geo_loc_country" : "Spain", + "geo_loc_state": "", + "geo_loc_city": "" + }, + { + "collecting_institution": "", + "geo_loc_country" : "Spain", + "geo_loc_state": "", + "geo_loc_city": "" + }, + { + "collecting_institution": "", + "geo_loc_country" : "Spain", + "geo_loc_state": "", + "geo_loc_city": "" + }, + { + "collecting_institution": "", + "geo_loc_country" : "Spain", + "geo_loc_state": "", + "geo_loc_city": "" + }, +] diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index beffcf89..e3465ab6 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -152,11 +152,11 @@ def read_metadata_file(self, meta_map_json): wb_file = openpyxl.load_workbook(self.metadata_file, data_only=True) ws_metadata_lab = wb_file["METADATA_LAB"] # removing the None columns in excel heading row - heading_without_none = [i.value.strip() for i in ws_metadata_lab[1] if i.value] + heading_without_none = [i.value.strip() for i in ws_metadata_lab[4] if i.value] heading = self.update_heading_to_json(heading_without_none, meta_map_json) metadata_values = [] errors = {} - for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row): + for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): sample_data_row = {} for idx in range(len(heading)): if "date" in heading[idx]: @@ -167,9 +167,11 @@ def read_metadata_file(self, meta_map_json): errors[row[0]] = {} errors[row[0]][heading[idx]] = "Invalid date format" else: - if heading[idx] == "host_age": - sample_data_row[heading[idx]] = row[idx] if row[idx] else "" + # if heading[idx] == "host_age": + # import pdb; pdb.set_trace() + sample_data_row[heading[idx]] = row[idx] if row[idx] else "" metadata_values.append(sample_data_row) + import pdb; pdb.set_trace() return metadata_values, errors def write_json_fo_file(self, completed_metadata, file_name): @@ -200,6 +202,7 @@ def create_metadata_json(self): meta_map_json = self.read_json_file(meta_map_json_file) valid_metadata_rows, errors = self.read_metadata_file(meta_map_json) + completed_metadata = self.add_extra_data( valid_metadata_rows, meta_map_json["Additional_fields"] ) From d2c08419242c4b38aad184bc1bb14727b54fb8e8 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 28 Mar 2022 17:04:09 +0200 Subject: [PATCH 0206/1454] Updating to read geo location from json --- relecov_tools/read_metadata.py | 65 ++++++++++++++++++++++++++++------ 1 file changed, 55 insertions(+), 10 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index e3465ab6..dc065f2d 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -73,17 +73,61 @@ def add_extra_data(self, metadata, extra_data): """ geo_loc_data = {} extra_metadata = [] + fh_lab = open( + os.path.join(os.path.dirname(__file__), "conf", "laboratory_address.json") + ) + + laboratory_json = json.load(fh_lab) + fh_lab.close() + fh_geo = open( + os.path.join(os.path.dirname(__file__), "conf", "geo_loc_cities.json") + ) + + geo_loc_json = json.load(fh_geo) + fh_geo.close() + for row in metadata: for new_field, value in extra_data.items(): row[new_field] = value - # get the geo location latitude and longitude + # from collecting_institution find city, and geo location latitude and longitude + for lab in laboratory_json: + if row["collecting_institution"] == lab["collecting_institution"]: + for key, value in lab.items(): + row[key] = value + if row["geo_loc_city"] in geo_loc_data: + row["geo_loc_latitude"] = geo_loc_data[row["geo_loc_city"]][ + "geo_loc_latitude" + ] + row["geo_loc_longitude"] = geo_loc_data[row["geo_loc_city"]][ + "geo_loc_longitude" + ] + break + else: + for city in geo_loc_json: + if city["geo_loc_city"] == row["geo_loc_city"]: + geo_loc_data[city["geo_loc_city"]] = {} + geo_loc_data[city["geo_loc_city"]][ + "geo_loc_latitude" + ] = city["geo_loc_latitude"] + geo_loc_data[city["geo_loc_city"]][ + "geo_loc_longitude" + ] = city["geo_loc_longitude"] + row["geo_loc_latitude"] = geo_loc_data[ + city["geo_loc_city"] + ]["geo_loc_latitude"] + row["geo_loc_longitude"] = geo_loc_data[ + city["geo_loc_city"] + ]["geo_loc_longitude"] + break + """ country = row["geo_loc_country"] city = row["geo_loc_state"] if city not in geo_loc_data: geo_loc_data[city] = self.get_geo_location_data(city, country) row["geo_loc_latitude"], row["geo_loc_longitude"] = geo_loc_data[city] + """ # update isolate qith the name of the sample - row["isolate"] = row["sample_name"] + row["isolate"] = row["collecting_lab_sample_id"] row["host_scientific_name"] = extra_data["host_scientific_name"][ row["host_common_name"] ] @@ -92,7 +136,7 @@ def add_extra_data(self, metadata, extra_data): return extra_metadata def compare_sample_in_metadata(self, completed_metadata): - """Compare te samples defined in metadata file and the ones in the + """Compare the samples defined in metadata file and the ones in the sample file """ not_found_samples = [] @@ -102,8 +146,8 @@ def compare_sample_in_metadata(self, completed_metadata): with open(self.sample_list_file, "r") as fh: samples = fh.read().split("\n") for line_metadata in completed_metadata: - if line_metadata["sample_name"] not in samples: - not_found_samples.append(line_metadata["sample_name"]) + if line_metadata["collecting_institution"] not in samples: + not_found_samples.append(line_metadata["collecting_institution"]) if len(not_found_samples) > 0: return not_found_samples return True @@ -167,19 +211,20 @@ def read_metadata_file(self, meta_map_json): errors[row[0]] = {} errors[row[0]][heading[idx]] = "Invalid date format" else: - # if heading[idx] == "host_age": - # import pdb; pdb.set_trace() sample_data_row[heading[idx]] = row[idx] if row[idx] else "" metadata_values.append(sample_data_row) - import pdb; pdb.set_trace() return metadata_values, errors def write_json_fo_file(self, completed_metadata, file_name): """Write metadata to json file""" os.makedirs(self.output_folder, exist_ok=True) json_file = os.path.join(self.output_folder, file_name) - with open(json_file, "w") as fh: - fh.write(json.dumps(completed_metadata)) + with open(json_file, "w", encoding="utf-8") as fh: + fh.write( + json.dumps( + completed_metadata, indent=4, sort_keys=True, ensure_ascii=False + ) + ) return True def create_metadata_json(self): From 4f271c1d1076b0ce30abe10044b990fa4372610c Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 28 Mar 2022 17:04:58 +0200 Subject: [PATCH 0207/1454] first draft laboratory and changes in mapping with the new changes --- relecov_tools/conf/laboratory_address.json | 2 +- relecov_tools/schema/mapping_metadata_to_json.json | 10 +++++----- relecov_tools/schema/phage_plus_schema.json | 12 ++++++------ 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 256fe123..f2afd170 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -130,5 +130,5 @@ "geo_loc_country" : "Spain", "geo_loc_state": "", "geo_loc_city": "" - }, + } ] diff --git a/relecov_tools/schema/mapping_metadata_to_json.json b/relecov_tools/schema/mapping_metadata_to_json.json index 0de5c9a0..debcf610 100644 --- a/relecov_tools/schema/mapping_metadata_to_json.json +++ b/relecov_tools/schema/mapping_metadata_to_json.json @@ -1,10 +1,10 @@ { "Public Health sample id (SIVIES)": "XXXXXXXXXXX", - "Sample ID given by originating laboratory": "sample_name", + "Sample ID given by originating laboratory": "collecting_lab_sample_id", "Sample ID given by the submitting laboratory" : "submitting_lab_sequence_id", - "Sample ID given in the microbiology lab": "XXXXXXX", - "Sample ID given if multiple rna-extraction or passages": "XXXXXXXXXXXX", - "Sample ID given for sequencing": "sequencing_sample_id", + "Sample ID given in the microbiology lab": "microbiology_lab_sample_id", + "Sample ID given if multiple rna-extraction or passages": "isolate_sample_id", + "Sample ID given for sequencing": "isolate_sample_id", "ENA Sample ID": "biosample_accession_ENA", "GISAID Virus Name": "virus_name", "GISAID id": "gisaid_id", @@ -15,7 +15,7 @@ "Purpose of sampling": "purpose_of_sampling", "Biological Sample Storage Condition": "sample_storage_conditions", "Specimen source": "anatomical_material", - "Anatomical Structure": "XXXXXXXXXXXXXXX", + "Anatomical Structure": "anatomical_part", "Environmental Material": "environmental_material", "Environmental System": "environmental_site", "Source material": "biomaterial_extracted", diff --git a/relecov_tools/schema/phage_plus_schema.json b/relecov_tools/schema/phage_plus_schema.json index ed7382aa..5cc27761 100644 --- a/relecov_tools/schema/phage_plus_schema.json +++ b/relecov_tools/schema/phage_plus_schema.json @@ -1,7 +1,7 @@ { "schema": "PHAGE_PLUS", "required": [ - "sample_name", + "collecting_lab_sample_id", "collecting_institution", "submitting_institution", "sample_collection_date", @@ -16,7 +16,7 @@ ], "type": "object", "properties": { - "sample_name": { + "collecting_lab_sample_id": { "examples": [ "prov_rona_99" ], @@ -24,7 +24,7 @@ "type": "string", "description": "The user-defined name for the sample.", "clasification": "Database Identifiers", - "label": "Collecting Sample id" + "label": "Sample ID given by originating laboratory" }, "collecting_institution": { "examples": [ @@ -801,7 +801,7 @@ "Blood [UBERON:0000178]" ], "classification": "Sample collection and processing", - "label": "Organism Substance" + "label": "Specimen source" }, "anatomical_part": { "Enums": [ @@ -1248,11 +1248,11 @@ "examples": [ "" ], - "ontology": "0", + "ontology": "GENEPIO:0000079", "type": "number", "description": "If the information is unknown or can not be shared, leave blank.", "clasification": "Database Identifiers", - "label": "Sequencing Sample Id" + "label": "Sample ID given for sequencing" }, "passage_details": { "examples": [ From c3b0cf5af5d04a23cf308f8121a02f3878740be8 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 28 Mar 2022 18:52:36 +0200 Subject: [PATCH 0208/1454] create json file with the samples , location_folder and md5 file --- relecov_tools/read_metadata.py | 16 +++++++++++----- relecov_tools/sftp_handled.py | 15 ++++++++++----- 2 files changed, 21 insertions(+), 10 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index dc065f2d..4e4dfaa1 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -76,16 +76,18 @@ def add_extra_data(self, metadata, extra_data): fh_lab = open( os.path.join(os.path.dirname(__file__), "conf", "laboratory_address.json") ) - laboratory_json = json.load(fh_lab) fh_lab.close() fh_geo = open( os.path.join(os.path.dirname(__file__), "conf", "geo_loc_cities.json") ) - geo_loc_json = json.load(fh_geo) fh_geo.close() - + samples_data = {} + fh_samples = open(self.sample_list_file, "r") + for line in fh_samples.readlines(): + line_split = line.strip().split(",") + samples_data[line_split[0]] = [line_split[1], line_split[2]] for row in metadata: for new_field, value in extra_data.items(): row[new_field] = value @@ -119,6 +121,10 @@ def add_extra_data(self, metadata, extra_data): city["geo_loc_city"] ]["geo_loc_longitude"] break + try: + row["sequence_file_R1_fastq"] = samples_data[row["collecting_lab_sample_id"]] + except KeyError: + pass """ country = row["geo_loc_country"] city = row["geo_loc_state"] @@ -146,8 +152,8 @@ def compare_sample_in_metadata(self, completed_metadata): with open(self.sample_list_file, "r") as fh: samples = fh.read().split("\n") for line_metadata in completed_metadata: - if line_metadata["collecting_institution"] not in samples: - not_found_samples.append(line_metadata["collecting_institution"]) + if line_metadata["collecting_lab_sample_id"] not in samples: + not_found_samples.append(line_metadata["collecting_lab_sample_id"]) if len(not_found_samples) > 0: return not_found_samples return True diff --git a/relecov_tools/sftp_handled.py b/relecov_tools/sftp_handled.py index 441d3257..f3bdc8b4 100644 --- a/relecov_tools/sftp_handled.py +++ b/relecov_tools/sftp_handled.py @@ -1,6 +1,7 @@ #!/usr/bin/env python from datetime import datetime import logging +import json import rich.console import paramiko import sys @@ -217,18 +218,22 @@ def create_tmp_files_with_metadata_info(self, local_folder, file_list, md5_data) except OSError as e: log.error("Unable to copy Metadata file %s", e) stderr.print("[red] Unable to copy Metadata file") - sample_data = [] + sample_data = {} for key, values in md5_data.items(): if key.endswith(tuple(self.allowed_sample_ext)): - sample_data.append(key + "," + ",".join(values)) + if key.split(".")[0] not in sample_data: + sample_data[key.split(".")[0]] = {} + sample_data[key.split(".")[0]][key] = values + # sample_data.append(key + "," + ",".join(values)) if len(sample_data) == 0: log.error("There is no samples in folder %s", local_folder) stderr.print("[red] There is no samples for this local folder") else: - with open(sample_data_file, "w") as fh: - for sample in sample_data: - fh.write(sample + "\n") + with open(sample_data_file, "w" , encoding="utf-8") as fh: + fh.write(json.dumps( + sample_data, indent=4, sort_keys=True, ensure_ascii=False + )) return def create_main_folders(self, root_directory_list): From 599eb430149cf874e2ca14c6be268fbfb355c7c5 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 28 Mar 2022 22:12:56 +0200 Subject: [PATCH 0209/1454] Modify sample_file to json. --- relecov_tools/sftp_handled.py | 22 ++++++++++++++-------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/relecov_tools/sftp_handled.py b/relecov_tools/sftp_handled.py index f3bdc8b4..eb9cc9e7 100644 --- a/relecov_tools/sftp_handled.py +++ b/relecov_tools/sftp_handled.py @@ -219,21 +219,27 @@ def create_tmp_files_with_metadata_info(self, local_folder, file_list, md5_data) log.error("Unable to copy Metadata file %s", e) stderr.print("[red] Unable to copy Metadata file") sample_data = {} + for f_name, values in md5_data.items(): + if f_name.endswith(tuple(self.allowed_sample_ext)): + sample = f_name.split(".")[0] + if sample not in sample_data: + sample_data[sample] = {} + sample_data[sample][f_name] = {} + sample_data[sample][f_name]["local_folder"] = values[0] + sample_data[sample][f_name]["md5"] = values[1] - for key, values in md5_data.items(): - if key.endswith(tuple(self.allowed_sample_ext)): - if key.split(".")[0] not in sample_data: - sample_data[key.split(".")[0]] = {} - sample_data[key.split(".")[0]][key] = values # sample_data.append(key + "," + ",".join(values)) if len(sample_data) == 0: log.error("There is no samples in folder %s", local_folder) stderr.print("[red] There is no samples for this local folder") else: - with open(sample_data_file, "w" , encoding="utf-8") as fh: - fh.write(json.dumps( + with open(sample_data_file, "w", encoding="utf-8") as fh: + fh.write( + json.dumps( sample_data, indent=4, sort_keys=True, ensure_ascii=False - )) + ) + ) + fh.close() return def create_main_folders(self, root_directory_list): From 17162f5cdcd006429573c1c9cbc1b4dfe89b7e6d Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 28 Mar 2022 22:13:40 +0200 Subject: [PATCH 0210/1454] reformating for litin --- relecov_tools/read_metadata.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 4e4dfaa1..b8e4ce19 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -122,7 +122,9 @@ def add_extra_data(self, metadata, extra_data): ]["geo_loc_longitude"] break try: - row["sequence_file_R1_fastq"] = samples_data[row["collecting_lab_sample_id"]] + row["sequence_file_R1_fastq"] = samples_data[ + row["collecting_lab_sample_id"] + ] except KeyError: pass """ From 923039aaafee4db30ef507c6c70670b950e30921 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 29 Mar 2022 00:43:03 +0200 Subject: [PATCH 0211/1454] Including samples information inside the extra data --- relecov_tools/conf/configuration.json | 2 + relecov_tools/read_metadata.py | 140 ++++++++++++++------------ 2 files changed, 75 insertions(+), 67 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 66a74a5f..3c6da228 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -17,6 +17,8 @@ "fastq.gz", "fasta" ], + "laboratory_data": "laboratory_address.json", + "geo_location_data" : "geo_loc_cities", "study": { "alias": "RELECOV", "title": "Example project for ENA submission RELECOV", diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index b8e4ce19..a0ab7b57 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -62,78 +62,79 @@ def fetch_metadata_file(folder, file_name): for cell in ws_metadata_lab[1]: heading.append(cell.value) - def validate_metadata_sample(row_sample): - """Validate sample information""" + def read_json_file(self, j_file): + """Read json file.""" + with open(j_file, "r") as fh: + data = json.load(fh) + return data - def add_extra_data(self, metadata, extra_data): + def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): + """Fetch the laboratory location and return a dictionary""" + data = {} + for lab in lab_json: + if lab_name == lab["collecting_institution"]: + for key, value in lab_name.items(): + data[key] = value + break + for city in geo_loc_json: + if city["geo_loc_city"] == data["geo_loc_city"]: + data[city["geo_loc_city"]] = {} + data[city["geo_loc_city"]]["geo_loc_latitude"] = city[ + "geo_loc_latitude" + ] + data[city["geo_loc_city"]]["geo_loc_longitude"] = city[ + "geo_loc_longitude" + ] + break + return data + + def add_extra_data(self, metadata, extra_data, lab_json_file, geo_loc_file): """Add the additional information that must be included in final metadata metadata Origin metadata extra_data additional data to be included result_metadata final metadata after adding the additional data """ - geo_loc_data = {} + lab_data = {} extra_metadata = [] - fh_lab = open( - os.path.join(os.path.dirname(__file__), "conf", "laboratory_address.json") - ) - laboratory_json = json.load(fh_lab) - fh_lab.close() - fh_geo = open( - os.path.join(os.path.dirname(__file__), "conf", "geo_loc_cities.json") - ) - geo_loc_json = json.load(fh_geo) - fh_geo.close() - samples_data = {} - fh_samples = open(self.sample_list_file, "r") - for line in fh_samples.readlines(): - line_split = line.strip().split(",") - samples_data[line_split[0]] = [line_split[1], line_split[2]] + lab_json = self.read_json_file(lab_json_file) + geo_loc_json = self.read_json_file(geo_loc_file) + samples_json = self.read_json_file(self.sample_list_file) + for row in metadata: for new_field, value in extra_data.items(): row[new_field] = value - # from collecting_institution find city, and geo location latitude and longitude - for lab in laboratory_json: - if row["collecting_institution"] == lab["collecting_institution"]: - for key, value in lab.items(): - row[key] = value - if row["geo_loc_city"] in geo_loc_data: - row["geo_loc_latitude"] = geo_loc_data[row["geo_loc_city"]][ - "geo_loc_latitude" - ] - row["geo_loc_longitude"] = geo_loc_data[row["geo_loc_city"]][ - "geo_loc_longitude" - ] - break - else: - for city in geo_loc_json: - if city["geo_loc_city"] == row["geo_loc_city"]: - geo_loc_data[city["geo_loc_city"]] = {} - geo_loc_data[city["geo_loc_city"]][ - "geo_loc_latitude" - ] = city["geo_loc_latitude"] - geo_loc_data[city["geo_loc_city"]][ - "geo_loc_longitude" - ] = city["geo_loc_longitude"] - row["geo_loc_latitude"] = geo_loc_data[ - city["geo_loc_city"] - ]["geo_loc_latitude"] - row["geo_loc_longitude"] = geo_loc_data[ - city["geo_loc_city"] - ]["geo_loc_longitude"] - break + if row["collecting_institution"] not in lab_data: + # from collecting_institution find city, and geo location latitude and longitude + l_data = self.get_laboratory_data( + lab_json, geo_loc_json, row["collecting_institution"] + ) + row.update(l_data) + lab_data[row["collecting_institution"]] = l_data + else: + row.update(lab_data[row["collecting_institution"]]) + try: - row["sequence_file_R1_fastq"] = samples_data[ - row["collecting_lab_sample_id"] - ] + s_data = samples_json[row["collecting_lab_sample_id"]] + for key, values in s_data.items(): + if key.endswith("_R1_fastq.gz"): + row["sequence_file_R1_fastq"] = key + row["r1_fastq_filepath"] = values["local_folder"] + row["fastq_md5"] = values["md5"] + elif key.endswith("_R2_fastq.gz"): + row["sequence_file_R2_fastq"] = key + row["r2_fastq_filepath"] = values["local_folder"] + # # WARNING: no md5 value for R2 is deficned on schena + # row["fastq_md5"] = values["md5"] + elif key.endswith(".fasta"): + file_path = os.path.join(values["local_folder"], key) + row["consensus_sequence_filepath"] = file_path + # # WARNING: no md5 value for fasta is deficned on schena + # row["fastq_md5"] = values["md5"] except KeyError: - pass - """ - country = row["geo_loc_country"] - city = row["geo_loc_state"] - if city not in geo_loc_data: - geo_loc_data[city] = self.get_geo_location_data(city, country) - row["geo_loc_latitude"], row["geo_loc_longitude"] = geo_loc_data[city] - """ + log.error( + "There is no files for sample %s", row["collecting_lab_sample_id"] + ) + # update isolate qith the name of the sample row["isolate"] = row["collecting_lab_sample_id"] row["host_scientific_name"] = extra_data["host_scientific_name"][ @@ -190,12 +191,6 @@ def update_heading_to_json(self, heading, meta_map_json): mapped_heading.append(cell) return mapped_heading - def read_json_file(self, j_file): - """Read json file.""" - with open(j_file, "r") as fh: - data = json.load(fh) - return data - def read_metadata_file(self, meta_map_json): """Read the input metadata file, mapping the metadata heading with the values used in json. Convert the date colunms value to the @@ -248,6 +243,14 @@ def create_metadata_json(self): phage_plus_schema = relecov_tools.schema_json.PhagePlusSchema(schema_json) properties_in_schema = phage_plus_schema.get_schema_properties() """ + geo_loc_json = config_json.get_configuration("geo_location_data") + geo_loc_file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), "conf", geo_loc_json + ) + lab_json = config_json.get_configuration("laboratory_data") + lab_json_file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), "conf", lab_json + ) metadata_mapping_json = config_json.get_configuration("mapping_metadata_json") meta_map_json_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", metadata_mapping_json @@ -257,7 +260,10 @@ def create_metadata_json(self): valid_metadata_rows, errors = self.read_metadata_file(meta_map_json) completed_metadata = self.add_extra_data( - valid_metadata_rows, meta_map_json["Additional_fields"] + valid_metadata_rows, + meta_map_json["Additional_fields"], + lab_json_file, + geo_loc_file, ) comp_result = self.compare_sample_in_metadata(completed_metadata) if isinstance(comp_result, list): From 3ec150ac1b015a4ad527fdbbc0b8627bcd9c6129 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 29 Mar 2022 13:36:35 +0200 Subject: [PATCH 0212/1454] removing and cleaning stuff --- relecov-tools | 14 -------------- relecov_tools/example_data/dummy_data.xlsx | Bin 8770 -> 0 bytes relecov_tools/example_data/dummy_data_new.xlsx | Bin 7390 -> 0 bytes relecov_tools/example_data/dummy_data_small.xlsx | Bin 7683 -> 0 bytes relecov_tools/example_data/metadata_leyenda.xlsx | Bin 9920 -> 0 bytes .../samples/programmatic/._samples.xml | Bin 212 -> 0 bytes .../{conversion_schema.py => map_schema.py} | 0 .../{sftp_handled.py => sftp_handle.py} | 0 8 files changed, 14 deletions(-) delete mode 100644 relecov-tools delete mode 100644 relecov_tools/example_data/dummy_data.xlsx delete mode 100644 relecov_tools/example_data/dummy_data_new.xlsx delete mode 100644 relecov_tools/example_data/dummy_data_small.xlsx delete mode 100644 relecov_tools/example_data/metadata_leyenda.xlsx delete mode 100644 relecov_tools/example_data/samples/programmatic/._samples.xml rename relecov_tools/{conversion_schema.py => map_schema.py} (100%) rename relecov_tools/{sftp_handled.py => sftp_handle.py} (100%) diff --git a/relecov-tools b/relecov-tools deleted file mode 100644 index a2bf5d2c..00000000 --- a/relecov-tools +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/bash - -echo -n Password: - -read -s password - -usuario=bioinfoadm -host=sftprelecov.isciii.es - -SSHPASS=$password sshpass -e sftp $usuario@$host <5YBAPH4*+G?E7aEH%kY1Zmx&_io_8G zWFCTuL;vV_uy+Hgj0LPUax_cM|4sVft(i~;klfQB9D<<_Ekciz4>%qYlFnQrvO0}^ zCmRiNF4Jd+#Qp++3v%(!cPU%#b%yANwG|lf&HKwHyB$tw6P*xiDS@+wYMr{qBHv7l z9)F6kSh4_zIvSZE-&t&(MMBS(ZI-WNv?I<#)2gAnpa}0ZV<2lb+K-_#S zgeoI48d`Z2%FPbk-j`ry43=qwny- 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zcmZQz6=P>$Vqox1Ojhs@R)|o50+1L3ClDI}@gg7w@vi_e5x_AdBnYYuq+J^qI7A5ADWagzZ6zUroSQuKH8Jeb;r&(B7J7*N-=cZblxHwxn lS(;hux*3|A>6#cA8tXbbn!4&58kv|myO@}mx|kU=004fSA2a{} diff --git a/relecov_tools/conversion_schema.py b/relecov_tools/map_schema.py similarity index 100% rename from relecov_tools/conversion_schema.py rename to relecov_tools/map_schema.py diff --git a/relecov_tools/sftp_handled.py b/relecov_tools/sftp_handle.py similarity index 100% rename from relecov_tools/sftp_handled.py rename to relecov_tools/sftp_handle.py From d3ea5f77a4b12de2e12160c76148d085c60089e8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 29 Mar 2022 13:37:29 +0200 Subject: [PATCH 0213/1454] more cleaning renaming --- .../schema/mapping_metadata_to_json.json | 100 ------------------ ...e_plus_schema.json => relecov_schema.json} | 0 2 files changed, 100 deletions(-) delete mode 100644 relecov_tools/schema/mapping_metadata_to_json.json rename relecov_tools/schema/{phage_plus_schema.json => relecov_schema.json} (100%) diff --git a/relecov_tools/schema/mapping_metadata_to_json.json b/relecov_tools/schema/mapping_metadata_to_json.json deleted file mode 100644 index ba891e56..00000000 --- a/relecov_tools/schema/mapping_metadata_to_json.json +++ /dev/null @@ -1,100 +0,0 @@ -{ - "Collecting Sample id": "sample_name", - "Sample ID given by the submitting laboratory" : "submitting_lab_sequence_id", - "Passage details": "passage_details", - "Sequencing sample id": "sequencing_sample_id", - "ENA Sample ID": "biosample_accession_ENA", - "GISAID Virus Name": "virus_name", - "GISAID id": "submitter", - "Country": "geo_loc_country", - "Autonomic community": "geo_loc_state", - "Province": "geo_loc_region", - "City":"geo_loc_city", - "Originating Laboratory": "collecting_institution", - "Originating Laboratory email": "collecting_institution_email", - "Originating Laboratory Address": "collecting_institution_address", - "Submitting Institution": "submitting_institution", - "Submitting Institution Email": "submitting_institution_email", - "Submitting Institution Address": "submitting_institution_address", - "Sample Collection Date": "sample_collection_date", - "Sample Received Date": "sample_received_date", - "Purpose of sampling": "purpose_of_sequencing", - "Biological Sample Storage Condition": "sample_storage_conditions", - "Specimen source": "anatomical_material", - "Anatomical Structure": "anatomical_part", - "Environmental Material": "environmental_material", - "Environmental System": "environmental_site", - "Sampling Device": "collection_device", - "Sampling method": "collection_method", - "Sampling Protocol": "collection_protocol", - "Specimen Processing": "specimen_processing", - "Lab passage Host": "lab_host", - "Passage Number": "passage_number", - "Passage Method": "passage_method", - "Nucleic acid extraction methods": "biomaterial_extracted", - "Host Common Name": "host_common_name", - "Host Age": "host_age", - "Host Age Unit": "host_age_unit", - "Host Age Bin": "host_age_bin", - "Host Gender": "host_gender", - "Outbreak Exposure Event Location": "outbreak", - "Additional Host Information": "additional_host_information", - "Purpose Of Sequencing Details": "purpose_of_sequencing", - "Sequencing Date": "sequencing_date", - "Rna Extraction Protocol": "rna_extraction_protocol", - "Library preparation kit": "library_preparation_kit", - "Enrichment Protocol": "enrichment_protocol", - "If Enrichment Protocol Is Other, Specify": "if_enrichment_protocol_is_other_specify", - "Amplicon Protocol": "amplicon_protocol", - "If Amplicon Protocol If Other, Especify": "if_amplicon_protocol_if_other_especify", - "Amplicon Version": "amplicon_protocol", - "Amplicon Size": "amplicon_size", - "Was Phix Used?": "was_phix_used?", - "Number Of Samples In Run": "number_of_samples_in_run", - "Flowcell Kit": "flowcell_kit", - "Runid": "runID", - "Sequencing Platforms": "sequencing_platforms", - "Library Preparation Kit": "library_kit", - "Flow Cell Barcode": "flow_cell_barcode", - "Sequencing Instrument Model": "sequencing_instrument_model", - "Sequencing Protocol Name": "sequencing_protocol_name", - "Sequencing Protocol": "sequencing_protocol", - "Sequencing Kit Number": "sequencing_kit_number", - "Amplicon Pcr Primer Scheme": "amplicon_pcr_primer_scheme", - "Library Source": "library_source", - "Library Selection": "library_selection", - "Library Strategy": "library_strategy", - "Library Layout": "library_layout", - "Library Name": "library_name", - "Nominal Length": "nominal_length", - "PCR Target 1": "gene_name_1", - "Diagnostic Pcr Protocol 1": "diagnostic_pcr_protocol_1", - "Diagnostic Pcr Ct Value 1": "diagnostic_pcr_Ct_value_1", - "PCR Target 2": "gene_name_2", - "Diagnostic Pcr Protocol 2": "diagnostic_pcr_protocol_2", - "Diagnostic Pcr Ct Value-2": "diagnostic_pcr_Ct_value_2", - "Analysis Authors": "analysis_author", - "Author Submitter": "author_submitter", - "Authors": "authors", - "Additional_fields": { - "geo_loc_latitude": "", - "geo_loc_longitude": "", - "organism": "sars_cov_2", - "isolate": "", - "host_scientific_name": { - "Human": "Homo sapiens" - }, - "host_disease":"COVID-19", - "sequence_file_R1_fastq": "", - "sequence_file_R2_fastq": "", - "type" : "betacoronavirus", - "tax_id": "2697049", - "scientific_name": "Severe acute respiratory syndrome coronavirus 2", - "study_alias": "", - "experiment_alias": "", - "run_alias": "", - "study_title": "", - "experiment_title": "", - - } -} diff --git a/relecov_tools/schema/phage_plus_schema.json b/relecov_tools/schema/relecov_schema.json similarity index 100% rename from relecov_tools/schema/phage_plus_schema.json rename to relecov_tools/schema/relecov_schema.json From c2023e675d392eb1ec8f70bd091eea069f0b5ba4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 29 Mar 2022 13:38:44 +0200 Subject: [PATCH 0214/1454] more renaming --- relecov_tools/{schema_json.py => json_schema.py} | 0 relecov_tools/{validation_json.py => json_validation.py} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename relecov_tools/{schema_json.py => json_schema.py} (100%) rename relecov_tools/{validation_json.py => json_validation.py} (100%) diff --git a/relecov_tools/schema_json.py b/relecov_tools/json_schema.py similarity index 100% rename from relecov_tools/schema_json.py rename to relecov_tools/json_schema.py diff --git a/relecov_tools/validation_json.py b/relecov_tools/json_validation.py similarity index 100% rename from relecov_tools/validation_json.py rename to relecov_tools/json_validation.py From be2e337fe8e48bfcdefb08680ccfd995498ccdd2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 29 Mar 2022 13:40:56 +0200 Subject: [PATCH 0215/1454] rename imports in main and download method name --- relecov_tools/__main__.py | 11 +++++------ relecov_tools/sftp_handle.py | 2 +- 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 2b0d6623..cafc2cf3 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -10,10 +10,10 @@ import relecov_tools.utils import relecov_tools.read_metadata -import relecov_tools.sftp_handled +import relecov_tools.sftp_handle import relecov_tools.ena_upload -import relecov_tools.validation_json -import relecov_tools.conversion_schema +import relecov_tools.json_validation +import relecov_tools.map_schema log = logging.getLogger() @@ -160,9 +160,8 @@ def list(keywords, sort, json, show_archived): ) def download_sftp(user, password, conf_file): """Download files located in sftp server.""" - sftp_connection = relecov_tools.sftp_handled.SftpHandle(user, password, conf_file) - sftp_connection.download_from_sftp() - + sftp_connection = relecov_tools.sftp_handle.SftpHandle(user, password, conf_file) + sftp_connection.download() # metadata @relecov_tools_cli.command(help_priority=3) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 65ac3df8..ccf29d8a 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -232,7 +232,7 @@ def create_main_folders(self, root_directory_list): os.makedirs(full_folder, exist_ok=True) return True - def download_from_sftp(self): + def download(self): try: os.makedirs(self.storage_local_folder, exist_ok=True) except OSError as e: From a375b3da3bd2be93117fd309473ab7045b13ea06 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 29 Mar 2022 13:51:38 +0200 Subject: [PATCH 0216/1454] added left functionalities to main, fixed names --- relecov_tools/__main__.py | 44 +++++++++++++++++++++++--------- relecov_tools/json_validation.py | 2 +- 2 files changed, 33 insertions(+), 13 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index cafc2cf3..a55f69da 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -158,7 +158,7 @@ def list(keywords, sort, json, show_archived): "--conf_file", help="Configuration file Create Nextflow command with params (no params file)", ) -def download_sftp(user, password, conf_file): +def download(user, password, conf_file): """Download files located in sftp server.""" sftp_connection = relecov_tools.sftp_handle.SftpHandle(user, password, conf_file) sftp_connection.download() @@ -201,13 +201,13 @@ def read_metadata(metadata_file, sample_list_file, metadata_out): @click.option("-j", "--json_file", help="Json file to validate") @click.option("-s", "--json_schema", help="Json schema") @click.option("-o", "--out_folder", help="Path to save validate json file") -def validation(json_file, json_schema, out_folder): +def validate(json_file, json_schema, out_folder): """Validate json file against schema.""" ( validated_json_data, invalid_json, errors, - ) = relecov_tools.validation_json.validate_json_vs_schema( + ) = relecov_tools.json_validation.validate( json_file, json_schema, out_folder ) if len(invalid_json) > 0: @@ -228,7 +228,7 @@ def validation(json_file, json_schema, out_folder): ) @click.option("-f", "--schema_file", help="file with the custom schema") @click.option("-o", "--output", help="File name and path to store the mapped json") -def mapped_schema( +def map( phage_plus_schema, json_data, destination_schema, schema_file, output ): """Convert data between phage plus schema to ENA, GISAID, or any other schema""" @@ -239,25 +239,45 @@ def mapped_schema( @relecov_tools_cli.command(help_priority=6) -@click.option("-u", "--user", help="User name for login to sftp server") +@click.option("-u", "--user", help="user name for login to ena") @click.option("-p", "--password", help="password for the user to login") -@click.option("-e", "--ena_json", help="Where the validated json is") +@click.option("-e", "--ena_json", help="where the validated json is") @click.option("-s", "--study", help="study/project name to include in xml files") @click.option( "-a", "--action", - type=click.Choice(["add", "modify", "cancel", "release"], case_sensitive=False), - help="Select one of the available options", + type=click.choice(["add", "modify", "cancel", "release"], case_sensitive=false), + help="select one of the available options", ) -@click.option("--dev/--production", default=True) -@click.option("-o", "--output_path", help="Output folder for the xml generated files") +@click.option("--dev/--production", default=true) +@click.option("-o", "--output_path", help="output folder for the xml generated files") def upload_to_ena(user, password, ena_json, dev, study, action, output_path): - """Parsed data to create xml files to upload to ENA""" - upload_ena = relecov_tools.ena_upload.EnaUpload( + """parsed data to create xml files to upload to ena""" + upload_ena = relecov_tools.ena_upload.enaupload( user, password, ena_json, dev, study, action, output_path ) upload_ena.upload_files_to_ena() +@relecov_tools_cli.command(help_priority=7) +@click.option("-u", "--user", help="user name for login") +@click.option("-p", "--password", help="password for the user to login") +@click.option("-e", "--gisaid_json", help="where the validated json is") +@click.option("-o", "--output_path", help="output folder for the xml generated files") +def upload_to_gisaid(user, password, gisaid_json, output_path): + """parsed data to create files to upload to gisaid""" + pass + +@relecov_tools_cli.command(help_priority=8) +@click.option("-u", "--user", help="user name for connecting to the server") +def launch(user): + """launch viralrecon in hpc""" + pass + +@relecov_tools_cli.command(help_priority=9) +@click.option("-j", "--json", help="data in json format") +def update_db(user): + """feed database with metadata jsons""" + pass if __name__ == "__main__": run_relecov_tools() diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 1206d34f..9b9f41c4 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -20,7 +20,7 @@ ) -def validate_json_vs_schema( +def validate( json_data_file=None, json_schema_file=None, out_folder=None ): """Validate json file against the schema""" From 1e2855a1f23e765a2282de88aeef0a558df832a1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 29 Mar 2022 13:52:53 +0200 Subject: [PATCH 0217/1454] removed empty download.py --- relecov_tools/download.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 relecov_tools/download.py diff --git a/relecov_tools/download.py b/relecov_tools/download.py deleted file mode 100644 index e69de29b..00000000 From eeb26f9dd4a2f1f8d84770fba7a2533053d63d23 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 29 Mar 2022 13:57:49 +0200 Subject: [PATCH 0218/1454] fixed renaming --- relecov_tools/read_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index beffcf89..f66b652b 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -11,7 +11,7 @@ import sys import relecov_tools.utils from relecov_tools.config_json import ConfigJson -import relecov_tools.schema_json +import relecov_tools.json_schema log = logging.getLogger(__name__) stderr = rich.console.Console( From df6944f2b4c2df3434015540b388993ae92d661b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 29 Mar 2022 14:10:12 +0200 Subject: [PATCH 0219/1454] black linting --- relecov_tools/__main__.py | 13 +++++++------ relecov_tools/json_validation.py | 4 +--- 2 files changed, 8 insertions(+), 9 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index a55f69da..e93d502b 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -163,6 +163,7 @@ def download(user, password, conf_file): sftp_connection = relecov_tools.sftp_handle.SftpHandle(user, password, conf_file) sftp_connection.download() + # metadata @relecov_tools_cli.command(help_priority=3) @click.option( @@ -207,9 +208,7 @@ def validate(json_file, json_schema, out_folder): validated_json_data, invalid_json, errors, - ) = relecov_tools.json_validation.validate( - json_file, json_schema, out_folder - ) + ) = relecov_tools.json_validation.validate(json_file, json_schema, out_folder) if len(invalid_json) > 0: log.error("Some of the samples in json metadata were not validated") else: @@ -228,9 +227,7 @@ def validate(json_file, json_schema, out_folder): ) @click.option("-f", "--schema_file", help="file with the custom schema") @click.option("-o", "--output", help="File name and path to store the mapped json") -def map( - phage_plus_schema, json_data, destination_schema, schema_file, output -): +def map(phage_plus_schema, json_data, destination_schema, schema_file, output): """Convert data between phage plus schema to ENA, GISAID, or any other schema""" new_schema = relecov_tools.conversion_schema.MappingSchema( phage_plus_schema, json_data, destination_schema, schema_file, output @@ -258,6 +255,7 @@ def upload_to_ena(user, password, ena_json, dev, study, action, output_path): ) upload_ena.upload_files_to_ena() + @relecov_tools_cli.command(help_priority=7) @click.option("-u", "--user", help="user name for login") @click.option("-p", "--password", help="password for the user to login") @@ -267,17 +265,20 @@ def upload_to_gisaid(user, password, gisaid_json, output_path): """parsed data to create files to upload to gisaid""" pass + @relecov_tools_cli.command(help_priority=8) @click.option("-u", "--user", help="user name for connecting to the server") def launch(user): """launch viralrecon in hpc""" pass + @relecov_tools_cli.command(help_priority=9) @click.option("-j", "--json", help="data in json format") def update_db(user): """feed database with metadata jsons""" pass + if __name__ == "__main__": run_relecov_tools() diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 9b9f41c4..c737cd0a 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -20,9 +20,7 @@ ) -def validate( - json_data_file=None, json_schema_file=None, out_folder=None -): +def validate(json_data_file=None, json_schema_file=None, out_folder=None): """Validate json file against the schema""" if json_data_file is None: json_data_file = relecov_tools.utils.prompt_path( From be13c40d0284b3edc0c5858cc72ea46fc14ef4c6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 29 Mar 2022 14:13:21 +0200 Subject: [PATCH 0220/1454] fixed true false typo --- relecov_tools/__main__.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index e93d502b..bb02eba1 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -243,10 +243,10 @@ def map(phage_plus_schema, json_data, destination_schema, schema_file, output): @click.option( "-a", "--action", - type=click.choice(["add", "modify", "cancel", "release"], case_sensitive=false), + type=click.choice(["add", "modify", "cancel", "release"], case_sensitive=False), help="select one of the available options", ) -@click.option("--dev/--production", default=true) +@click.option("--dev/--production", default=True) @click.option("-o", "--output_path", help="output folder for the xml generated files") def upload_to_ena(user, password, ena_json, dev, study, action, output_path): """parsed data to create xml files to upload to ena""" From b6178f57896531c9e5749512497108e3084d4654 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 29 Mar 2022 14:16:25 +0200 Subject: [PATCH 0221/1454] continue fixed renaming --- relecov_tools/__main__.py | 4 ++-- relecov_tools/ena_upload.py | 2 +- relecov_tools/json_validation.py | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index bb02eba1..fa362274 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -208,7 +208,7 @@ def validate(json_file, json_schema, out_folder): validated_json_data, invalid_json, errors, - ) = relecov_tools.json_validation.validate(json_file, json_schema, out_folder) + ) = relecov_tools.json_validation.validate_json(json_file, json_schema, out_folder) if len(invalid_json) > 0: log.error("Some of the samples in json metadata were not validated") else: @@ -250,7 +250,7 @@ def map(phage_plus_schema, json_data, destination_schema, schema_file, output): @click.option("-o", "--output_path", help="output folder for the xml generated files") def upload_to_ena(user, password, ena_json, dev, study, action, output_path): """parsed data to create xml files to upload to ena""" - upload_ena = relecov_tools.ena_upload.enaupload( + upload_ena = relecov_tools.ena_upload.upload( user, password, ena_json, dev, study, action, output_path ) upload_ena.upload_files_to_ena() diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 25a9968f..cb843356 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -116,7 +116,7 @@ def create_structure_to_ena(self): schema_dataframe[xml_file] = df return schema_dataframe - def upload_files_to_ena(self): + def upload(self): """Create the required files and upload to ENA""" self.convert_input_json_to_ena() self.create_structure_to_ena() diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index c737cd0a..509a3469 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -20,7 +20,7 @@ ) -def validate(json_data_file=None, json_schema_file=None, out_folder=None): +def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): """Validate json file against the schema""" if json_data_file is None: json_data_file = relecov_tools.utils.prompt_path( From 7daf70889593d590dd913f445b864c7ecdd2d4a0 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 29 Mar 2022 14:31:45 +0200 Subject: [PATCH 0222/1454] Added test parameter for testing and create sftp config for testing --- relecov_tools/__main__.py | 3 ++- relecov_tools/example_data/samples/sftp_config.yaml | 11 +++++++++++ relecov_tools/sftp_handled.py | 6 +++++- 3 files changed, 18 insertions(+), 2 deletions(-) create mode 100644 relecov_tools/example_data/samples/sftp_config.yaml diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 2b0d6623..19300645 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -158,9 +158,10 @@ def list(keywords, sort, json, show_archived): "--conf_file", help="Configuration file Create Nextflow command with params (no params file)", ) +@click.option("--test", is_flag=True, default=False, help="download files for testing") def download_sftp(user, password, conf_file): """Download files located in sftp server.""" - sftp_connection = relecov_tools.sftp_handled.SftpHandle(user, password, conf_file) + sftp_connection = relecov_tools.sftp_handled.SftpHandle(user, password, conf_file, test) sftp_connection.download_from_sftp() diff --git a/relecov_tools/example_data/samples/sftp_config.yaml b/relecov_tools/example_data/samples/sftp_config.yaml new file mode 100644 index 00000000..d6ded6ae --- /dev/null +++ b/relecov_tools/example_data/samples/sftp_config.yaml @@ -0,0 +1,11 @@ +sftp_serve": "sftprelecov.isciii.es", +sftp_port": "22", +sftp_user : "usuario_test", +sftp_passwd : "U[9[Gpyu3.", +storage_local_folder: "/tmp/relecov", +tmp_folder_for_metadata: "/tmp/relecov/tmp", +allowed_sample_extensions: extensions + +extensions: + -fastq.gz + -fasta diff --git a/relecov_tools/sftp_handled.py b/relecov_tools/sftp_handled.py index eb9cc9e7..ca24d264 100644 --- a/relecov_tools/sftp_handled.py +++ b/relecov_tools/sftp_handled.py @@ -21,7 +21,7 @@ class SftpHandle: - def __init__(self, user=None, passwd=None, conf_file=None): + def __init__(self, user=None, passwd=None, conf_file=None, test=None): """Initializes the sftp object""" config_json = ConfigJson() self.allowed_sample_ext = config_json.get_configuration( @@ -81,6 +81,10 @@ def __init__(self, user=None, passwd=None, conf_file=None): else: self.passwd = passwd self.client = None + if test is None: + self.test = False + else: + self.test = True def open_connection(self): """Establish sftp connection""" From 8874eaeef600ae35202ef1b36fb1f8b43a2f94c7 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 29 Mar 2022 16:11:07 +0200 Subject: [PATCH 0223/1454] changes in schemas --- relecov_tools/schema/ena_schema.json | 4 +-- relecov_tools/schema/phage_plus_schema.json | 2 +- relecov_tools/schema/phage_schema.json | 27 +++++++++++++-------- 3 files changed, 20 insertions(+), 13 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 6c944e74..0337308c 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -29,7 +29,7 @@ "type": "string", "description": "The user-defined name for the sample.", "clasification": "Database Identifiers", - "label": "Collecting Sample id" + "label": "Sample ID given by originating laboratory" }, "collecting_institution": { "examples": [ @@ -399,7 +399,7 @@ ], "genepio_label": "isolate identifier", "clasification": "Sample collection and processing", - "label": "Isolate" + "label": "Sample ID given by originating laboratory" }, "purpose_sampling": { "examples": [ diff --git a/relecov_tools/schema/phage_plus_schema.json b/relecov_tools/schema/phage_plus_schema.json index e920d682..75f58b1a 100644 --- a/relecov_tools/schema/phage_plus_schema.json +++ b/relecov_tools/schema/phage_plus_schema.json @@ -24,7 +24,7 @@ "type": "string", "description": "The user-defined name for the sample.", "clasification": "Database Identifiers", - "label": "Collecting Sample id" + "label": "Sample ID given by originating laboratory" }, "sample_description": { "examples": [ diff --git a/relecov_tools/schema/phage_schema.json b/relecov_tools/schema/phage_schema.json index deb1330b..544b3be2 100644 --- a/relecov_tools/schema/phage_schema.json +++ b/relecov_tools/schema/phage_schema.json @@ -572,7 +572,8 @@ "description": "The self-identified ethnicity(ies) of the host.", "examples": [ "Indigenous, European" - ] + ], + "label": "Host ethnicity" }, "collection_device": { "Enums": [ @@ -1177,7 +1178,8 @@ "description": "The name of the sample plan implemented for sample collection.", "examples": [ "CanCOGeN Sampling Strategy 1.0" - ] + ], + "label": "Sample plan name" }, "treatment": { "ontology": "OGMS:0000090", @@ -2015,7 +2017,7 @@ "type": "string", "description": "The user-defined name for the sample.", "clasification": "Database Identifiers", - "label": "Collecting Sample id" + "label": "Sample ID given by originating laboratory" }, "host_scientific_name": { "Enums": [ @@ -2143,7 +2145,8 @@ "ontology": "GENEPIO:0001399", "type": "string", "description": "The date on which the symptoms began or were first noted.", - "format": "date" + "format": "date", + "label": "Symptom onset date" }, "r2 fastq filename": { "examples": [ @@ -2435,7 +2438,7 @@ "clasification": "Pathogen diagnostic testing", "label": "reference genome accession" }, - "host_residence_geo_loc_name_country": { + "host_residence_country": { "Enums": [ "Afghanistan [GAZ:00006882]", "Albania [GAZ:00002953]", @@ -2719,7 +2722,8 @@ "description": "The country where the host resides.", "examples": [ "South Africa [GAZ:00001094]" - ] + ], + "label": "Host residence country" }, "travel_history": { "ontology": "GENEPIO:0001416", @@ -3173,7 +3177,8 @@ "description": "Whether the sample was collected from an individual in quarantine.", "examples": [ "Yes [NCIT:C49488]" - ] + ], + "label": "Sample collected in quarantine" }, "sample_collected_by": { "examples": [ @@ -3267,7 +3272,8 @@ "description": "Further details pertaining to the health or disease status of the host at time of collection.", "examples": [ "Hospitalized (ICU) [GENEPIO:0100046]" - ] + ], + "label": "Host health status details" }, "isolate": { "ontology": "GENEPIO:0001644", @@ -3277,7 +3283,7 @@ "SARS-CoV-2/human/USA/CA-CDPH-001/2020" ], "clasification": "Sample collection and processing", - "label": "Isolate" + "label": "Sample ID given by originating laboratory" }, "host_health_state": { "Enums": [ @@ -3435,7 +3441,8 @@ "description": "A description of how any data elements were altered to preserve patient privacy.", "examples": [ "Jitter added to publicly shared collection dates to prevent re-identifiability." - ] + ], + "label": "Data abstraction details" }, "consensus_sequence_filename": { "ontology": "GENEPIO:0001461", From c3c1a04c48f197164b083668573cd78fc1f47460 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 29 Mar 2022 16:24:40 +0200 Subject: [PATCH 0224/1454] changes for using test configuration yaml --- relecov_tools/__main__.py | 2 +- .../example_data/samples/sftp_config.yaml | 11 ----- relecov_tools/sftp_handled.py | 45 +++++++++++-------- relecov_tools/test/sftp_config.yaml | 9 ++++ 4 files changed, 36 insertions(+), 31 deletions(-) delete mode 100644 relecov_tools/example_data/samples/sftp_config.yaml create mode 100644 relecov_tools/test/sftp_config.yaml diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 19300645..12a1cc09 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -159,7 +159,7 @@ def list(keywords, sort, json, show_archived): help="Configuration file Create Nextflow command with params (no params file)", ) @click.option("--test", is_flag=True, default=False, help="download files for testing") -def download_sftp(user, password, conf_file): +def download_sftp(user, password, conf_file, test): """Download files located in sftp server.""" sftp_connection = relecov_tools.sftp_handled.SftpHandle(user, password, conf_file, test) sftp_connection.download_from_sftp() diff --git a/relecov_tools/example_data/samples/sftp_config.yaml b/relecov_tools/example_data/samples/sftp_config.yaml deleted file mode 100644 index d6ded6ae..00000000 --- a/relecov_tools/example_data/samples/sftp_config.yaml +++ /dev/null @@ -1,11 +0,0 @@ -sftp_serve": "sftprelecov.isciii.es", -sftp_port": "22", -sftp_user : "usuario_test", -sftp_passwd : "U[9[Gpyu3.", -storage_local_folder: "/tmp/relecov", -tmp_folder_for_metadata: "/tmp/relecov/tmp", -allowed_sample_extensions: extensions - -extensions: - -fastq.gz - -fasta diff --git a/relecov_tools/sftp_handled.py b/relecov_tools/sftp_handled.py index ca24d264..68f9cdc0 100644 --- a/relecov_tools/sftp_handled.py +++ b/relecov_tools/sftp_handled.py @@ -27,7 +27,8 @@ def __init__(self, user=None, passwd=None, conf_file=None, test=None): self.allowed_sample_ext = config_json.get_configuration( "allowed_sample_extensions" ) - + self.sftp_user = user + self.sftp_passwd = passwd if conf_file is None: self.server = config_json.get_topic_data("sftp_connection", "sftp_server") self.port = config_json.get_topic_data("sftp_connection", "sftp_port") @@ -66,35 +67,41 @@ def __init__(self, user=None, passwd=None, conf_file=None, test=None): self.metadata_tmp_folder = config_json.get_configuration( "tmp_folder_for_metadata" ) - self.user = config["user_sftp"] - self.passwd = config["password"] + try: + self.abort_if_md5_mismatch = ( + True + if config["abort_if_md5_mismatch"] == "True" + else False + ) + except KeyError: + self.abort_if_md5_mismatch = ( + True + if config_json.get_configuration("abort_if_md5_mismatch") == "True" + else False + ) + self.sftp_user = config["sftp_user"] + self.sftp_passwd = config["sftp_passwd"] + self.pp = config["allowed_sample_extensions"] except KeyError as e: log.error("Invalid configuration file %s", e) stderr.print("[red] Invalide configuration file {e} !") sys.exit(1) - if user is None: - self.user = relecov_tools.utils.text(msg="Enter the userid") - else: - self.user = user - if passwd is None: - self.passwd = relecov_tools.utils.password(msg="Enter your password") - else: - self.passwd = passwd + if self.sftp_user is None: + self.sftp_user = relecov_tools.utils.prompt_text(msg="Enter the userid") + if self.sftp_passwd is None: + self.sftp_passwd = relecov_tools.utils.prompt_password(msg="Enter your password") self.client = None - if test is None: - self.test = False - else: - self.test = True + self.test = test def open_connection(self): """Establish sftp connection""" self.client = paramiko.SSHClient() self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) self.client.connect( - hostname=self.server, - port=self.port, - username=self.user, - password=self.passwd, + hostname=self.sftp_server, + port=self.sftp_port, + username=self.sftp_user, + password=self.sftp_passwd, allow_agent=False, look_for_keys=False, ) diff --git a/relecov_tools/test/sftp_config.yaml b/relecov_tools/test/sftp_config.yaml new file mode 100644 index 00000000..07d84433 --- /dev/null +++ b/relecov_tools/test/sftp_config.yaml @@ -0,0 +1,9 @@ +sftp_server: "sftprelecov.isciii.es" +sftp_port: "22" +sftp_user : "usuario_test" +sftp_passwd : "U[9[Gpyu3." +storage_local_folder: "/tmp/relecov" +tmp_folder_for_metadata: "/tmp/relecov/tmp" +allowed_sample_extensions: + - .fastq.gz + - .fasta From e23195f2e40b685a94bc00bb93ca3641aa154cca Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 29 Mar 2022 17:11:39 +0200 Subject: [PATCH 0225/1454] Fixed error typing for choice click and incompleted changes at merging --- relecov_tools/__main__.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 4b093653..2b75132c 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -161,8 +161,7 @@ def list(keywords, sort, json, show_archived): @click.option("--test", is_flag=True, default=False, help="download files for testing") def download(user, password, conf_file, test): """Download files located in sftp server.""" - sftp_connection = relecov_tools.sftp_handled.SftpHandle(user, password, conf_file, test) - sftp_connection.download_from_sftp() + sftp_connection = relecov_tools.sftp_handle.SftpHandle(user, password, conf_file, test) sftp_connection.download() @@ -245,7 +244,7 @@ def map(phage_plus_schema, json_data, destination_schema, schema_file, output): @click.option( "-a", "--action", - type=click.choice(["add", "modify", "cancel", "release"], case_sensitive=False), + type=click.Choice(["add", "modify", "cancel", "release"], case_sensitive=False), help="select one of the available options", ) @click.option("--dev/--production", default=True) From cee03bab42b7b2bae85a56da57814f744715528b Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 29 Mar 2022 17:12:33 +0200 Subject: [PATCH 0226/1454] This file must be remain. the one to remove is the mapping_ena_to_upload_ena.json --- .../schema/mapping_metadata_to_json.json | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 relecov_tools/schema/mapping_metadata_to_json.json diff --git a/relecov_tools/schema/mapping_metadata_to_json.json b/relecov_tools/schema/mapping_metadata_to_json.json new file mode 100644 index 00000000..debcf610 --- /dev/null +++ b/relecov_tools/schema/mapping_metadata_to_json.json @@ -0,0 +1,74 @@ +{ + "Public Health sample id (SIVIES)": "XXXXXXXXXXX", + "Sample ID given by originating laboratory": "collecting_lab_sample_id", + "Sample ID given by the submitting laboratory" : "submitting_lab_sequence_id", + "Sample ID given in the microbiology lab": "microbiology_lab_sample_id", + "Sample ID given if multiple rna-extraction or passages": "isolate_sample_id", + "Sample ID given for sequencing": "isolate_sample_id", + "ENA Sample ID": "biosample_accession_ENA", + "GISAID Virus Name": "virus_name", + "GISAID id": "gisaid_id", + "Originating Laboratory": "collecting_institution", + "Submitting Institution": "submitting_institution", + "Sample Collection Date": "sample_collection_date", + "Sample Received Date": "sample_received_date", + "Purpose of sampling": "purpose_of_sampling", + "Biological Sample Storage Condition": "sample_storage_conditions", + "Specimen source": "anatomical_material", + "Anatomical Structure": "anatomical_part", + "Environmental Material": "environmental_material", + "Environmental System": "environmental_site", + "Source material": "biomaterial_extracted", + "Collection Device": "collection_device", + "Host": "host_common_name", + "Host Age": "host_age", + "Host Gender": "host_gender", + "Sequencing Date": "sequencing_date", + "Rna Extraction Protocol": "rna_extraction_protocol", + "Commercial All-in-one library kit": "library_kit", + "Library preparation kit": "library_preparation_kit", + "Enrichment Protocol": "enrichment_protocol", + "If Enrichment Protocol Is Other, Specify": "if_enrichment_protocol_is_other_specify", + "Amplicon panel/assay": "amplicon_protocol", + "If Amplicon Protocol If Other, Especify": "if_amplicon_protocol_if_other_especify", + "Amplicon Version": "amplicon_version", + "Number Of Samples In Run": "number_of_samples_in_run", + "Runid": "runID", + "Sequencing Instrument Model": "sequencing_instrument_model", + "Flowcell Kit": "flowcell_kit", + "Source material": "biomaterial_extracted", + "Capture method": "library_selection", + "Sequencing technique": "library_strategy", + "Library Layout": "library_layout", + "Gene Name 1" : "gene_name_1", + "Diagnostic Pcr Ct Value 1": "diagnostic_pcr_Ct_value_1", + "Gene Name 2" : "gene_name_2", + "Diagnostic Pcr Ct Value 2": "diagnostic_pcr_Ct_value_2", + "Analysis Authors": "analysis_author", + "Author Submitter": "author_submitter", + "Authors": "authors", + "Additional_fields": { + "geo_loc_country" : "", + "geo_loc_state": "", + "geo_loc_latitude": "", + "geo_loc_longitude": "", + "organism": "sars_cov_2", + "isolate": "", + "host_scientific_name": { + "Human": "Homo sapiens" + }, + "host_disease":"COVID-19", + "sequence_file_R1_fastq": "", + "sequence_file_R2_fastq": "", + "type" : "betacoronavirus", + "tax_id": "2697049", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "study_alias": "", + "experiment_alias": "", + "run_alias": "", + "study_title": "", + "experiment_title": "", + "sequencing_instrument_platform": "" + + } +} From adb17de139471925cdbd578881d6c9e48c95733a Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 29 Mar 2022 17:17:33 +0200 Subject: [PATCH 0227/1454] added metadata lab test --- .../example_data/METADATA_LAB_TEST.xlsx | Bin 0 -> 494447 bytes relecov_tools/schema/ena_schema.json | 16 +++++++-- relecov_tools/schema/phage_plus_schema.json | 34 ++++++++++++++++-- relecov_tools/schema/phage_schema.json | 3 +- 4 files changed, 46 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zC^K1KeeRdFJ^C}{he`yq?v>TL7(`rG1_1D;!2T4igO5K0!LshPsH^jdtNUf`2EhD& zw7{%;WsOEy4R#LRc4WMtqjePcGY~B6UeDt^>>$2h)|C?M@5=(S?v?f94|n|brVFX^ zGY~B6UK9QCmoI*65E_(lzc1_8pZxgQw|>mY_^m7JQvD1B%evo{e@tq)OW^qRz|!~` z^F!nMA)VuAVL#>t+$BT&df;oq{rA*}pHKgBwe#J`_Sb_}3oPj8RDz!YKfVCM{`KtJ zPqDgSz<*mJ{WIamIjg%DMZX@c4!;oo>$TC(r~Wu&a5t&->!INOU*Y`EDXyPS{_!FA zZc^db1IY_~@-G$e-=-LT=KT0{c=rtW>yhXU_u~Wd&nN!)yz$!;bA7-9{_|1t=M#S% kwEnizUi!k__i&;l2Xi~70sv@k|IFNuMg0742S Date: Tue, 29 Mar 2022 17:22:50 +0200 Subject: [PATCH 0228/1454] removing mapping, data willbe collected from schema --- .../schema/mapping_metadata_to_json.json | 74 ------------------- 1 file changed, 74 deletions(-) delete mode 100644 relecov_tools/schema/mapping_metadata_to_json.json diff --git a/relecov_tools/schema/mapping_metadata_to_json.json b/relecov_tools/schema/mapping_metadata_to_json.json deleted file mode 100644 index debcf610..00000000 --- a/relecov_tools/schema/mapping_metadata_to_json.json +++ /dev/null @@ -1,74 +0,0 @@ -{ - "Public Health sample id (SIVIES)": "XXXXXXXXXXX", - "Sample ID given by originating laboratory": "collecting_lab_sample_id", - "Sample ID given by the submitting laboratory" : "submitting_lab_sequence_id", - "Sample ID given in the microbiology lab": "microbiology_lab_sample_id", - "Sample ID given if multiple rna-extraction or passages": "isolate_sample_id", - "Sample ID given for sequencing": "isolate_sample_id", - "ENA Sample ID": "biosample_accession_ENA", - "GISAID Virus Name": "virus_name", - "GISAID id": "gisaid_id", - "Originating Laboratory": "collecting_institution", - "Submitting Institution": "submitting_institution", - "Sample Collection Date": "sample_collection_date", - "Sample Received Date": "sample_received_date", - "Purpose of sampling": "purpose_of_sampling", - "Biological Sample Storage Condition": "sample_storage_conditions", - "Specimen source": "anatomical_material", - "Anatomical Structure": "anatomical_part", - "Environmental Material": "environmental_material", - "Environmental System": "environmental_site", - "Source material": "biomaterial_extracted", - "Collection Device": "collection_device", - "Host": "host_common_name", - "Host Age": "host_age", - "Host Gender": "host_gender", - "Sequencing Date": "sequencing_date", - "Rna Extraction Protocol": "rna_extraction_protocol", - "Commercial All-in-one library kit": "library_kit", - "Library preparation kit": "library_preparation_kit", - "Enrichment Protocol": "enrichment_protocol", - "If Enrichment Protocol Is Other, Specify": "if_enrichment_protocol_is_other_specify", - "Amplicon panel/assay": "amplicon_protocol", - "If Amplicon Protocol If Other, Especify": "if_amplicon_protocol_if_other_especify", - "Amplicon Version": "amplicon_version", - "Number Of Samples In Run": "number_of_samples_in_run", - "Runid": "runID", - "Sequencing Instrument Model": "sequencing_instrument_model", - "Flowcell Kit": "flowcell_kit", - "Source material": "biomaterial_extracted", - "Capture method": "library_selection", - "Sequencing technique": "library_strategy", - "Library Layout": "library_layout", - "Gene Name 1" : "gene_name_1", - "Diagnostic Pcr Ct Value 1": "diagnostic_pcr_Ct_value_1", - "Gene Name 2" : "gene_name_2", - "Diagnostic Pcr Ct Value 2": "diagnostic_pcr_Ct_value_2", - "Analysis Authors": "analysis_author", - "Author Submitter": "author_submitter", - "Authors": "authors", - "Additional_fields": { - "geo_loc_country" : "", - "geo_loc_state": "", - "geo_loc_latitude": "", - "geo_loc_longitude": "", - "organism": "sars_cov_2", - "isolate": "", - "host_scientific_name": { - "Human": "Homo sapiens" - }, - "host_disease":"COVID-19", - "sequence_file_R1_fastq": "", - "sequence_file_R2_fastq": "", - "type" : "betacoronavirus", - "tax_id": "2697049", - "scientific_name": "Severe acute respiratory syndrome coronavirus 2", - "study_alias": "", - "experiment_alias": "", - "run_alias": "", - "study_title": "", - "experiment_title": "", - "sequencing_instrument_platform": "" - - } -} From 3b6b5ae3c1453f20abbd201876a3577ad841c19b Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 29 Mar 2022 17:34:23 +0200 Subject: [PATCH 0229/1454] fixin litin --- relecov_tools/__main__.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 2b75132c..b8f84e84 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -161,7 +161,9 @@ def list(keywords, sort, json, show_archived): @click.option("--test", is_flag=True, default=False, help="download files for testing") def download(user, password, conf_file, test): """Download files located in sftp server.""" - sftp_connection = relecov_tools.sftp_handle.SftpHandle(user, password, conf_file, test) + sftp_connection = relecov_tools.sftp_handle.SftpHandle( + user, password, conf_file, test + ) sftp_connection.download() From d4290eeb4bdd5937ef7b926052a26946d8f9e8d5 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 30 Mar 2022 01:03:59 +0200 Subject: [PATCH 0230/1454] Validating if all fastq files are downloaded --- relecov_tools/sftp_handle.py | 69 +++++++++++++++++++++++++++++++----- 1 file changed, 60 insertions(+), 9 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 6b75b3cf..bd78ab17 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -1,5 +1,6 @@ #!/usr/bin/env python from datetime import datetime +from itertools import islice import logging import json import rich.console @@ -8,6 +9,7 @@ import os import shutil import yaml +import openpyxl import relecov_tools.utils from relecov_tools.config_json import ConfigJson @@ -69,14 +71,13 @@ def __init__(self, user=None, passwd=None, conf_file=None, test=None): ) try: self.abort_if_md5_mismatch = ( - True - if config["abort_if_md5_mismatch"] == "True" - else False + True if config["abort_if_md5_mismatch"] == "True" else False ) except KeyError: self.abort_if_md5_mismatch = ( True - if config_json.get_configuration("abort_if_md5_mismatch") == "True" + if config_json.get_configuration("abort_if_md5_mismatch") + == "True" else False ) self.sftp_user = config["sftp_user"] @@ -89,7 +90,9 @@ def __init__(self, user=None, passwd=None, conf_file=None, test=None): if self.sftp_user is None: self.sftp_user = relecov_tools.utils.prompt_text(msg="Enter the userid") if self.sftp_passwd is None: - self.sftp_passwd = relecov_tools.utils.prompt_password(msg="Enter your password") + self.sftp_passwd = relecov_tools.utils.prompt_password( + msg="Enter your password" + ) self.client = None self.test = test @@ -260,6 +263,50 @@ def create_main_folders(self, root_directory_list): os.makedirs(full_folder, exist_ok=True) return True + def get_sample_fastq_file_names(self, ws_metadata_lab): + """ """ + sample_file_list = {} + # find out the index for file names + for col in ws_metadata_lab[4]: + if "Sequence file R1 fastq" == col.value: + index_fastq_r1 = col.column - 1 + elif "Sequence file R2 fastq" == col.value: + index_fastq_r2 = col.column - 1 + for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): + if row[2] is not None: + if row[2].value not in sample_file_list: + sample_file_list[row[2]] = {} + if row[index_fastq_r1] is not None: + sample_file_list[row[2]]["fastq_r1"] = row[index_fastq_r1] + else: + log.error( + "Fastq_R1 not defined in Metadata file for sample %s", row[2] + ) + stderr.print("[red] No fastq R1 file for sample " + row[2]) + return False + if row[index_fastq_r2] is not None: + sample_file_list[row[2]]["fastq_r2"] = row[index_fastq_r2] + return sample_file_list + + def validate_download_files(self, local_folder): + """Check if download sample files are the ones defined on metadata file""" + meta_f_path = os.path.join(local_folder, "METADATA_LAB.xlsx") + if not os.path.isfile(meta_f_path): + log.error("Metadata file does not exists on %s", local_folder) + stderr.print("[red] METADATA_LAB.xlsx do not exist in" + local_folder) + return False + wb_file = openpyxl.load_workbook(meta_f_path, data_only=True) + sample_file_list = self.get_sample_fastq_file_names(wb_file["METADATA_LAB"]) + if not sample_file_list: + return False + for sample, files in sample_file_list.items(): + for file in files.values(): + if not os.path.isfile(os.path.join(local_folder, file)): + log.error("File %s does not exist", file) + stderr.print("[red] File " + file + " does not exist") + return False + return True + def delete_remote_files(self, folder, files): """Delete files from remote server""" self.open_connection() @@ -319,9 +366,13 @@ def download(self): f"[red] Stop processing folder {folder} because of corrupted files {corrupted}" ) continue - self.create_tmp_files_with_metadata_info( - result_data["local_folder"], result_data["fetched_files"], md5_files - ) - self.delete_remote_files(folder, files) + if self.validate_download_files(self, local_folder): + + self.create_tmp_files_with_metadata_info( + result_data["local_folder"], result_data["fetched_files"], md5_files + ) + self.delete_remote_files(folder, files) + else: + self.delete_local_folder(local_folder) self.close_connection() return From aa097abe754550ac2f6a743630469ee2900d4cf3 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 30 Mar 2022 09:04:36 +0200 Subject: [PATCH 0231/1454] Change the validate method, get_sample_fastq_file_names is calling from main --- relecov_tools/sftp_handle.py | 27 ++++++++++++++++----------- 1 file changed, 16 insertions(+), 11 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index bd78ab17..0ba4910f 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -263,8 +263,15 @@ def create_main_folders(self, root_directory_list): os.makedirs(full_folder, exist_ok=True) return True - def get_sample_fastq_file_names(self, ws_metadata_lab): + def get_sample_fastq_file_names(self, local_folder): """ """ + meta_f_path = os.path.join(local_folder, "METADATA_LAB.xlsx") + if not os.path.isfile(meta_f_path): + log.error("Metadata file does not exists on %s", local_folder) + stderr.print("[red] METADATA_LAB.xlsx do not exist in" + local_folder) + return False + wb_file = openpyxl.load_workbook(meta_f_path, data_only=True) + ws_metadata_lab = wb_file["METADATA_LAB"] sample_file_list = {} # find out the index for file names for col in ws_metadata_lab[4]: @@ -288,15 +295,8 @@ def get_sample_fastq_file_names(self, ws_metadata_lab): sample_file_list[row[2]]["fastq_r2"] = row[index_fastq_r2] return sample_file_list - def validate_download_files(self, local_folder): + def validate_download_files(self, sample_file_list, local_folder): """Check if download sample files are the ones defined on metadata file""" - meta_f_path = os.path.join(local_folder, "METADATA_LAB.xlsx") - if not os.path.isfile(meta_f_path): - log.error("Metadata file does not exists on %s", local_folder) - stderr.print("[red] METADATA_LAB.xlsx do not exist in" + local_folder) - return False - wb_file = openpyxl.load_workbook(meta_f_path, data_only=True) - sample_file_list = self.get_sample_fastq_file_names(wb_file["METADATA_LAB"]) if not sample_file_list: return False for sample, files in sample_file_list.items(): @@ -366,13 +366,18 @@ def download(self): f"[red] Stop processing folder {folder} because of corrupted files {corrupted}" ) continue - if self.validate_download_files(self, local_folder): + sample_file_list = self.get_sample_fastq_file_names( + result_data["local_folder"] + ) + if self.validate_download_files( + self, sample_file_list, result_data["local_folder"] + ): self.create_tmp_files_with_metadata_info( result_data["local_folder"], result_data["fetched_files"], md5_files ) self.delete_remote_files(folder, files) else: - self.delete_local_folder(local_folder) + self.delete_local_folder(result_data["local_folder"]) self.close_connection() return From 01f215e615a92700dd69735bc066104b616ffb6d Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 30 Mar 2022 09:16:49 +0200 Subject: [PATCH 0232/1454] Added sample_list when creating files on tmp folder --- relecov_tools/sftp_handle.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 0ba4910f..ed38c5c1 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -232,6 +232,7 @@ def create_tmp_files_with_metadata_info(self, local_folder, file_list, md5_data) except OSError as e: log.error("Unable to copy Metadata file %s", e) stderr.print("[red] Unable to copy Metadata file") + return False sample_data = {} for f_name, values in md5_data.items(): if f_name.endswith(tuple(self.allowed_sample_ext)): @@ -254,7 +255,7 @@ def create_tmp_files_with_metadata_info(self, local_folder, file_list, md5_data) ) ) fh.close() - return + return True def create_main_folders(self, root_directory_list): """Create the main folder structure if not exists""" @@ -374,7 +375,7 @@ def download(self): ): self.create_tmp_files_with_metadata_info( - result_data["local_folder"], result_data["fetched_files"], md5_files + result_data["local_folder"], sample_file_list, md5_files ) self.delete_remote_files(folder, files) else: From b00d355d054c87ced9c8f2f95f1cba4e2548c31d Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 30 Mar 2022 12:54:27 +0200 Subject: [PATCH 0233/1454] added table labels to ena shcema --- relecov_tools/schema/ena_schema.json | 245 +++++++++++++++++++++++---- 1 file changed, 214 insertions(+), 31 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 48b04519..0d2beccd 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -29,7 +29,11 @@ "type": "string", "description": "The user-defined name for the sample.", "clasification": "Database Identifiers", - "label": "Sample ID given by originating laboratory" + "label": "Sample ID given by originating laboratory", + "table": [ + "sample", + "experiments" + ] }, "collecting_institution": { "examples": [ @@ -38,7 +42,8 @@ "ontology": "GENEPIO:0001153", "type": "string", "description": "Name of the institution to which the person collecting the specimen belongs. Format: Institute Name, Institute Address", - "label": "Originating Laboratory" + "label": "Originating Laboratory", + "table": "sample" }, "collector_name": { "examples": [ @@ -48,7 +53,8 @@ "type": "string", "description": "Name of the person who collected the specimen", "clasification": "Sample collection and processing", - "label": "Collector name" + "label": "Collector name", + "table": "sample" }, "collection_date": { "examples": [ @@ -59,7 +65,8 @@ "description": "The date on which the sample was collected.", "format": "date", "classification": "Sample collection and processing", - "label": "Sample Collection Date" + "label": "Sample Collection Date", + "table": "sample" }, "receipt_date": { "examples": [ @@ -72,6 +79,19 @@ "clasification": "Sample collection and processing", "label": "Sample Received Date" }, + "design_description": { + "examples": [ + "design_description_1" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "", + "label": "Design description", + "table": [ + "experiments" + ] + }, "geographic_location_(country_and/or_sea)": { "Enums": [ "Afghanistan [GAZ:00006882]", @@ -358,7 +378,8 @@ "South Africa [GAZ:00001094]" ], "clasification": "Sample collection and processing", - "label": "Geo Loc Autonomic Country" + "label": "Geo Loc Autonomic Country", + "table": "sample" }, "geographic location (region and locality)": { "ontology": "GENEPIO:0100280", @@ -399,7 +420,8 @@ ], "genepio_label": "isolate identifier", "clasification": "Sample collection and processing", - "label": "Sample ID given by originating laboratory" + "label": "Sample ID given by originating laboratory", + "table": "sample" }, "purpose_sampling": { "examples": [ @@ -486,7 +508,7 @@ "clasification": "Sample collection and processing", "label": "Environmental Material" }, - "host common name": { + "host_common_name": { "Enums": [ "Human [NCBITaxon:9606]", "Bat [NCBITaxon:9397]", @@ -514,9 +536,10 @@ "Human [NCBITaxon:9606]" ], "classification": "Host information", - "label": "Host Common Name" + "label": "Host Common Name", + "table": "sample" }, - "host scientific name": { + "host_scientific_name": { "Enums": [ "Bos taurus [NCBITaxon:9913]", "Canis lupus familiaris [NCBITaxon:9615]", @@ -547,7 +570,8 @@ "Homo sapiens [NCBITaxon:9606]" ], "clasification": "Host information", - "label": "Host Scientific Name" + "label": "Host Scientific Name", + "table": "runs" }, "host_subject_id": { "examples": [ @@ -557,7 +581,31 @@ "type": "string", "description": "a unique identifier by which each subject can be referred to, de-identified.", "clasification": "Host information", - "label": "Host Subject Id" + "label": "Host Subject Id", + "table": "sample" + }, + "host_gender": { + "Enums": [ + "Female [NCIT:C46110]", + "Male [NCIT:C46109]", + "Non-binary Gender [GSSO:000132]", + "Transgender (assigned male at birth) [GSSO:004004]", + "Transgender (assigned female at birth) [GSSO:004005]", + "Undeclared [NCIT:C110959]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001395", + "type": "string", + "description": "The gender of the host at the time of sample collection.", + "examples": [ + "Male [NCIT:C46109]" + ], + "label": "Host Gender", + "table": "sample" }, "type exposure": { "examples": [ @@ -640,7 +688,10 @@ "Oxford Nanopore MinION [GENEPIO:0100142]" ], "classification": "Sequencing", - "label": "Sequencing Instrument Model" + "label": "Sequencing Instrument Model", + "table": [ + "experiments" + ] }, "instrument_platform": { "examples": [ @@ -649,7 +700,10 @@ "ontology": "GENEPIO_0000071", "type": "string", "description": "The model of the sequencing instrument used.", - "label": "Sequencing Platforms " + "label": "Sequencing Platforms ", + "table": [ + "experiments" + ] }, "file_name": { "examples": [ @@ -659,7 +713,30 @@ "type": "string", "description": "The user-specified filename of the r1 FASTQ file.", "clasification": "Bioinformatics and QC metrics", - "label": "Sequence file R1 fastq" + "label": "Sequence file R1 fastq", + "table": "runs" + }, + "file_type": { + "examples": [ + "fastq" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Bioinformatics and QC metrics", + "label": "file type", + "table": "runs" + }, + "file_checksum": { + "examples": [ + "3e69af1f875fab020aed82f5edbc1f03" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Bioinformatics and QC metrics", + "label": "file checksum", + "table": "runs" }, "tax_id": { "examples": [ @@ -669,7 +746,8 @@ "type": "string", "description": "The NCBITaxon identifier for the organism being sequenced.", "clasification": "Sample collection and processing", - "label": "Tax ID" + "label": "Tax ID", + "table": "sample" }, "scientific_name": { "Enums": [ @@ -689,7 +767,8 @@ "description": "The taxonomic name of the organism.", "clasification": "Sample collection and processing", "classification": "Sample collection and processing", - "label": "Organism" + "label": "Organism", + "table": "sample" }, "common_name": { "examples": [ @@ -709,7 +788,8 @@ "type": "string", "description": "Free text description of the sample.", "clasification": "Sample collection and processing", - "label": "Sample Description" + "label": "Sample Description", + "table": "sample" }, "sample_storage_conditions": { "examples": [ @@ -755,7 +835,10 @@ "type": "string", "description": "Molecule type used to make the library.", "clasification": "Sequencing", - "label": "Source material" + "label": "Source material", + "table": [ + "experiments" + ] }, "library_selection": { "examples": [ @@ -765,7 +848,23 @@ "type": "string", "description": "Library capture method.", "clasification": "Sequencing", - "label": "Capture method" + "label": "Capture method", + "table": [ + "experiments" + ] + }, + "library_construction_protocol": { + "examples": [ + "library_construction_protocol_1" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Library Construction protocol", + "table": [ + "experiments" + ] }, "library_strategy": { "Enums": [ @@ -797,7 +896,10 @@ "type": "string", "description": "Overall sequencing strategy or approach.", "clasification": "Sequencing", - "label": "Sequencing technique" + "label": "Sequencing technique", + "table": [ + "experiments" + ] }, "library_layout": { "examples": [ @@ -807,7 +909,10 @@ "type": "string", "description": "Single or paired.", "clasification": "Sequencing", - "label": "Library Layout" + "label": "Library Layout", + "table": [ + "experiments" + ] }, "library_name": { "examples": [ @@ -817,7 +922,10 @@ "type": "string", "description": "The submitter's name for this library.", "clasification": "Sequencing", - "label": "Library Name" + "label": "Library Name", + "table": [ + "experiments" + ] }, "nominal_length ": { "examples": [ @@ -939,6 +1047,19 @@ "clasification": "Submission ENA", "label": "Base count" }, + "insert_size": { + "examples": [ + "250" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Insert size", + "table": [ + "experiments" + ] + }, "center_name": { "examples": [ " KAROLINSKA INSITUTET" @@ -971,13 +1092,27 @@ }, "experiment_title": { "examples": [ - "e.g Illumina MiSeq paired end sequencing" + "experiment_title_1" ], - "ontology": "ORNASEQ_0000004", + "ontology": "0", "type": "string", "description": "", "clasification": "Submission ENA", - "label": "Experiment title" + "label": "Experiment title", + "table": [ + "experiments" + ] + }, + "sample_title": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Sample title", + "table": "sample" }, "study_title": { "examples": [ @@ -987,7 +1122,45 @@ "type": "string", "description": "", "clasification": "Submission ENA", - "label": "Study title" + "label": "Study title", + "table": "study" + }, + "study_type": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Study type", + "table": "study" + }, + "pubmed_id": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "pubmed id", + "table": [ + "study" + ] + }, + "study_abstract": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Study abstract", + "table": [ + "study" + ] }, "study_alias": { "examples": [ @@ -997,17 +1170,24 @@ "type": "string", "description": "", "clasification": "Submission ENA", - "label": "Study alias" + "label": "Study alias", + "table": [ + "study", + "experiments" + ] }, "experiment_alias": { "examples": [ - "e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092" + "experiment_alias_7a" ], - "ontology": "NCIT_C42790", + "ontology": "0", "type": "string", "description": "", "clasification": "Submission ENA", - "label": "Experiment alias" + "label": "Experiment alias", + "table": [ + "experiments" + ] }, "run_alias": { "examples": [ @@ -1017,7 +1197,10 @@ "type": "string", "description": "", "clasification": "Submission ENA", - "label": "Run Alias" + "label": "Run Alias", + "table": [ + "runs" + ] }, "fastq_bytes": { "examples": [ From 96a96fb7cb9f2f8fcbda6a1f458167cfd0546d6e Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 30 Mar 2022 13:43:52 +0200 Subject: [PATCH 0234/1454] Fixed bug after testing --- relecov_tools/sftp_handle.py | 84 ++++++++++++++++++++++-------------- 1 file changed, 52 insertions(+), 32 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index ed38c5c1..e25c10d0 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -1,7 +1,9 @@ #!/usr/bin/env python from datetime import datetime from itertools import islice +import copy import logging +import glob import json import rich.console import paramiko @@ -215,46 +217,40 @@ def verify_md5_checksum(self, local_folder, file_list): ) return sftp_md5, required_retransmition - def create_tmp_files_with_metadata_info(self, local_folder, file_list, md5_data): + def create_tmp_files_with_metadata_info(self, local_folder, file_list, md5_data, metadata_file): """Copy metadata file from folder and create a file with the sample names """ out_folder = self.metadata_tmp_folder os.makedirs(out_folder, exist_ok=True) prefix_file_name = "_".join(local_folder.split("/")[-2:]) - metadata_file = prefix_file_name + "_metadata_lab.xlsx" - sample_data_file = os.path.join(out_folder, prefix_file_name + "samples.csv") + new_metadata_file = "metadata_lab_" + prefix_file_name + ".xlsx" + sample_data_file = "samples_data_" + prefix_file_name + ".json" + sample_data_path = os.path.join(out_folder, sample_data_file) try: shutil.copy( - os.path.join(local_folder, "Metadata_lab.xlsx"), - os.path.join(out_folder, metadata_file), + os.path.join(local_folder, metadata_file), + os.path.join(out_folder, new_metadata_file), ) except OSError as e: log.error("Unable to copy Metadata file %s", e) stderr.print("[red] Unable to copy Metadata file") return False - sample_data = {} - for f_name, values in md5_data.items(): - if f_name.endswith(tuple(self.allowed_sample_ext)): - sample = f_name.split(".")[0] - if sample not in sample_data: - sample_data[sample] = {} - sample_data[sample][f_name] = {} - sample_data[sample][f_name]["local_folder"] = values[0] - sample_data[sample][f_name]["md5"] = values[1] + data = copy.deepcopy(file_list) - # sample_data.append(key + "," + ",".join(values)) - if len(sample_data) == 0: - log.error("There is no samples in folder %s", local_folder) - stderr.print("[red] There is no samples for this local folder") - else: - with open(sample_data_file, "w", encoding="utf-8") as fh: - fh.write( - json.dumps( - sample_data, indent=4, sort_keys=True, ensure_ascii=False - ) + for s_name, values in file_list.items(): + for f_type , f_name in values.items(): + if not f_name.endswith(tuple(self.allowed_sample_ext)): + stderr.print("[red] " + f_name + " has a not valid extension") + data[s_name]["local_folder"] = md5_data[f_name][0] + data[s_name][f_type + "_md5"] = md5_data[f_name][1] + with open(sample_data_path, "w", encoding="utf-8") as fh: + fh.write( + json.dumps( + data, indent=4, sort_keys=True, ensure_ascii=False ) - fh.close() + ) + return True def create_main_folders(self, root_directory_list): @@ -264,9 +260,22 @@ def create_main_folders(self, root_directory_list): os.makedirs(full_folder, exist_ok=True) return True - def get_sample_fastq_file_names(self, local_folder): + def find_metadata_file(self, local_folder): + """Find excel extension file which contains metatada """ + reg_for_xlsx = os.path.join(local_folder, "*.xlsx") + ex_files = glob.glob(reg_for_xlsx) + if len(ex_files) == 0: + log.error("Excel file for metadata does not exist on %s", local_folder) + stderr.print("[red] Metadata file does not exist on " + local_folder) + return False + if len(ex_files) > 1: + log.error("Too many Excel files on folder %s", local_folder) + stderr.print("[red] Metadata file does not exist on " + local_folder) + return False + return ex_files[0] + + def get_sample_fastq_file_names(self, local_folder, meta_f_path): """ """ - meta_f_path = os.path.join(local_folder, "METADATA_LAB.xlsx") if not os.path.isfile(meta_f_path): log.error("Metadata file does not exists on %s", local_folder) stderr.print("[red] METADATA_LAB.xlsx do not exist in" + local_folder) @@ -282,7 +291,7 @@ def get_sample_fastq_file_names(self, local_folder): index_fastq_r2 = col.column - 1 for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): if row[2] is not None: - if row[2].value not in sample_file_list: + if row[2] not in sample_file_list: sample_file_list[row[2]] = {} if row[index_fastq_r1] is not None: sample_file_list[row[2]]["fastq_r1"] = row[index_fastq_r1] @@ -300,6 +309,7 @@ def validate_download_files(self, sample_file_list, local_folder): """Check if download sample files are the ones defined on metadata file""" if not sample_file_list: return False + for sample, files in sample_file_list.items(): for file in files.values(): if not os.path.isfile(os.path.join(local_folder, file)): @@ -319,6 +329,11 @@ def delete_remote_files(self, folder, files): continue return + def delete_local_folder(self, local_folder): + """Delete download folder because files does not complain requisites""" + shutil.rmtree(local_folder, ignore_errors=True) + return True + def download(self): try: os.makedirs(self.storage_local_folder, exist_ok=True) @@ -347,6 +362,8 @@ def download(self): sys.exit(0) for folder, files in folders_to_download.items(): + log.info("Processing folder %s", folder) + stderr.print("Processing folder " + folder) # get the files in each folder result_data = self.get_files_from_sftp_folder(folder, files) md5_files, req_retransmition = self.verify_md5_checksum( @@ -367,18 +384,21 @@ def download(self): f"[red] Stop processing folder {folder} because of corrupted files {corrupted}" ) continue + meta_file = self.find_metadata_file(result_data["local_folder"]) sample_file_list = self.get_sample_fastq_file_names( - result_data["local_folder"] + result_data["local_folder"], meta_file ) if self.validate_download_files( - self, sample_file_list, result_data["local_folder"] + sample_file_list, result_data["local_folder"] ): self.create_tmp_files_with_metadata_info( - result_data["local_folder"], sample_file_list, md5_files + result_data["local_folder"], sample_file_list, md5_files, meta_file ) - self.delete_remote_files(folder, files) + # self.delete_remote_files(folder, files) else: + log.info("Deleting local folder %s", result_data["local_folder"]) self.delete_local_folder(result_data["local_folder"]) + self.close_connection() return From 6c8dc543957f2af7d7898c18e02047d7ef11d46e Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 30 Mar 2022 13:44:27 +0200 Subject: [PATCH 0235/1454] Fixed bug after testing and litin --- relecov_tools/sftp_handle.py | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index e25c10d0..46fcee1c 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -217,7 +217,9 @@ def verify_md5_checksum(self, local_folder, file_list): ) return sftp_md5, required_retransmition - def create_tmp_files_with_metadata_info(self, local_folder, file_list, md5_data, metadata_file): + def create_tmp_files_with_metadata_info( + self, local_folder, file_list, md5_data, metadata_file + ): """Copy metadata file from folder and create a file with the sample names """ @@ -239,17 +241,13 @@ def create_tmp_files_with_metadata_info(self, local_folder, file_list, md5_data, data = copy.deepcopy(file_list) for s_name, values in file_list.items(): - for f_type , f_name in values.items(): + for f_type, f_name in values.items(): if not f_name.endswith(tuple(self.allowed_sample_ext)): stderr.print("[red] " + f_name + " has a not valid extension") data[s_name]["local_folder"] = md5_data[f_name][0] data[s_name][f_type + "_md5"] = md5_data[f_name][1] with open(sample_data_path, "w", encoding="utf-8") as fh: - fh.write( - json.dumps( - data, indent=4, sort_keys=True, ensure_ascii=False - ) - ) + fh.write(json.dumps(data, indent=4, sort_keys=True, ensure_ascii=False)) return True @@ -261,7 +259,7 @@ def create_main_folders(self, root_directory_list): return True def find_metadata_file(self, local_folder): - """Find excel extension file which contains metatada """ + """Find excel extension file which contains metatada""" reg_for_xlsx = os.path.join(local_folder, "*.xlsx") ex_files = glob.glob(reg_for_xlsx) if len(ex_files) == 0: From e4f9aa43b541e905ade153e07873a095ceebb25f Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 30 Mar 2022 13:56:05 +0200 Subject: [PATCH 0236/1454] minor change in main --- relecov_tools/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index fa362274..446614a2 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -188,7 +188,7 @@ def download(user, password, conf_file): ) def read_metadata(metadata_file, sample_list_file, metadata_out): """ - Create the json complaining the relecov schema from the Metadata file. + Create the json compliant to the relecov schema from the Metadata file. """ new_metadata = relecov_tools.read_metadata.RelecovMetadata( metadata_file, sample_list_file, metadata_out From f1405b3be815295f8d1fb0e32530d0acd91d1a1a Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 30 Mar 2022 13:59:25 +0200 Subject: [PATCH 0237/1454] include required testing file for read_metadata module --- .../samples_data_COD_test_01_20220330.json | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 relecov_tools/example_data/samples_data_COD_test_01_20220330.json diff --git a/relecov_tools/example_data/samples_data_COD_test_01_20220330.json b/relecov_tools/example_data/samples_data_COD_test_01_20220330.json new file mode 100644 index 00000000..ab634772 --- /dev/null +++ b/relecov_tools/example_data/samples_data_COD_test_01_20220330.json @@ -0,0 +1,72 @@ +{ + "1197663.0": { + "fastq_r1": "ABC123_S1_L001_R1_008.fastq.gz", + "fastq_r1_md5": "83043c429b0ab94375236cf7f51860f0", + "fastq_r2": "ABC123_S1_L001_R2_008.fastq.gz", + "fastq_r2_md5": "c00859a1f83e2364cca953fb25da3cf2", + "local_folder": "/tmp/relecov/COD_test_01/20220330" + }, + "1197677.0": { + "fastq_r1": "ABC123_S1_L001_R1_005.fastq.gz", + "fastq_r1_md5": "b0a13671031ef5aa7e0e6559a925a688", + "fastq_r2": "ABC123_S1_L001_R2_005.fastq.gz", + "fastq_r2_md5": "8c420a603c81823e68436003825b1e1f", + "local_folder": "/tmp/relecov/COD_test_01/20220330" + }, + "1197678.0": { + "fastq_r1": "ABC123_S1_L001_R1_006.fastq.gz", + "fastq_r1_md5": "13e01498a0526303f5e32f3eef077b5a", + "fastq_r2": "ABC123_S1_L001_R2_006.fastq.gz", + "fastq_r2_md5": "61d1f52e84237320d97fd7fc2da56116", + "local_folder": "/tmp/relecov/COD_test_01/20220330" + }, + "1197685.0": { + "fastq_r1": "ABC123_S1_L001_R1_0010.fastq.gz", + "fastq_r1_md5": "a86f4fa0c92d76df34fd000a29d1cdd3", + "fastq_r2": "ABC123_S1_L001_R2_0010.fastq.gz", + "fastq_r2_md5": "8c4309dc00d725496c48bee6da0e4bbf", + "local_folder": "/tmp/relecov/COD_test_01/20220330" + }, + "1197689.0": { + "fastq_r1": "ABC123_S1_L001_R1_009.fastq.gz", + "fastq_r1_md5": "bc720a024263a518f6a6cd9301b308ac", + "fastq_r2": "ABC123_S1_L001_R2_009.fastq.gz", + "fastq_r2_md5": "6bf6d95b59c950691effcaf8a0e83068", + "local_folder": "/tmp/relecov/COD_test_01/20220330" + }, + "1197737.0": { + "fastq_r1": "ABC123_S1_L001_R1_007.fastq.gz", + "fastq_r1_md5": "f5b60a93b39a0b98781efb434d577a57", + "fastq_r2": "ABC123_S1_L001_R2_007.fastq.gz", + "fastq_r2_md5": "e19f883b4e05045895f990c2296009a8", + "local_folder": "/tmp/relecov/COD_test_01/20220330" + }, + "1197767.0": { + "fastq_r1": "ABC123_S1_L001_R1_003.fastq.gz", + "fastq_r1_md5": "c78fcb585a0f44734ce8c2aebf3eff33", + "fastq_r2": "ABC123_S1_L001_R2_003.fastq.gz", + "fastq_r2_md5": "8361d5a6b50279fbc8c93226ecc3568a", + "local_folder": "/tmp/relecov/COD_test_01/20220330" + }, + "1197824.0": { + "fastq_r1": "ABC123_S1_L001_R1_002.fastq.gz", + "fastq_r1_md5": "9a460a812086516536c1a1023ab5f7fe", + "fastq_r2": "ABC123_S1_L001_R2_002.fastq.gz", + "fastq_r2_md5": "41cd79b8a167d85eb06309207fd120cf", + "local_folder": "/tmp/relecov/COD_test_01/20220330" + }, + "1197860.0": { + "fastq_r1": "ABC123_S1_L001_R1_001.fastq.gz", + "fastq_r1_md5": "f2facbd1d6c7e0972074ced31ccbfd8e", + "fastq_r2": "ABC123_S1_L001_R2_001.fastq.gz", + "fastq_r2_md5": "fd9948be8da7a38b0f80659dfc21aeea", + "local_folder": "/tmp/relecov/COD_test_01/20220330" + }, + "8328199.0": { + "fastq_r1": "ABC123_S1_L001_R1_004.fastq.gz", + "fastq_r1_md5": "aa557fc40d3a9e16f470ac595fb5eb3e", + "fastq_r2": "ABC123_S1_L001_R2_004.fastq.gz", + "fastq_r2_md5": "a2dd5e08b75815dab892e392cb8468fc", + "local_folder": "/tmp/relecov/COD_test_01/20220330" + } +} \ No newline at end of file From f278a886abad2bee5464308325df0ee96958fc6a Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 30 Mar 2022 16:05:53 +0200 Subject: [PATCH 0238/1454] added last table labels --- relecov_tools/schema/ena_schema.json | 36 +++++++++++++++++++++------- 1 file changed, 27 insertions(+), 9 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 0d2beccd..39e1b5ad 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -571,7 +571,9 @@ ], "clasification": "Host information", "label": "Host Scientific Name", - "table": "runs" + "table": [ + "runs" + ] }, "host_subject_id": { "examples": [ @@ -582,7 +584,9 @@ "description": "a unique identifier by which each subject can be referred to, de-identified.", "clasification": "Host information", "label": "Host Subject Id", - "table": "sample" + "table": [ + "sample" + ] }, "host_gender": { "Enums": [ @@ -605,7 +609,9 @@ "Male [NCIT:C46109]" ], "label": "Host Gender", - "table": "sample" + "table": [ + "sample" + ] }, "type exposure": { "examples": [ @@ -714,7 +720,9 @@ "description": "The user-specified filename of the r1 FASTQ file.", "clasification": "Bioinformatics and QC metrics", "label": "Sequence file R1 fastq", - "table": "runs" + "table": [ + "runs" + ] }, "file_type": { "examples": [ @@ -725,7 +733,9 @@ "description": "", "clasification": "Bioinformatics and QC metrics", "label": "file type", - "table": "runs" + "table": [ + "runs" + ] }, "file_checksum": { "examples": [ @@ -736,7 +746,9 @@ "description": "", "clasification": "Bioinformatics and QC metrics", "label": "file checksum", - "table": "runs" + "table": [ + "runs" + ] }, "tax_id": { "examples": [ @@ -747,7 +759,9 @@ "description": "The NCBITaxon identifier for the organism being sequenced.", "clasification": "Sample collection and processing", "label": "Tax ID", - "table": "sample" + "table": [ + "sample" + ] }, "scientific_name": { "Enums": [ @@ -1112,7 +1126,9 @@ "description": "", "clasification": "Submission ENA", "label": "Sample title", - "table": "sample" + "table": [ + "sample" + ] }, "study_title": { "examples": [ @@ -1123,7 +1139,9 @@ "description": "", "clasification": "Submission ENA", "label": "Study title", - "table": "study" + "table": [ + "study" + ] }, "study_type": { "examples": [ From 45c3324b0ac5fe9a42de45438a32aade1604ef8d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 30 Mar 2022 16:56:55 +0200 Subject: [PATCH 0239/1454] updated readme and setup.py now command is relecov-tools --- README.md | 16 +++++++++++++++- setup.py | 4 ++-- 2 files changed, 17 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 6d4757f6..91f1d747 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![python_lint](https://github.com/BU-ISCIII/relecov-tools/actions/workflows/python_lint.yml/badge.svg)](https://github.com/BU-ISCIII/relecov-tools/actions/workflows/python_lint.yml) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) -A Python package with helper tools for the relecov project. +relecov-tools is a set of helper tools for the assembly of the different elements in the RELECOV platform (Spanish Network for genomic surveillance of SARS-Cov-2) as data download, processing, validation and upload to publica databases, as well as analysis runs and database storage. ## Table of contents @@ -12,5 +12,19 @@ A Python package with helper tools for the relecov project. ## Install +### Bioconda +soon + +### Pip +soon + +### Development version +If you want to install the latest code in the repository: + +``` +pip install --force-reinstall --upgrade git+https://github.com/bu-isciii/relecov-tools.git@develop + +``` + diff --git a/setup.py b/setup.py index 40521d90..27555f97 100644 --- a/setup.py +++ b/setup.py @@ -26,10 +26,10 @@ ], author="Sara Monzon", author_email="smonzon@isciii.es", - url="https://github.com/BU-ISCIII/relecov_tools", + url="https://github.com/BU-ISCIII/relecov-tools", license="GNU GENERAL PUBLIC LICENSE v.3", entry_points={ - "console_scripts": ["relecov_tools=relecov_tools.__main__:run_relecov_tools"] + "console_scripts": ["relecov-tools=relecov_tools.__main__:run_relecov_tools"] }, install_requires=required, packages=find_packages(exclude=("docs")), From 354b0ab16e3de918d45897a5bc2f0bda0642122a Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 30 Mar 2022 17:16:24 +0200 Subject: [PATCH 0240/1454] adding .json extension to geo_loc_cities that was missing --- relecov_tools/conf/configuration.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 3c6da228..6d0a3698 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -18,7 +18,7 @@ "fasta" ], "laboratory_data": "laboratory_address.json", - "geo_location_data" : "geo_loc_cities", + "geo_location_data" : "geo_loc_cities.json", "study": { "alias": "RELECOV", "title": "Example project for ENA submission RELECOV", From 93982bdfe4e105c3d6a97c55efd9f6584c5277c2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 30 Mar 2022 17:22:34 +0200 Subject: [PATCH 0241/1454] modified readme and removed list module --- README.md | 62 +++++++++++++++++++++++++++++++++++++-- relecov_tools/__main__.py | 41 +++++++++++++------------- 2 files changed, 79 insertions(+), 24 deletions(-) diff --git a/README.md b/README.md index 91f1d747..693f2b8c 100644 --- a/README.md +++ b/README.md @@ -6,11 +6,18 @@ relecov-tools is a set of helper tools for the assembly of the different element ## Table of contents -* [Install](#installation) +* [Installation](#installation) * [Usage](#usage) +* [download](#download) +* [read-metadata](#read-metadata) +* [validate](#validate) +* [map](#map) +* [upload-to-ena](#upload-to-ena) +* [upload-to-gisaid](#upload-to-gisaid) +* [launch](#launch) +* [update-db](#update-db) -## Install - +## Installation ### Bioconda soon @@ -22,9 +29,58 @@ soon If you want to install the latest code in the repository: ``` +conda create -n relecov_dev pip pip install --force-reinstall --upgrade git+https://github.com/bu-isciii/relecov-tools.git@develop +``` + +## Usage + +### Command-line +relecov-tools provides a command-line version with help descriptions and params prompt if needed. + +``` +$ relecov-tools --help + ___ ___ ___ ___ ___ +\ |--| | \ | | | | | | \ / +\ \ / |__ / |__ | |___ | | | \ / +/ / \ | \ | | | | | | \ / +/ |--| | \ |___ |___ |___ |___ |___| \/ +RELECOV-tools version 0.0.1 +Usage: relecov-tools [OPTIONS] COMMAND [ARGS]... + +Options: +--version Show the version and exit. +-v, --verbose Print verbose output to the console. +-l, --log-file Save a verbose log to a file. +--help Show this message and exit. + +Commands: + download Download files located in sftp server. + read-metadata Create the json compliant to the relecov schema from... + validate Validate json file against schema. + map Convert data between phage plus schema to ENA,... + upload-to-ena parsed data to create xml files to upload to ena + upload-to-gisaid parsed data to create files to upload to gisaid + launch launch viralrecon in hpc + update-db feed database with metadata jsons +``` + + +# Python package mode +relecov-tools is designed in a way that you can use import the different modules and use them in your own scripts, for example: + +``` +import relecov_tools.sftp_handle +user="admin" +passwd="1234" +conf_file="/path/to/conf" +sftp_connection = relecov_tools.sftp_handle.SftpHandle( + user, password, conf_file +) +sftp_connection.download() ``` +DOCs soon!! diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index cf1e5e3e..c3468173 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -126,27 +126,26 @@ def relecov_tools_cli(verbose, log_file): log.addHandler(log_fh) -# pipeline list -@relecov_tools_cli.command(help_priority=1) -@click.argument("keywords", required=False, nargs=-1, metavar="") -@click.option( - "-s", - "--sort", - type=click.Choice(["release", "pulled", "name", "stars"]), - default="release", - help="How to sort listed pipelines", -) -@click.option("--json", is_flag=True, default=False, help="Print full output as JSON") -@click.option( - "--show-archived", is_flag=True, default=False, help="Print archived workflows" -) -def list(keywords, sort, json, show_archived): - """ - List available bu-isciii workflows used for relecov. - Checks the web for a list of nf-core pipelines with their latest releases. - Shows which nf-core pipelines you have pulled locally and whether they are up to date. - """ - pass +#@relecov_tools_cli.command(help_priority=1) +#@click.argument("keywords", required=False, nargs=-1, metavar="") +#@click.option( +# "-s", +# "--sort", +# type=click.Choice(["release", "pulled", "name", "stars"]), +# default="release", +# help="How to sort listed pipelines", +#) +#@click.option("--json", is_flag=True, default=False, help="Print full output as JSON") +#@click.option( +# "--show-archived", is_flag=True, default=False, help="Print archived workflows" +#) +#def list(keywords, sort, json, show_archived): +# """ +# List available bu-isciii workflows used for relecov. +# Checks the web for a list of nf-core pipelines with their latest releases. +# Shows which nf-core pipelines you have pulled locally and whether they are up to date. +# """ +# pass # sftp From bb49bb1bc7ae75608c90419375fa1aae8ed7df72 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 30 Mar 2022 17:40:08 +0200 Subject: [PATCH 0242/1454] removing mapping json --- relecov_tools/conf/configuration.json | 2 -- 1 file changed, 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 6d0a3698..449d5aaf 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -4,8 +4,6 @@ "ena_schema": "ena_schema.json", "gisaid_schema": "gisaid_schema.json" }, - "mapping_metadata_json": "mapping_metadata_to_json.json", - "mapping_upload_ena": "mapping_ena_to_upload_ena.json", "sftp_connection": { "sftp_server": "sftprelecov.isciii.es", "sftp_port": "50122" From c90b456de66a970427f4f0aab409351ab49975fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 30 Mar 2022 17:43:43 +0200 Subject: [PATCH 0243/1454] removed test param from main and sftp class, updating readme --- relecov_tools/__main__.py | 7 +++---- relecov_tools/sftp_handle.py | 3 +-- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index c3468173..24e3c584 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -155,13 +155,12 @@ def relecov_tools_cli(verbose, log_file): @click.option( "-f", "--conf_file", - help="Configuration file Create Nextflow command with params (no params file)", + help="Configuration file (no params file)", ) -@click.option("--test", is_flag=True, default=False, help="download files for testing") -def download(user, password, conf_file, test): +def download(user, password, conf_file): """Download files located in sftp server.""" sftp_connection = relecov_tools.sftp_handle.SftpHandle( - user, password, conf_file, test + user, password, conf_file ) sftp_connection.download() diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 46fcee1c..a922563b 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -25,7 +25,7 @@ class SftpHandle: - def __init__(self, user=None, passwd=None, conf_file=None, test=None): + def __init__(self, user=None, passwd=None, conf_file=None): """Initializes the sftp object""" config_json = ConfigJson() self.allowed_sample_ext = config_json.get_configuration( @@ -96,7 +96,6 @@ def __init__(self, user=None, passwd=None, conf_file=None, test=None): msg="Enter your password" ) self.client = None - self.test = test def open_connection(self): """Establish sftp connection""" From 2d4533d5fbd7681cfed433216d9baca5ec2de7e3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 30 Mar 2022 17:47:35 +0200 Subject: [PATCH 0244/1454] add validate docs in readme --- README.md | 89 +++++++++++++++++++++++++++++++++++++-- relecov_tools/__main__.py | 20 ++++----- 2 files changed, 95 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index 693f2b8c..61e20616 100644 --- a/README.md +++ b/README.md @@ -20,10 +20,10 @@ relecov-tools is a set of helper tools for the assembly of the different element ## Installation ### Bioconda -soon +Soon ### Pip -soon +Soon ### Development version If you want to install the latest code in the repository: @@ -64,9 +64,92 @@ Commands: launch launch viralrecon in hpc update-db feed database with metadata jsons ``` +#### download +The command `download` connects to a transfer protocol (currently sftp) and downloads all files in the different foldes available in the passed credentials. In addition, it checks if the files in the folder match the files in the metadata file and checks if there are md5sum for each file, if not it creates one before storing in the final repository. +``` +$ relecov-tools download --help +Usage: relecov-tools download [OPTIONS] + + Download files located in sftp server. + + Options: + -u, --user TEXT User name for login to sftp server + -p, --password TEXT password for the user to login + -f, --conf_file TEXT Configuration file in yaml format (no params file) + --help Show this message and exit. +``` + +Configuration can be passed in several formats: +- if no config_file is passed default values are fetched from conf/configuration.json, and user and password are asked in prompt. +- Default values can be overwritten using a yml config file, so you can input user, password, sftp_server, etc. + +Config file example with all available options: +``` +sftp_server: "sftprelecov.isciii.es" +sftp_port: "22" +sftp_user : "user" +sftp_passwd : "pass" +storage_local_folder: "/tmp/relecov" +tmp_folder_for_metadata: "/tmp/relecov/tmp" +allowed_sample_extensions: + - .fastq.gz + - .fasta +``` + +#### read-metadata +`read-metadata` command reads the excel file with laboratory metadata and processes it adding aditional needed fields. + +``` +$ relecov-tools read-metadata --help +Usage: relecov-tools read-metadata [OPTIONS] + + Create the json compliant to the relecov schema from the Metadata file. + + Options: + -m, --metadata_file PATH file containing metadata in xlsx format. + -s, --sample_list_file PATH Json with the additional metadata to add to the + received user metadata. + -o, --metadata-out PATH Path to save output metadata file in json format. + --help Show this message and exit. +``` + + +An example for the metadata excel file can be found [here](./relecov_tools/example_data/METADATA_LAB_TEST.xlsx) + +#### validate +`validate` commands validate the data in json format outputted by `read-metadata` command against a json schema, in this case the relecov [schema specification](./relecov_tools/schema/relecov_schema.json). + +``` +$ relecov-tools validate --help +Usage: relecov-tools validate [OPTIONS] + + Validate json file against schema. + + Options: + -j, --json_file TEXT Json file to validate + -s, --json_schema TEXT Json schema + -o, --out_folder TEXT Path to save validate json file + --help Show this message and exit. + +``` + +#### map + + +#### upload-to-ena + + +#### upload-to-gisaid +SOON + +#### launch +SOON + +#### update-db +SOON -# Python package mode +#### Python package mode relecov-tools is designed in a way that you can use import the different modules and use them in your own scripts, for example: ``` diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 24e3c584..72a849be 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -126,20 +126,20 @@ def relecov_tools_cli(verbose, log_file): log.addHandler(log_fh) -#@relecov_tools_cli.command(help_priority=1) -#@click.argument("keywords", required=False, nargs=-1, metavar="") -#@click.option( +# @relecov_tools_cli.command(help_priority=1) +# @click.argument("keywords", required=False, nargs=-1, metavar="") +# @click.option( # "-s", # "--sort", # type=click.Choice(["release", "pulled", "name", "stars"]), # default="release", # help="How to sort listed pipelines", -#) -#@click.option("--json", is_flag=True, default=False, help="Print full output as JSON") -#@click.option( +# ) +# @click.option("--json", is_flag=True, default=False, help="Print full output as JSON") +# @click.option( # "--show-archived", is_flag=True, default=False, help="Print archived workflows" -#) -#def list(keywords, sort, json, show_archived): +# ) +# def list(keywords, sort, json, show_archived): # """ # List available bu-isciii workflows used for relecov. # Checks the web for a list of nf-core pipelines with their latest releases. @@ -159,9 +159,7 @@ def relecov_tools_cli(verbose, log_file): ) def download(user, password, conf_file): """Download files located in sftp server.""" - sftp_connection = relecov_tools.sftp_handle.SftpHandle( - user, password, conf_file - ) + sftp_connection = relecov_tools.sftp_handle.SftpHandle(user, password, conf_file) sftp_connection.download() From f180109cbb3c0ea57941ec69a24831495ec8bbbb Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 30 Mar 2022 17:48:43 +0200 Subject: [PATCH 0245/1454] Removed test parameter from sft_handle --- relecov_tools/__main__.py | 1 - relecov_tools/sftp_handle.py | 3 +-- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index b8f84e84..b162fc34 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -158,7 +158,6 @@ def list(keywords, sort, json, show_archived): "--conf_file", help="Configuration file Create Nextflow command with params (no params file)", ) -@click.option("--test", is_flag=True, default=False, help="download files for testing") def download(user, password, conf_file, test): """Download files located in sftp server.""" sftp_connection = relecov_tools.sftp_handle.SftpHandle( diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 46fcee1c..a922563b 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -25,7 +25,7 @@ class SftpHandle: - def __init__(self, user=None, passwd=None, conf_file=None, test=None): + def __init__(self, user=None, passwd=None, conf_file=None): """Initializes the sftp object""" config_json = ConfigJson() self.allowed_sample_ext = config_json.get_configuration( @@ -96,7 +96,6 @@ def __init__(self, user=None, passwd=None, conf_file=None, test=None): msg="Enter your password" ) self.client = None - self.test = test def open_connection(self): """Establish sftp connection""" From afda8a8b658db533e466957b475ee1f02b23e48d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 30 Mar 2022 17:57:49 +0200 Subject: [PATCH 0246/1454] upload readme with remaining modules --- README.md | 35 +++++++++++++++++++++++++++++++++++ relecov_tools/__main__.py | 4 ++-- 2 files changed, 37 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 61e20616..3197d7fd 100644 --- a/README.md +++ b/README.md @@ -135,10 +135,43 @@ Usage: relecov-tools validate [OPTIONS] ``` #### map +The command `map` converts a data in json format from relecov data model to ena or gisaid data model using their own schemas acording to their annotated ontoly terms. +``` +$ relecov-tools map --help +Usage: relecov-tools map [OPTIONS] + + Convert data between phage plus schema to ENA, GISAID, or any other schema + + Options: + -p, --origin_schema TEXT File with the origin (relecov) schema + -j, --json_data TEXT File with the json data to convert + -d, --destination_schema [ENA|GSAID|other] + schema to be mapped + -f, --schema_file TEXT file with the custom schema + -o, --output TEXT File name and path to store the mapped json + --help Show this message and exit. +``` #### upload-to-ena +`upload-to-ena` command uses json data mapped to ena schema to use the [ena_upload_cli](https://github.com/usegalaxy-eu/ena-upload-cli) package to upload raw data and metadata to ENA db. +``` +Usage: relecov-tools upload-to-ena [OPTIONS] + + parsed data to create xml files to upload to ena + + Options: + -u, --user TEXT user name for login to ena + -p, --password TEXT password for the user to login + -e, --ena_json TEXT where the validated json is + -s, --study TEXT study/project name to include in xml files + -a, --action [add|modify|cancel|release] select one of the available options + --dev / --production + -o, --output_path TEXT output folder for the xml generated files + --help Show this message and exit. + +``` #### upload-to-gisaid SOON @@ -167,3 +200,5 @@ sftp_connection.download() DOCs soon!! +## Acknowledgements +Python package idea and designed is really inspired in [nf-core/tools](https://github.com/nf-core/tools). diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 72a849be..f0b688bd 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -216,7 +216,7 @@ def validate(json_file, json_schema, out_folder): # mapping to ENA schema @relecov_tools_cli.command(help_priority=5) -@click.option("-p", "--phage_plus_schema", help="File with the phage plus schema") +@click.option("-p", "--origin_schema", help="File with the origin (relecov) schema") @click.option("-j", "--json_data", help="File with the json data to convert") @click.option( "-d", @@ -229,7 +229,7 @@ def validate(json_file, json_schema, out_folder): def map(phage_plus_schema, json_data, destination_schema, schema_file, output): """Convert data between phage plus schema to ENA, GISAID, or any other schema""" new_schema = relecov_tools.conversion_schema.MappingSchema( - phage_plus_schema, json_data, destination_schema, schema_file, output + origin_schema, json_data, destination_schema, schema_file, output ) new_schema.map_to_data_to_new_schema() From 161048b6e83db01c4fec81eaadb78c0fdda8e6dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 30 Mar 2022 17:59:00 +0200 Subject: [PATCH 0247/1454] minor format change readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3197d7fd..f2b7a47b 100644 --- a/README.md +++ b/README.md @@ -182,7 +182,7 @@ SOON #### update-db SOON -#### Python package mode +### Python package mode relecov-tools is designed in a way that you can use import the different modules and use them in your own scripts, for example: ``` From 7cddb310415b56a8a41271659f14c10eaace24a5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 30 Mar 2022 18:02:43 +0200 Subject: [PATCH 0248/1454] fix typo from renaming in main --- relecov_tools/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index f0b688bd..0d8e3726 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -226,7 +226,7 @@ def validate(json_file, json_schema, out_folder): ) @click.option("-f", "--schema_file", help="file with the custom schema") @click.option("-o", "--output", help="File name and path to store the mapped json") -def map(phage_plus_schema, json_data, destination_schema, schema_file, output): +def map(origin_schema, json_data, destination_schema, schema_file, output): """Convert data between phage plus schema to ENA, GISAID, or any other schema""" new_schema = relecov_tools.conversion_schema.MappingSchema( origin_schema, json_data, destination_schema, schema_file, output From 5017e89087348016a6b426b3a5277424911643c6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 30 Mar 2022 18:08:20 +0200 Subject: [PATCH 0249/1454] added warning of active development --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index f2b7a47b..4a77438c 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,8 @@ [![python_lint](https://github.com/BU-ISCIII/relecov-tools/actions/workflows/python_lint.yml/badge.svg)](https://github.com/BU-ISCIII/relecov-tools/actions/workflows/python_lint.yml) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) +> THIS REPO IS IN ACTIVE DEVELOPMENT WITH NO RELEASE VERSION YET. + relecov-tools is a set of helper tools for the assembly of the different elements in the RELECOV platform (Spanish Network for genomic surveillance of SARS-Cov-2) as data download, processing, validation and upload to publica databases, as well as analysis runs and database storage. ## Table of contents From 0d71380408b99b39c919d894e13f33f3b6dde532 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 30 Mar 2022 18:08:27 +0200 Subject: [PATCH 0250/1454] added warning of active development --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 4a77438c..4fa7e23f 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![python_lint](https://github.com/BU-ISCIII/relecov-tools/actions/workflows/python_lint.yml/badge.svg)](https://github.com/BU-ISCIII/relecov-tools/actions/workflows/python_lint.yml) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) -> THIS REPO IS IN ACTIVE DEVELOPMENT WITH NO RELEASE VERSION YET. +> THIS REPO IS IN ACTIVE DEVELOPMENT. relecov-tools is a set of helper tools for the assembly of the different elements in the RELECOV platform (Spanish Network for genomic surveillance of SARS-Cov-2) as data download, processing, validation and upload to publica databases, as well as analysis runs and database storage. From 6088dca2884147dc7d93eed690cbf3bb06eb65cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 30 Mar 2022 18:14:18 +0200 Subject: [PATCH 0251/1454] updated paramiko version due to vulnerabilities --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 0e38527e..df6c9d32 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,7 +6,7 @@ prompt_toolkit>=3.0.3 rich>=10.0.0 requests==2.27.1 geopy==2.2.0 -paramiko==2.9.2 +paramiko>=2.10.1 pyyaml openpyxl ena-upload-cli From 608ff9b1f9156fddde2e31b5cee3a57515770547 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 30 Mar 2022 18:16:12 +0200 Subject: [PATCH 0252/1454] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 4fa7e23f..1a037f62 100644 --- a/README.md +++ b/README.md @@ -203,4 +203,4 @@ DOCs soon!! ## Acknowledgements -Python package idea and designed is really inspired in [nf-core/tools](https://github.com/nf-core/tools). +Python package idea and design is really inspired in [nf-core/tools](https://github.com/nf-core/tools). From 4237948086520af780e859db60a934eb39d6e7ef Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 30 Mar 2022 18:20:09 +0200 Subject: [PATCH 0253/1454] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1a037f62..68fa6bd4 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ > THIS REPO IS IN ACTIVE DEVELOPMENT. -relecov-tools is a set of helper tools for the assembly of the different elements in the RELECOV platform (Spanish Network for genomic surveillance of SARS-Cov-2) as data download, processing, validation and upload to publica databases, as well as analysis runs and database storage. +relecov-tools is a set of helper tools for the assembly of the different elements in the RELECOV platform (Spanish Network for genomic surveillance of SARS-Cov-2) as data download, processing, validation and upload to public databases, as well as analysis runs and database storage. ## Table of contents From 3f9ba5cec65bc95048b4e5b9d776a3f94ab908cb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 30 Mar 2022 18:22:24 +0200 Subject: [PATCH 0254/1454] Update README.md --- README.md | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 68fa6bd4..cc025622 100644 --- a/README.md +++ b/README.md @@ -10,14 +10,15 @@ relecov-tools is a set of helper tools for the assembly of the different element * [Installation](#installation) * [Usage](#usage) -* [download](#download) -* [read-metadata](#read-metadata) -* [validate](#validate) -* [map](#map) -* [upload-to-ena](#upload-to-ena) -* [upload-to-gisaid](#upload-to-gisaid) -* [launch](#launch) -* [update-db](#update-db) + * [download](#download) + * [read-metadata](#read-metadata) + * [validate](#validate) + * [map](#map) + * [upload-to-ena](#upload-to-ena) + * [upload-to-gisaid](#upload-to-gisaid) + * [launch](#launch) + * [update-db](#update-db) +* [Aknowledgements](#aknowledgements) ## Installation From abde81c469991c5d4d8ff249e454fa98c6b65449 Mon Sep 17 00:00:00 2001 From: Alema91 Date: Wed, 30 Mar 2022 18:39:54 +0200 Subject: [PATCH 0255/1454] Some english misprints --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index cc025622..17df3c52 100644 --- a/README.md +++ b/README.md @@ -68,9 +68,9 @@ Commands: update-db feed database with metadata jsons ``` #### download -The command `download` connects to a transfer protocol (currently sftp) and downloads all files in the different foldes available in the passed credentials. In addition, it checks if the files in the folder match the files in the metadata file and checks if there are md5sum for each file, if not it creates one before storing in the final repository. +The command `download` connects to a transfer protocol (currently sftp) and downloads all files in the different available folders in the passed credentials. In addition, it checks if the files in the current folder match the files in the metadata file and also checks if there are md5sum for each file. If not, it creates one before storing in the final repository. -``` +``` $ relecov-tools download --help Usage: relecov-tools download [OPTIONS] @@ -138,7 +138,7 @@ Usage: relecov-tools validate [OPTIONS] ``` #### map -The command `map` converts a data in json format from relecov data model to ena or gisaid data model using their own schemas acording to their annotated ontoly terms. +The command `map` converts a data in json format from relecov data model to ena or gisaid data model using their own schemas acording to their annotated ontology terms. ``` $ relecov-tools map --help @@ -204,4 +204,4 @@ DOCs soon!! ## Acknowledgements -Python package idea and design is really inspired in [nf-core/tools](https://github.com/nf-core/tools). +Python package idea and design is really inspired in [nf-core/tools](https://github.com/nf-core/tools). \ No newline at end of file From eaf1144b2ea6553166622053c5392181d544706a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 30 Mar 2022 19:31:25 +0200 Subject: [PATCH 0256/1454] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 17df3c52..45dc033a 100644 --- a/README.md +++ b/README.md @@ -68,7 +68,7 @@ Commands: update-db feed database with metadata jsons ``` #### download -The command `download` connects to a transfer protocol (currently sftp) and downloads all files in the different available folders in the passed credentials. In addition, it checks if the files in the current folder match the files in the metadata file and also checks if there are md5sum for each file. If not, it creates one before storing in the final repository. +The command `download` connects to a transfer protocol (currently sftp) and downloads all files in the different available folders in the passed credentials. In addition, it checks if the files in the current folder match the files in the metadata file and also checks if there are md5sum for each file. Else, it creates one before storing in the final repository. ``` $ relecov-tools download --help @@ -84,7 +84,7 @@ Usage: relecov-tools download [OPTIONS] ``` Configuration can be passed in several formats: -- if no config_file is passed default values are fetched from conf/configuration.json, and user and password are asked in prompt. +- if no config_file is passed, default values are fetched from conf/configuration.json, and user and password are asked in prompt. - Default values can be overwritten using a yml config file, so you can input user, password, sftp_server, etc. Config file example with all available options: @@ -204,4 +204,4 @@ DOCs soon!! ## Acknowledgements -Python package idea and design is really inspired in [nf-core/tools](https://github.com/nf-core/tools). \ No newline at end of file +Python package idea and design is really inspired in [nf-core/tools](https://github.com/nf-core/tools). From ce9b7fb9a92b1d855076ed95cb83ba4611e8794a Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 30 Mar 2022 22:11:46 +0200 Subject: [PATCH 0257/1454] Rename the PHAGE_PLUS to RELECOV --- relecov_tools/schema/relecov_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index bdba659d..86f8eac5 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1,5 +1,5 @@ { - "schema": "PHAGE_PLUS", + "schema": "RELECOV", "required": [ "collecting_lab_sample_id", "collecting_institution", @@ -3225,4 +3225,4 @@ "clasification": "Database Identifiers" } } -} \ No newline at end of file +} From 7aa93c41b715f169d499e533a08f8f8e328509d4 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 30 Mar 2022 22:16:01 +0200 Subject: [PATCH 0258/1454] Set the prompt to unsafe_ask() --- relecov_tools/utils.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 3b29e75e..662d6787 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -97,12 +97,12 @@ def rich_force_colors(): def prompt_text(msg): - source = questionary.text(msg).ask() + source = questionary.text(msg).unsafe_ask() return source def prompt_password(msg): - source = questionary.password(msg).ask() + source = questionary.password(msg).unsafe_ask() return source From c843d45f238877d2c9eb273c3ded1e83d784495b Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 30 Mar 2022 22:35:03 +0200 Subject: [PATCH 0259/1454] rename to relecov the references to phage_plus schema --- relecov_tools/conf/configuration.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 449d5aaf..02e45c1d 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -1,6 +1,6 @@ { "json_schemas": { - "phage_plus_schema": "phage_plus_schema.json", + "relecov_schema": "relecov_schema.json", "ena_schema": "ena_schema.json", "gisaid_schema": "gisaid_schema.json" }, From 1d2b45a8ae3ee6d8fe0b80842b4620bd5e79f16c Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 31 Mar 2022 00:22:57 +0200 Subject: [PATCH 0260/1454] changes in the label field not matched with Metadata file --- relecov_tools/schema/relecov_schema.json | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 86f8eac5..0c7e16e7 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -573,7 +573,8 @@ ], "ontology": "0", "type": "string", - "description": "Sample ID given by the submitting laboratory" + "description": "Sample ID given by the submitting laboratory", + "label": "Sample ID given by the submitting laboratory" }, "bioproject_umbrella_accession_ENA": { "examples": [ @@ -603,7 +604,7 @@ "type": "string", "description": "The identifier assigned to a BioSample in INSDC archives.", "clasification": "Database Identifiers", - "label": "ENA Sample Id" + "label": "ENA Sample ID" }, "sra_accession": { "examples": [ @@ -1295,7 +1296,7 @@ "Human [NCBITaxon:9606]" ], "classification": "Host information", - "label": "Host Common Name" + "label": "Host" }, "host_residence_country": { "Enums": [ @@ -1673,7 +1674,7 @@ "examples": [ "Diagnostic Testing [GENEPIO:0100002]" ], - "label": "Purpose of Sampling" + "label": "Purpose of sampling" }, "purpose_of_sampling_details": { "ontology": "GENEPIO:0001200", @@ -1743,7 +1744,7 @@ "description": "The date the sample was sequenced.", "format": "date", "clasification": "Sequencing", - "label": "Sequencing date" + "label": "Sequencing Date" }, "rna_extraction_protocol": { "examples": [ @@ -1763,7 +1764,7 @@ "type": "string", "description": "", "clasification": "Sequencing", - "label": "Library Kit" + "label": "Commercial All-in-one library kit" }, "library_id": { "examples": [ @@ -1783,7 +1784,7 @@ "type": "string", "description": "", "clasification": "Sequencing", - "label": "Enrichment_protocol" + "label": "Enrichment Protocol" }, "if_enrichment_protocol_is_other_specify": { "examples": [ @@ -1803,7 +1804,7 @@ "type": "string", "description": "", "clasification": "Sequencing", - "label": "Amplicon Protocol" + "label": "Amplicon panel/assay" }, "if_amplicon_protocol_if_other_especify": { "examples": [ @@ -1813,7 +1814,7 @@ "type": "string", "description": "", "clasification": "Sequencing", - "labe": "If Amplicon Protocol If Other, Especify" + "label": "If Amplicon Protocol If Other, Especify" }, "amplicon_version": { "examples": [ @@ -1863,7 +1864,7 @@ "type": "string", "description": "", "clasification": "Sequencing", - "labe": "Flowcell Kit" + "label": "Flowcell Kit" }, "runID": { "examples": [ @@ -1873,7 +1874,7 @@ "type": "string", "description": "", "clasification": "Sequencing", - "label": "RunID" + "label": "Runid" }, "sequencing_platforms": { "examples": [ From 5c0001e31e7585bcf11c7556877e6114c3e5a6ea Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 31 Mar 2022 00:24:57 +0200 Subject: [PATCH 0261/1454] Starting mapping metadata using label field in schema --- relecov_tools/read_metadata.py | 57 +++++++++++++++++++++++++--------- 1 file changed, 42 insertions(+), 15 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index ac794da7..857f8a2a 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -32,19 +32,35 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None self.metadata_file = metadata_file if not os.path.exists(self.metadata_file): log.error("Metadata file %s does not exist ", self.metadata_file) + stderr.print("[red] Metadata file " + self.meta_file + " does not exist") sys.exit(1) if sample_list_file is None: self.sample_list_file = relecov_tools.utils.prompt_path( - msg="Select the file which contains the sample list" + msg="Select the file which contains the sample information" ) else: self.sample_list_file = sample_list_file + if not os.path.exists(self.sample_list_file): + log.error("Sample information file %s does not exist ", self.metadata_file) + stderr.print("[red] Sample information " + self.sample_list_file + " does not exist") + sys.exit(1) if output_folder is None: self.output_folder = relecov_tools.utils.prompt_path( msg="Select the output folder" ) else: self.output_folder = output_folder + config_json = ConfigJson() + relecov_schema = config_json.get_topic_data("json_schemas", "relecov_schema") + relecov_sch_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), "schema", relecov_schema) + with open(relecov_sch_path, "r") as fh: + self.relecov_sch_json = json.load(fh) + self.label_prop_dict = {} + for prop, values in self.relecov_sch_json['properties'].items(): + try: + self.label_prop_dict[values["label"]] = prop + except KeyError: + continue def check_new_metadata(folder): """Check if there is a new metadata to be processed @@ -191,30 +207,40 @@ def update_heading_to_json(self, heading, meta_map_json): mapped_heading.append(cell) return mapped_heading - def read_metadata_file(self, meta_map_json): - """Read the input metadata file, mapping the metadata heading with - the values used in json. Convert the date colunms value to the - dd/mm/yyyy format. Return list of dict with data, and errors + def read_metadata_file(self): + """Read the input metadata file, changing the metadata heading with + their property name values defined in schema. + Convert the date colunms value to the dd/mm/yyyy format. + Return list of dict with data, and errors """ wb_file = openpyxl.load_workbook(self.metadata_file, data_only=True) ws_metadata_lab = wb_file["METADATA_LAB"] # removing the None columns in excel heading row - heading_without_none = [i.value.strip() for i in ws_metadata_lab[4] if i.value] - heading = self.update_heading_to_json(heading_without_none, meta_map_json) + heading = [i.value.strip() for i in ws_metadata_lab[4] if i.value] + # heading = self.update_heading_to_json(heading_without_none, meta_map_json) metadata_values = [] errors = {} for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): sample_data_row = {} - for idx in range(len(heading)): + # Ignore the empty rows + if row[2] is None: + continue + for idx in range(2, len(heading)): if "date" in heading[idx]: try: - sample_data_row[heading[idx]] = row[idx].strftime("%Y/%m/%d") + sample_data_row[self.label_prop_dict[heading[idx]]] = row[idx].strftime("%Y/%m/%d") except AttributeError: - if row[0] not in errors: - errors[row[0]] = {} - errors[row[0]][heading[idx]] = "Invalid date format" + if row[2] not in errors: + errors[row[2]] = {} + errors[row[2]][heading[idx]] = "Invalid date format" + log.error("Invalid date format in sample", row[2]) + stderr.print("[red] Invalid date format in sample", row[2] + " column " + heading[idx]) else: - sample_data_row[heading[idx]] = row[idx] if row[idx] else "" + try: + sample_data_row[self.label_prop_dict[heading[idx]]] = row[idx] if row[idx] else "" + except KeyError as e: + print (e) + import pdb; pdb.set_trace() metadata_values.append(sample_data_row) return metadata_values, errors @@ -251,13 +277,14 @@ def create_metadata_json(self): lab_json_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "conf", lab_json ) + """ metadata_mapping_json = config_json.get_configuration("mapping_metadata_json") meta_map_json_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", metadata_mapping_json ) meta_map_json = self.read_json_file(meta_map_json_file) - - valid_metadata_rows, errors = self.read_metadata_file(meta_map_json) + """ + valid_metadata_rows, errors = self.read_metadata_file() completed_metadata = self.add_extra_data( valid_metadata_rows, From 3a78040b780ca17d8933ec021e67207fa1a771b8 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 31 Mar 2022 00:31:35 +0200 Subject: [PATCH 0262/1454] Removing debuging tags --- relecov_tools/read_metadata.py | 31 +++++++++++++++++++++---------- 1 file changed, 21 insertions(+), 10 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 857f8a2a..e4767f34 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -42,7 +42,9 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None self.sample_list_file = sample_list_file if not os.path.exists(self.sample_list_file): log.error("Sample information file %s does not exist ", self.metadata_file) - stderr.print("[red] Sample information " + self.sample_list_file + " does not exist") + stderr.print( + "[red] Sample information " + self.sample_list_file + " does not exist" + ) sys.exit(1) if output_folder is None: self.output_folder = relecov_tools.utils.prompt_path( @@ -52,11 +54,13 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None self.output_folder = output_folder config_json = ConfigJson() relecov_schema = config_json.get_topic_data("json_schemas", "relecov_schema") - relecov_sch_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), "schema", relecov_schema) + relecov_sch_path = os.path.join( + os.path.dirname(os.path.realpath(__file__)), "schema", relecov_schema + ) with open(relecov_sch_path, "r") as fh: self.relecov_sch_json = json.load(fh) self.label_prop_dict = {} - for prop, values in self.relecov_sch_json['properties'].items(): + for prop, values in self.relecov_sch_json["properties"].items(): try: self.label_prop_dict[values["label"]] = prop except KeyError: @@ -104,7 +108,7 @@ def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): break return data - def add_extra_data(self, metadata, extra_data, lab_json_file, geo_loc_file): + def add_extra_data(self, metadata, lab_json_file, geo_loc_file): """Add the additional information that must be included in final metadata metadata Origin metadata extra_data additional data to be included @@ -112,6 +116,7 @@ def add_extra_data(self, metadata, extra_data, lab_json_file, geo_loc_file): """ lab_data = {} extra_metadata = [] + extra_data = "" lab_json = self.read_json_file(lab_json_file) geo_loc_json = self.read_json_file(geo_loc_file) samples_json = self.read_json_file(self.sample_list_file) @@ -228,19 +233,26 @@ def read_metadata_file(self): for idx in range(2, len(heading)): if "date" in heading[idx]: try: - sample_data_row[self.label_prop_dict[heading[idx]]] = row[idx].strftime("%Y/%m/%d") + sample_data_row[self.label_prop_dict[heading[idx]]] = row[ + idx + ].strftime("%Y/%m/%d") except AttributeError: if row[2] not in errors: errors[row[2]] = {} errors[row[2]][heading[idx]] = "Invalid date format" log.error("Invalid date format in sample", row[2]) - stderr.print("[red] Invalid date format in sample", row[2] + " column " + heading[idx]) + stderr.print( + "[red] Invalid date format in sample", + row[2] + " column " + heading[idx], + ) else: try: - sample_data_row[self.label_prop_dict[heading[idx]]] = row[idx] if row[idx] else "" + sample_data_row[self.label_prop_dict[heading[idx]]] = ( + row[idx] if row[idx] else "" + ) except KeyError as e: - print (e) - import pdb; pdb.set_trace() + print(e) + metadata_values.append(sample_data_row) return metadata_values, errors @@ -288,7 +300,6 @@ def create_metadata_json(self): completed_metadata = self.add_extra_data( valid_metadata_rows, - meta_map_json["Additional_fields"], lab_json_file, geo_loc_file, ) From 4f7246f25538e9b4763600edc92d74e3f12efce4 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 31 Mar 2022 13:56:48 +0200 Subject: [PATCH 0263/1454] working with extra data --- relecov_tools/read_metadata.py | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index e4767f34..c68566f4 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -1,6 +1,7 @@ #!/usr/bin/env python from itertools import islice -from geopy.geocoders import Nominatim + +# from geopy.geocoders import Nominatim import json import logging import rich.console @@ -165,10 +166,11 @@ def add_extra_data(self, metadata, lab_json_file, geo_loc_file): extra_metadata.append(row) return extra_metadata - def compare_sample_in_metadata(self, completed_metadata): + # def compare_sample_in_metadata(self, completed_metadata): """Compare the samples defined in metadata file and the ones in the sample file """ + """ not_found_samples = [] if not os.path.exists(self.sample_list_file): return False @@ -181,6 +183,7 @@ def compare_sample_in_metadata(self, completed_metadata): if len(not_found_samples) > 0: return not_found_samples return True + """ def request_information(external_url, request): """Get information from external database server using Rest API @@ -194,16 +197,19 @@ def store_information(external_url, request, data): """Update information""" pass - def get_geo_location_data(self, state, country): + # def get_geo_location_data(self, state, country): """Get the geo_loc_latitude and geo_loc_longitude from state""" + """ geolocator = Nominatim(user_agent="geoapiRelecov") loc = geolocator.geocode(state + "," + country) return [str(loc.latitude), str(loc.longitude)] + """ - def update_heading_to_json(self, heading, meta_map_json): + # def update_heading_to_json(self, heading, meta_map_json): """Change the heading values from the metadata file for the ones defined in the json schema """ + """ mapped_heading = [] for cell in heading: if cell in meta_map_json: @@ -211,6 +217,7 @@ def update_heading_to_json(self, heading, meta_map_json): else: mapped_heading.append(cell) return mapped_heading + """ def read_metadata_file(self): """Read the input metadata file, changing the metadata heading with @@ -230,7 +237,7 @@ def read_metadata_file(self): # Ignore the empty rows if row[2] is None: continue - for idx in range(2, len(heading)): + for idx in range(1, len(heading)): if "date" in heading[idx]: try: sample_data_row[self.label_prop_dict[heading[idx]]] = row[ @@ -240,7 +247,7 @@ def read_metadata_file(self): if row[2] not in errors: errors[row[2]] = {} errors[row[2]][heading[idx]] = "Invalid date format" - log.error("Invalid date format in sample", row[2]) + log.error("Invalid date format in sample %s", row[2]) stderr.print( "[red] Invalid date format in sample", row[2] + " column " + heading[idx], @@ -252,8 +259,8 @@ def read_metadata_file(self): ) except KeyError as e: print(e) - metadata_values.append(sample_data_row) + # import pdb; pdb.set_trace() return metadata_values, errors def write_json_fo_file(self, completed_metadata, file_name): From 9a6a63a98f33fda7aca688e7a077354402a1c741 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 31 Mar 2022 13:58:09 +0200 Subject: [PATCH 0264/1454] update relecov schema --- relecov_tools/schema/relecov_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 0c7e16e7..b9d9d2eb 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2758,7 +2758,7 @@ "type": "string", "description": "", "clasification": "enter your GISAID-Username", - "label": "GISAID Id" + "label": "GISAID id" }, "authors": { "examples": [ From 891a92d1a21dad83111601b92901dfdae2aa4d38 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 31 Mar 2022 16:28:19 +0200 Subject: [PATCH 0265/1454] latest changes in the schema --- relecov_tools/__main__.py | 5 ++- relecov_tools/ena_upload.py | 20 +++++++++- .../schema/mapping_ena_to_upload_ena.json | 38 ++++++++++--------- 3 files changed, 42 insertions(+), 21 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index cf1e5e3e..767cef09 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -238,6 +238,7 @@ def map(phage_plus_schema, json_data, destination_schema, schema_file, output): new_schema.map_to_data_to_new_schema() +# upload to ENA @relecov_tools_cli.command(help_priority=6) @click.option("-u", "--user", help="user name for login to ena") @click.option("-p", "--password", help="password for the user to login") @@ -253,10 +254,10 @@ def map(phage_plus_schema, json_data, destination_schema, schema_file, output): @click.option("-o", "--output_path", help="output folder for the xml generated files") def upload_to_ena(user, password, ena_json, dev, study, action, output_path): """parsed data to create xml files to upload to ena""" - upload_ena = relecov_tools.ena_upload.upload( + upload_ena = relecov_tools.ena_upload.EnaUpload( user, password, ena_json, dev, study, action, output_path ) - upload_ena.upload_files_to_ena() + upload_ena.upload() @relecov_tools_cli.command(help_priority=7) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index cb843356..2ce63fff 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,3 +1,4 @@ +from bdb import set_trace import os import logging import rich.console @@ -86,15 +87,28 @@ def create_structure_to_ena(self): schema_dataframe = {} config_json = ConfigJson() - map_to_upload = config_json.get_configuration("mapping_ena_to_upload_ena") + + map_to_upload = config_json.get_topic_data("json_schemas", "ena_schema") + map_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", map_to_upload ) fh = open(map_file) map_structure_json = json.load(fh) fh.close() + lista = ["study", "runs", "samples", "experiments"] + + for i in map_structure_json["properties"].keys(): + import pdb + + pdb.set_trace() - for xml_file in map_structure_json["xml_files"]: + if "table" in i.keys() and "study" in i["table"]: + + print(i["table"]) + + """ + for xml_file in lista: if self.project is not None and xml_file in self.project: pass elif config_json.get_configuration(xml_file): @@ -115,11 +129,13 @@ def create_structure_to_ena(self): df = ena_upload.check_columns(df, xml_file, self.action, self.dev, False) schema_dataframe[xml_file] = df return schema_dataframe + """ def upload(self): """Create the required files and upload to ENA""" self.convert_input_json_to_ena() self.create_structure_to_ena() + # df_study = pd.DataFrame.from_dict(data["study"]) # df_samples = pd.DataFrame.from_dict(data["samples"]) # df_runs = pd.DataFrame.from_dict(data["runs"]) diff --git a/relecov_tools/schema/mapping_ena_to_upload_ena.json b/relecov_tools/schema/mapping_ena_to_upload_ena.json index 4b663473..44456b71 100644 --- a/relecov_tools/schema/mapping_ena_to_upload_ena.json +++ b/relecov_tools/schema/mapping_ena_to_upload_ena.json @@ -1,6 +1,13 @@ { - "xml_files":["study","runs","samples","experiment"], - "one_loop_in_mapping": ["study"] + "xml_files": [ + "study", + "runs", + "samples", + "experiment" + ], + "one_loop_in_mapping": [ + "study" + ], "study": { "study_alias": "alias", "study_title": "title", @@ -11,7 +18,7 @@ "runs": { "file_name": "", "experiment_alias": "", - "host_scientific_name": "" + "host_scientific_name": "", "file_name": "", "file_type": "", "file_checksum": "" @@ -19,7 +26,7 @@ "samples": { "": "alias", "title": "", - "taxon_id":"" + "taxon_id": "", "sample_description": "", "scientific_name": "", "common_name": "", @@ -27,8 +34,7 @@ "host common name": "", "isolate": "", "collecting institution": "", - "geographic location (country and/or sea)":"", - + "geographic location (country and/or sea)": "", "host subject id": [ "host_subject_id_1", "host_subject_id_2" @@ -41,18 +47,14 @@ "male", "female" ], - [ - "host_scientific_name_1", - "host_scientific_name_2" - ], + "host_scientific_name_1": [], + "host_scientific_name_2": [], "collector name": "", - - - "collection date": + "collection date": "" }, - "experiments": { - "experiment_alias": "alias" + "experiment_alias": [ + "alias" ], "title": [ "experiment_title_1", @@ -100,7 +102,9 @@ "single" ], "insert_size": [ - "250","None","None" + "250", + "None", + "None" ], "library_construction_protocol": [ "library_construction_protocol_1", @@ -118,4 +122,4 @@ "Illumina Genome Analyzer" ] } -} +} \ No newline at end of file From 3a1e00841a9a757f455c10750cf65692d52d6df6 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 31 Mar 2022 16:51:49 +0200 Subject: [PATCH 0266/1454] added fields to schema --- relecov_tools/schema/ena_schema.json | 32 ++++++++++- relecov_tools/schema/relecov_schema.json | 67 ++++++++++++------------ 2 files changed, 65 insertions(+), 34 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 39e1b5ad..129e15eb 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -53,9 +53,39 @@ "type": "string", "description": "Name of the person who collected the specimen", "clasification": "Sample collection and processing", - "label": "Collector name", + "label": "Sample collector name", "table": "sample" }, + "public_health_sample_id_sivies": { + "examples": [ + "2022CEU03926" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Sample collection and processing", + "label": "Public Health sample id (SIVIES)" + }, + "microbiology_lab_sample_id": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Sample collection and processing", + "label": "Sample ID given in the microbiology lab" + }, + "isolate_sample_id": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "", + "label": "Sample ID given if multiple rna-extraction or passages" + }, "collection_date": { "examples": [ "3/19/2020" diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index b9d9d2eb..cf29c565 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -825,6 +825,36 @@ ], "label": "Host Gender" }, + "microbiology_lab_sample_id": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Sample collection and processing", + "label": "Sample ID given in the microbiology lab" + }, + "public_health_sample_id_sivies": { + "examples": [ + "2022CEU03926" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Sample collection and processing", + "label": "Public Health sample id (SIVIES)" + }, + "isolate_sample_id": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "", + "label": "Sample ID given if multiple rna-extraction or passages" + }, "geo_loc_region": { "examples": [ "Derbyshire" @@ -1218,36 +1248,6 @@ "clasification": "Sample collection and processing", "label": "Passage Method" }, - "biomaterial_extracted": { - "Enums": [ - "mRNA (cDNA) [OBI:0002754]", - "RNA (Total) [OBI:0000895]", - "RNA (Poly-A) [OBI:0000869]", - "RNA (Ribo-Depleted) [OBI:0002627]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO_0001965", - "type": "string", - "description": "The biomaterial extracted from samples for the purpose of sequencing.", - "examples": [ - "RNA (Total) [OBI:0000895]" - ], - "classification": "Sample collection and processing", - "label": "Source material" - }, - "data_abstraction_details": { - "ontology": "GENEPIO:0100278", - "type": "string", - "description": "A description of how any data elements were altered to preserve patient privacy.", - "examples": [ - "Jitter added to publicly shared collection dates to prevent re-identifiability." - ], - "label": "Data abstraction details" - }, "tax_id": { "examples": [ "probably 2697049 in all cases" @@ -2783,11 +2783,12 @@ "examples": [ "John Smith" ], - "ontology": "GENEPIO:0001153", + "ontology": "NCIT:C164471", "type": "string", "description": "Name of the person who collected the specimen", "clasification": "Sample collection and processing", - "label": "Originating Laboratory" + "label": "Sample collector name", + "table": "sample" }, "library_source": { "Enums": [ @@ -3226,4 +3227,4 @@ "clasification": "Database Identifiers" } } -} +} \ No newline at end of file From bb4baa0ce908d09cf53d787c334448c48de01f4f Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 31 Mar 2022 18:18:42 +0200 Subject: [PATCH 0267/1454] working on additional data --- relecov_tools/read_metadata.py | 79 +++++++++++++++++++--------------- 1 file changed, 44 insertions(+), 35 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index c68566f4..48ecbe64 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -109,62 +109,71 @@ def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): break return data - def add_extra_data(self, metadata, lab_json_file, geo_loc_file): + def include_fixed_data(): + """Include fixed data that are always the same for each samples""" + fixed_data = { + "host_disease": "COVID-19", + "type": "betacoronavirus", + "tax_id": "2697049", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "study_alias": "", + "experiment_alias": "", + "run_alias": "", + "study_title": "", + "experiment_title": "", + } + return fixed_data + + def add_additional_data(self, metadata, lab_json_file, geo_loc_file): """Add the additional information that must be included in final metadata metadata Origin metadata extra_data additional data to be included result_metadata final metadata after adding the additional data """ lab_data = {} - extra_metadata = [] + additional_metadata = [] extra_data = "" lab_json = self.read_json_file(lab_json_file) geo_loc_json = self.read_json_file(geo_loc_file) samples_json = self.read_json_file(self.sample_list_file) - for row in metadata: - for new_field, value in extra_data.items(): - row[new_field] = value - if row["collecting_institution"] not in lab_data: + for row_sample in metadata: + """Include sample data from sample json""" + for row_sample_data in samples_json: + if row_sample_data == row_sample: + for key, value in row_sample_data.items(): + row_sample[key] = value + + """ Fetch the information related to the laboratory. + Info is stored in lab_data, to prevent to call get_laboratory_data + each time for each sample that belongs to the same lab + """ + if row_sample["collecting_institution"] not in lab_data: # from collecting_institution find city, and geo location latitude and longitude l_data = self.get_laboratory_data( - lab_json, geo_loc_json, row["collecting_institution"] + lab_json, geo_loc_json, row_sample["collecting_institution"] ) - row.update(l_data) - lab_data[row["collecting_institution"]] = l_data + row_sample.update(l_data) + lab_data[row_sample["collecting_institution"]] = l_data else: - row.update(lab_data[row["collecting_institution"]]) + row_sample.update(lab_data[row_sample["collecting_institution"]]) - try: - s_data = samples_json[row["collecting_lab_sample_id"]] - for key, values in s_data.items(): - if key.endswith("_R1_fastq.gz"): - row["sequence_file_R1_fastq"] = key - row["r1_fastq_filepath"] = values["local_folder"] - row["fastq_md5"] = values["md5"] - elif key.endswith("_R2_fastq.gz"): - row["sequence_file_R2_fastq"] = key - row["r2_fastq_filepath"] = values["local_folder"] - # # WARNING: no md5 value for R2 is deficned on schena - # row["fastq_md5"] = values["md5"] - elif key.endswith(".fasta"): - file_path = os.path.join(values["local_folder"], key) - row["consensus_sequence_filepath"] = file_path - # # WARNING: no md5 value for fasta is deficned on schena - # row["fastq_md5"] = values["md5"] - except KeyError: - log.error( - "There is no files for sample %s", row["collecting_lab_sample_id"] - ) + """ Add Fixed information + """ + row_sample.update(self.include_fixed_data()) + + """Add information which is already fetched but required + """ - # update isolate qith the name of the sample + """ row["isolate"] = row["collecting_lab_sample_id"] row["host_scientific_name"] = extra_data["host_scientific_name"][ row["host_common_name"] ] row["sequencing_instrument_platform"] = "To change" - extra_metadata.append(row) - return extra_metadata + """ + additional_metadata.append(row_sample) + return additional_metadata # def compare_sample_in_metadata(self, completed_metadata): """Compare the samples defined in metadata file and the ones in the @@ -305,7 +314,7 @@ def create_metadata_json(self): """ valid_metadata_rows, errors = self.read_metadata_file() - completed_metadata = self.add_extra_data( + completed_metadata = self.add_additional_data( valid_metadata_rows, lab_json_file, geo_loc_file, From a908bbfd811420c06758719687a998e9f0cfc2f3 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 31 Mar 2022 23:16:28 +0200 Subject: [PATCH 0268/1454] testing code --- relecov_tools/read_metadata.py | 24 +++++++++++++++--------- 1 file changed, 15 insertions(+), 9 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 48ecbe64..f154b9c8 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -67,12 +67,6 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None except KeyError: continue - def check_new_metadata(folder): - """Check if there is a new metadata to be processed - folder Directory to be checked - """ - pass - def fetch_metadata_file(folder, file_name): """Fetch the metadata file folder Directory to fetch metadata file file_name metadata file name @@ -124,6 +118,17 @@ def include_fixed_data(): } return fixed_data + def include_processed_data(self, metadata): + """Include the data that requires to be processed to set the value + """ + new_data = {} + p_data = {"host_common_name": {"Human": ["host_scientific_name", "Homo Sapiens"]}} + for key, values in p_data.items(): + v_data = metadata[key] + if v_data in values: + new_data[values[v_data][0]] = values[v_data][1] + return new_data + def add_additional_data(self, metadata, lab_json_file, geo_loc_file): """Add the additional information that must be included in final metadata metadata Origin metadata @@ -132,7 +137,7 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): """ lab_data = {} additional_metadata = [] - extra_data = "" + lab_json = self.read_json_file(lab_json_file) geo_loc_json = self.read_json_file(geo_loc_file) samples_json = self.read_json_file(self.sample_list_file) @@ -162,9 +167,9 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): """ row_sample.update(self.include_fixed_data()) - """Add information which is already fetched but required + """Add information which requires processing """ - + row_sample.update(self.include_processed_data(row_sample)) """ row["isolate"] = row["collecting_lab_sample_id"] row["host_scientific_name"] = extra_data["host_scientific_name"][ @@ -173,6 +178,7 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): row["sequencing_instrument_platform"] = "To change" """ additional_metadata.append(row_sample) + import pdb; pdb.set_trace() return additional_metadata # def compare_sample_in_metadata(self, completed_metadata): From f7a6560c769071bf050db392a04695619df84bd0 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 1 Apr 2022 00:58:38 +0200 Subject: [PATCH 0269/1454] Error when saving json beacuse of date is object datetime --- relecov_tools/read_metadata.py | 32 ++++++++++++++++++++------------ 1 file changed, 20 insertions(+), 12 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index f154b9c8..fb796616 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -88,7 +88,7 @@ def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): data = {} for lab in lab_json: if lab_name == lab["collecting_institution"]: - for key, value in lab_name.items(): + for key, value in lab.items(): data[key] = value break for city in geo_loc_json: @@ -103,7 +103,7 @@ def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): break return data - def include_fixed_data(): + def include_fixed_data(self): """Include fixed data that are always the same for each samples""" fixed_data = { "host_disease": "COVID-19", @@ -122,11 +122,17 @@ def include_processed_data(self, metadata): """Include the data that requires to be processed to set the value """ new_data = {} - p_data = {"host_common_name": {"Human": ["host_scientific_name", "Homo Sapiens"]}} + p_data = {"host_common_name": {"Human": ["host_scientific_name", "Homo Sapiens"]}, + "collecting_lab_sample_id": ["isolate", metadata["collecting_lab_sample_id"]] + } + for key, values in p_data.items(): v_data = metadata[key] - if v_data in values: - new_data[values[v_data][0]] = values[v_data][1] + if isinstance(values, dict): + if v_data in values: + new_data[values[v_data][0]] = values[v_data][1] + else: + new_data[values[0]] = values[1] return new_data def add_additional_data(self, metadata, lab_json_file, geo_loc_file): @@ -162,7 +168,6 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): lab_data[row_sample["collecting_institution"]] = l_data else: row_sample.update(lab_data[row_sample["collecting_institution"]]) - """ Add Fixed information """ row_sample.update(self.include_fixed_data()) @@ -178,7 +183,6 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): row["sequencing_instrument_platform"] = "To change" """ additional_metadata.append(row_sample) - import pdb; pdb.set_trace() return additional_metadata # def compare_sample_in_metadata(self, completed_metadata): @@ -275,17 +279,18 @@ def read_metadata_file(self): except KeyError as e: print(e) metadata_values.append(sample_data_row) - # import pdb; pdb.set_trace() + return metadata_values, errors - def write_json_fo_file(self, completed_metadata, file_name): + def write_json_fo_file(self, data, file_name): """Write metadata to json file""" os.makedirs(self.output_folder, exist_ok=True) json_file = os.path.join(self.output_folder, file_name) + import pdb; pdb.set_trace() with open(json_file, "w", encoding="utf-8") as fh: fh.write( json.dumps( - completed_metadata, indent=4, sort_keys=True, ensure_ascii=False + data, indent=4, sort_keys=True, ensure_ascii=False ) ) return True @@ -325,7 +330,8 @@ def create_metadata_json(self): lab_json_file, geo_loc_file, ) - comp_result = self.compare_sample_in_metadata(completed_metadata) + # comp_result = self.compare_sample_in_metadata(completed_metadata) + """ if isinstance(comp_result, list): missing_samples = ",".join(comp_result) log.error("Missing samples %s", missing_samples) @@ -333,5 +339,7 @@ def create_metadata_json(self): log.info("Samples in metadata matches with the ones uploaded") else: log.error("There is missing samples in metadata and/or uploaded") - self.write_json_fo_file(completed_metadata, "completed_metadata.json") + """ + file_name = "processed_" + os.path.basename(self.metadata_file) + ".json" + 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zC^K1KeeRdFJ^C}{he`yq?v>TL7(`rG1_1D;!2T4igO5K0!LshPsH^jdtNUf`2EhD& zw7{%;WsOEy4R#LRc4WMtqjePcGY~B6UeDt^>>$2h)|C?M@5=(S?v?f94|n|brVFX^ zGY~B6UK9QCmoI*65E_(lzc1_8pZxgQw|>mY_^m7JQvD1B%evo{e@tq)OW^qRz|!~` z^F!nMA)VuAVL#>t+$BT&df;oq{rA*}pHKgBwe#J`_Sb_}3oPj8RDz!YKfVCM{`KtJ zPqDgSz<*mJ{WIamIjg%DMZX@c4!;oo>$TC(r~Wu&a5t&->!INOU*Y`EDXyPS{_!FA zZc^db1IY_~@-G$e-=-LT=KT0{c=rtW>yhXU_u~Wd&nN!)yz$!;bA7-9{_|1t=M#S% kwEnizUi!k__i&;l2Xi~70sv@k|IFNuMg0742S Date: Fri, 1 Apr 2022 10:55:36 +0200 Subject: [PATCH 0271/1454] added label for gisaid virus name --- relecov_tools/schema/relecov_schema.json | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index cf29c565..ccd96b11 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -643,7 +643,8 @@ "ontology": "GENEPIO:0100282", "type": "string", "description": "The user-defined GISAID virus name assigned to the sequence.", - "clasification": "Database Identifiers" + "clasification": "Database Identifiers", + "label": "GISAID Virus Name" }, "collecting_institution_email": { "examples": [ @@ -3227,4 +3228,4 @@ "clasification": "Database Identifiers" } } -} \ No newline at end of file +} From 1e72c6096a48ce95a7d9b72825ded5e6c424ad71 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 1 Apr 2022 10:56:52 +0200 Subject: [PATCH 0272/1454] Json file is created. pending testing for validation --- relecov_tools/read_metadata.py | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index fb796616..fd833874 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -119,12 +119,15 @@ def include_fixed_data(self): return fixed_data def include_processed_data(self, metadata): - """Include the data that requires to be processed to set the value - """ + """Include the data that requires to be processed to set the value""" new_data = {} - p_data = {"host_common_name": {"Human": ["host_scientific_name", "Homo Sapiens"]}, - "collecting_lab_sample_id": ["isolate", metadata["collecting_lab_sample_id"]] - } + p_data = { + "host_common_name": {"Human": ["host_scientific_name", "Homo Sapiens"]}, + "collecting_lab_sample_id": [ + "isolate", + metadata["collecting_lab_sample_id"], + ], + } for key, values in p_data.items(): v_data = metadata[key] @@ -257,7 +260,8 @@ def read_metadata_file(self): if row[2] is None: continue for idx in range(1, len(heading)): - if "date" in heading[idx]: + if "date" in heading[idx].lower(): + # import pdb; pdb.set_trace() try: sample_data_row[self.label_prop_dict[heading[idx]]] = row[ idx @@ -286,13 +290,11 @@ def write_json_fo_file(self, data, file_name): """Write metadata to json file""" os.makedirs(self.output_folder, exist_ok=True) json_file = os.path.join(self.output_folder, file_name) - import pdb; pdb.set_trace() + import pdb + + pdb.set_trace() with open(json_file, "w", encoding="utf-8") as fh: - fh.write( - json.dumps( - data, indent=4, sort_keys=True, ensure_ascii=False - ) - ) + fh.write(json.dumps(data, indent=4, sort_keys=True, ensure_ascii=False)) return True def create_metadata_json(self): From 003542b47cb8ca61f9b107958c993608f81803c1 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 1 Apr 2022 11:35:21 +0200 Subject: [PATCH 0273/1454] Fixed bug when including geo location data --- relecov_tools/read_metadata.py | 55 ++-------------------------------- 1 file changed, 3 insertions(+), 52 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index fd833874..437c03fc 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -93,13 +93,8 @@ def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): break for city in geo_loc_json: if city["geo_loc_city"] == data["geo_loc_city"]: - data[city["geo_loc_city"]] = {} - data[city["geo_loc_city"]]["geo_loc_latitude"] = city[ - "geo_loc_latitude" - ] - data[city["geo_loc_city"]]["geo_loc_longitude"] = city[ - "geo_loc_longitude" - ] + data["geo_loc_latitude"] = city["geo_loc_latitude"] + data["geo_loc_longitude"] = city["geo_loc_longitude"] break return data @@ -171,6 +166,7 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): lab_data[row_sample["collecting_institution"]] = l_data else: row_sample.update(lab_data[row_sample["collecting_institution"]]) + """ Add Fixed information """ row_sample.update(self.include_fixed_data()) @@ -188,25 +184,6 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): additional_metadata.append(row_sample) return additional_metadata - # def compare_sample_in_metadata(self, completed_metadata): - """Compare the samples defined in metadata file and the ones in the - sample file - """ - """ - not_found_samples = [] - if not os.path.exists(self.sample_list_file): - return False - # get the smaples defined in json - with open(self.sample_list_file, "r") as fh: - samples = fh.read().split("\n") - for line_metadata in completed_metadata: - if line_metadata["collecting_lab_sample_id"] not in samples: - not_found_samples.append(line_metadata["collecting_lab_sample_id"]) - if len(not_found_samples) > 0: - return not_found_samples - return True - """ - def request_information(external_url, request): """Get information from external database server using Rest API @@ -219,28 +196,6 @@ def store_information(external_url, request, data): """Update information""" pass - # def get_geo_location_data(self, state, country): - """Get the geo_loc_latitude and geo_loc_longitude from state""" - """ - geolocator = Nominatim(user_agent="geoapiRelecov") - loc = geolocator.geocode(state + "," + country) - return [str(loc.latitude), str(loc.longitude)] - """ - - # def update_heading_to_json(self, heading, meta_map_json): - """Change the heading values from the metadata file for the ones defined - in the json schema - """ - """ - mapped_heading = [] - for cell in heading: - if cell in meta_map_json: - mapped_heading.append(meta_map_json[cell]) - else: - mapped_heading.append(cell) - return mapped_heading - """ - def read_metadata_file(self): """Read the input metadata file, changing the metadata heading with their property name values defined in schema. @@ -261,7 +216,6 @@ def read_metadata_file(self): continue for idx in range(1, len(heading)): if "date" in heading[idx].lower(): - # import pdb; pdb.set_trace() try: sample_data_row[self.label_prop_dict[heading[idx]]] = row[ idx @@ -290,9 +244,6 @@ def write_json_fo_file(self, data, file_name): """Write metadata to json file""" os.makedirs(self.output_folder, exist_ok=True) json_file = os.path.join(self.output_folder, file_name) - import pdb - - pdb.set_trace() with open(json_file, "w", encoding="utf-8") as fh: fh.write(json.dumps(data, indent=4, sort_keys=True, ensure_ascii=False)) return True From 33ce37ff42d5c3a5a55e1cc64228bbda4d87cd9e Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 1 Apr 2022 13:14:38 +0200 Subject: [PATCH 0274/1454] Preform the json validation on webpage --- relecov_tools/read_metadata.py | 42 +++++++++++++++++++++++++++------- 1 file changed, 34 insertions(+), 8 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 437c03fc..cc82b32a 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -104,7 +104,7 @@ def include_fixed_data(self): "host_disease": "COVID-19", "type": "betacoronavirus", "tax_id": "2697049", - "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "organism": "Severe acute respiratory syndrome coronavirus 2", "study_alias": "", "experiment_alias": "", "run_alias": "", @@ -123,7 +123,16 @@ def include_processed_data(self, metadata): metadata["collecting_lab_sample_id"], ], } - + seq_inst_plat = { + "Illumina": [ + "Illumina iSeq 100", + "Illumina MiSeq", + "Illumina NextSeq550", + "Illumina NovaSeq 6000", + ], + "MinION": ["Oxford Nanopore"], + "Ion Torrent": ["Ion Torrent S5", "Ion Torrent PGM"], + } for key, values in p_data.items(): v_data = metadata[key] if isinstance(values, dict): @@ -131,6 +140,11 @@ def include_processed_data(self, metadata): new_data[values[v_data][0]] = values[v_data][1] else: new_data[values[0]] = values[1] + """New fields that required processing from other field """ + for key, values in seq_inst_plat.items(): + if metadata["sequencing_instrument_model"] in values: + new_data["sequencing_instrument_platform"] = key + break return new_data def add_additional_data(self, metadata, lab_json_file, geo_loc_file): @@ -202,6 +216,7 @@ def read_metadata_file(self): Convert the date colunms value to the dd/mm/yyyy format. Return list of dict with data, and errors """ + exc_format_num = ["Host Age", "Sample ID given for sequencing"] wb_file = openpyxl.load_workbook(self.metadata_file, data_only=True) ws_metadata_lab = wb_file["METADATA_LAB"] # removing the None columns in excel heading row @@ -230,12 +245,23 @@ def read_metadata_file(self): row[2] + " column " + heading[idx], ) else: - try: - sample_data_row[self.label_prop_dict[heading[idx]]] = ( - row[idx] if row[idx] else "" - ) - except KeyError as e: - print(e) + + if isinstance(row[idx], float): + if heading[idx] in exc_format_num: + val = int(row[idx]) + else: + val = str(int(row[idx])) + try: + sample_data_row[self.label_prop_dict[heading[idx]]] = val + except TypeError as e: + stderr.print("[red] Error when reading " + row[2] + e) + else: + try: + sample_data_row[self.label_prop_dict[heading[idx]]] = ( + row[idx] if row[idx] else "" + ) + except KeyError as e: + stderr.print("[red] Error when reading " + row[2] + e) metadata_values.append(sample_data_row) return metadata_values, errors From 2b4618a3f161f57bdc784d88a7c6cd56705d85e6 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 1 Apr 2022 13:48:09 +0200 Subject: [PATCH 0275/1454] Pending to update ENA settings --- .../processed_METADATA_LAB_TEST.json | 672 ++++++++++++++++++ 1 file changed, 672 insertions(+) create mode 100644 relecov_tools/example_data/processed_METADATA_LAB_TEST.json diff --git a/relecov_tools/example_data/processed_METADATA_LAB_TEST.json b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json new file mode 100644 index 00000000..26ab8790 --- /dev/null +++ b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json @@ -0,0 +1,672 @@ +[ + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_part": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123456", + "collecting_institution": "Hospital Universitario Miguel Servet", + "collecting_lab_sample_id": "1197860", + "collection_device": "Swab", + "diagnostic_pcr_Ct_value_1": "45", + "diagnostic_pcr_Ct_value_2": "34", + "enrichment_protocol": "Amplicon", + "environmental_material": "Other", + "environmental_site": "Earth surface", + "experiment_alias": "", + "experiment_title": "", + "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", + "gene_name_1": "ORF 1ab", + "gene_name_2": "S", + "geo_loc_city": "Zaragoza", + "geo_loc_country": "Spain", + "geo_loc_latitude": "41.6483", + "geo_loc_longitude": "-0.8830", + "geo_loc_state": "Aragon", + "gisaid_id": "EPI_ISL_11222687", + "host_age": 55, + "host_common_name": "Human", + "host_disease": "COVID-19", + "host_gender": "Mujer", + "host_scientific_name": "Homo Sapiens", + "if_amplicon_protocol_if_other_especify": "", + "if_enrichment_protocol_is_other_specify": "", + "isolate": "1197860", + "isolate_sample_id": "220407", + "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_layout": "Single End", + "library_preparation_kit": "Truseq Nano", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "microbiology_lab_sample_id": "220407", + "number_of_samples_in_run": "96", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "2022CEU01394", + "purpose_of_sampling": "Surveillance", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2021/04/13", + "sample_received_date": "2021/05/13", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_001.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_001.fastq.gz", + "sequencing_date": "2022/02/22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 214824, + "study_alias": "", + "study_title": "", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202201751", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2022" + }, + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_part": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123457", + "collecting_institution": "Hospital Universitario Miguel Servet", + "collecting_lab_sample_id": "1197824", + "collection_device": "Swab", + "diagnostic_pcr_Ct_value_1": "12", + "diagnostic_pcr_Ct_value_2": "16", + "enrichment_protocol": "Amplicon", + "environmental_material": "Other", + "environmental_site": "Earth surface", + "experiment_alias": "", + "experiment_title": "", + "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", + "gene_name_1": "ORF 1ab", + "gene_name_2": "S", + "geo_loc_city": "Zaragoza", + "geo_loc_country": "Spain", + "geo_loc_latitude": "41.6483", + "geo_loc_longitude": "-0.8830", + "geo_loc_state": "Aragon", + "gisaid_id": "EPI_ISL_11222688", + "host_age": 59, + "host_common_name": "Human", + "host_disease": "COVID-19", + "host_gender": "Hombre", + "host_scientific_name": "Homo Sapiens", + "if_amplicon_protocol_if_other_especify": "", + "if_enrichment_protocol_is_other_specify": "", + "isolate": "1197824", + "isolate_sample_id": "220433", + "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_layout": "Single End", + "library_preparation_kit": "Truseq Nano", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "microbiology_lab_sample_id": "220433", + "number_of_samples_in_run": "96", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "2022CEU01469", + "purpose_of_sampling": "Surveillance", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2021/03/31", + "sample_received_date": "2021/05/13", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_002.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_002.fastq.gz", + "sequencing_date": "2022/02/22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 214832, + "study_alias": "", + "study_title": "", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202201678", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2023" + }, + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_part": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123458", + "collecting_institution": "Hospital Universitario Miguel Servet", + "collecting_lab_sample_id": "1197767", + "collection_device": "Swab", + "diagnostic_pcr_Ct_value_1": "45", + "diagnostic_pcr_Ct_value_2": "41", + "enrichment_protocol": "Amplicon", + "environmental_material": "Other", + "environmental_site": "Earth surface", + "experiment_alias": "", + "experiment_title": "", + "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", + "gene_name_1": "ORF 1ab", + "gene_name_2": "S", + "geo_loc_city": "Zaragoza", + "geo_loc_country": "Spain", + "geo_loc_latitude": "41.6483", + "geo_loc_longitude": "-0.8830", + "geo_loc_state": "Aragon", + "gisaid_id": "EPI_ISL_11222689", + "host_age": 8, + "host_common_name": "Human", + "host_disease": "COVID-19", + "host_gender": "Mujer", + "host_scientific_name": "Homo Sapiens", + "if_amplicon_protocol_if_other_especify": "", + "if_enrichment_protocol_is_other_specify": "", + "isolate": "1197767", + "isolate_sample_id": "220435", + "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_layout": "Single End", + "library_preparation_kit": "Truseq Nano", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "microbiology_lab_sample_id": "220435", + "number_of_samples_in_run": "96", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "2022CEU03926", + "purpose_of_sampling": "Surveillance", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2022/01/13", + "sample_received_date": "2022/01/18", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_003.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_003.fastq.gz", + "sequencing_date": "2022/02/22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 220338, + "study_alias": "", + "study_title": "", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202201853", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2024" + }, + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_part": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123459", + "collecting_institution": "Hospital Universitario Miguel Servet", + "collecting_lab_sample_id": "8328199", + "collection_device": "Swab", + "diagnostic_pcr_Ct_value_1": "23", + "diagnostic_pcr_Ct_value_2": "23", + "enrichment_protocol": 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"Single End", + "library_preparation_kit": "Truseq Nano", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "microbiology_lab_sample_id": "220625", + "number_of_samples_in_run": "96", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "2022CEU03901", + "purpose_of_sampling": "Surveillance", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2022/01/12", + "sample_received_date": "2022/01/20", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_006.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_006.fastq.gz", + "sequencing_date": "2022/02/22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 220625, + "study_alias": "", + "study_title": "", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202203146", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2027" + }, + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_part": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123462", + "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", + "collecting_lab_sample_id": "1197737", + "collection_device": "Swab", + "diagnostic_pcr_Ct_value_1": "11", + "diagnostic_pcr_Ct_value_2": "11", + "enrichment_protocol": "Amplicon", + "environmental_material": "Other", + "environmental_site": "Earth surface", + "experiment_alias": "", + "experiment_title": "", + "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", + "gene_name_1": "ORF 1ab", + "gene_name_2": "S", + "geo_loc_city": "Zaragoza", + "geo_loc_country": "Spain", + "geo_loc_latitude": "41.6483", + "geo_loc_longitude": "-0.8830", + "geo_loc_state": "Aragon", + "gisaid_id": "EPI_ISL_11222693", + "host_age": 42, + "host_common_name": "Human", + "host_disease": "COVID-19", + "host_gender": "Mujer", + "host_scientific_name": "Homo Sapiens", + "if_amplicon_protocol_if_other_especify": "", + "if_enrichment_protocol_is_other_specify": "", + "isolate": "1197737", + "isolate_sample_id": "220629", + "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_layout": "Single End", + "library_preparation_kit": "Truseq Nano", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "microbiology_lab_sample_id": "220629", + "number_of_samples_in_run": "96", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "2022CEU03862", + "purpose_of_sampling": "Surveillance", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2022/01/02", + "sample_received_date": "2022/01/20", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_007.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_007.fastq.gz", + "sequencing_date": "2022/02/22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 220629, + "study_alias": "", + "study_title": "", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202203153", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2028" + }, + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_part": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123463", + "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", + "collecting_lab_sample_id": "1197663", + "collection_device": "Swab", + "diagnostic_pcr_Ct_value_1": "34", + "diagnostic_pcr_Ct_value_2": "36", + "enrichment_protocol": "Amplicon", + "environmental_material": "Other", + "environmental_site": "Earth surface", + "experiment_alias": "", + "experiment_title": "", + "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", + "gene_name_1": "ORF 1ab", + "gene_name_2": "S", + "geo_loc_city": "Zaragoza", + "geo_loc_country": "Spain", + "geo_loc_latitude": "41.6483", + "geo_loc_longitude": "-0.8830", + "geo_loc_state": "Aragon", + "gisaid_id": "EPI_ISL_11222694", + "host_age": 40, + "host_common_name": "Human", + "host_disease": "COVID-19", + "host_gender": "Hombre", + "host_scientific_name": "Homo Sapiens", + "if_amplicon_protocol_if_other_especify": "", + "if_enrichment_protocol_is_other_specify": "", + "isolate": "1197663", + "isolate_sample_id": "220634", + "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_layout": "Single End", + "library_preparation_kit": "Truseq Nano", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "microbiology_lab_sample_id": "220634", + "number_of_samples_in_run": "96", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "2022CEU03614", + "purpose_of_sampling": "Surveillance", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2022/01/23", + "sample_received_date": "2022/01/25", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_008.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_008.fastq.gz", + "sequencing_date": "2022/02/22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 220634, + "study_alias": "", + "study_title": "", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202203163", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2029" + }, + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_part": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123464", + "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", + "collecting_lab_sample_id": "1197689", + "collection_device": "Swab", + "diagnostic_pcr_Ct_value_1": "23", + "diagnostic_pcr_Ct_value_2": "20", + "enrichment_protocol": "Amplicon", + "environmental_material": "Other", + "environmental_site": "Earth surface", + "experiment_alias": "", + "experiment_title": "", + "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", + "gene_name_1": "ORF 1ab", + "gene_name_2": "S", + "geo_loc_city": "Zaragoza", + "geo_loc_country": "Spain", + "geo_loc_latitude": "41.6483", + "geo_loc_longitude": "-0.8830", + "geo_loc_state": "Aragon", + "gisaid_id": "EPI_ISL_11222695", + "host_age": 53, + "host_common_name": "Human", + "host_disease": "COVID-19", + "host_gender": "Hombre", + "host_scientific_name": "Homo Sapiens", + "if_amplicon_protocol_if_other_especify": "", + "if_enrichment_protocol_is_other_specify": "", + "isolate": "1197689", + "isolate_sample_id": "220636", + "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_layout": "Single End", + "library_preparation_kit": "Truseq Nano", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "microbiology_lab_sample_id": "220636", + "number_of_samples_in_run": "96", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "2022CEU04252", + "purpose_of_sampling": "Surveillance", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2022/01/18", + "sample_received_date": "2022/01/26", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_009.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_009.fastq.gz", + "sequencing_date": "2022/02/22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 220636, + "study_alias": "", + "study_title": "", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202203170", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2030" + }, + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_part": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123465", + "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", + "collecting_lab_sample_id": "1197685", + "collection_device": "Swab", + "diagnostic_pcr_Ct_value_1": "32", + "diagnostic_pcr_Ct_value_2": "32", + "enrichment_protocol": "Amplicon", + "environmental_material": "Other", + "environmental_site": "Earth surface", + "experiment_alias": "", + "experiment_title": "", + "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", + "gene_name_1": "ORF 1ab", + "gene_name_2": "S", + "geo_loc_city": "Zaragoza", + "geo_loc_country": "Spain", + "geo_loc_latitude": "41.6483", + "geo_loc_longitude": "-0.8830", + "geo_loc_state": "Aragon", + "gisaid_id": "EPI_ISL_11222696", + "host_age": 96, + "host_common_name": "Human", + "host_disease": "COVID-19", + "host_gender": "Male", + "host_scientific_name": "Homo Sapiens", + "if_amplicon_protocol_if_other_especify": "", + "if_enrichment_protocol_is_other_specify": "", + "isolate": "1197685", + "isolate_sample_id": "220639", + "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_layout": "Single End", + "library_preparation_kit": "Truseq Nano", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "microbiology_lab_sample_id": "220639", + "number_of_samples_in_run": "96", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "2022CEU04223", + "purpose_of_sampling": "Surveillance", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2022/01/19", + "sample_received_date": "2022/01/26", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_0010.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_0010.fastq.gz", + "sequencing_date": "2022/02/22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 220639, + "study_alias": "", + "study_title": "", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202203166", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2031" + } +] From 0c075bb9335e2346f26bbdb12720e3fc3a928534 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 1 Apr 2022 15:42:21 +0200 Subject: [PATCH 0276/1454] defining ENA fixed values in configuration json file --- relecov_tools/conf/configuration.json | 10 +-- .../processed_METADATA_LAB_TEST.json | 62 +++++++++---------- relecov_tools/read_metadata.py | 7 +-- 3 files changed, 39 insertions(+), 40 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 02e45c1d..4cd3fa9b 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -17,9 +17,11 @@ ], "laboratory_data": "laboratory_address.json", "geo_location_data" : "geo_loc_cities.json", - "study": { - "alias": "RELECOV", - "title": "Example project for ENA submission RELECOV", - "study_type": "This study was created as part of an ENA submissions example RELECOV" + "ENA_configuration": { + "study_alias": "RELECOV", + "experiment_alias": "", + "run_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance" } } diff --git a/relecov_tools/example_data/processed_METADATA_LAB_TEST.json b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json index 26ab8790..fda2fd6c 100644 --- a/relecov_tools/example_data/processed_METADATA_LAB_TEST.json +++ b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json @@ -16,7 +16,7 @@ "environmental_material": "Other", "environmental_site": "Earth surface", "experiment_alias": "", - "experiment_title": "", + "experiment_title": "Example project for ENA submission RELECOV", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -58,8 +58,8 @@ "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 214824, - "study_alias": "", - "study_title": "", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202201751", "tax_id": "2697049", @@ -83,7 +83,7 @@ "environmental_material": "Other", "environmental_site": "Earth surface", "experiment_alias": "", - "experiment_title": "", + "experiment_title": "Example project for ENA submission RELECOV", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -125,8 +125,8 @@ "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 214832, - "study_alias": "", - "study_title": "", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202201678", "tax_id": "2697049", @@ -150,7 +150,7 @@ "environmental_material": "Other", "environmental_site": "Earth surface", "experiment_alias": "", - "experiment_title": "", + "experiment_title": "Example project for ENA submission RELECOV", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -192,8 +192,8 @@ "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 220338, - "study_alias": "", - "study_title": "", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202201853", "tax_id": "2697049", @@ -217,7 +217,7 @@ "environmental_material": "Other", "environmental_site": "Earth surface", "experiment_alias": "", - "experiment_title": "", + "experiment_title": "Example project for ENA submission RELECOV", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -259,8 +259,8 @@ "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 220407, - "study_alias": "", - "study_title": "", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202202165", "tax_id": "2697049", @@ -284,7 +284,7 @@ "environmental_material": "Other", "environmental_site": "Earth surface", "experiment_alias": "", - "experiment_title": "", + "experiment_title": "Example project for ENA submission RELECOV", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -326,8 +326,8 @@ "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 220624, - "study_alias": "", - "study_title": "", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202203144", "tax_id": "2697049", @@ -351,7 +351,7 @@ "environmental_material": "Other", "environmental_site": "Earth surface", "experiment_alias": "", - "experiment_title": "", + "experiment_title": "Example project for ENA submission RELECOV", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -393,8 +393,8 @@ "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 220625, - "study_alias": "", - "study_title": "", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202203146", "tax_id": "2697049", @@ -418,7 +418,7 @@ "environmental_material": "Other", "environmental_site": "Earth surface", "experiment_alias": "", - "experiment_title": "", + "experiment_title": "Example project for ENA submission RELECOV", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -460,8 +460,8 @@ "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 220629, - "study_alias": "", - "study_title": "", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202203153", "tax_id": "2697049", @@ -485,7 +485,7 @@ "environmental_material": "Other", "environmental_site": "Earth surface", "experiment_alias": "", - "experiment_title": "", + "experiment_title": "Example project for ENA submission RELECOV", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -527,8 +527,8 @@ "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 220634, - "study_alias": "", - "study_title": "", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202203163", "tax_id": "2697049", @@ -552,7 +552,7 @@ "environmental_material": "Other", "environmental_site": "Earth surface", "experiment_alias": "", - "experiment_title": "", + "experiment_title": "Example project for ENA submission RELECOV", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -594,8 +594,8 @@ "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 220636, - "study_alias": "", - "study_title": "", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202203170", "tax_id": "2697049", @@ -619,7 +619,7 @@ "environmental_material": "Other", "environmental_site": "Earth surface", "experiment_alias": "", - "experiment_title": "", + "experiment_title": "Example project for ENA submission RELECOV", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -661,12 +661,12 @@ "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 220639, - "study_alias": "", - "study_title": "", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202203166", "tax_id": "2697049", "type": "betacoronavirus", "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2031" } -] +] \ No newline at end of file diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index cc82b32a..914c3cee 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -58,6 +58,7 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None relecov_sch_path = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", relecov_schema ) + self.configuration = config_json with open(relecov_sch_path, "r") as fh: self.relecov_sch_json = json.load(fh) self.label_prop_dict = {} @@ -105,12 +106,8 @@ def include_fixed_data(self): "type": "betacoronavirus", "tax_id": "2697049", "organism": "Severe acute respiratory syndrome coronavirus 2", - "study_alias": "", - "experiment_alias": "", - "run_alias": "", - "study_title": "", - "experiment_title": "", } + fixed_data.update(self.configuration.get_configuration("ENA_configuration")) return fixed_data def include_processed_data(self, metadata): From f1e194ae010f90ee97103737e0c5638e5035758e Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 1 Apr 2022 15:49:33 +0200 Subject: [PATCH 0277/1454] fixin litin issues --- relecov_tools/ena_upload.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 2ce63fff..c42da157 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,11 +1,10 @@ -from bdb import set_trace import os import logging import rich.console import json -import pandas as pd + +# import pandas as pd import sys -from ena_upload import ena_upload import relecov_tools.utils from relecov_tools.config_json import ConfigJson @@ -84,7 +83,7 @@ def convert_input_json_to_ena(self): def create_structure_to_ena(self): """Convert json to dataframe required by ena-upload-cli package""" - schema_dataframe = {} + # schema_dataframe = {} config_json = ConfigJson() @@ -96,7 +95,7 @@ def create_structure_to_ena(self): fh = open(map_file) map_structure_json = json.load(fh) fh.close() - lista = ["study", "runs", "samples", "experiments"] + # lista = ["study", "runs", "samples", "experiments"] for i in map_structure_json["properties"].keys(): import pdb From 8d7271e72fca2549831ea560c9388041f7a19fb3 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 1 Apr 2022 15:58:26 +0200 Subject: [PATCH 0278/1454] Changed python version to 3.9.12 in worlflows --- .github/workflows/python_lint.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml index 791ba18f..12d3beb8 100644 --- a/.github/workflows/python_lint.yml +++ b/.github/workflows/python_lint.yml @@ -15,7 +15,7 @@ jobs: - name: Setup Python uses: actions/setup-python@v1 with: - python-version: 3.9.10 + python-version: 3.9.12 architecture: x64 - name: Checkout PyTorch uses: actions/checkout@master From 35a13c72ba3728b77d20783cd894ae3110140000 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 4 Apr 2022 14:39:50 +0200 Subject: [PATCH 0279/1454] Validate when all samples in json are ok --- relecov_tools/json_validation.py | 5 +++-- relecov_tools/utils.py | 8 ++++++++ 2 files changed, 11 insertions(+), 2 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 509a3469..a1b87909 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -4,10 +4,10 @@ import jsonschema from jsonschema import validate from jsonschema import Draft202012Validator - import json import sys import os + import relecov_tools.utils from relecov_tools.config_json import ConfigJson @@ -28,7 +28,7 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): ) if json_schema_file is None: config_json = ConfigJson() - schema_name = config_json.get_topic_data("json_schemas", "phage_plus_schema") + schema_name = config_json.get_topic_data("json_schemas", "relecov_schema") json_schema_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", schema_name ) @@ -43,6 +43,7 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): if not os.path.isfile(json_data_file): stderr.print("[red] Json file does not exists") sys.exit(1) + json_data = relecov_tools.utils.read_json_file(json_data_file) with open(json_data_file, "r") as fh: json_data = json.load(fh) validated_json_data = [] diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 662d6787..e6fd447b 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -8,6 +8,7 @@ import logging from rich.console import Console import questionary +import json log = logging.getLogger(__name__) @@ -24,6 +25,13 @@ def file_exists(file_to_check): return False +def read_json_file(j_file): + """Read json file.""" + with open(j_file, "r") as fh: + data = json.load(fh) + return data + + def get_md5_from_local_folder(local_folder): """Fetch the md5 values for each file in the file list""" md5_results = {} From 0875597bd56be0a3568a75f91dd1329f83b3c4e7 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 4 Apr 2022 18:04:18 +0200 Subject: [PATCH 0280/1454] working on invalid metadata file --- relecov_tools/__main__.py | 15 +- .../invalid_METADATA_LAB_TEST.json | 136 ++++++++++++++++++ relecov_tools/json_validation.py | 35 +++++ 3 files changed, 185 insertions(+), 1 deletion(-) create mode 100644 relecov_tools/example_data/invalid_METADATA_LAB_TEST.json diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 6103ec51..fdd6cd8a 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -200,9 +200,17 @@ def read_metadata(metadata_file, sample_list_file, metadata_out): @relecov_tools_cli.command(help_priority=4) @click.option("-j", "--json_file", help="Json file to validate") @click.option("-s", "--json_schema", help="Json schema") +@click.option( + "-m", + "--metadata", + type=click.Path(), + help="Origin file containing metadata", +) @click.option("-o", "--out_folder", help="Path to save validate json file") -def validate(json_file, json_schema, out_folder): +def validate(json_file, json_schema, metadata, out_folder): """Validate json file against schema.""" + relecov_tools.json_validation.create_invalid_metadata(metadata, json_file, out_folder) + import pdb; pdb.set_trace() ( validated_json_data, invalid_json, @@ -210,6 +218,11 @@ def validate(json_file, json_schema, out_folder): ) = relecov_tools.json_validation.validate_json(json_file, json_schema, out_folder) if len(invalid_json) > 0: log.error("Some of the samples in json metadata were not validated") + if not os.isfile(metadata): + log.error("Metadata file %s does not exists", metadata) + exit(1) + relecov_tools.json_validation.create_invalid_metadata(metadata, invalid_json, out_folder) + else: log.info("All data in json were validated") diff --git a/relecov_tools/example_data/invalid_METADATA_LAB_TEST.json b/relecov_tools/example_data/invalid_METADATA_LAB_TEST.json new file mode 100644 index 00000000..9e1e6dd3 --- /dev/null +++ b/relecov_tools/example_data/invalid_METADATA_LAB_TEST.json @@ -0,0 +1,136 @@ +[ + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_part": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123464", + "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", + "collecting_lab_sample_id": "1197689", + "collection_device": "Swab", + "diagnostic_pcr_Ct_value_1": "23", + "diagnostic_pcr_Ct_value_2": "20", + "enrichment_protocol": "Amplicon", + "environmental_material": "Other", + "environmental_site": "Earth surface", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", + "gene_name_1": "ORF 1ab", + "gene_name_2": "S", + "geo_loc_city": "Zaragoza", + "geo_loc_country": "Spain", + "geo_loc_latitude": "41.6483", + "geo_loc_longitude": "-0.8830", + "geo_loc_state": "Aragon", + "gisaid_id": "EPI_ISL_11222695", + "host_age": 53, + "host_common_name": "Human", + "host_disease": "COVID-19", + "host_gender": "Hombre", + "host_scientific_name": "Homo Sapiens", + "if_amplicon_protocol_if_other_especify": "", + "if_enrichment_protocol_is_other_specify": "", + "isolate": "1197689", + "isolate_sample_id": "220636", + "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_layout": "Single End", + "library_preparation_kit": "Truseq Nano", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "microbiology_lab_sample_id": "220636", + "number_of_samples_in_run": "96", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "2022CEU04252", + "purpose_of_sampling": "Surveillance", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2022/01/18", + "sample_received_date": "2022/01/26", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_009.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_009.fastq.gz", + "sequencing_date": "2022/02/22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 220636, + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202203170", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2030" + }, + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_part": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123465", + "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", + "collecting_lab_sample_id": "1197685", + "collection_device": "Swab", + "diagnostic_pcr_Ct_value_1": "32", + "diagnostic_pcr_Ct_value_2": "32", + "enrichment_protocol": "Amplicon", + "environmental_material": "Other", + "environmental_site": "Earth surface", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", + "gene_name_1": "ORF 1ab", + "gene_name_2": "S", + "geo_loc_city": "Zaragoza", + "geo_loc_country": "Spain", + "geo_loc_latitude": "41.6483", + "geo_loc_longitude": "-0.8830", + "geo_loc_state": "Aragon", + "gisaid_id": "EPI_ISL_11222696", + "host_age": 96, + "host_common_name": "Human", + "host_disease": "COVID-19", + "host_gender": "Male", + "host_scientific_name": "Homo Sapiens", + "if_amplicon_protocol_if_other_especify": "", + "if_enrichment_protocol_is_other_specify": "", + "isolate": "1197685", + "isolate_sample_id": "220639", + "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_layout": "Single End", + "library_preparation_kit": "Truseq Nano", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "microbiology_lab_sample_id": "220639", + "number_of_samples_in_run": "96", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "2022CEU04223", + "purpose_of_sampling": "Surveillance", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2022/01/19", + "sample_received_date": "2022/01/26", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_0010.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_0010.fastq.gz", + "sequencing_date": "2022/02/22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 220639, + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202203166", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2031" + } +] diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index a1b87909..bcce30c1 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -7,6 +7,7 @@ import json import sys import os +import openpyxl import relecov_tools.utils from relecov_tools.config_json import ConfigJson @@ -57,3 +58,37 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): log.error("Invalid sample data %s", e) invalid_json.append(item_row) return validated_json_data, invalid_json, errors + + +def create_invalid_metadata(metadata_file, invalid_json, out_folder): + """Create a new sub excel file having only the samples that were invalid + """ + invalid_metadata = "" + sample_id_head = "Sequencing sample id" + wb_inv = openpyxl.Workbook() + sample_list = [] + + json_data = relecov_tools.utils.read_json_file(invalid_json) + for row in json_data: + sample_list.append(row["collecting_lab_sample_id"]) + wb = openpyxl.load_workbook(metadata_file) + import pdb; pdb.set_trace() + for sheet in wb.sheetnames: + ws_sheet = wb[sheet] + ws_inv = wb_inv.create_sheet(sheet) + head_list = [cell.value for cell in ws_sheet[1]] + import pdb; pdb.set_trace() + try: + s_index = head_list.index(sample_id_head) + except: + + for row in ws_sheet.iter_rows(): + if row[s_index].value in sample_list: + ws_inv.append(row) + import pdb; pdb.set_trace() + target = wb_inv.copy_worksheet(ws_inv) + target.title(sheet) + import pdb; pdb.set_trace() + + + wb_inv.save(filename=invalid_metadata) From 3d0df513ffc8b53fa0f7cc0db7a73c1f985200b7 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 5 Apr 2022 16:47:43 +0200 Subject: [PATCH 0281/1454] changes in schema relecov and created bioinfo_schema.json --- relecov_tools/ena_upload.py | 6 +- relecov_tools/example_data/ena_upload.json | 178 ---- relecov_tools/example_data/to_ena.json | 39 + relecov_tools/schema/bioinfo_schema.json | 512 +++++++++++ relecov_tools/schema/relecov_schema.json | 8 +- relecov_tools/schema/sample_relecov.xml | 1 + relecov_tools/test/pruebas.ipynb | 849 ++++++++++++++++++ relecov_tools/test/try_01.ipynb | 4 +- .../xml_files/samples/submission_add.xml | 10 + .../xml_files/samples/submission_modify.xml | 10 + relecov_tools/xml_files/study/project.xml | 9 + relecov_tools/xml_files/study/receipt.xml | 12 + relecov_tools/xml_files/study/submission.xml | 10 + 13 files changed, 1461 insertions(+), 187 deletions(-) delete mode 100644 relecov_tools/example_data/ena_upload.json create mode 100644 relecov_tools/example_data/to_ena.json create mode 100644 relecov_tools/schema/bioinfo_schema.json create mode 100644 relecov_tools/schema/sample_relecov.xml create mode 100644 relecov_tools/test/pruebas.ipynb create mode 100644 relecov_tools/xml_files/samples/submission_add.xml create mode 100644 relecov_tools/xml_files/samples/submission_modify.xml create mode 100644 relecov_tools/xml_files/study/project.xml create mode 100644 relecov_tools/xml_files/study/receipt.xml create mode 100644 relecov_tools/xml_files/study/submission.xml diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index c42da157..fac92f33 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -96,11 +96,11 @@ def create_structure_to_ena(self): map_structure_json = json.load(fh) fh.close() # lista = ["study", "runs", "samples", "experiments"] + import pdb - for i in map_structure_json["properties"].keys(): - import pdb + pdb.set_trace() - pdb.set_trace() + for i in map_structure_json["properties"].keys(): if "table" in i.keys() and "study" in i["table"]: diff --git a/relecov_tools/example_data/ena_upload.json b/relecov_tools/example_data/ena_upload.json deleted file mode 100644 index 92aaefb9..00000000 --- a/relecov_tools/example_data/ena_upload.json +++ /dev/null @@ -1,178 +0,0 @@ -{ - "study": { - "alias": [ - "study_alias_4", - "study_alias_5" - ], - "title": [ - "study_title_1", - "study_title_2" - ], - "study_type": [ - "Transcriptome Analysis", - "RNASeq" - ], - "study_abstract": [ - "study_abstract_1", - "study_abstract_2" - ], - "pubmed_id": ["None", - "pubmed_id_2" - ] - }, - "samples": { - "alias": [ - "sample_alias_4", - "sample_alias_5" - ], - "title": [ - "sample_title_2", - "sample_title_3" - ], - "taxon_id": [ - "2697049", - "2697049" - ], - "sample_description": [ - "sample_description_1", - "sample_description_2" - ], - "collection date": [ - "2020-10-11", - "2008-01-24" - ], - "geographic location (country and/or sea)": [ - "Argentina", - "Belgium" - ], - "host common name": [ - "host_common_name_1", - "host_common_name_2" - ], - "host subject id": [ - "host_subject_id_1", - "host_subject_id_2" - ], - "host health state": [ - "diseased", - "restricted access" - ], - "host sex": [ - "male", - "female" - ], - "host scientific name": [ - "host_scientific_name_1", - "host_scientific_name_2" - ], - "collector name": [ - "collector_name_1", - "collector_name_2" - ], - "collecting institution": [ - "collecting_institution_1", - "collecting_institution_2" - ], - "isolate": [ - "isolate_1", - "isolate_2" - ] - }, - "runs": { - "alias": [ - "run_alias_1a", - "run_alias_1a", - "run_alias_3c" - ], - "experiment_alias": [ - "experiment_alias_7a", - "experiment_alias_7a", - "experiment_alias_9c" - ], - "file_name": [ - "ENA_TEST2.R1.fastq.gz", - "ENA_TEST2.R2.fastq.gz", - "ENA_TEST1.R1.fastq.gz" - ], - "file_type": [ - "fastq", - "fastq", - "fastq" - ], - "file_checksum": [ - "3e69af1f875fab020aed82f5edbc1f03", - "3e69af1f875fab020aed82f5edbc1f03", - "3e69af1f875fab020aed82f5edbc1f03" - ] - }, - "experiments": { - "alias": [ - "experiment_alias_7a", - "experiment_alias_8b", - "experiment_alias_9c" - ], - "title": [ - "experiment_title_1", - "experiment_title_2", - "experiment_title_3" - ], - "study_alias": [ - "study_alias_4", - "study_alias_5", - "study_alias_5" - ], - "sample_alias": [ - "study_alias_4", - "study_alias_5", - "study_alias_5" - ], - "design_description": [ - "design_description_1", - "design_description_2", - "design_description_3" - ], - "library_name": [ - "library_name_1", - "library_name_2", - "library_name_3" - ], - "library_strategy": [ - "WGA", - "RNA-Seq", - "RNA-Seq" - ], - "library_source": [ - "GENOMIC", - "TRANSCRIPTOMIC", - "TRANSCRIPTOMIC" - ], - "library_selection": [ - "RANDOM", - "repeat fractionation", - "repeat fractionation" - ], - "library_layout": [ - "paired", - "single", - "single" - ], - "insert_size": [ - "250","None","None" - ], - "library_construction_protocol": [ - "library_construction_protocol_1", - "library_construction_protocol_2", - "library_construction_protocol_2" - ], - "platform": [ - "LS454", - "illumina", - "illumina" - ], - "instrument_model": [ - "454 GS 20", - "Illumina Genome Analyzer", - "Illumina Genome Analyzer" - ] - } -} \ No newline at end of file diff --git a/relecov_tools/example_data/to_ena.json b/relecov_tools/example_data/to_ena.json new file mode 100644 index 00000000..fa46d819 --- /dev/null +++ b/relecov_tools/example_data/to_ena.json @@ -0,0 +1,39 @@ +{ + "sample_name": "ID_001", + "sample_title": "sample_title_2", + "tax_id": "2697049", + "collecting_institution": "Hospital Universitario de Basurto", + "geographic_location_(country_and/or_sea)": "Spain", + "isolate": "ID_001", + "host_scientific_name": "Homo sapiens", + "host_common_name": "Human", + "host_health_state": "diseased", + "host_gender": "male", + "host_subject_id": "#131", + "instrument_model": "Illumina MiSeq", + "file_name": "ABC123_S1_L001_R1_001.fasstq.gz", + "collection_date": "2020-10-11", + "scientific_name": "severe acute respiratory syndrome coronavirus 2", + "common_name": "SARS-CoV-2", + "collector_name": "John Smith", + "sample_description": "SARS-CoV-2 Sample #1", + "library_source": "METAGENOMIC", + "library_selection": "RANDOM PCR", + "library_strategy": "WGS", + "library_layout": "PAIRED", + "library_name": "library_name_1", + "study_alias": "study_alias_1", + "study_title": "study_title", + "study_type": "RNASeq", + "study_abstract": "study_abstract_1", + "pubmed_id": "pubmed_id_2", + "run_alias": "run_alias_1a", + "experiment_alias": "experiment_alias_7a", + "file_type": "fastq", + "file_checksum": "3e69af1f875fab020aed82f5edbc1f03", + "experiment_title": "experiment_title_1", + "design_description": "design_description_1", + "insert_size": "250", + "library_construction_protocol": "library_construction_protocol_1", + "platform": "LS454" +} \ No newline at end of file diff --git a/relecov_tools/schema/bioinfo_schema.json b/relecov_tools/schema/bioinfo_schema.json new file mode 100644 index 00000000..872c9882 --- /dev/null +++ b/relecov_tools/schema/bioinfo_schema.json @@ -0,0 +1,512 @@ +{ + "schema": "bioinfo_metadata", + "type": "object", + "properties": { + "dehosting_method": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "assembly": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "if_assembly_other": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "assembly_params": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "variant_calling": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "if_variant_calling_other": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "variant_calling_params": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "consensus_sequence_name": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "consensus_sequence_name_md5": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "consensus_sequence_filepath": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "consensus_sequence_software_name": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "if_consensus_other": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "consensus_sequence_software_version": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "consensus_criteria": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": 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"clasification": "", + "label": "", + "table": [] + }, + "bioinformatics_protocol": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "if_bioinformatic_protocol_other": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "bioinformatic_protocol_version": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "commercial/open-source/both": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "preprocessing": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "if_preprocessing_other": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "preprocessing_params": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "mapping": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "if_mapping_other": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "mapping_params": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "lineage/clade_name": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "lineage/clade_analysis_software_name": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "if_lineage_identification_other": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "lineage/clade_analysis_software_version": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "variant_designation": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "gene_name_1": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "%qc_filtered": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "%reads_host": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "%reads_virus": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "%unmapped": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "% genome _greater_10x": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "mean_depth_of_coverage_value": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "%Ns": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "Number_of_variants_(AF_greater_75%)": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "Numer_of_variants_with_effect": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + }, + "long_table_path": { + "examples": [ + "" + ], + "ontology": "", + "type": "", + "description": "", + "clasification": "", + "label": "", + "table": [] + } + } +} \ No newline at end of file diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index ccd96b11..66a3bcff 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1805,7 +1805,7 @@ "type": "string", "description": "", "clasification": "Sequencing", - "label": "Amplicon panel/assay" + "label": "Enrichment panel/assay" }, "if_amplicon_protocol_if_other_especify": { "examples": [ @@ -1815,7 +1815,7 @@ "type": "string", "description": "", "clasification": "Sequencing", - "label": "If Amplicon Protocol If Other, Especify" + "label": "If Enrichment panel/assay If Other, Especify" }, "amplicon_version": { "examples": [ @@ -1825,7 +1825,7 @@ "type": "string", "description": "", "clasification": "Sequencing", - "label": "Amplicon Version" + "label": "Enrichment panel/assay version" }, "amplicon_size": { "examples": [ @@ -3228,4 +3228,4 @@ "clasification": "Database Identifiers" } } -} +} \ No newline at end of file diff --git a/relecov_tools/schema/sample_relecov.xml b/relecov_tools/schema/sample_relecov.xml new file mode 100644 index 00000000..4715010b --- /dev/null +++ b/relecov_tools/schema/sample_relecov.xml @@ -0,0 +1 @@ +SARS Sample 12697049Severe acute respiratory syndrome coronavirus 2SARS-CoV-2 Sample #1sample_nameID_001collecting_institutionHospital Universitario de Basurtogeographic_location_(country_and/or_sea)SpainisolateID_001host_scientific_nameHomo sapienshost_common_nameHumanhost_subject_id#131instrument_modelIllumina MiSeqfile_nameABC123_S1_L001_R1_001.fasstq.gztax_id2697049scientific_namesevere acute respiratory syndrome coronavirus 2common_nameSARS-CoV-2sample_descriptionSARS-CoV-2 Sample #1library_sourceMETAGENOMIClibrary_selectionRANDOM PCRlibrary_strategyWGSlibrary_layoutPAIRED \ No newline at end of file diff --git a/relecov_tools/test/pruebas.ipynb b/relecov_tools/test/pruebas.ipynb new file mode 100644 index 00000000..1f1fb881 --- /dev/null +++ b/relecov_tools/test/pruebas.ipynb @@ -0,0 +1,849 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 3, + "id": "a99df8ae", + "metadata": {}, + "outputs": [], + "source": [ + "import json\n", + "import openpyxl" + ] + }, + { + "cell_type": "code", + "execution_count": 220, + "id": "dd64f661", + "metadata": {}, + "outputs": [], + "source": [ + "f = open(\"schema/small_schema.json\")\n", + "json_phage_plus_schema = json.load(f)" + ] + }, + { + "cell_type": "code", + "execution_count": 221, + "id": "9057ba90", + "metadata": {}, + "outputs": [], + "source": [ + "json_phage_plus_schema;" + ] + }, + { + "cell_type": "code", + "execution_count": 222, + "id": "97b35c6a", + "metadata": {}, + "outputs": [], + "source": [ + " wb_file = openpyxl.load_workbook(\"example_data/dummy_data_small.xlsx\", data_only=True)\n", + "ws_metadata_lab = wb_file[\"METADATA_LAB\"]\n", + "heading = []\n", + "for cell in ws_metadata_lab[1]:\n", + " heading.append(cell.value)\n" + ] + }, + { + "cell_type": "code", + "execution_count": 223, + "id": "986c372a", + "metadata": {}, + "outputs": [], + "source": [ + "heading;" + ] + }, + { + "cell_type": "code", + "execution_count": 224, + "id": "895b82c2", + "metadata": {}, + "outputs": [], + "source": [ + "for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row):\n", + " sample_data_row = {}\n", + " for idx in range(len(heading)):\n", + " if \"date\" in heading[idx]:\n", + " sample_data_row[heading[idx]] = row[idx].strftime(\"%d/%m/%Y\")\n", + " else:\n", + " sample_data_row[heading[idx]] = row[idx]\n", + " \n", + "fila = sample_data_row" + ] + }, + { + "cell_type": "code", + "execution_count": 225, + "id": "c441ba9d", + "metadata": {}, + "outputs": [], + "source": [ + "list(fila.keys());" + ] + }, + { + "cell_type": "code", + "execution_count": 226, + "id": "a2f1610b", + "metadata": {}, + "outputs": [], + "source": [ + "json_phage_plus_schema['properties'];" + ] + }, + { + "cell_type": "code", + "execution_count": 227, + "id": "2b3da23d", + "metadata": {}, + "outputs": [], + "source": [ + "instance = [{}, 3, \"foo\"]" + ] + }, + { + "cell_type": "code", + "execution_count": 228, + "id": "2b30fc71", + "metadata": {}, + "outputs": [], + "source": [ + "validate(instance = list(fila.keys()), schema =json_phage_plus_schema['properties']) " + ] + }, + { + "cell_type": "code", + "execution_count": 229, + "id": "cc3c4bac", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'prov_rona_99'" + ] + }, + "execution_count": 229, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "sample_data_row[\"Collecting Sample id\"]" + ] + }, + { + "cell_type": "code", + "execution_count": 63, + "id": "72587d32", + "metadata": {}, + "outputs": [], + "source": [ + "heading =['Collecting Sample id', 'Originating Laboratory', 'Submitting Institution', 'Sample Collection Date', 'geo_loc_country', 'geo_loc_state', 'organism', 'isolate', 'host_scientific_name', 'Host Common Name', 'host_disease', 'Sequencing Instrument Model', 'Sequencing Platforms', 'consensus_sequence_software_name', 'consensus_sequence_software_version', 'file_name', 'tax_id', 'sample_description', 'Library Source', 'Library Selection', 'Library Strategy', 'Library Layout', 'type', 'GISAID Virus Name', 'GISAID Id', 'Originating Laboratory Address']\n" + ] + }, + { + "cell_type": "code", + "execution_count": 71, + "id": "7ea69469", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "26" + ] + }, + "execution_count": 71, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "len(heading)" + ] + }, + { + "cell_type": "code", + "execution_count": 64, + "id": "54afd367", + "metadata": {}, + "outputs": [], + "source": [ + "map_file = open(\"schema/mapping_file.json\")\n", + "mapping_file = json.load(map_file)" + ] + }, + { + "cell_type": "code", + "execution_count": 65, + "id": "3d1e0f63", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'Collecting Sample id': 'sample_name',\n", + " 'Originating Laboratory': 'collecting_institution',\n", + " 'Submitting Institution': 'submitting_institution',\n", + " 'Sample Collection Date': 'sample_collection_date',\n", + " 'geo_loc_country': 'geo_loc_country',\n", + " 'geo_loc_state': 'geo_loc_state',\n", + " 'organism': 'organism',\n", + " 'isolate': 'isolate',\n", + " 'host_scientific_name': 'host_scientific_name',\n", + " 'Host Common Name': 'host_common_name',\n", + " 'host_disease': 'host_disease',\n", + " 'Sequencing Instrument Model': 'sequencing_instrument_model',\n", + " 'Sequencing Platforms': 'sequencing_instrument_platform',\n", + " 'consensus_sequence_software_name': 'consensus_sequence_software_name',\n", + " 'consensus_sequence_software_version': 'consensus_sequence_software_version',\n", + " 'file_name': 'file_name',\n", + " 'tax_id': 'tax_id',\n", + " 'sample_description': 'sample_description',\n", + " 'Library Source': 'library_source',\n", + " 'Library Selection': 'library_selection',\n", + " 'Library Strategy': 'library_strategy',\n", + " 'Library Layout': 'library_layout',\n", + " 'type': 'type',\n", + " 'GISAID Virus Name': 'virus_name',\n", + " 'GISAID Id': 'submitter',\n", + " 'Originating Laboratory Address': 'collecting_address'}" + ] + }, + "execution_count": 65, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "mapping_file" + ] + }, + { + "cell_type": "code", + "execution_count": 54, + "id": "def77932", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'sample_name'" + ] + }, + "execution_count": 54, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "list(mapping_file.values())[0]" + ] + }, + { + "cell_type": "code", + "execution_count": 70, + "id": "34b84069", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "0\n", + "1\n", + "2\n", + "3\n", + "4\n", + "5\n", + "6\n", + "7\n", + "8\n", + "9\n", + "10\n", + "11\n", + "12\n", + "13\n", + "14\n", + "15\n", + "16\n", + "17\n", + "18\n", + "19\n", + "20\n", + "21\n", + "22\n", + "23\n", + "24\n", + "25\n" + ] + } + ], + "source": [ + "for i in range(len(heading)):\n", + " print(i)" + ] + }, + { + "cell_type": "code", + "execution_count": 72, + "id": "1caa1045", + "metadata": {}, + "outputs": [], + "source": [ + "for i in range(len(heading)):\n", + " if heading[i] in list(mapping_file.keys()):\n", + " index = list(mapping_file).index(heading[i])\n", + " heading[index] = list(mapping_file.values())[index]\n", + " \n", + " \n" + ] + }, + { + "cell_type": "code", + "execution_count": 73, + "id": "8ab4a0c2", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['sample_name',\n", + " 'collecting_institution',\n", + " 'submitting_institution',\n", + " 'sample_collection_date',\n", + " 'geo_loc_country',\n", + " 'geo_loc_state',\n", + " 'organism',\n", + " 'isolate',\n", + " 'host_scientific_name',\n", + " 'host_common_name',\n", + " 'host_disease',\n", + " 'sequencing_instrument_model',\n", + " 'sequencing_instrument_platform',\n", + " 'consensus_sequence_software_name',\n", + " 'consensus_sequence_software_version',\n", + " 'file_name',\n", + " 'tax_id',\n", + " 'sample_description',\n", + " 'library_source',\n", + " 'library_selection',\n", + " 'library_strategy',\n", + " 'library_layout',\n", + " 'type',\n", + " 'virus_name',\n", + " 'submitter',\n", + " 'collecting_address']" + ] + }, + "execution_count": 73, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "heading" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4689d46e", + "metadata": {}, + "outputs": [], + "source": [ + "dictionary = {'test':{1,3}, 'test2':{2}, 'test3':{2,3}}\n", + "\n", + "if 'test' in dictionary:\n", + " print(list(dictionary).index('test'))" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "id": "5ae4de88", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['Collecting Sample id',\n", + " 'Originating Laboratory',\n", + " 'Submitting Institution',\n", + " 'Sample Collection Date',\n", + " 'geo_loc_country',\n", + " 'geo_loc_state',\n", + " 'organism',\n", + " 'isolate',\n", + " 'host_scientific_name',\n", + " 'Host Common Name',\n", + " 'host_disease',\n", + " 'Sequencing Instrument Model',\n", + " 'Sequencing Platforms',\n", + " 'consensus_sequence_software_name',\n", + " 'consensus_sequence_software_version',\n", + " 'file_name',\n", + " 'tax_id',\n", + " 'sample_description',\n", + " 'Library Source',\n", + " 'Library Selection',\n", + " 'Library Strategy',\n", + " 'Library Layout',\n", + " 'type',\n", + " 'GISAID Virus Name',\n", + " 'GISAID Id',\n", + " 'Originating Laboratory Address']" + ] + }, + "execution_count": 27, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "heading" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b212e5ee", + "metadata": {}, + "outputs": [], + "source": [ + " 'sample_name',\n", + " 'collecting_institution',\n", + " 'submitting_institution',\n", + "'sample_collection_date',\n", + " 'geo_loc_country',\n", + " 'geo_loc_state',\n", + " 'organism',\n", + " 'isolate',\n", + " 'host_scientific_name',\n", + " 'host_common_name',\n", + " 'host_disease',\n", + " 'sequencing_instrument_model',\n", + " 'sequencing_instrument_platform',\n", + " 'consensus_sequence_software_name',\n", + " 'consensus_sequence_software_version',\n", + " 'file_name',\n", + " 'tax_id',\n", + " 'sample_description',\n", + " 'library_source',\n", + " 'library_selection',\n", + " 'library_strategy',\n", + " 'library_layout',\n", + " 'type',\n", + " 'virus_name',\n", + " 'submitter',\n", + " 'collecting_institution_address'],\n" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "697682c3", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "prueba.py pruebas.ipynb to_ena.json\r\n" + ] + } + ], + "source": [ + "ls" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "id": "3124de94", + "metadata": {}, + "outputs": [], + "source": [ + "d = {'collecting_institution': 'Hospital Universitario de Basurto',\n", + "'collecting_institution_address': 'Avda. Montevideo, 18,Bilbao,Vizcaya, ',\n", + "'consensus_sequence_software_name': 'CLC Genomics Workbench 12',\n", + "'consensus_sequence_software_version': '. CLC Genomics Workbench 12,',\n", + "'file_name': 'filename2',\n", + "'geo_loc_country': 'Spain',\n", + "'geo_loc_state': 'Madrid',\n", + "'host_common_name': 'Human',\n", + "'host_disease': 'SARS-CoV2',\n", + "'host_scientific_name': 'Homo sapiens',\n", + "'isolate': 'SARS-CoV-2/human/USA/CA-CDPH-001/2020',\n", + "'library_layout': 'PAIRED',\n", + "'library_selection': 'RANDOM PCR',\n", + "'library_source': 'METAGENOMIC',\n", + "'library_strategy': 'WGS',\n", + "'organism': 'Severe acute respiratory syndrome coronavirus 2',\n", + "'sample_description': 'madnatory ENA description sample',\n", + "'sample_name': 'ID_001',\n", + "'sequencing_instrument_model': 'Illumina MiSeq',\n", + "'sequencing_instrument_platform': 'ILLUMINA',\n", + "'submitter': 'GISAID-Username',\n", + "'submitting_institution': 'Laboratorio de Microbiología de Bibao ',\n", + "'tax_id': 2697049,\n", + "'type': 'betacoronavirus',\n", + "'virus_name': 'hCoV-19/España/Vizcaya-01/2020'}\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "5c390e91", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'collecting_institution': 'Hospital Universitario de Basurto',\n", + " 'collecting_institution_address': 'Avda. Montevideo, 18,Bilbao,Vizcaya, ',\n", + " 'consensus_sequence_software_name': 'CLC Genomics Workbench 12',\n", + " 'consensus_sequence_software_version': '. CLC Genomics Workbench 12,',\n", + " 'file_name': 'filename2',\n", + " 'geo_loc_country': 'Spain',\n", + " 'geo_loc_state': 'Madrid',\n", + " 'host_common_name': 'Human',\n", + " 'host_disease': 'SARS-CoV2',\n", + " 'host_scientific_name': 'Homo sapiens',\n", + " 'isolate': 'SARS-CoV-2/human/USA/CA-CDPH-001/2020',\n", + " 'library_layout': 'PAIRED',\n", + " 'library_selection': 'RANDOM PCR',\n", + " 'library_source': 'METAGENOMIC',\n", + " 'library_strategy': 'WGS',\n", + " 'organism': 'Severe acute respiratory syndrome coronavirus 2',\n", + " 'sample_description': 'madnatory ENA description sample',\n", + " 'sample_name': 'ID_001',\n", + " 'sequencing_instrument_model': 'Illumina MiSeq',\n", + " 'sequencing_instrument_platform': 'ILLUMINA',\n", + " 'submitter': 'GISAID-Username',\n", + " 'submitting_institution': 'Laboratorio de Microbiología de Bibao ',\n", + " 'tax_id': 2697049,\n", + " 'type': 'betacoronavirus',\n", + " 'virus_name': 'hCoV-19/España/Vizcaya-01/2020'}" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "d" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "2939d552", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/schema'" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "pwd\n" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "88c37daa", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Directory xml_outout Created \n" + ] + } + ], + "source": [ + "# Create directory\n", + "import os \n", + "dirName = 'xml_outout'\n", + "try:\n", + " # Create target Directory\n", + " os.mkdir(dirName)\n", + " print(\"Directory \" , dirName , \" Created \") \n", + "except FileExistsError:\n", + " print(\"Directory \" , dirName , \" already exists\")" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "e0ff2698", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "ena_v01.json mapping_metadata_json_v01.json pruebas.ipynb to_ena.json\r\n", + "genepio.owl phage_plus_V0.json sample_relecov.xml\r\n", + "gisaid_V0.json phage_V0.json small_schema.json\r\n" + ] + } + ], + "source": [ + "ls\n" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "id": "42698e3a", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 29, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import json as j\n", + "import xml.etree.cElementTree as e\n", + "\n", + "\n", + "with open(\"to_ena.json\") as json_format_file:\n", + " d = j.load(json_format_file)\n", + " \n", + "\n", + "data_keys = list(d.keys())\n", + "\n", + "\n", + "r = e.Element(\"SUBMISSION_SET\")\n", + "\n", + "\n", + "sample = e.SubElement(r,\"SUBMISSION\")\n", + "actions = e.SubElement(sample,'ACTIONS')\n", + "action = e.SubElement(actions,\"ACTION\")\n", + "\n", + "e.SubElement(action,\"ADD\")\n", + "\n", + "\n", + " \n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "id": "8f06bf42", + "metadata": {}, + "outputs": [], + "source": [ + "\n", + "a = e.ElementTree(r)\n", + "a.write(\"xml_outout/submission.xml\")" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "id": "914fc897", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/schema'" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "pwd" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "id": "b20e77ff", + "metadata": {}, + "outputs": [ + { + "ename": "SyntaxError", + "evalue": "EOL while scanning string literal (3660535544.py, line 1)", + "output_type": "error", + "traceback": [ + "\u001b[0;36m Input \u001b[0;32mIn [18]\u001b[0;36m\u001b[0m\n\u001b[0;31m xml = '\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m EOL while scanning string literal\n" + ] + } + ], + "source": [ + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "id": "2e794989", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/schema'" + ] + }, + "execution_count": 1, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import os\n", + "os.getcwd()" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "id": "5fd9f694", + "metadata": {}, + "outputs": [], + "source": [ + "os.chdir('xml_files/')" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "id": "39fb227a", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/xml_files'" + ] + }, + "execution_count": 26, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "os.getcwd()" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "b76abb51", + "metadata": {}, + "outputs": [], + "source": [ + "import json\n", + "\n", + "conf_dict = {\n", + " \"json_schemas\": {\n", + " \"phage_plus_schema\": \"phage_plus_V0.json\",\n", + " \"ene_schema\": \"ena_v01.json\",\n", + " \"gisaid_schema\": \"gisaid_v01.json\"\n", + " },\n", + " \"mapping_metadata_json\": \"mapping_metadata_json_v01.json\",\n", + " \"additional_metadata\": \"additional_metadata_v01.json\",\n", + " \"sftp_connection\": {\n", + " \"sftp_server\": \"sftprelecov.isciii.es\",\n", + " \"sftp_port\": \"50122\"\n", + " },\n", + " \"storage_local_folder\": \"/tmp/relecov\",\n", + " \"tmp_folder_for_metadata\": \"/tmp/relecov/tmp\",\n", + " \"allowed_sample_extensions\": [\n", + " \"fastq.gz\",\n", + " \"fasta\"\n", + " ],\n", + " \"project_relecov_xml\": {\n", + " \"alias\": \"RELECOV\",\n", + " \"TITLE\": \"Example project for ENA submission RELECOV\",\n", + " \"DESCRIPTION\": \"This study was created as part of an ENA submissions example RELECOV\"\n", + " }\n", + "}\n", + "\n", + "\n", + "\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "id": "74cfbcea", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'RELECOV'" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "conf_dict[\"project_relecov_xml\"][\"alias\"]\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d13efc61", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.9.5" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/relecov_tools/test/try_01.ipynb b/relecov_tools/test/try_01.ipynb index df0f0e80..384ef60c 100644 --- a/relecov_tools/test/try_01.ipynb +++ b/relecov_tools/test/try_01.ipynb @@ -239,7 +239,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -253,7 +253,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.3" + "version": "3.9.5" } }, "nbformat": 4, diff --git a/relecov_tools/xml_files/samples/submission_add.xml b/relecov_tools/xml_files/samples/submission_add.xml new file mode 100644 index 00000000..8edfc2ad --- /dev/null +++ b/relecov_tools/xml_files/samples/submission_add.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/relecov_tools/xml_files/samples/submission_modify.xml b/relecov_tools/xml_files/samples/submission_modify.xml new file mode 100644 index 00000000..d9bc1a3a --- /dev/null +++ b/relecov_tools/xml_files/samples/submission_modify.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/relecov_tools/xml_files/study/project.xml b/relecov_tools/xml_files/study/project.xml new file mode 100644 index 00000000..5e244c5a --- /dev/null +++ b/relecov_tools/xml_files/study/project.xml @@ -0,0 +1,9 @@ + + + Example project for ENA submission workshop + This study was created as part of an ENA submissions workshop + + + + + diff --git a/relecov_tools/xml_files/study/receipt.xml b/relecov_tools/xml_files/study/receipt.xml new file mode 100644 index 00000000..06d1e5ba --- /dev/null +++ b/relecov_tools/xml_files/study/receipt.xml @@ -0,0 +1,12 @@ +curl -u Webin-60330:W2b3nENA%2021 -F "SUBMISSION=@submission.xml" -F "PROJECT=@project.xml" "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/" + + + + + + + In project, alias:"workshop_project", accession:"". The object being added already exists in the submission account with accession: "PRJEB51674". + This submission is a TEST submission and will be discarded within 24 hours + + ADD + diff --git a/relecov_tools/xml_files/study/submission.xml b/relecov_tools/xml_files/study/submission.xml new file mode 100644 index 00000000..8edfc2ad --- /dev/null +++ b/relecov_tools/xml_files/study/submission.xml @@ -0,0 +1,10 @@ + + + + + + + + + + From c93d6b678fce93cd7b9162091ea362815bb1153b Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 5 Apr 2022 22:50:09 +0200 Subject: [PATCH 0282/1454] Create a new METADATA file with the invalid samples --- relecov_tools/__main__.py | 6 ++-- relecov_tools/json_validation.py | 47 ++++++++++++++++++-------------- 2 files changed, 29 insertions(+), 24 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index fdd6cd8a..d4fd2a13 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -209,8 +209,6 @@ def read_metadata(metadata_file, sample_list_file, metadata_out): @click.option("-o", "--out_folder", help="Path to save validate json file") def validate(json_file, json_schema, metadata, out_folder): """Validate json file against schema.""" - relecov_tools.json_validation.create_invalid_metadata(metadata, json_file, out_folder) - import pdb; pdb.set_trace() ( validated_json_data, invalid_json, @@ -221,7 +219,9 @@ def validate(json_file, json_schema, metadata, out_folder): if not os.isfile(metadata): log.error("Metadata file %s does not exists", metadata) exit(1) - relecov_tools.json_validation.create_invalid_metadata(metadata, invalid_json, out_folder) + relecov_tools.json_validation.create_invalid_metadata( + metadata, invalid_json, out_folder + ) else: log.info("All data in json were validated") diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index bcce30c1..a6eb28be 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -61,34 +61,39 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): def create_invalid_metadata(metadata_file, invalid_json, out_folder): - """Create a new sub excel file having only the samples that were invalid + """Create a new sub excel file having only the samples that were invalid. + Samples name are checking the Sequencing sample id which are in + column B (index 1). + The rows that match the value collected from json file on tag + collecting_lab_sample_id are removed from excel """ - invalid_metadata = "" - sample_id_head = "Sequencing sample id" - wb_inv = openpyxl.Workbook() sample_list = [] - json_data = relecov_tools.utils.read_json_file(invalid_json) for row in json_data: sample_list.append(row["collecting_lab_sample_id"]) wb = openpyxl.load_workbook(metadata_file) - import pdb; pdb.set_trace() + exclude_sheet = ["Overview", "METADATA_LAB", "DATA VALIDATION"] for sheet in wb.sheetnames: + if sheet in exclude_sheet: + continue ws_sheet = wb[sheet] - ws_inv = wb_inv.create_sheet(sheet) - head_list = [cell.value for cell in ws_sheet[1]] - import pdb; pdb.set_trace() - try: - s_index = head_list.index(sample_id_head) - except: - - for row in ws_sheet.iter_rows(): - if row[s_index].value in sample_list: - ws_inv.append(row) - import pdb; pdb.set_trace() - target = wb_inv.copy_worksheet(ws_inv) - target.title(sheet) - import pdb; pdb.set_trace() + row_to_del = [] + # Findout where the sample index is + idx_sample = 2 if ws_sheet.title == "1.Database Identifiers" else 1 + for row in ws_sheet.iter_rows(min_row=4, max_row=ws_sheet.max_row): + if not row[2].value and not row[1].value: + if len(row_to_del) > 0: + row_to_del.sort(reverse=True) + for idx in row_to_del: + ws_sheet.delete_rows(idx) + break + if row[0].value == "CAMPO": + continue + if str(row[idx_sample].value) not in sample_list: + row_to_del.append(row[0].row) - wb_inv.save(filename=invalid_metadata) + new_name = "invalid_" + os.path.basename(metadata_file) + m_file = os.path.join(out_folder, new_name) + wb.save(m_file) + return From 2dc3d1951d4e1715e691cb1a7442dded28515b98 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 6 Apr 2022 00:10:54 +0200 Subject: [PATCH 0283/1454] update metadata parameter in validate module --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 45dc033a..e8d42b6c 100644 --- a/README.md +++ b/README.md @@ -70,7 +70,7 @@ Commands: #### download The command `download` connects to a transfer protocol (currently sftp) and downloads all files in the different available folders in the passed credentials. In addition, it checks if the files in the current folder match the files in the metadata file and also checks if there are md5sum for each file. Else, it creates one before storing in the final repository. -``` +``` $ relecov-tools download --help Usage: relecov-tools download [OPTIONS] @@ -101,7 +101,7 @@ allowed_sample_extensions: ``` #### read-metadata -`read-metadata` command reads the excel file with laboratory metadata and processes it adding aditional needed fields. +`read-metadata` command reads the excel file with laboratory metadata and processes it adding additional needed fields. ``` $ relecov-tools read-metadata --help @@ -132,6 +132,7 @@ Usage: relecov-tools validate [OPTIONS] Options: -j, --json_file TEXT Json file to validate -s, --json_schema TEXT Json schema + -m, --metadata PATH Origin file containing metadata -o, --out_folder TEXT Path to save validate json file --help Show this message and exit. From 52943826f112f362e12ef382827069d154c92af8 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 6 Apr 2022 00:45:35 +0200 Subject: [PATCH 0284/1454] Working on mapping to ENA --- relecov_tools/__main__.py | 2 +- relecov_tools/map_schema.py | 63 ++++++++++++++++++++----------------- 2 files changed, 35 insertions(+), 30 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index d4fd2a13..a49ee039 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -241,7 +241,7 @@ def validate(json_file, json_schema, metadata, out_folder): @click.option("-o", "--output", help="File name and path to store the mapped json") def map(origin_schema, json_data, destination_schema, schema_file, output): """Convert data between phage plus schema to ENA, GISAID, or any other schema""" - new_schema = relecov_tools.conversion_schema.MappingSchema( + new_schema = relecov_tools.map_schema.MappingSchema( origin_schema, json_data, destination_schema, schema_file, output ) new_schema.map_to_data_to_new_schema() diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 91fc112b..dbcc399b 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -25,43 +25,46 @@ class MappingSchema: def __init__( self, - phage_plus_schema=None, - json_data=None, + relecov_schema=None, + json_file=None, destination_schema=None, schema_file=None, output=None, ): config_json = ConfigJson() - if phage_plus_schema is None: - phage_plus_schema_file = os.path.join( + if relecov_schema is None: + relecov_schema = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", - config_json.get_topic_data("json_schemas", "phage_plus_schema"), + config_json.get_topic_data("json_schemas", "relecov_schema"), ) - with open(phage_plus_schema_file, "r") as fh: - self.phage_plus_schema = json.load(fh) else: - with open(phage_plus_schema, "r") as fh: - json_schema = json.load(fh) - try: - Draft202012Validator.check_schema(json_schema) - except jsonschema.ValidationError: + if os.path.isfile(relecov_schema): + log.error("Relecov schema file %s does not exists", relecov_schema) stderr.print( - "[red] phage plus schema does not fulfil Draft 202012 Validation" + "[red] Relecov schema " + relecov_schema + "does not exists" ) - sys.exit(1) - self.phage_plus_schema = json.load(fh) + exit(1) + rel_schema_json = relecov_tools.utils.read_json_file(relecov_schema) + try: + Draft202012Validator.check_schema(rel_schema_json) + except jsonschema.ValidationError: + log.error("Relecov schema does not fulfil Draft 202012 Validation ") + stderr.print( + "[red] phage plus schema does not fulfil Draft 202012 Validation" + ) + sys.exit(1) + self.relecov_schema = rel_schema_json - if json_data is None: - self.json_data_file = relecov_tools.utils.prompt_path( - msg="Select the json which have the data to map" + if json_file is None: + json_file = relecov_tools.utils.prompt_path( + msg="Select the json file which have the data to map" ) - else: - self.json_data_file = json_data - if not os.path.isfile(self.json_data_file): - log.error("json data file %s does not exist ", self.json_data_file) - stderr.print(f"json data file {self.json_data_file} does not exist") + if not os.path.isfile(json_file): + log.error("json data file %s does not exist ", json_file) + stderr.print(f"[red] json data file {json_file} does not exist") sys.exit(1) + self.json_data = relecov_tools.utils.read_json_file(json_file) if destination_schema is None: self.destination_schema = relecov_tools.utils.prompt_selection( @@ -111,7 +114,7 @@ def __init__( self.mapped_to_schema = json.load(fh) self.ontology = {} - for key, values in self.phage_plus_schema["properties"].items(): + for key, values in self.relecov_schema["properties"].items(): self.ontology[values["ontology"]] = key def maping_schemas_based_on_geontology(self): @@ -131,12 +134,14 @@ def maping_schemas_based_on_geontology(self): def mapping_json_data(self, mapping_schema_dict): """Convert phage plus data to the requested schema""" mapped_data = [] - with open(self.json_data, "r") as fh: - json_data = json.load(fh) - for data in json_data: + + for data in self.json_data: map_sample_dict = OrderedDict() - for item, value in mapping_schema_dict.items: - map_sample_dict[item] = self.data[value] + for item, value in mapping_schema_dict.items(): + try: + map_sample_dict[item] = data[value] + except KeyError as e: + print(e) mapped_data.append(map_sample_dict) return mapped_data From 052b2f0c815fcd5928ce258fca83015b466bd6a4 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 6 Apr 2022 14:27:47 +0200 Subject: [PATCH 0285/1454] Remove duplicated nominal_length --- relecov_tools/schema/relecov_schema.json | 9 --------- 1 file changed, 9 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index ccd96b11..4b4c7b20 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2827,15 +2827,6 @@ "clasification": "Sequencing", "label": "Source material" }, - "nominal_length": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "clasification": "Sequencing" - }, "analysis_accession": { "examples": [ "" From 6e46de827a6c814e19395a2d2ed610fa3349158b Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 6 Apr 2022 14:35:44 +0200 Subject: [PATCH 0286/1454] added changes in schema --- relecov_tools/schema/relecov_schema.json | 338 +++++++++++------------ 1 file changed, 169 insertions(+), 169 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 66a3bcff..546bdcbf 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -23,7 +23,7 @@ "ontology": "GENEPIO:0001123", "type": "string", "description": "The user-defined name for the sample.", - "clasification": "Database Identifiers", + "classification": "Database Identifiers", "label": "Sample ID given by originating laboratory" }, "sample_description": { @@ -33,7 +33,7 @@ "ontology": "GENEPIO:0001156", "type": "string", "description": "Free text description of the sample.", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Sample Description" }, "collecting_institution": { @@ -71,7 +71,7 @@ "ontology": "GENEPIO:0001398", "type": "string", "description": "a unique identifier by which each subject can be referred to, de-identified.", - "clasification": "Host information", + "classification": "Host information", "label": "Host Subject Id" }, "geo_loc_country": { @@ -475,7 +475,7 @@ "examples": [ "Homo sapiens [NCBITaxon:9606]" ], - "clasification": "Host information", + "classification": "Host information", "label": "Host Scientific Name" }, "host_disease": { @@ -583,7 +583,7 @@ "ontology": "GENEPIO:0001133", "type": "string", "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", - "clasification": "Database Identifiers", + "classification": "Database Identifiers", "label": "Bioproject umbrella accession ENA" }, "bioproject_accession_ENA": { @@ -593,7 +593,7 @@ "ontology": "GENEPIO:0001136", "type": "string", "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", - "clasification": "Database Identifiers", + "classification": "Database Identifiers", "label": "Bioproject accession ENA" }, "biosample_accession_ENA": { @@ -603,7 +603,7 @@ "ontology": "GENEPIO:0001139", "type": "string", "description": "The identifier assigned to a BioSample in INSDC archives.", - "clasification": "Database Identifiers", + "classification": "Database Identifiers", "label": "ENA Sample ID" }, "sra_accession": { @@ -613,7 +613,7 @@ "ontology": "GENEPIO:0001142", "type": "string", "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "clasification": "Database Identifiers", + "classification": "Database Identifiers", "label": "SRA Accession" }, "genBank/ENA/DDBJ_accession": { @@ -623,7 +623,7 @@ "ontology": "GENEPIO_0001145", "type": "string", "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", - "clasification": "Database Identifiers", + "classification": "Database Identifiers", "label": "GenBank/ENA/DDBJ accession" }, "GISAID_accession": { @@ -633,7 +633,7 @@ "ontology": "GENEPIO:0001147", "type": "string", "description": "The GISAID accession number assigned to the sequence.", - "clasification": "Database Identifiers", + "classification": "Database Identifiers", "label": "GISAID Accession" }, "virus_name": { @@ -643,7 +643,7 @@ "ontology": "GENEPIO:0100282", "type": "string", "description": "The user-defined GISAID virus name assigned to the sequence.", - "clasification": "Database Identifiers", + "classification": "Database Identifiers", "label": "GISAID Virus Name" }, "collecting_institution_email": { @@ -653,7 +653,7 @@ "ontology": "OBI:0001890", "type": "string", "description": "The email address of the contact responsible for follow-up regarding the sample.", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Originating Laboratory Email" }, "collecting_institution_address": { @@ -663,7 +663,7 @@ "ontology": "GENEPIO:0001158", "type": "string", "description": "The mailing address of the agency submitting the sample.", - "clasification": "Originating Laboratory Address" + "classification": "Originating Laboratory Address" }, "submitting_institution_email": { "examples": [ @@ -672,7 +672,7 @@ "ontology": "GENEPIO:0001165", "type": "string", "description": "The email address of the contact responsible for follow-up regarding the sequence.", - "clasification": "Sample collection and processing" + "classification": "Sample collection and processing" }, "submitting_institution_address": { "examples": [ @@ -681,7 +681,7 @@ "ontology": "GENEPIO:0001167", "type": "string", "description": "The mailing address of the agency submitting the sequence.", - "clasification": "Sample collection and processing" + "classification": "Sample collection and processing" }, "sample_received_date": { "examples": [ @@ -691,7 +691,7 @@ "type": "string", "description": "The date on which the sample was received.", "format": "date", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Sample Received Date" }, "shipping_date": { @@ -702,7 +702,7 @@ "type": "string", "description": "The date on which the sample was sent.", "format": "date", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Shipping Date" }, "results_emission_date": { @@ -713,7 +713,7 @@ "type": "string", "description": "The date on which the results were emitted.", "format": "date", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Results Emission Date" }, "sample_storage_conditions": { @@ -723,7 +723,7 @@ "ontology": "NCIT_C115535", "type": "string", "description": "The name and version of a particular protocol used for sampling.", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Biological Sample Storage Condition" }, "culture_collection": { @@ -833,7 +833,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Sample ID given in the microbiology lab" }, "public_health_sample_id_sivies": { @@ -843,7 +843,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Public Health sample id (SIVIES)" }, "isolate_sample_id": { @@ -853,7 +853,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "", + "classification": "", "label": "Sample ID given if multiple rna-extraction or passages" }, "geo_loc_region": { @@ -863,7 +863,7 @@ "ontology": "GENEPIO:0100280", "type": "string", "description": "The county/region of origin of the sample.", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Province" }, "geo_loc_city": { @@ -873,7 +873,7 @@ "ontology": "GENEPIO:0001189", "type": "string", "description": "The city of origin of the sample.", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "City" }, "geo_loc_latitude": { @@ -883,7 +883,7 @@ "ontology": "OBI:0001620", "type": "string", "description": "The latitude coordinates of the geographical location of sample collection.", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Geo Loc Latitude" }, "geo_loc_longitude": { @@ -893,7 +893,7 @@ "ontology": "OBI:0001621", "type": "string", "description": "The longitude coordinates of the geographical location of sample collection.", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Geo Loc Longitude" }, "anatomical_material": { @@ -1035,7 +1035,7 @@ "examples": [ "Face Mask [OBI:0002787]" ], - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Environmental Material" }, "environmental_site": { @@ -1125,7 +1125,7 @@ "examples": [ "Swab [GENEPIO:0100027]" ], - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Collection Device" }, "collection_method": { @@ -1163,7 +1163,7 @@ "examples": [ "Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]" ], - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Collection Method" }, "collection_protocol": { @@ -1173,7 +1173,7 @@ "ontology": "GENEPIO:0001243", "type": "string", "description": "The name and version of a particular protocol used for sampling.", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Collection Protocol" }, "specimen_processing": { @@ -1236,7 +1236,7 @@ "ontology": "GENEPIO:0001261", "type": "string", "description": "Number of passages.", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Passage Number" }, "passage_method": { @@ -1246,7 +1246,7 @@ "ontology": "GENEPIO:0001264", "type": "string", "description": "Description of how organism was passaged.", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Passage Method" }, "tax_id": { @@ -1256,7 +1256,7 @@ "ontology": "GENEPIO_0001724", "type": "string", "description": "The NCBITaxon identifier for the organism being sequenced.", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Tax ID" }, "center_name": { @@ -1266,7 +1266,7 @@ "ontology": "NCIT_C19983", "type": "string", "description": "The name of the institution", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Center Name" }, "host_common_name": { @@ -1593,7 +1593,7 @@ "ontology": "GENEPIO:0001417", "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", - "clasification": "Host information", + "classification": "Host information", "label": "Outbreak Exposure Event Location" }, "additional_host_information": { @@ -1603,7 +1603,7 @@ "ontology": "GENEPIO_0001268", "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", - "clasification": "Host information", + "classification": "Host information", "label": "Additional Host Information" }, "host_ethnicity": { @@ -1693,7 +1693,7 @@ "ontology": "GENEPIO:0000079", "type": "number", "description": "If the information is unknown or can not be shared, leave blank.", - "clasification": "Database Identifiers", + "classification": "Database Identifiers", "label": "Sample ID given for sequencing" }, "passage_details": { @@ -1706,7 +1706,7 @@ "number" ], "description": "If the information is unknown or can not be shared, leave blank.", - "clasification": "Database Identifiers", + "classification": "Database Identifiers", "label": "Passage Details" }, "purpose_of_sequencing_details": { @@ -1733,7 +1733,7 @@ "examples": [ "Screened for S gene target failure (S dropout)" ], - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Purpose Of Sequencing Details" }, "sequencing_date": { @@ -1744,7 +1744,7 @@ "type": "string", "description": "The date the sample was sequenced.", "format": "date", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Sequencing Date" }, "rna_extraction_protocol": { @@ -1754,7 +1754,7 @@ "ontology": "OBI_0302884", "type": "string", "description": "", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Rna Extraction Protocol" }, "library_kit": { @@ -1764,7 +1764,7 @@ "ontology": "GENEPIO_0000085", "type": "string", "description": "", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Commercial All-in-one library kit" }, "library_id": { @@ -1774,7 +1774,7 @@ "ontology": "GENEPIO:0001448", "type": "string", "description": "The user-specified identifier for the library prepared for sequencing.", - "clasification": "Sequencing", + "classification": "Sequencing", "labe": "Library Id" }, "enrichment_protocol": { @@ -1784,7 +1784,7 @@ "ontology": "EFO_0009089", "type": "string", "description": "", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Enrichment Protocol" }, "if_enrichment_protocol_is_other_specify": { @@ -1794,7 +1794,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "If Enrichment Protocol Is Other, Specify" }, "amplicon_protocol": { @@ -1804,7 +1804,7 @@ "ontology": "EFO_0003747", "type": "string", "description": "", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Enrichment panel/assay" }, "if_amplicon_protocol_if_other_especify": { @@ -1814,7 +1814,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "If Enrichment panel/assay If Other, Especify" }, "amplicon_version": { @@ -1824,7 +1824,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Enrichment panel/assay version" }, "amplicon_size": { @@ -1834,7 +1834,7 @@ "ontology": "GENEPIO:0001449", "type": "string", "description": "The length of the amplicon generated by PCR amplification.", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Amplicon Size" }, "was_phix_used?": { @@ -1844,7 +1844,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Was Phix Used" }, "number_of_samples_in_run": { @@ -1854,7 +1854,7 @@ "ontology": "KISAO_0000326", "type": "string", "description": "", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Number Of Samples In Run" }, "flowcell_kit": { @@ -1864,7 +1864,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Flowcell Kit" }, "runID": { @@ -1874,7 +1874,7 @@ "ontology": "NCIT_C117058", "type": "string", "description": "", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Runid" }, "sequencing_platforms": { @@ -1884,7 +1884,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Sequencing Platforms " }, "library_preparation_kit": { @@ -1894,7 +1894,7 @@ "ontology": "GENEPIO:0001450", "type": "string", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Library Preparation Kit" }, "flow_cell_barcode": { @@ -1904,7 +1904,7 @@ "ontology": "GENEPIO:0001451", "type": "string", "description": "The barcode of the flow cell used for sequencing.", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Flow Cell Barcode" }, "sequencing_protocol_name": { @@ -1914,7 +1914,7 @@ "ontology": "GENEPIO:0001453", "type": "string", "description": "The name and version number of the sequencing protocol used.", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Sequencing Protocol Name" }, "sequencing_protocol": { @@ -1924,7 +1924,7 @@ "ontology": "GENEPIO:0001454", "type": "string", "description": "The protocol used to generate the sequence.", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Sequencing Protocol" }, "sequencing_kit_number": { @@ -1934,7 +1934,7 @@ "ontology": "GENEPIO:0001455", "type": "string", "description": "The manufacturer's kit number.", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Sequencing Kit Number" }, "amplicon_pcr_primer_scheme": { @@ -1944,7 +1944,7 @@ "ontology": "GENEPIO:0001456", "type": "string", "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Amplicon Pcr Primer Scheme" }, "library_selection": { @@ -1954,7 +1954,7 @@ "ontology": "GENPIO_0001940", "type": "string", "description": "Library capture method.", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Capture method" }, "library_strategy": { @@ -1986,7 +1986,7 @@ "ontology": "GENPIO_0001973", "type": "string", "description": "Overall sequencing strategy or approach.", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Sequencing technique" }, "library_layout": { @@ -1996,7 +1996,7 @@ "ontology": "NCIT:C175894", "type": "string", "description": "Single or paired.", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Library Layout" }, "library_name": { @@ -2006,7 +2006,7 @@ "ontology": "GENEPIO_0001995", "type": "string", "description": "Name of the used library", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Library Name" }, "nominal_length ": { @@ -2016,7 +2016,7 @@ "ontology": "GENEPIO_0000076", "type": "string", "description": "", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Nominal Length" }, "raw_sequence_data_processing_method": { @@ -2026,7 +2026,7 @@ "ontology": "GENEPIO:0001458", "type": "string", "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Raw sequence data processin method" }, "dehosting_method": { @@ -2036,7 +2036,7 @@ "ontology": "GENEPIO:0001459", "type": "string", "description": "The method used to remove host reads from the pathogen sequence.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Dehosting Method" }, "personal_protective_equipment": { @@ -2046,7 +2046,7 @@ "ontology": "NCIT:C173748", "type": "string", "description": "Use of personal protective equipment, such as gloves, gowns, during any type of exposure.", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Personal protective equipment" }, "assembly": { @@ -2056,7 +2056,7 @@ "ontology": "NCIT_C63548", "type": "string", "description": "", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Assembly" }, "if_assembly_other": { @@ -2066,7 +2066,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "If assembly Is Other, Specify" }, "assembly_params": { @@ -2076,7 +2076,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Assambly params" }, "variant_calling": { @@ -2086,7 +2086,7 @@ "ontology": "operation_3227", "type": "string", "description": "", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Variant Calling" }, "if_variant_calling_other": { @@ -2096,7 +2096,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "If variant calling Is Other, Specify" }, "variant_calling_params": { @@ -2106,7 +2106,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Variant Calling params" }, "consensus_sequence_name": { @@ -2134,7 +2134,7 @@ "ontology": "GENEPIO:0001462", "type": "string", "description": "The filepath of the consesnsus sequence file.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Consensus sequence filepath" }, "consensus_sequence_software_name": { @@ -2144,7 +2144,7 @@ "ontology": "GENEPIO:0001463", "type": "string", "description": "The name of software used to generate the consensus sequence.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Consensus sequence software name" }, "if_consensus_other": { @@ -2154,7 +2154,7 @@ "ontology": "0", "type": "string", "description": "The version of the software used to generate the consensus sequence.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "If consensus Is Other, Specify" }, "consensus_sequence_software_version": { @@ -2164,7 +2164,7 @@ "ontology": "GENEPIO:0001469", "type": "string", "description": "The version of the software used to generate the consensus sequence.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Consensus sequence software version" }, "consensus_criteria": { @@ -2174,7 +2174,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Consensus criteria" }, "quality_control_metrics": { @@ -2184,7 +2184,7 @@ "ontology": "data_3914", "type": "string", "description": "", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Quality control metrics " }, "breadth_of_coverage_value": { @@ -2194,7 +2194,7 @@ "ontology": "GENEPIO:0001472", "type": "string", "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Breadth of coverage value" }, "depth_of_coverage_value": { @@ -2204,7 +2204,7 @@ "ontology": "GENEPIO:0001474", "type": "string", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Depth of coverage value " }, "depth_of_coverage_threshold": { @@ -2214,7 +2214,7 @@ "ontology": "GENEPIO:0001475", "type": "string", "description": "The threshold used as a cut-off for the depth of coverage.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Depth of coverage threshold" }, "sequence_file_R1_fastq": { @@ -2224,7 +2224,7 @@ "ontology": "GENEPIO:0001476", "type": "string", "description": "The user-specified filename of the r1 FASTQ file.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Sequence file R1 fastq" }, "sequence_file_R2_fastq": { @@ -2234,7 +2234,7 @@ "ontology": "GENEPIO:0001477", "type": "string", "description": "The user-specified filename of the r2 FASTQ file.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Sequence file R2 fastq" }, "r1_fastq_filepath": { @@ -2244,7 +2244,7 @@ "ontology": "GENEPIO:0001478", "type": "string", "description": "The filepath of the r1 FASTQ file.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Filepath R1 fastq" }, "r2_fastq_filepath": { @@ -2254,7 +2254,7 @@ "ontology": "GENEPIO:0001479", "type": "string", "description": "The filepath of the r2 FASTQ file.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Filepath R2 fastq" }, "fast5_filename": { @@ -2264,7 +2264,7 @@ "ontology": "GENEPIO:0001480", "type": "string", "description": "The user-specified filename of the FAST5 file.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Filename fast5" }, "fast5_filepath": { @@ -2274,7 +2274,7 @@ "ontology": "GENEPIO:0001481", "type": "string", "description": "The filepath of the FAST5 file.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Filepath fast5" }, "number_of_base_pairs_sequenced": { @@ -2284,7 +2284,7 @@ "ontology": "GENEPIO:0001482", "type": "string", "description": "The number of total base pairs generated by the sequencing process.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Number of base pairs sequenced " }, "consensus_genome_length": { @@ -2294,7 +2294,7 @@ "ontology": "GENEPIO:0001483", "type": "string", "description": "Size of the assembled genome described as the number of base pairs.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Consensus genome length" }, "ns_per_100_kbp": { @@ -2304,7 +2304,7 @@ "ontology": "GENEPIO:0001484", "type": "string", "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Ns per 100 kbp" }, "reference_genome_accession": { @@ -2314,7 +2314,7 @@ "ontology": "GENEPIO:0001485", "type": "string", "description": "A persistent, unique identifier of a genome database entry.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Reference genome accession" }, "bioinformatics_protocol": { @@ -2324,7 +2324,7 @@ "ontology": "GENEPIO:0001489", "type": "string", "description": "The name of the bioinformatics protocol used.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Bioinformatics protocol" }, "if_bioinformatic_protocol_is_other_specify": { @@ -2334,7 +2334,7 @@ "ontology": "0", "type": "string", "description": "The name of the bioinformatics protocol used.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "If bioinformatic protocol Is Other, Specify" }, "bioinformatic_protocol_version": { @@ -2344,7 +2344,7 @@ "ontology": "NCIT:C93490", "type": "string", "description": "The version number of the bioinformatics protocol used.", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "bioinformatics protocol version" }, "commercial/open-source/both": { @@ -2354,7 +2354,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Commercial/Open-source/both" }, "sample_plan_name": { @@ -2373,7 +2373,7 @@ "ontology": "MS_1002386", "type": "string", "description": "", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Preprocessing" }, "if_preprocessing_other": { @@ -2383,7 +2383,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "If preprocessing Is Other, Specify" }, "preprocessing_params": { @@ -2393,7 +2393,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics", "label": "Preprocessing params" }, "mapping": { @@ -2403,7 +2403,7 @@ "ontology": "topic:0102", "type": "string", "description": "", - "clasification": "Lineage and Variant information", + "classification": "Lineage and Variant information", "label": "Mapping" }, "if_mapping_other": { @@ -2413,7 +2413,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Lineage and Variant information", + "classification": "Lineage and Variant information", "label": "If mapping Is Other, Specify" }, "mapping_params": { @@ -2423,7 +2423,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Lineage and Variant information", + "classification": "Lineage and Variant information", "label": "Mapping params" }, "lineage/clade_name": { @@ -2433,7 +2433,7 @@ "ontology": "GENEPIO:0001500", "type": "string", "description": "The name of the lineage or clade.", - "clasification": "Lineage and Variant information", + "classification": "Lineage and Variant information", "label": "Lineage/clade name" }, "lineage/clade_analysis_software_name": { @@ -2443,7 +2443,7 @@ "ontology": "GENEPIO:0001501", "type": "string", "description": "The name of the software used to determine the lineage/clade.", - "clasification": "Lineage and Variant information", + "classification": "Lineage and Variant information", "label": "lineage/clade analysis software name" }, "if_lineage_identification_other": { @@ -2453,7 +2453,7 @@ "ontology": "0", "type": "string", "description": "The name of the software used to determine the lineage/clade.", - "clasification": "Lineage and Variant information", + "classification": "Lineage and Variant information", "label": "If lineage identification Is Other, Specify" }, "lineage/clade_analysis_software_version": { @@ -2463,7 +2463,7 @@ "ontology": "GENEPIO:0001502", "type": "string", "description": "The version of the software used to determine the lineage/clade.", - "clasification": "Lineage and Variant information", + "classification": "Lineage and Variant information", "label": "Lineage/clade analysis software version" }, "variant_designation": { @@ -2488,7 +2488,7 @@ "ontology": "GENEPIO:0001504", "type": "string", "description": "The evidence used to make the variant determination.", - "clasification": "Lineage and Variant information", + "classification": "Lineage and Variant information", "label": "Variant evidence" }, "gene_name_1": { @@ -2548,7 +2548,7 @@ "ontology": "CIDO_0020274", "type": "string", "description": "", - "clasification": "Pathogen diagnostic testing", + "classification": "Pathogen diagnostic testing", "label": "Protocol SARS-CoV-2 detection" }, "%qc_filtered": { @@ -2558,7 +2558,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Pathogen diagnostic testing", + "classification": "Pathogen diagnostic testing", "label": "%qc filtered" }, "%reads_host": { @@ -2568,7 +2568,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Pathogen diagnostic testing", + "classification": "Pathogen diagnostic testing", "label": "%reads host" }, "%reads_virus": { @@ -2578,7 +2578,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Pathogen diagnostic testing", + "classification": "Pathogen diagnostic testing", "label": "%reads virus" }, "%unmapped": { @@ -2588,7 +2588,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Pathogen diagnostic testing", + "classification": "Pathogen diagnostic testing", "label": "%unmapped" }, "%genome _greater_10x": { @@ -2598,7 +2598,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Pathogen diagnostic testing", + "classification": "Pathogen diagnostic testing", "label": "% genome greater 10x" }, "mean_depth_of_coverage_value": { @@ -2608,7 +2608,7 @@ "ontology": "NCIT:C167285", "type": "string", "description": "", - "clasification": "Pathogen diagnostic testing", + "classification": "Pathogen diagnostic testing", "label": "mean depth of coverage value" }, "%Ns": { @@ -2618,7 +2618,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Pathogen diagnostic testing", + "classification": "Pathogen diagnostic testing", "label": "%Ns" }, "Number_of_variants_(AF_greater_75%)": { @@ -2628,7 +2628,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Pathogen diagnostic testing", + "classification": "Pathogen diagnostic testing", "label": "Number of variants (AF greater 75%)" }, "Numer_of_variants_with_effect": { @@ -2638,7 +2638,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Pathogen diagnostic testing", + "classification": "Pathogen diagnostic testing", "label": "Numer of variants with effect" }, "diagnostic_pcr_protocol_1": { @@ -2648,7 +2648,7 @@ "ontology": "GENEPIO:0001508", "type": "string", "description": "The name and version number of the protocol used for diagnostic marker amplification.", - "clasification": "Pathogen diagnostic testing", + "classification": "Pathogen diagnostic testing", "label": "Diagnostic Pcr Protocol 1" }, "diagnostic_pcr_Ct_value_1": { @@ -2658,7 +2658,7 @@ "ontology": "GENEPIO:0001509", "type": "string", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "clasification": "Pathogen diagnostic testing", + "classification": "Pathogen diagnostic testing", "label": "Diagnostic Pcr Ct Value 1" }, "gene_name_2": { @@ -2718,7 +2718,7 @@ "ontology": "GENEPIO:0001511", "type": "string", "description": "The name and version number of the protocol used for diagnostic marker amplification.", - "clasification": "Pathogen diagnostic testing", + "classification": "Pathogen diagnostic testing", "label": "Diagnostic Pcr Protocol 2" }, "diagnostic_pcr_Ct_value_2": { @@ -2728,7 +2728,7 @@ "ontology": "GENEPIO:0001512", "type": "string", "description": "The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "clasification": "Pathogen diagnostic testing", + "classification": "Pathogen diagnostic testing", "label": "Diagnostic Pcr Ct Value-2" }, "analysis_author": { @@ -2738,7 +2738,7 @@ "ontology": "NCIT:C42781", "type": "string", "description": "", - "clasification": "Contributor Acknowledgement", + "classification": "Contributor Acknowledgement", "label": "Analysis Authors" }, "author_submitter": { @@ -2748,7 +2748,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Contributor Acknowledgement", + "classification": "Contributor Acknowledgement", "label": "Author Submitter" }, "gisaid_id": { @@ -2758,7 +2758,7 @@ "ontology": "NCIT:C54269", "type": "string", "description": "", - "clasification": "enter your GISAID-Username", + "classification": "enter your GISAID-Username", "label": "GISAID id" }, "authors": { @@ -2768,7 +2768,7 @@ "ontology": "GENEPIO:0001517", "type": "string", "description": "", - "clasification": "Contributor Acknowledgement", + "classification": "Contributor Acknowledgement", "label": "Authors" }, "common_name": { @@ -2778,7 +2778,7 @@ "ontology": "NCIT:C164471", "type": "string", "description": "The common name of the organism.", - "clasification": "Sample collection and processing" + "classification": "Sample collection and processing" }, "collector_name": { "examples": [ @@ -2787,7 +2787,7 @@ "ontology": "NCIT:C164471", "type": "string", "description": "Name of the person who collected the specimen", - "clasification": "Sample collection and processing", + "classification": "Sample collection and processing", "label": "Sample collector name", "table": "sample" }, @@ -2824,7 +2824,7 @@ "ontology": "GENEPIO_0001965", "type": "string", "description": "Molecule type used to make the library.", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Source material" }, "nominal_length": { @@ -2834,7 +2834,7 @@ "ontology": "0", "type": "string", "description": "", - "clasification": "Sequencing" + "classification": "Sequencing" }, "analysis_accession": { "examples": [ @@ -2843,7 +2843,7 @@ "ontology": "GENEPIO_0001145", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Analysis Accession" }, "study_accession": { @@ -2853,7 +2853,7 @@ "ontology": "GENEPIO_0001136", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Study accession" }, "secondary_study_accession": { @@ -2863,7 +2863,7 @@ "ontology": "BU_ISCIII:012", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Secondary study accession" }, "sample_accession": { @@ -2873,7 +2873,7 @@ "ontology": "GENEPIO_0001139", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Sample accession" }, "secondary_sample_accession": { @@ -2883,7 +2883,7 @@ "ontology": "BU_ISCIII:014", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Secondary sample accession" }, "experiment_accession": { @@ -2893,7 +2893,7 @@ "ontology": "BU_ISCIII:015", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Experiment Accession" }, "run_accession": { @@ -2903,7 +2903,7 @@ "ontology": "BU_ISCIII:016", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Run Accession" }, "submission_accession": { @@ -2913,7 +2913,7 @@ "ontology": "BU_ISCIII:017", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Submission Accession" }, "read_count": { @@ -2923,7 +2923,7 @@ "ontology": "STATO_0000064", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Read count" }, "read_length": { @@ -2933,7 +2933,7 @@ "ontology": "STATO_0000064", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Read length" }, "base_count": { @@ -2943,7 +2943,7 @@ "ontology": "UO_0000244", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Base count" }, "first_public": { @@ -2953,7 +2953,7 @@ "ontology": "NCIT_C142711", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "First Public date" }, "last_updated": { @@ -2963,7 +2963,7 @@ "ontology": "OMIABIS_0001005", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "format": "date", "label": "Last Updated" }, @@ -2974,7 +2974,7 @@ "ontology": "ORNASEQ_0000004", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Experiment title" }, "study_title": { @@ -2984,7 +2984,7 @@ "ontology": "OPMI_0000380", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Study title" }, "study_alias": { @@ -2994,7 +2994,7 @@ "ontology": "SIO_001066", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Study alias" }, "experiment_alias": { @@ -3004,7 +3004,7 @@ "ontology": "NCIT_C42790", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Experiment alias" }, "run_alias": { @@ -3014,7 +3014,7 @@ "ontology": "NCIT_C47911", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Run Alias" }, "fastq_bytes": { @@ -3024,7 +3024,7 @@ "ontology": "NCIT_C48047", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Fastq bytes" }, "fastq_md5_r1": { @@ -3034,7 +3034,7 @@ "ontology": "MS_1000568", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Fastq md5 r1" }, "fastq_md5_r2": { @@ -3044,7 +3044,7 @@ "ontology": "MS_1000568", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Fastq md5 r2" }, "fastq_ftp": { @@ -3054,7 +3054,7 @@ "ontology": "PRIDE_0000469", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Fastq ftp" }, "fastq_aspera": { @@ -3064,7 +3064,7 @@ "ontology": "BU_ISCIII:032", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Fastq aspera" }, "fastq_galaxy": { @@ -3074,7 +3074,7 @@ "ontology": "ENVO_01000807", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Fastq galaxy" }, "submitted_bytes": { @@ -3084,7 +3084,7 @@ "ontology": "NCIT_C172872", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Submitted bytes " }, "submitted_md5": { @@ -3094,7 +3094,7 @@ "ontology": "BU_ISCIII:035", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Submitted md5" }, "submitted_ftp": { @@ -3104,7 +3104,7 @@ "ontology": "BU_ISCIII:036", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Submitted ftp" }, "submitted_aspera": { @@ -3114,7 +3114,7 @@ "ontology": "BU_ISCIII:037", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Submitted aspera" }, "submitted_galaxy": { @@ -3124,7 +3124,7 @@ "ontology": "BU_ISCIII:038", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Submitted Galaxy" }, "submitted_format": { @@ -3134,7 +3134,7 @@ "ontology": "BU_ISCIII:039", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Submitted Format" }, "sra_bytes": { @@ -3144,7 +3144,7 @@ "ontology": "BU_ISCIII:040", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "SRA bytes" }, "sra_md5": { @@ -3154,7 +3154,7 @@ "ontology": "BU_ISCIII:041", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "SRA md5" }, "sra_ftp": { @@ -3164,7 +3164,7 @@ "ontology": "BU_ISCIII:042", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "SRA ftp" }, "sra_aspera": { @@ -3174,7 +3174,7 @@ "ontology": "BU_ISCIII:043", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "SRA aspera" }, "sra_galaxy": { @@ -3184,7 +3184,7 @@ "ontology": "BU_ISCIII:044", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "SRA galaxy" }, "broker_name": { @@ -3194,7 +3194,7 @@ "ontology": "BU_ISCIII:045", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Broker Name" }, "nominal_sdev": { @@ -3204,7 +3204,7 @@ "ontology": "STATO_0000237", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Nominal sdev" }, "first_created_date": { @@ -3215,7 +3215,7 @@ "type": "string", "format": "date", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "First created date" }, "type": { @@ -3225,7 +3225,7 @@ "ontology": "NCIT:C25284", "type": "string", "description": "default must remain 'betacoronavirus'", - "clasification": "Database Identifiers" + "classification": "Database Identifiers" } } } \ No newline at end of file From 1d497c92787c6ca8689f8021f53506ed0e7daac7 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 6 Apr 2022 15:33:31 +0200 Subject: [PATCH 0287/1454] removed library name and insert size --- relecov_tools/schema/relecov_schema.json | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 5ce188e8..0d241846 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1999,16 +1999,6 @@ "classification": "Sequencing", "label": "Library Layout" }, - "library_name": { - "examples": [ - "P17157_1007" - ], - "ontology": "GENEPIO_0001995", - "type": "string", - "description": "Name of the used library", - "classification": "Sequencing", - "label": "Library Name" - }, "nominal_length ": { "examples": [ "350" From 24e0a89421407a59622c30638aca31ceee68b7f2 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 6 Apr 2022 15:36:40 +0200 Subject: [PATCH 0288/1454] added analysis and lineage date --- relecov_tools/schema/relecov_schema.json | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 0d241846..5846f4ce 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2711,6 +2711,28 @@ "classification": "Pathogen diagnostic testing", "label": "Diagnostic Pcr Protocol 2" }, + "analysis_date": { + "examples": [ + "" + ], + "ontology": "0", + "type": "date", + "format": "date", + "description": "", + "classification": "Bioinformatics and QC metrics", + "label": "Analysis date" + }, + "lineage_identification_date": { + "examples": [ + "" + ], + "ontology": "0", + "type": "date", + "format": "date", + "description": "", + "classification": "Bioinformatics and QC metrics", + "label": "Lineage identification date" + }, "diagnostic_pcr_Ct_value_2": { "examples": [ "36" From 9f09f65926949d2f7c2898fd78c8a3de5f697daa Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 6 Apr 2022 15:55:16 +0200 Subject: [PATCH 0289/1454] Required fields for creating files to ENA are set in required --- relecov_tools/schema/ena_schema.json | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 129e15eb..dae74691 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -17,7 +17,12 @@ "library_source", "library_selection", "library_strategy", - "library_layout" + "library_layout", + "study_alias", + "experiment_alias", + "run_alias", + "experiment_title", + "study_title" ], "type": "object", "properties": { @@ -1452,4 +1457,4 @@ "label": "First created date" } } -} \ No newline at end of file +} From 59422bef56f0688b0cb3ef18d8f756cedbb64a1e Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 6 Apr 2022 15:56:42 +0200 Subject: [PATCH 0290/1454] checking result mapping --- relecov_tools/map_schema.py | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index dbcc399b..0367053a 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -29,7 +29,7 @@ def __init__( json_file=None, destination_schema=None, schema_file=None, - output=None, + output_folder=None, ): config_json = ConfigJson() if relecov_schema is None: @@ -65,7 +65,7 @@ def __init__( stderr.print(f"[red] json data file {json_file} does not exist") sys.exit(1) self.json_data = relecov_tools.utils.read_json_file(json_file) - + self.json_file = json_file if destination_schema is None: self.destination_schema = relecov_tools.utils.prompt_selection( msg="Select ENA, GISAID for already defined schemas or other for custom", @@ -116,6 +116,7 @@ def __init__( self.ontology = {} for key, values in self.relecov_schema["properties"].items(): self.ontology[values["ontology"]] = key + self.output_folder = output_folder def maping_schemas_based_on_geontology(self): """Return a dictionnary with the properties of the mapped_to_schema as key and @@ -129,6 +130,7 @@ def maping_schemas_based_on_geontology(self): # There is no exact match on ontology. Search for the parent # to be implemented later stderr.print(f"[red] Ontology value {e} not in phage plus schema") + import pdb; pdb.set_trace() return mapped_dict def mapping_json_data(self, mapping_schema_dict): @@ -141,6 +143,7 @@ def mapping_json_data(self, mapping_schema_dict): try: map_sample_dict[item] = data[value] except KeyError as e: + log.warning("Property %s not set in the source data", e) print(e) mapped_data.append(map_sample_dict) return mapped_data @@ -149,11 +152,11 @@ def write_json_fo_file(self, mapped_json_data): """Write metadata to json file""" os.makedirs(self.output_folder, exist_ok=True) time = datetime.now().strftime("%Y_%m_%d_%H_%M") - f_sub_name = os.path.basename(self.json_data).split(".")[0] - file_name = f_sub_name + "_" + time + "_ena_mapped.json" + f_sub_name = os.path.basename(self.json_file).split(".")[0] + file_name = f_sub_name + "_" + time + "_" + self.destination_schema + "_mapped.json" json_file = os.path.join(self.output_folder, file_name) - with open(json_file, "w") as fh: - fh.write(json.dumps(mapped_json_data)) + with open(json_file, "w", encoding="utf-8") as fh: + fh.write(json.dumps(mapped_json_data, indent=4, sort_keys=True, ensure_ascii=False)) return True def map_to_data_to_new_schema(self): @@ -161,3 +164,4 @@ def map_to_data_to_new_schema(self): mapping_schema_dict = self.maping_schemas_based_on_geontology() mapped_json_data = self.mapping_json_data(mapping_schema_dict) self.write_json_fo_file(mapped_json_data) + return From d6a74e97bbd73988cec49c867f20ca9ef317399c Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 6 Apr 2022 17:40:50 +0200 Subject: [PATCH 0291/1454] update METADATA test and include file for testing --- .../example_data/METADATA_LAB_TEST.xlsx | Bin 492337 -> 495600 bytes relecov_tools/test/test_cases.txt | 4 ++++ 2 files changed, 4 insertions(+) create mode 100644 relecov_tools/test/test_cases.txt diff --git a/relecov_tools/example_data/METADATA_LAB_TEST.xlsx 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/dev/null +++ b/relecov_tools/test/test_cases.txt @@ -0,0 +1,4 @@ + +read-metadata -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -s relecov_toold/example_data/samples_data_COD_test_01_20220330.json -o /tmp +relecov-tools validate -j relecov_tools/example_data/invalid_METADATA_LAB_TEST.json -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx +relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -o /tmp From 6602984295cfe0d58a69b827d4bc1364fc13938f Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 6 Apr 2022 17:46:26 +0200 Subject: [PATCH 0292/1454] Update schema and configuration for mapping to ENA --- relecov_tools/conf/configuration.json | 1 + relecov_tools/map_schema.py | 2 ++ relecov_tools/schema/ena_schema.json | 23 ++++++++++++++++++----- 3 files changed, 21 insertions(+), 5 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 4cd3fa9b..1eb337d2 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -19,6 +19,7 @@ "geo_location_data" : "geo_loc_cities.json", "ENA_configuration": { "study_alias": "RELECOV", + "design_description":"Design Description", "experiment_alias": "", "run_alias": "", "experiment_title": "Example project for ENA submission RELECOV", diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 0367053a..6a7b7d86 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -115,6 +115,8 @@ def __init__( self.ontology = {} for key, values in self.relecov_schema["properties"].items(): + if values["ontology"] == "0": + continue self.ontology[values["ontology"]] = key self.output_folder = output_folder diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index dae74691..679c91fb 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -772,11 +772,24 @@ "runs" ] }, - "file_checksum": { + "fastq_md5_r1": { "examples": [ "3e69af1f875fab020aed82f5edbc1f03" ], - "ontology": "0", + "ontology": "MS_1000568", + "type": "string", + "description": "", + "clasification": "Bioinformatics and QC metrics", + "label": "file checksum", + "table": [ + "runs" + ] + }, + "fastq_md5_r2": { + "examples": [ + "3e69af1f875fab020aed82f5edbc1f03" + ], + "ontology": "MS_1000568", "type": "string", "description": "", "clasification": "Bioinformatics and QC metrics", @@ -1143,7 +1156,7 @@ "examples": [ "experiment_title_1" ], - "ontology": "0", + "ontology": "ORNASEQ_0000004", "type": "string", "description": "", "clasification": "Submission ENA", @@ -1182,7 +1195,7 @@ "examples": [ "" ], - "ontology": "0", + "ontology": "OPMI_0000380", "type": "string", "description": "", "clasification": "Submission ENA", @@ -1233,7 +1246,7 @@ "examples": [ "experiment_alias_7a" ], - "ontology": "0", + "ontology": "NCIT_C42790", "type": "string", "description": "", "clasification": "Submission ENA", From 0cb9eecfadbe705c10a0ba2fb49e9ea4f9cd3c2c Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 6 Apr 2022 18:09:01 +0200 Subject: [PATCH 0293/1454] fixed bug for printing keyerror --- relecov_tools/read_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 914c3cee..6f92f68d 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -258,7 +258,7 @@ def read_metadata_file(self): row[idx] if row[idx] else "" ) except KeyError as e: - stderr.print("[red] Error when reading " + row[2] + e) + stderr.print("[red] Error when reading " + str(row[2]) + str(e)) metadata_values.append(sample_data_row) return metadata_values, errors From 999268be22bdfbc5f35470bf17712ce75af80489 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 6 Apr 2022 18:09:22 +0200 Subject: [PATCH 0294/1454] update test --- relecov_tools/test/test_cases.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/test/test_cases.txt b/relecov_tools/test/test_cases.txt index 37d93062..804e7e61 100644 --- a/relecov_tools/test/test_cases.txt +++ b/relecov_tools/test/test_cases.txt @@ -1,4 +1,4 @@ -read-metadata -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -s relecov_toold/example_data/samples_data_COD_test_01_20220330.json -o /tmp +relecov-tools read-metadata -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -s relecov_tools/example_data/samples_data_COD_test_01_20220330.json -o /tmp relecov-tools validate -j relecov_tools/example_data/invalid_METADATA_LAB_TEST.json -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -o /tmp From e01c0b1b3c4ed233fe8b60b3d3aecbfb71f5f00a Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 6 Apr 2022 23:07:07 +0200 Subject: [PATCH 0295/1454] Remove the xslx extension in the ouput json --- relecov_tools/read_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 6f92f68d..8e60206c 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -316,6 +316,6 @@ def create_metadata_json(self): else: log.error("There is missing samples in metadata and/or uploaded") """ - file_name = "processed_" + os.path.basename(self.metadata_file) + ".json" + file_name = "processed_" + os.path.splitext(os.path.basename(self.metadata_file))[0] + ".json" self.write_json_fo_file(completed_metadata, file_name) return True From ead87e238edfc6453c95f88dee5847d14fe33ddb Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 6 Apr 2022 23:07:32 +0200 Subject: [PATCH 0296/1454] Remove the xslx extension in the ouput json --- relecov_tools/read_metadata.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 8e60206c..1b201fc8 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -258,7 +258,9 @@ def read_metadata_file(self): row[idx] if row[idx] else "" ) except KeyError as e: - stderr.print("[red] Error when reading " + str(row[2]) + str(e)) + stderr.print( + "[red] Error when reading " + str(row[2]) + str(e) + ) metadata_values.append(sample_data_row) return metadata_values, errors @@ -316,6 +318,10 @@ def create_metadata_json(self): else: log.error("There is missing samples in metadata and/or uploaded") """ - file_name = "processed_" + os.path.splitext(os.path.basename(self.metadata_file))[0] + ".json" + file_name = ( + "processed_" + + os.path.splitext(os.path.basename(self.metadata_file))[0] + + ".json" + ) self.write_json_fo_file(completed_metadata, file_name) return True From 1cb0129ee6e9718168f9b3cd66e14f440bf5b833 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 6 Apr 2022 23:08:26 +0200 Subject: [PATCH 0297/1454] Update the testing files with new changes --- 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    " + ], "text/plain": [ - "['Collecting Sample id',\n", - " 'Originating Laboratory',\n", - " 'Submitting Institution',\n", - " 'Sample Collection Date',\n", - " 'geo_loc_country',\n", - " 'geo_loc_state',\n", - " 'organism',\n", - " 'isolate',\n", - " 'host_scientific_name',\n", - " 'Host Common Name',\n", - " 'host_disease',\n", - " 'Sequencing Instrument Model',\n", - " 'Sequencing Platforms',\n", - " 'consensus_sequence_software_name',\n", - " 'consensus_sequence_software_version',\n", - " 'file_name',\n", - " 'tax_id',\n", - " 'sample_description',\n", - " 'Library Source',\n", - " 'Library Selection',\n", - " 'Library Strategy',\n", - " 'Library Layout',\n", - " 'type',\n", - " 'GISAID Virus Name',\n", - " 'GISAID Id',\n", - " 'Originating Laboratory Address']" + " collection_date common_name experiment_alias \\\n", + "0 2021/04/13 PEPITO \n", + "\n", + " experiment_title \\\n", + "0 Example project for ENA submission RELECOV \n", + "\n", + " fastq_r1_md5 fastq_r2_md5 \\\n", + "0 f2facbd1d6c7e0972074ced31ccbfd8e fd9948be8da7a38b0f80659dfc21aeea \n", + "\n", + " geographic location (latitude) geographic location (longitude) \\\n", + "0 41.6483 -0.8830 \n", + "\n", + " geographic_location_(country_and/or_sea) host_common_name ... \\\n", + "0 Spain Human ... \n", + "\n", + " sample_description sample_name sample_storage_conditions \\\n", + "0 Sample for surveillance 1197860 -80ºC \n", + "\n", + " scientific_name \\\n", + "0 Severe acute respiratory syndrome coronavirus 2 \n", + "\n", + " sequence_file_R1_fastq sequence_file_R2_fastq study_alias \\\n", + "0 ABC123_S1_L001_R1_001.fastq.gz ABC123_S1_L001_R2_001.fastq.gz RELECOV \n", + "\n", + " study_title \\\n", + "0 RELECOV Spanish Network for genomics surveillance \n", + "\n", + " study_type tax_id \n", + "0 RELECOV Spanish Network for genomics surveillance 2697049 \n", + "\n", + "[1 rows x 36 columns]" ] }, - "execution_count": 27, + "execution_count": 25, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "heading" + "df1_transposed = df.T\n", + "df1_transposed" ] }, { "cell_type": "code", - "execution_count": null, - "id": "b212e5ee", - "metadata": {}, - "outputs": [], - "source": [ - " 'sample_name',\n", - " 'collecting_institution',\n", - " 'submitting_institution',\n", - "'sample_collection_date',\n", - " 'geo_loc_country',\n", - " 'geo_loc_state',\n", - " 'organism',\n", - " 'isolate',\n", - " 'host_scientific_name',\n", - " 'host_common_name',\n", - " 'host_disease',\n", - " 'sequencing_instrument_model',\n", - " 'sequencing_instrument_platform',\n", - " 'consensus_sequence_software_name',\n", - " 'consensus_sequence_software_version',\n", - " 'file_name',\n", - " 'tax_id',\n", - " 'sample_description',\n", - " 'library_source',\n", - " 'library_selection',\n", - " 'library_strategy',\n", - " 'library_layout',\n", - " 'type',\n", - " 'virus_name',\n", - " 'submitter',\n", - " 'collecting_institution_address'],\n" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "697682c3", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "prueba.py pruebas.ipynb to_ena.json\r\n" - ] - } - ], - "source": [ - "ls" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "id": "3124de94", + "execution_count": 26, + "id": "0817f87d", "metadata": {}, "outputs": [], "source": [ - "d = {'collecting_institution': 'Hospital Universitario de Basurto',\n", - "'collecting_institution_address': 'Avda. Montevideo, 18,Bilbao,Vizcaya, ',\n", - "'consensus_sequence_software_name': 'CLC Genomics Workbench 12',\n", - "'consensus_sequence_software_version': '. CLC Genomics Workbench 12,',\n", - "'file_name': 'filename2',\n", - "'geo_loc_country': 'Spain',\n", - "'geo_loc_state': 'Madrid',\n", - "'host_common_name': 'Human',\n", - "'host_disease': 'SARS-CoV2',\n", - "'host_scientific_name': 'Homo sapiens',\n", - "'isolate': 'SARS-CoV-2/human/USA/CA-CDPH-001/2020',\n", - "'library_layout': 'PAIRED',\n", - "'library_selection': 'RANDOM PCR',\n", - "'library_source': 'METAGENOMIC',\n", - "'library_strategy': 'WGS',\n", - "'organism': 'Severe acute respiratory syndrome coronavirus 2',\n", - "'sample_description': 'madnatory ENA description sample',\n", - "'sample_name': 'ID_001',\n", - "'sequencing_instrument_model': 'Illumina MiSeq',\n", - "'sequencing_instrument_platform': 'ILLUMINA',\n", - "'submitter': 'GISAID-Username',\n", - "'submitting_institution': 'Laboratorio de Microbiología de Bibao ',\n", - "'tax_id': 2697049,\n", - "'type': 'betacoronavirus',\n", - "'virus_name': 'hCoV-19/España/Vizcaya-01/2020'}\n", - "\n" + "df_study = df1_transposed[[\"study_alias\",\"study_title\",\"study_type\"]]" ] }, { "cell_type": "code", - "execution_count": 2, - "id": "5c390e91", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'collecting_institution': 'Hospital Universitario de Basurto',\n", - " 'collecting_institution_address': 'Avda. Montevideo, 18,Bilbao,Vizcaya, ',\n", - " 'consensus_sequence_software_name': 'CLC Genomics Workbench 12',\n", - " 'consensus_sequence_software_version': '. CLC Genomics Workbench 12,',\n", - " 'file_name': 'filename2',\n", - " 'geo_loc_country': 'Spain',\n", - " 'geo_loc_state': 'Madrid',\n", - " 'host_common_name': 'Human',\n", - " 'host_disease': 'SARS-CoV2',\n", - " 'host_scientific_name': 'Homo sapiens',\n", - " 'isolate': 'SARS-CoV-2/human/USA/CA-CDPH-001/2020',\n", - " 'library_layout': 'PAIRED',\n", - " 'library_selection': 'RANDOM PCR',\n", - " 'library_source': 'METAGENOMIC',\n", - " 'library_strategy': 'WGS',\n", - " 'organism': 'Severe acute respiratory syndrome coronavirus 2',\n", - " 'sample_description': 'madnatory ENA description sample',\n", - " 'sample_name': 'ID_001',\n", - " 'sequencing_instrument_model': 'Illumina MiSeq',\n", - " 'sequencing_instrument_platform': 'ILLUMINA',\n", - " 'submitter': 'GISAID-Username',\n", - " 'submitting_institution': 'Laboratorio de Microbiología de Bibao ',\n", - " 'tax_id': 2697049,\n", - " 'type': 'betacoronavirus',\n", - " 'virus_name': 'hCoV-19/España/Vizcaya-01/2020'}" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "d" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "id": "2939d552", + "execution_count": 27, + "id": "c8783948", "metadata": {}, "outputs": [ { "data": { + "text/html": [ + "
    \n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
    study_aliasstudy_titlestudy_type
    0RELECOVRELECOV Spanish Network for genomics surveillanceRELECOV Spanish Network for genomics surveillance
    \n", + "
    " + ], "text/plain": [ - "'/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/schema'" + " study_alias study_title \\\n", + "0 RELECOV RELECOV Spanish Network for genomics surveillance \n", + "\n", + " study_type \n", + "0 RELECOV Spanish Network for genomics surveillance " ] }, - "execution_count": 5, + "execution_count": 27, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "pwd\n" - ] - }, - { - "cell_type": "code", - "execution_count": 13, - "id": "88c37daa", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Directory xml_outout Created \n" - ] - } - ], - "source": [ - "# Create directory\n", - "import os \n", - "dirName = 'xml_outout'\n", - "try:\n", - " # Create target Directory\n", - " os.mkdir(dirName)\n", - " print(\"Directory \" , dirName , \" Created \") \n", - "except FileExistsError:\n", - " print(\"Directory \" , dirName , \" already exists\")" + "df_study \n", + "#falta study abstract y pubmed_id " ] }, { "cell_type": "code", - "execution_count": 9, - "id": "e0ff2698", + "execution_count": 28, + "id": "1a2f62ab", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "ena_v01.json mapping_metadata_json_v01.json pruebas.ipynb to_ena.json\r\n", - "genepio.owl phage_plus_V0.json sample_relecov.xml\r\n", - "gisaid_V0.json phage_V0.json small_schema.json\r\n" - ] - } - ], + "outputs": [], "source": [ - "ls\n" + "df_samples = df1_transposed[['sample_name','tax_id','sample_description','collection_date','geographic_location_(country_and/or_sea)','host_common_name','host_gender','host_scientific_name','isolate' ]]" ] }, { "cell_type": "code", "execution_count": 29, - "id": "42698e3a", + "id": "254eb9bc", "metadata": {}, "outputs": [ { "data": { + "text/html": [ + "
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    sample_nametax_idsample_descriptioncollection_dategeographic_location_(country_and/or_sea)host_common_namehost_genderhost_scientific_nameisolate
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    " + ], "text/plain": [ - "" + " sample_name tax_id sample_description collection_date \\\n", + "0 1197860 2697049 Sample for surveillance 2021/04/13 \n", + "\n", + " geographic_location_(country_and/or_sea) host_common_name host_gender \\\n", + "0 Spain Human Mujer \n", + "\n", + " host_scientific_name isolate \n", + "0 Homo Sapiens 1197860 " ] }, "execution_count": 29, @@ -626,200 +560,173 @@ } ], "source": [ - "import json as j\n", - "import xml.etree.cElementTree as e\n", - "\n", - "\n", - "with open(\"to_ena.json\") as json_format_file:\n", - " d = j.load(json_format_file)\n", - " \n", - "\n", - "data_keys = list(d.keys())\n", - "\n", - "\n", - "r = e.Element(\"SUBMISSION_SET\")\n", - "\n", - "\n", - "sample = e.SubElement(r,\"SUBMISSION\")\n", - "actions = e.SubElement(sample,'ACTIONS')\n", - "action = e.SubElement(actions,\"ACTION\")\n", - "\n", - "e.SubElement(action,\"ADD\")\n", - "\n", - "\n", - " \n", - "\n" + "df_samples\n", + "#FALTA:sample_title, host_subject_id, host_health_state, collector_name, collecting institutions\n" ] }, { "cell_type": "code", - "execution_count": 30, - "id": "8f06bf42", + "execution_count": 32, + "id": "b699c031", "metadata": {}, "outputs": [], "source": [ - "\n", - "a = e.ElementTree(r)\n", - "a.write(\"xml_outout/submission.xml\")" + "df_runs = df1_transposed[['experiment_alias','sequence_file_R1_fastq','sequence_file_R2_fastq']]\n", + "#FALTA: run alias, file_type, flie_checksum" ] }, { "cell_type": "code", - "execution_count": 14, - "id": "914fc897", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/schema'" - ] - }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "pwd" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "id": "b20e77ff", - "metadata": {}, - "outputs": [ - { - "ename": "SyntaxError", - "evalue": "EOL while scanning string literal (3660535544.py, line 1)", - "output_type": "error", - "traceback": [ - "\u001b[0;36m Input \u001b[0;32mIn [18]\u001b[0;36m\u001b[0m\n\u001b[0;31m xml = '\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m EOL while scanning string literal\n" - ] - } - ], - "source": [ - "\n" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "id": "2e794989", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/schema'" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "import os\n", - "os.getcwd()" - ] - }, - { - "cell_type": "code", - "execution_count": 25, - "id": "5fd9f694", - "metadata": {}, - "outputs": [], - "source": [ - "os.chdir('xml_files/')" - ] - }, - { - "cell_type": "code", - "execution_count": 26, - "id": "39fb227a", + "execution_count": 33, + "id": "f44ab490", "metadata": {}, "outputs": [ { "data": { + "text/html": [ + "
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    experiment_aliassequence_file_R1_fastqsequence_file_R2_fastq
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    " + ], "text/plain": [ - "'/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/xml_files'" + " experiment_alias sequence_file_R1_fastq \\\n", + "0 ABC123_S1_L001_R1_001.fastq.gz \n", + "\n", + " sequence_file_R2_fastq \n", + "0 ABC123_S1_L001_R2_001.fastq.gz " ] }, - "execution_count": 26, + "execution_count": 33, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "os.getcwd()" + "df_runs\n" ] }, { "cell_type": "code", - "execution_count": 13, - "id": "b76abb51", + "execution_count": 35, + "id": "4e3037fd", "metadata": {}, "outputs": [], "source": [ - "import json\n", - "\n", - "conf_dict = {\n", - " \"json_schemas\": {\n", - " \"phage_plus_schema\": \"phage_plus_V0.json\",\n", - " \"ene_schema\": \"ena_v01.json\",\n", - " \"gisaid_schema\": \"gisaid_v01.json\"\n", - " },\n", - " \"mapping_metadata_json\": \"mapping_metadata_json_v01.json\",\n", - " \"additional_metadata\": \"additional_metadata_v01.json\",\n", - " \"sftp_connection\": {\n", - " \"sftp_server\": \"sftprelecov.isciii.es\",\n", - " \"sftp_port\": \"50122\"\n", - " },\n", - " \"storage_local_folder\": \"/tmp/relecov\",\n", - " \"tmp_folder_for_metadata\": \"/tmp/relecov/tmp\",\n", - " \"allowed_sample_extensions\": [\n", - " \"fastq.gz\",\n", - " \"fasta\"\n", - " ],\n", - " \"project_relecov_xml\": {\n", - " \"alias\": \"RELECOV\",\n", - " \"TITLE\": \"Example project for ENA submission RELECOV\",\n", - " \"DESCRIPTION\": \"This study was created as part of an ENA submissions example RELECOV\"\n", - " }\n", - "}\n", - "\n", - "\n", - "\n", - "\n" + "df_runs = df1_transposed[['experiment_alias','study_title','sample_name','library_strategy', 'library_source','library_selection', 'library_layout', 'instrument_platform', 'instrument_model']]\n", + "#FALTA: sample alias lo he llamado sample name\n", + "#FALTA platform lo he llamado instrument_platform\n", + "#FALTA: design_description, library_name, 'insert_size', library_construction_protocol ,'experiemnt_title'\n" ] }, { "cell_type": "code", - "execution_count": 17, - "id": "74cfbcea", + "execution_count": 36, + "id": "18fe6ccc", "metadata": {}, "outputs": [ { "data": { + "text/html": [ + "
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    experiment_aliasstudy_titlesample_namelibrary_strategylibrary_sourcelibrary_selectionlibrary_layoutinstrument_platforminstrument_model
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    " + ], "text/plain": [ - "'RELECOV'" + " experiment_alias study_title \\\n", + "0 RELECOV Spanish Network for genomics surveillance \n", + "\n", + " sample_name library_strategy library_source library_selection \\\n", + "0 1197860 WGS strategy RNA RT-PCR \n", + "\n", + " library_layout instrument_platform instrument_model \n", + "0 Single End Illumina Illumina MiSeq " ] }, - "execution_count": 17, + "execution_count": 36, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "conf_dict[\"project_relecov_xml\"][\"alias\"]\n" + "df_runs" ] }, { "cell_type": "code", "execution_count": null, - "id": "d13efc61", + "id": "a649c726", "metadata": {}, "outputs": [], "source": [] From e98d2cf9ab710730553719d6bb20bd8ff02171db Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 12 Apr 2022 13:03:15 +0200 Subject: [PATCH 0327/1454] removed jupyter notebooks for trials --- relecov_tools/test/pruebas.ipynb | 756 ------------------------------- relecov_tools/test/try_01.ipynb | 261 ----------- 2 files changed, 1017 deletions(-) delete mode 100644 relecov_tools/test/pruebas.ipynb delete mode 100644 relecov_tools/test/try_01.ipynb diff --git a/relecov_tools/test/pruebas.ipynb b/relecov_tools/test/pruebas.ipynb deleted file mode 100644 index f3727b96..00000000 --- a/relecov_tools/test/pruebas.ipynb +++ /dev/null @@ -1,756 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "id": "ca2ef1c4", - "metadata": {}, - "outputs": [], - "source": [ - "esquema_json = {'collection_date': '2021/04/13', 'common_name': 'PEPITO', 'experiment_alias': '', 'experiment_title': 'Example project for ENA submission RELECOV', 'fastq_r1_md5': 'f2facbd1d6c7e0972074ced31ccbfd8e', 'fastq_r2_md5': 'fd9948be8da7a38b0f80659dfc21aeea', 'geographic location (latitude)': '41.6483', 'geographic location (longitude)': '-0.8830', 'geographic_location_(country_and/or_sea)': 'Spain', 'host_common_name': 'Human', 'host_gender': 'Mujer', 'host_scientific_name': 'Homo Sapiens', 'instrument_model': 'Illumina MiSeq', 'instrument_platform': 'Illumina', 'isolate': '1197860', 'isolation source host-associated': 'Nasopharynx aspirate', 'isolation source non-host-associated': 'Other', 'library_layout': 'Single End', 'library_selection': 'RT-PCR', 'library_source': 'RNA', 'library_strategy': 'WGS strategy', 'purpose_sampling': 'Surveillance', 'r1_fastq_filepath': '/tmp/relecov/COD_test_01/20220408', 'r2_fastq_filepath': '/tmp/relecov/COD_test_01/20220408', 'receipt_date': '2021/05/13', 'run_alias': '', 'sample_description': 'Sample for surveillance', 'sample_name': '1197860', 'sample_storage_conditions': ' -80ºC', 'scientific_name': 'Severe acute respiratory syndrome coronavirus 2', 'sequence_file_R1_fastq': 'ABC123_S1_L001_R1_001.fastq.gz', 'sequence_file_R2_fastq': 'ABC123_S1_L001_R2_001.fastq.gz', 'study_alias': 'RELECOV', 'study_title': 'RELECOV Spanish Network for genomics surveillance', 'study_type': 'RELECOV Spanish Network for genomics surveillance', 'tax_id': '2697049'}\n" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "226a90e0", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'collection_date': '2021/04/13',\n", - " 'common_name': 'PEPITO',\n", - " 'experiment_alias': '',\n", - " 'experiment_title': 'Example project for ENA submission RELECOV',\n", - " 'fastq_r1_md5': 'f2facbd1d6c7e0972074ced31ccbfd8e',\n", - " 'fastq_r2_md5': 'fd9948be8da7a38b0f80659dfc21aeea',\n", - " 'geographic location (latitude)': '41.6483',\n", - " 'geographic location (longitude)': '-0.8830',\n", - " 'geographic_location_(country_and/or_sea)': 'Spain',\n", - " 'host_common_name': 'Human',\n", - " 'host_gender': 'Mujer',\n", - " 'host_scientific_name': 'Homo Sapiens',\n", - " 'instrument_model': 'Illumina MiSeq',\n", - " 'instrument_platform': 'Illumina',\n", - " 'isolate': '1197860',\n", - " 'isolation source host-associated': 'Nasopharynx aspirate',\n", - " 'isolation source non-host-associated': 'Other',\n", - " 'library_layout': 'Single End',\n", - " 'library_selection': 'RT-PCR',\n", - " 'library_source': 'RNA',\n", - " 'library_strategy': 'WGS strategy',\n", - " 'purpose_sampling': 'Surveillance',\n", - " 'r1_fastq_filepath': '/tmp/relecov/COD_test_01/20220408',\n", - " 'r2_fastq_filepath': '/tmp/relecov/COD_test_01/20220408',\n", - " 'receipt_date': '2021/05/13',\n", - " 'run_alias': '',\n", - " 'sample_description': 'Sample for surveillance',\n", - " 'sample_name': '1197860',\n", - " 'sample_storage_conditions': ' -80ºC',\n", - " 'scientific_name': 'Severe acute respiratory syndrome coronavirus 2',\n", - " 'sequence_file_R1_fastq': 'ABC123_S1_L001_R1_001.fastq.gz',\n", - " 'sequence_file_R2_fastq': 'ABC123_S1_L001_R2_001.fastq.gz',\n", - " 'study_alias': 'RELECOV',\n", - " 'study_title': 'RELECOV Spanish Network for genomics surveillance',\n", - " 'study_type': 'RELECOV Spanish Network for genomics surveillance',\n", - " 'tax_id': '2697049'}" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "esquema_json" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "id": "be0cb85c", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "dict_keys(['collection_date', 'common_name', 'experiment_alias', 'experiment_title', 'fastq_r1_md5', 'fastq_r2_md5', 'geographic location (latitude)', 'geographic location (longitude)', 'geographic_location_(country_and/or_sea)', 'host_common_name', 'host_gender', 'host_scientific_name', 'instrument_model', 'instrument_platform', 'isolate', 'isolation source host-associated', 'isolation source non-host-associated', 'library_layout', 'library_selection', 'library_source', 'library_strategy', 'purpose_sampling', 'r1_fastq_filepath', 'r2_fastq_filepath', 'receipt_date', 'run_alias', 'sample_description', 'sample_name', 'sample_storage_conditions', 'scientific_name', 'sequence_file_R1_fastq', 'sequence_file_R2_fastq', 'study_alias', 'study_title', 'study_type', 'tax_id'])" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "esquema_json.keys()" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "id": "8d390edf", - "metadata": {}, - "outputs": [], - "source": [ - "llaves = list(esquema_json.keys())" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "id": "ec640155", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['collection_date',\n", - " 'common_name',\n", - " 'experiment_alias',\n", - " 'experiment_title',\n", - " 'fastq_r1_md5',\n", - " 'fastq_r2_md5',\n", - " 'geographic location (latitude)',\n", - " 'geographic location (longitude)',\n", - " 'geographic_location_(country_and/or_sea)',\n", - " 'host_common_name',\n", - " 'host_gender',\n", - " 'host_scientific_name',\n", - " 'instrument_model',\n", - " 'instrument_platform',\n", - " 'isolate',\n", - " 'isolation source host-associated',\n", - " 'isolation source non-host-associated',\n", - " 'library_layout',\n", - " 'library_selection',\n", - " 'library_source',\n", - " 'library_strategy',\n", - " 'purpose_sampling',\n", - " 'r1_fastq_filepath',\n", - " 'r2_fastq_filepath',\n", - " 'receipt_date',\n", - " 'run_alias',\n", - " 'sample_description',\n", - " 'sample_name',\n", - " 'sample_storage_conditions',\n", - " 'scientific_name',\n", - " 'sequence_file_R1_fastq',\n", - " 'sequence_file_R2_fastq',\n", - " 'study_alias',\n", - " 'study_title',\n", - " 'study_type',\n", - " 'tax_id']" - ] - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "llaves" - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "id": "85d6577f", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "collection_date\n", - "common_name\n", - "experiment_alias\n", - "experiment_title\n", - "fastq_r1_md5\n", - "fastq_r2_md5\n", - "geographic location (latitude)\n", - "geographic location (longitude)\n", - "geographic_location_(country_and/or_sea)\n", - "host_common_name\n", - "host_gender\n", - "host_scientific_name\n", - "instrument_model\n", - "instrument_platform\n", - "isolate\n", - "isolation source host-associated\n", - "isolation source non-host-associated\n", - "library_layout\n", - "library_selection\n", - "library_source\n", - "library_strategy\n", - "purpose_sampling\n", - "r1_fastq_filepath\n", - "r2_fastq_filepath\n", - "receipt_date\n", - "run_alias\n", - "sample_description\n", - "sample_name\n", - "sample_storage_conditions\n", - "scientific_name\n", - "sequence_file_R1_fastq\n", - "sequence_file_R2_fastq\n", - "study_alias\n", - "study_title\n", - "study_type\n", - "tax_id\n" - ] - } - ], - "source": [ - "for key, value in esquema_json.items():\n", - " print (key)" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "id": "961f966c", - "metadata": {}, - "outputs": [], - "source": [ - "import pandas as pd" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "id": "04bb5f74", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['collection_date',\n", - " 'common_name',\n", - " 'experiment_alias',\n", - " 'experiment_title',\n", - " 'fastq_r1_md5',\n", - " 'fastq_r2_md5',\n", - " 'geographic location (latitude)',\n", - " 'geographic location (longitude)',\n", - " 'geographic_location_(country_and/or_sea)',\n", - " 'host_common_name',\n", - " 'host_gender',\n", - " 'host_scientific_name',\n", - " 'instrument_model',\n", - " 'instrument_platform',\n", - " 'isolate',\n", - " 'isolation source host-associated',\n", - " 'isolation source non-host-associated',\n", - " 'library_layout',\n", - " 'library_selection',\n", - " 'library_source',\n", - " 'library_strategy',\n", - " 'purpose_sampling',\n", - " 'r1_fastq_filepath',\n", - " 'r2_fastq_filepath',\n", - " 'receipt_date',\n", - " 'run_alias',\n", - " 'sample_description',\n", - " 'sample_name',\n", - " 'sample_storage_conditions',\n", - " 'scientific_name',\n", - " 'sequence_file_R1_fastq',\n", - " 'sequence_file_R2_fastq',\n", - 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    " - ], - "text/plain": [ - " study\n", - "alias [study_alias_4, study_alias_5]" - ] - }, - "execution_count": 26, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "df" - ] - }, - { - "cell_type": "code", - "execution_count": 39, - "id": "95cf4dd2", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "(2,)" - ] - }, - "execution_count": 39, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lista = data[\"study\"][\"alias\"]\n", - "import numpy as np\n", - "a = np.array(lista)\n", - "a.shape" - ] - }, - { - "cell_type": "code", - "execution_count": 40, - "id": "f1a7dcf1", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'study': {'alias': ['study_alias_4', 'study_alias_5']}}" - ] - }, - "execution_count": 40, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "data" - ] - }, - { - "cell_type": "code", - "execution_count": 52, - "id": "6f6c7f87", - "metadata": {}, - "outputs": [], - "source": [ - "import json\n", - "# load data using Python JSON module\n", - "with open('../example_data/ena_upload.json','r') as f:\n", - " data = json.loads(f.read())\n", - "\n", - "lista = data[\"study\"]\n", - "df_study = pd.DataFrame(lista, columns=['alias',\"title\",\"study_type\",\"study_abstract\",\"pubmed_id\"])\n", - "\n", - "#study_df pd.DataFrame(columns=[\"alias\"], )\n" - ] - }, - { - "cell_type": "code", - "execution_count": 53, - "id": "a8066308", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'alias': ['study_alias_4', 'study_alias_5'],\n", - " 'title': ['study_title_1', 'study_title_2'],\n", - " 'study_type': ['Transcriptome Analysis', 'RNASeq'],\n", - " 'study_abstract': ['study_abstract_1', 'study_abstract_2'],\n", - " 'pubmed_id': ['None', 'pubmed_id_2']}" - ] - }, - "execution_count": 53, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "lista" - ] - }, - { - "cell_type": "code", - "execution_count": 54, - "id": "5dcb05c6", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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3d710e506806fb10849a2e8e6b5583738c5c7068 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 13 Apr 2022 15:41:11 +0200 Subject: [PATCH 0328/1454] added changes in the labels in relecov schema and ena_upload script --- relecov_tools/ena_upload.py | 12 ++-- relecov_tools/schema/relecov_schema.json | 90 ++++++++---------------- 2 files changed, 39 insertions(+), 63 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index d482396d..bbcdac6d 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -7,6 +7,7 @@ import sys import relecov_tools.utils from relecov_tools.config_json import ConfigJson +from ena_upload.ena_upload import extract_targets log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -102,10 +103,7 @@ def create_structure_to_ena(self): fh_esquema.close() # lista = ["study", "runs", "samples", "experiments"] - llaves = esquema_json.keys() - import pdb - - pdb.set_trace() + # llaves = esquema_json.keys() df = pd.DataFrame.from_dict(esquema_json, orient="index") df_transposed = df.T @@ -140,6 +138,12 @@ def create_structure_to_ena(self): ] ] + extract_targets(self.action, df_study) + + import pdb + + pdb.set_trace() + def upload(self): """Create the required files and upload to ENA""" self.convert_input_json_to_ena() diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 1bff8211..006f3db8 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2096,6 +2096,7 @@ "examples": [ "ncov123assembly3" ], + "classification": "Bioinformatics and QC metrics", "label": "Consensus sequence name" }, "consensus_sequence_name_md5": { @@ -2105,6 +2106,7 @@ "examples": [ "ncov123assembly3" ], + "classification": "Bioinformatics and QC metrics", "label": "Consensus sequence name md5" }, "consensus_sequence_filepath": { @@ -2167,16 +2169,6 @@ "classification": "Bioinformatics and QC metrics", "label": "Quality control metrics " }, - "breadth_of_coverage_value": { - "examples": [ - "95%" - ], - "ontology": "GENEPIO:0001472", - "type": "string", - "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", - "classification": "Bioinformatics and QC metrics", - "label": "Breadth of coverage value" - }, "depth_of_coverage_value": { "examples": [ "400x" @@ -2214,7 +2206,7 @@ "ontology": "GENEPIO:0001476", "type": "string", "description": "The user-specified filename of the r1 FASTQ file.", - "classification": "Bioinformatics and QC metrics", + "classification": "", "label": "Sequence file R1 fastq" }, "sequence_file_R2_fastq": { @@ -2224,7 +2216,7 @@ "ontology": "GENEPIO:0001477", "type": "string", "description": "The user-specified filename of the r2 FASTQ file.", - "classification": "Bioinformatics and QC metrics", + "classification": "", "label": "Sequence file R2 fastq" }, "r1_fastq_filepath": { @@ -2234,7 +2226,7 @@ "ontology": "GENEPIO:0001478", "type": "string", "description": "The filepath of the r1 FASTQ file.", - "classification": "Bioinformatics and QC metrics", + "classification": "", "label": "Filepath R1 fastq" }, "r2_fastq_filepath": { @@ -2244,7 +2236,7 @@ "ontology": "GENEPIO:0001479", "type": "string", "description": "The filepath of the r2 FASTQ file.", - "classification": "Bioinformatics and QC metrics", + "classification": "", "label": "Filepath R2 fastq" }, "fast5_filename": { @@ -2254,7 +2246,7 @@ "ontology": "GENEPIO:0001480", "type": "string", "description": "The user-specified filename of the FAST5 file.", - "classification": "Bioinformatics and QC metrics", + "classification": "", "label": "Filename fast5" }, "fast5_filepath": { @@ -2264,7 +2256,7 @@ "ontology": "GENEPIO:0001481", "type": "string", "description": "The filepath of the FAST5 file.", - "classification": "Bioinformatics and QC metrics", + "classification": "", "label": "Filepath fast5" }, "number_of_base_pairs_sequenced": { @@ -2393,7 +2385,7 @@ "ontology": "topic:0102", "type": "string", "description": "", - "classification": "Lineage and Variant information", + "classification": "Bioinformatics and QC metrics", "label": "Mapping" }, "if_mapping_other": { @@ -2403,7 +2395,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Lineage and Variant information", + "classification": "Bioinformatics and QC metrics", "label": "If mapping Is Other, Specify" }, "mapping_params": { @@ -2413,7 +2405,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Lineage and Variant information", + "classification": "Bioinformatics and QC metrics", "label": "Mapping params" }, "lineage_name": { @@ -2423,7 +2415,7 @@ "ontology": "GENEPIO:0001500", "type": "string", "description": "The name of the lineage or clade.", - "classification": "Lineage and Variant information", + "classification": "Bioinformatics and QC metrics", "label": "Lineage/clade name" }, "lineage_analysis_software_name": { @@ -2433,7 +2425,7 @@ "ontology": "GENEPIO:0001501", "type": "string", "description": "The name of the software used to determine the lineage/clade.", - "classification": "Lineage and Variant information", + "classification": "Bioinformatics and QC metrics", "label": "lineage/clade analysis software name" }, "if_lineage_identification_other": { @@ -2443,7 +2435,7 @@ "ontology": "0", "type": "string", "description": "The name of the software used to determine the lineage/clade.", - "classification": "Lineage and Variant information", + "classification": "Bioinformatics and QC metrics", "label": "If lineage identification Is Other, Specify" }, "lineage_analysis_software_version": { @@ -2453,7 +2445,7 @@ "ontology": "GENEPIO:0001502", "type": "string", "description": "The version of the software used to determine the lineage/clade.", - "classification": "Lineage and Variant information", + "classification": "Bioinformatics and QC metrics", "label": "Lineage/clade analysis software version" }, "design_description": { @@ -2488,19 +2480,9 @@ "examples": [ "Variant of Concern (VOC) [GENEPIO:0100083]" ], - "classification": "Lineage and Variant information", + "classification": "Bioinformatics and QC metrics", "label": "Variant designation" }, - "variant_evidence": { - "examples": [ - "lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)" - ], - "ontology": "GENEPIO:0001504", - "type": "string", - "description": "The evidence used to make the variant determination.", - "classification": "Lineage and Variant information", - "label": "Variant evidence" - }, "gene_name_1": { "Enums": [ "E gene (orf4) [GENEPIO:0100151]", @@ -2548,19 +2530,9 @@ "examples": [ "E gene (orf4) [GENEPIO:0100151]" ], - "classification": "Pathogen diagnostic testing", + "classification": "Bioinformatics and QC metrics", "label": "Gene Name 1" }, - "protocol_SARS-CoV-2_detection": { - "examples": [ - "" - ], - "ontology": "CIDO_0020274", - "type": "string", - "description": "", - "classification": "Pathogen diagnostic testing", - "label": "Protocol SARS-CoV-2 detection" - }, "per_qc_filtered": { "examples": [ "" @@ -2568,7 +2540,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Pathogen diagnostic testing", + "classification": "Bioinformatics and QC metrics", "label": "%qc filtered" }, "per_reads_host": { @@ -2578,7 +2550,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Pathogen diagnostic testing", + "classification": "Bioinformatics and QC metrics", "label": "%reads host" }, "per_reads_virus": { @@ -2588,7 +2560,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Pathogen diagnostic testing", + "classification": "Bioinformatics and QC metrics", "label": "%reads virus" }, "per_unmapped": { @@ -2598,7 +2570,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Pathogen diagnostic testing", + "classification": "Bioinformatics and QC metrics", "label": "%unmapped" }, "per_genome _greater_10x": { @@ -2608,7 +2580,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Pathogen diagnostic testing", + "classification": "Bioinformatics and QC metrics", "label": "% genome greater 10x" }, "mean_depth_of_coverage_value": { @@ -2618,7 +2590,7 @@ "ontology": "NCIT:C167285", "type": "string", "description": "", - "classification": "Pathogen diagnostic testing", + "classification": "Bioinformatics and QC metrics", "label": "mean depth of coverage value" }, "per_Ns": { @@ -2628,28 +2600,28 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Pathogen diagnostic testing", + "classification": "Bioinformatics and QC metrics", "label": "%Ns" }, - "Number_of_variants_AF_greater_75percent": { + "number_of_variants_AF_greater_75percent": { "examples": [ "" ], "ontology": "0", "type": "string", "description": "", - "classification": "Pathogen diagnostic testing", + "classification": "Bioinformatics and QC metrics", "label": "Number of variants (AF greater 75%)" }, - "Numer_of_variants_with_effect": { + "number_of_variants_with_effect": { "examples": [ "" ], "ontology": "0", "type": "string", "description": "", - "classification": "Pathogen diagnostic testing", - "label": "Numer of variants with effect" + "classification": "Bioinformatics and QC metrics", + "label": "Number of variants with effect" }, "diagnostic_pcr_protocol_1": { "examples": [ @@ -2733,7 +2705,7 @@ }, "analysis_date": { "examples": [ - "e.g 2020-08-07" + "e.g 2020-08-07" ], "ontology": "0", "type": "string", @@ -3251,4 +3223,4 @@ "classification": "Database Identifiers" } } -} +} \ No newline at end of file From 081d42fa4d2580bc7a8e75d44b2e8d5d51eae1e2 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 16 Apr 2022 11:41:49 +0200 Subject: [PATCH 0329/1454] define parameters for update_db --- relecov_tools/__main__.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index a49ee039..2b1877cb 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -287,10 +287,17 @@ def launch(user): @relecov_tools_cli.command(help_priority=9) +@click.option("-u", "--user", help="user name for login") +@click.option("-p", "--password", help="password for the user to login") @click.option("-j", "--json", help="data in json format") -def update_db(user): +@click.option("-i", "--iskylims", help="url for sending request to iSkyLIMs") +@click.option("-r", "--relecov", help="url for sending request to Relecov Platform") +def update_db(user, password, json, iskylims, relecov): """feed database with metadata jsons""" - pass + feed_databases = relecov_tools.feed_databases.FeedDatabases( + user, password, json, iskylims, relecov + ) + feed_databases.store_data() if __name__ == "__main__": From c027260042d26fb286bb5c7c629039b6ed1eb9ac Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 16 Apr 2022 12:44:23 +0200 Subject: [PATCH 0330/1454] Include external url to feed database --- relecov_tools/conf/configuration.json | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 1eb337d2..6c5f9926 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -24,5 +24,18 @@ "run_alias": "", "experiment_title": "Example project for ENA submission RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance" + }, + "external_url":{ + "iskylims": { + "url": "http://relecov-iskylims.isciiides.es/wetlab/api/", + "store_samples": "createSampleData", + "get_project_fields": "sampleProjectFields", + "token": "" + }, + "relecov": { + "url": "http://relecov-platform.isciiides.es/api/", + "store_samples": "storeData", + "token": "" + } } } From fe6f4476726d4f82a9b5b410ad93f9d678baca3a Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 16 Apr 2022 13:06:42 +0200 Subject: [PATCH 0331/1454] RestApi is include to send the requests --- relecov_tools/rest_api.py | 42 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 relecov_tools/rest_api.py diff --git a/relecov_tools/rest_api.py b/relecov_tools/rest_api.py new file mode 100644 index 00000000..f234dd18 --- /dev/null +++ b/relecov_tools/rest_api.py @@ -0,0 +1,42 @@ +#!/usr/bin/env python +import logging +import json +import requests + +log = logging.getLogger(__name__) + + +class RestApi: + def __init__(self, server, url): + self.request_url = server + url + self.headers = {"content-type": "application/json"} + + def get_request(self, request_info, parameter, value): + url_http = str(self.request_url + request_info + "?" + parameter + "=" + value) + try: + req = requests.get(url_http, headers=self.headers) + if req.status_code > 201: + return False + return json.loads(req.text) + except requests.ConnectionError: + log.error("Unable to open connection towards %s", self.server) + return False + + def put_request(self, request_info, parameter, value): + url_http = str(self.request_url + request_info + "?" + parameter + "=" + value) + try: + requests.get(url_http, headers=self.headers) + return True + except requests.ConnectionError: + log.error("Unable to open connection towards %s", self.server) + return False + + def post_request(self, data): + try: + req = requests.post(self.request_url, data=data, headers=self.headers) + if req.status_code > 201: + log.error(str(req.status_code)) + return False + except requests.ConnectionError: + log.error("Unable to open connection towards %s", self.server) + return True From 3fb24046a2690b423750c6cb08d6dcbf4def8905 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 16 Apr 2022 13:07:58 +0200 Subject: [PATCH 0332/1454] First draft for feed_database --- relecov_tools/feed_databases.py | 51 +++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 relecov_tools/feed_databases.py diff --git a/relecov_tools/feed_databases.py b/relecov_tools/feed_databases.py new file mode 100644 index 00000000..ec2afcbf --- /dev/null +++ b/relecov_tools/feed_databases.py @@ -0,0 +1,51 @@ +#!/usr/bin/env python +import sys +import os + +import logging +import rich.console +import relecov_tools.utils +from relecov_tools.config_json import ConfigJson +import relecov_tools.json_schema + +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + + +class RelecovMetadata: + def __init__( + self, + user=None, + passwd=None, + json_file=None, + iskylims_url=None, + relecov_url=None, + ): + config_json = ConfigJson() + if json_file is None: + json_file = relecov_tools.utils.prompt_path( + msg="Select the json file which have the data to map" + ) + if not os.path.isfile(json_file): + log.error("json data file %s does not exist ", json_file) + stderr.print(f"[red] json data file {json_file} does not exist") + sys.exit(1) + self.json_data = relecov_tools.utils.read_json_file(json_file) + self.json_file = json_file + + def split_json(): + """Split the information in the input json to populate iSkyLIMS and + Relecov platform + """ + pass + + def store_data(self): + """Collect data from json file and split them to store data in iSkyLIMS + amd in Relecov Platform + """ + split_data = self.split_json() From bc655793a1ec0061be0ba69422a69a3f1d6c1ecb Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 16 Apr 2022 13:13:16 +0200 Subject: [PATCH 0333/1454] fixing litin --- relecov_tools/read_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index d3ef2aa7..b68b4f9d 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -108,7 +108,7 @@ def include_fixed_data(self): "tax_id": "2697049", "organism": "Severe acute respiratory syndrome coronavirus 2", "common_name": "PEPITO", - "sample_description" : "Sample for surveillance", + "sample_description": "Sample for surveillance", } fixed_data.update(self.configuration.get_configuration("ENA_configuration")) return fixed_data From ea030b59833bcaf39ab421f352c778631e98059d Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 16 Apr 2022 13:52:45 +0200 Subject: [PATCH 0334/1454] Include fields for iskylims --- relecov_tools/conf/configuration.json | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 6c5f9926..4b7675c4 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -37,5 +37,19 @@ "store_samples": "storeData", "token": "" } + }, + "iskylims_sample_fields": [ + ["patientCore", "collector_name"], + ["sampleName", "collecting_lab_sample_id"], + ["labRequest","collecting_institution"], + ["sampleType", "anatomical_material"], + ["species", "host_common_name"], + ["sampleEntryDate", "sample_received_date"], + ["sampleCollectionDate", "sample_collection_date"] + ], + "iskylims_fixed_values": { + "sampleProject": "Relecov", + "onlyRecorded": "Yes", + "sampleLocation": "Not defined" } } From 71ec2610db8414589cde4c466d63b57405693e3f Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 16 Apr 2022 15:59:42 +0200 Subject: [PATCH 0335/1454] split external url into server and url --- relecov_tools/conf/configuration.json | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 4b7675c4..6c5ad2b0 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -27,13 +27,15 @@ }, "external_url":{ "iskylims": { - "url": "http://relecov-iskylims.isciiides.es/wetlab/api/", + "server": "http://relecov-iskylims.isciiides.es/", + "url": "wetlab/api/", "store_samples": "createSampleData", "get_project_fields": "sampleProjectFields", "token": "" }, "relecov": { - "url": "http://relecov-platform.isciiides.es/api/", + "server": "http://relecov-platform.isciiides.es/", + "url": "api/", "store_samples": "storeData", "token": "" } From cd5bfcbda6a22f6f6753321dd345707eaacb1dbb Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 16 Apr 2022 16:53:56 +0200 Subject: [PATCH 0336/1454] included project name in configuration --- relecov_tools/conf/configuration.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 6c5ad2b0..ae1ab622 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -30,7 +30,8 @@ "server": "http://relecov-iskylims.isciiides.es/", "url": "wetlab/api/", "store_samples": "createSampleData", - "get_project_fields": "sampleProjectFields", + "url_project_fields": "sampleProjectFields", + "project_name" = "Relecov", "token": "" }, "relecov": { From bad105363dbbe6140a18d979db26414de96f67c9 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 16 Apr 2022 16:54:30 +0200 Subject: [PATCH 0337/1454] testing creation class for feed_bd --- relecov_tools/feed_databases.py | 47 ++++++++++++++++++++++++++++++--- 1 file changed, 43 insertions(+), 4 deletions(-) diff --git a/relecov_tools/feed_databases.py b/relecov_tools/feed_databases.py index ec2afcbf..be030d11 100644 --- a/relecov_tools/feed_databases.py +++ b/relecov_tools/feed_databases.py @@ -6,6 +6,7 @@ import rich.console import relecov_tools.utils from relecov_tools.config_json import ConfigJson +from relecov_tools.rest_api import RestApi import relecov_tools.json_schema log = logging.getLogger(__name__) @@ -17,7 +18,7 @@ ) -class RelecovMetadata: +class FeedDatabases: def __init__( self, user=None, @@ -26,7 +27,7 @@ def __init__( iskylims_url=None, relecov_url=None, ): - config_json = ConfigJson() + self.config_json = ConfigJson() if json_file is None: json_file = relecov_tools.utils.prompt_path( msg="Select the json file which have the data to map" @@ -37,12 +38,50 @@ def __init__( sys.exit(1) self.json_data = relecov_tools.utils.read_json_file(json_file) self.json_file = json_file + # Get iSkyLIMS settings + self.iskylims_settings = self.config_json.get_topic_data("external_url", "iskylims") + self.iskylims_server = self.iskylims_settings['server'] + self.iskylims_url = self.iskylims_settings['url'] + if iskylims_url: + split = iskylims_url.split("/") + self.iskylims_server = split[0] + "/" + self.iskylims_url = "/".join(split[1:]) + "/" - def split_json(): + self.relecov_settings = self.config_json.get_topic_data("external_url", "relecov") + self.relecov_server = self.relecov_settings['server'] + self.relecov_url = self.relecov_settings['url'] + if relecov_url: + split = relecov_url.split("/") + self.relecov_server = split[0] + "/" + self.relecov_url = "/".join(split[1:]) + "/" + + self.iskylims_rest_api = RestApi(self.iskylims_server, self.iskylims_url) + self.relecov_rest_api = RestApi(self.relecov_server, self.relecov_url) + + def fetch_sample_project_fields(self): + s_project = self.iskylims_rest_api.get_request(self.iskylims_settings["url_project_fields"], "project", self.iskylims_settings["project_name"]) + if not s_project: + return False + + def get_fields_sample(self): + """Get from configuration file the mandatory fields for Sample""" + sample_fields = {} + sample_fields["iskylims_s_fields"] = self.config_json.get_configuration("iskylims_sample_fields") + sample_fields["relecov_fields"] = self.config_json.get_configuration("relecov_fields") + req_data = self.fetch_sample_project_fields() + if not req_data: + stderr.print("[red] Unable to fetch fields for sample project ") + log.error("Unable to fetch fields for sample project") + sys.exit(1) + sample_fields["iskylims_s_proj_fields"] = req_data + return sample_fields + + def split_json(self): """Split the information in the input json to populate iSkyLIMS and Relecov platform """ - pass + sample_fields = self.get_fields_sample() + def store_data(self): """Collect data from json file and split them to store data in iSkyLIMS From 2c6245c07a8331aed4622997f8036bc1b2664d26 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 16 Apr 2022 17:07:27 +0200 Subject: [PATCH 0338/1454] add import feed_database that was missing --- relecov_tools/__main__.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 2b1877cb..85c4f19b 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -14,6 +14,7 @@ import relecov_tools.ena_upload import relecov_tools.json_validation import relecov_tools.map_schema +import relecov_tools.feed_databases log = logging.getLogger() From 1d5a48cc836480534c58f244d1c19fe874bbb86b Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 16 Apr 2022 19:26:58 +0200 Subject: [PATCH 0339/1454] fixed ikylims url for deployment --- relecov_tools/test/test_cases.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/test/test_cases.txt b/relecov_tools/test/test_cases.txt index 0e810fa9..6b63b9f5 100644 --- a/relecov_tools/test/test_cases.txt +++ b/relecov_tools/test/test_cases.txt @@ -3,3 +3,4 @@ relecov-tools -l /tmp/logs.log download -f relecov_tools/test/sftp_config.yaml relecov-tools read-metadata -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -s relecov_tools/example_data/samples_data_COD_test_01_20220408.json -o /tmp relecov-tools validate -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -o /tmp relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -o /tmp +relecov-tools update-db -i http://iskylims.isciiides.es/wetlab/api/ -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json From 272fb229fe6fd0b757f59df7a60de759b681d25f Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 16 Apr 2022 19:28:27 +0200 Subject: [PATCH 0340/1454] Include http protocol to isklims settings --- relecov_tools/conf/configuration.json | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index ae1ab622..49d02676 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -27,16 +27,16 @@ }, "external_url":{ "iskylims": { - "server": "http://relecov-iskylims.isciiides.es/", - "url": "wetlab/api/", + "server": "http://relecov-iskylims.isciiides.es", + "url": "/wetlab/api/", "store_samples": "createSampleData", "url_project_fields": "sampleProjectFields", - "project_name" = "Relecov", + "project_name" : "Relecov", "token": "" }, "relecov": { - "server": "http://relecov-platform.isciiides.es/", - "url": "api/", + "server": "http://relecov-platform.isciiides.es", + "url": "/api/", "store_samples": "storeData", "token": "" } From d2a379c809c4c1d6ee4dde8853c6a30b928cdbeb Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 16 Apr 2022 19:28:58 +0200 Subject: [PATCH 0341/1454] working on sending request to iSkyLIMS --- relecov_tools/feed_databases.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/feed_databases.py b/relecov_tools/feed_databases.py index be030d11..7707316e 100644 --- a/relecov_tools/feed_databases.py +++ b/relecov_tools/feed_databases.py @@ -29,6 +29,7 @@ def __init__( ): self.config_json = ConfigJson() if json_file is None: + self.config_json = ConfigJson() json_file = relecov_tools.utils.prompt_path( msg="Select the json file which have the data to map" ) @@ -53,12 +54,13 @@ def __init__( if relecov_url: split = relecov_url.split("/") self.relecov_server = split[0] + "/" - self.relecov_url = "/".join(split[1:]) + "/" + self.relecov_url = "/".join(split[1:]) self.iskylims_rest_api = RestApi(self.iskylims_server, self.iskylims_url) self.relecov_rest_api = RestApi(self.relecov_server, self.relecov_url) def fetch_sample_project_fields(self): + import pdb; pdb.set_trace() s_project = self.iskylims_rest_api.get_request(self.iskylims_settings["url_project_fields"], "project", self.iskylims_settings["project_name"]) if not s_project: return False From 3e83c4a2cdf9c54bd6b726a2ea080c81e07db74b Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 18 Apr 2022 12:41:22 +0200 Subject: [PATCH 0342/1454] changes in ena upload --- relecov_tools/ena_upload.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index bbcdac6d..0b7fbda2 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -138,7 +138,7 @@ def create_structure_to_ena(self): ] ] - extract_targets(self.action, df_study) + targets = extract_targets(self.action, df_study) import pdb From 0edd782c8cd0172bff786585996352514c12b132 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 18 Apr 2022 18:02:57 +0200 Subject: [PATCH 0343/1454] extract target function implemented --- relecov_tools/ena_upload.py | 39 ++++++++++++++++++------ relecov_tools/example_data/to_ena_2.json | 5 +-- 2 files changed, 32 insertions(+), 12 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 0b7fbda2..631f755d 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,3 +1,4 @@ +from bdb import set_trace import os import logging import rich.console @@ -8,6 +9,7 @@ import relecov_tools.utils from relecov_tools.config_json import ConfigJson from ena_upload.ena_upload import extract_targets +from ena_upload.ena_upload import check_filenames log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -108,6 +110,7 @@ def create_structure_to_ena(self): df = pd.DataFrame.from_dict(esquema_json, orient="index") df_transposed = df.T df_study = df_transposed[["study_alias", "study_title", "study_type"]] + df_study["status"] = self.action df_samples = df_transposed[ [ "sample_name", @@ -121,9 +124,11 @@ def create_structure_to_ena(self): "isolate", ] ] + df_samples["status"] = self.action df_runs = df_transposed[ ["experiment_alias", "sequence_file_R1_fastq", "sequence_file_R2_fastq"] ] + df_runs["status"] = self.action df_experiments = df_transposed[ [ "experiment_alias", @@ -137,19 +142,33 @@ def create_structure_to_ena(self): "instrument_model", ] ] + df_experiments["status"] = self.action + + schema_dataframe = {} + schema_dataframe["study"] = df_study + schema_dataframe["samples"] = df_samples + schema_dataframe["runs"] = df_runs + schema_dataframe["experiments"] = df_experiments + + schema_targets = extract_targets(self.action, schema_dataframe) + if not schema_targets: + sys.exit( + f"There is no table submitted having at least one row with {self.action} as action in the status column." + ) - targets = extract_targets(self.action, df_study) - - import pdb - - pdb.set_trace() + if self.action == "add": + if "run" in schema_targets: + # a dictionary of filename:file_path + df = schema_targets["run"] + file_paths = {} + if self.source_json: + for path in self.source_json: + file_paths[os.path.basename(path)] = os.path.abspath(path) + # check if file names identical between command line and table + # if not, system exits + check_filenames(file_paths, df_runs) def upload(self): """Create the required files and upload to ENA""" self.convert_input_json_to_ena() self.create_structure_to_ena() - - # df_study = pd.DataFrame.from_dict(data["study"]) - # df_samples = pd.DataFrame.from_dict(data["samples"]) - # df_runs = pd.DataFrame.from_dict(data["runs"]) - # df_experiments = pd.DataFrame.from_dict(data["experiments"]) diff --git a/relecov_tools/example_data/to_ena_2.json b/relecov_tools/example_data/to_ena_2.json index 951803d8..9fd0de80 100644 --- a/relecov_tools/example_data/to_ena_2.json +++ b/relecov_tools/example_data/to_ena_2.json @@ -34,5 +34,6 @@ "study_alias": "RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "RELECOV Spanish Network for genomics surveillance", - "tax_id": "2697049" -} \ No newline at end of file + "tax_id": "2697049", + "query":"" +} From e370217ed8b621d1afcc8163c5f8086399201f92 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 18 Apr 2022 23:34:38 +0200 Subject: [PATCH 0344/1454] modified rest api and completed for sending request to iSkyLIMS --- relecov_tools/__main__.py | 5 +- relecov_tools/feed_databases.py | 140 ++++++++++++++++++++++++++------ relecov_tools/map_schema.py | 4 +- relecov_tools/rest_api.py | 55 ++++++++++--- 4 files changed, 164 insertions(+), 40 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 85c4f19b..af938bd0 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -291,12 +291,13 @@ def launch(user): @click.option("-u", "--user", help="user name for login") @click.option("-p", "--password", help="password for the user to login") @click.option("-j", "--json", help="data in json format") +@click.option("-s", "--schema", help="json schema if relecov is not used") @click.option("-i", "--iskylims", help="url for sending request to iSkyLIMs") @click.option("-r", "--relecov", help="url for sending request to Relecov Platform") -def update_db(user, password, json, iskylims, relecov): +def update_db(user, password, json, schema, iskylims, relecov): """feed database with metadata jsons""" feed_databases = relecov_tools.feed_databases.FeedDatabases( - user, password, json, iskylims, relecov + user, password, json, schema, iskylims, relecov ) feed_databases.store_data() diff --git a/relecov_tools/feed_databases.py b/relecov_tools/feed_databases.py index 7707316e..baaf5954 100644 --- a/relecov_tools/feed_databases.py +++ b/relecov_tools/feed_databases.py @@ -1,13 +1,17 @@ #!/usr/bin/env python import sys import os - +import jsonschema import logging import rich.console +from jsonschema import Draft202012Validator +import time + import relecov_tools.utils from relecov_tools.config_json import ConfigJson from relecov_tools.rest_api import RestApi -import relecov_tools.json_schema + +# import relecov_tools.json_schema log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -24,9 +28,20 @@ def __init__( user=None, passwd=None, json_file=None, + schema=None, iskylims_url=None, relecov_url=None, ): + if user is None: + user = relecov_tools.utils.prompt_text( + msg="Enter username for iskylims and relecov_plaform" + ) + self.user = user + if passwd is None: + passwd = relecov_tools.utils.prompt_text( + msg="Enter credential password for iskylims and relecov_plaform" + ) + self.passwd = passwd self.config_json = ConfigJson() if json_file is None: self.config_json = ConfigJson() @@ -39,18 +54,42 @@ def __init__( sys.exit(1) self.json_data = relecov_tools.utils.read_json_file(json_file) self.json_file = json_file + if schema is None: + schema = os.path.join( + os.path.dirname(os.path.realpath(__file__)), + "schema", + self.config_json.get_topic_data("json_schemas", "relecov_schema"), + ) + else: + if os.path.isfile(schema): + log.error("Relecov schema file %s does not exists", schema) + stderr.print("[red] Relecov schema " + schema + "does not exists") + sys.exit(1) + rel_schema_json = relecov_tools.utils.read_json_file(schema) + try: + Draft202012Validator.check_schema(rel_schema_json) + except jsonschema.ValidationError: + log.error("Schema does not fulfil Draft 202012 Validation ") + stderr.print("[red] Schema does not fulfil Draft 202012 Validation") + sys.exit(1) + self.schema = rel_schema_json + # Get iSkyLIMS settings - self.iskylims_settings = self.config_json.get_topic_data("external_url", "iskylims") - self.iskylims_server = self.iskylims_settings['server'] - self.iskylims_url = self.iskylims_settings['url'] + self.iskylims_settings = self.config_json.get_topic_data( + "external_url", "iskylims" + ) + self.iskylims_server = self.iskylims_settings["server"] + self.iskylims_url = self.iskylims_settings["url"] if iskylims_url: split = iskylims_url.split("/") self.iskylims_server = split[0] + "/" self.iskylims_url = "/".join(split[1:]) + "/" - self.relecov_settings = self.config_json.get_topic_data("external_url", "relecov") - self.relecov_server = self.relecov_settings['server'] - self.relecov_url = self.relecov_settings['url'] + self.relecov_settings = self.config_json.get_topic_data( + "external_url", "relecov" + ) + self.relecov_server = self.relecov_settings["server"] + self.relecov_url = self.relecov_settings["url"] if relecov_url: split = relecov_url.split("/") self.relecov_server = split[0] + "/" @@ -59,34 +98,87 @@ def __init__( self.iskylims_rest_api = RestApi(self.iskylims_server, self.iskylims_url) self.relecov_rest_api = RestApi(self.relecov_server, self.relecov_url) - def fetch_sample_project_fields(self): - import pdb; pdb.set_trace() - s_project = self.iskylims_rest_api.get_request(self.iskylims_settings["url_project_fields"], "project", self.iskylims_settings["project_name"]) - if not s_project: - return False + def mapping_sample_project_fields(self, s_project_fields): + """Map the label defined in the sample project fields with the name + in json schema based on label + """ + label_prop_dict = {} + map_list = {} # key is the label, value the property + for prop, values in self.schema["properties"].items(): + try: + self.label_prop_dict[values["label"]] = prop + except KeyError: + continue + + for field in s_project_fields: + try: + map_list[field] = label_prop_dict[field] + except KeyError as e: + log.error("Unable to map in the schema the label %s", e) + stderr.print("[red] Unable to map in the schema the label ", e) + sys.exit(1) + return map_list def get_fields_sample(self): """Get from configuration file the mandatory fields for Sample""" sample_fields = {} - sample_fields["iskylims_s_fields"] = self.config_json.get_configuration("iskylims_sample_fields") - sample_fields["relecov_fields"] = self.config_json.get_configuration("relecov_fields") - req_data = self.fetch_sample_project_fields() - if not req_data: - stderr.print("[red] Unable to fetch fields for sample project ") - log.error("Unable to fetch fields for sample project") + sample_fields["iskylims_s_fields"] = self.config_json.get_configuration( + "iskylims_sample_fields" + ) + sample_fields["relecov_fields"] = self.config_json.get_configuration( + "relecov_fields" + ) + + s_project = self.iskylims_rest_api.get_request( + self.iskylims_settings["url_project_fields"], + "project", + self.iskylims_settings["project_name"], + ) + if "ERROR" in s_project: + log.error( + "Unable to get parameters. Received error code %s", s_project["ERROR"] + ) + stderr.print( + "[red] Unable to fetch data. Received error ", s_project["ERROR"] + ) sys.exit(1) - sample_fields["iskylims_s_proj_fields"] = req_data + s_project_fields = list(s_project.values()) + sample_fields["iskylims_s_fields"].update( + self.mapping_sample_project_fields(s_project_fields) + ) + return sample_fields - def split_json(self): + def update_databases(self, sample_fields): """Split the information in the input json to populate iSkyLIMS and Relecov platform """ - sample_fields = self.get_fields_sample() - + for sample in self.json_file: + iskylims_data = {} + for label, value in sample_fields["iskylims_s_fields"]: + iskylims_data[label] = sample[value] + result = self.iskylims_rest_api.post_request( + iskylims_data, {"user": self.user, "passwd": self.passwd} + ) + if "ERROR" in result: + for i in range(10): + # wait 5 sec before resending the request + time.sleep(5) + result = self.iskylims_rest_api.post_request( + iskylims_data, {"user": self.user, "passwd": self.passwd} + ) + if "ERROR" not in result: + break + if i == 9 and "ERROR" in result: + log.error("Unable to sent the request to iSlyLIMS") + stderr.print("[red] Unable to sent the request to iSlyLIMS") + sys.exit(1) + log.info("stored data in iskylims %s", sample["sampleName"]) + return def store_data(self): """Collect data from json file and split them to store data in iSkyLIMS amd in Relecov Platform """ - split_data = self.split_json() + sample_fields = self.get_fields_sample() + self.update_databases(sample_fields) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index fb227f4a..6e7e94f1 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -50,9 +50,7 @@ def __init__( Draft202012Validator.check_schema(rel_schema_json) except jsonschema.ValidationError: log.error("Relecov schema does not fulfil Draft 202012 Validation ") - stderr.print( - "[red] phage plus schema does not fulfil Draft 202012 Validation" - ) + stderr.print("[red] Relecov schema does not fulfil Draft 202012 Validation") sys.exit(1) self.relecov_schema = rel_schema_json diff --git a/relecov_tools/rest_api.py b/relecov_tools/rest_api.py index f234dd18..3c617741 100644 --- a/relecov_tools/rest_api.py +++ b/relecov_tools/rest_api.py @@ -2,25 +2,45 @@ import logging import json import requests +import sys +import rich.console +import relecov_tools.utils log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + class RestApi: def __init__(self, server, url): self.request_url = server + url self.headers = {"content-type": "application/json"} - def get_request(self, request_info, parameter, value): + def get_request(self, request_info, parameter, value, safe=True): url_http = str(self.request_url + request_info + "?" + parameter + "=" + value) try: req = requests.get(url_http, headers=self.headers) - if req.status_code > 201: - return False - return json.loads(req.text) + if req.status_code != 200: + if safe: + log.error( + "Unable to get parameters. Received error code %s", + req.status_code, + ) + stderr.print( + "[red] Unable to fetch data. Received error ", req.status_code + ) + sys.exit(1) + return {"ERROR": req.status_code} + return {"DATA": json.loads(req.text)} except requests.ConnectionError: log.error("Unable to open connection towards %s", self.server) - return False + stderr.print("[red] Unable to open connection towards ", self.server) + return {"ERROR": "Server not available"} def put_request(self, request_info, parameter, value): url_http = str(self.request_url + request_info + "?" + parameter + "=" + value) @@ -31,12 +51,25 @@ def put_request(self, request_info, parameter, value): log.error("Unable to open connection towards %s", self.server) return False - def post_request(self, data): + def post_request(self, data, credentials): + if isinstance(credentials, dict): + auth = (credentials["user"], credentials["pass"]) try: - req = requests.post(self.request_url, data=data, headers=self.headers) - if req.status_code > 201: - log.error(str(req.status_code)) - return False + req = requests.post( + self.request_url, data=data, headers=self.headers, auth=auth + ) + if req.status_code != 201: + log.error( + "Unable to store parameters. Received error code %s", + req.status_code, + ) + stderr.print( + "[red] Unable to store data. Received error ", req.status_code + ) + sys.exit(1) + return True except requests.ConnectionError: log.error("Unable to open connection towards %s", self.server) - return True + stderr.print("[red] Unable to open connection towards ", self.server) + return {"ERROR": "Server not available"} + return {"Success": "Data are store in requested server"} From 65e7ee2e1ce82f177a5d62ac1494a58dc018c5d8 Mon Sep 17 00:00:00 2001 From: Erika <39902241+ErikaKvalem@users.noreply.github.com> Date: Tue, 19 Apr 2022 10:24:57 +0200 Subject: [PATCH 0345/1454] Update relecov_tools/ena_upload.py Co-authored-by: luissian --- relecov_tools/ena_upload.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 631f755d..dfefb28c 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -152,9 +152,9 @@ def create_structure_to_ena(self): schema_targets = extract_targets(self.action, schema_dataframe) if not schema_targets: - sys.exit( - f"There is no table submitted having at least one row with {self.action} as action in the status column." - ) + stderr.print(f"[red] There is no table submitted having at least one row with {self.action} as action in the status column.") + sys.exit(1) + if self.action == "add": if "run" in schema_targets: From 8743d2538a8e1ea89b5963c5feca8583343aa555 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 20 Apr 2022 14:01:49 +0200 Subject: [PATCH 0346/1454] adding new functions from ena-upload lci --- relecov_tools/ena_upload.py | 96 +++++++++++++++++++++++++++++++------ 1 file changed, 82 insertions(+), 14 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index dfefb28c..61957e85 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -10,6 +10,10 @@ from relecov_tools.config_json import ConfigJson from ena_upload.ena_upload import extract_targets from ena_upload.ena_upload import check_filenames +from ena_upload.ena_upload import check_file_checksum +from ena_upload.ena_upload import get_md5 +from ena_upload.ena_upload import get_taxon_id +from ena_upload.ena_upload import get_scientific_name log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -103,14 +107,11 @@ def create_structure_to_ena(self): fh_esquema = open(esquema) esquema_json = json.load(fh_esquema) fh_esquema.close() - # lista = ["study", "runs", "samples", "experiments"] - - # llaves = esquema_json.keys() df = pd.DataFrame.from_dict(esquema_json, orient="index") df_transposed = df.T df_study = df_transposed[["study_alias", "study_title", "study_type"]] - df_study["status"] = self.action + df_study.insert(3, "status", self.action) df_samples = df_transposed[ [ "sample_name", @@ -124,11 +125,11 @@ def create_structure_to_ena(self): "isolate", ] ] - df_samples["status"] = self.action + df_samples.insert(3, "status", self.action) df_runs = df_transposed[ ["experiment_alias", "sequence_file_R1_fastq", "sequence_file_R2_fastq"] ] - df_runs["status"] = self.action + df_runs.insert(3, "status", self.action) df_experiments = df_transposed[ [ "experiment_alias", @@ -142,7 +143,7 @@ def create_structure_to_ena(self): "instrument_model", ] ] - df_experiments["status"] = self.action + df_experiments.insert(3, "status", self.action) schema_dataframe = {} schema_dataframe["study"] = df_study @@ -151,12 +152,20 @@ def create_structure_to_ena(self): schema_dataframe["experiments"] = df_experiments schema_targets = extract_targets(self.action, schema_dataframe) + import pdb + + pdb.set_trace() + if not schema_targets: - stderr.print(f"[red] There is no table submitted having at least one row with {self.action} as action in the status column.") + stderr.print( + f"[red] There is no table submitted having at least one row with {self.action} as action in the status column." + ) sys.exit(1) - - if self.action == "add": + if self.action == "ADD": + # when adding run object + # update schema_targets wit md5 hash + # submit data if "run" in schema_targets: # a dictionary of filename:file_path df = schema_targets["run"] @@ -168,7 +177,66 @@ def create_structure_to_ena(self): # if not, system exits check_filenames(file_paths, df_runs) - def upload(self): - """Create the required files and upload to ENA""" - self.convert_input_json_to_ena() - self.create_structure_to_ena() + +""" + # generate MD5 sum if not supplied in table + if file_paths and not check_file_checksum(df): + print("No valid checksums found, generate now...", end=" ") + file_md5 = {filename: get_md5(path) for filename, path + in file_paths.items()} + + # update schema_targets wih md5 hash + md5 = df['file_name'].apply(lambda x: file_md5[x]).values + # SettingWithCopyWarning causes false positive + # e.g at df.loc[:, 'file_checksum'] = md5 + pd.options.mode.chained_assignment = None + df.loc[:, 'file_checksum'] = md5 + print("done.") + elif check_file_checksum(df): + print("Valid checksums found", end=" ") + else: + sys.exit("No valid checksums found and no files given to generate checksum from. Please list the files using the --data option or specify the checksums in the run-table when the data is uploaded separately.") + + schema_targets['run'] = df + + # submit data to webin ftp server + if args.no_data_upload: + print( + "No files will be uploaded, remove `--no_data_upload' argument to perform upload.") + elif draft: + print( + "No files will be uploaded, remove `--draft' argument to perform upload.") + else: + submit_data(file_paths, password, webin_id) + + # when adding sample + # update schema_targets with taxon ids or scientific names + if 'sample' in schema_targets: + df = schema_targets['sample'] + print('Retrieving taxon IDs and scientific names if needed') + for index, row in df.iterrows(): + if pd.notna(row['scientific_name']) and pd.isna(row['taxon_id']): + # retrieve taxon id using scientific name + taxonID = get_taxon_id(row['scientific_name']) + df.loc[index, 'taxon_id'] = taxonID + elif pd.notna(row['taxon_id']) and pd.isna(row['scientific_name']): + # retrieve scientific name using taxon id + scientificName = get_scientific_name(row['taxon_id']) + df.loc[index, 'scientific_name'] = scientificName + elif pd.isna(row['taxon_id']) and pd.isna(row['scientific_name']): + sys.exit( + f"No taxon_id or scientific_name was given with sample {row['alias']}.") + print('Taxon IDs and scientific names are retrieved') + schema_targets['sample'] = df + + # ? need to add a place holder for setting up + base_path = os.path.abspath(os.path.dirname(__file__)) + template_path = os.path.join(base_path, 'templates' + + """ + + +def upload(self): + """Create the required files and upload to ENA""" + self.convert_input_json_to_ena() + self.create_structure_to_ena() From 97e15151adfcbda9b49ce97f874dca353a31901c Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 20 Apr 2022 15:59:35 +0200 Subject: [PATCH 0347/1454] changes in main, enaupload and json file to_ena_2.json stuck with checkfilename funciton --- relecov_tools/__main__.py | 5 +- relecov_tools/ena_upload.py | 129 +++++++++-------------- relecov_tools/example_data/to_ena_2.json | 4 +- 3 files changed, 56 insertions(+), 82 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index a49ee039..4ae2da1a 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -253,6 +253,7 @@ def map(origin_schema, json_data, destination_schema, schema_file, output): @click.option("-p", "--password", help="password for the user to login") @click.option("-e", "--ena_json", help="where the validated json is") @click.option("-s", "--study", help="study/project name to include in xml files") +@click.option("-f", "--filename", help="data for submitting RUN objec") @click.option( "-a", "--action", @@ -261,10 +262,10 @@ def map(origin_schema, json_data, destination_schema, schema_file, output): ) @click.option("--dev/--production", default=True) @click.option("-o", "--output_path", help="output folder for the xml generated files") -def upload_to_ena(user, password, ena_json, dev, study, action, output_path): +def upload_to_ena(user, password, ena_json, dev, study, action, output_path, filename): """parsed data to create xml files to upload to ena""" upload_ena = relecov_tools.ena_upload.EnaUpload( - user, password, ena_json, dev, study, action, output_path + user, password, ena_json, dev, study, action, output_path, filename ) upload_ena.upload() diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 61957e85..7e631d0b 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -34,6 +34,7 @@ def __init__( customized_project=None, action=None, output_path=None, + filename=None, ): if user is None: self.user = relecov_tools.utils.prompt_text( @@ -83,6 +84,22 @@ def __init__( sys.exit(1) with open(self.source_json_file, "r") as fh: self.json_data = json.loads(fh.read()) + # check if data is given when adding a 'run' table + + if filename is None: + self.filename = relecov_tools.utils.prompt_path( + msg="Oops, requires data for submitting RUN object" + ) + else: + self.filename = filename + """ + else: + # validate if given data is file + for path in filename: + if not os.path.isfile(path): + msg = f"Oops, the file {path} does not exist" + log.error(msg) + """ def convert_input_json_to_ena(self): """Split the input ena json, in samples and runs json""" @@ -108,8 +125,8 @@ def create_structure_to_ena(self): esquema_json = json.load(fh_esquema) fh_esquema.close() - df = pd.DataFrame.from_dict(esquema_json, orient="index") - df_transposed = df.T + df_schemas = pd.DataFrame.from_dict(esquema_json, orient="index") + df_transposed = df_schemas.T df_study = df_transposed[["study_alias", "study_title", "study_type"]] df_study.insert(3, "status", self.action) df_samples = df_transposed[ @@ -126,10 +143,10 @@ def create_structure_to_ena(self): ] ] df_samples.insert(3, "status", self.action) - df_runs = df_transposed[ - ["experiment_alias", "sequence_file_R1_fastq", "sequence_file_R2_fastq"] + df_run = df_transposed[ + ["experiment_alias", "file_name", "sequence_file_R2_fastq"] ] - df_runs.insert(3, "status", self.action) + df_run.insert(3, "status", self.action) df_experiments = df_transposed[ [ "experiment_alias", @@ -148,21 +165,19 @@ def create_structure_to_ena(self): schema_dataframe = {} schema_dataframe["study"] = df_study schema_dataframe["samples"] = df_samples - schema_dataframe["runs"] = df_runs + schema_dataframe["run"] = df_run schema_dataframe["experiments"] = df_experiments schema_targets = extract_targets(self.action, schema_dataframe) - import pdb - - pdb.set_trace() - + """ if not schema_targets: stderr.print( f"[red] There is no table submitted having at least one row with {self.action} as action in the status column." ) sys.exit(1) + """ - if self.action == "ADD": + if self.action == "ADD" or self.action == "add": # when adding run object # update schema_targets wit md5 hash # submit data @@ -170,73 +185,31 @@ def create_structure_to_ena(self): # a dictionary of filename:file_path df = schema_targets["run"] file_paths = {} - if self.source_json: - for path in self.source_json: + if self.filename: + for path in self.source_json_file: file_paths[os.path.basename(path)] = os.path.abspath(path) # check if file names identical between command line and table # if not, system exits - check_filenames(file_paths, df_runs) - - -""" - # generate MD5 sum if not supplied in table - if file_paths and not check_file_checksum(df): - print("No valid checksums found, generate now...", end=" ") - file_md5 = {filename: get_md5(path) for filename, path - in file_paths.items()} - - # update schema_targets wih md5 hash - md5 = df['file_name'].apply(lambda x: file_md5[x]).values - # SettingWithCopyWarning causes false positive - # e.g at df.loc[:, 'file_checksum'] = md5 - pd.options.mode.chained_assignment = None - df.loc[:, 'file_checksum'] = md5 - print("done.") - elif check_file_checksum(df): - print("Valid checksums found", end=" ") - else: - sys.exit("No valid checksums found and no files given to generate checksum from. Please list the files using the --data option or specify the checksums in the run-table when the data is uploaded separately.") - - schema_targets['run'] = df - - # submit data to webin ftp server - if args.no_data_upload: - print( - "No files will be uploaded, remove `--no_data_upload' argument to perform upload.") - elif draft: - print( - "No files will be uploaded, remove `--draft' argument to perform upload.") - else: - submit_data(file_paths, password, webin_id) - - # when adding sample - # update schema_targets with taxon ids or scientific names - if 'sample' in schema_targets: - df = schema_targets['sample'] - print('Retrieving taxon IDs and scientific names if needed') - for index, row in df.iterrows(): - if pd.notna(row['scientific_name']) and pd.isna(row['taxon_id']): - # retrieve taxon id using scientific name - taxonID = get_taxon_id(row['scientific_name']) - df.loc[index, 'taxon_id'] = taxonID - elif pd.notna(row['taxon_id']) and pd.isna(row['scientific_name']): - # retrieve scientific name using taxon id - scientificName = get_scientific_name(row['taxon_id']) - df.loc[index, 'scientific_name'] = scientificName - elif pd.isna(row['taxon_id']) and pd.isna(row['scientific_name']): - sys.exit( - f"No taxon_id or scientific_name was given with sample {row['alias']}.") - print('Taxon IDs and scientific names are retrieved') - schema_targets['sample'] = df - - # ? need to add a place holder for setting up - base_path = os.path.abspath(os.path.dirname(__file__)) - template_path = os.path.join(base_path, 'templates' - - """ - - -def upload(self): - """Create the required files and upload to ENA""" - self.convert_input_json_to_ena() - self.create_structure_to_ena() + check_filenames(file_paths, df_run) + # generate MD5 sum if not supplied in table + if file_paths and not check_file_checksum(df): + print("No valid checksums found, generate now...", end=" ") + file_md5 = { + filename: get_md5(path) for filename, path in file_paths.items() + } + df_experiments.insert(1, "status", self.action) + import pdb + + pdb.set_trace() + # update schema_targets wih md5 hash + md5 = df["file_name"].apply(lambda x: file_md5[x]).values + # SettingWithCopyWarning causes false positive + # e.g at df.loc[:, 'file_checksum'] = md5 + pd.options.mode.chained_assignment = None + df.loc[:, "file_checksum"] = md5 + print("done.") + + def upload(self): + """Create the required files and upload to ENA""" + self.convert_input_json_to_ena() + self.create_structure_to_ena() diff --git a/relecov_tools/example_data/to_ena_2.json b/relecov_tools/example_data/to_ena_2.json index 9fd0de80..3f3aee55 100644 --- a/relecov_tools/example_data/to_ena_2.json +++ b/relecov_tools/example_data/to_ena_2.json @@ -21,8 +21,8 @@ "library_source": "RNA", "library_strategy": "WGS strategy", "purpose_sampling": "Surveillance", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "file_name": "/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/example_data/ENA_TEST1.R1.fastq", + "r2_fastq_filepath": "/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/example_data/", "receipt_date": "2021/05/13", "run_alias": "", "sample_description": "Sample for surveillance", From 9552263148d825627089d65a2a72924aedd3b278 Mon Sep 17 00:00:00 2001 From: ErikaKvalem Date: Thu, 21 Apr 2022 11:12:56 +0200 Subject: [PATCH 0348/1454] fixing lintin --- relecov_tools/ena_upload.py | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 7e631d0b..cf6b8091 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,5 +1,5 @@ -from bdb import set_trace -import os +#from pdb import set_trace +import python3 get-pip.py import logging import rich.console import json @@ -12,8 +12,8 @@ from ena_upload.ena_upload import check_filenames from ena_upload.ena_upload import check_file_checksum from ena_upload.ena_upload import get_md5 -from ena_upload.ena_upload import get_taxon_id -from ena_upload.ena_upload import get_scientific_name +# from ena_upload.ena_upload import get_taxon_id +# from ena_upload.ena_upload import get_scientific_name log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -111,6 +111,7 @@ def create_structure_to_ena(self): config_json = ConfigJson() + """ map_to_upload = config_json.get_topic_data("json_schemas", "ena_schema") map_file = os.path.join( @@ -119,6 +120,7 @@ def create_structure_to_ena(self): fh = open(map_file) map_structure_json = json.load(fh) fh.close() + """ esquema = self.source_json_file fh_esquema = open(esquema) @@ -213,3 +215,8 @@ def upload(self): """Create the required files and upload to ENA""" self.convert_input_json_to_ena() self.create_structure_to_ena() + + + + + From a562f7228f86573cea147f41bf2de015d65593f0 Mon Sep 17 00:00:00 2001 From: ErikaKvalem Date: Thu, 21 Apr 2022 11:31:47 +0200 Subject: [PATCH 0349/1454] changed import for linting --- relecov_tools/ena_upload.py | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index cf6b8091..45dd125e 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,5 +1,5 @@ -#from pdb import set_trace -import python3 get-pip.py +# from pdb import set_trace +# import python3 get-pip.py import logging import rich.console import json @@ -12,6 +12,7 @@ from ena_upload.ena_upload import check_filenames from ena_upload.ena_upload import check_file_checksum from ena_upload.ena_upload import get_md5 + # from ena_upload.ena_upload import get_taxon_id # from ena_upload.ena_upload import get_scientific_name @@ -215,8 +216,3 @@ def upload(self): """Create the required files and upload to ENA""" self.convert_input_json_to_ena() self.create_structure_to_ena() - - - - - From 4c723518e78eaf87cd7fc1b1c36a7749b74a4cd7 Mon Sep 17 00:00:00 2001 From: ErikaKvalem Date: Thu, 21 Apr 2022 11:37:53 +0200 Subject: [PATCH 0350/1454] fixing linting 2 --- relecov_tools/ena_upload.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 45dd125e..acdf36a0 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -6,6 +6,7 @@ import pandas as pd import sys +import os import relecov_tools.utils from relecov_tools.config_json import ConfigJson from ena_upload.ena_upload import extract_targets @@ -110,7 +111,7 @@ def create_structure_to_ena(self): """Convert json to dataframe required by ena-upload-cli package""" # schema_dataframe = {} - config_json = ConfigJson() + # config_json = ConfigJson() """ map_to_upload = config_json.get_topic_data("json_schemas", "ena_schema") From 9b2d23f8686cb2fe9bbd443c2d42cfa31c1b5615 Mon Sep 17 00:00:00 2001 From: ErikaKvalem Date: Thu, 21 Apr 2022 11:41:16 +0200 Subject: [PATCH 0351/1454] fixing linting 3 --- relecov_tools/ena_upload.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index acdf36a0..c8588668 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -8,7 +8,8 @@ import sys import os import relecov_tools.utils -from relecov_tools.config_json import ConfigJson + +# from relecov_tools.config_json import ConfigJson from ena_upload.ena_upload import extract_targets from ena_upload.ena_upload import check_filenames from ena_upload.ena_upload import check_file_checksum From fb3e1be44aa48f7bf34639ea0fe53f00b69a8372 Mon Sep 17 00:00:00 2001 From: ErikaKvalem Date: Thu, 21 Apr 2022 15:32:55 +0200 Subject: [PATCH 0352/1454] adding center name, removed filename for input in terminal --- relecov_tools/__main__.py | 6 +- relecov_tools/ena_upload.py | 142 +++++++++++------------ relecov_tools/example_data/to_ena_2.json | 12 +- 3 files changed, 78 insertions(+), 82 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index fb4d0725..e5e6db57 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -252,9 +252,9 @@ def map(origin_schema, json_data, destination_schema, schema_file, output): @relecov_tools_cli.command(help_priority=6) @click.option("-u", "--user", help="user name for login to ena") @click.option("-p", "--password", help="password for the user to login") +@click.option("-c", "--center", help="center name") @click.option("-e", "--ena_json", help="where the validated json is") @click.option("-s", "--study", help="study/project name to include in xml files") -@click.option("-f", "--filename", help="data for submitting RUN objec") @click.option( "-a", "--action", @@ -263,10 +263,10 @@ def map(origin_schema, json_data, destination_schema, schema_file, output): ) @click.option("--dev/--production", default=True) @click.option("-o", "--output_path", help="output folder for the xml generated files") -def upload_to_ena(user, password, ena_json, dev, study, action, output_path, filename): +def upload_to_ena(user, password, center, ena_json, dev, study, action, output_path): """parsed data to create xml files to upload to ena""" upload_ena = relecov_tools.ena_upload.EnaUpload( - user, password, ena_json, dev, study, action, output_path, filename + user, password, center, ena_json, dev, study, action, output_path ) upload_ena.upload() diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index c8588668..011e208d 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,5 +1,3 @@ -# from pdb import set_trace -# import python3 get-pip.py import logging import rich.console import json @@ -9,14 +7,12 @@ import os import relecov_tools.utils -# from relecov_tools.config_json import ConfigJson + from ena_upload.ena_upload import extract_targets -from ena_upload.ena_upload import check_filenames -from ena_upload.ena_upload import check_file_checksum -from ena_upload.ena_upload import get_md5 +from ena_upload.ena_upload import submit_data +from ena_upload.ena_upload import run_construct +from ena_upload.ena_upload import construct_submission -# from ena_upload.ena_upload import get_taxon_id -# from ena_upload.ena_upload import get_scientific_name log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -32,12 +28,12 @@ def __init__( self, user=None, passwd=None, + center = None, source_json=None, dev=None, customized_project=None, action=None, output_path=None, - filename=None, ): if user is None: self.user = relecov_tools.utils.prompt_text( @@ -51,6 +47,12 @@ def __init__( ) else: self.passwd = passwd + if center is None: + self.center = relecov_tools.utils.prompt_text( + msg="Enter your center name" + ) + else: + self.center = center if source_json is None: self.source_json_file = relecov_tools.utils.prompt_path( msg="Select the ENA json file to upload" @@ -89,21 +91,6 @@ def __init__( self.json_data = json.loads(fh.read()) # check if data is given when adding a 'run' table - if filename is None: - self.filename = relecov_tools.utils.prompt_path( - msg="Oops, requires data for submitting RUN object" - ) - else: - self.filename = filename - """ - else: - # validate if given data is file - for path in filename: - if not os.path.isfile(path): - msg = f"Oops, the file {path} does not exist" - log.error(msg) - """ - def convert_input_json_to_ena(self): """Split the input ena json, in samples and runs json""" pass @@ -114,17 +101,6 @@ def create_structure_to_ena(self): # config_json = ConfigJson() - """ - map_to_upload = config_json.get_topic_data("json_schemas", "ena_schema") - - map_file = os.path.join( - os.path.dirname(os.path.realpath(__file__)), "schema", map_to_upload - ) - fh = open(map_file) - map_structure_json = json.load(fh) - fh.close() - """ - esquema = self.source_json_file fh_esquema = open(esquema) esquema_json = json.load(fh_esquema) @@ -149,9 +125,16 @@ def create_structure_to_ena(self): ] df_samples.insert(3, "status", self.action) df_run = df_transposed[ - ["experiment_alias", "file_name", "sequence_file_R2_fastq"] + [ + "experiment_alias", + "sequence_file_R1_fastq", + "sequence_file_R2_fastq", + "r1_fastq_filepath", + "r2_fastq_filepath", + ] ] df_run.insert(3, "status", self.action) + df_experiments = df_transposed[ [ "experiment_alias", @@ -174,47 +157,60 @@ def create_structure_to_ena(self): schema_dataframe["experiments"] = df_experiments schema_targets = extract_targets(self.action, schema_dataframe) - """ - if not schema_targets: - stderr.print( - f"[red] There is no table submitted having at least one row with {self.action} as action in the status column." - ) - sys.exit(1) - """ if self.action == "ADD" or self.action == "add": - # when adding run object - # update schema_targets wit md5 hash - # submit data - if "run" in schema_targets: - # a dictionary of filename:file_path - df = schema_targets["run"] - file_paths = {} - if self.filename: - for path in self.source_json_file: - file_paths[os.path.basename(path)] = os.path.abspath(path) - # check if file names identical between command line and table - # if not, system exits - check_filenames(file_paths, df_run) - # generate MD5 sum if not supplied in table - if file_paths and not check_file_checksum(df): - print("No valid checksums found, generate now...", end=" ") - file_md5 = { - filename: get_md5(path) for filename, path in file_paths.items() - } - df_experiments.insert(1, "status", self.action) - import pdb - - pdb.set_trace() - # update schema_targets wih md5 hash - md5 = df["file_name"].apply(lambda x: file_md5[x]).values - # SettingWithCopyWarning causes false positive - # e.g at df.loc[:, 'file_checksum'] = md5 - pd.options.mode.chained_assignment = None - df.loc[:, "file_checksum"] = md5 - print("done.") + file_paths = {} + + for path in df_run["r1_fastq_filepath"]: + file_paths[os.path.basename(path)] = os.path.abspath(path) + import pdb + + pdb.set_trace() + + # submit data to webin ftp server + if self.dev == "dev": + print( + "No files will be uploaded, remove `--no_data_upload' argument to perform upload." + ) + else: + submit_data(file_paths, self.passwd, self.user) + + # when ADD/MODIFY, + # requires source XMLs for 'run', 'experiment', 'sample', 'experiment' + # schema_xmls record XMLs for all these schema and following 'submission' + tool = "ena-upload-cli" + checklist = "ERC000033" + schema_xmls = run_construct( + template_path, schema_targets, center, checklist, tool + ) + + submission_xml = construct_submission( + template_path, action, schema_xmls, center, checklist, tool + ) def upload(self): """Create the required files and upload to ENA""" self.convert_input_json_to_ena() self.create_structure_to_ena() + + +""" +def check_filenames(file_paths, run_df): + + Compare data filenames from command line and from RUN table. + :param file_paths: a dictionary of filename string and file_path string + :param df: dataframe built from RUN table + + + cmd_input = file_paths.keys() + table_input = run_df['file_name'].values + + # symmetric difference between two sets + difference = set(cmd_input) ^ set(table_input) + + if difference: + msg = f"different file names between command line and RUN table: {difference}" + sys.exit(msg) + + +""" diff --git a/relecov_tools/example_data/to_ena_2.json b/relecov_tools/example_data/to_ena_2.json index 3f3aee55..4c69ecc6 100644 --- a/relecov_tools/example_data/to_ena_2.json +++ b/relecov_tools/example_data/to_ena_2.json @@ -21,19 +21,19 @@ "library_source": "RNA", "library_strategy": "WGS strategy", "purpose_sampling": "Surveillance", - "file_name": "/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/example_data/ENA_TEST1.R1.fastq", - "r2_fastq_filepath": "/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/example_data/", + "r1_fastq_filepath": "/Users/erika/Desktop/relecov-tools/relecov_tools/example_data/ENA_TEST1.R1.fastq", + "r2_fastq_filepath": "/Users/erika/Desktop/relecov-tools/relecov_tools/example_data/ENA_TEST1.R2.fastq", "receipt_date": "2021/05/13", "run_alias": "", "sample_description": "Sample for surveillance", "sample_name": "1197860", "sample_storage_conditions": " -80ºC", "scientific_name": "Severe acute respiratory syndrome coronavirus 2", - "sequence_file_R1_fastq": "ABC123_S1_L001_R1_001.fastq.gz", - "sequence_file_R2_fastq": "ABC123_S1_L001_R2_001.fastq.gz", + "sequence_file_R1_fastq": "ENA_TEST1.R1.fastq", + "sequence_file_R2_fastq": "ENA_TEST1.R2.fastq", "study_alias": "RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "RELECOV Spanish Network for genomics surveillance", "tax_id": "2697049", - "query":"" -} + "query": "" +} \ No newline at end of file From 47bf6c727d9c022834d200a7cf2a9713b68d0448 Mon Sep 17 00:00:00 2001 From: ErikaKvalem Date: Thu, 21 Apr 2022 17:39:48 +0200 Subject: [PATCH 0353/1454] added templates folder, 2 fields to configuration.json and modified ena_upload --- relecov_tools/conf/configuration.json | 53 ++-- relecov_tools/ena_upload.py | 55 ++--- .../templates/ENA_template_experiments.xml | 51 ++++ relecov_tools/templates/ENA_template_runs.xml | 36 +++ .../ENA_template_samples_ERC000033.xml | 228 ++++++++++++++++++ .../templates/ENA_template_studies.xml | 49 ++++ .../templates/ENA_template_submission.xml | 36 +++ 7 files changed, 458 insertions(+), 50 deletions(-) create mode 100644 relecov_tools/templates/ENA_template_experiments.xml create mode 100644 relecov_tools/templates/ENA_template_runs.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000033.xml create mode 100644 relecov_tools/templates/ENA_template_studies.xml create mode 100644 relecov_tools/templates/ENA_template_submission.xml diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 49d02676..22ed5aa4 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -16,43 +16,66 @@ "fasta" ], "laboratory_data": "laboratory_address.json", - "geo_location_data" : "geo_loc_cities.json", + "geo_location_data": "geo_loc_cities.json", "ENA_configuration": { "study_alias": "RELECOV", - "design_description":"Design Description", + "design_description": "Design Description", "experiment_alias": "", "run_alias": "", "experiment_title": "Example project for ENA submission RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance" }, - "external_url":{ + "external_url": { "iskylims": { "server": "http://relecov-iskylims.isciiides.es", "url": "/wetlab/api/", "store_samples": "createSampleData", "url_project_fields": "sampleProjectFields", - "project_name" : "Relecov", + "project_name": "Relecov", "token": "" - }, + }, "relecov": { "server": "http://relecov-platform.isciiides.es", "url": "/api/", "store_samples": "storeData", "token": "" - } + } }, "iskylims_sample_fields": [ - ["patientCore", "collector_name"], - ["sampleName", "collecting_lab_sample_id"], - ["labRequest","collecting_institution"], - ["sampleType", "anatomical_material"], - ["species", "host_common_name"], - ["sampleEntryDate", "sample_received_date"], - ["sampleCollectionDate", "sample_collection_date"] + [ + "patientCore", + "collector_name" + ], + [ + "sampleName", + "collecting_lab_sample_id" + ], + [ + "labRequest", + "collecting_institution" + ], + [ + "sampleType", + "anatomical_material" + ], + [ + "species", + "host_common_name" + ], + [ + "sampleEntryDate", + "sample_received_date" + ], + [ + "sampleCollectionDate", + "sample_collection_date" + ] ], "iskylims_fixed_values": { "sampleProject": "Relecov", "onlyRecorded": "Yes", "sampleLocation": "Not defined" - } -} + }, + "tool": "ena-upload-cli", + "checklist": "ERC000033" +} \ No newline at end of file diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 011e208d..24a1f879 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -6,6 +6,7 @@ import sys import os import relecov_tools.utils +from relecov_tools.config_json import ConfigJson from ena_upload.ena_upload import extract_targets @@ -28,7 +29,7 @@ def __init__( self, user=None, passwd=None, - center = None, + center=None, source_json=None, dev=None, customized_project=None, @@ -48,9 +49,7 @@ def __init__( else: self.passwd = passwd if center is None: - self.center = relecov_tools.utils.prompt_text( - msg="Enter your center name" - ) + self.center = relecov_tools.utils.prompt_text(msg="Enter your center name") else: self.center = center if source_json is None: @@ -163,54 +162,40 @@ def create_structure_to_ena(self): for path in df_run["r1_fastq_filepath"]: file_paths[os.path.basename(path)] = os.path.abspath(path) - import pdb - - pdb.set_trace() # submit data to webin ftp server - if self.dev == "dev": + if self.dev: print( "No files will be uploaded, remove `--no_data_upload' argument to perform upload." ) + else: - submit_data(file_paths, self.passwd, self.user) + + submit_data(file_paths, self.passwd, self.user) # when ADD/MODIFY, # requires source XMLs for 'run', 'experiment', 'sample', 'experiment' # schema_xmls record XMLs for all these schema and following 'submission' - tool = "ena-upload-cli" - checklist = "ERC000033" + + # No me está funcionando con el absolute path + # base_path = os.path.abspath(os.path.dirname(__file__)) + base_path = os.getcwd() + template_path = os.path.join(base_path, "relecov_tools", "templates") + config_json = ConfigJson() + tool = config_json.get_configuration("tool") + checklist = config_json.get_configuration("checklist") + import pdb + + pdb.set_trace() schema_xmls = run_construct( - template_path, schema_targets, center, checklist, tool + template_path, schema_targets, self.center, checklist, tool ) submission_xml = construct_submission( - template_path, action, schema_xmls, center, checklist, tool + template_path, self.action, schema_xmls, self.center, checklist, tool ) def upload(self): """Create the required files and upload to ENA""" self.convert_input_json_to_ena() self.create_structure_to_ena() - - -""" -def check_filenames(file_paths, run_df): - - Compare data filenames from command line and from RUN table. - :param file_paths: a dictionary of filename string and file_path string - :param df: dataframe built from RUN table - - - cmd_input = file_paths.keys() - table_input = run_df['file_name'].values - - # symmetric difference between two sets - difference = set(cmd_input) ^ set(table_input) - - if difference: - msg = f"different file names between command line and RUN table: {difference}" - sys.exit(msg) - - -""" diff --git a/relecov_tools/templates/ENA_template_experiments.xml b/relecov_tools/templates/ENA_template_experiments.xml new file mode 100644 index 00000000..b2c77ce5 --- /dev/null +++ b/relecov_tools/templates/ENA_template_experiments.xml @@ -0,0 +1,51 @@ + + + + + + ${row.title} + + + ${row.design_description} + + ${row.spot_descriptor} + + + + ${row.library_name} + + + + + + + + + ${row.library_construction_protocol} + + + + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_runs.xml b/relecov_tools/templates/ENA_template_runs.xml new file mode 100644 index 00000000..ade3e42f --- /dev/null +++ b/relecov_tools/templates/ENA_template_runs.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000033.xml b/relecov_tools/templates/ENA_template_samples_ERC000033.xml new file mode 100644 index 00000000..46e57d86 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000033.xml @@ -0,0 +1,228 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + + subject exposure + ${row['subject exposure']} + + + + + subject exposure duration + ${row['subject exposure duration']} + + + + + type exposure + ${row['type exposure']} + + + + + personal protective equipment + ${row['personal protective equipment']} + + + + + hospitalisation + ${row['hospitalisation']} + + + + + illness duration + ${row['illness duration']} + + + + + illness symptoms + ${row['illness symptoms']} + + + + + collection date + ${row['collection date']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + sample capture status + ${row['sample capture status']} + + + + + host disease outcome + ${row['host disease outcome']} + + + + host common name + ${row['host common name']} + + + host subject id + ${row['host subject id']} + + + + host age + ${row['host age']} + + + + host health state + ${row['host health state']} + + + host sex + ${row['host sex']} + + + host scientific name + ${row['host scientific name']} + + + + virus identifier + ${row['virus identifier']} + + + + collector name + ${row['collector name']} + + + collecting institution + ${row['collecting institution']} + + + + receipt date + ${row['receipt date']} + + + + + sample storage conditions + ${row['sample storage conditions']} + + + + + definition for seropositive sample + ${row['definition for seropositive sample']} + + + + + serotype (required for a seropositive sample) + ${row['serotype (required for a seropositive sample)']} + + + + isolate + ${row['isolate']} + + + + strain + ${row['strain']} + + + + + host habitat + ${row['host habitat']} + + + + + isolation source host-associated + ${row['isolation source host-associated']} + + + + + host description + ${row['host description']} + + + + + gravidity + ${row['gravidity']} + + + + + host behaviour + ${row['host behaviour']} + + + + + isolation source non-host-associated + ${row['isolation source non-host-associated']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_studies.xml b/relecov_tools/templates/ENA_template_studies.xml new file mode 100644 index 00000000..2316d410 --- /dev/null +++ b/relecov_tools/templates/ENA_template_studies.xml @@ -0,0 +1,49 @@ + + + + + + + ${row.title} + + ${row.study_abstract} + + ${row.center_project_name} + + + ${row.study_description} + + + + + + + PUBMED + ${row.pubmed_id} + + + + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_submission.xml b/relecov_tools/templates/ENA_template_submission.xml new file mode 100644 index 00000000..7cf27072 --- /dev/null +++ b/relecov_tools/templates/ENA_template_submission.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file From b779d99f1b66e9b0dfb135282dd1fd5d6f4c6346 Mon Sep 17 00:00:00 2001 From: ErikaKvalem Date: Thu, 21 Apr 2022 17:43:47 +0200 Subject: [PATCH 0354/1454] changed templates path to og --- relecov_tools/ena_upload.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 24a1f879..8177c9d9 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -178,9 +178,8 @@ def create_structure_to_ena(self): # schema_xmls record XMLs for all these schema and following 'submission' # No me está funcionando con el absolute path - # base_path = os.path.abspath(os.path.dirname(__file__)) - base_path = os.getcwd() - template_path = os.path.join(base_path, "relecov_tools", "templates") + base_path = os.path.abspath(os.path.dirname(__file__)) + template_path = os.path.join(base_path, "templates") config_json = ConfigJson() tool = config_json.get_configuration("tool") checklist = config_json.get_configuration("checklist") From fd0f012cb087842cd48cc9e12eac9164001e3201 Mon Sep 17 00:00:00 2001 From: ErikaKvalem Date: Thu, 21 Apr 2022 20:09:04 +0200 Subject: [PATCH 0355/1454] added changes to dict tools --- relecov_tools/conf/configuration.json | 5 ++++- relecov_tools/ena_upload.py | 11 ++++++++--- 2 files changed, 12 insertions(+), 4 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 22ed5aa4..1c23b6c7 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -76,6 +76,9 @@ "onlyRecorded": "Yes", "sampleLocation": "Not defined" }, - "tool": "ena-upload-cli", + "tool": { + "tool_name": "ena-upload-cli", + "tool_version": "1.0" + }, "checklist": "ERC000033" } \ No newline at end of file diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 8177c9d9..8b25a7a0 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -13,6 +13,9 @@ from ena_upload.ena_upload import submit_data from ena_upload.ena_upload import run_construct from ena_upload.ena_upload import construct_submission +import site + +template_path = os.path.join(site.getsitepackages()[0], "ena_upload", "templates") log = logging.getLogger(__name__) @@ -178,10 +181,12 @@ def create_structure_to_ena(self): # schema_xmls record XMLs for all these schema and following 'submission' # No me está funcionando con el absolute path - base_path = os.path.abspath(os.path.dirname(__file__)) - template_path = os.path.join(base_path, "templates") + # base_path = os.path.abspath(os.path.dirname(__file__)) + # base_path = "miniconda3/envs/relecov/lib/python3.1/site-packages/ena_upload" + # template_path = os.path.join(base_path, "templates") config_json = ConfigJson() - tool = config_json.get_configuration("tool") + # tool = config_json.get_topic_data("tool") + tool = {"tool_name": "ena-upload-cli", "tool_version": "1.0"} checklist = config_json.get_configuration("checklist") import pdb From f17336aed6f4debafa26bfd2bfa402d7e2527e1e Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 22 Apr 2022 12:26:12 +0200 Subject: [PATCH 0356/1454] include json for testing upload ENA --- ..._LAB_TEST_2022_04_22_12_23_ENA_mapped.json | 382 ++++++++++++++++++ 1 file changed, 382 insertions(+) create mode 100644 relecov_tools/example_data/processed_METADATA_LAB_TEST_2022_04_22_12_23_ENA_mapped.json diff --git a/relecov_tools/example_data/processed_METADATA_LAB_TEST_2022_04_22_12_23_ENA_mapped.json b/relecov_tools/example_data/processed_METADATA_LAB_TEST_2022_04_22_12_23_ENA_mapped.json new file mode 100644 index 00000000..610d84b2 --- /dev/null +++ b/relecov_tools/example_data/processed_METADATA_LAB_TEST_2022_04_22_12_23_ENA_mapped.json @@ -0,0 +1,382 @@ +[ + { + "collection_date": "2021/04/13", + "common_name": "PEPITO", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "f2facbd1d6c7e0972074ced31ccbfd8e", + "fastq_r2_md5": "fd9948be8da7a38b0f80659dfc21aeea", + "geographic location (latitude)": "41.6483", + "geographic location (longitude)": "-0.8830", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_gender": "Mujer", + "host_scientific_name": "Homo Sapiens", + "instrument_model": "Illumina MiSeq", + "instrument_platform": "Illumina", + "isolate": "1197860", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "Single End", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "purpose_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "receipt_date": "2021/05/13", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197860", + "sample_storage_conditions": " -80ºC", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_001.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_001.fastq.gz", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "RELECOV Spanish Network for genomics surveillance", + "tax_id": "2697049" + }, + { + "collection_date": "2021/03/31", + "common_name": "PEPITO", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "9a460a812086516536c1a1023ab5f7fe", + "fastq_r2_md5": "41cd79b8a167d85eb06309207fd120cf", + "geographic location (latitude)": "41.6483", + "geographic location (longitude)": "-0.8830", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_gender": "Hombre", + "host_scientific_name": "Homo Sapiens", + "instrument_model": "Illumina MiSeq", + "instrument_platform": "Illumina", + "isolate": "1197824", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "Single End", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "purpose_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "receipt_date": "2021/05/13", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197824", + "sample_storage_conditions": " -80ºC", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_002.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_002.fastq.gz", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "RELECOV Spanish Network for genomics surveillance", + "tax_id": "2697049" + }, + { + "collection_date": "2022/01/13", + "common_name": "PEPITO", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "c78fcb585a0f44734ce8c2aebf3eff33", + "fastq_r2_md5": "8361d5a6b50279fbc8c93226ecc3568a", + "geographic location (latitude)": "41.6483", + "geographic location (longitude)": "-0.8830", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_gender": "Mujer", + "host_scientific_name": "Homo Sapiens", + "instrument_model": "Illumina MiSeq", + "instrument_platform": "Illumina", + "isolate": "1197767", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "Single End", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "purpose_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "receipt_date": "2022/01/18", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197767", + "sample_storage_conditions": " -80ºC", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_003.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_003.fastq.gz", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "RELECOV Spanish Network for genomics surveillance", + "tax_id": "2697049" + }, + { + "collection_date": "2022/01/11", + "common_name": "PEPITO", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "aa557fc40d3a9e16f470ac595fb5eb3e", + "fastq_r2_md5": "a2dd5e08b75815dab892e392cb8468fc", + "geographic location (latitude)": "41.6483", + "geographic location (longitude)": "-0.8830", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_gender": "Mujer", + "host_scientific_name": "Homo Sapiens", + "instrument_model": "Illumina MiSeq", + "instrument_platform": "Illumina", + "isolate": "8328199", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "Single End", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "purpose_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "receipt_date": "2022/01/20", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "8328199", + "sample_storage_conditions": " -80ºC", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_004.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_004.fastq.gz", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "RELECOV Spanish Network for genomics surveillance", + "tax_id": "2697049" + }, + { + "collection_date": "2022/01/10", + "common_name": "PEPITO", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "b0a13671031ef5aa7e0e6559a925a688", + "fastq_r2_md5": "8c420a603c81823e68436003825b1e1f", + "geographic location (latitude)": "41.6483", + "geographic location (longitude)": "-0.8830", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_gender": "Hombre", + "host_scientific_name": "Homo Sapiens", + "instrument_model": "Illumina MiSeq", + "instrument_platform": "Illumina", + "isolate": "1197677", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "Single End", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "purpose_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "receipt_date": "2022/01/20", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197677", + "sample_storage_conditions": " -80ºC", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_005.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_005.fastq.gz", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "RELECOV Spanish Network for genomics surveillance", + "tax_id": "2697049" + }, + { + "collection_date": "2022/01/12", + "common_name": "PEPITO", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "13e01498a0526303f5e32f3eef077b5a", + "fastq_r2_md5": "61d1f52e84237320d97fd7fc2da56116", + "geographic location (latitude)": "41.6483", + "geographic location (longitude)": "-0.8830", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_gender": "Mujer", + "host_scientific_name": "Homo Sapiens", + "instrument_model": "Illumina MiSeq", + "instrument_platform": "Illumina", + "isolate": "1197678", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "Single End", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "purpose_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "receipt_date": "2022/01/20", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197678", + "sample_storage_conditions": " -80ºC", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_006.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_006.fastq.gz", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "RELECOV Spanish Network for genomics surveillance", + "tax_id": "2697049" + }, + { + "collection_date": "2022/01/02", + "common_name": "PEPITO", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "f5b60a93b39a0b98781efb434d577a57", + "fastq_r2_md5": "e19f883b4e05045895f990c2296009a8", + "geographic location (latitude)": "41.6483", + "geographic location (longitude)": "-0.8830", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_gender": "Mujer", + "host_scientific_name": "Homo Sapiens", + "instrument_model": "Illumina MiSeq", + "instrument_platform": "Illumina", + "isolate": "1197737", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "Single End", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "purpose_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "receipt_date": "2022/01/20", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197737", + "sample_storage_conditions": " -80ºC", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_007.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_007.fastq.gz", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "RELECOV Spanish Network for genomics surveillance", + "tax_id": "2697049" + }, + { + "collection_date": "2022/01/23", + "common_name": "PEPITO", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "83043c429b0ab94375236cf7f51860f0", + "fastq_r2_md5": "c00859a1f83e2364cca953fb25da3cf2", + "geographic location (latitude)": "41.6483", + "geographic location (longitude)": "-0.8830", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_gender": "Hombre", + "host_scientific_name": "Homo Sapiens", + "instrument_model": "Illumina MiSeq", + "instrument_platform": "Illumina", + "isolate": "1197663", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "Single End", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "purpose_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "receipt_date": "2022/01/25", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197663", + "sample_storage_conditions": " -80ºC", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_008.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_008.fastq.gz", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "RELECOV Spanish Network for genomics surveillance", + "tax_id": "2697049" + }, + { + "collection_date": "2022/01/18", + "common_name": "PEPITO", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "bc720a024263a518f6a6cd9301b308ac", + "fastq_r2_md5": "6bf6d95b59c950691effcaf8a0e83068", + "geographic location (latitude)": "41.6483", + "geographic location (longitude)": "-0.8830", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_gender": "Hombre", + "host_scientific_name": "Homo Sapiens", + "instrument_model": "Illumina MiSeq", + "instrument_platform": "Illumina", + "isolate": "1197689", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "Single End", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "purpose_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "receipt_date": "2022/01/26", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197689", + "sample_storage_conditions": " -80ºC", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_009.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_009.fastq.gz", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "RELECOV Spanish Network for genomics surveillance", + "tax_id": "2697049" + }, + { + "collection_date": "2022/01/19", + "common_name": "PEPITO", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "a86f4fa0c92d76df34fd000a29d1cdd3", + "fastq_r2_md5": "8c4309dc00d725496c48bee6da0e4bbf", + "geographic location (latitude)": "41.6483", + "geographic location (longitude)": "-0.8830", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_gender": "Male", + "host_scientific_name": "Homo Sapiens", + "instrument_model": "Illumina MiSeq", + "instrument_platform": "Illumina", + "isolate": "1197685", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "Single End", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "purpose_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "receipt_date": "2022/01/26", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197685", + "sample_storage_conditions": " -80ºC", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_0010.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_0010.fastq.gz", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "RELECOV Spanish Network for genomics surveillance", + "tax_id": "2697049" + } +] \ No newline at end of file From f81b2efc1b0035b4328ed9d4b778079a2d8e8631 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 22 Apr 2022 13:56:56 +0200 Subject: [PATCH 0357/1454] ena-upload almost working removed templates folder --- relecov_tools/ena_upload.py | 93 +++++-- relecov_tools/example_data/to_ena_2.json | 41 ++-- .../templates/ENA_template_experiments.xml | 51 ---- relecov_tools/templates/ENA_template_runs.xml | 36 --- .../ENA_template_samples_ERC000033.xml | 228 ------------------ .../templates/ENA_template_studies.xml | 49 ---- .../templates/ENA_template_submission.xml | 36 --- 7 files changed, 93 insertions(+), 441 deletions(-) delete mode 100644 relecov_tools/templates/ENA_template_experiments.xml delete mode 100644 relecov_tools/templates/ENA_template_runs.xml delete mode 100644 relecov_tools/templates/ENA_template_samples_ERC000033.xml delete mode 100644 relecov_tools/templates/ENA_template_studies.xml delete mode 100644 relecov_tools/templates/ENA_template_submission.xml diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 8b25a7a0..ffc8b362 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -13,6 +13,10 @@ from ena_upload.ena_upload import submit_data from ena_upload.ena_upload import run_construct from ena_upload.ena_upload import construct_submission +from ena_upload.ena_upload import send_schemas +from ena_upload.ena_upload import process_receipt +from ena_upload.ena_upload import update_table +from ena_upload.ena_upload import save_update import site template_path = os.path.join(site.getsitepackages()[0], "ena_upload", "templates") @@ -91,7 +95,6 @@ def __init__( sys.exit(1) with open(self.source_json_file, "r") as fh: self.json_data = json.loads(fh.read()) - # check if data is given when adding a 'run' table def convert_input_json_to_ena(self): """Split the input ena json, in samples and runs json""" @@ -99,9 +102,6 @@ def convert_input_json_to_ena(self): def create_structure_to_ena(self): """Convert json to dataframe required by ena-upload-cli package""" - # schema_dataframe = {} - - # config_json = ConfigJson() esquema = self.source_json_file fh_esquema = open(esquema) @@ -110,21 +110,33 @@ def create_structure_to_ena(self): df_schemas = pd.DataFrame.from_dict(esquema_json, orient="index") df_transposed = df_schemas.T - df_study = df_transposed[["study_alias", "study_title", "study_type"]] + df_study = df_transposed[ + ["study_alias", "study_title", "study_type", "study_abstract"] + ] + df_study.rename(columns={"study_alias": "alias"}, inplace=True) + df_study.rename(columns={"study_title": "title"}, inplace=True) df_study.insert(3, "status", self.action) df_samples = df_transposed[ [ "sample_name", - "tax_id", + "sample_title", + "taxon_id", "sample_description", - "collection_date", - "geographic_location_(country_and/or_sea)", - "host_common_name", - "host_gender", - "host_scientific_name", + "collection date", + "geographic location (country and/or sea)", + "host common name", + "host scientific name", + "host subject id", + "host health state", + "host sex", + "scientific_name", + "collector name", + "collecting institution", "isolate", ] ] + df_samples.rename(columns={"sample_name": "alias"}, inplace=True) + df_samples.rename(columns={"sample_title": "title"}, inplace=True) df_samples.insert(3, "status", self.action) df_run = df_transposed[ [ @@ -133,30 +145,40 @@ def create_structure_to_ena(self): "sequence_file_R2_fastq", "r1_fastq_filepath", "r2_fastq_filepath", + "file_type", + "file_checksum", ] ] df_run.insert(3, "status", self.action) + df_run.insert(4, "alias", df_run["experiment_alias"]) + df_run.insert(4, "file_name", df_run["sequence_file_R1_fastq"]) df_experiments = df_transposed[ [ "experiment_alias", "study_title", + "study_alias", + "design_description", "sample_name", + "library_name", "library_strategy", "library_source", "library_selection", "library_layout", - "instrument_platform", + "platform", "instrument_model", ] ] df_experiments.insert(3, "status", self.action) + df_experiments.insert(4, "alias", df_experiments["experiment_alias"]) + df_experiments.rename(columns={"study_title": "title"}, inplace=True) + df_experiments.rename(columns={"sample_name": "sample_alias"}, inplace=True) schema_dataframe = {} schema_dataframe["study"] = df_study - schema_dataframe["samples"] = df_samples + schema_dataframe["sample"] = df_samples schema_dataframe["run"] = df_run - schema_dataframe["experiments"] = df_experiments + schema_dataframe["experiment"] = df_experiments schema_targets = extract_targets(self.action, schema_dataframe) @@ -168,29 +190,23 @@ def create_structure_to_ena(self): # submit data to webin ftp server if self.dev: - print( + log.error( "No files will be uploaded, remove `--no_data_upload' argument to perform upload." ) - else: submit_data(file_paths, self.passwd, self.user) - # when ADD/MODIFY, # requires source XMLs for 'run', 'experiment', 'sample', 'experiment' # schema_xmls record XMLs for all these schema and following 'submission' - - # No me está funcionando con el absolute path - # base_path = os.path.abspath(os.path.dirname(__file__)) - # base_path = "miniconda3/envs/relecov/lib/python3.1/site-packages/ena_upload" - # template_path = os.path.join(base_path, "templates") config_json = ConfigJson() - # tool = config_json.get_topic_data("tool") - tool = {"tool_name": "ena-upload-cli", "tool_version": "1.0"} - checklist = config_json.get_configuration("checklist") import pdb pdb.set_trace() + tool = config_json.get_configuration("tool") + # tool = {"tool_name": "ena-upload-cli", "tool_version": "1.0"} + checklist = config_json.get_configuration("checklist") + schema_xmls = run_construct( template_path, schema_targets, self.center, checklist, tool ) @@ -198,6 +214,33 @@ def create_structure_to_ena(self): submission_xml = construct_submission( template_path, self.action, schema_xmls, self.center, checklist, tool ) + import pdb + + pdb.set_trace() + if self.dev: + url = "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" + else: + url = "https://www.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" + + print(f"\nSubmitting XMLs to ENA server: {url}") + receipt = send_schemas(schema_xmls, url, self.passwd, self.user).text + print("Printing receipt to ./receipt.xml") + + with open("receipt.xml", "w") as fw: + fw.write(receipt) + try: + schema_update = process_receipt(receipt.encode("utf-8"), self.action) + except ValueError: + log.error("There was an ERROR during submission:") + sys.exit(receipt) + + if self.action in ["ADD", "MODIFY"] or self.action in ["add", "modify"]: + schema_dataframe = update_table( + schema_dataframe, schema_targets, schema_update + ) + + # save updates in new tables + # save_update(schema_tables, schema_dataframe) def upload(self): """Create the required files and upload to ENA""" diff --git a/relecov_tools/example_data/to_ena_2.json b/relecov_tools/example_data/to_ena_2.json index 4c69ecc6..6a9b4c9a 100644 --- a/relecov_tools/example_data/to_ena_2.json +++ b/relecov_tools/example_data/to_ena_2.json @@ -1,39 +1,48 @@ { - "collection_date": "2021/04/13", - "common_name": "PEPITO", - "experiment_alias": "", + "collection date": "2021/04/13", + "collector name": "CNM", + "experiment_alias": "45321", "experiment_title": "Example project for ENA submission RELECOV", "fastq_r1_md5": "f2facbd1d6c7e0972074ced31ccbfd8e", "fastq_r2_md5": "fd9948be8da7a38b0f80659dfc21aeea", "geographic location (latitude)": "41.6483", "geographic location (longitude)": "-0.8830", - "geographic_location_(country_and/or_sea)": "Spain", - "host_common_name": "Human", - "host_gender": "Mujer", - "host_scientific_name": "Homo Sapiens", + "geographic location (country and/or sea)": "Spain", + "host subject id": "host_subject_id_1", + "host common name": "Human", + "host health state": "diseased", + "collecting institution": "ISCIII", + "host sex": "Mujer", + "host scientific name": "Homo Sapiens", "instrument_model": "Illumina MiSeq", - "instrument_platform": "Illumina", + "platform": "Illumina", "isolate": "1197860", "isolation source host-associated": "Nasopharynx aspirate", "isolation source non-host-associated": "Other", - "library_layout": "Single End", + "library_name": "", + "library_layout": "Single", "library_selection": "RT-PCR", - "library_source": "RNA", - "library_strategy": "WGS strategy", + "library_source": "viral RNA", + "library_strategy": "WGS", "purpose_sampling": "Surveillance", - "r1_fastq_filepath": "/Users/erika/Desktop/relecov-tools/relecov_tools/example_data/ENA_TEST1.R1.fastq", - "r2_fastq_filepath": "/Users/erika/Desktop/relecov-tools/relecov_tools/example_data/ENA_TEST1.R2.fastq", + "r1_fastq_filepath": "home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/example_data/ENA_TEST1.R1.fastq", + "r2_fastq_filepath": "home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/example_data/ENA_TEST1.R2.fastq", "receipt_date": "2021/05/13", "run_alias": "", "sample_description": "Sample for surveillance", - "sample_name": "1197860", + "design_description": "", + "sample_name": "sample_alias_4", + "sample_title": "sample_title_1", "sample_storage_conditions": " -80ºC", "scientific_name": "Severe acute respiratory syndrome coronavirus 2", "sequence_file_R1_fastq": "ENA_TEST1.R1.fastq", "sequence_file_R2_fastq": "ENA_TEST1.R2.fastq", + "file_type": "fastq", + "file_checksum": "41ca-bcf0-cbfd43e06d29", "study_alias": "RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "RELECOV Spanish Network for genomics surveillance", - "tax_id": "2697049", + "study_type": "Whole Genome Sequencing", + "study_abstract": "", + "taxon_id": "2697049", "query": "" } \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_experiments.xml b/relecov_tools/templates/ENA_template_experiments.xml deleted file mode 100644 index b2c77ce5..00000000 --- a/relecov_tools/templates/ENA_template_experiments.xml +++ /dev/null @@ -1,51 +0,0 @@ - - - - - - ${row.title} - - - ${row.design_description} - - ${row.spot_descriptor} - - - - ${row.library_name} - - - - - - - - - ${row.library_construction_protocol} - - - - - - - SUBMISSION_TOOL - ${tool_name} - - - SUBMISSION_TOOL_VERSION - ${tool_version} - - - - - \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_runs.xml b/relecov_tools/templates/ENA_template_runs.xml deleted file mode 100644 index ade3e42f..00000000 --- a/relecov_tools/templates/ENA_template_runs.xml +++ /dev/null @@ -1,36 +0,0 @@ - - - - - - - - - - - - - - - - SUBMISSION_TOOL - ${tool_name} - - - SUBMISSION_TOOL_VERSION - ${tool_version} - - - - - \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000033.xml b/relecov_tools/templates/ENA_template_samples_ERC000033.xml deleted file mode 100644 index 46e57d86..00000000 --- a/relecov_tools/templates/ENA_template_samples_ERC000033.xml +++ /dev/null @@ -1,228 +0,0 @@ - - - - - - ${row.title} - - ${row.taxon_id} - ${row.scientific_name} - - ${row.common_name} - - - ${row.sample_description} - - - - subject exposure - ${row['subject exposure']} - - - - - subject exposure duration - ${row['subject exposure duration']} - - - - - type exposure - ${row['type exposure']} - - - - - personal protective equipment - ${row['personal protective equipment']} - - - - - hospitalisation - ${row['hospitalisation']} - - - - - illness duration - ${row['illness duration']} - - - - - illness symptoms - ${row['illness symptoms']} - - - - - collection date - ${row['collection date']} - - - - geographic location (country and/or sea) - ${row['geographic location (country and/or sea)']} - - - - geographic location (latitude) - ${row['geographic location (latitude)']} - - - - - geographic location (longitude) - ${row['geographic location (longitude)']} - - - - - geographic location (region and locality) - ${row['geographic location (region and locality)']} - - - - - sample capture status - ${row['sample capture status']} - - - - - host disease outcome - ${row['host disease outcome']} - - - - host common name - ${row['host common name']} - - - host subject id - ${row['host subject id']} - - - - host age - ${row['host age']} - - - - host health state - ${row['host health state']} - - - host sex - ${row['host sex']} - - - host scientific name - ${row['host scientific name']} - - - - virus identifier - ${row['virus identifier']} - - - - collector name - ${row['collector name']} - - - collecting institution - ${row['collecting institution']} - - - - receipt date - ${row['receipt date']} - - - - - sample storage conditions - ${row['sample storage conditions']} - - - - - definition for seropositive sample - ${row['definition for seropositive sample']} - - - - - serotype (required for a seropositive sample) - ${row['serotype (required for a seropositive sample)']} - - - - isolate - ${row['isolate']} - - - - strain - ${row['strain']} - - - - - host habitat - ${row['host habitat']} - - - - - isolation source host-associated - ${row['isolation source host-associated']} - - - - - host description - ${row['host description']} - - - - - gravidity - ${row['gravidity']} - - - - - host behaviour - ${row['host behaviour']} - - - - - isolation source non-host-associated - ${row['isolation source non-host-associated']} - - - - SUBMISSION_TOOL - ${tool_name} - - - SUBMISSION_TOOL_VERSION - ${tool_version} - - - - - \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_studies.xml b/relecov_tools/templates/ENA_template_studies.xml deleted file mode 100644 index 2316d410..00000000 --- a/relecov_tools/templates/ENA_template_studies.xml +++ /dev/null @@ -1,49 +0,0 @@ - - - - - - - ${row.title} - - ${row.study_abstract} - - ${row.center_project_name} - - - ${row.study_description} - - - - - - - PUBMED - ${row.pubmed_id} - - - - - - - SUBMISSION_TOOL - ${tool_name} - - - SUBMISSION_TOOL_VERSION - ${tool_version} - - - - - \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_submission.xml b/relecov_tools/templates/ENA_template_submission.xml deleted file mode 100644 index 7cf27072..00000000 --- a/relecov_tools/templates/ENA_template_submission.xml +++ /dev/null @@ -1,36 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file From a5fc7ec30a845a9f4d6297ba76de916a143d8e88 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 22 Apr 2022 13:59:14 +0200 Subject: [PATCH 0358/1454] fixing linting --- relecov_tools/conf/configuration.json | 2 +- relecov_tools/ena_upload.py | 6 ++++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 1c23b6c7..c02328dd 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -78,7 +78,7 @@ }, "tool": { "tool_name": "ena-upload-cli", - "tool_version": "1.0" + "tool_version": "0.5.3" }, "checklist": "ERC000033" } \ No newline at end of file diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index ffc8b362..ad9965e8 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -16,7 +16,8 @@ from ena_upload.ena_upload import send_schemas from ena_upload.ena_upload import process_receipt from ena_upload.ena_upload import update_table -from ena_upload.ena_upload import save_update + +# from ena_upload.ena_upload import save_update import site template_path = os.path.join(site.getsitepackages()[0], "ena_upload", "templates") @@ -211,7 +212,8 @@ def create_structure_to_ena(self): template_path, schema_targets, self.center, checklist, tool ) - submission_xml = construct_submission( + # submission_xml = 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wGXpTeBLRtWtfm+mU^51}EJDq`U)Ewb24V^;u$Wn+a literal 0 HcmV?d00001 diff --git a/relecov_tools/example_data/samples_data_COD_test_01_20220408.json b/relecov_tools/example_data/samples_data_COD_test_01_20220422.json similarity index 68% rename from relecov_tools/example_data/samples_data_COD_test_01_20220408.json rename to relecov_tools/example_data/samples_data_COD_test_01_20220422.json index 5403a0e1..18568ea1 100644 --- a/relecov_tools/example_data/samples_data_COD_test_01_20220408.json +++ b/relecov_tools/example_data/samples_data_COD_test_01_20220422.json @@ -2,80 +2,80 @@ "1197663": { "fastq_r1_md5": "83043c429b0ab94375236cf7f51860f0", "fastq_r2_md5": "c00859a1f83e2364cca953fb25da3cf2", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_008.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_008.fastq.gz" }, "1197677": { "fastq_r1_md5": "b0a13671031ef5aa7e0e6559a925a688", "fastq_r2_md5": "8c420a603c81823e68436003825b1e1f", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_005.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_005.fastq.gz" }, "1197678": { "fastq_r1_md5": "13e01498a0526303f5e32f3eef077b5a", "fastq_r2_md5": "61d1f52e84237320d97fd7fc2da56116", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_006.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_006.fastq.gz" }, "1197685": { "fastq_r1_md5": "a86f4fa0c92d76df34fd000a29d1cdd3", "fastq_r2_md5": "8c4309dc00d725496c48bee6da0e4bbf", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_0010.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_0010.fastq.gz" }, "1197689": { "fastq_r1_md5": "bc720a024263a518f6a6cd9301b308ac", "fastq_r2_md5": "6bf6d95b59c950691effcaf8a0e83068", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_009.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_009.fastq.gz" }, "1197737": { "fastq_r1_md5": "f5b60a93b39a0b98781efb434d577a57", "fastq_r2_md5": "e19f883b4e05045895f990c2296009a8", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_007.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_007.fastq.gz" }, "1197767": { "fastq_r1_md5": "c78fcb585a0f44734ce8c2aebf3eff33", "fastq_r2_md5": "8361d5a6b50279fbc8c93226ecc3568a", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_003.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_003.fastq.gz" }, "1197824": { "fastq_r1_md5": "9a460a812086516536c1a1023ab5f7fe", "fastq_r2_md5": "41cd79b8a167d85eb06309207fd120cf", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_002.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_002.fastq.gz" }, "1197860": { "fastq_r1_md5": "f2facbd1d6c7e0972074ced31ccbfd8e", "fastq_r2_md5": "fd9948be8da7a38b0f80659dfc21aeea", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_001.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_001.fastq.gz" }, "8328199": { "fastq_r1_md5": "aa557fc40d3a9e16f470ac595fb5eb3e", "fastq_r2_md5": "a2dd5e08b75815dab892e392cb8468fc", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_004.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_004.fastq.gz" } From 50da257fbfe96b88a48a3dbd91ce7b6332d6d637 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 22 Apr 2022 17:32:54 +0200 Subject: [PATCH 0361/1454] fixed bug when checking invalid json --- relecov_tools/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index e5e6db57..042249f0 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -217,7 +217,7 @@ def validate(json_file, json_schema, metadata, out_folder): ) = relecov_tools.json_validation.validate_json(json_file, json_schema, out_folder) if len(invalid_json) > 0: log.error("Some of the samples in json metadata were not validated") - if not os.isfile(metadata): + if not os.path.isfile(metadata): log.error("Metadata file %s does not exists", metadata) exit(1) relecov_tools.json_validation.create_invalid_metadata( From 1715197030bef8cb884e7a4d2b80160027671a23 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 22 Apr 2022 17:49:11 +0200 Subject: [PATCH 0362/1454] Fixed bug when sample is an integer and checking with a string --- relecov_tools/json_validation.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index b096886e..090062b9 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -68,9 +68,10 @@ def create_invalid_metadata(metadata_file, invalid_json, out_folder): collecting_lab_sample_id are removed from excel """ sample_list = [] - json_data = relecov_tools.utils.read_json_file(invalid_json) - for row in json_data: - sample_list.append(row["collecting_lab_sample_id"]) + # import pdb; pdb.set_trace() + # json_data = relecov_tools.utils.read_json_file(invalid_json) + for row in invalid_json: + sample_list.append(str(row["collecting_lab_sample_id"])) wb = openpyxl.load_workbook(metadata_file) ws_sheet = wb["METADATA_LAB"] row_to_del = [] @@ -84,7 +85,7 @@ def create_invalid_metadata(metadata_file, invalid_json, out_folder): for idx in row_to_del: ws_sheet.delete_rows(idx) break - + import pdb; pdb.set_trace() if str(row[2].value) not in sample_list: row_to_del.append(row[0].row) From f94fef75b5025ff637cee9d804e8574a6412e2e7 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 22 Apr 2022 17:50:02 +0200 Subject: [PATCH 0363/1454] update test parameters with the new metadatada test file --- relecov_tools/test/test_cases.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/test/test_cases.txt b/relecov_tools/test/test_cases.txt index 6b63b9f5..31fdb85a 100644 --- a/relecov_tools/test/test_cases.txt +++ b/relecov_tools/test/test_cases.txt @@ -1,6 +1,6 @@ relecov-tools -l /tmp/logs.log download -u usuario_test -p U[9[Gpyu3. relecov-tools -l /tmp/logs.log download -f relecov_tools/test/sftp_config.yaml -relecov-tools read-metadata -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -s relecov_tools/example_data/samples_data_COD_test_01_20220408.json -o /tmp +relecov-tools read-metadata -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -s relecov_tools/example_data/samples_data_COD_test_01_20220422.json -o /tmp relecov-tools validate -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -o /tmp relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -o /tmp relecov-tools update-db -i http://iskylims.isciiides.es/wetlab/api/ -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json From 32dcd33e7487d3963d8d9bb095c3766fc9eae159 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 22 Apr 2022 17:53:23 +0200 Subject: [PATCH 0364/1454] removed debugging tag --- relecov_tools/json_validation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 090062b9..f648c7d2 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -85,7 +85,7 @@ def create_invalid_metadata(metadata_file, invalid_json, out_folder): for idx in row_to_del: ws_sheet.delete_rows(idx) break - import pdb; pdb.set_trace() + if str(row[2].value) not in sample_list: row_to_del.append(row[0].row) From e2ae5e1f7fad2fc80a2478b3cdbc9c0a2358e11f Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 22 Apr 2022 18:24:26 +0200 Subject: [PATCH 0365/1454] Update relecov schema with latest changes --- relecov_tools/schema/relecov_schema.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 006f3db8..6eaf4227 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -8,7 +8,7 @@ "geo_loc_country", "geo_loc_state", "organism", - "isolate", + "isolate_sample_id", "host_scientific_name", "host_disease", "sequencing_instrument_model", @@ -2466,7 +2466,7 @@ "type": "string", "description": "", "classification": "", - "label": "" + "label": "Sample ID given if multiple rna-extraction or passages" }, "variant_designation": { "Enums": [ @@ -3223,4 +3223,4 @@ "classification": "Database Identifiers" } } -} \ No newline at end of file +} From 6e067669172fd9dbb223b7fe75c9af4823c0dc2a Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 22 Apr 2022 18:29:22 +0200 Subject: [PATCH 0366/1454] fixed changes done on metadata file --- relecov_tools/read_metadata.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index b68b4f9d..5ff92b3b 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -119,7 +119,7 @@ def include_processed_data(self, metadata): p_data = { "host_common_name": {"Human": ["host_scientific_name", "Homo Sapiens"]}, "collecting_lab_sample_id": [ - "isolate", + "isolate_sample_id", metadata["collecting_lab_sample_id"], ], } @@ -248,7 +248,7 @@ def read_metadata_file(self): ) else: - if isinstance(row[idx], float): + if isinstance(row[idx], float) or isinstance(row[idx], int): if heading[idx] in exc_format_num: val = int(row[idx]) else: From d855a6af260355d03b95a8aefc4ce28624c73fd8 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 22 Apr 2022 18:30:25 +0200 Subject: [PATCH 0367/1454] example for processed data after the changes in metadata file --- .../processed_METADATA_LAB_TEST.json | 110 ++++++++---------- 1 file changed, 50 insertions(+), 60 deletions(-) diff --git a/relecov_tools/example_data/processed_METADATA_LAB_TEST.json b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json index cdb3cbc7..643009ed 100644 --- a/relecov_tools/example_data/processed_METADATA_LAB_TEST.json +++ b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json @@ -37,21 +37,20 @@ "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", - "isolate": "1197860", - "isolate_sample_id": "220407", + "isolate_sample_id": "1197860", "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "library_layout": "Single End", + "library_layout": "SINGLE", "library_preparation_kit": "Truseq Nano", "library_selection": "RT-PCR", "library_source": "RNA", - "library_strategy": "WGS strategy", + "library_strategy": "WGS", "microbiology_lab_sample_id": "220407", "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU01394", "purpose_of_sampling": "Surveillance", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -111,21 +110,20 @@ "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", - "isolate": "1197824", - "isolate_sample_id": "220433", + "isolate_sample_id": "1197824", "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "library_layout": "Single End", + "library_layout": "SINGLE", "library_preparation_kit": "Truseq Nano", "library_selection": "RT-PCR", "library_source": "RNA", - "library_strategy": "WGS strategy", + "library_strategy": "WGS", "microbiology_lab_sample_id": "220433", "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU01469", "purpose_of_sampling": "Surveillance", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -185,21 +183,20 @@ "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", - "isolate": "1197767", - "isolate_sample_id": "220435", + "isolate_sample_id": "1197767", "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "library_layout": "Single End", + "library_layout": "SINGLE", "library_preparation_kit": "Truseq Nano", "library_selection": "RT-PCR", "library_source": "RNA", - "library_strategy": "WGS strategy", + "library_strategy": "WGS", "microbiology_lab_sample_id": "220435", "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU03926", "purpose_of_sampling": "Surveillance", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -259,21 +256,20 @@ "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", - "isolate": "8328199", - "isolate_sample_id": "220436", + "isolate_sample_id": "8328199", "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "library_layout": "Single End", + "library_layout": "SINGLE", "library_preparation_kit": "Truseq Nano", "library_selection": "RT-PCR", "library_source": "RNA", - "library_strategy": "WGS strategy", + "library_strategy": "WGS", "microbiology_lab_sample_id": "220436", "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU06554", "purpose_of_sampling": "Surveillance", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -333,21 +329,20 @@ "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", - "isolate": "1197677", - "isolate_sample_id": "220624", + "isolate_sample_id": "1197677", "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "library_layout": "Single End", + "library_layout": "SINGLE", "library_preparation_kit": "Truseq Nano", "library_selection": "RT-PCR", "library_source": "RNA", - "library_strategy": "WGS strategy", + "library_strategy": "WGS", "microbiology_lab_sample_id": "220624", "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU03790", "purpose_of_sampling": "Surveillance", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -407,21 +402,20 @@ "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", - "isolate": "1197678", - "isolate_sample_id": "220625", + "isolate_sample_id": "1197678", "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "library_layout": "Single End", + "library_layout": "SINGLE", "library_preparation_kit": "Truseq Nano", "library_selection": "RT-PCR", "library_source": "RNA", - "library_strategy": "WGS strategy", + "library_strategy": "WGS", "microbiology_lab_sample_id": "220625", "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU03901", "purpose_of_sampling": "Surveillance", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -481,21 +475,20 @@ "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", - "isolate": "1197737", - "isolate_sample_id": "220629", + "isolate_sample_id": "1197737", "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "library_layout": "Single End", + "library_layout": "SINGLE", "library_preparation_kit": "Truseq Nano", "library_selection": "RT-PCR", "library_source": "RNA", - "library_strategy": "WGS strategy", + "library_strategy": "WGS", "microbiology_lab_sample_id": "220629", "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU03862", "purpose_of_sampling": "Surveillance", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -555,21 +548,20 @@ "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", - "isolate": "1197663", - "isolate_sample_id": "220634", + "isolate_sample_id": "1197663", "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "library_layout": "Single End", + "library_layout": "SINGLE", "library_preparation_kit": "Truseq Nano", "library_selection": "RT-PCR", "library_source": "RNA", - "library_strategy": "WGS strategy", + "library_strategy": "WGS", "microbiology_lab_sample_id": "220634", "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU03614", "purpose_of_sampling": "Surveillance", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -629,21 +621,20 @@ "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", - "isolate": "1197689", - "isolate_sample_id": "220636", + "isolate_sample_id": "1197689", "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "library_layout": "Single End", + "library_layout": "SINGLE", "library_preparation_kit": "Truseq Nano", "library_selection": "RT-PCR", "library_source": "RNA", - "library_strategy": "WGS strategy", + "library_strategy": "WGS", "microbiology_lab_sample_id": "220636", "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU04252", "purpose_of_sampling": "Surveillance", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -703,21 +694,20 @@ "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", - "isolate": "1197685", - "isolate_sample_id": "220639", + "isolate_sample_id": "1197685", "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "library_layout": "Single End", + "library_layout": "SINGLE", "library_preparation_kit": "Truseq Nano", "library_selection": "RT-PCR", "library_source": "RNA", - "library_strategy": "WGS strategy", + "library_strategy": "WGS", "microbiology_lab_sample_id": "220639", "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU04223", "purpose_of_sampling": "Surveillance", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", From 7d2a45f42146ee974af9da58269afc66e1a551a0 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 22 Apr 2022 19:39:38 +0200 Subject: [PATCH 0368/1454] change host_sex and include GO for design_description --- relecov_tools/schema/ena_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 40327552..5f33df8d 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -116,7 +116,7 @@ "examples": [ "design_description_1" ], - "ontology": "0", + "ontology": "NCIT:C147139", "type": "string", "description": "", "clasification": "", @@ -621,7 +621,7 @@ "sample" ] }, - "host_gender": { + "host_sex": { "Enums": [ "Female [NCIT:C46110]", "Male [NCIT:C46109]", From 73a9a56a110da652ae9dc99f53afdfdfb1819d0b Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 22 Apr 2022 19:41:18 +0200 Subject: [PATCH 0369/1454] change platform for instrument_platform --- relecov_tools/example_data/to_ena_2.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/example_data/to_ena_2.json b/relecov_tools/example_data/to_ena_2.json index 6a9b4c9a..fb281980 100644 --- a/relecov_tools/example_data/to_ena_2.json +++ b/relecov_tools/example_data/to_ena_2.json @@ -15,7 +15,7 @@ "host sex": "Mujer", "host scientific name": "Homo Sapiens", "instrument_model": "Illumina MiSeq", - "platform": "Illumina", + "instrument_platform": "Illumina", "isolate": "1197860", "isolation source host-associated": "Nasopharynx aspirate", "isolation source non-host-associated": "Other", @@ -45,4 +45,4 @@ "study_abstract": "", "taxon_id": "2697049", "query": "" -} \ No newline at end of file +} From 8a01c80338fb31da50d982c58b5574373946da45 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 24 Apr 2022 18:23:52 +0200 Subject: [PATCH 0370/1454] Define study title in configuration for ENA --- relecov_tools/conf/configuration.json | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index c02328dd..e684bdf7 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -23,7 +23,8 @@ "experiment_alias": "", "run_alias": "", "experiment_title": "Example project for ENA submission RELECOV", - "study_title": "RELECOV Spanish Network for genomics surveillance" + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type" : "" }, "external_url": { "iskylims": { @@ -81,4 +82,4 @@ "tool_version": "0.5.3" }, "checklist": "ERC000033" -} \ No newline at end of file +} From 8024bb5fdcd52770bdf2ef6c21a9c4d22b457295 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 24 Apr 2022 18:24:24 +0200 Subject: [PATCH 0371/1454] Update mapping to ENA with Sara's comments --- relecov_tools/map_schema.py | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 6e7e94f1..1fbf5d78 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -159,6 +159,27 @@ def additional_formating(self, mapped_json_data): mapped_json_data[idx]["fastq_r2_md5"] = self.json_data[idx][ "fastq_r2_md5" ] + mapped_json_data[idx]["r1_fastq_filepath"] = ( + self.json_data[idx]["r1_fastq_filepath"] + + self.json_data[idx]["sequence_file_R1_fastq"] + ) + mapped_json_data[idx]["r2_fastq_filepath"] = ( + self.json_data[idx]["r2_fastq_filepath"] + + self.json_data[idx]["sequence_file_R2_fastq"] + ) + mapped_json_data[idx]["collecting_institution"] = self.json_data[idx][ + "collecting_institution" + ] + mapped_json_data[idx]["collector_name"] = self.json_data[idx][ + "collector_name" + ] + mapped_json_data[idx]["library_name"] = self.json_data[idx][ + "collecting_lab_sample_id" + ] + mapped_json_data[idx]["sample_title"] = self.json_data[idx][ + "collecting_lab_sample_id" + ] + mapped_json_data[idx]["file_type"] = "fastq" return mapped_json_data From 63941cdb8307c493e259c97cfd6770ead785036b Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 25 Apr 2022 00:07:48 +0200 Subject: [PATCH 0372/1454] Fixed typing error on GISAID --- relecov_tools/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 042249f0..a87d1d57 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -235,7 +235,7 @@ def validate(json_file, json_schema, metadata, out_folder): @click.option( "-d", "--destination_schema", - type=click.Choice(["ENA", "GSAID", "other"], case_sensitive=True), + type=click.Choice(["ENA", "GISAID", "other"], case_sensitive=True), help="schema to be mapped", ) @click.option("-f", "--schema_file", help="file with the custom schema") From b1c975938b5d64e6143ae2f93c8b94625a4aa663 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 25 Apr 2022 00:08:54 +0200 Subject: [PATCH 0373/1454] Added configuration for GISAID --- relecov_tools/conf/configuration.json | 3 +++ 1 file changed, 3 insertions(+) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index e684bdf7..8c14b1aa 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -26,6 +26,9 @@ "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type" : "" }, + "GISATD_configuration": { + "submitter" : "GISAID_ID" + }, "external_url": { "iskylims": { "server": "http://relecov-iskylims.isciiides.es", From 2ecf093cf1cbca15bafcaf14e9b6f5e2819450de Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 25 Apr 2022 00:09:38 +0200 Subject: [PATCH 0374/1454] Addind mor laboratories to the file --- relecov_tools/conf/laboratory_address.json | 184 +++++++++++++-------- 1 file changed, 114 insertions(+), 70 deletions(-) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index f2afd170..8757be7a 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -1,134 +1,178 @@ [ { "collecting_institution": "Microbiología HUC San Cecilio", - "geo_loc_country" : "Spain", + "collecting_institution_address": "Av. del Conocimiento S/N,", + "collecting_institution_email": "fegarcia@ugr.es", "geo_loc_state": "Andalucia", - "geo_loc_city": "Granada" + "geo_loc_city": "Granada", + "geo_loc_country": "Spain" }, { "collecting_institution": "Microbiología. Hospital Universitario Virgen del Rocio", - "geo_loc_country" : "Spain", + "collecting_institution_address": "Avenida Manuel Siurot s/n", + "collecting_institution_email": "josea.lepe.sspa@juntadeandalucia.es", "geo_loc_state": "Andalucia", - "geo_loc_city": "Sevilla" + "geo_loc_city": "Sevilla", + "geo_loc_country": "Spain" }, { "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", - "geo_loc_country" : "Spain", + "collecting_institution_address": "S. Juan Bosco, 15", + "collecting_institution_email": "rbenito@salud.aragon.es", "geo_loc_state": "Aragon", - "geo_loc_city": "Zaragoza" + "geo_loc_city": "Zaragoza", + "geo_loc_country": "Spain" }, { "collecting_institution": "Hospital Universitario Miguel Servet", - "geo_loc_country" : "Spain", + "collecting_institution_address": "P.º Isabel la Católica, 1-3", + "collecting_institution_email": "rbenito@salud.aragon.es", "geo_loc_state": "Aragon", - "geo_loc_city": "Zaragoza" + "geo_loc_city": "Zaragoza", + "geo_loc_country": "Spain" }, { "collecting_institution": "Centro de Investigación Biomédica de Aragón", - "geo_loc_country" : "Spain", + "collecting_institution_address": "Avenida San Juan Bosco 13", + "collecting_institution_email": "mhpstrunk.iacs@aragon.es", "geo_loc_state": "Aragon", - "geo_loc_city": "Zaragoza" + "geo_loc_city": "Zaragoza", + "geo_loc_country": "Spain" }, { "collecting_institution": "Hospital Universitario Central de Asturias", - "geo_loc_country" : "Spain", + "collecting_institution_address": " Av. Roma, s/n,", + "collecting_institution_email": "santiago.melon@sespa.es", "geo_loc_state": "Asturias", - "geo_loc_city": "Oviedo" + "geo_loc_city": "Oviedo", + "geo_loc_country": "Spain" }, { "collecting_institution": "Servicio de Microbiologia HU Son Espases", - "geo_loc_country" : "Spain", + "collecting_institution_address": " Ctra. Valldemossa 79", + "collecting_institution_email": "antonio.oliver@ssib.es", "geo_loc_state": "Baleares", - "geo_loc_city": "Palma de Mallorca" + "geo_loc_city": "Palma de Mallorca", + "geo_loc_country": "Spain" }, { - "collecting_institution": "", - "geo_loc_country" : "Spain", - "geo_loc_state": "", - "geo_loc_city": "" + "collecting_institution": "Hospital Universitario Ntra. Sra de Candelaria", + "collecting_institution_address": "Carretera del Rosario 145", + "collecting_institution_email": "Not available", + "geo_loc_state": "Canarias", + "geo_loc_city": "Santa Cruz de Tenerife", + "geo_loc_country": "Spain" }, { - "collecting_institution": "", - "geo_loc_country" : "Spain", - "geo_loc_state": "", - "geo_loc_city": "" + "collecting_institution": "Hospital Universitario de Gran Canaria", + "collecting_institution_address": "Bco. de la Ballena s/n", + "collecting_institution_email": "", + "geo_loc_state": "Canarias", + "geo_loc_city": "Las Palmas", + "geo_loc_country": "Spain" }, { - "collecting_institution": "", - "geo_loc_country" : "Spain", - "geo_loc_state": "", - "geo_loc_city": "" + "collecting_institution": "Hospital Universitario Marqués de Valdecilla", + "collecting_institution_address": "Av. Valdecilla s/n", + "collecting_institution_email": "", + "geo_loc_state": "Cantabria", + "geo_loc_city": "Santander", + "geo_loc_country": "Spain" }, { - "collecting_institution": "", - "geo_loc_country" : "Spain", - "geo_loc_state": "", - "geo_loc_city": "" + "collecting_institution": "Hospital General Universitario de Ciudad Real.", + "collecting_institution_address": "Calle Obispo Rafael Torija s/n", + "collecting_institution_email": "", + "geo_loc_state": "Castilla la Mancha", + "geo_loc_city": "Ciudad Real", + "geo_loc_country": "Spain" }, { - "collecting_institution": "", - "geo_loc_country" : "Spain", - "geo_loc_state": "", - "geo_loc_city": "" + "collecting_institution": "Hospital Virgen de la Salud", + "collecting_institution_address": "Calle Barber 30", + "collecting_institution_email": "", + "geo_loc_state": "Castilla la Mancha", + "geo_loc_city": "Toledo", + "geo_loc_country": "Spain" }, { - "collecting_institution": "", - "geo_loc_country" : "Spain", - "geo_loc_state": "", - "geo_loc_city": "" + "collecting_institution": "Hospital General Universitario de Albacete", + "collecting_institution_address": "Calle Hermanos Falcó 37", + "collecting_institution_email": "", + "geo_loc_state": "Castilla la Mancha", + "geo_loc_city": "Albacete", + "geo_loc_country": "Spain" }, { - "collecting_institution": "", - "geo_loc_country" : "Spain", - "geo_loc_state": "", - "geo_loc_city": "" + "collecting_institution": "Consorcio LUCIA (SACYL,ITACYL UBU,UVa)", + "collecting_institution_address": "Paseo de Belen 19", + "collecting_institution_email": "", + "geo_loc_state": "Castilla y León", + "geo_loc_city": "Valladolid", + "geo_loc_country": "Spain" }, { - "collecting_institution": "", - "geo_loc_country" : "Spain", - "geo_loc_state": "", - "geo_loc_city": "" + "collecting_institution": "Hospital Universitari Vall d’Hebron", + "collecting_institution_address": " Passeig de la Vall d’Hebron, 119-129", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_city": "Barcelona", + "geo_loc_country": "Spain" }, { - "collecting_institution": "", - "geo_loc_country" : "Spain", - "geo_loc_state": "", - "geo_loc_city": "" + "collecting_institution": "Hospital Universitari Germans Trias i Pujol", + "collecting_institution_address": " Crta del Canyet s/n", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_city": "Barcelona", + "geo_loc_country": "Spain" }, { - "collecting_institution": "", - "geo_loc_country" : "Spain", - "geo_loc_state": "", - "geo_loc_city": "" + "collecting_institution": "Hospital Clínic de Barcelona", + "collecting_institution_address": "C/Villarroel 170", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_city": "Barcelona", + "geo_loc_country": "Spain" }, { - "collecting_institution": "", - "geo_loc_country" : "Spain", - "geo_loc_state": "", - "geo_loc_city": "" + "collecting_institution": "Hospital Universitari Bellvitge", + "collecting_institution_address": "Carrer Feixa Llarga s/n ", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_city": "Barcelona", + "geo_loc_country": "Spain" }, { - "collecting_institution": "", - "geo_loc_country" : "Spain", - "geo_loc_state": "", - "geo_loc_city": "" + "collecting_institution": "Lab Clínic ICS Camp de Tarragona-Terres de l'Ebre. Hospital Joan XXIII", + "collecting_institution_address": "c/ Dr. Mallafrè Guasch, 4,", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_city": "Tarragona", + "geo_loc_country": "Spain" }, { - "collecting_institution": "", - "geo_loc_country" : "Spain", + "collecting_institution": "LABORATORI DE REFERENCIA DE CATALUNYA", + "collecting_institution_address": "", + "collecting_institution_email": "", "geo_loc_state": "", - "geo_loc_city": "" + "geo_loc_city": "", + "geo_loc_country": "Spain" }, { - "collecting_institution": "", + "collecting_institution": "Banc de Sang i Teixits Catalunya", + "collecting_institution_address": "", "geo_loc_country" : "Spain", "geo_loc_state": "", - "geo_loc_city": "" + "geo_loc_city": "", + "geo_loc_country": "Spain" }, { - "collecting_institution": "", - "geo_loc_country" : "Spain", + "collecting_institution": "Unitat de Genòmica i Medicina Personalitzada - Hospital Dr. Josep Trueta", + "collecting_institution_address": "", + "collecting_institution_email": "", "geo_loc_state": "", - "geo_loc_city": "" + "geo_loc_city": "", + "geo_loc_country": "Spain" } ] From e412ac073f41459f822e71f3b8a602d560e8e60d Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 25 Apr 2022 00:11:40 +0200 Subject: [PATCH 0375/1454] Updated with the information of laboratory, country and address --- .../processed_METADATA_LAB_TEST.json | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/relecov_tools/example_data/processed_METADATA_LAB_TEST.json b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json index 643009ed..a2884048 100644 --- a/relecov_tools/example_data/processed_METADATA_LAB_TEST.json +++ b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json @@ -8,6 +8,8 @@ "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123456", "collecting_institution": "Hospital Universitario Miguel Servet", + "collecting_institution_address": "P.º Isabel la Católica, 1-3", + "collecting_institution_email": "rbenito@salud.aragon.es", "collecting_lab_sample_id": "1197860", "collection_device": "Swab", "common_name": "PEPITO", @@ -66,6 +68,7 @@ "sequencing_sample_id": 214824, "study_alias": "RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202201751", "tax_id": "2697049", @@ -81,6 +84,8 @@ "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123457", "collecting_institution": "Hospital Universitario Miguel Servet", + "collecting_institution_address": "P.º Isabel la Católica, 1-3", + "collecting_institution_email": "rbenito@salud.aragon.es", "collecting_lab_sample_id": "1197824", "collection_device": "Swab", "common_name": "PEPITO", @@ -139,6 +144,7 @@ "sequencing_sample_id": 214832, "study_alias": "RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202201678", "tax_id": "2697049", @@ -154,6 +160,8 @@ "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123458", "collecting_institution": "Hospital Universitario Miguel Servet", + "collecting_institution_address": "P.º Isabel la Católica, 1-3", + "collecting_institution_email": "rbenito@salud.aragon.es", "collecting_lab_sample_id": "1197767", "collection_device": "Swab", "common_name": "PEPITO", @@ -212,6 +220,7 @@ "sequencing_sample_id": 220338, "study_alias": "RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202201853", "tax_id": "2697049", @@ -227,6 +236,8 @@ "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123459", "collecting_institution": "Hospital Universitario Miguel Servet", + "collecting_institution_address": "P.º Isabel la Católica, 1-3", + "collecting_institution_email": "rbenito@salud.aragon.es", "collecting_lab_sample_id": "8328199", "collection_device": "Swab", "common_name": "PEPITO", @@ -285,6 +296,7 @@ "sequencing_sample_id": 220407, "study_alias": "RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202202165", "tax_id": "2697049", @@ -300,6 +312,8 @@ "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123460", "collecting_institution": "Hospital Universitario Miguel Servet", + "collecting_institution_address": "P.º Isabel la Católica, 1-3", + "collecting_institution_email": "rbenito@salud.aragon.es", "collecting_lab_sample_id": "1197677", "collection_device": "Swab", "common_name": "PEPITO", @@ -358,6 +372,7 @@ "sequencing_sample_id": 220624, "study_alias": "RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202203144", "tax_id": "2697049", @@ -373,6 +388,8 @@ "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123461", "collecting_institution": "Hospital Universitario Miguel Servet", + "collecting_institution_address": "P.º Isabel la Católica, 1-3", + "collecting_institution_email": "rbenito@salud.aragon.es", "collecting_lab_sample_id": "1197678", "collection_device": "Swab", "common_name": "PEPITO", @@ -431,6 +448,7 @@ "sequencing_sample_id": 220625, "study_alias": "RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202203146", "tax_id": "2697049", @@ -446,6 +464,8 @@ "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123462", "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", + "collecting_institution_address": "S. Juan Bosco, 15", + "collecting_institution_email": "rbenito@salud.aragon.es", "collecting_lab_sample_id": "1197737", "collection_device": "Swab", "common_name": "PEPITO", @@ -504,6 +524,7 @@ "sequencing_sample_id": 220629, "study_alias": "RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202203153", "tax_id": "2697049", @@ -519,6 +540,8 @@ "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123463", "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", + "collecting_institution_address": "S. Juan Bosco, 15", + "collecting_institution_email": "rbenito@salud.aragon.es", "collecting_lab_sample_id": "1197663", "collection_device": "Swab", "common_name": "PEPITO", @@ -577,6 +600,7 @@ "sequencing_sample_id": 220634, "study_alias": "RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202203163", "tax_id": "2697049", @@ -592,6 +616,8 @@ "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123464", "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", + "collecting_institution_address": "S. Juan Bosco, 15", + "collecting_institution_email": "rbenito@salud.aragon.es", "collecting_lab_sample_id": "1197689", "collection_device": "Swab", "common_name": "PEPITO", @@ -650,6 +676,7 @@ "sequencing_sample_id": 220636, "study_alias": "RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202203170", "tax_id": "2697049", @@ -665,6 +692,8 @@ "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123465", "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", + "collecting_institution_address": "S. Juan Bosco, 15", + "collecting_institution_email": "rbenito@salud.aragon.es", "collecting_lab_sample_id": "1197685", "collection_device": "Swab", "common_name": "PEPITO", @@ -723,6 +752,7 @@ "sequencing_sample_id": 220639, "study_alias": "RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", "submitting_lab_sequence_id": "202203166", "tax_id": "2697049", From f13393cfd304c4bd5a4239061934dbec941beec2 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 25 Apr 2022 00:12:29 +0200 Subject: [PATCH 0376/1454] Testing mapping for gisaid test --- ...B_TEST_2022_04_25_00_03_GISAID_mapped.json | 152 ++++++++++++++++++ 1 file changed, 152 insertions(+) create mode 100644 relecov_tools/example_data/processed_METADATA_LAB_TEST_2022_04_25_00_03_GISAID_mapped.json diff --git a/relecov_tools/example_data/processed_METADATA_LAB_TEST_2022_04_25_00_03_GISAID_mapped.json b/relecov_tools/example_data/processed_METADATA_LAB_TEST_2022_04_25_00_03_GISAID_mapped.json new file mode 100644 index 00000000..edf69533 --- /dev/null +++ b/relecov_tools/example_data/processed_METADATA_LAB_TEST_2022_04_25_00_03_GISAID_mapped.json @@ -0,0 +1,152 @@ +[ + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "P.º Isabel la Católica, 1-3", + "collection_date": "2021/04/13", + "gender": "Mujer", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 55, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222687", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2022" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "P.º Isabel la Católica, 1-3", + "collection_date": "2021/03/31", + "gender": "Hombre", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 59, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222688", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2023" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "P.º Isabel la Católica, 1-3", + "collection_date": "2022/01/13", + "gender": "Mujer", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 8, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222689", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2024" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "P.º Isabel la Católica, 1-3", + "collection_date": "2022/01/11", + "gender": "Mujer", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 9, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222690", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2025" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "P.º Isabel la Católica, 1-3", + "collection_date": "2022/01/10", + "gender": "Hombre", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 31, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222691", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2026" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "P.º Isabel la Católica, 1-3", + "collection_date": "2022/01/12", + "gender": "Mujer", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 27, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222692", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2027" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "S. Juan Bosco, 15", + "collection_date": "2022/01/02", + "gender": "Mujer", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 42, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222693", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2028" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "S. Juan Bosco, 15", + "collection_date": "2022/01/23", + "gender": "Hombre", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 40, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222694", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2029" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "S. Juan Bosco, 15", + "collection_date": "2022/01/18", + "gender": "Hombre", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 53, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222695", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2030" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "S. Juan Bosco, 15", + "collection_date": "2022/01/19", + "gender": "Male", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 96, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222696", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2031" + } +] \ No newline at end of file From 8e31aee112fad90615d9d3c4fbb30ad51fcae887 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 25 Apr 2022 00:14:48 +0200 Subject: [PATCH 0377/1454] Used the right function get_topic_data to fetch data from config file --- relecov_tools/map_schema.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 1fbf5d78..7c716cab 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -103,7 +103,7 @@ def __init__( self.schema_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", - config_json.get_item("json_schemas", "gisaid_schema"), + config_json.get_topic_data("json_schemas", "gisaid_schema"), ) else: stderr.print("[red] Invalid option for mapping to schena") From 0f3178cf0e561de219bbcada76c33af26f9cad7b Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 25 Apr 2022 00:15:41 +0200 Subject: [PATCH 0378/1454] update patient data --- relecov_tools/schema/gisaid_schema.json | 44 ++++++++++--------------- 1 file changed, 17 insertions(+), 27 deletions(-) diff --git a/relecov_tools/schema/gisaid_schema.json b/relecov_tools/schema/gisaid_schema.json index 8aae7cf1..cb2a2cf9 100644 --- a/relecov_tools/schema/gisaid_schema.json +++ b/relecov_tools/schema/gisaid_schema.json @@ -20,7 +20,7 @@ "examples": [ "betacoronavirus" ], - "ontology": "NCBITaxon:694002", + "ontology": "NCIT:C25284", "type": "string", "description": "default must remain 'betacoronavirus'", "clasification": "Database Identifiers" @@ -99,7 +99,7 @@ "examples": [ "e.g. Europe / Germany / Bavaria / Munich" ], - "ontology": "GENEPIO:0001181 ", + "ontology": "GENEPIO:0001181", "type": "string", "description": "The country of origin of the sample.", "clasification": "Sample collection and processing", @@ -116,31 +116,21 @@ "label": "Host Scientific Name" }, "patient_age": { - "Enums": [ - "0 - 9 [GENEPIO:0100049]", - "10 - 19 [GENEPIO:0100050]", - "20 - 29 [GENEPIO:0100051]", - "30 - 39 [GENEPIO:0100052]", - "40 - 49 [GENEPIO:0100053]", - "50 - 59 [GENEPIO:0100054]", - "60 - 69 [GENEPIO:0100055]", - "70 - 79 [GENEPIO:0100056]", - "80 - 89 [GENEPIO:0100057]", - "90 - 99 [GENEPIO:0100058]", - "100+ [GENEPIO:0100059]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" + "ontology": "GENEPIO:0001392", + "anyOf": [ + { + "type": "integer" + }, + { + "pattern": "\\d+-\\d+", + "type": "string" + } ], + "description": "Age of host at the time of sampling.", "examples": [ - "50 - 59 [GENEPIO:0100054]" + 79 ], - "ontology": "GENEPIO:0001394", - "type": "string", - "description": "The age category of the host at the time of sampling.", - "clasification": "Host information" + "label": "Host Age" }, "specimen_source": { "Enums": [ @@ -234,7 +224,7 @@ "examples": [ "" ], - "ontology": "GENEPIO:0001156", + "ontology": "GENEPIO:0001460", "type": "string", "description": "Filename that contains the sequence without path", "clasification": "Bioinformatics and QC metrics" @@ -253,7 +243,7 @@ "examples": [ "e.g. 04/09/2021" ], - "ontology": "GENEPIO:0001156", + "ontology": "0", "type": "string", "description": "The date the host received their last dose of vaccine.", "format": "date", @@ -298,4 +288,4 @@ "label": "Submitting Institution" } } -} \ No newline at end of file +} From 926a6e6d73f4f5d20c4d03a30887351fd0bc4ae4 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 25 Apr 2022 00:16:25 +0200 Subject: [PATCH 0379/1454] Update test after software updated --- relecov_tools/test/test_cases.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/test/test_cases.txt b/relecov_tools/test/test_cases.txt index 31fdb85a..c2c532e3 100644 --- a/relecov_tools/test/test_cases.txt +++ b/relecov_tools/test/test_cases.txt @@ -2,5 +2,6 @@ relecov-tools -l /tmp/logs.log download -u usuario_test -p U[9[Gpyu3. relecov-tools -l /tmp/logs.log download -f relecov_tools/test/sftp_config.yaml relecov-tools read-metadata -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -s relecov_tools/example_data/samples_data_COD_test_01_20220422.json -o /tmp relecov-tools validate -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -o /tmp -relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -o /tmp +relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json - d ENA -o /tmp +relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -d GISAID -o /tmp relecov-tools update-db -i http://iskylims.isciiides.es/wetlab/api/ -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json From df5ab219e69e871a945adc47940b5fa016bbecb2 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 25 Apr 2022 12:08:28 +0200 Subject: [PATCH 0380/1454] added desplegable to metadata en field purpose of surveillance --- .../example_data/METADATA_LAB_TEST.xlsx | Bin 490767 -> 490959 bytes relecov_tools/example_data/to_ena.json | 37 ------------------ relecov_tools/example_data/to_ena_2.json | 5 +-- relecov_tools/schema/relecov_schema.json | 15 ++++++- 4 files changed, 16 insertions(+), 41 deletions(-) delete mode 100644 relecov_tools/example_data/to_ena.json diff --git a/relecov_tools/example_data/METADATA_LAB_TEST.xlsx b/relecov_tools/example_data/METADATA_LAB_TEST.xlsx index 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wGXpTeBLRtWtfm+mU^51}EJDq`U)Ewb24V^;u$Wn+a diff --git a/relecov_tools/example_data/to_ena.json b/relecov_tools/example_data/to_ena.json deleted file mode 100644 index e9d06f17..00000000 --- a/relecov_tools/example_data/to_ena.json +++ /dev/null @@ -1,37 +0,0 @@ -{ - "sample_name": "ID_001", - "sample_title": "sample_title_2", - "tax_id": "2697049", - "collecting_institution": "Hospital Universitario de Basurto", - "geographic_location_(country_and/or_sea)": "Spain", - "isolate": "ID_001", - "host_scientific_name": "Homo sapiens", - "host_common_name": "Human", - "host_health_state": "diseased", - "host_gender": "male", - "host_subject_id": "#131", - "instrument_model": "Illumina MiSeq", - "file_name": "ABC123_S1_L001_R1_001.fasstq.gz", - "collection_date": "2020-10-11", - "scientific_name": "severe acute respiratory syndrome coronavirus 2", - "common_name": "SARS-CoV-2", - "collector_name": "John Smith", - "sample_description": "SARS-CoV-2 Sample #1", - "library_source": "METAGENOMIC", - "library_selection": "RANDOM PCR", - "library_strategy": "WGS", - "library_layout": "PAIRED", - "library_name": "library_name_1", - "study_alias": "study_alias_1", - "study_title": "study_title", - "study_type": "RNASeq", - "run_alias": "run_alias_1a", - "experiment_alias": "experiment_alias_7a", - "file_type": "fastq", - "file_checksum": "3e69af1f875fab020aed82f5edbc1f03", - "experiment_title": "experiment_title_1", - "design_description": "design_description_1", - "insert_size": "250", - "library_construction_protocol": "library_construction_protocol_1", - "platform": "LS454" -} \ No newline at end of file diff --git a/relecov_tools/example_data/to_ena_2.json b/relecov_tools/example_data/to_ena_2.json index fb281980..077aabed 100644 --- a/relecov_tools/example_data/to_ena_2.json +++ b/relecov_tools/example_data/to_ena_2.json @@ -43,6 +43,5 @@ "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "Whole Genome Sequencing", "study_abstract": "", - "taxon_id": "2697049", - "query": "" -} + "taxon_id": "2697049" +} \ No newline at end of file diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 6eaf4227..5be00cbe 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1757,6 +1757,19 @@ "classification": "Sequencing", "label": "Commercial All-in-one library kit" }, + "library_name": { + "examples": [ + "e.g PAIRED" + ], + "ontology": "GENEPIO_0001995", + "type": "string", + "description": "The submitter's name for this library.", + "clasification": "Sequencing", + "label": "Library Name", + "table": [ + "experiments" + ] + }, "library_id": { "examples": [ "XYZ_123345" @@ -3223,4 +3236,4 @@ "classification": "Database Identifiers" } } -} +} \ No newline at end of file From 9981ef8c7c5a17a80c89c5b1414d4d7add8d866a Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 25 Apr 2022 15:58:15 +0200 Subject: [PATCH 0381/1454] changes in Santa cruz de tenerife --- relecov_tools/conf/geo_loc_cities.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/geo_loc_cities.json b/relecov_tools/conf/geo_loc_cities.json index 8ff1a201..dbd0fc2e 100644 --- a/relecov_tools/conf/geo_loc_cities.json +++ b/relecov_tools/conf/geo_loc_cities.json @@ -130,7 +130,7 @@ "geo_loc_longitude": "-6.1378" }, { - "geo_loc_city": "Santa Cruz", + "geo_loc_city": "Santa Cruz de Tenerife", "geo_loc_latitude": "28.4667", "geo_loc_longitude": "-16.2500" }, From 0acb3993ecc74dda6cca393a5ed5466ef7266304 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 26 Apr 2022 10:57:24 +0200 Subject: [PATCH 0382/1454] latest chenges in ena.json and script to upload --- relecov_tools/ena_upload.py | 23 ++++++++--------------- relecov_tools/example_data/to_ena_2.json | 12 ++++++------ 2 files changed, 14 insertions(+), 21 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index ad9965e8..e7331bce 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,4 +1,5 @@ import logging +from tkinter.tix import CheckList import rich.console import json @@ -7,7 +8,7 @@ import os import relecov_tools.utils from relecov_tools.config_json import ConfigJson - +from lxml import etree from ena_upload.ena_upload import extract_targets from ena_upload.ena_upload import submit_data @@ -190,42 +191,34 @@ def create_structure_to_ena(self): file_paths[os.path.basename(path)] = os.path.abspath(path) # submit data to webin ftp server - if self.dev: - log.error( - "No files will be uploaded, remove `--no_data_upload' argument to perform upload." - ) - else: + submit_data(file_paths, self.passwd, self.user) - submit_data(file_paths, self.passwd, self.user) # when ADD/MODIFY, # requires source XMLs for 'run', 'experiment', 'sample', 'experiment' # schema_xmls record XMLs for all these schema and following 'submission' config_json = ConfigJson() - import pdb - pdb.set_trace() tool = config_json.get_configuration("tool") - # tool = {"tool_name": "ena-upload-cli", "tool_version": "1.0"} - checklist = config_json.get_configuration("checklist") - + checklist = "ERC000011" + # checklist = config_json.get_configuration("checklist") + print(checklist) schema_xmls = run_construct( template_path, schema_targets, self.center, checklist, tool ) + print(schema_xmls) # submission_xml = construct_submission(template_path, self.action, schema_xmls, self.center, checklist, tool) construct_submission( template_path, self.action, schema_xmls, self.center, checklist, tool ) - import pdb - pdb.set_trace() if self.dev: url = "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" else: url = "https://www.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" print(f"\nSubmitting XMLs to ENA server: {url}") - receipt = send_schemas(schema_xmls, url, self.passwd, self.user).text + receipt = send_schemas(schema_xmls, url, self.user, self.passwd).text print("Printing receipt to ./receipt.xml") with open("receipt.xml", "w") as fw: diff --git a/relecov_tools/example_data/to_ena_2.json b/relecov_tools/example_data/to_ena_2.json index 077aabed..5335408f 100644 --- a/relecov_tools/example_data/to_ena_2.json +++ b/relecov_tools/example_data/to_ena_2.json @@ -15,7 +15,7 @@ "host sex": "Mujer", "host scientific name": "Homo Sapiens", "instrument_model": "Illumina MiSeq", - "instrument_platform": "Illumina", + "platform": "Illumina", "isolate": "1197860", "isolation source host-associated": "Nasopharynx aspirate", "isolation source non-host-associated": "Other", @@ -25,8 +25,8 @@ "library_source": "viral RNA", "library_strategy": "WGS", "purpose_sampling": "Surveillance", - "r1_fastq_filepath": "home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/example_data/ENA_TEST1.R1.fastq", - "r2_fastq_filepath": "home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/example_data/ENA_TEST1.R2.fastq", + "r1_fastq_filepath": "/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/example_data/ENA_TEST1.R1.fastq", + "r2_fastq_filepath": "/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/example_data/ENA_TEST1.R2.fastq", "receipt_date": "2021/05/13", "run_alias": "", "sample_description": "Sample for surveillance", @@ -35,10 +35,10 @@ "sample_title": "sample_title_1", "sample_storage_conditions": " -80ºC", "scientific_name": "Severe acute respiratory syndrome coronavirus 2", - "sequence_file_R1_fastq": "ENA_TEST1.R1.fastq", - "sequence_file_R2_fastq": "ENA_TEST1.R2.fastq", + "sequence_file_R1_fastq": "ENA_TEST1.R1.fastq.gz", + "sequence_file_R2_fastq": "ENA_TEST1.R2.fastq.gz", "file_type": "fastq", - "file_checksum": "41ca-bcf0-cbfd43e06d29", + "file_checksum": "f2facbd1d6c7e0972074ced31ccbfd8e", "study_alias": "RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "Whole Genome Sequencing", From 09d0fe19d2f9e57a203a83da56cad87a59817b23 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 26 Apr 2022 13:56:39 +0200 Subject: [PATCH 0383/1454] changes in confinguration json --- relecov_tools/conf/configuration.json | 7 ++++--- relecov_tools/ena_upload.py | 25 ++++++++++++++++++------- 2 files changed, 22 insertions(+), 10 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 8c14b1aa..ef0626ef 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -24,10 +24,11 @@ "run_alias": "", "experiment_title": "Example project for ENA submission RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type" : "" + "study_type": "", + "study_id": "ERP137164" }, "GISATD_configuration": { - "submitter" : "GISAID_ID" + "submitter": "GISAID_ID" }, "external_url": { "iskylims": { @@ -85,4 +86,4 @@ "tool_version": "0.5.3" }, "checklist": "ERC000033" -} +} \ No newline at end of file diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index e7331bce..b91903eb 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,5 +1,6 @@ import logging from tkinter.tix import CheckList +from numpy import empty import rich.console import json @@ -176,13 +177,24 @@ def create_structure_to_ena(self): df_experiments.rename(columns={"study_title": "title"}, inplace=True) df_experiments.rename(columns={"sample_name": "sample_alias"}, inplace=True) - schema_dataframe = {} - schema_dataframe["study"] = df_study - schema_dataframe["sample"] = df_samples - schema_dataframe["run"] = df_run - schema_dataframe["experiment"] = df_experiments + config_json = ConfigJson() + ena_config = config_json.get_configuration("ENA_configuration") - schema_targets = extract_targets(self.action, schema_dataframe) + if ena_config["study_id"] is empty: + schema_dataframe = {} + schema_dataframe["study"] = df_study + schema_dataframe["sample"] = df_samples + schema_dataframe["run"] = df_run + schema_dataframe["experiment"] = df_experiments + + schema_targets = extract_targets(self.action, schema_dataframe) + else: + schema_dataframe = {} + schema_dataframe["sample"] = df_samples + schema_dataframe["run"] = df_run + schema_dataframe["experiment"] = df_experiments + + schema_targets = extract_targets(self.action, schema_dataframe) if self.action == "ADD" or self.action == "add": file_paths = {} @@ -196,7 +208,6 @@ def create_structure_to_ena(self): # when ADD/MODIFY, # requires source XMLs for 'run', 'experiment', 'sample', 'experiment' # schema_xmls record XMLs for all these schema and following 'submission' - config_json = ConfigJson() tool = config_json.get_configuration("tool") checklist = "ERC000011" From c281b30367c6d778ddd6ea5b1b4e2ef5c0094525 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 26 Apr 2022 16:39:37 +0200 Subject: [PATCH 0384/1454] latest changes in config and script --- relecov_tools/conf/configuration.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index ef0626ef..ef61a750 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -25,7 +25,7 @@ "experiment_title": "Example project for ENA submission RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "", - "study_id": "ERP137164" + "study_id": "" }, "GISATD_configuration": { "submitter": "GISAID_ID" From bc24256e392d885c43befcceeb0fae237791c414 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 26 Apr 2022 17:49:33 +0200 Subject: [PATCH 0385/1454] Vamos que casi lo tenemos --- relecov_tools/conf/configuration.json | 2 +- relecov_tools/ena_upload.py | 44 +++++++++++++----------- relecov_tools/example_data/to_ena_2.json | 2 +- 3 files changed, 26 insertions(+), 22 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index ef61a750..ef0626ef 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -25,7 +25,7 @@ "experiment_title": "Example project for ENA submission RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "", - "study_id": "" + "study_id": "ERP137164" }, "GISATD_configuration": { "submitter": "GISAID_ID" diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index b91903eb..839b8ff4 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -116,6 +116,9 @@ def create_structure_to_ena(self): df_study = df_transposed[ ["study_alias", "study_title", "study_type", "study_abstract"] ] + # df_study.columns.values[0] = "alias" + # df_study.columns.values[1] = "title" + df_study.rename(columns={"study_alias": "alias"}, inplace=True) df_study.rename(columns={"study_title": "title"}, inplace=True) df_study.insert(3, "status", self.action) @@ -138,9 +141,16 @@ def create_structure_to_ena(self): "isolate", ] ] + # df_samples.columns.values[0] = "alias" + # df_samples.columns.values[1] = "title" + df_samples.rename(columns={"sample_name": "alias"}, inplace=True) df_samples.rename(columns={"sample_title": "title"}, inplace=True) df_samples.insert(3, "status", self.action) + config_json = ConfigJson() + checklist = config_json.get_configuration("checklist") + df_samples.insert(4, "ENA_CHECKLIST", checklist) + df_run = df_transposed[ [ "experiment_alias", @@ -174,29 +184,24 @@ def create_structure_to_ena(self): ] df_experiments.insert(3, "status", self.action) df_experiments.insert(4, "alias", df_experiments["experiment_alias"]) + + # df_experiments.columns.values[0] = "title" + # df_experiments.columns.values[1] = "sample_alias" + df_experiments.rename(columns={"study_title": "title"}, inplace=True) df_experiments.rename(columns={"sample_name": "sample_alias"}, inplace=True) - config_json = ConfigJson() ena_config = config_json.get_configuration("ENA_configuration") + schema_dataframe = {} + schema_dataframe["sample"] = df_samples + schema_dataframe["run"] = df_run + schema_dataframe["experiment"] = df_experiments + schema_targets = extract_targets(self.action, schema_dataframe) - if ena_config["study_id"] is empty: - schema_dataframe = {} + if ena_config["study_id"] is not None: schema_dataframe["study"] = df_study - schema_dataframe["sample"] = df_samples - schema_dataframe["run"] = df_run - schema_dataframe["experiment"] = df_experiments - - schema_targets = extract_targets(self.action, schema_dataframe) - else: - schema_dataframe = {} - schema_dataframe["sample"] = df_samples - schema_dataframe["run"] = df_run - schema_dataframe["experiment"] = df_experiments - schema_targets = extract_targets(self.action, schema_dataframe) - - if self.action == "ADD" or self.action == "add": + if self.action == "ADD" or self.action == "add" or self.action == "modify": file_paths = {} for path in df_run["r1_fastq_filepath"]: @@ -210,18 +215,17 @@ def create_structure_to_ena(self): # schema_xmls record XMLs for all these schema and following 'submission' tool = config_json.get_configuration("tool") - checklist = "ERC000011" - # checklist = config_json.get_configuration("checklist") + print(checklist) schema_xmls = run_construct( template_path, schema_targets, self.center, checklist, tool ) - print(schema_xmls) # submission_xml = construct_submission(template_path, self.action, schema_xmls, self.center, checklist, tool) - construct_submission( + submission_xml = construct_submission( template_path, self.action, schema_xmls, self.center, checklist, tool ) + schema_xmls["submission"] = submission_xml if self.dev: url = "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" diff --git a/relecov_tools/example_data/to_ena_2.json b/relecov_tools/example_data/to_ena_2.json index 5335408f..dff3d6dd 100644 --- a/relecov_tools/example_data/to_ena_2.json +++ b/relecov_tools/example_data/to_ena_2.json @@ -1,5 +1,5 @@ { - "collection date": "2021/04/13", + "collection date": "2021-04-13", "collector name": "CNM", "experiment_alias": "45321", "experiment_title": "Example project for ENA submission RELECOV", From 7902ce0bc2a32ff6262a518a3e4c9f2d3ee23618 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 26 Apr 2022 22:54:22 +0200 Subject: [PATCH 0386/1454] changes in ENA mapping from Erika comments --- relecov_tools/map_schema.py | 15 +++++++++++++++ relecov_tools/schema/ena_schema.json | 6 +++--- 2 files changed, 18 insertions(+), 3 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 7c716cab..239c6c23 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -180,6 +180,21 @@ def additional_formating(self, mapped_json_data): "collecting_lab_sample_id" ] mapped_json_data[idx]["file_type"] = "fastq" + mapped_json_data[idx]["collector_name"] = self.json_data[idx][ + "author_submitter" + ] + mapped_json_data[idx]["library_name"] = self.json_data[idx][ + "library_kit" + ] + mapped_json_data[idx]["sample_name"] = self.json_data[idx][ + "sample_title" + ] + mapped_json_data[idx]["study_type"] = self.json_data[idx][ + "purpose_of_sampling" + ] + mapped_json_data[idx]["study_abstract"] = self.json_data[idx][ + "study_title" + ] return mapped_json_data diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 5f33df8d..aca6249e 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -8,7 +8,7 @@ "host_scientific_name", "host_common_name", "instrument_model", - "tax_id", + "taxon_id", "scientific_name", "common_name", "sample_description", @@ -732,7 +732,7 @@ "experiments" ] }, - "instrument_platform": { + "platform": { "examples": [ "MinIon" ], @@ -823,7 +823,7 @@ "runs" ] }, - "tax_id": { + "taxon_id": { "examples": [ "probably 2697049 in all cases" ], From 97c00271298dbaf92da2da7aa454d77833b230b1 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 27 Apr 2022 21:35:11 +0200 Subject: [PATCH 0387/1454] Change date format to Y-m-d --- relecov_tools/read_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 5ff92b3b..55a62996 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -236,7 +236,7 @@ def read_metadata_file(self): try: sample_data_row[self.label_prop_dict[heading[idx]]] = row[ idx - ].strftime("%Y/%m/%d") + ].strftime("%Y-%m-%d") except AttributeError: if row[2] not in errors: errors[row[2]] = {} From 88f1b51890b636174f5be14576e46adcd65e27c3 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 28 Apr 2022 11:47:40 +0200 Subject: [PATCH 0388/1454] latest changes in example files that worked --- relecov_tools/ena_upload.py | 17 +++++++++-------- relecov_tools/example_data/to_ena_2.json | 22 +++++++++++++--------- 2 files changed, 22 insertions(+), 17 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 839b8ff4..69d30948 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -119,8 +119,8 @@ def create_structure_to_ena(self): # df_study.columns.values[0] = "alias" # df_study.columns.values[1] = "title" - df_study.rename(columns={"study_alias": "alias"}, inplace=True) - df_study.rename(columns={"study_title": "title"}, inplace=True) + df_study = df_study.rename(columns={"study_alias": "alias"}) + df_study = df_study.rename(columns={"study_title": "title"}) df_study.insert(3, "status", self.action) df_samples = df_transposed[ [ @@ -144,8 +144,8 @@ def create_structure_to_ena(self): # df_samples.columns.values[0] = "alias" # df_samples.columns.values[1] = "title" - df_samples.rename(columns={"sample_name": "alias"}, inplace=True) - df_samples.rename(columns={"sample_title": "title"}, inplace=True) + df_samples = df_samples.rename(columns={"sample_name": "alias"}) + df_samples = df_samples.rename(columns={"sample_title": "title"}) df_samples.insert(3, "status", self.action) config_json = ConfigJson() checklist = config_json.get_configuration("checklist") @@ -188,8 +188,8 @@ def create_structure_to_ena(self): # df_experiments.columns.values[0] = "title" # df_experiments.columns.values[1] = "sample_alias" - df_experiments.rename(columns={"study_title": "title"}, inplace=True) - df_experiments.rename(columns={"sample_name": "sample_alias"}, inplace=True) + df_experiments = df_experiments.rename(columns={"study_title": "title"}) + df_experiments = df_experiments.rename(columns={"sample_name": "sample_alias"}) ena_config = config_json.get_configuration("ENA_configuration") schema_dataframe = {} @@ -201,14 +201,15 @@ def create_structure_to_ena(self): if ena_config["study_id"] is not None: schema_dataframe["study"] = df_study - if self.action == "ADD" or self.action == "add" or self.action == "modify": + if self.action == "ADD" or self.action == "add": file_paths = {} for path in df_run["r1_fastq_filepath"]: file_paths[os.path.basename(path)] = os.path.abspath(path) # submit data to webin ftp server - submit_data(file_paths, self.passwd, self.user) + chec = submit_data(file_paths, self.passwd, self.user) + print(chec) # when ADD/MODIFY, # requires source XMLs for 'run', 'experiment', 'sample', 'experiment' diff --git a/relecov_tools/example_data/to_ena_2.json b/relecov_tools/example_data/to_ena_2.json index dff3d6dd..89f10805 100644 --- a/relecov_tools/example_data/to_ena_2.json +++ b/relecov_tools/example_data/to_ena_2.json @@ -1,7 +1,7 @@ { "collection date": "2021-04-13", "collector name": "CNM", - "experiment_alias": "45321", + "experiment_alias": "45499", "experiment_title": "Example project for ENA submission RELECOV", "fastq_r1_md5": "f2facbd1d6c7e0972074ced31ccbfd8e", "fastq_r2_md5": "fd9948be8da7a38b0f80659dfc21aeea", @@ -12,7 +12,7 @@ "host common name": "Human", "host health state": "diseased", "collecting institution": "ISCIII", - "host sex": "Mujer", + "host sex": "Female", "host scientific name": "Homo Sapiens", "instrument_model": "Illumina MiSeq", "platform": "Illumina", @@ -25,23 +25,27 @@ "library_source": "viral RNA", "library_strategy": "WGS", "purpose_sampling": "Surveillance", - "r1_fastq_filepath": "/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/example_data/ENA_TEST1.R1.fastq", - "r2_fastq_filepath": "/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/example_data/ENA_TEST1.R2.fastq", - "receipt_date": "2021/05/13", + "r1_fastq_filepath": "/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/example_data/ENA_TEST1_V1.R1.fastq.gz", + "r2_fastq_filepath": "/home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/example_data/ENA_TEST1_V1.R2.fastq.gz", + "receipt_date": "2021-05-13", "run_alias": "", "sample_description": "Sample for surveillance", "design_description": "", - "sample_name": "sample_alias_4", + "sample_name": 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zYbrwK6j@|GZ(+`7dVsn@BrX8;D_vGy7^Lldm<0|CUt4kd4fS*F%%<#5PhN1wQ zOT{7$hO<`Z76I;6BAmzOed&NBv1A@{?U$jCq7S_iwFCsTwn_;8`M06(r&aV82yYhz zRETrz*-*YJZWXosZBzn27Y8h6@W5{l!h8TOC!ROf6z8`vN(PqMO+U~wgR~GWIB#dK&}G3)o<~y zF|YgyC$QBFa^494^*8s+HnfI2)Fah+UoR19Vw#@_e?4ARN8~tB{D?@LzHTCq-a=z4 zZu-eVsz$O)v>&~@jdhIpF7uAXsM)dQBN?|&dxY;oC)jbtU#Ac2H7&RWKKZ$R>B~F3 zCSC#~;x7g}MG7`~x?gvFj9hpo{yJ7fS$5A6cTSJqdQ|6@uZ#_`H_|lEYMdN9I)19Y z6!sC{gAr*2qMoCw6+TGHg}28ZwYu?BlFR+p@aNBq6$D~VZTtApIo|8RalcdY?#9Up zp%;!`x&P?-{q6BrFYM{u?T%ce>iZD7v~Z!>Dd}Fc%0oGRNXnSI<--*2<~-Aj&W}#U z|GFCbJEhzsayrMWi+0hjJjg$?|Eq=%BWWdGY3?DCa7%*t?ITlSIP zUc-r(XmKZo>~k$otOoX=HGL{`S4bo}aj~A>=7zeI&&l8~ZkOR_n*>}LkFgIOA4=Ui zu29||Q^_Y(Ad+!Y_wKbft$30zxT4SBG3xbRnc$Aj1Z?Z0z4Gpw-j`eR-XR5F5a>6v zRqIaRw^BWThSVmNw!V$=@I6>ay1`x`w$`CL$LbxgnN}KBvvNa;AvuHehV?^BEjim4 ziaXj`m~w#JU6n5th_@}D4BpSoo4v}JOkdHOuI$ozl0E?M-*=$bb4Dx?4czWZi)FYx zo(bZ#1%+n6V!W_F`qQM>!MhQX68g~{K8gr(&RD)e+?QeKUHQTJ7FzVZfI#-A4d9z{ z-TLhU+XXgk*dVZc{xM!KNJL9;?S+1jh%WRZC`d#{47_5I(h6*NTe?nQBfcg`mU5JR`#a9r`!TKYn}u&jA4NAp5oPscWu%gZ@93_m6*R`ZM?8 zr11B=q;MizcCFRm-#21G0qH;0pcjk3j}zH}w+CIJTK{o%{5k9^d>l^XfH1g3zzF{j Du_uZ^ From d45e020e40228dc2e6ba4571e81e9f5d5b28779d Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 28 Apr 2022 16:40:03 +0200 Subject: [PATCH 0392/1454] include isciii in lab address --- relecov_tools/conf/laboratory_address.json | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 8757be7a..3f13d429 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -1,4 +1,12 @@ [ + { + "collecting_institution": "Instituto de Salud Carlos III ", + "collecting_institution_address": "Crta. Pozuelo Majadahonda S/N,", + "collecting_institution_email": "info@isciii.es", + "geo_loc_state": "Madrid", + "geo_loc_city": "Madrid", + "geo_loc_country": "Spain" + }, { "collecting_institution": "Microbiología HUC San Cecilio", "collecting_institution_address": "Av. del Conocimiento S/N,", From 93d27a9784b449d56d23f3abee79a590bbf42bf0 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 28 Apr 2022 17:39:05 +0200 Subject: [PATCH 0393/1454] Fill with empty values if no originating lab is given --- relecov_tools/read_metadata.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 55a62996..47492739 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -87,6 +87,14 @@ def read_json_file(self, j_file): def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): """Fetch the laboratory location and return a dictionary""" data = {} + if lab_name == "": + data["geo_loc_city"] = "" + data["geo_loc_latitude"] = "" + data["geo_loc_longitude"] = "" + data["geo_loc_country"] = "" + stderr.print("[red] Empty Originating Laboratory.") + log.error("Found empti Originating Laboratory") + return data for lab in lab_json: if lab_name == lab["collecting_institution"]: for key, value in lab.items(): From 787ec9a39c8069d31071ff1527fc4c602cc9492f Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 28 Apr 2022 20:21:30 +0200 Subject: [PATCH 0394/1454] change host age from integer to string --- relecov_tools/schema/relecov_schema.json | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 5be00cbe..0c297502 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -744,18 +744,10 @@ }, "host_age": { "ontology": "GENEPIO:0001392", - "anyOf": [ - { - "type": "integer" - }, - { - "pattern": "\\d+-\\d+", - "type": "string" - } - ], + "type": "string", "description": "Age of host at the time of sampling.", "examples": [ - 79 + "79" ], "label": "Host Age" }, @@ -3236,4 +3228,4 @@ "classification": "Database Identifiers" } } -} \ No newline at end of file +} From b2d0004a92cf41d940f2c7c078549867ada1eefa Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 28 Apr 2022 20:35:39 +0200 Subject: [PATCH 0395/1454] Fixing space in parameter for ENA mapping --- relecov_tools/test/test_cases.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/test/test_cases.txt b/relecov_tools/test/test_cases.txt index c2c532e3..81f87fa1 100644 --- a/relecov_tools/test/test_cases.txt +++ b/relecov_tools/test/test_cases.txt @@ -2,6 +2,6 @@ relecov-tools -l /tmp/logs.log download -u usuario_test -p U[9[Gpyu3. relecov-tools -l /tmp/logs.log download -f relecov_tools/test/sftp_config.yaml relecov-tools read-metadata -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -s relecov_tools/example_data/samples_data_COD_test_01_20220422.json -o /tmp relecov-tools validate -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -o /tmp -relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json - d ENA -o /tmp +relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -d ENA -o /tmp relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -d GISAID -o /tmp relecov-tools update-db -i http://iskylims.isciiides.es/wetlab/api/ -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json From f8fac7b5e5ecf6fd5a138b3cbbc4e19500557e06 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 28 Apr 2022 20:39:26 +0200 Subject: [PATCH 0396/1454] host age is now a string --- relecov_tools/read_metadata.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 47492739..9ec45cec 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -100,6 +100,7 @@ def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): for key, value in lab.items(): data[key] = value break + for city in geo_loc_json: if city["geo_loc_city"] == data["geo_loc_city"]: data["geo_loc_latitude"] = city["geo_loc_latitude"] @@ -226,7 +227,7 @@ def read_metadata_file(self): Convert the date colunms value to the dd/mm/yyyy format. Return list of dict with data, and errors """ - exc_format_num = ["Host Age", "Sample ID given for sequencing"] + exc_format_num = ["Sample ID given for sequencing"] wb_file = openpyxl.load_workbook(self.metadata_file, data_only=True) ws_metadata_lab = wb_file["METADATA_LAB"] # removing the None columns in excel heading row From 8b49f42ce23dd0531a78a5068dad32117d526834 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 28 Apr 2022 22:15:15 +0200 Subject: [PATCH 0397/1454] adding more laboratories --- relecov_tools/conf/laboratory_address.json | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 3f13d429..625f267a 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -182,5 +182,21 @@ "geo_loc_state": "", "geo_loc_city": "", "geo_loc_country": "Spain" + }, + { + "collecting_institution": "HU Virgen de la Arrixaca", + "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", + "collecting_institution_email": "", + "geo_loc_state": "Murcia", + "geo_loc_city": "Murcia", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "HU de Donostia", + "collecting_institution_address": "Begiristain Doktorea Pasealekua, s/n", + "collecting_institution_email": "", + "geo_loc_state": "País Vasco", + "geo_loc_city": "Donostia", + "geo_loc_country": "Spain" } ] From 41b5430ba15364ccac7c127c08d707eed74d1923 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 28 Apr 2022 22:17:01 +0200 Subject: [PATCH 0398/1454] Select several lab for testing --- .../example_data/METADATA_LAB_TEST.xlsx | Bin 490978 -> 490183 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/relecov_tools/example_data/METADATA_LAB_TEST.xlsx b/relecov_tools/example_data/METADATA_LAB_TEST.xlsx index 00adc3238f8f19428d353699d1800bf2ee3cdb6d..02846bb96e5866dce68b2f330327bc16ab089895 100644 GIT binary patch literal 490183 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zax;R5Ut6w1V*Y)fn7Yuj(ej6n*9UmBa};Htn#6gEfnmiR4u$}4MkWyk5e5zp4u(%L zb3)QqHEn;uz`$V5#K6D}q)|b9QEE=Hz8;7~*BH|Lv*-{|lM)*P13!u`Nk#^SiX8p& z{G#ln{QPXairgG@&82GR9QipI7&^8vFz}*imS6#EE-tCeNiD{vRY`1<#)~bC47{0w z3=$|>lX&3v7H6cUmK5uQDI;vAOv_ge;sv@>j-7!)3dNKO2N^-Ghxi=X4_HItrNYYx z@<0P-Ol1HDDl&L_2y9MqMq*KFN^nV0W?nj0|9tb?*A)zONf$6I1(6M4aJ$RMkdmJq zP?TR#te>1;l#0zG?3v#cUjwyO1C0-c0&KefZ*r_|0P0lWVqg$P(ardP zks;bSKd&S;uOvRCvLLlM7MlUNn$rCaSAnVEI44?c9C`@$KPUu|W5W`gDg8g&Uhh1{ zz`$sRZi>ftCRkcRHpK#)DV_&IX%mP+yZZW}T z%E{In0ekcq7*;K1LUYRt4>oM37-KW#<{d$WX=V%zW Date: Thu, 28 Apr 2022 22:17:52 +0200 Subject: [PATCH 0399/1454] Update test file after changes --- .../processed_METADATA_LAB_TEST.json | 280 ++++++++++-------- 1 file changed, 150 insertions(+), 130 deletions(-) diff --git a/relecov_tools/example_data/processed_METADATA_LAB_TEST.json b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json index a2884048..b5bd53e1 100644 --- a/relecov_tools/example_data/processed_METADATA_LAB_TEST.json +++ b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json @@ -7,11 +7,12 @@ "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123456", - "collecting_institution": "Hospital Universitario Miguel Servet", - "collecting_institution_address": "P.º Isabel la Católica, 1-3", - "collecting_institution_email": "rbenito@salud.aragon.es", + "collecting_institution": "HU Virgen de la Arrixaca", + "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", + "collecting_institution_email": "", "collecting_lab_sample_id": "1197860", "collection_device": "Swab", + "collector_name": "Maria de la Montaña", "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "45", @@ -26,16 +27,16 @@ "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", - "geo_loc_city": "Zaragoza", + "geo_loc_city": "Murcia", "geo_loc_country": "Spain", - "geo_loc_latitude": "41.6483", - "geo_loc_longitude": "-0.8830", - "geo_loc_state": "Aragon", + "geo_loc_latitude": "37.9861", + "geo_loc_longitude": "-1.1303", + "geo_loc_state": "Murcia", "gisaid_id": "EPI_ISL_11222687", - "host_age": 55, + "host_age": "55", "host_common_name": "Human", "host_disease": "COVID-19", - "host_gender": "Mujer", + "host_gender": "Female", "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", @@ -50,23 +51,24 @@ "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU01394", - "purpose_of_sampling": "Surveillance", + "purpose_of_sampling": "Whole Genome Sequencing", "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", - "sample_collection_date": "2021/04/13", + "sample_collection_date": "2021-04-13", "sample_description": "Sample for surveillance", - "sample_received_date": "2021/05/13", + "sample_received_date": "2021-05-13", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_001.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_001.fastq.gz", - "sequencing_date": "2022/02/22", + "sequencing_date": "2022-02-22", "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 214824, "study_alias": "RELECOV", + "study_id": "ERP137164", "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", @@ -83,11 +85,12 @@ "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123457", - "collecting_institution": "Hospital Universitario Miguel Servet", - "collecting_institution_address": "P.º Isabel la Católica, 1-3", - "collecting_institution_email": "rbenito@salud.aragon.es", + "collecting_institution": "HU Virgen de la Arrixaca", + "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", + "collecting_institution_email": "", "collecting_lab_sample_id": "1197824", "collection_device": "Swab", + "collector_name": "Maria de la Montaña", "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "12", @@ -102,16 +105,16 @@ "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", - "geo_loc_city": "Zaragoza", + "geo_loc_city": "Murcia", "geo_loc_country": "Spain", - "geo_loc_latitude": "41.6483", - "geo_loc_longitude": "-0.8830", - "geo_loc_state": "Aragon", + "geo_loc_latitude": "37.9861", + "geo_loc_longitude": "-1.1303", + "geo_loc_state": "Murcia", "gisaid_id": "EPI_ISL_11222688", - "host_age": 59, + "host_age": "59", "host_common_name": "Human", "host_disease": "COVID-19", - "host_gender": "Hombre", + "host_gender": "Male", "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", @@ -126,23 +129,24 @@ "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU01469", - "purpose_of_sampling": "Surveillance", + "purpose_of_sampling": "Whole Genome Sequencing", "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", - "sample_collection_date": "2021/03/31", + "sample_collection_date": "2021-03-31", "sample_description": "Sample for surveillance", - "sample_received_date": "2021/05/13", + "sample_received_date": "2021-05-13", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_002.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_002.fastq.gz", - "sequencing_date": "2022/02/22", + "sequencing_date": "2022-02-22", "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 214832, "study_alias": "RELECOV", + "study_id": "ERP137164", "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", @@ -159,11 +163,12 @@ "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123458", - "collecting_institution": "Hospital Universitario Miguel Servet", - "collecting_institution_address": "P.º Isabel la Católica, 1-3", - "collecting_institution_email": "rbenito@salud.aragon.es", + "collecting_institution": "HU Virgen de la Arrixaca", + "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", + "collecting_institution_email": "", "collecting_lab_sample_id": "1197767", "collection_device": "Swab", + "collector_name": "Maria de la Montaña", "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "45", @@ -178,16 +183,16 @@ "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", - "geo_loc_city": "Zaragoza", + "geo_loc_city": "Murcia", "geo_loc_country": "Spain", - "geo_loc_latitude": "41.6483", - "geo_loc_longitude": "-0.8830", - "geo_loc_state": "Aragon", + "geo_loc_latitude": "37.9861", + "geo_loc_longitude": "-1.1303", + "geo_loc_state": "Murcia", "gisaid_id": "EPI_ISL_11222689", - "host_age": 8, + "host_age": "8", "host_common_name": "Human", "host_disease": "COVID-19", - "host_gender": "Mujer", + "host_gender": "Female", "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", @@ -202,23 +207,24 @@ "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU03926", - "purpose_of_sampling": "Surveillance", + "purpose_of_sampling": "Whole Genome Sequencing", "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", - "sample_collection_date": "2022/01/13", + "sample_collection_date": "2022-01-13", "sample_description": "Sample for surveillance", - "sample_received_date": "2022/01/18", + "sample_received_date": "2022-01-18", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_003.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_003.fastq.gz", - "sequencing_date": "2022/02/22", + "sequencing_date": "2022-02-22", "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 220338, "study_alias": "RELECOV", + "study_id": "ERP137164", "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", @@ -235,11 +241,12 @@ "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123459", - "collecting_institution": "Hospital Universitario Miguel Servet", - "collecting_institution_address": "P.º Isabel la Católica, 1-3", - "collecting_institution_email": "rbenito@salud.aragon.es", + "collecting_institution": "HU Virgen de la Arrixaca", + "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", + "collecting_institution_email": "", "collecting_lab_sample_id": "8328199", "collection_device": "Swab", + "collector_name": "Maria de la Montaña", "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "23", @@ -254,16 +261,16 @@ "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", - "geo_loc_city": "Zaragoza", + "geo_loc_city": "Murcia", "geo_loc_country": "Spain", - "geo_loc_latitude": "41.6483", - "geo_loc_longitude": "-0.8830", - "geo_loc_state": "Aragon", + "geo_loc_latitude": "37.9861", + "geo_loc_longitude": "-1.1303", + "geo_loc_state": "Murcia", "gisaid_id": "EPI_ISL_11222690", - "host_age": 9, + "host_age": "9", "host_common_name": "Human", "host_disease": "COVID-19", - "host_gender": "Mujer", + "host_gender": "Male", "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", @@ -278,23 +285,24 @@ "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU06554", - "purpose_of_sampling": "Surveillance", + "purpose_of_sampling": "Whole Genome Sequencing", "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", - "sample_collection_date": "2022/01/11", + "sample_collection_date": "2022-01-11", "sample_description": "Sample for surveillance", - "sample_received_date": "2022/01/20", + "sample_received_date": "2022-01-20", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_004.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_004.fastq.gz", - "sequencing_date": "2022/02/22", + "sequencing_date": "2022-02-22", "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 220407, "study_alias": "RELECOV", + "study_id": "ERP137164", "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", @@ -311,11 +319,12 @@ "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123460", - "collecting_institution": "Hospital Universitario Miguel Servet", - "collecting_institution_address": "P.º Isabel la Católica, 1-3", - "collecting_institution_email": "rbenito@salud.aragon.es", + "collecting_institution": "HU de Donostia", + "collecting_institution_address": "Begiristain Doktorea Pasealekua, s/n", + "collecting_institution_email": "", "collecting_lab_sample_id": "1197677", "collection_device": "Swab", + "collector_name": "Maria de la Montaña", "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "12", @@ -330,16 +339,16 @@ "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", - "geo_loc_city": "Zaragoza", + "geo_loc_city": "Donostia", "geo_loc_country": "Spain", - "geo_loc_latitude": "41.6483", - "geo_loc_longitude": "-0.8830", - "geo_loc_state": "Aragon", + "geo_loc_latitude": "43.3200", + "geo_loc_longitude": "-1.9800", + "geo_loc_state": "País Vasco", "gisaid_id": "EPI_ISL_11222691", - "host_age": 31, + "host_age": "31", "host_common_name": "Human", "host_disease": "COVID-19", - "host_gender": "Hombre", + "host_gender": "Male", "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", @@ -354,23 +363,24 @@ "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU03790", - "purpose_of_sampling": "Surveillance", + "purpose_of_sampling": "Whole Genome Sequencing", "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", - "sample_collection_date": "2022/01/10", + "sample_collection_date": "2022-01-10", "sample_description": "Sample for surveillance", - "sample_received_date": "2022/01/20", + "sample_received_date": "2022-01-20", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_005.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_005.fastq.gz", - "sequencing_date": "2022/02/22", + "sequencing_date": "2022-02-22", "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 220624, "study_alias": "RELECOV", + "study_id": "ERP137164", "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", @@ -387,11 +397,12 @@ "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123461", - "collecting_institution": "Hospital Universitario Miguel Servet", - "collecting_institution_address": "P.º Isabel la Católica, 1-3", - "collecting_institution_email": "rbenito@salud.aragon.es", + "collecting_institution": "HU de Donostia", + "collecting_institution_address": "Begiristain Doktorea Pasealekua, s/n", + "collecting_institution_email": "", "collecting_lab_sample_id": "1197678", "collection_device": "Swab", + "collector_name": "Maria de la Montaña", "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "56", @@ -406,16 +417,16 @@ "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", - "geo_loc_city": "Zaragoza", + "geo_loc_city": "Donostia", "geo_loc_country": "Spain", - "geo_loc_latitude": "41.6483", - "geo_loc_longitude": "-0.8830", - "geo_loc_state": "Aragon", + "geo_loc_latitude": "43.3200", + "geo_loc_longitude": "-1.9800", + "geo_loc_state": "País Vasco", "gisaid_id": "EPI_ISL_11222692", - "host_age": 27, + "host_age": "27", "host_common_name": "Human", "host_disease": "COVID-19", - "host_gender": "Mujer", + "host_gender": "Male", "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", @@ -430,23 +441,24 @@ "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU03901", - "purpose_of_sampling": "Surveillance", + "purpose_of_sampling": "Whole Genome Sequencing", "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", - "sample_collection_date": "2022/01/12", + "sample_collection_date": "2022-01-12", "sample_description": "Sample for surveillance", - "sample_received_date": "2022/01/20", + "sample_received_date": "2022-01-20", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_006.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_006.fastq.gz", - "sequencing_date": "2022/02/22", + "sequencing_date": "2022-02-22", "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 220625, "study_alias": "RELECOV", + "study_id": "ERP137164", "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", @@ -463,11 +475,12 @@ "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123462", - "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", - "collecting_institution_address": "S. Juan Bosco, 15", - "collecting_institution_email": "rbenito@salud.aragon.es", + "collecting_institution": "HU de Donostia", + "collecting_institution_address": "Begiristain Doktorea Pasealekua, s/n", + "collecting_institution_email": "", "collecting_lab_sample_id": "1197737", "collection_device": "Swab", + "collector_name": "Maria de la Montaña", "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "11", @@ -482,16 +495,16 @@ "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", - "geo_loc_city": "Zaragoza", + "geo_loc_city": "Donostia", "geo_loc_country": "Spain", - "geo_loc_latitude": "41.6483", - "geo_loc_longitude": "-0.8830", - "geo_loc_state": "Aragon", + "geo_loc_latitude": "43.3200", + "geo_loc_longitude": "-1.9800", + "geo_loc_state": "País Vasco", "gisaid_id": "EPI_ISL_11222693", - "host_age": 42, + "host_age": "42", "host_common_name": "Human", "host_disease": "COVID-19", - "host_gender": "Mujer", + "host_gender": "Male", "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", @@ -506,23 +519,24 @@ "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU03862", - "purpose_of_sampling": "Surveillance", + "purpose_of_sampling": "Whole Genome Sequencing", "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", - "sample_collection_date": "2022/01/02", + "sample_collection_date": "2022-01-02", "sample_description": "Sample for surveillance", - "sample_received_date": "2022/01/20", + "sample_received_date": "2022-01-20", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_007.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_007.fastq.gz", - "sequencing_date": "2022/02/22", + "sequencing_date": "2022-02-22", "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 220629, "study_alias": "RELECOV", + "study_id": "ERP137164", "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", @@ -539,11 +553,12 @@ "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123463", - "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", - "collecting_institution_address": "S. Juan Bosco, 15", - "collecting_institution_email": "rbenito@salud.aragon.es", + "collecting_institution": "HU de Donostia", + "collecting_institution_address": "Begiristain Doktorea Pasealekua, s/n", + "collecting_institution_email": "", "collecting_lab_sample_id": "1197663", "collection_device": "Swab", + "collector_name": "Maria de la Montaña", "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "34", @@ -558,16 +573,16 @@ "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", - "geo_loc_city": "Zaragoza", + "geo_loc_city": "Donostia", "geo_loc_country": "Spain", - "geo_loc_latitude": "41.6483", - "geo_loc_longitude": "-0.8830", - "geo_loc_state": "Aragon", + "geo_loc_latitude": "43.3200", + "geo_loc_longitude": "-1.9800", + "geo_loc_state": "País Vasco", "gisaid_id": "EPI_ISL_11222694", - "host_age": 40, + "host_age": "40", "host_common_name": "Human", "host_disease": "COVID-19", - "host_gender": "Hombre", + "host_gender": "Female", "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", @@ -582,23 +597,24 @@ "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU03614", - "purpose_of_sampling": "Surveillance", + "purpose_of_sampling": "Whole Genome Sequencing", "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", - "sample_collection_date": "2022/01/23", + "sample_collection_date": "2022-01-23", "sample_description": "Sample for surveillance", - "sample_received_date": "2022/01/25", + "sample_received_date": "2022-01-25", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_008.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_008.fastq.gz", - "sequencing_date": "2022/02/22", + "sequencing_date": "2022-02-22", "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 220634, "study_alias": "RELECOV", + "study_id": "ERP137164", "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", @@ -615,11 +631,12 @@ "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123464", - "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", - "collecting_institution_address": "S. Juan Bosco, 15", - "collecting_institution_email": "rbenito@salud.aragon.es", + "collecting_institution": "HU de Donostia", + "collecting_institution_address": "Begiristain Doktorea Pasealekua, s/n", + "collecting_institution_email": "", "collecting_lab_sample_id": "1197689", "collection_device": "Swab", + "collector_name": "Maria de la Montaña", "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "23", @@ -634,16 +651,16 @@ "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", - "geo_loc_city": "Zaragoza", + "geo_loc_city": "Donostia", "geo_loc_country": "Spain", - "geo_loc_latitude": "41.6483", - "geo_loc_longitude": "-0.8830", - "geo_loc_state": "Aragon", + "geo_loc_latitude": "43.3200", + "geo_loc_longitude": "-1.9800", + "geo_loc_state": "País Vasco", "gisaid_id": "EPI_ISL_11222695", - "host_age": 53, + "host_age": "53", "host_common_name": "Human", "host_disease": "COVID-19", - "host_gender": "Hombre", + "host_gender": "Male", "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", @@ -658,23 +675,24 @@ "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU04252", - "purpose_of_sampling": "Surveillance", + "purpose_of_sampling": "Whole Genome Sequencing", "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", - "sample_collection_date": "2022/01/18", + "sample_collection_date": "2022-01-18", "sample_description": "Sample for surveillance", - "sample_received_date": "2022/01/26", + "sample_received_date": "2022-01-26", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_009.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_009.fastq.gz", - "sequencing_date": "2022/02/22", + "sequencing_date": "2022-02-22", "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 220636, "study_alias": "RELECOV", + "study_id": "ERP137164", "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", @@ -691,11 +709,12 @@ "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123465", - "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", - "collecting_institution_address": "S. Juan Bosco, 15", - "collecting_institution_email": "rbenito@salud.aragon.es", + "collecting_institution": "HU de Donostia", + "collecting_institution_address": "Begiristain Doktorea Pasealekua, s/n", + "collecting_institution_email": "", "collecting_lab_sample_id": "1197685", "collection_device": "Swab", + "collector_name": "Maria de la Montaña", "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "32", @@ -710,16 +729,16 @@ "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", - "geo_loc_city": "Zaragoza", + "geo_loc_city": "Donostia", "geo_loc_country": "Spain", - "geo_loc_latitude": "41.6483", - "geo_loc_longitude": "-0.8830", - "geo_loc_state": "Aragon", + "geo_loc_latitude": "43.3200", + "geo_loc_longitude": "-1.9800", + "geo_loc_state": "País Vasco", "gisaid_id": "EPI_ISL_11222696", - "host_age": 96, + "host_age": "96", "host_common_name": "Human", "host_disease": "COVID-19", - "host_gender": "Male", + "host_gender": "Female", "host_scientific_name": "Homo Sapiens", "if_amplicon_protocol_if_other_especify": "", "if_enrichment_protocol_is_other_specify": "", @@ -734,23 +753,24 @@ "number_of_samples_in_run": "96", "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU04223", - "purpose_of_sampling": "Surveillance", + "purpose_of_sampling": "Whole Genome Sequencing", "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", - "sample_collection_date": "2022/01/19", + "sample_collection_date": "2022-01-19", "sample_description": "Sample for surveillance", - "sample_received_date": "2022/01/26", + "sample_received_date": "2022-01-26", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_0010.fastq.gz", "sequence_file_R2_fastq": "ABC123_S1_L001_R2_0010.fastq.gz", - "sequencing_date": "2022/02/22", + "sequencing_date": "2022-02-22", "sequencing_instrument_model": "Illumina MiSeq", "sequencing_instrument_platform": "Illumina", "sequencing_sample_id": 220639, "study_alias": "RELECOV", + "study_id": "ERP137164", "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "", "submitting_institution": "Instituto de Salud Carlos III ", From 5686856accd917320234eb2a069ab37708fbf9c7 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 28 Apr 2022 22:18:43 +0200 Subject: [PATCH 0400/1454] Update ENA test file after changes in mapping --- ..._LAB_TEST_2022_04_22_12_23_ENA_mapped.json | 382 ------------------ 1 file changed, 382 deletions(-) delete mode 100644 relecov_tools/example_data/processed_METADATA_LAB_TEST_2022_04_22_12_23_ENA_mapped.json diff --git a/relecov_tools/example_data/processed_METADATA_LAB_TEST_2022_04_22_12_23_ENA_mapped.json b/relecov_tools/example_data/processed_METADATA_LAB_TEST_2022_04_22_12_23_ENA_mapped.json deleted file mode 100644 index 610d84b2..00000000 --- a/relecov_tools/example_data/processed_METADATA_LAB_TEST_2022_04_22_12_23_ENA_mapped.json +++ /dev/null @@ -1,382 +0,0 @@ -[ - { - "collection_date": "2021/04/13", - "common_name": "PEPITO", - "experiment_alias": "", - "experiment_title": "Example project for ENA submission RELECOV", - "fastq_r1_md5": "f2facbd1d6c7e0972074ced31ccbfd8e", - "fastq_r2_md5": "fd9948be8da7a38b0f80659dfc21aeea", - "geographic location (latitude)": "41.6483", - "geographic location (longitude)": "-0.8830", - "geographic_location_(country_and/or_sea)": "Spain", - "host_common_name": "Human", - "host_gender": "Mujer", - "host_scientific_name": "Homo Sapiens", - "instrument_model": "Illumina MiSeq", - "instrument_platform": "Illumina", - "isolate": "1197860", - "isolation source host-associated": "Nasopharynx aspirate", - "isolation source non-host-associated": "Other", - "library_layout": "Single End", - "library_selection": "RT-PCR", - "library_source": "RNA", - "library_strategy": "WGS strategy", - "purpose_sampling": "Surveillance", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "receipt_date": "2021/05/13", - "run_alias": "", - "sample_description": "Sample for surveillance", - "sample_name": "1197860", - "sample_storage_conditions": " -80ºC", - "scientific_name": "Severe acute respiratory syndrome coronavirus 2", - "sequence_file_R1_fastq": "ABC123_S1_L001_R1_001.fastq.gz", - "sequence_file_R2_fastq": "ABC123_S1_L001_R2_001.fastq.gz", - "study_alias": "RELECOV", - "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "RELECOV Spanish Network for genomics surveillance", - "tax_id": "2697049" - }, - { - "collection_date": "2021/03/31", - "common_name": "PEPITO", - "experiment_alias": "", - "experiment_title": "Example project for ENA submission RELECOV", - "fastq_r1_md5": "9a460a812086516536c1a1023ab5f7fe", - "fastq_r2_md5": "41cd79b8a167d85eb06309207fd120cf", - "geographic location (latitude)": "41.6483", - "geographic location (longitude)": "-0.8830", - "geographic_location_(country_and/or_sea)": "Spain", - "host_common_name": "Human", - "host_gender": "Hombre", - "host_scientific_name": "Homo Sapiens", - "instrument_model": "Illumina MiSeq", - "instrument_platform": "Illumina", - "isolate": "1197824", - "isolation source host-associated": "Nasopharynx aspirate", - "isolation source non-host-associated": "Other", - "library_layout": "Single End", - "library_selection": "RT-PCR", - "library_source": "RNA", - "library_strategy": "WGS strategy", - "purpose_sampling": "Surveillance", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", - "receipt_date": "2021/05/13", - "run_alias": "", - "sample_description": "Sample for surveillance", - "sample_name": 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"ABC123_S1_L001_R2_0010.fastq.gz", - "study_alias": "RELECOV", - "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "RELECOV Spanish Network for genomics surveillance", - "tax_id": "2697049" - } -] \ No newline at end of file From bc19df73c4c6cfefada8000d2ac126c05e68e813 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 28 Apr 2022 22:20:33 +0200 Subject: [PATCH 0401/1454] fixing bugs during mapping --- relecov_tools/map_schema.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 239c6c23..3755ff4f 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -187,7 +187,7 @@ def additional_formating(self, mapped_json_data): "library_kit" ] mapped_json_data[idx]["sample_name"] = self.json_data[idx][ - "sample_title" + "collecting_lab_sample_id" ] mapped_json_data[idx]["study_type"] = self.json_data[idx][ "purpose_of_sampling" From 4b0f8a9c0377f857062bdc5232db96c7cd56e2f2 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 28 Apr 2022 22:21:33 +0200 Subject: [PATCH 0402/1454] add collector_name to json data --- relecov_tools/read_metadata.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 9ec45cec..162e43b8 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -122,6 +122,12 @@ def include_fixed_data(self): fixed_data.update(self.configuration.get_configuration("ENA_configuration")) return fixed_data + def include_fields_already_set(self, row_sample): + processed_data = {} + processed_data["collector_name"] = row_sample['author_submitter'] + + return processed_data + def include_processed_data(self, metadata): """Include the data that requires to be processed to set the value""" new_data = {} @@ -196,6 +202,9 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): """ row_sample.update(self.include_fixed_data()) + """ Add fields that are already in other fields + """ + row_sample.update(self.include_fields_already_set(row_sample)) """Add information which requires processing """ row_sample.update(self.include_processed_data(row_sample)) From e5c41fc07eb6bd95ed1f76ea60f2c287a372f55f Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 28 Apr 2022 22:21:59 +0200 Subject: [PATCH 0403/1454] remove old file --- ..._LAB_TEST_2022_04_28_21_05_ENA_mapped.json | 452 ++++++++++++++++++ 1 file changed, 452 insertions(+) create mode 100644 relecov_tools/example_data/processed_METADATA_LAB_TEST_2022_04_28_21_05_ENA_mapped.json diff --git a/relecov_tools/example_data/processed_METADATA_LAB_TEST_2022_04_28_21_05_ENA_mapped.json b/relecov_tools/example_data/processed_METADATA_LAB_TEST_2022_04_28_21_05_ENA_mapped.json new file mode 100644 index 00000000..684be7bc --- /dev/null +++ b/relecov_tools/example_data/processed_METADATA_LAB_TEST_2022_04_28_21_05_ENA_mapped.json @@ -0,0 +1,452 @@ +[ + { + "collecting_institution": "HU Virgen de la Arrixaca", + "collection_date": "2021-04-13", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "f2facbd1d6c7e0972074ced31ccbfd8e", + "fastq_r2_md5": "fd9948be8da7a38b0f80659dfc21aeea", + "file_type": "fastq", + "geographic location (latitude)": "37.9861", + "geographic location (longitude)": "-1.1303", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_scientific_name": "Homo Sapiens", + "host_sex": "Female", + "instrument_model": "Illumina MiSeq", + "isolate": "1197860", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": 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"study_type": "Whole Genome Sequencing", + "taxon_id": "2697049" + }, + { + "collecting_institution": "HU Virgen de la Arrixaca", + "collection_date": "2021-03-31", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "9a460a812086516536c1a1023ab5f7fe", + "fastq_r2_md5": "41cd79b8a167d85eb06309207fd120cf", + "file_type": "fastq", + "geographic location (latitude)": "37.9861", + "geographic location (longitude)": "-1.1303", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_scientific_name": "Homo Sapiens", + "host_sex": "Male", + "instrument_model": "Illumina MiSeq", + "isolate": "1197824", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "SINGLE", + "library_name": "NEBNext® Fast DNA 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"taxon_id": "2697049" + }, + { + "collecting_institution": "HU Virgen de la Arrixaca", + "collection_date": "2022-01-13", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "c78fcb585a0f44734ce8c2aebf3eff33", + "fastq_r2_md5": "8361d5a6b50279fbc8c93226ecc3568a", + "file_type": "fastq", + "geographic location (latitude)": "37.9861", + "geographic location (longitude)": "-1.1303", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_scientific_name": "Homo Sapiens", + "host_sex": "Female", + "instrument_model": "Illumina MiSeq", + "isolate": "1197767", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "SINGLE", + "library_name": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "platform": "Illumina", + "purpose_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_003.fastq.gz", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_003.fastq.gz", + "receipt_date": "2022-01-18", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197767", + "sample_storage_conditions": " -80ºC", + "sample_title": "1197767", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_003.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_003.fastq.gz", + "study_abstract": "RELECOV Spanish Network for genomics surveillance", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "Whole Genome Sequencing", + "taxon_id": "2697049" + }, + { + "collecting_institution": "HU Virgen de la Arrixaca", + "collection_date": "2022-01-11", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "aa557fc40d3a9e16f470ac595fb5eb3e", + "fastq_r2_md5": "a2dd5e08b75815dab892e392cb8468fc", + "file_type": "fastq", + "geographic location (latitude)": "37.9861", + "geographic location (longitude)": "-1.1303", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_scientific_name": "Homo Sapiens", + "host_sex": "Male", + "instrument_model": "Illumina MiSeq", + "isolate": "8328199", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "SINGLE", + "library_name": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "platform": "Illumina", + "purpose_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_004.fastq.gz", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_004.fastq.gz", + "receipt_date": "2022-01-20", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "8328199", + "sample_storage_conditions": " -80ºC", + "sample_title": "8328199", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_004.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_004.fastq.gz", + "study_abstract": "RELECOV Spanish Network for genomics surveillance", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "Whole Genome Sequencing", + "taxon_id": "2697049" + }, + { + "collecting_institution": "HU de Donostia", + "collection_date": "2022-01-10", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "b0a13671031ef5aa7e0e6559a925a688", + "fastq_r2_md5": "8c420a603c81823e68436003825b1e1f", + "file_type": "fastq", + "geographic location (latitude)": "43.3200", + "geographic location (longitude)": "-1.9800", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_scientific_name": "Homo Sapiens", + "host_sex": "Male", + "instrument_model": "Illumina MiSeq", + "isolate": "1197677", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "SINGLE", + "library_name": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "platform": "Illumina", + "purpose_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_005.fastq.gz", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_005.fastq.gz", + "receipt_date": "2022-01-20", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197677", + "sample_storage_conditions": " -80ºC", + "sample_title": "1197677", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_005.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_005.fastq.gz", + "study_abstract": "RELECOV Spanish Network for genomics surveillance", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "Whole Genome Sequencing", + "taxon_id": "2697049" + }, + { + "collecting_institution": "HU de Donostia", + "collection_date": "2022-01-12", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "13e01498a0526303f5e32f3eef077b5a", + "fastq_r2_md5": "61d1f52e84237320d97fd7fc2da56116", + "file_type": "fastq", + "geographic location (latitude)": "43.3200", + "geographic location (longitude)": "-1.9800", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_scientific_name": "Homo Sapiens", + "host_sex": "Male", + "instrument_model": "Illumina MiSeq", + "isolate": "1197678", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "SINGLE", + "library_name": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "platform": "Illumina", + "purpose_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_006.fastq.gz", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_006.fastq.gz", + "receipt_date": "2022-01-20", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197678", + "sample_storage_conditions": " -80ºC", + "sample_title": "1197678", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_006.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_006.fastq.gz", + "study_abstract": "RELECOV Spanish Network for genomics surveillance", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "Whole Genome Sequencing", + "taxon_id": "2697049" + }, + { + "collecting_institution": "HU de Donostia", + "collection_date": "2022-01-02", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "f5b60a93b39a0b98781efb434d577a57", + "fastq_r2_md5": "e19f883b4e05045895f990c2296009a8", + "file_type": "fastq", + "geographic location (latitude)": "43.3200", + "geographic location (longitude)": "-1.9800", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_scientific_name": "Homo Sapiens", + "host_sex": "Male", + "instrument_model": "Illumina MiSeq", + "isolate": "1197737", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "SINGLE", + "library_name": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "platform": "Illumina", + "purpose_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_007.fastq.gz", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_007.fastq.gz", + "receipt_date": "2022-01-20", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197737", + "sample_storage_conditions": " -80ºC", + "sample_title": "1197737", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_007.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_007.fastq.gz", + "study_abstract": "RELECOV Spanish Network for genomics surveillance", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "Whole Genome Sequencing", + "taxon_id": "2697049" + }, + { + "collecting_institution": "HU de Donostia", + "collection_date": "2022-01-23", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "83043c429b0ab94375236cf7f51860f0", + "fastq_r2_md5": "c00859a1f83e2364cca953fb25da3cf2", + "file_type": "fastq", + "geographic location (latitude)": "43.3200", + "geographic location (longitude)": "-1.9800", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_scientific_name": "Homo Sapiens", + "host_sex": "Female", + "instrument_model": "Illumina MiSeq", + "isolate": "1197663", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "SINGLE", + "library_name": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "platform": "Illumina", + "purpose_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_008.fastq.gz", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_008.fastq.gz", + "receipt_date": "2022-01-25", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197663", + "sample_storage_conditions": " -80ºC", + "sample_title": "1197663", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_008.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_008.fastq.gz", + "study_abstract": "RELECOV Spanish Network for genomics surveillance", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "Whole Genome Sequencing", + "taxon_id": "2697049" + }, + { + "collecting_institution": "HU de Donostia", + "collection_date": "2022-01-18", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "bc720a024263a518f6a6cd9301b308ac", + "fastq_r2_md5": "6bf6d95b59c950691effcaf8a0e83068", + "file_type": "fastq", + "geographic location (latitude)": "43.3200", + "geographic location (longitude)": "-1.9800", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_scientific_name": "Homo Sapiens", + "host_sex": "Male", + "instrument_model": "Illumina MiSeq", + "isolate": "1197689", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "SINGLE", + "library_name": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "platform": "Illumina", + "purpose_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_009.fastq.gz", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_009.fastq.gz", + "receipt_date": "2022-01-26", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197689", + "sample_storage_conditions": " -80ºC", + "sample_title": "1197689", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_009.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_009.fastq.gz", + "study_abstract": "RELECOV Spanish Network for genomics surveillance", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "Whole Genome Sequencing", + "taxon_id": "2697049" + }, + { + "collecting_institution": "HU de Donostia", + "collection_date": "2022-01-19", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "a86f4fa0c92d76df34fd000a29d1cdd3", + "fastq_r2_md5": "8c4309dc00d725496c48bee6da0e4bbf", + "file_type": "fastq", + "geographic location (latitude)": "43.3200", + "geographic location (longitude)": "-1.9800", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_scientific_name": "Homo Sapiens", + "host_sex": "Female", + "instrument_model": "Illumina MiSeq", + "isolate": "1197685", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "SINGLE", + "library_name": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "platform": "Illumina", + "purpose_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_0010.fastq.gz", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_0010.fastq.gz", + "receipt_date": "2022-01-26", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197685", + "sample_storage_conditions": " -80ºC", + "sample_title": "1197685", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_0010.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_0010.fastq.gz", + "study_abstract": "RELECOV Spanish Network for genomics surveillance", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "Whole Genome Sequencing", + "taxon_id": "2697049" + } +] \ No newline at end of file From b1d4c1f923c490526a7ac344e9024d2e8fdc8bf2 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 28 Apr 2022 22:26:57 +0200 Subject: [PATCH 0404/1454] fix litin --- relecov_tools/ena_upload.py | 3 --- relecov_tools/read_metadata.py | 2 +- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 69d30948..b56dbb57 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,6 +1,4 @@ import logging -from tkinter.tix import CheckList -from numpy import empty import rich.console import json @@ -9,7 +7,6 @@ import os import relecov_tools.utils from relecov_tools.config_json import ConfigJson -from lxml import etree from ena_upload.ena_upload import extract_targets from ena_upload.ena_upload import submit_data diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 162e43b8..9a103de1 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -124,7 +124,7 @@ def include_fixed_data(self): def include_fields_already_set(self, row_sample): processed_data = {} - processed_data["collector_name"] = row_sample['author_submitter'] + processed_data["collector_name"] = row_sample["author_submitter"] return processed_data From 4c88cd4ad38bef85ede673aee8c4319624837362 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 29 Apr 2022 15:00:09 +0200 Subject: [PATCH 0405/1454] Adding more lab in json --- relecov_tools/conf/laboratory_address.json | 35 +++++++++++++++------- 1 file changed, 25 insertions(+), 10 deletions(-) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 625f267a..0b0f7045 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -161,26 +161,41 @@ }, { "collecting_institution": "LABORATORI DE REFERENCIA DE CATALUNYA", - "collecting_institution_address": "", + "collecting_institution_address": "Carrer de la Selva, 10", "collecting_institution_email": "", - "geo_loc_state": "", - "geo_loc_city": "", + "geo_loc_state": "Cataluña", + "geo_loc_city": "Barcelona", "geo_loc_country": "Spain" }, { "collecting_institution": "Banc de Sang i Teixits Catalunya", - "collecting_institution_address": "", - "geo_loc_country" : "Spain", - "geo_loc_state": "", - "geo_loc_city": "", + "collecting_institution_address": "Passeig del Taulat, 116", + "geo_loc_state": "Cataluña", + "geo_loc_city": "Barcelona", "geo_loc_country": "Spain" }, { "collecting_institution": "Unitat de Genòmica i Medicina Personalitzada - Hospital Dr. Josep Trueta", - "collecting_institution_address": "", + "collecting_institution_address": "Avinguda de França, S/N,", "collecting_institution_email": "", - "geo_loc_state": "", - "geo_loc_city": "", + "geo_loc_state": "Cataluña", + "geo_loc_city": "Girona", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Universitario de Ceuta", + "collecting_institution_address": "Colmenar s/n", + "collecting_institution_email": "", + "geo_loc_state": "Ceuta", + "geo_loc_city": "Ceuta", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital de Mostoles", + "collecting_institution_address": "C. Dr. Luis Montes, S/N ", + "collecting_institution_email": "", + "geo_loc_state": "Madrid", + "geo_loc_city": "Madrid", "geo_loc_country": "Spain" }, { From c24d82b80c4f8473fc163c61cf45e26daca0ea60 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 2 May 2022 14:12:56 +0200 Subject: [PATCH 0406/1454] remove / form the url in update_db command --- relecov_tools/test/test_cases.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/test/test_cases.txt b/relecov_tools/test/test_cases.txt index 81f87fa1..7ddd6d58 100644 --- a/relecov_tools/test/test_cases.txt +++ b/relecov_tools/test/test_cases.txt @@ -4,4 +4,4 @@ relecov-tools read-metadata -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx relecov-tools validate -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -o /tmp relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -d ENA -o /tmp relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -d GISAID -o /tmp -relecov-tools update-db -i http://iskylims.isciiides.es/wetlab/api/ -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json +relecov-tools update-db -i http://iskylims.isciiides.es/wetlab/api -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json From 62a16a16287047e78887614d738a02ca364b3b9d Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 2 May 2022 14:14:09 +0200 Subject: [PATCH 0407/1454] replace anatomical_part for anatomical_material, and add label for Type --- relecov_tools/schema/relecov_schema.json | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 0c297502..051bd1a3 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -904,7 +904,7 @@ "classification": "Sample collection and processing", "label": "Specimen source" }, - "anatomical_part": { + "anatomical_material": { "Enums": [ "Anus [UBERON:0001245]", "Duodenum [UBERON:0002114]", @@ -3225,7 +3225,8 @@ "ontology": "NCIT:C25284", "type": "string", "description": "default must remain 'betacoronavirus'", - "classification": "Database Identifiers" + "classification": "Database Identifiers", + "label": "Type" } } } From 98ffae317ec831d10a4ef88fe4589a67d674a2a9 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 2 May 2022 14:15:15 +0200 Subject: [PATCH 0408/1454] Add url for post and update the return error messages --- relecov_tools/rest_api.py | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/relecov_tools/rest_api.py b/relecov_tools/rest_api.py index 3c617741..616ecf6a 100644 --- a/relecov_tools/rest_api.py +++ b/relecov_tools/rest_api.py @@ -51,25 +51,24 @@ def put_request(self, request_info, parameter, value): log.error("Unable to open connection towards %s", self.server) return False - def post_request(self, data, credentials): + def post_request(self, data, credentials, url): if isinstance(credentials, dict): auth = (credentials["user"], credentials["pass"]) + url_http = str(self.request_url + url) try: - req = requests.post( - self.request_url, data=data, headers=self.headers, auth=auth - ) + req = requests.post(url_http, data=data, headers=self.headers, auth=auth) if req.status_code != 201: log.error( - "Unable to store parameters. Received error code %s", + "Unable to post parameters. Received error code %s", req.status_code, ) stderr.print( - "[red] Unable to store data. Received error ", req.status_code + f"[red] Unable to post data. Received error {req.status_code}" ) - sys.exit(1) - return True + # sys.exit(1) + return {"ERROR": req.status_code} + return {"Success": req.data} except requests.ConnectionError: log.error("Unable to open connection towards %s", self.server) stderr.print("[red] Unable to open connection towards ", self.server) return {"ERROR": "Server not available"} - return {"Success": "Data are store in requested server"} From 0bad7522b168fa47f815d820a7b456db5920a259 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 2 May 2022 14:19:09 +0200 Subject: [PATCH 0409/1454] reformat to dict the sampleData to send to iSkyLIMS and starting adding data for relecov post request --- relecov_tools/conf/configuration.json | 50 ++++++++++----------------- 1 file changed, 19 insertions(+), 31 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index ef0626ef..b3f6882a 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -46,44 +46,32 @@ "token": "" } }, - "iskylims_sample_fields": [ - [ - "patientCore", - "collector_name" - ], - [ - "sampleName", - "collecting_lab_sample_id" - ], - [ - "labRequest", - "collecting_institution" - ], - [ - "sampleType", - "anatomical_material" - ], - [ - "species", - "host_common_name" - ], - [ - "sampleEntryDate", - "sample_received_date" - ], - [ - "sampleCollectionDate", - "sample_collection_date" - ] - ], + "iskylims_sample_fields": { + "patientCore": "collector_name", + "sampleName": "collecting_lab_sample_id", + "labRequest": "collecting_institution", + "sampleType": "anatomical_material", + "species": "host_common_name", + "sampleEntryDate": "sample_received_date", + "sampleCollectionDate": "sample_collection_date" + }, "iskylims_fixed_values": { "sampleProject": "Relecov", "onlyRecorded": "Yes", "sampleLocation": "Not defined" }, + "relecov_metadata":[ + "collecting_lab_sample_id", + "sequencing_sample_id", + "biosample_accession_ENA", + "virus_name", + "gisaid_id", + "sequencing_date" + ], "tool": { "tool_name": "ena-upload-cli", "tool_version": "0.5.3" }, "checklist": "ERC000033" -} \ No newline at end of file + +} From 713e663b4057e4f614543f2f2563fd905da2843f Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 2 May 2022 14:20:28 +0200 Subject: [PATCH 0410/1454] manualy replace anatomical_part by anatomical_material --- .../processed_METADATA_LAB_TEST.json | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/relecov_tools/example_data/processed_METADATA_LAB_TEST.json b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json index b5bd53e1..eb51fcc1 100644 --- a/relecov_tools/example_data/processed_METADATA_LAB_TEST.json +++ b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json @@ -3,7 +3,7 @@ "amplicon_protocol": "ARTIC", "amplicon_version": "v.4", "analysis_author": "Inmaculada Casas", - "anatomical_part": "Nasopharynx aspirate", + "anatomical_material": "Nasopharynx aspirate", "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123456", @@ -81,7 +81,7 @@ "amplicon_protocol": "ARTIC", "amplicon_version": "v.4", "analysis_author": "Inmaculada Casas", - "anatomical_part": "Nasopharynx aspirate", + "anatomical_material": "Nasopharynx aspirate", "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123457", @@ -159,7 +159,7 @@ "amplicon_protocol": "ARTIC", "amplicon_version": "v.4", "analysis_author": "Inmaculada Casas", - "anatomical_part": "Nasopharynx aspirate", + "anatomical_material": "Nasopharynx aspirate", "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123458", @@ -237,7 +237,7 @@ "amplicon_protocol": "ARTIC", "amplicon_version": "v.4", "analysis_author": "Inmaculada Casas", - "anatomical_part": "Nasopharynx aspirate", + "anatomical_material": "Nasopharynx aspirate", "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123459", @@ -315,7 +315,7 @@ "amplicon_protocol": "ARTIC", "amplicon_version": "v.4", "analysis_author": "Inmaculada Casas", - "anatomical_part": "Nasopharynx aspirate", + "anatomical_material": "Nasopharynx aspirate", "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123460", @@ -393,7 +393,7 @@ "amplicon_protocol": "ARTIC", "amplicon_version": "v.4", "analysis_author": "Inmaculada Casas", - "anatomical_part": "Nasopharynx aspirate", + "anatomical_material": "Nasopharynx aspirate", "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123461", @@ -471,7 +471,7 @@ "amplicon_protocol": "ARTIC", "amplicon_version": "v.4", "analysis_author": "Inmaculada Casas", - "anatomical_part": "Nasopharynx aspirate", + "anatomical_material": "Nasopharynx aspirate", "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123462", @@ -549,7 +549,7 @@ "amplicon_protocol": "ARTIC", "amplicon_version": "v.4", "analysis_author": "Inmaculada Casas", - "anatomical_part": "Nasopharynx aspirate", + "anatomical_material": "Nasopharynx aspirate", "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123463", @@ -627,7 +627,7 @@ "amplicon_protocol": "ARTIC", "amplicon_version": "v.4", "analysis_author": "Inmaculada Casas", - "anatomical_part": "Nasopharynx aspirate", + "anatomical_material": "Nasopharynx aspirate", "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123464", @@ -705,7 +705,7 @@ "amplicon_protocol": "ARTIC", "amplicon_version": "v.4", "analysis_author": "Inmaculada Casas", - "anatomical_part": "Nasopharynx aspirate", + "anatomical_material": "Nasopharynx aspirate", "author_submitter": "Maria de la Montaña", "authors": "Inmaculada Casas,Maria de la Montaña", "biosample_accession_ENA": "ERS123465", @@ -779,4 +779,4 @@ "type": "betacoronavirus", "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2031" } -] \ No newline at end of file +] From 4cafa131305e3aa5dbc277071e01537c616de77c Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 2 May 2022 14:21:47 +0200 Subject: [PATCH 0411/1454] fixing error when sending request to iSkyLIMS --- relecov_tools/feed_databases.py | 63 +++++++++++++++++++++++---------- 1 file changed, 44 insertions(+), 19 deletions(-) diff --git a/relecov_tools/feed_databases.py b/relecov_tools/feed_databases.py index baaf5954..efc8bb05 100644 --- a/relecov_tools/feed_databases.py +++ b/relecov_tools/feed_databases.py @@ -2,6 +2,7 @@ import sys import os import jsonschema +import json import logging import rich.console from jsonschema import Draft202012Validator @@ -106,10 +107,9 @@ def mapping_sample_project_fields(self, s_project_fields): map_list = {} # key is the label, value the property for prop, values in self.schema["properties"].items(): try: - self.label_prop_dict[values["label"]] = prop + label_prop_dict[values["label"]] = prop except KeyError: continue - for field in s_project_fields: try: map_list[field] = label_prop_dict[field] @@ -142,7 +142,8 @@ def get_fields_sample(self): "[red] Unable to fetch data. Received error ", s_project["ERROR"] ) sys.exit(1) - s_project_fields = list(s_project.values()) + s_project_fields = [x["sampleProjectFieldName"] for x in s_project['DATA']] + sample_fields["iskylims_s_fields"].update( self.mapping_sample_project_fields(s_project_fields) ) @@ -153,27 +154,51 @@ def update_databases(self, sample_fields): """Split the information in the input json to populate iSkyLIMS and Relecov platform """ - for sample in self.json_file: + for sample in self.json_data: iskylims_data = {} - for label, value in sample_fields["iskylims_s_fields"]: - iskylims_data[label] = sample[value] + for label, value in sample_fields["iskylims_s_fields"].items(): + try: + iskylims_data[label] = sample[value] + except KeyError as e: + import pdb; pdb.set_trace() + log.error("Found %s when mapping data for sending to iSkyLIMS") + stderr.print(f"[red] {e} not found in mapping") + sys.exit(1) + iskylims_data["project"] = self.iskylims_settings["project_name"] result = self.iskylims_rest_api.post_request( - iskylims_data, {"user": self.user, "passwd": self.passwd} + json.dumps(iskylims_data), {"user": self.user, "pass": self.passwd}, + self.iskylims_settings['store_samples'] ) - if "ERROR" in result: - for i in range(10): - # wait 5 sec before resending the request - time.sleep(5) - result = self.iskylims_rest_api.post_request( - iskylims_data, {"user": self.user, "passwd": self.passwd} - ) - if "ERROR" not in result: - break - if i == 9 and "ERROR" in result: - log.error("Unable to sent the request to iSlyLIMS") - stderr.print("[red] Unable to sent the request to iSlyLIMS") + if "ERROR" in result : + if result["ERROR"] == "Server not available": + # retry to connect to server + for i in range(10): + # wait 5 sec before resending the request + time.sleep(5) + result = self.iskylims_rest_api.post_request( + iskylims_data, {"user": self.user, "passwd": self.passwd}, + self.iskylims_settings['store_samples'] + ) + if "ERROR" not in result: + break + if i == 9 and "ERROR" in result: + log.error("Unable to sent the request to iSkyLIMS") + stderr.print("[red] Unable to sent the request to iSkyLIMS") + sys.exit(1) + else: + log.error("Unable to sent the request to iSkyLIMS") + stderr.print(f"[red] Error {result['ERROR']} when sending request to iSkyLIMS ") sys.exit(1) + import pdb; pdb.set_trace() log.info("stored data in iskylims %s", sample["sampleName"]) + # send request to releco-latform + relecov_data = {} + for label, value in sample.items(): + if label not in sample_fields["iskylims_s_fields"]: + relecov_data[label] = sample[value] + result = self.relecov_rest_api.post_request( + relecov_data, {"user": self.user, "passwd": self.passwd} + ) return def store_data(self): From 885e12e7eb17663872c511e676cdeeaa9ddc47f7 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 2 May 2022 14:22:53 +0200 Subject: [PATCH 0412/1454] fixing litin --- relecov_tools/feed_databases.py | 26 +++++++++++++++++--------- 1 file changed, 17 insertions(+), 9 deletions(-) diff --git a/relecov_tools/feed_databases.py b/relecov_tools/feed_databases.py index efc8bb05..e917a5c6 100644 --- a/relecov_tools/feed_databases.py +++ b/relecov_tools/feed_databases.py @@ -142,7 +142,7 @@ def get_fields_sample(self): "[red] Unable to fetch data. Received error ", s_project["ERROR"] ) sys.exit(1) - s_project_fields = [x["sampleProjectFieldName"] for x in s_project['DATA']] + s_project_fields = [x["sampleProjectFieldName"] for x in s_project["DATA"]] sample_fields["iskylims_s_fields"].update( self.mapping_sample_project_fields(s_project_fields) @@ -160,24 +160,28 @@ def update_databases(self, sample_fields): try: iskylims_data[label] = sample[value] except KeyError as e: - import pdb; pdb.set_trace() + import pdb + + pdb.set_trace() log.error("Found %s when mapping data for sending to iSkyLIMS") stderr.print(f"[red] {e} not found in mapping") sys.exit(1) iskylims_data["project"] = self.iskylims_settings["project_name"] result = self.iskylims_rest_api.post_request( - json.dumps(iskylims_data), {"user": self.user, "pass": self.passwd}, - self.iskylims_settings['store_samples'] + json.dumps(iskylims_data), + {"user": self.user, "pass": self.passwd}, + self.iskylims_settings["store_samples"], ) - if "ERROR" in result : + if "ERROR" in result: if result["ERROR"] == "Server not available": # retry to connect to server for i in range(10): # wait 5 sec before resending the request time.sleep(5) result = self.iskylims_rest_api.post_request( - iskylims_data, {"user": self.user, "passwd": self.passwd}, - self.iskylims_settings['store_samples'] + iskylims_data, + {"user": self.user, "passwd": self.passwd}, + self.iskylims_settings["store_samples"], ) if "ERROR" not in result: break @@ -187,9 +191,13 @@ def update_databases(self, sample_fields): sys.exit(1) else: log.error("Unable to sent the request to iSkyLIMS") - stderr.print(f"[red] Error {result['ERROR']} when sending request to iSkyLIMS ") + stderr.print( + f"[red] Error {result['ERROR']} when sending request to iSkyLIMS " + ) sys.exit(1) - import pdb; pdb.set_trace() + import pdb + + pdb.set_trace() log.info("stored data in iskylims %s", sample["sampleName"]) # send request to releco-latform relecov_data = {} From 306b3202ac405e0ec61e0432f487044969dcd0b3 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 2 May 2022 21:28:58 +0200 Subject: [PATCH 0413/1454] remove patientCore and change collectionSampleDate --- relecov_tools/conf/configuration.json | 3 +-- relecov_tools/feed_databases.py | 12 +++++++----- relecov_tools/rest_api.py | 7 +++++-- 3 files changed, 13 insertions(+), 9 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index b3f6882a..f5ea31a9 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -47,13 +47,12 @@ } }, "iskylims_sample_fields": { - "patientCore": "collector_name", "sampleName": "collecting_lab_sample_id", "labRequest": "collecting_institution", "sampleType": "anatomical_material", "species": "host_common_name", "sampleEntryDate": "sample_received_date", - "sampleCollectionDate": "sample_collection_date" + "collectionSampleDate": "sample_collection_date" }, "iskylims_fixed_values": { "sampleProject": "Relecov", diff --git a/relecov_tools/feed_databases.py b/relecov_tools/feed_databases.py index e917a5c6..83446ce2 100644 --- a/relecov_tools/feed_databases.py +++ b/relecov_tools/feed_databases.py @@ -166,7 +166,11 @@ def update_databases(self, sample_fields): log.error("Found %s when mapping data for sending to iSkyLIMS") stderr.print(f"[red] {e} not found in mapping") sys.exit(1) - iskylims_data["project"] = self.iskylims_settings["project_name"] + # add fxxed valuurs before sending request + iskylims_data["patientCore"] = "" + iskylims_data["sampleLocation"] = "" + iskylims_data["onlyRecorded"] = "Yes" + iskylims_data["sampleProject"] = self.iskylims_settings["project_name"] result = self.iskylims_rest_api.post_request( json.dumps(iskylims_data), {"user": self.user, "pass": self.passwd}, @@ -190,15 +194,13 @@ def update_databases(self, sample_fields): stderr.print("[red] Unable to sent the request to iSkyLIMS") sys.exit(1) else: - log.error("Unable to sent the request to iSkyLIMS") + log.error("Request to iSkyLIMS was not accepted") stderr.print( f"[red] Error {result['ERROR']} when sending request to iSkyLIMS " ) sys.exit(1) - import pdb - pdb.set_trace() - log.info("stored data in iskylims %s", sample["sampleName"]) + log.info("stored data in iskylims for sample %s", iskylims_data["sampleName"]) # send request to releco-latform relecov_data = {} for label, value in sample.items(): diff --git a/relecov_tools/rest_api.py b/relecov_tools/rest_api.py index 616ecf6a..516ca748 100644 --- a/relecov_tools/rest_api.py +++ b/relecov_tools/rest_api.py @@ -63,11 +63,14 @@ def post_request(self, data, credentials, url): req.status_code, ) stderr.print( - f"[red] Unable to post data. Received error {req.status_code}" + f"[red] Unable to post data because {req.text}" + ) + stderr.print( + f"[red] Received error {req.status_code}" ) # sys.exit(1) return {"ERROR": req.status_code} - return {"Success": req.data} + return {"Success": req.text} except requests.ConnectionError: log.error("Unable to open connection towards %s", self.server) stderr.print("[red] Unable to open connection towards ", self.server) From c653e5f846791bddf0b23ca452a1180e7ff9e426 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 7 May 2022 16:58:18 +0200 Subject: [PATCH 0414/1454] fixing missing data in schema --- relecov_tools/schema/relecov_schema.json | 26 ++++++++++++++++++------ 1 file changed, 20 insertions(+), 6 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 051bd1a3..c6cd829c 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -43,6 +43,7 @@ "ontology": "GENEPIO:0001153", "type": "string", "description": "The name of the agency that collected the original sample.", + "classification": "Sample collection and processing", "label": "Originating Laboratory" }, "submitting_institution": { @@ -52,6 +53,7 @@ "ontology": "GENEPIO:0001159", "type": "string", "description": "The name of the agency that generated the sequence.", + "classification": "Sample collection and processing", "label": "Submitting Institution" }, "sample_collection_date": { @@ -62,6 +64,7 @@ "type": "string", "description": "The date on which the sample was collected.", "format": "date", + "classification": "Sample collection and processing", "label": "Sample Collection Date" }, "host_subject_id": { @@ -152,7 +155,7 @@ "Eswatini [GAZ:00001099]", "Ethiopia [GAZ:00000567]", "Europa Island [GAZ:00005811]", - "Falkland Islands (Islas Malvinas) [GAZ:00001412]", + "Falkland Islands [GAZ:00001412]", "Faroe Islands [GAZ:00059206]", "Fiji [GAZ:00006891]", "Finland [GAZ:00002937]", @@ -399,6 +402,7 @@ "type": "string", "description": "The date on which the symptoms began or were first noted.", "format": "date", + "classification": "Host information", "label": "Symptom onset date" }, "host_health_state": { @@ -420,6 +424,7 @@ "examples": [ "Asymptomatic [NCIT:C3833]" ], + "classification": "Host information", "label": "Host health state" }, "host_health_status_details": { @@ -443,6 +448,7 @@ "examples": [ "Hospitalized (ICU) [GENEPIO:0100046]" ], + "classification": "Host information", "label": "Host health status details" }, "host_scientific_name": { @@ -493,7 +499,8 @@ "examples": [ "COVID-19 [MONDO:0100096]" ], - "host_disease": "Host disease" + "classification": "Host information", + "label": "Host disease" }, "sequencing_instrument_model": { "Enums": [ @@ -565,6 +572,7 @@ "ontology": "GENEPIO_0000071", "type": "string", "description": "The model of the sequencing instrument used.", + "classification": "Sequencing", "label": "Sequencing Instrument Platform" }, "submitting_lab_sequence_id": { @@ -574,6 +582,7 @@ "ontology": "0", "type": "string", "description": "Sample ID given by the submitting laboratory", + "classification": "Sequencing", "label": "Sample ID given by the submitting laboratory" }, "bioproject_umbrella_accession_ENA": { @@ -663,7 +672,8 @@ "ontology": "GENEPIO:0001158", "type": "string", "description": "The mailing address of the agency submitting the sample.", - "classification": "Originating Laboratory Address" + "classification": "Sample collection and processing", + "label": "Originating Laboratory Address" }, "submitting_institution_email": { "examples": [ @@ -672,7 +682,8 @@ "ontology": "GENEPIO:0001165", "type": "string", "description": "The email address of the contact responsible for follow-up regarding the sequence.", - "classification": "Sample collection and processing" + "classification": "Sample collection and processing", + "label": "Submitting Institution Email" }, "submitting_institution_address": { "examples": [ @@ -681,7 +692,8 @@ "ontology": "GENEPIO:0001167", "type": "string", "description": "The mailing address of the agency submitting the sequence.", - "classification": "Sample collection and processing" + "classification": "Sample collection and processing", + "label": "Submitting Institution Address" }, "sample_received_date": { "examples": [ @@ -733,6 +745,7 @@ "examples": [ "/culture_collection=\"ATCC:26370\"" ], + "classification": "Sample collection and processing", "label": "Culture collection" }, "treatment": { @@ -740,6 +753,7 @@ "type": "string", "description": "Include drug name, dosage", "examples": [], + "classification": "Sample collection and processing", "label": "Treatment" }, "host_age": { @@ -1756,7 +1770,7 @@ "ontology": "GENEPIO_0001995", "type": "string", "description": "The submitter's name for this library.", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Library Name", "table": [ "experiments" From cc40143ab131e21d5e2586497eea382aed253e6b Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 8 May 2022 08:48:20 +0200 Subject: [PATCH 0415/1454] added test for feed database --- relecov_tools/test/test_cases.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/test/test_cases.txt b/relecov_tools/test/test_cases.txt index 7ddd6d58..c9b80f05 100644 --- a/relecov_tools/test/test_cases.txt +++ b/relecov_tools/test/test_cases.txt @@ -5,3 +5,4 @@ relecov-tools validate -j relecov_tools/example_data/processed_METADATA_LAB_TEST relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -d ENA -o /tmp relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -d GISAID -o /tmp relecov-tools update-db -i http://iskylims.isciiides.es/wetlab/api -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json +relecov-tools update-db -i http://localhost:8001/wetlab/api -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -u admin -p Apple@123 From 35c842c6e70650a8e122bc20bf451c7e0ccd1eac Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 8 May 2022 08:49:12 +0200 Subject: [PATCH 0416/1454] fixed error for sending to iskylims --- relecov_tools/feed_databases.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/relecov_tools/feed_databases.py b/relecov_tools/feed_databases.py index 83446ce2..ef205ef7 100644 --- a/relecov_tools/feed_databases.py +++ b/relecov_tools/feed_databases.py @@ -201,11 +201,12 @@ def update_databases(self, sample_fields): sys.exit(1) log.info("stored data in iskylims for sample %s", iskylims_data["sampleName"]) - # send request to releco-latform + # send request to releco-platform relecov_data = {} for label, value in sample.items(): if label not in sample_fields["iskylims_s_fields"]: - relecov_data[label] = sample[value] + relecov_data[label] = value + import pdb; pdb.set_trace() result = self.relecov_rest_api.post_request( relecov_data, {"user": self.user, "passwd": self.passwd} ) From 7a2b1602fecd2112ef32fb5ea08b29eb40e5ffcc Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 9 May 2022 11:52:28 +0200 Subject: [PATCH 0417/1454] changes in relecov schema and bioinfo metadata --- relecov_tools/schema/bioinfo_schema.json | 526 ++++++++++------------- relecov_tools/schema/relecov_schema.json | 45 +- 2 files changed, 235 insertions(+), 336 deletions(-) diff --git a/relecov_tools/schema/bioinfo_schema.json b/relecov_tools/schema/bioinfo_schema.json index 872c9882..e68e29c5 100644 --- a/relecov_tools/schema/bioinfo_schema.json +++ b/relecov_tools/schema/bioinfo_schema.json @@ -4,498 +4,438 @@ "properties": { "dehosting_method": { "examples": [ - "" + "Nanostripper" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "ontology": "GENEPIO:0001459", + "type": "string", + "description": "The method used to remove host reads from the pathogen sequence.", + "classification": "Bioinformatics and QC metrics", + "label": "Dehosting Method" }, "assembly": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "NCIT_C63548", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "Assembly" }, "if_assembly_other": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "If assembly Is Other, Specify" }, "assembly_params": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "Assambly params" }, "variant_calling": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "operation_3227", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "Variant Calling" }, "if_variant_calling_other": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "If variant calling Is Other, Specify" }, "variant_calling_params": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "Variant Calling params" }, "consensus_sequence_name": { + "ontology": "GENEPIO:0001460", + "type": "string", + "description": "The name of the consensus sequence.", "examples": [ - "" + "ncov123assembly3" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "Consensus sequence name" }, "consensus_sequence_name_md5": { + "ontology": "NMR:1000568", + "type": "string", + "description": "The name of the consensus sequence.", "examples": [ - "" + "ncov123assembly3" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "Consensus sequence name md5" }, "consensus_sequence_filepath": { "examples": [ - "" + "/User/Documents/RespLab/Data/ncov123assembly.fasta" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "ontology": "GENEPIO:0001462", + "type": "string", + "description": "The filepath of the consesnsus sequence file.", + "classification": "Bioinformatics and QC metrics", + "label": "Consensus sequence filepath" }, "consensus_sequence_software_name": { "examples": [ - "" + "Ivar" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "ontology": "GENEPIO:0001463", + "type": "string", + "description": "The name of software used to generate the consensus sequence.", + "classification": "Bioinformatics and QC metrics", + "label": "Consensus sequence software name" }, "if_consensus_other": { "examples": [ - "" + "1.3" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "ontology": "0", + "type": "string", + "description": "The version of the software used to generate the consensus sequence.", + "classification": "Bioinformatics and QC metrics", + "label": "If consensus Is Other, Specify" }, "consensus_sequence_software_version": { "examples": [ - "" + "1.3" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "ontology": "GENEPIO:0001469", + "type": "string", + "description": "The version of the software used to generate the consensus sequence.", + "classification": "Bioinformatics and QC metrics", + "label": "Consensus sequence software version" }, "consensus_criteria": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] - }, - "quality_control_metrics": { - "examples": [ - "" - ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] - }, - "depth_of_coverage_value": { - "examples": [ - "" - ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "Consensus criteria" }, "depth_of_coverage_threshold": { "examples": [ - "" + "100x" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "ontology": "GENEPIO:0001475", + "type": "string", + "description": "The threshold used as a cut-off for the depth of coverage.", + "classification": "Bioinformatics and QC metrics", + "label": "Depth of coverage threshold" }, "number_of_base_pairs_sequenced": { "examples": [ - "" + "387566" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "ontology": "GENEPIO:0001482", + "type": "string", + "description": "The number of total base pairs generated by the sequencing process.", + "classification": "Bioinformatics and QC metrics", + "label": "Number of base pairs sequenced " }, "consensus_genome_length": { "examples": [ - "" + "38677" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "ontology": "GENEPIO:0001483", + "type": "string", + "description": "Size of the assembled genome described as the number of base pairs.", + "classification": "Bioinformatics and QC metrics", + "label": "Consensus genome length" + }, + "ns_per_100_kbp": { + "examples": [ + "300" + ], + "ontology": "GENEPIO:0001484", + "type": "string", + "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", + "classification": "Bioinformatics and QC metrics", + "label": "Ns per 100 kbp" }, "reference_genome_accession": { "examples": [ - "" + "NC_045512.2" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "ontology": "GENEPIO:0001485", + "type": "string", + "description": "A persistent, unique identifier of a genome database entry.", + "classification": "Bioinformatics and QC metrics", + "label": "Reference genome accession" }, "bioinformatics_protocol": { "examples": [ - "" + "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "ontology": "GENEPIO:0001489", + "type": "string", + "description": "The name of the bioinformatics protocol used.", + "classification": "Bioinformatics and QC metrics", + "label": "Bioinformatics protocol" }, - "if_bioinformatic_protocol_other": { + "if_bioinformatic_protocol_is_other_specify": { "examples": [ - "" + "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "ontology": "0", + "type": "string", + "description": "The name of the bioinformatics protocol used.", + "classification": "Bioinformatics and QC metrics", + "label": "If bioinformatic protocol Is Other, Specify" }, "bioinformatic_protocol_version": { "examples": [ - "" + "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "ontology": "NCIT:C93490", + "type": "string", + "description": "The version number of the bioinformatics protocol used.", + "classification": "Bioinformatics and QC metrics", + "label": "bioinformatics protocol version" }, "commercial/open-source/both": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "Commercial/Open-source/both" }, "preprocessing": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "MS_1002386", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "Preprocessing" }, "if_preprocessing_other": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "If preprocessing Is Other, Specify" }, "preprocessing_params": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "Preprocessing params" }, "mapping": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "topic:0102", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "Mapping" }, "if_mapping_other": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "If mapping Is Other, Specify" }, "mapping_params": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "Mapping params" }, - "lineage/clade_name": { + "lineage_name": { "examples": [ - "" + "B.1.1.7" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "ontology": "GENEPIO:0001500", + "type": "string", + "description": "The name of the lineage or clade.", + "classification": "Bioinformatics and QC metrics", + "label": "Lineage/clade name" }, - "lineage/clade_analysis_software_name": { + "lineage_analysis_software_name": { "examples": [ - "" + "Pangolin" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "ontology": "GENEPIO:0001501", + "type": "string", + "description": "The name of the software used to determine the lineage/clade.", + "classification": "Bioinformatics and QC metrics", + "label": "lineage/clade analysis software name" }, "if_lineage_identification_other": { "examples": [ - "" + "Other than Pangolin" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "ontology": "0", + "type": "string", + "description": "The name of the software used to determine the lineage/clade.", + "classification": "Bioinformatics and QC metrics", + "label": "If lineage identification Is Other, Specify" }, - "lineage/clade_analysis_software_version": { + "lineage_analysis_software_version": { "examples": [ - "" + "2.1.10" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "ontology": "GENEPIO:0001502", + "type": "string", + "description": "The version of the software used to determine the lineage/clade.", + "classification": "Bioinformatics and QC metrics", + "label": "Lineage/clade analysis software version" }, "variant_designation": { - "examples": [ - "" + "Enums": [ + "Variant of Interest (VOI) [GENEPIO:0100082]", + "Variant of Concern (VOC) [GENEPIO:0100083]", + "Variant Under Monitoring (VUM) [GENEPIO:0100279]" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] - }, - "gene_name_1": { + "ontology": "GENEPIO:0001503", + "type": "string", + "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", "examples": [ - "" + "Variant of Concern (VOC) [GENEPIO:0100083]" ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "Variant designation" }, - "%qc_filtered": { + "per_qc_filtered": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "%qc filtered" }, - "%reads_host": { + "per_reads_host": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "%reads host" }, - "%reads_virus": { + "per_reads_virus": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "%reads virus" }, - "%unmapped": { + "per_unmapped": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "%unmapped" }, - "% genome _greater_10x": { + "per_genome _greater_10x": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "% genome greater 10x" }, - "mean_depth_of_coverage_value": { + "median_depth_of_coverage_value": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "NCIT:C167285", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "mean depth of coverage value" }, - "%Ns": { + "per_Ns": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "%Ns" }, - "Number_of_variants_(AF_greater_75%)": { + "number_of_variants_AF_greater_75percent": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "Number of variants (AF greater 75%)" }, - "Numer_of_variants_with_effect": { + "number_of_variants_with_effect": { "examples": [ "" ], - "ontology": "", - "type": "", + "ontology": "0", + "type": "string", "description": "", - "clasification": "", - "label": "", - "table": [] + "classification": "Bioinformatics and QC metrics", + "label": "Number of variants with effect" }, "long_table_path": { "examples": [ diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index c6cd829c..f1e47ad8 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -918,47 +918,6 @@ "classification": "Sample collection and processing", "label": "Specimen source" }, - "anatomical_material": { - "Enums": [ - "Anus [UBERON:0001245]", - "Duodenum [UBERON:0002114]", - "Eye [UBERON:0000970]", - "Intestine [UBERON:0000160]", - "Lower respiratory tract [UBERON:0001558]", - "Bronchus [UBERON:0002185]", - "Lung [UBERON:0002048]", - "Bronchiole [UBERON:0002186]", - "Alveolar sac [UBERON:0002169]", - "Pleural sac [UBERON:0009778]", - "Pleural cavity [UBERON:0002402]", - "Trachea [UBERON:0003126]", - "Rectum [UBERON:0001052]", - "Skin [UBERON:0001003]", - "Stomach [UBERON:0000945]", - "Upper respiratory tract [UBERON:0001557]", - "Anterior Nares [UBERON:2001427]", - "Esophagus [UBERON:0001043]", - "Ethmoid sinus [UBERON:0002453]", - "Nasal Cavity [UBERON:0001707]", - "Middle Nasal Turbinate [UBERON:0005921]", - "Inferior Nasal Turbinate [UBERON:0005922]", - "Nasopharynx (NP) [UBERON:0001728]", - "Oropharynx (OP) [UBERON:0001729]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001211", - "type": "string", - "description": "An anatomical part of an organism e.g. oropharynx. ", - "examples": [ - "Nasopharynx (NP) [UBERON:0001728]" - ], - "classification": "Sample collection and processing", - "label": "Specimen source" - }, "body_product": { "Enums": [ "Breast Milk [UBERON:0001913]", @@ -2602,7 +2561,7 @@ "classification": "Bioinformatics and QC metrics", "label": "% genome greater 10x" }, - "mean_depth_of_coverage_value": { + "median_depth_of_coverage_value": { "examples": [ "" ], @@ -3243,4 +3202,4 @@ "label": "Type" } } -} +} \ No newline at end of file From 2925c75cce95845e12c2b99650395218617c54f5 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 9 May 2022 11:57:24 +0200 Subject: [PATCH 0418/1454] changes in relecov schema classification attribute all filled --- relecov_tools/schema/relecov_schema.json | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index f1e47ad8..4d90d3a9 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2174,7 +2174,7 @@ "ontology": "", "type": "string", "description": "", - "classification": "", + "classification": "Bioinformatics and QC metrics", "label": "" }, "sequence_file_R1_fastq": { @@ -2184,7 +2184,7 @@ "ontology": "GENEPIO:0001476", "type": "string", "description": "The user-specified filename of the r1 FASTQ file.", - "classification": "", + "classification": "Bioinformatics and QC metrics", "label": "Sequence file R1 fastq" }, "sequence_file_R2_fastq": { @@ -2194,7 +2194,7 @@ "ontology": "GENEPIO:0001477", "type": "string", "description": "The user-specified filename of the r2 FASTQ file.", - "classification": "", + "classification": "Bioinformatics and QC metrics", "label": "Sequence file R2 fastq" }, "r1_fastq_filepath": { @@ -2204,7 +2204,7 @@ "ontology": "GENEPIO:0001478", "type": "string", "description": "The filepath of the r1 FASTQ file.", - "classification": "", + "classification": "Bioinformatics and QC metrics", "label": "Filepath R1 fastq" }, "r2_fastq_filepath": { @@ -2214,7 +2214,7 @@ "ontology": "GENEPIO:0001479", "type": "string", "description": "The filepath of the r2 FASTQ file.", - "classification": "", + "classification": "Bioinformatics and QC metrics", "label": "Filepath R2 fastq" }, "fast5_filename": { @@ -2224,7 +2224,7 @@ "ontology": "GENEPIO:0001480", "type": "string", "description": "The user-specified filename of the FAST5 file.", - "classification": "", + "classification": "Bioinformatics and QC metrics", "label": "Filename fast5" }, "fast5_filepath": { @@ -2234,7 +2234,7 @@ "ontology": "GENEPIO:0001481", "type": "string", "description": "The filepath of the FAST5 file.", - "classification": "", + "classification": "Bioinformatics and QC metrics", "label": "Filepath fast5" }, "number_of_base_pairs_sequenced": { @@ -2433,7 +2433,7 @@ "ontology": "NCIT:C147139", "type": "string", "description": "", - "classification": "", + "classification": "Bioinformatics and QC metrics", "label": "" }, "isolate_sample_id": { @@ -2443,7 +2443,7 @@ "ontology": "NCIT:C53471", "type": "string", "description": "", - "classification": "", + "classification": "Database Identifiers", "label": "Sample ID given if multiple rna-extraction or passages" }, "variant_designation": { From 400096f259b7f19e89c7d0c3a4cf5cf80d36136b Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 9 May 2022 12:17:01 +0200 Subject: [PATCH 0419/1454] created json with metadata bioinfo --- .../example_data/bioinfo_metadata.json | 45 ++ relecov_tools/schema/bioinfo_schema.json | 452 ------------------ 2 files changed, 45 insertions(+), 452 deletions(-) create mode 100644 relecov_tools/example_data/bioinfo_metadata.json delete mode 100644 relecov_tools/schema/bioinfo_schema.json diff --git a/relecov_tools/example_data/bioinfo_metadata.json b/relecov_tools/example_data/bioinfo_metadata.json new file mode 100644 index 00000000..d77fb38f --- /dev/null +++ b/relecov_tools/example_data/bioinfo_metadata.json @@ -0,0 +1,45 @@ +{ + "dehosting_method": "", + "if_assembly_other": "", + "assembly_params": "", + "variant_calling": "", + "if_variant_calling_other": "", + "variant_calling_params": "", + "consensus_sequence_name": "", + "consensus_sequence_name_md5": "", + "consensus_sequence_filepath": "", + "consensus_sequence_software_name": "", + "if_consensus_other": "", + "consensus_sequence_software_version": "", + "consensus_criteria": "", + "depth_of_coverage_threshold": "", + "number_of_base_pairs_sequenced": "", + "consensus_genome_length": "", + "ns_per_100_kbp": "", + "reference_genome_accession": "", + "bioinformatics_protocol": "", + "if_bioinformatic_protocol_is_other_specify": "", + "bioinformatic_protocol_version": "", + "commercial/open-source/both": "", + "preprocessing": "", + "if_preprocessing_other": "", + "preprocessing_params": "", + "mapping": "", + "if_mapping_other": "", + "mapping_params": "", + "lineage_name": "", + "lineage_analysis_software_name": "", + "if_lineage_identification_other": "", + "lineage_analysis_software_version": "", + "variant_designation": "", + "per_qc_filtered": "", + "per_reads_host": "", + "per_reads_virus": "", + "per_unmapped": "", + "per_genome _greater_10x": "", + "median_depth_of_coverage_value": "", + "per_Ns": "", + "number_of_variants_AF_greater_75percent": "", + "number_of_variants_with_effect": "", + "long_table_path": "" +} \ No newline at end of file diff --git a/relecov_tools/schema/bioinfo_schema.json b/relecov_tools/schema/bioinfo_schema.json deleted file mode 100644 index e68e29c5..00000000 --- a/relecov_tools/schema/bioinfo_schema.json +++ /dev/null @@ -1,452 +0,0 @@ -{ - "schema": "bioinfo_metadata", - "type": "object", - "properties": { - "dehosting_method": { - "examples": [ - "Nanostripper" - ], - "ontology": "GENEPIO:0001459", - "type": "string", - "description": "The method used to remove host reads from the pathogen sequence.", - "classification": "Bioinformatics and QC metrics", - "label": "Dehosting Method" - }, - "assembly": { - "examples": [ - "" - ], - "ontology": "NCIT_C63548", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "Assembly" - }, - "if_assembly_other": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "If assembly Is Other, Specify" - }, - "assembly_params": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "Assambly params" - }, - "variant_calling": { - "examples": [ - "" - ], - "ontology": "operation_3227", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "Variant Calling" - }, - "if_variant_calling_other": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "If variant calling Is Other, Specify" - }, - "variant_calling_params": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "Variant Calling params" - }, - "consensus_sequence_name": { - "ontology": "GENEPIO:0001460", - "type": "string", - "description": "The name of the consensus sequence.", - "examples": [ - "ncov123assembly3" - ], - "classification": "Bioinformatics and QC metrics", - "label": "Consensus sequence name" - }, - "consensus_sequence_name_md5": { - "ontology": "NMR:1000568", - "type": "string", - "description": "The name of the consensus sequence.", - "examples": [ - "ncov123assembly3" - ], - "classification": "Bioinformatics and QC metrics", - "label": "Consensus sequence name md5" - }, - "consensus_sequence_filepath": { - "examples": [ - "/User/Documents/RespLab/Data/ncov123assembly.fasta" - ], - "ontology": "GENEPIO:0001462", - "type": "string", - "description": "The filepath of the consesnsus sequence file.", - "classification": "Bioinformatics and QC metrics", - "label": "Consensus sequence filepath" - }, - "consensus_sequence_software_name": { - "examples": [ - "Ivar" - ], - "ontology": "GENEPIO:0001463", - "type": "string", - "description": "The name of software used to generate the consensus sequence.", - "classification": "Bioinformatics and QC metrics", - "label": "Consensus sequence software name" - }, - "if_consensus_other": { - "examples": [ - "1.3" - ], - "ontology": "0", - "type": "string", - "description": "The version of the software used to generate the consensus sequence.", - "classification": "Bioinformatics and QC metrics", - "label": "If consensus Is Other, Specify" - }, - "consensus_sequence_software_version": { - "examples": [ - "1.3" - ], - "ontology": "GENEPIO:0001469", - "type": "string", - "description": "The version of the software used to generate the consensus sequence.", - "classification": "Bioinformatics and QC metrics", - "label": "Consensus sequence software version" - }, - "consensus_criteria": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "Consensus criteria" - }, - "depth_of_coverage_threshold": { - "examples": [ - "100x" - ], - "ontology": "GENEPIO:0001475", - "type": "string", - "description": "The threshold used as a cut-off for the depth of coverage.", - "classification": "Bioinformatics and QC metrics", - "label": "Depth of coverage threshold" - }, - "number_of_base_pairs_sequenced": { - "examples": [ - "387566" - ], - "ontology": "GENEPIO:0001482", - "type": "string", - "description": "The number of total base pairs generated by the sequencing process.", - "classification": "Bioinformatics and QC metrics", - "label": "Number of base pairs sequenced " - }, - "consensus_genome_length": { - "examples": [ - "38677" - ], - "ontology": "GENEPIO:0001483", - "type": "string", - "description": "Size of the assembled genome described as the number of base pairs.", - "classification": "Bioinformatics and QC metrics", - "label": "Consensus genome length" - }, - "ns_per_100_kbp": { - "examples": [ - "300" - ], - "ontology": "GENEPIO:0001484", - "type": "string", - "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", - "classification": "Bioinformatics and QC metrics", - "label": "Ns per 100 kbp" - }, - "reference_genome_accession": { - "examples": [ - "NC_045512.2" - ], - "ontology": "GENEPIO:0001485", - "type": "string", - "description": "A persistent, unique identifier of a genome database entry.", - "classification": "Bioinformatics and QC metrics", - "label": "Reference genome accession" - }, - "bioinformatics_protocol": { - "examples": [ - "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" - ], - "ontology": "GENEPIO:0001489", - "type": "string", - "description": "The name of the bioinformatics protocol used.", - "classification": "Bioinformatics and QC metrics", - "label": "Bioinformatics protocol" - }, - "if_bioinformatic_protocol_is_other_specify": { - "examples": [ - "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" - ], - "ontology": "0", - "type": "string", - "description": "The name of the bioinformatics protocol used.", - "classification": "Bioinformatics and QC metrics", - "label": "If bioinformatic protocol Is Other, Specify" - }, - "bioinformatic_protocol_version": { - "examples": [ - "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" - ], - "ontology": "NCIT:C93490", - "type": "string", - "description": "The version number of the bioinformatics protocol used.", - "classification": "Bioinformatics and QC metrics", - "label": "bioinformatics protocol version" - }, - "commercial/open-source/both": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "Commercial/Open-source/both" - }, - "preprocessing": { - "examples": [ - "" - ], - "ontology": "MS_1002386", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "Preprocessing" - }, - "if_preprocessing_other": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "If preprocessing Is Other, Specify" - }, - "preprocessing_params": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "Preprocessing params" - }, - "mapping": { - "examples": [ - "" - ], - "ontology": "topic:0102", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "Mapping" - }, - "if_mapping_other": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "If mapping Is Other, Specify" - }, - "mapping_params": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "Mapping params" - }, - "lineage_name": { - "examples": [ - "B.1.1.7" - ], - "ontology": "GENEPIO:0001500", - "type": "string", - "description": "The name of the lineage or clade.", - "classification": "Bioinformatics and QC metrics", - "label": "Lineage/clade name" - }, - "lineage_analysis_software_name": { - "examples": [ - "Pangolin" - ], - "ontology": "GENEPIO:0001501", - "type": "string", - "description": "The name of the software used to determine the lineage/clade.", - "classification": "Bioinformatics and QC metrics", - "label": "lineage/clade analysis software name" - }, - "if_lineage_identification_other": { - "examples": [ - "Other than Pangolin" - ], - "ontology": "0", - "type": "string", - "description": "The name of the software used to determine the lineage/clade.", - "classification": "Bioinformatics and QC metrics", - "label": "If lineage identification Is Other, Specify" - }, - "lineage_analysis_software_version": { - "examples": [ - "2.1.10" - ], - "ontology": "GENEPIO:0001502", - "type": "string", - "description": "The version of the software used to determine the lineage/clade.", - "classification": "Bioinformatics and QC metrics", - "label": "Lineage/clade analysis software version" - }, - "variant_designation": { - "Enums": [ - "Variant of Interest (VOI) [GENEPIO:0100082]", - "Variant of Concern (VOC) [GENEPIO:0100083]", - "Variant Under Monitoring (VUM) [GENEPIO:0100279]" - ], - "ontology": "GENEPIO:0001503", - "type": "string", - "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", - "examples": [ - "Variant of Concern (VOC) [GENEPIO:0100083]" - ], - "classification": "Bioinformatics and QC metrics", - "label": "Variant designation" - }, - "per_qc_filtered": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "%qc filtered" - }, - "per_reads_host": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "%reads host" - }, - "per_reads_virus": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "%reads virus" - }, - "per_unmapped": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "%unmapped" - }, - "per_genome _greater_10x": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "% genome greater 10x" - }, - "median_depth_of_coverage_value": { - "examples": [ - "" - ], - "ontology": "NCIT:C167285", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "mean depth of coverage value" - }, - "per_Ns": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "%Ns" - }, - "number_of_variants_AF_greater_75percent": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "Number of variants (AF greater 75%)" - }, - "number_of_variants_with_effect": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "Number of variants with effect" - }, - "long_table_path": { - "examples": [ - "" - ], - "ontology": "", - "type": "", - "description": "", - "clasification": "", - "label": "", - "table": [] - } - } -} \ No newline at end of file From 6e0dc00157f0f3b398584f524fde7ab0abdd5a5c Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 9 May 2022 14:08:46 +0200 Subject: [PATCH 0420/1454] added fill_mode and Files info classification changed --- .../example_data/bioinfo_metadata.json | 1 + relecov_tools/schema/relecov_schema.json | 630 ++++++++++++------ 2 files changed, 419 insertions(+), 212 deletions(-) diff --git a/relecov_tools/example_data/bioinfo_metadata.json b/relecov_tools/example_data/bioinfo_metadata.json index d77fb38f..f8831cc5 100644 --- a/relecov_tools/example_data/bioinfo_metadata.json +++ b/relecov_tools/example_data/bioinfo_metadata.json @@ -1,4 +1,5 @@ { + "sample_name": "", "dehosting_method": "", "if_assembly_other": "", "assembly_params": "", diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 4d90d3a9..9caab8f8 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -24,7 +24,8 @@ "type": "string", "description": "The user-defined name for the sample.", "classification": "Database Identifiers", - "label": "Sample ID given by originating laboratory" + "label": "Sample ID given by originating laboratory", + "fill_mode": "sample" }, "sample_description": { "examples": [ @@ -34,7 +35,8 @@ "type": "string", "description": "Free text description of the sample.", "classification": "Sample collection and processing", - "label": "Sample Description" + "label": "Sample Description", + "fill_mode": "batch" }, "collecting_institution": { "examples": [ @@ -44,7 +46,8 @@ "type": "string", "description": "The name of the agency that collected the original sample.", "classification": "Sample collection and processing", - "label": "Originating Laboratory" + "label": "Originating Laboratory", + "fill_mode": "sample" }, "submitting_institution": { "examples": [ @@ -54,7 +57,8 @@ "type": "string", "description": "The name of the agency that generated the sequence.", "classification": "Sample collection and processing", - "label": "Submitting Institution" + "label": "Submitting Institution", + "fill_mode": "sample" }, "sample_collection_date": { "examples": [ @@ -65,7 +69,8 @@ "description": "The date on which the sample was collected.", "format": "date", "classification": "Sample collection and processing", - "label": "Sample Collection Date" + "label": "Sample Collection Date", + "fill_mode": "sample" }, "host_subject_id": { "examples": [ @@ -75,7 +80,8 @@ "type": "string", "description": "a unique identifier by which each subject can be referred to, de-identified.", "classification": "Host information", - "label": "Host Subject Id" + "label": "Host Subject Id", + "fill_mode": "batch" }, "geo_loc_country": { "Enums": [ @@ -363,7 +369,8 @@ "South Africa [GAZ:00001094]" ], "classification": "Sample collection and processing", - "label": "Country" + "label": "Country", + "fill_mode": "batch" }, "geo_loc_state": { "examples": [ @@ -373,7 +380,8 @@ "type": "string", "description": "The state/province/territory of origin of the sample.", "classification": "Sample collection and processing", - "label": "Autonomic Community" + "label": "Autonomic Community", + "fill_mode": "batch" }, "organism": { "Enums": [ @@ -392,7 +400,8 @@ "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]" ], "classification": "Sample collection and processing", - "label": "Organism" + "label": "Organism", + "fill_mode": "batch" }, "symptom_onset_date": { "examples": [ @@ -403,7 +412,8 @@ "description": "The date on which the symptoms began or were first noted.", "format": "date", "classification": "Host information", - "label": "Symptom onset date" + "label": "Symptom onset date", + "fill_mode": "batch" }, "host_health_state": { "Enums": [ @@ -425,7 +435,8 @@ "Asymptomatic [NCIT:C3833]" ], "classification": "Host information", - "label": "Host health state" + "label": "Host health state", + "fill_mode": "batch" }, "host_health_status_details": { "Enums": [ @@ -449,7 +460,8 @@ "Hospitalized (ICU) [GENEPIO:0100046]" ], "classification": "Host information", - "label": "Host health status details" + "label": "Host health status details", + "fill_mode": "batch" }, "host_scientific_name": { "Enums": [ @@ -482,7 +494,8 @@ "Homo sapiens [NCBITaxon:9606]" ], "classification": "Host information", - "label": "Host Scientific Name" + "label": "Host Scientific Name", + "fill_mode": "batch" }, "host_disease": { "Enums": [ @@ -500,7 +513,8 @@ "COVID-19 [MONDO:0100096]" ], "classification": "Host information", - "label": "Host disease" + "label": "Host disease", + "fill_mode": "batch" }, "sequencing_instrument_model": { "Enums": [ @@ -563,7 +577,8 @@ "Oxford Nanopore MinION [GENEPIO:0100142]" ], "classification": "Sequencing", - "label": "Sequencing Instrument Model" + "label": "Sequencing Instrument Model", + "fill_mode": "batch" }, "sequencing_instrument_platform": { "examples": [ @@ -573,7 +588,8 @@ "type": "string", "description": "The model of the sequencing instrument used.", "classification": "Sequencing", - "label": "Sequencing Instrument Platform" + "label": "Sequencing Instrument Platform", + "fill_mode": "batch" }, "submitting_lab_sequence_id": { "examples": [ @@ -583,7 +599,8 @@ "type": "string", "description": "Sample ID given by the submitting laboratory", "classification": "Sequencing", - "label": "Sample ID given by the submitting laboratory" + "label": "Sample ID given by the submitting laboratory", + "fill_mode": "sample" }, "bioproject_umbrella_accession_ENA": { "examples": [ @@ -593,7 +610,8 @@ "type": "string", "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", "classification": "Database Identifiers", - "label": "Bioproject umbrella accession ENA" + "label": "Bioproject umbrella accession ENA", + "fill_mode": "batch" }, "bioproject_accession_ENA": { "examples": [ @@ -603,7 +621,8 @@ "type": "string", "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", "classification": "Database Identifiers", - "label": "Bioproject accession ENA" + "label": "Bioproject accession ENA", + "fill_mode": "batch" }, "biosample_accession_ENA": { "examples": [ @@ -613,7 +632,8 @@ "type": "string", "description": "The identifier assigned to a BioSample in INSDC archives.", "classification": "Database Identifiers", - "label": "ENA Sample ID" + "label": "ENA Sample ID", + "fill_mode": "sample" }, "sra_accession": { "examples": [ @@ -623,7 +643,8 @@ "type": "string", "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", "classification": "Database Identifiers", - "label": "SRA Accession" + "label": "SRA Accession", + "fill_mode": "batch" }, "genBank/ENA/DDBJ_accession": { "examples": [ @@ -633,7 +654,8 @@ "type": "string", "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", "classification": "Database Identifiers", - "label": "GenBank/ENA/DDBJ accession" + "label": "GenBank/ENA/DDBJ accession", + "fill_mode": "batch" }, "GISAID_accession": { "examples": [ @@ -643,7 +665,8 @@ "type": "string", "description": "The GISAID accession number assigned to the sequence.", "classification": "Database Identifiers", - "label": "GISAID Accession" + "label": "GISAID Accession", + "fill_mode": "batch" }, "virus_name": { "examples": [ @@ -653,7 +676,8 @@ "type": "string", "description": "The user-defined GISAID virus name assigned to the sequence.", "classification": "Database Identifiers", - "label": "GISAID Virus Name" + "label": "GISAID Virus Name", + "fill_mode": "sample" }, "collecting_institution_email": { "examples": [ @@ -663,7 +687,8 @@ "type": "string", "description": "The email address of the contact responsible for follow-up regarding the sample.", "classification": "Sample collection and processing", - "label": "Originating Laboratory Email" + "label": "Originating Laboratory Email", + "fill_mode": "batch" }, "collecting_institution_address": { "examples": [ @@ -673,7 +698,8 @@ "type": "string", "description": "The mailing address of the agency submitting the sample.", "classification": "Sample collection and processing", - "label": "Originating Laboratory Address" + "label": "Originating Laboratory Address", + "fill_mode": "batch" }, "submitting_institution_email": { "examples": [ @@ -683,7 +709,8 @@ "type": "string", "description": "The email address of the contact responsible for follow-up regarding the sequence.", "classification": "Sample collection and processing", - "label": "Submitting Institution Email" + "label": "Submitting Institution Email", + "fill_mode": "batch" }, "submitting_institution_address": { "examples": [ @@ -693,7 +720,8 @@ "type": "string", "description": "The mailing address of the agency submitting the sequence.", "classification": "Sample collection and processing", - "label": "Submitting Institution Address" + "label": "Submitting Institution Address", + "fill_mode": "batch" }, "sample_received_date": { "examples": [ @@ -704,7 +732,8 @@ "description": "The date on which the sample was received.", "format": "date", "classification": "Sample collection and processing", - "label": "Sample Received Date" + "label": "Sample Received Date", + "fill_mode": "sample" }, "shipping_date": { "examples": [ @@ -715,7 +744,8 @@ "description": "The date on which the sample was sent.", "format": "date", "classification": "Sample collection and processing", - "label": "Shipping Date" + "label": "Shipping Date", + "fill_mode": "batch" }, "results_emission_date": { "examples": [ @@ -726,7 +756,8 @@ "description": "The date on which the results were emitted.", "format": "date", "classification": "Sample collection and processing", - "label": "Results Emission Date" + "label": "Results Emission Date", + "fill_mode": "batch" }, "sample_storage_conditions": { "examples": [ @@ -736,7 +767,8 @@ "type": "string", "description": "The name and version of a particular protocol used for sampling.", "classification": "Sample collection and processing", - "label": "Biological Sample Storage Condition" + "label": "Biological Sample Storage Condition", + "fill_mode": "batch" }, "culture_collection": { "ontology": "GENEPIO:0100284", @@ -746,7 +778,8 @@ "/culture_collection=\"ATCC:26370\"" ], "classification": "Sample collection and processing", - "label": "Culture collection" + "label": "Culture collection", + "fill_mode": "batch" }, "treatment": { "ontology": "OGMS:0000090", @@ -754,7 +787,8 @@ "description": "Include drug name, dosage", "examples": [], "classification": "Sample collection and processing", - "label": "Treatment" + "label": "Treatment", + "fill_mode": "batch" }, "host_age": { "ontology": "GENEPIO:0001392", @@ -763,7 +797,8 @@ "examples": [ "79" ], - "label": "Host Age" + "label": "Host Age", + "fill_mode": "sample" }, "host_age_unit": { "Enums": [ @@ -781,7 +816,8 @@ "examples": [ "years [UO:0000036]" ], - "label": "Host Age unit" + "label": "Host Age unit", + "fill_mode": "batch" }, "host_age_bin": { "Enums": [ @@ -808,7 +844,8 @@ "examples": [ "50 - 59 [GENEPIO:0100054]" ], - "label": "Host Age Bin" + "label": "Host Age Bin", + "fill_mode": "batch" }, "host_gender": { "Enums": [ @@ -830,7 +867,8 @@ "examples": [ "Male [NCIT:C46109]" ], - "label": "Host Gender" + "label": "Host Gender", + "fill_mode": "sample" }, "microbiology_lab_sample_id": { "examples": [ @@ -840,7 +878,8 @@ "type": "string", "description": "", "classification": "Sample collection and processing", - "label": "Sample ID given in the microbiology lab" + "label": "Sample ID given in the microbiology lab", + "fill_mode": "sample" }, "public_health_sample_id_sivies": { "examples": [ @@ -850,7 +889,8 @@ "type": "string", "description": "", "classification": "Sample collection and processing", - "label": "Public Health sample id (SIVIES)" + "label": "Public Health sample id (SIVIES)", + "fill_mode": "sample" }, "geo_loc_region": { "examples": [ @@ -860,7 +900,8 @@ "type": "string", "description": "The county/region of origin of the sample.", "classification": "Sample collection and processing", - "label": "Province" + "label": "Province", + "fill_mode": "batch" }, "geo_loc_city": { "examples": [ @@ -870,7 +911,8 @@ "type": "string", "description": "The city of origin of the sample.", "classification": "Sample collection and processing", - "label": "City" + "label": "City", + "fill_mode": "batch" }, "geo_loc_latitude": { "examples": [ @@ -880,7 +922,8 @@ "type": "string", "description": "The latitude coordinates of the geographical location of sample collection.", "classification": "Sample collection and processing", - "label": "Geo Loc Latitude" + "label": "Geo Loc Latitude", + "fill_mode": "batch" }, "geo_loc_longitude": { "examples": [ @@ -890,7 +933,8 @@ "type": "string", "description": "The longitude coordinates of the geographical location of sample collection.", "classification": "Sample collection and processing", - "label": "Geo Loc Longitude" + "label": "Geo Loc Longitude", + "fill_mode": "batch" }, "anatomical_material": { "Enums": [ @@ -916,7 +960,8 @@ "Blood [UBERON:0000178]" ], "classification": "Sample collection and processing", - "label": "Specimen source" + "label": "Specimen source", + "fill_mode": "batch" }, "body_product": { "Enums": [ @@ -941,7 +986,8 @@ "Feces [UBERON:0001988]" ], "classification": "Sample collection and processing", - "label": "Body product" + "label": "Body product", + "fill_mode": "batch" }, "environmental_material": { "Enums": [ @@ -991,7 +1037,8 @@ "Face Mask [OBI:0002787]" ], "classification": "Sample collection and processing", - "label": "Environmental Material" + "label": "Environmental Material", + "fill_mode": "batch" }, "environmental_site": { "Enums": [ @@ -1029,7 +1076,8 @@ "Hospital [ENVO:00002173]" ], "classification": "Sample collection and processing", - "label": "Environmental System" + "label": "Environmental System", + "fill_mode": "batch" }, "sample_collected_in_quarantine": { "Enums": [ @@ -1047,7 +1095,8 @@ "examples": [ "Yes [NCIT:C49488]" ], - "label": "Sample collected in quarantine" + "label": "Sample collected in quarantine", + "fill_mode": "batch" }, "collection_device": { "Enums": [ @@ -1081,7 +1130,8 @@ "Swab [GENEPIO:0100027]" ], "classification": "Sample collection and processing", - "label": "Collection Device" + "label": "Collection Device", + "fill_mode": "batch" }, "collection_method": { "Enums": [ @@ -1119,7 +1169,8 @@ "Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]" ], "classification": "Sample collection and processing", - "label": "Collection Method" + "label": "Collection Method", + "fill_mode": "batch" }, "collection_protocol": { "examples": [ @@ -1129,7 +1180,8 @@ "type": "string", "description": "The name and version of a particular protocol used for sampling.", "classification": "Sample collection and processing", - "label": "Collection Protocol" + "label": "Collection Protocol", + "fill_mode": "batch" }, "specimen_processing": { "Enums": [ @@ -1149,7 +1201,8 @@ "Virus Passage [GENEPIO:0100039]" ], "classification": "Sample collection and processing", - "label": "Specimen Processing" + "label": "Specimen Processing", + "fill_mode": "batch" }, "lab_host": { "Enums": [ @@ -1182,7 +1235,8 @@ "Vero E6 Cell Line [BTO:0004755]" ], "classification": "Sample collection and processing", - "label": "Lab passage Host" + "label": "Lab passage Host", + "fill_mode": "batch" }, "passage_number": { "examples": [ @@ -1192,7 +1246,8 @@ "type": "string", "description": "Number of passages.", "classification": "Sample collection and processing", - "label": "Passage Number" + "label": "Passage Number", + "fill_mode": "batch" }, "passage_method": { "examples": [ @@ -1202,7 +1257,8 @@ "type": "string", "description": "Description of how organism was passaged.", "classification": "Sample collection and processing", - "label": "Passage Method" + "label": "Passage Method", + "fill_mode": "batch" }, "tax_id": { "examples": [ @@ -1212,7 +1268,8 @@ "type": "string", "description": "The NCBITaxon identifier for the organism being sequenced.", "classification": "Sample collection and processing", - "label": "Tax ID" + "label": "Tax ID", + "fill_mode": "batch" }, "center_name": { "examples": [ @@ -1222,7 +1279,8 @@ "type": "string", "description": "The name of the institution", "classification": "Sample collection and processing", - "label": "Center Name" + "label": "Center Name", + "fill_mode": "batch" }, "host_common_name": { "Enums": [ @@ -1252,7 +1310,8 @@ "Human [NCBITaxon:9606]" ], "classification": "Host information", - "label": "Host" + "label": "Host", + "fill_mode": "batch" }, "host_residence_country": { "Enums": [ @@ -1539,7 +1598,8 @@ "examples": [ "South Africa [GAZ:00001094]" ], - "label": "Host residence country" + "label": "Host residence country", + "fill_mode": "batch" }, "outbreak": { "examples": [ @@ -1549,7 +1609,8 @@ "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", "classification": "Host information", - "label": "Outbreak Exposure Event Location" + "label": "Outbreak Exposure Event Location", + "fill_mode": "batch" }, "additional_host_information": { "examples": [ @@ -1559,7 +1620,8 @@ "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", "classification": "Host information", - "label": "Additional Host Information" + "label": "Additional Host Information", + "fill_mode": "batch" }, "host_ethnicity": { "ontology": "GECKO:0000061", @@ -1568,7 +1630,8 @@ "examples": [ "Indigenous, European" ], - "label": "Host ethnicity" + "label": "Host ethnicity", + "fill_mode": "batch" }, "purpose_of_sequencing": { "Enums": [ @@ -1609,7 +1672,8 @@ "Baseline surveillance (random sampling) [GENEPIO:0100005]" ], "classification": "Sequencing", - "label": "Purpose of Sequencing" + "label": "Purpose of Sequencing", + "fill_mode": "batch" }, "purpose_of_sampling": { "Enums": [ @@ -1630,7 +1694,8 @@ "examples": [ "Diagnostic Testing [GENEPIO:0100002]" ], - "label": "Purpose of sampling" + "label": "Purpose of sampling", + "fill_mode": "batch" }, "purpose_of_sampling_details": { "ontology": "GENEPIO:0001200", @@ -1639,7 +1704,8 @@ "examples": [ "Screening of bat specimens in museum collections." ], - "label": "Purpose of sampling details" + "label": "Purpose of sampling details", + "fill_mode": "batch" }, "sequencing_sample_id": { "examples": [ @@ -1649,7 +1715,8 @@ "type": "number", "description": "If the information is unknown or can not be shared, leave blank.", "classification": "Database Identifiers", - "label": "Sample ID given for sequencing" + "label": "Sample ID given for sequencing", + "fill_mode": "sample" }, "passage_details": { "examples": [ @@ -1662,7 +1729,8 @@ ], "description": "If the information is unknown or can not be shared, leave blank.", "classification": "Database Identifiers", - "label": "Passage Details" + "label": "Passage Details", + "fill_mode": "batch" }, "purpose_of_sequencing_details": { "Enums": [ @@ -1689,7 +1757,8 @@ "Screened for S gene target failure (S dropout)" ], "classification": "Sequencing", - "label": "Purpose Of Sequencing Details" + "label": "Purpose Of Sequencing Details", + "fill_mode": "batch" }, "sequencing_date": { "examples": [ @@ -1700,7 +1769,8 @@ "description": "The date the sample was sequenced.", "format": "date", "classification": "Sequencing", - "label": "Sequencing Date" + "label": "Sequencing Date", + "fill_mode": "batch" }, "rna_extraction_protocol": { "examples": [ @@ -1710,7 +1780,8 @@ "type": "string", "description": "", "classification": "Sequencing", - "label": "Rna Extraction Protocol" + "label": "Rna Extraction Protocol", + "fill_mode": "batch" }, "library_kit": { "examples": [ @@ -1720,7 +1791,8 @@ "type": "string", "description": "", "classification": "Sequencing", - "label": "Commercial All-in-one library kit" + "label": "Commercial All-in-one library kit", + "fill_mode": "batch" }, "library_name": { "examples": [ @@ -1733,7 +1805,8 @@ "label": "Library Name", "table": [ "experiments" - ] + ], + "fill_mode": "batch" }, "library_id": { "examples": [ @@ -1743,7 +1816,8 @@ "type": "string", "description": "The user-specified identifier for the library prepared for sequencing.", "classification": "Sequencing", - "labe": "Library Id" + "labe": "Library Id", + "fill_mode": "batch" }, "enrichment_protocol": { "examples": [ @@ -1753,7 +1827,8 @@ "type": "string", "description": "", "classification": "Sequencing", - "label": "Enrichment Protocol" + "label": "Enrichment Protocol", + "fill_mode": "batch" }, "if_enrichment_protocol_is_other_specify": { "examples": [ @@ -1763,7 +1838,8 @@ "type": "string", "description": "", "classification": "Sequencing", - "label": "If Enrichment Protocol Is Other, Specify" + "label": "If Enrichment Protocol Is Other, Specify", + "fill_mode": "batch" }, "amplicon_protocol": { "examples": [ @@ -1773,7 +1849,8 @@ "type": "string", "description": "", "classification": "Sequencing", - "label": "Enrichment panel/assay" + "label": "Enrichment panel/assay", + "fill_mode": "batch" }, "if_amplicon_protocol_if_other_especify": { "examples": [ @@ -1783,7 +1860,8 @@ "type": "string", "description": "", "classification": "Sequencing", - "label": "If Enrichment panel/assay If Other, Especify" + "label": "If Enrichment panel/assay If Other, Especify", + "fill_mode": "batch" }, "amplicon_version": { "examples": [ @@ -1793,7 +1871,8 @@ "type": "string", "description": "", "classification": "Sequencing", - "label": "Enrichment panel/assay version" + "label": "Enrichment panel/assay version", + "fill_mode": "batch" }, "amplicon_size": { "examples": [ @@ -1803,7 +1882,8 @@ "type": "string", "description": "The length of the amplicon generated by PCR amplification.", "classification": "Sequencing", - "label": "Amplicon Size" + "label": "Amplicon Size", + "fill_mode": "batch" }, "was_phix_used?": { "examples": [ @@ -1813,7 +1893,8 @@ "type": "string", "description": "", "classification": "Sequencing", - "label": "Was Phix Used" + "label": "Was Phix Used", + "fill_mode": "batch" }, "number_of_samples_in_run": { "examples": [ @@ -1823,7 +1904,8 @@ "type": "string", "description": "", "classification": "Sequencing", - "label": "Number Of Samples In Run" + "label": "Number Of Samples In Run", + "fill_mode": "batch" }, "flowcell_kit": { "examples": [ @@ -1833,7 +1915,8 @@ "type": "string", "description": "", "classification": "Sequencing", - "label": "Flowcell Kit" + "label": "Flowcell Kit", + "fill_mode": "batch" }, "runID": { "examples": [ @@ -1843,7 +1926,8 @@ "type": "string", "description": "", "classification": "Sequencing", - "label": "Runid" + "label": "Runid", + "fill_mode": "batch" }, "sequencing_platforms": { "examples": [ @@ -1853,7 +1937,8 @@ "type": "string", "description": "", "classification": "Sequencing", - "label": "Sequencing Platforms " + "label": "Sequencing Platforms ", + "fill_mode": "batch" }, "library_preparation_kit": { "examples": [ @@ -1863,7 +1948,8 @@ "type": "string", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "classification": "Sequencing", - "label": "Library Preparation Kit" + "label": "Library Preparation Kit", + "fill_mode": "batch" }, "flow_cell_barcode": { "examples": [ @@ -1873,7 +1959,8 @@ "type": "string", "description": "The barcode of the flow cell used for sequencing.", "classification": "Sequencing", - "label": "Flow Cell Barcode" + "label": "Flow Cell Barcode", + "fill_mode": "batch" }, "sequencing_protocol_name": { "examples": [ @@ -1883,7 +1970,8 @@ "type": "string", "description": "The name and version number of the sequencing protocol used.", "classification": "Sequencing", - "label": "Sequencing Protocol Name" + "label": "Sequencing Protocol Name", + "fill_mode": "batch" }, "sequencing_protocol": { "examples": [ @@ -1893,7 +1981,8 @@ "type": "string", "description": "The protocol used to generate the sequence.", "classification": "Sequencing", - "label": "Sequencing Protocol" + "label": "Sequencing Protocol", + "fill_mode": "batch" }, "sequencing_kit_number": { "examples": [ @@ -1903,7 +1992,8 @@ "type": "string", "description": "The manufacturer's kit number.", "classification": "Sequencing", - "label": "Sequencing Kit Number" + "label": "Sequencing Kit Number", + "fill_mode": "batch" }, "amplicon_pcr_primer_scheme": { "examples": [ @@ -1913,7 +2003,8 @@ "type": "string", "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", "classification": "Sequencing", - "label": "Amplicon Pcr Primer Scheme" + "label": "Amplicon Pcr Primer Scheme", + "fill_mode": "batch" }, "library_selection": { "examples": [ @@ -1923,7 +2014,8 @@ "type": "string", "description": "Library capture method.", "classification": "Sequencing", - "label": "Capture method" + "label": "Capture method", + "fill_mode": "batch" }, "library_strategy": { "Enums": [ @@ -1955,7 +2047,8 @@ "type": "string", "description": "Overall sequencing strategy or approach.", "classification": "Sequencing", - "label": "Sequencing technique" + "label": "Sequencing technique", + "fill_mode": "batch" }, "library_layout": { "examples": [ @@ -1965,7 +2058,8 @@ "type": "string", "description": "Single or paired.", "classification": "Sequencing", - "label": "Library Layout" + "label": "Library Layout", + "fill_mode": "batch" }, "nominal_length ": { "examples": [ @@ -1975,7 +2069,8 @@ "type": "string", "description": "", "classification": "Sequencing", - "label": "Nominal Length" + "label": "Nominal Length", + "fill_mode": "batch" }, "raw_sequence_data_processing_method": { "examples": [ @@ -1985,7 +2080,8 @@ "type": "string", "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", "classification": "Bioinformatics and QC metrics", - "label": "Raw sequence data processin method" + "label": "Raw sequence data processin method", + "fill_mode": "batch" }, "dehosting_method": { "examples": [ @@ -1995,7 +2091,8 @@ "type": "string", "description": "The method used to remove host reads from the pathogen sequence.", "classification": "Bioinformatics and QC metrics", - "label": "Dehosting Method" + "label": "Dehosting Method", + "fill_mode": "batch" }, "personal_protective_equipment": { "examples": [ @@ -2005,7 +2102,8 @@ "type": "string", "description": "Use of personal protective equipment, such as gloves, gowns, during any type of exposure.", "classification": "Sample collection and processing", - "label": "Personal protective equipment" + "label": "Personal protective equipment", + "fill_mode": "batch" }, "assembly": { "examples": [ @@ -2015,7 +2113,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Assembly" + "label": "Assembly", + "fill_mode": "batch" }, "if_assembly_other": { "examples": [ @@ -2025,7 +2124,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "If assembly Is Other, Specify" + "label": "If assembly Is Other, Specify", + "fill_mode": "batch" }, "assembly_params": { "examples": [ @@ -2035,7 +2135,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Assambly params" + "label": "Assambly params", + "fill_mode": "batch" }, "variant_calling": { "examples": [ @@ -2045,7 +2146,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Variant Calling" + "label": "Variant Calling", + "fill_mode": "batch" }, "if_variant_calling_other": { "examples": [ @@ -2055,7 +2157,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "If variant calling Is Other, Specify" + "label": "If variant calling Is Other, Specify", + "fill_mode": "batch" }, "variant_calling_params": { "examples": [ @@ -2065,7 +2168,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Variant Calling params" + "label": "Variant Calling params", + "fill_mode": "batch" }, "consensus_sequence_name": { "ontology": "GENEPIO:0001460", @@ -2075,7 +2179,8 @@ "ncov123assembly3" ], "classification": "Bioinformatics and QC metrics", - "label": "Consensus sequence name" + "label": "Consensus sequence name", + "fill_mode": "batch" }, "consensus_sequence_name_md5": { "ontology": "NMR:1000568", @@ -2085,7 +2190,8 @@ "ncov123assembly3" ], "classification": "Bioinformatics and QC metrics", - "label": "Consensus sequence name md5" + "label": "Consensus sequence name md5", + "fill_mode": "batch" }, "consensus_sequence_filepath": { "examples": [ @@ -2095,7 +2201,8 @@ "type": "string", "description": "The filepath of the consesnsus sequence file.", "classification": "Bioinformatics and QC metrics", - "label": "Consensus sequence filepath" + "label": "Consensus sequence filepath", + "fill_mode": "batch" }, "consensus_sequence_software_name": { "examples": [ @@ -2105,7 +2212,8 @@ "type": "string", "description": "The name of software used to generate the consensus sequence.", "classification": "Bioinformatics and QC metrics", - "label": "Consensus sequence software name" + "label": "Consensus sequence software name", + "fill_mode": "batch" }, "if_consensus_other": { "examples": [ @@ -2115,7 +2223,8 @@ "type": "string", "description": "The version of the software used to generate the consensus sequence.", "classification": "Bioinformatics and QC metrics", - "label": "If consensus Is Other, Specify" + "label": "If consensus Is Other, Specify", + "fill_mode": "batch" }, "consensus_sequence_software_version": { "examples": [ @@ -2125,7 +2234,8 @@ "type": "string", "description": "The version of the software used to generate the consensus sequence.", "classification": "Bioinformatics and QC metrics", - "label": "Consensus sequence software version" + "label": "Consensus sequence software version", + "fill_mode": "batch" }, "consensus_criteria": { "examples": [ @@ -2135,7 +2245,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Consensus criteria" + "label": "Consensus criteria", + "fill_mode": "batch" }, "quality_control_metrics": { "examples": [ @@ -2145,7 +2256,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Quality control metrics " + "label": "Quality control metrics ", + "fill_mode": "batch" }, "depth_of_coverage_value": { "examples": [ @@ -2155,7 +2267,8 @@ "type": "string", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", "classification": "Bioinformatics and QC metrics", - "label": "Depth of coverage value " + "label": "Depth of coverage value ", + "fill_mode": "batch" }, "depth_of_coverage_threshold": { "examples": [ @@ -2165,7 +2278,8 @@ "type": "string", "description": "The threshold used as a cut-off for the depth of coverage.", "classification": "Bioinformatics and QC metrics", - "label": "Depth of coverage threshold" + "label": "Depth of coverage threshold", + "fill_mode": "batch" }, "file_type": { "examples": [ @@ -2175,7 +2289,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "" + "label": "", + "fill_mode": "batch" }, "sequence_file_R1_fastq": { "examples": [ @@ -2184,8 +2299,9 @@ "ontology": "GENEPIO:0001476", "type": "string", "description": "The user-specified filename of the r1 FASTQ file.", - "classification": "Bioinformatics and QC metrics", - "label": "Sequence file R1 fastq" + "classification": "Files info", + "label": "Sequence file R1 fastq", + "fill_mode": "sample" }, "sequence_file_R2_fastq": { "examples": [ @@ -2194,8 +2310,9 @@ "ontology": "GENEPIO:0001477", "type": "string", "description": "The user-specified filename of the r2 FASTQ file.", - "classification": "Bioinformatics and QC metrics", - "label": "Sequence file R2 fastq" + "classification": "Files info", + "label": "Sequence file R2 fastq", + "fill_mode": "sample" }, "r1_fastq_filepath": { "examples": [ @@ -2204,8 +2321,9 @@ "ontology": "GENEPIO:0001478", "type": "string", "description": "The filepath of the r1 FASTQ file.", - "classification": "Bioinformatics and QC metrics", - "label": "Filepath R1 fastq" + "classification": "Files info", + "label": "Filepath R1 fastq", + "fill_mode": "batch" }, "r2_fastq_filepath": { "examples": [ @@ -2214,8 +2332,9 @@ "ontology": "GENEPIO:0001479", "type": "string", "description": "The filepath of the r2 FASTQ file.", - "classification": "Bioinformatics and QC metrics", - "label": "Filepath R2 fastq" + "classification": "Files info", + "label": "Filepath R2 fastq", + "fill_mode": "batch" }, "fast5_filename": { "examples": [ @@ -2224,8 +2343,9 @@ "ontology": "GENEPIO:0001480", "type": "string", "description": "The user-specified filename of the FAST5 file.", - "classification": "Bioinformatics and QC metrics", - "label": "Filename fast5" + "classification": "Files info", + "label": "Filename fast5", + "fill_mode": "batch" }, "fast5_filepath": { "examples": [ @@ -2234,8 +2354,9 @@ "ontology": "GENEPIO:0001481", "type": "string", "description": "The filepath of the FAST5 file.", - "classification": "Bioinformatics and QC metrics", - "label": "Filepath fast5" + "classification": "Files info", + "label": "Filepath fast5", + "fill_mode": "batch" }, "number_of_base_pairs_sequenced": { "examples": [ @@ -2245,7 +2366,8 @@ "type": "string", "description": "The number of total base pairs generated by the sequencing process.", "classification": "Bioinformatics and QC metrics", - "label": "Number of base pairs sequenced " + "label": "Number of base pairs sequenced ", + "fill_mode": "batch" }, "consensus_genome_length": { "examples": [ @@ -2255,7 +2377,8 @@ "type": "string", "description": "Size of the assembled genome described as the number of base pairs.", "classification": "Bioinformatics and QC metrics", - "label": "Consensus genome length" + "label": "Consensus genome length", + "fill_mode": "batch" }, "ns_per_100_kbp": { "examples": [ @@ -2265,7 +2388,8 @@ "type": "string", "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", "classification": "Bioinformatics and QC metrics", - "label": "Ns per 100 kbp" + "label": "Ns per 100 kbp", + "fill_mode": "batch" }, "reference_genome_accession": { "examples": [ @@ -2275,7 +2399,8 @@ "type": "string", "description": "A persistent, unique identifier of a genome database entry.", "classification": "Bioinformatics and QC metrics", - "label": "Reference genome accession" + "label": "Reference genome accession", + "fill_mode": "batch" }, "bioinformatics_protocol": { "examples": [ @@ -2285,7 +2410,8 @@ "type": "string", "description": "The name of the bioinformatics protocol used.", "classification": "Bioinformatics and QC metrics", - "label": "Bioinformatics protocol" + "label": "Bioinformatics protocol", + "fill_mode": "batch" }, "if_bioinformatic_protocol_is_other_specify": { "examples": [ @@ -2295,7 +2421,8 @@ "type": "string", "description": "The name of the bioinformatics protocol used.", "classification": "Bioinformatics and QC metrics", - "label": "If bioinformatic protocol Is Other, Specify" + "label": "If bioinformatic protocol Is Other, Specify", + "fill_mode": "batch" }, "bioinformatic_protocol_version": { "examples": [ @@ -2305,7 +2432,8 @@ "type": "string", "description": "The version number of the bioinformatics protocol used.", "classification": "Bioinformatics and QC metrics", - "label": "bioinformatics protocol version" + "label": "bioinformatics protocol version", + "fill_mode": "batch" }, "commercial/open-source/both": { "examples": [ @@ -2315,7 +2443,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Commercial/Open-source/both" + "label": "Commercial/Open-source/both", + "fill_mode": "batch" }, "sample_plan_name": { "ontology": "GENEPIO:0100285", @@ -2324,7 +2453,8 @@ "examples": [ "CanCOGeN Sampling Strategy 1.0" ], - "label": "Sample plan name" + "label": "Sample plan name", + "fill_mode": "batch" }, "preprocessing": { "examples": [ @@ -2334,7 +2464,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Preprocessing" + "label": "Preprocessing", + "fill_mode": "batch" }, "if_preprocessing_other": { "examples": [ @@ -2344,7 +2475,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "If preprocessing Is Other, Specify" + "label": "If preprocessing Is Other, Specify", + "fill_mode": "batch" }, "preprocessing_params": { "examples": [ @@ -2354,7 +2486,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Preprocessing params" + "label": "Preprocessing params", + "fill_mode": "batch" }, "mapping": { "examples": [ @@ -2364,7 +2497,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Mapping" + "label": "Mapping", + "fill_mode": "batch" }, "if_mapping_other": { "examples": [ @@ -2374,7 +2508,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "If mapping Is Other, Specify" + "label": "If mapping Is Other, Specify", + "fill_mode": "batch" }, "mapping_params": { "examples": [ @@ -2384,7 +2519,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Mapping params" + "label": "Mapping params", + "fill_mode": "batch" }, "lineage_name": { "examples": [ @@ -2394,7 +2530,8 @@ "type": "string", "description": "The name of the lineage or clade.", "classification": "Bioinformatics and QC metrics", - "label": "Lineage/clade name" + "label": "Lineage/clade name", + "fill_mode": "batch" }, "lineage_analysis_software_name": { "examples": [ @@ -2404,7 +2541,8 @@ "type": "string", "description": "The name of the software used to determine the lineage/clade.", "classification": "Bioinformatics and QC metrics", - "label": "lineage/clade analysis software name" + "label": "lineage/clade analysis software name", + "fill_mode": "batch" }, "if_lineage_identification_other": { "examples": [ @@ -2414,7 +2552,8 @@ "type": "string", "description": "The name of the software used to determine the lineage/clade.", "classification": "Bioinformatics and QC metrics", - "label": "If lineage identification Is Other, Specify" + "label": "If lineage identification Is Other, Specify", + "fill_mode": "batch" }, "lineage_analysis_software_version": { "examples": [ @@ -2424,7 +2563,8 @@ "type": "string", "description": "The version of the software used to determine the lineage/clade.", "classification": "Bioinformatics and QC metrics", - "label": "Lineage/clade analysis software version" + "label": "Lineage/clade analysis software version", + "fill_mode": "batch" }, "design_description": { "examples": [ @@ -2434,7 +2574,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "" + "label": "", + "fill_mode": "batch" }, "isolate_sample_id": { "examples": [ @@ -2444,7 +2585,8 @@ "type": "string", "description": "", "classification": "Database Identifiers", - "label": "Sample ID given if multiple rna-extraction or passages" + "label": "Sample ID given if multiple rna-extraction or passages", + "fill_mode": "sample" }, "variant_designation": { "Enums": [ @@ -2459,7 +2601,8 @@ "Variant of Concern (VOC) [GENEPIO:0100083]" ], "classification": "Bioinformatics and QC metrics", - "label": "Variant designation" + "label": "Variant designation", + "fill_mode": "batch" }, "gene_name_1": { "Enums": [ @@ -2509,7 +2652,8 @@ "E gene (orf4) [GENEPIO:0100151]" ], "classification": "Bioinformatics and QC metrics", - "label": "Gene Name 1" + "label": "Gene Name 1", + "fill_mode": "batch" }, "per_qc_filtered": { "examples": [ @@ -2519,7 +2663,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "%qc filtered" + "label": "%qc filtered", + "fill_mode": "batch" }, "per_reads_host": { "examples": [ @@ -2529,7 +2674,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "%reads host" + "label": "%reads host", + "fill_mode": "batch" }, "per_reads_virus": { "examples": [ @@ -2539,7 +2685,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "%reads virus" + "label": "%reads virus", + "fill_mode": "batch" }, "per_unmapped": { "examples": [ @@ -2549,7 +2696,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "%unmapped" + "label": "%unmapped", + "fill_mode": "batch" }, "per_genome _greater_10x": { "examples": [ @@ -2559,7 +2707,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "% genome greater 10x" + "label": "% genome greater 10x", + "fill_mode": "batch" }, "median_depth_of_coverage_value": { "examples": [ @@ -2569,7 +2718,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "mean depth of coverage value" + "label": "mean depth of coverage value", + "fill_mode": "batch" }, "per_Ns": { "examples": [ @@ -2579,7 +2729,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "%Ns" + "label": "%Ns", + "fill_mode": "batch" }, "number_of_variants_AF_greater_75percent": { "examples": [ @@ -2589,7 +2740,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Number of variants (AF greater 75%)" + "label": "Number of variants (AF greater 75%)", + "fill_mode": "batch" }, "number_of_variants_with_effect": { "examples": [ @@ -2599,7 +2751,8 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Number of variants with effect" + "label": "Number of variants with effect", + "fill_mode": "batch" }, "diagnostic_pcr_protocol_1": { "examples": [ @@ -2609,7 +2762,8 @@ "type": "string", "description": "The name and version number of the protocol used for diagnostic marker amplification.", "classification": "Pathogen diagnostic testing", - "label": "Diagnostic Pcr Protocol 1" + "label": "Diagnostic Pcr Protocol 1", + "fill_mode": "batch" }, "diagnostic_pcr_Ct_value_1": { "examples": [ @@ -2619,7 +2773,8 @@ "type": "string", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "classification": "Pathogen diagnostic testing", - "label": "Diagnostic Pcr Ct Value 1" + "label": "Diagnostic Pcr Ct Value 1", + "fill_mode": "batch" }, "gene_name_2": { "Enums": [ @@ -2669,7 +2824,8 @@ "RdRp gene (nsp12) [GENEPIO:0100168]" ], "classification": "Pathogen diagnostic testing", - "label": "Gene Name 2" + "label": "Gene Name 2", + "fill_mode": "batch" }, "diagnostic_pcr_protocol_2": { "examples": [ @@ -2679,7 +2835,8 @@ "type": "string", "description": "The name and version number of the protocol used for diagnostic marker amplification.", "classification": "Pathogen diagnostic testing", - "label": "Diagnostic Pcr Protocol 2" + "label": "Diagnostic Pcr Protocol 2", + "fill_mode": "batch" }, "analysis_date": { "examples": [ @@ -2690,7 +2847,8 @@ "format": "date", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Analysis date" + "label": "Analysis date", + "fill_mode": "batch" }, "lineage_identification_date": { "examples": [ @@ -2701,7 +2859,8 @@ "format": "date", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Lineage identification date" + "label": "Lineage identification date", + "fill_mode": "batch" }, "diagnostic_pcr_Ct_value_2": { "examples": [ @@ -2711,7 +2870,8 @@ "type": "string", "description": "The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.", "classification": "Pathogen diagnostic testing", - "label": "Diagnostic Pcr Ct Value-2" + "label": "Diagnostic Pcr Ct Value-2", + "fill_mode": "batch" }, "analysis_author": { "examples": [ @@ -2721,7 +2881,8 @@ "type": "string", "description": "", "classification": "Contributor Acknowledgement", - "label": "Analysis Authors" + "label": "Analysis Authors", + "fill_mode": "batch" }, "author_submitter": { "examples": [ @@ -2731,7 +2892,8 @@ "type": "string", "description": "", "classification": "Contributor Acknowledgement", - "label": "Author Submitter" + "label": "Author Submitter", + "fill_mode": "batch" }, "gisaid_id": { "examples": [ @@ -2741,7 +2903,8 @@ "type": "string", "description": "", "classification": "enter your GISAID-Username", - "label": "GISAID id" + "label": "GISAID id", + "fill_mode": "sample" }, "authors": { "examples": [ @@ -2751,7 +2914,8 @@ "type": "string", "description": "", "classification": "Contributor Acknowledgement", - "label": "Authors" + "label": "Authors", + "fill_mode": "batch" }, "common_name": { "examples": [ @@ -2760,7 +2924,8 @@ "ontology": "NCIT:C164471", "type": "string", "description": "The common name of the organism.", - "classification": "Sample collection and processing" + "classification": "Sample collection and processing", + "fill_mode": "batch" }, "collector_name": { "examples": [ @@ -2771,7 +2936,8 @@ "description": "Name of the person who collected the specimen", "classification": "Sample collection and processing", "label": "Sample collector name", - "table": "sample" + "table": "sample", + "fill_mode": "batch" }, "library_source": { "Enums": [ @@ -2807,7 +2973,8 @@ "type": "string", "description": "Molecule type used to make the library.", "classification": "Sequencing", - "label": "Source material" + "label": "Source material", + "fill_mode": "batch" }, "analysis_accession": { "examples": [ @@ -2817,7 +2984,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Analysis Accession" + "label": "Analysis Accession", + "fill_mode": "batch" }, "study_accession": { "examples": [ @@ -2827,7 +2995,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Study accession" + "label": "Study accession", + "fill_mode": "batch" }, "secondary_study_accession": { "examples": [ @@ -2837,7 +3006,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Secondary study accession" + "label": "Secondary study accession", + "fill_mode": "batch" }, "sample_accession": { "examples": [ @@ -2847,7 +3017,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Sample accession" + "label": "Sample accession", + "fill_mode": "batch" }, "secondary_sample_accession": { "examples": [ @@ -2857,7 +3028,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Secondary sample accession" + "label": "Secondary sample accession", + "fill_mode": "batch" }, "experiment_accession": { "examples": [ @@ -2867,7 +3039,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Experiment Accession" + "label": "Experiment Accession", + "fill_mode": "batch" }, "run_accession": { "examples": [ @@ -2877,7 +3050,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Run Accession" + "label": "Run Accession", + "fill_mode": "batch" }, "submission_accession": { "examples": [ @@ -2887,7 +3061,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Submission Accession" + "label": "Submission Accession", + "fill_mode": "batch" }, "read_count": { "examples": [ @@ -2897,7 +3072,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Read count" + "label": "Read count", + "fill_mode": "batch" }, "read_length": { "examples": [ @@ -2907,7 +3083,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Read length" + "label": "Read length", + "fill_mode": "batch" }, "base_count": { "examples": [ @@ -2917,7 +3094,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Base count" + "label": "Base count", + "fill_mode": "batch" }, "first_public": { "examples": [ @@ -2927,7 +3105,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "First Public date" + "label": "First Public date", + "fill_mode": "batch" }, "last_updated": { "examples": [ @@ -2938,7 +3117,8 @@ "description": "", "classification": "Submission ENA", "format": "date", - "label": "Last Updated" + "label": "Last Updated", + "fill_mode": "batch" }, "experiment_title": { "examples": [ @@ -2948,7 +3128,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Experiment title" + "label": "Experiment title", + "fill_mode": "batch" }, "study_title": { "examples": [ @@ -2958,7 +3139,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Study title" + "label": "Study title", + "fill_mode": "batch" }, "study_alias": { "examples": [ @@ -2968,7 +3150,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Study alias" + "label": "Study alias", + "fill_mode": "batch" }, "experiment_alias": { "examples": [ @@ -2978,7 +3161,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Experiment alias" + "label": "Experiment alias", + "fill_mode": "batch" }, "run_alias": { "examples": [ @@ -2988,7 +3172,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Run Alias" + "label": "Run Alias", + "fill_mode": "batch" }, "fastq_bytes": { "examples": [ @@ -2998,7 +3183,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Fastq bytes" + "label": "Fastq bytes", + "fill_mode": "batch" }, "fastq_md5_r1": { "examples": [ @@ -3008,7 +3194,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Fastq md5 r1" + "label": "Fastq md5 r1", + "fill_mode": "batch" }, "fastq_md5_r2": { "examples": [ @@ -3018,7 +3205,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Fastq md5 r2" + "label": "Fastq md5 r2", + "fill_mode": "batch" }, "fastq_ftp": { "examples": [ @@ -3028,7 +3216,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Fastq ftp" + "label": "Fastq ftp", + "fill_mode": "batch" }, "fastq_aspera": { "examples": [ @@ -3038,7 +3227,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Fastq aspera" + "label": "Fastq aspera", + "fill_mode": "batch" }, "fastq_galaxy": { "examples": [ @@ -3048,7 +3238,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Fastq galaxy" + "label": "Fastq galaxy", + "fill_mode": "batch" }, "submitted_bytes": { "examples": [ @@ -3058,7 +3249,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Submitted bytes " + "label": "Submitted bytes ", + "fill_mode": "batch" }, "submitted_md5": { "examples": [ @@ -3068,7 +3260,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Submitted md5" + "label": "Submitted md5", + "fill_mode": "batch" }, "submitted_ftp": { "examples": [ @@ -3078,7 +3271,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Submitted ftp" + "label": "Submitted ftp", + "fill_mode": "batch" }, "submitted_aspera": { "examples": [ @@ -3088,7 +3282,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Submitted aspera" + "label": "Submitted aspera", + "fill_mode": "batch" }, "submitted_galaxy": { "examples": [ @@ -3098,7 +3293,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Submitted Galaxy" + "label": "Submitted Galaxy", + "fill_mode": "batch" }, "submitted_format": { "examples": [ @@ -3108,7 +3304,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Submitted Format" + "label": "Submitted Format", + "fill_mode": "batch" }, "sra_bytes": { "examples": [ @@ -3118,7 +3315,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "SRA bytes" + "label": "SRA bytes", + "fill_mode": "batch" }, "sra_md5": { "examples": [ @@ -3128,7 +3326,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "SRA md5" + "label": "SRA md5", + "fill_mode": "batch" }, "sra_ftp": { "examples": [ @@ -3138,7 +3337,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "SRA ftp" + "label": "SRA ftp", + "fill_mode": "batch" }, "sra_aspera": { "examples": [ @@ -3148,7 +3348,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "SRA aspera" + "label": "SRA aspera", + "fill_mode": "batch" }, "sra_galaxy": { "examples": [ @@ -3158,7 +3359,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "SRA galaxy" + "label": "SRA galaxy", + "fill_mode": "batch" }, "broker_name": { "examples": [ @@ -3168,7 +3370,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Broker Name" + "label": "Broker Name", + "fill_mode": "batch" }, "nominal_sdev": { "examples": [ @@ -3178,7 +3381,8 @@ "type": "string", "description": "", "classification": "Submission ENA", - "label": "Nominal sdev" + "label": "Nominal sdev", + "fill_mode": "batch" }, "first_created_date": { "examples": [ @@ -3189,7 +3393,8 @@ "format": "date", "description": "", "classification": "Submission ENA", - "label": "First created date" + "label": "First created date", + "fill_mode": "batch" }, "type": { "examples": [ @@ -3199,7 +3404,8 @@ "type": "string", "description": "default must remain 'betacoronavirus'", "classification": "Database Identifiers", - "label": "Type" + "label": "Type", + "fill_mode": "batch" } } } \ No newline at end of file From 0cd324fdc1cf12ec46f539a40ab5402976be3bc3 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 9 May 2022 15:33:28 +0200 Subject: [PATCH 0421/1454] minor change --- .../schema/mapping_ena_to_upload_ena.json | 125 ------------------ relecov_tools/schema/relecov_schema.json | 2 +- 2 files changed, 1 insertion(+), 126 deletions(-) delete mode 100644 relecov_tools/schema/mapping_ena_to_upload_ena.json diff --git a/relecov_tools/schema/mapping_ena_to_upload_ena.json b/relecov_tools/schema/mapping_ena_to_upload_ena.json deleted file mode 100644 index 44456b71..00000000 --- a/relecov_tools/schema/mapping_ena_to_upload_ena.json +++ /dev/null @@ -1,125 +0,0 @@ -{ - "xml_files": [ - "study", - "runs", - "samples", - "experiment" - ], - "one_loop_in_mapping": [ - "study" - ], - "study": { - "study_alias": "alias", - "study_title": "title", - "study_type": "", - "study_abstract": "", - "pubmed_id": "" - }, - "runs": { - "file_name": "", - "experiment_alias": "", - "host_scientific_name": "", - "file_name": "", - "file_type": "", - "file_checksum": "" - }, - "samples": { - "": "alias", - "title": "", - "taxon_id": "", - "sample_description": "", - "scientific_name": "", - "common_name": "", - "host scientific name": "", - "host common name": "", - "isolate": "", - "collecting institution": "", - "geographic location (country and/or sea)": "", - "host subject id": [ - "host_subject_id_1", - "host_subject_id_2" - ], - "host health state": [ - "diseased", - "restricted access" - ], - "host sex": [ - "male", - "female" - ], - "host_scientific_name_1": [], - "host_scientific_name_2": [], - "collector name": "", - "collection date": "" - }, - "experiments": { - "experiment_alias": [ - "alias" - ], - "title": [ - "experiment_title_1", - "experiment_title_2", - "experiment_title_3" - ], - "study_alias": [ - "study_alias_4", - "study_alias_5", - "study_alias_5" - ], - "sample_alias": [ - "study_alias_4", - "study_alias_5", - "study_alias_5" - ], - "design_description": [ - "design_description_1", - "design_description_2", - "design_description_3" - ], - "library_name": [ - "library_name_1", - "library_name_2", - "library_name_3" - ], - "library_strategy": [ - "WGA", - "RNA-Seq", - "RNA-Seq" - ], - "library_source": [ - "GENOMIC", - "TRANSCRIPTOMIC", - "TRANSCRIPTOMIC" - ], - "library_selection": [ - "RANDOM", - "repeat fractionation", - "repeat fractionation" - ], - "library_layout": [ - "paired", - "single", - "single" - ], - "insert_size": [ - "250", - "None", - "None" - ], - "library_construction_protocol": [ - "library_construction_protocol_1", - "library_construction_protocol_2", - "library_construction_protocol_2" - ], - "platform": [ - "LS454", - "illumina", - "illumina" - ], - "instrument_model": [ - "454 GS 20", - "Illumina Genome Analyzer", - "Illumina Genome Analyzer" - ] - } -} \ No newline at end of file diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 9caab8f8..d71be668 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2305,7 +2305,7 @@ }, "sequence_file_R2_fastq": { "examples": [ - "ABC123_S1_L001_R2_001.fastq.gz" + "ABC123_S1_L001_R2_002.fastq.gz" ], "ontology": "GENEPIO:0001477", "type": "string", From 88e41732878b505574e1afc318b92117f2825976 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 9 May 2022 15:33:28 +0200 Subject: [PATCH 0422/1454] minor change --- .../schema/mapping_ena_to_upload_ena.json | 125 ------------------ relecov_tools/schema/relecov_schema.json | 2 +- 2 files changed, 1 insertion(+), 126 deletions(-) delete mode 100644 relecov_tools/schema/mapping_ena_to_upload_ena.json diff --git a/relecov_tools/schema/mapping_ena_to_upload_ena.json b/relecov_tools/schema/mapping_ena_to_upload_ena.json deleted file mode 100644 index 44456b71..00000000 --- a/relecov_tools/schema/mapping_ena_to_upload_ena.json +++ /dev/null @@ -1,125 +0,0 @@ -{ - "xml_files": [ - "study", - "runs", - "samples", - "experiment" - ], - "one_loop_in_mapping": [ - "study" - ], - "study": { - "study_alias": "alias", - "study_title": "title", - "study_type": "", - "study_abstract": "", - "pubmed_id": "" - }, - "runs": { - "file_name": "", - "experiment_alias": "", - "host_scientific_name": "", - "file_name": "", - "file_type": "", - "file_checksum": "" - }, - "samples": { - "": "alias", - "title": "", - "taxon_id": "", - "sample_description": "", - "scientific_name": "", - "common_name": "", - "host scientific name": "", - "host common name": "", - "isolate": "", - "collecting institution": "", - "geographic location (country and/or sea)": "", - "host subject id": [ - "host_subject_id_1", - "host_subject_id_2" - ], - "host health state": [ - "diseased", - "restricted access" - ], - "host sex": [ - "male", - "female" - ], - "host_scientific_name_1": [], - "host_scientific_name_2": [], - "collector name": "", - "collection date": "" - }, - "experiments": { - "experiment_alias": [ - "alias" - ], - "title": [ - "experiment_title_1", - "experiment_title_2", - "experiment_title_3" - ], - "study_alias": [ - "study_alias_4", - "study_alias_5", - "study_alias_5" - ], - "sample_alias": [ - "study_alias_4", - "study_alias_5", - "study_alias_5" - ], - "design_description": [ - "design_description_1", - "design_description_2", - "design_description_3" - ], - "library_name": [ - "library_name_1", - "library_name_2", - "library_name_3" - ], - "library_strategy": [ - "WGA", - "RNA-Seq", - "RNA-Seq" - ], - "library_source": [ - "GENOMIC", - "TRANSCRIPTOMIC", - "TRANSCRIPTOMIC" - ], - "library_selection": [ - "RANDOM", - "repeat fractionation", - "repeat fractionation" - ], - "library_layout": [ - "paired", - "single", - "single" - ], - "insert_size": [ - "250", - "None", - "None" - ], - "library_construction_protocol": [ - "library_construction_protocol_1", - "library_construction_protocol_2", - "library_construction_protocol_2" - ], - "platform": [ - "LS454", - "illumina", - "illumina" - ], - "instrument_model": [ - "454 GS 20", - "Illumina Genome Analyzer", - "Illumina Genome Analyzer" - ] - } -} \ No newline at end of file diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 9caab8f8..d71be668 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2305,7 +2305,7 @@ }, "sequence_file_R2_fastq": { "examples": [ - "ABC123_S1_L001_R2_001.fastq.gz" + "ABC123_S1_L001_R2_002.fastq.gz" ], "ontology": "GENEPIO:0001477", "type": "string", From 2e93a6f8e0d9d1352cff089b3e682b09567421a8 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 9 May 2022 16:57:09 +0200 Subject: [PATCH 0423/1454] added BioinfoMetadata class --- relecov_tools/__main__.py | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index a87d1d57..0368721b 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -15,6 +15,7 @@ import relecov_tools.json_validation import relecov_tools.map_schema import relecov_tools.feed_databases +import relecov_tools.bioinfo_metadata log = logging.getLogger() @@ -303,5 +304,27 @@ def update_db(user, password, json, schema, iskylims, relecov): feed_databases.store_data() +# metadata bioinformatics +@relecov_tools_cli.command(help_priority=3) +@click.option( + "-m", + "--metadata_file", + type=click.Path(), + help="file containing metadata", +) +@click.option( + "-o", "--metadata-out", type=click.Path(), help="Path to save output metadata file" +) +def bioinfo_metadata(metadata_file, metadata_out): + """ + Create the json compliant from the Bioinfo Metadata. + """ + new_metadata = relecov_tools.bioinfo_metadata.BioinfoMetadata( + metadata_file, metadata_out + ) + bioinfo_json = new_metadata.create_metadata_json() + return bioinfo_json + + if __name__ == "__main__": run_relecov_tools() From 94cff03e5cb034f317dec9f52b333236c71703f0 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 9 May 2022 21:21:00 +0200 Subject: [PATCH 0424/1454] fixin litin --- relecov_tools/feed_databases.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/relecov_tools/feed_databases.py b/relecov_tools/feed_databases.py index ef205ef7..949d737a 100644 --- a/relecov_tools/feed_databases.py +++ b/relecov_tools/feed_databases.py @@ -200,13 +200,15 @@ def update_databases(self, sample_fields): ) sys.exit(1) - log.info("stored data in iskylims for sample %s", iskylims_data["sampleName"]) + log.info( + "stored data in iskylims for sample %s", iskylims_data["sampleName"] + ) # send request to releco-platform relecov_data = {} for label, value in sample.items(): if label not in sample_fields["iskylims_s_fields"]: relecov_data[label] = value - import pdb; pdb.set_trace() + result = self.relecov_rest_api.post_request( relecov_data, {"user": self.user, "passwd": self.passwd} ) From 7f4fcebbc02b51d5e06af8dd0035aa6758e31456 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 9 May 2022 21:23:21 +0200 Subject: [PATCH 0425/1454] fixin litin --- relecov_tools/rest_api.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/relecov_tools/rest_api.py b/relecov_tools/rest_api.py index 516ca748..ee5f579f 100644 --- a/relecov_tools/rest_api.py +++ b/relecov_tools/rest_api.py @@ -62,12 +62,8 @@ def post_request(self, data, credentials, url): "Unable to post parameters. Received error code %s", req.status_code, ) - stderr.print( - f"[red] Unable to post data because {req.text}" - ) - stderr.print( - f"[red] Received error {req.status_code}" - ) + stderr.print(f"[red] Unable to post data because {req.text}") + stderr.print(f"[red] Received error {req.status_code}") # sys.exit(1) return {"ERROR": req.status_code} return {"Success": req.text} From 1e43fc90ae8268310cfa7c4cd754c5f6d126df3b Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 10 May 2022 11:33:05 +0200 Subject: [PATCH 0426/1454] minor changes in bioinfo_metadata.py --- relecov_tools/__main__.py | 11 +++++- relecov_tools/bioinfo_metadata.py | 64 +++++++++++++++++++++++++++++++ 2 files changed, 73 insertions(+), 2 deletions(-) create mode 100644 relecov_tools/bioinfo_metadata.py diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 0368721b..442d3224 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -319,12 +319,19 @@ def bioinfo_metadata(metadata_file, metadata_out): """ Create the json compliant from the Bioinfo Metadata. """ - new_metadata = relecov_tools.bioinfo_metadata.BioinfoMetadata( + + new_bioinfo_metadata = relecov_tools.bioinfo_metadata.BioinfoMetadata( metadata_file, metadata_out ) - bioinfo_json = new_metadata.create_metadata_json() + bioinfo_json = new_bioinfo_metadata.create_metadata_json() return bioinfo_json if __name__ == "__main__": run_relecov_tools() + + +def read_metadata(metadata_file, sample_list_file, metadata_out): + """ + Create the json compliant to the relecov schema from the Metadata file. + """ diff --git a/relecov_tools/bioinfo_metadata.py b/relecov_tools/bioinfo_metadata.py new file mode 100644 index 00000000..4b7106bb --- /dev/null +++ b/relecov_tools/bioinfo_metadata.py @@ -0,0 +1,64 @@ +#!/usr/bin/env python +from itertools import islice + +# from geopy.geocoders import Nominatim +import json +import logging +import rich.console + +# from openpyxl import Workbook +import openpyxl +import os +import sys +import relecov_tools.utils +from relecov_tools.config_json import ConfigJson +import relecov_tools.json_schema + +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + + +class BioinfoMetadata: + def __init__(self, metadata_file=None, output_folder=None): + if metadata_file is None: + self.metadata_file = relecov_tools.utils.prompt_path( + msg="Select the excel file which contains metadata" + ) + else: + self.metadata_file = metadata_file + if not os.path.exists(self.metadata_file): + log.error("Metadata file %s does not exist ", self.metadata_file) + stderr.print("[red] Metadata file " + self.meta_file + " does not exist") + sys.exit(1) + if output_folder is None: + self.output_folder = relecov_tools.utils.prompt_path( + msg="Select the output folder" + ) + else: + self.output_folder = output_folder + + def fetch_metadata_file(folder, file_name): + """Fetch the metadata file folder Directory to fetch metadata file + file_name metadata file name + """ + wb_file = openpyxl.load_workbook(file_name, data_only=True) + ws_metadata_lab = wb_file["METADATA_LAB"] + heading = [] + for cell in ws_metadata_lab[1]: + heading.append(cell.value) + + def read_json_file(self, j_file): + """Read json file.""" + with open(j_file, "r") as fh: + data = json.load(fh) + return data + + +# esto es una prueba + +print("Hello esto es una prueba ") From 636e123f15427dabf043b07892a68489caa479d7 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 10 May 2022 11:58:36 +0200 Subject: [PATCH 0427/1454] removed a repetition at the enf of main --- relecov_tools/__main__.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 442d3224..af449506 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -329,9 +329,3 @@ def bioinfo_metadata(metadata_file, metadata_out): if __name__ == "__main__": run_relecov_tools() - - -def read_metadata(metadata_file, sample_list_file, metadata_out): - """ - Create the json compliant to the relecov schema from the Metadata file. - """ From 147eae5f1874abbfa4d472f6597834ed2c94b6c5 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 10 May 2022 12:00:54 +0200 Subject: [PATCH 0428/1454] fixing linting --- relecov_tools/bioinfo_metadata.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/relecov_tools/bioinfo_metadata.py b/relecov_tools/bioinfo_metadata.py index 4b7106bb..d3d971bf 100644 --- a/relecov_tools/bioinfo_metadata.py +++ b/relecov_tools/bioinfo_metadata.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -from itertools import islice +# from itertools import islice # from geopy.geocoders import Nominatim import json @@ -11,7 +11,8 @@ import os import sys import relecov_tools.utils -from relecov_tools.config_json import ConfigJson + +# from relecov_tools.config_json import ConfigJson import relecov_tools.json_schema log = logging.getLogger(__name__) From 3a1a9205ed83b818be55f411ad3d190285492539 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 10 May 2022 12:23:50 +0200 Subject: [PATCH 0429/1454] changed names in read_metadata and bioinfo_metadta --- relecov_tools/__main__.py | 10 +++++----- .../{bioinfo_metadata.py => read_bioinfo_metadata.py} | 6 ++++-- .../{read_metadata.py => read_lab_metadata.py} | 0 3 files changed, 9 insertions(+), 7 deletions(-) rename relecov_tools/{bioinfo_metadata.py => read_bioinfo_metadata.py} (89%) rename relecov_tools/{read_metadata.py => read_lab_metadata.py} (100%) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index af449506..e5f3cd6f 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -9,13 +9,13 @@ import rich.traceback import relecov_tools.utils -import relecov_tools.read_metadata +import relecov_tools.read_lab_metadata import relecov_tools.sftp_handle import relecov_tools.ena_upload import relecov_tools.json_validation import relecov_tools.map_schema import relecov_tools.feed_databases -import relecov_tools.bioinfo_metadata +import relecov_tools.read_bioinfo_metadata log = logging.getLogger() @@ -187,11 +187,11 @@ def download(user, password, conf_file): @click.option( "-o", "--metadata-out", type=click.Path(), help="Path to save output metadata file" ) -def read_metadata(metadata_file, sample_list_file, metadata_out): +def read_lab_metadata(metadata_file, sample_list_file, metadata_out): """ Create the json compliant to the relecov schema from the Metadata file. """ - new_metadata = relecov_tools.read_metadata.RelecovMetadata( + new_metadata = relecov_tools.read_lab_metadata.RelecovMetadata( metadata_file, sample_list_file, metadata_out ) relecov_json = new_metadata.create_metadata_json() @@ -320,7 +320,7 @@ def bioinfo_metadata(metadata_file, metadata_out): Create the json compliant from the Bioinfo Metadata. """ - new_bioinfo_metadata = relecov_tools.bioinfo_metadata.BioinfoMetadata( + new_bioinfo_metadata = relecov_tools.read_bioinfo_metadata.BioinfoMetadata( metadata_file, metadata_out ) bioinfo_json = new_bioinfo_metadata.create_metadata_json() diff --git a/relecov_tools/bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py similarity index 89% rename from relecov_tools/bioinfo_metadata.py rename to relecov_tools/read_bioinfo_metadata.py index d3d971bf..67284d06 100644 --- a/relecov_tools/bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -25,7 +25,7 @@ class BioinfoMetadata: - def __init__(self, metadata_file=None, output_folder=None): + def __init__(self, metadata_file=None, input_folder=None, output_folder=None): if metadata_file is None: self.metadata_file = relecov_tools.utils.prompt_path( msg="Select the excel file which contains metadata" @@ -34,7 +34,9 @@ def __init__(self, metadata_file=None, output_folder=None): self.metadata_file = metadata_file if not os.path.exists(self.metadata_file): log.error("Metadata file %s does not exist ", self.metadata_file) - stderr.print("[red] Metadata file " + self.meta_file + " does not exist") + stderr.print( + "[red] Metadata file " + self.metadata_file + " does not exist" + ) sys.exit(1) if output_folder is None: self.output_folder = relecov_tools.utils.prompt_path( diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_lab_metadata.py similarity index 100% rename from relecov_tools/read_metadata.py rename to relecov_tools/read_lab_metadata.py From 6bca20e0b82fec539e52db38ca49c0a11d0f2637 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 10 May 2022 16:20:07 +0200 Subject: [PATCH 0430/1454] workin in read_bioinfo_metadtada --- relecov_tools/__main__.py | 11 ++- relecov_tools/conf/configuration.json | 14 ++- relecov_tools/read_bioinfo_metadata.py | 121 ++++++++++++++++++++++--- 3 files changed, 126 insertions(+), 20 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index e5f3cd6f..664f8f7d 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -304,7 +304,7 @@ def update_db(user, password, json, schema, iskylims, relecov): feed_databases.store_data() -# metadata bioinformatics +# read metadata bioinformatics @relecov_tools_cli.command(help_priority=3) @click.option( "-m", @@ -312,19 +312,20 @@ def update_db(user, password, json, schema, iskylims, relecov): type=click.Path(), help="file containing metadata", ) +@click.option("-i", "--input-folder", type=click.Path(), help="Path to input files") @click.option( "-o", "--metadata-out", type=click.Path(), help="Path to save output metadata file" ) -def bioinfo_metadata(metadata_file, metadata_out): +def read_bioinfo_metadata(metadata_file, input_folder, metadata_out): """ Create the json compliant from the Bioinfo Metadata. """ new_bioinfo_metadata = relecov_tools.read_bioinfo_metadata.BioinfoMetadata( - metadata_file, metadata_out + metadata_file, input_folder, metadata_out ) - bioinfo_json = new_bioinfo_metadata.create_metadata_json() - return bioinfo_json + + new_bioinfo_metadata.bioinfo_parse(metadata_file) if __name__ == "__main__": diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index f5ea31a9..f80f4c96 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -59,7 +59,7 @@ "onlyRecorded": "Yes", "sampleLocation": "Not defined" }, - "relecov_metadata":[ + "relecov_metadata": [ "collecting_lab_sample_id", "sequencing_sample_id", "biosample_accession_ENA", @@ -67,10 +67,18 @@ "gisaid_id", "sequencing_date" ], + "relecov_bioinfo_metadata": { + "dehosting_method_software_name": "kraken2", + "dehosting_method_software_version": "2.1.2", + "variant_calling_software_name": "IVAR_VARIANTS", + "variant_calling_software_version": "1.3.1", + "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", + "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", + "consensus_sequence_software_version": "1.14" + }, "tool": { "tool_name": "ena-upload-cli", "tool_version": "0.5.3" }, "checklist": "ERC000033" - -} +} \ No newline at end of file diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 67284d06..063bc280 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -4,7 +4,11 @@ # from geopy.geocoders import Nominatim import json import logging +from turtle import pd +import pandas as pd +from requests import head import rich.console +from itertools import islice # from openpyxl import Workbook import openpyxl @@ -12,7 +16,7 @@ import sys import relecov_tools.utils -# from relecov_tools.config_json import ConfigJson +from relecov_tools.config_json import ConfigJson import relecov_tools.json_schema log = logging.getLogger(__name__) @@ -38,6 +42,12 @@ def __init__(self, metadata_file=None, input_folder=None, output_folder=None): "[red] Metadata file " + self.metadata_file + " does not exist" ) sys.exit(1) + if input_folder is None: + self.input_folder = relecov_tools.utils.prompt_path( + msg="Select the input folder" + ) + else: + self.output_folder = output_folder if output_folder is None: self.output_folder = relecov_tools.utils.prompt_path( msg="Select the output folder" @@ -45,23 +55,110 @@ def __init__(self, metadata_file=None, input_folder=None, output_folder=None): else: self.output_folder = output_folder - def fetch_metadata_file(folder, file_name): + def bioinfo_parse(self, file_name): """Fetch the metadata file folder Directory to fetch metadata file file_name metadata file name """ + wb_file = openpyxl.load_workbook(file_name, data_only=True) ws_metadata_lab = wb_file["METADATA_LAB"] - heading = [] - for cell in ws_metadata_lab[1]: - heading.append(cell.value) + config_json = ConfigJson() + relecov_bioinfo_metadata = config_json.get_configuration( + "relecov_bioinfo_metadata" + ) + + for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): + # row = ws_metadata_lab[5] + sample_name = row[5] + fastq_r1 = row[47] + fastq_r2 = row[48] + bioinfo_dict = {} + bioinfo_dict["sample_name"] = sample_name + bioinfo_dict["fastq_r1"] = fastq_r1 + bioinfo_dict["dehosting_method_software_name"] = relecov_bioinfo_metadata[ + "dehosting_method_software_name" + ] # software_versions.yml + bioinfo_dict[ + "dehosting_method_software_version" + ] = relecov_bioinfo_metadata[ + "dehosting_method_software_version" + ] # software_versions.yml + bioinfo_dict["assembly"] = None + bioinfo_dict["if_assembly_other"] = None + bioinfo_dict["assembly_params"] = None + bioinfo_dict["variant_calling_software_name"] = relecov_bioinfo_metadata[ + "variant_calling_software_name" + ] # software_versions.yml + bioinfo_dict["variant_calling_software_version"] = relecov_bioinfo_metadata[ + "variant_calling_software_version" # software_versions.yml + ] + bioinfo_dict["variant_calling_params"] = relecov_bioinfo_metadata[ + "variant_calling_params" + ] + # bioinfo_dict["consensus_sequence_name"]= + # bioinfo_dict["consensus_sequence_name_md5"]= + # bioinfo_dict["consensus_sequence_filepath"]= input file path + + bioinfo_dict["consensus_sequence_software_name"] = relecov_bioinfo_metadata[ + "consensus_sequence_software_name" + ] # software_versions.yml + bioinfo_dict[ + "consensus_sequence_software_version" + ] = relecov_bioinfo_metadata[ + "consensus_sequence_software_version" # software_versions.yml + ] + + bioinfo_dict["if_consensus_other"] = self.input_folder + """ + "dehosting_method": "", + "if_assembly_other": "", + "assembly_params": "", + "variant_calling": "", + "if_variant_calling_other": "", + "variant_calling_params": "", + "consensus_sequence_name": "", + "consensus_sequence_name_md5": "", + "consensus_sequence_filepath": "", + + "consensus_sequence_software_name": "", + "if_consensus_other": "", + "consensus_sequence_software_version": "", - def read_json_file(self, j_file): - """Read json file.""" - with open(j_file, "r") as fh: - data = json.load(fh) - return data + "consensus_criteria": "", + "depth_of_coverage_threshold": "", + "number_of_base_pairs_sequenced": "", + "consensus_genome_length": "", + "ns_per_100_kbp": "", + "reference_genome_accession": "", + "bioinformatics_protocol": "", + "if_bioinformatic_protocol_is_other_specify": "", + "bioinformatic_protocol_version": "", + "commercial/open-source/both": "", + "preprocessing": "", + "if_preprocessing_other": "", + "preprocessing_params": "", + "mapping": "", + "if_mapping_other": "", + "mapping_params": "", + "lineage_name": "", + "lineage_analysis_software_name": "", + "if_lineage_identification_other": "", + "lineage_analysis_software_version": "", + "variant_designation": "", + "per_qc_filtered": "", + "per_reads_host": "", + "per_reads_virus": "", + "per_unmapped": "", + "per_genome _greater_10x": "", + "median_depth_of_coverage_value": "", + "per_Ns": "", + "number_of_variants_AF_greater_75percent": "", + "number_of_variants_with_effect": "", + "long_table_path": "" + """ -# esto es una prueba + print(bioinfo_dict) + import pdb -print("Hello esto es una prueba ") + pdb.set_trace() From 636afa80164ee7a00bb879f3c1df32175cba2d99 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 10 May 2022 16:31:10 +0200 Subject: [PATCH 0431/1454] linting --- relecov_tools/read_bioinfo_metadata.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 063bc280..8ee42b48 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -2,11 +2,9 @@ # from itertools import islice # from geopy.geocoders import Nominatim -import json +# import json import logging from turtle import pd -import pandas as pd -from requests import head import rich.console from itertools import islice @@ -75,6 +73,7 @@ def bioinfo_parse(self, file_name): bioinfo_dict = {} bioinfo_dict["sample_name"] = sample_name bioinfo_dict["fastq_r1"] = fastq_r1 + bioinfo_dict["fastq_r1"] = fastq_r2 bioinfo_dict["dehosting_method_software_name"] = relecov_bioinfo_metadata[ "dehosting_method_software_name" ] # software_versions.yml From b906d9e32a995fb4c3601b6c4585cee2cd339bf2 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 10 May 2022 16:32:23 +0200 Subject: [PATCH 0432/1454] linting2 --- relecov_tools/read_bioinfo_metadata.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 8ee42b48..18693fa4 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -4,7 +4,8 @@ # from geopy.geocoders import Nominatim # import json import logging -from turtle import pd + +# from turtle import pd import rich.console from itertools import islice From 338eff26ba9d632dcc8147d68da79669639f0e56 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 10 May 2022 17:58:27 +0200 Subject: [PATCH 0433/1454] working in read_bioinfo_metadata --- relecov_tools/read_bioinfo_metadata.py | 33 +++++++++++++++----------- 1 file changed, 19 insertions(+), 14 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 18693fa4..831448f3 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -4,6 +4,7 @@ # from geopy.geocoders import Nominatim # import json import logging +import yaml # from turtle import pd import rich.console @@ -77,54 +78,53 @@ def bioinfo_parse(self, file_name): bioinfo_dict["fastq_r1"] = fastq_r2 bioinfo_dict["dehosting_method_software_name"] = relecov_bioinfo_metadata[ "dehosting_method_software_name" - ] # software_versions.yml + ] # software_versions.yml software_list["KRAKEN2_KRAKEN2"].keys(0) bioinfo_dict[ "dehosting_method_software_version" ] = relecov_bioinfo_metadata[ "dehosting_method_software_version" - ] # software_versions.yml + ] # software_versions.yml software_list["KRAKEN2_KRAKEN2"].values(0) bioinfo_dict["assembly"] = None bioinfo_dict["if_assembly_other"] = None bioinfo_dict["assembly_params"] = None bioinfo_dict["variant_calling_software_name"] = relecov_bioinfo_metadata[ "variant_calling_software_name" - ] # software_versions.yml + ] # software_versions.yml software_list["IVAR_VARIANTS"].keys(0) bioinfo_dict["variant_calling_software_version"] = relecov_bioinfo_metadata[ - "variant_calling_software_version" # software_versions.yml + "variant_calling_software_version" # software_versions.yml software_list["IVAR_VARIANTS"].values(0) ] bioinfo_dict["variant_calling_params"] = relecov_bioinfo_metadata[ "variant_calling_params" ] # bioinfo_dict["consensus_sequence_name"]= # bioinfo_dict["consensus_sequence_name_md5"]= - # bioinfo_dict["consensus_sequence_filepath"]= input file path + bioinfo_dict["consensus_sequence_filepath"] = self.input_folder bioinfo_dict["consensus_sequence_software_name"] = relecov_bioinfo_metadata[ "consensus_sequence_software_name" - ] # software_versions.yml + ] # software_versions.yml software_list["BCFTOOLS_CONSENSUS"].keys(0) bioinfo_dict[ "consensus_sequence_software_version" ] = relecov_bioinfo_metadata[ - "consensus_sequence_software_version" # software_versions.yml + "consensus_sequence_software_version" # software_versions.yml software_list["BCFTOOLS_CONSENSUS"].values(0) ] - bioinfo_dict["if_consensus_other"] = self.input_folder + bioinfo_dict["if_consensus_other"] = None """ - "dehosting_method": "", + "dehosting_method": "", RENAMED to dehosting_software_name y dehosting_software_version "if_assembly_other": "", - "assembly_params": "", - "variant_calling": "", + "assembly_params": "", + "variant_calling": "", RENAMED to variant_calling_software_name y variant_calling_software_version "if_variant_calling_other": "", - "variant_calling_params": "", + "variant_calling_params": "", "consensus_sequence_name": "", "consensus_sequence_name_md5": "", "consensus_sequence_filepath": "", - "consensus_sequence_software_name": "", "if_consensus_other": "", "consensus_sequence_software_version": "", - "consensus_criteria": "", + "consensus_criteria": "", RENAMED to consensus_params "depth_of_coverage_threshold": "", "number_of_base_pairs_sequenced": "", "consensus_genome_length": "", @@ -157,6 +157,11 @@ def bioinfo_parse(self, file_name): "long_table_path": "" """ + path_software_version = os.path.join( + self.input_folder, "software_versions.yml" + ) + with open(path_software_version) as file: + software_list = yaml.load(file, Loader=yaml.FullLoader) print(bioinfo_dict) import pdb From b0e512b78fb56fd35f3de3eb313084d6188b0f4f Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 11 May 2022 13:47:21 +0200 Subject: [PATCH 0434/1454] linting --- relecov_tools/read_bioinfo_metadata.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 831448f3..456ae9a3 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -123,7 +123,6 @@ def bioinfo_parse(self, file_name): "consensus_sequence_software_name": "", "if_consensus_other": "", "consensus_sequence_software_version": "", - "consensus_criteria": "", RENAMED to consensus_params "depth_of_coverage_threshold": "", "number_of_base_pairs_sequenced": "", @@ -155,14 +154,16 @@ def bioinfo_parse(self, file_name): "number_of_variants_AF_greater_75percent": "", "number_of_variants_with_effect": "", "long_table_path": "" - + """ """ path_software_version = os.path.join( - self.input_folder, "software_versions.yml" + self.input_folder, "software_versions.yml" ) with open(path_software_version) as file: software_list = yaml.load(file, Loader=yaml.FullLoader) + """ + print(bioinfo_dict) import pdb From ce0b0a39e18175a1e5f114726539eb197caa59d0 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 11 May 2022 13:57:39 +0200 Subject: [PATCH 0435/1454] linting --- relecov_tools/read_bioinfo_metadata.py | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 456ae9a3..25aeff1e 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -4,7 +4,8 @@ # from geopy.geocoders import Nominatim # import json import logging -import yaml + +# import yaml # from turtle import pd import rich.console @@ -111,10 +112,10 @@ def bioinfo_parse(self, file_name): bioinfo_dict["if_consensus_other"] = None """ - "dehosting_method": "", RENAMED to dehosting_software_name y dehosting_software_version + "dehosting_method": "" RENAMED to dehosting_software_name y dehosting_software_version, "if_assembly_other": "", "assembly_params": "", - "variant_calling": "", RENAMED to variant_calling_software_name y variant_calling_software_version + "variant_calling": "" RENAMED to variant_calling_software_name y variant_calling_software_version, "if_variant_calling_other": "", "variant_calling_params": "", "consensus_sequence_name": "", @@ -155,14 +156,11 @@ def bioinfo_parse(self, file_name): "number_of_variants_with_effect": "", "long_table_path": "" """ - """ - path_software_version = os.path.join( - self.input_folder, "software_versions.yml" - ) - with open(path_software_version) as file: - software_list = yaml.load(file, Loader=yaml.FullLoader) - """ + # path_software_version = os.path.join( + # self.input_folder, "software_versions.yml") + # with open(path_software_version) as file: + # software_list = yaml.load(file, Loader=yaml.FullLoader) print(bioinfo_dict) import pdb From 5352ee9087a48c699a55a25650b0902891eaedb7 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 11 May 2022 14:02:43 +0200 Subject: [PATCH 0436/1454] linting3 --- relecov_tools/read_bioinfo_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 25aeff1e..9be4b209 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -48,7 +48,7 @@ def __init__(self, metadata_file=None, input_folder=None, output_folder=None): msg="Select the input folder" ) else: - self.output_folder = output_folder + self.input_folder = output_folder if output_folder is None: self.output_folder = relecov_tools.utils.prompt_path( msg="Select the output folder" From 557fded7e931f45d392cc03e8e1c2ad78cfde493 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 11 May 2022 14:05:15 +0200 Subject: [PATCH 0437/1454] linting3 --- relecov_tools/read_bioinfo_metadata.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 9be4b209..736fbe1a 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -112,12 +112,12 @@ def bioinfo_parse(self, file_name): bioinfo_dict["if_consensus_other"] = None """ - "dehosting_method": "" RENAMED to dehosting_software_name y dehosting_software_version, + "dehosting_method": "" RENAMED to dehosting_software_name y dehosting_software_version, "if_assembly_other": "", - "assembly_params": "", + "assembly_params": "", "variant_calling": "" RENAMED to variant_calling_software_name y variant_calling_software_version, "if_variant_calling_other": "", - "variant_calling_params": "", + "variant_calling_params": "", "consensus_sequence_name": "", "consensus_sequence_name_md5": "", "consensus_sequence_filepath": "", From f7ea20997379ede1ac105db0577ef12cbdd57cde Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 11 May 2022 15:45:37 +0200 Subject: [PATCH 0438/1454] Remove geopy from requirements file --- relecov_tools/read_lab_metadata.py | 2 -- requirements.txt | 1 - 2 files changed, 3 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 9a103de1..47439689 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -1,12 +1,10 @@ #!/usr/bin/env python from itertools import islice -# from geopy.geocoders import Nominatim import json import logging import rich.console -# from openpyxl import Workbook import openpyxl import os import sys diff --git a/requirements.txt b/requirements.txt index df6c9d32..d2533548 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,7 +5,6 @@ packaging prompt_toolkit>=3.0.3 rich>=10.0.0 requests==2.27.1 -geopy==2.2.0 paramiko>=2.10.1 pyyaml openpyxl From f346672167565abc0a8ac524e3dfd56862e13e0f Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 11 May 2022 15:52:30 +0200 Subject: [PATCH 0439/1454] change version to upload to pypi --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 27555f97..5f081b36 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import setup, find_packages -version = "0.0.1" +version = "0.0.2" with open("README.md") as f: readme = f.read() From c7df3f3477c68fe83b1bc2a9bead76ede24696cc Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 11 May 2022 16:31:55 +0200 Subject: [PATCH 0440/1454] changes in schema --- relecov_tools/conf/configuration.json | 27 +++++- relecov_tools/read_bioinfo_metadata.py | 110 ++++++++++++++++++----- relecov_tools/schema/relecov_schema.json | 62 +++++++++++-- 3 files changed, 167 insertions(+), 32 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index f80f4c96..967e0d67 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -70,11 +70,32 @@ "relecov_bioinfo_metadata": { "dehosting_method_software_name": "kraken2", "dehosting_method_software_version": "2.1.2", - "variant_calling_software_name": "IVAR_VARIANTS", + "assembly": "None", + "if_assembly_other": "None", + "assembly_params": "None", + "variant_calling_software_name": "ivar_variants", "variant_calling_software_version": "1.3.1", "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", - "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", - "consensus_sequence_software_version": "1.14" + "consensus_sequence_software_name": "bcftools_consensus", + "consensus_sequence_software_version": "1.14", + "if_consensur_other": "None", + "consensus_params": "-p vcf -f", + "depth_of_coverage_threshold": ">10x", + "bioinformatics_protocol_software_name": "nf-core/viralrecon", + "bioinformatics_protocol_software_version": "2.4.1", + "if_bioinformatic_protocol_is_other_specify": "None", + "commercial_open_source_both": "open-source", + "preprocessing_software_name": "fastp", + "preprocessing_software_version": "0.23.2", + "if_preprocessing_other": "None", + "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", + "mapping_software_name": "bowtie2", + "mapping_software_version": "2.4.4", + "if_mapping_other": "None", + "mapping_params": "--seed 1", + "lineage_analysis_software_name": "pangolin", + "lineage_analysis_software_version": "4.0.6", + "if_lineage_identification_other": "None" }, "tool": { "tool_name": "ena-upload-cli", diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 736fbe1a..b8ea1ea9 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -76,41 +76,111 @@ def bioinfo_parse(self, file_name): bioinfo_dict = {} bioinfo_dict["sample_name"] = sample_name bioinfo_dict["fastq_r1"] = fastq_r1 - bioinfo_dict["fastq_r1"] = fastq_r2 + bioinfo_dict["fastq_r2"] = fastq_r2 bioinfo_dict["dehosting_method_software_name"] = relecov_bioinfo_metadata[ "dehosting_method_software_name" - ] # software_versions.yml software_list["KRAKEN2_KRAKEN2"].keys(0) + ] bioinfo_dict[ "dehosting_method_software_version" - ] = relecov_bioinfo_metadata[ - "dehosting_method_software_version" - ] # software_versions.yml software_list["KRAKEN2_KRAKEN2"].values(0) - bioinfo_dict["assembly"] = None - bioinfo_dict["if_assembly_other"] = None - bioinfo_dict["assembly_params"] = None + ] = relecov_bioinfo_metadata["dehosting_method_software_version"] + bioinfo_dict["assembly"] = relecov_bioinfo_metadata["assembly"] + bioinfo_dict["if_assembly_other"] = relecov_bioinfo_metadata[ + "if_assembly_other" + ] + bioinfo_dict["assembly_params"] = relecov_bioinfo_metadata[ + "assembly_params" + ] bioinfo_dict["variant_calling_software_name"] = relecov_bioinfo_metadata[ "variant_calling_software_name" - ] # software_versions.yml software_list["IVAR_VARIANTS"].keys(0) + ] bioinfo_dict["variant_calling_software_version"] = relecov_bioinfo_metadata[ - "variant_calling_software_version" # software_versions.yml software_list["IVAR_VARIANTS"].values(0) + "variant_calling_software_version" ] bioinfo_dict["variant_calling_params"] = relecov_bioinfo_metadata[ "variant_calling_params" ] # bioinfo_dict["consensus_sequence_name"]= # bioinfo_dict["consensus_sequence_name_md5"]= + bioinfo_dict["consensus_sequence_filepath"] = self.input_folder bioinfo_dict["consensus_sequence_software_name"] = relecov_bioinfo_metadata[ "consensus_sequence_software_name" - ] # software_versions.yml software_list["BCFTOOLS_CONSENSUS"].keys(0) + ] bioinfo_dict[ "consensus_sequence_software_version" - ] = relecov_bioinfo_metadata[ - "consensus_sequence_software_version" # software_versions.yml software_list["BCFTOOLS_CONSENSUS"].values(0) + ] = relecov_bioinfo_metadata["consensus_sequence_software_version"] + bioinfo_dict["if_consensus_other"] = relecov_bioinfo_metadata[ + "if_consensur_other" ] - - bioinfo_dict["if_consensus_other"] = None + bioinfo_dict["consensus_params"] = relecov_bioinfo_metadata[ + "consensus_params" + ] + bioinfo_dict["depth_of_coverage_threshold"] = relecov_bioinfo_metadata[ + "depth_of_coverage_threshold" + ] + bioinfo_dict["depth_of_coverage_threshold"] = relecov_bioinfo_metadata[ + "depth_of_coverage_threshold" + ] + # "number_of_base_pairs_sequenced": "", + # "consensus_genome_length": "", + # "ns_per_100_kbp": "", + # "reference_genome_accession": "", + bioinfo_dict[ + "bioinformatics_protocol_software_name" + ] = relecov_bioinfo_metadata["bioinformatics_protocol_software_name"] + bioinfo_dict[ + "bioinformatics_protocol_software_version" + ] = relecov_bioinfo_metadata["bioinformatics_protocol_software_version"] + bioinfo_dict[ + "if_bioinformatic_protocol_is_other_specify" + ] = relecov_bioinfo_metadata["if_bioinformatic_protocol_is_other_specify"] + bioinfo_dict["commercial_open_source_both"] = relecov_bioinfo_metadata[ + "commercial_open_source_both" + ] + bioinfo_dict["preprocessing_software_name"] = relecov_bioinfo_metadata[ + "preprocessing_software_name" + ] + bioinfo_dict["preprocessing_software_version"] = relecov_bioinfo_metadata[ + "preprocessing_software_version" + ] + bioinfo_dict["if_preprocessing_other"] = relecov_bioinfo_metadata[ + "if_preprocessing_other" + ] + bioinfo_dict["preprocessing_params"] = relecov_bioinfo_metadata[ + "preprocessing_params" + ] + bioinfo_dict["mapping_software_name"] = relecov_bioinfo_metadata[ + "mapping_software_name" + ] + bioinfo_dict["mapping_software_version"] = relecov_bioinfo_metadata[ + "mapping_software_version" + ] + bioinfo_dict["if_mapping_other"] = relecov_bioinfo_metadata[ + "if_mapping_other" + ] + bioinfo_dict["mapping_params"] = relecov_bioinfo_metadata["mapping_params"] + # "lineage_name": "" + bioinfo_dict["lineage_analysis_software_name"] = relecov_bioinfo_metadata[ + "lineage_analysis_software_name" + ] + bioinfo_dict[ + "lineage_analysis_software_version" + ] = relecov_bioinfo_metadata["lineage_analysis_software_version"] + bioinfo_dict["if_lineage_identification_other"] = relecov_bioinfo_metadata[ + "if_lineage_identification_other" + ] + # "variant_designation": "", + # "per_qc_filtered": "", + # "per_reads_host": "", + # "per_reads_virus": "", + # "per_unmapped": "", + # "per_genome _greater_10x": "", + # "median_depth_of_coverage_value": "", + # "per_Ns": "", + # "number_of_variants_AF_greater_75percent": "", + # "number_of_variants_with_effect": "", + bioinfo_dict["long_table_path"] = self.input_folder """ "dehosting_method": "" RENAMED to dehosting_software_name y dehosting_software_version, "if_assembly_other": "", @@ -130,14 +200,14 @@ def bioinfo_parse(self, file_name): "consensus_genome_length": "", "ns_per_100_kbp": "", "reference_genome_accession": "", - "bioinformatics_protocol": "", + "bioinformatics_protocol": "", RENAMED to "bioinformatics_protocol_software_name" "if_bioinformatic_protocol_is_other_specify": "", - "bioinformatic_protocol_version": "", - "commercial/open-source/both": "", - "preprocessing": "", + "bioinformatic_protocol_version": "", RENAMED to "bioinformatics_protocol_software_version" + "commercial/open-source/both": "", RENAMED to "commercial_open_source_both" + "preprocessing": "", RENAMED to "preprocessing_software_name" y "preprocessing_software_version" "if_preprocessing_other": "", "preprocessing_params": "", - "mapping": "", + "mapping": "", RENAMED to "mapping_software_name" y ""mapping_software_version" "if_mapping_other": "", "mapping_params": "", "lineage_name": "", diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index d71be668..62caaa82 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2083,7 +2083,7 @@ "label": "Raw sequence data processin method", "fill_mode": "batch" }, - "dehosting_method": { + "dehosting_software_name": { "examples": [ "Nanostripper" ], @@ -2094,6 +2094,17 @@ "label": "Dehosting Method", "fill_mode": "batch" }, + "dehosting_software_version": { + "examples": [ + "2.4.1" + ], + "ontology": "0", + "type": "string", + "description": "The method version used to remove host reads from the pathogen sequence.", + "classification": "Bioinformatics and QC metrics", + "label": "Dehosting Method Version", + "fill_mode": "batch" + }, "personal_protective_equipment": { "examples": [ "mask" @@ -2138,7 +2149,7 @@ "label": "Assambly params", "fill_mode": "batch" }, - "variant_calling": { + "variant_calling_software_name": { "examples": [ "" ], @@ -2149,6 +2160,17 @@ "label": "Variant Calling", "fill_mode": "batch" }, + "variant_calling_software_version": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "classification": "Bioinformatics and QC metrics", + "label": "Variant Calling Version", + "fill_mode": "batch" + }, "if_variant_calling_other": { "examples": [ "" @@ -2237,7 +2259,7 @@ "label": "Consensus sequence software version", "fill_mode": "batch" }, - "consensus_criteria": { + "consensus_params": { "examples": [ "" ], @@ -2245,7 +2267,7 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Consensus criteria", + "label": "Consensus Params", "fill_mode": "batch" }, "quality_control_metrics": { @@ -2402,7 +2424,7 @@ "label": "Reference genome accession", "fill_mode": "batch" }, - "bioinformatics_protocol": { + "bioinformatics_protocol_software_name": { "examples": [ "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" ], @@ -2424,7 +2446,7 @@ "label": "If bioinformatic protocol Is Other, Specify", "fill_mode": "batch" }, - "bioinformatic_protocol_version": { + "bioinformatics_protocol_software_version": { "examples": [ "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" ], @@ -2435,7 +2457,7 @@ "label": "bioinformatics protocol version", "fill_mode": "batch" }, - "commercial/open-source/both": { + "commercial_open_source_both": { "examples": [ "" ], @@ -2456,7 +2478,7 @@ "label": "Sample plan name", "fill_mode": "batch" }, - "preprocessing": { + "preprocessing_software_name": { "examples": [ "" ], @@ -2467,6 +2489,17 @@ "label": "Preprocessing", "fill_mode": "batch" }, + "preprocessing_software_version": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "classification": "Bioinformatics and QC metrics", + "label": "Preprocessing Version", + "fill_mode": "batch" + }, "if_preprocessing_other": { "examples": [ "" @@ -2489,7 +2522,7 @@ "label": "Preprocessing params", "fill_mode": "batch" }, - "mapping": { + "mapping_software_name": { "examples": [ "" ], @@ -2500,6 +2533,17 @@ "label": "Mapping", "fill_mode": "batch" }, + "mapping_software_version": { + "examples": [ + "" + ], + "ontology": "topic:0102", + "type": "string", + "description": "", + "classification": "Bioinformatics and QC metrics", + "label": "Mapping Version", + "fill_mode": "batch" + }, "if_mapping_other": { "examples": [ "" From 648b481084a71d46084dc93cdfd8a1ad1781802f Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 11 May 2022 16:50:41 +0200 Subject: [PATCH 0441/1454] linting --- relecov_tools/read_bioinfo_metadata.py | 50 ------------------------ relecov_tools/schema/relecov_schema.json | 2 +- 2 files changed, 1 insertion(+), 51 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index b8ea1ea9..15d80e56 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -181,56 +181,6 @@ def bioinfo_parse(self, file_name): # "number_of_variants_AF_greater_75percent": "", # "number_of_variants_with_effect": "", bioinfo_dict["long_table_path"] = self.input_folder - """ - "dehosting_method": "" RENAMED to dehosting_software_name y dehosting_software_version, - "if_assembly_other": "", - "assembly_params": "", - "variant_calling": "" RENAMED to variant_calling_software_name y variant_calling_software_version, - "if_variant_calling_other": "", - "variant_calling_params": "", - "consensus_sequence_name": "", - "consensus_sequence_name_md5": "", - "consensus_sequence_filepath": "", - "consensus_sequence_software_name": "", - "if_consensus_other": "", - "consensus_sequence_software_version": "", - "consensus_criteria": "", RENAMED to consensus_params - "depth_of_coverage_threshold": "", - "number_of_base_pairs_sequenced": "", - "consensus_genome_length": "", - "ns_per_100_kbp": "", - "reference_genome_accession": "", - "bioinformatics_protocol": "", RENAMED to "bioinformatics_protocol_software_name" - "if_bioinformatic_protocol_is_other_specify": "", - "bioinformatic_protocol_version": "", RENAMED to "bioinformatics_protocol_software_version" - "commercial/open-source/both": "", RENAMED to "commercial_open_source_both" - "preprocessing": "", RENAMED to "preprocessing_software_name" y "preprocessing_software_version" - "if_preprocessing_other": "", - "preprocessing_params": "", - "mapping": "", RENAMED to "mapping_software_name" y ""mapping_software_version" - "if_mapping_other": "", - "mapping_params": "", - "lineage_name": "", - "lineage_analysis_software_name": "", - "if_lineage_identification_other": "", - "lineage_analysis_software_version": "", - "variant_designation": "", - "per_qc_filtered": "", - "per_reads_host": "", - "per_reads_virus": "", - "per_unmapped": "", - "per_genome _greater_10x": "", - "median_depth_of_coverage_value": "", - "per_Ns": "", - "number_of_variants_AF_greater_75percent": "", - "number_of_variants_with_effect": "", - "long_table_path": "" - """ - - # path_software_version = os.path.join( - # self.input_folder, "software_versions.yml") - # with open(path_software_version) as file: - # software_list = yaml.load(file, Loader=yaml.FullLoader) print(bioinfo_dict) import pdb diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 62caaa82..c7fe37a9 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2537,7 +2537,7 @@ "examples": [ "" ], - "ontology": "topic:0102", + "ontology": "0", "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", From 265ba7d6681e7cbce0934d9e37026b9f530b6706 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 11 May 2022 17:07:07 +0200 Subject: [PATCH 0442/1454] fixed repetition accessing dictionary --- relecov_tools/read_bioinfo_metadata.py | 213 +++++++++++++------------ 1 file changed, 107 insertions(+), 106 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 15d80e56..163c6342 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -73,116 +73,117 @@ def bioinfo_parse(self, file_name): sample_name = row[5] fastq_r1 = row[47] fastq_r2 = row[48] + bioinfo_dict = {} bioinfo_dict["sample_name"] = sample_name bioinfo_dict["fastq_r1"] = fastq_r1 bioinfo_dict["fastq_r2"] = fastq_r2 - bioinfo_dict["dehosting_method_software_name"] = relecov_bioinfo_metadata[ - "dehosting_method_software_name" - ] - bioinfo_dict[ - "dehosting_method_software_version" - ] = relecov_bioinfo_metadata["dehosting_method_software_version"] - bioinfo_dict["assembly"] = relecov_bioinfo_metadata["assembly"] - bioinfo_dict["if_assembly_other"] = relecov_bioinfo_metadata[ - "if_assembly_other" - ] - bioinfo_dict["assembly_params"] = relecov_bioinfo_metadata[ - "assembly_params" - ] - bioinfo_dict["variant_calling_software_name"] = relecov_bioinfo_metadata[ - "variant_calling_software_name" - ] - bioinfo_dict["variant_calling_software_version"] = relecov_bioinfo_metadata[ - "variant_calling_software_version" - ] - bioinfo_dict["variant_calling_params"] = relecov_bioinfo_metadata[ - "variant_calling_params" - ] - # bioinfo_dict["consensus_sequence_name"]= - # bioinfo_dict["consensus_sequence_name_md5"]= - - bioinfo_dict["consensus_sequence_filepath"] = self.input_folder + for key in relecov_bioinfo_metadata.keys(): + bioinfo_dict[key] = relecov_bioinfo_metadata[key] + """ + + bioinfo_dict["dehosting_method_software_name"] = relecov_bioinfo_metadata[ + "dehosting_method_software_name" + ] + bioinfo_dict["dehosting_method_software_version"] = relecov_bioinfo_metadata[ + "dehosting_method_software_version" + ] # NO HARCODED + bioinfo_dict["assembly"] = relecov_bioinfo_metadata["assembly"] + bioinfo_dict["if_assembly_other"] = relecov_bioinfo_metadata[ + "if_assembly_other" + ] + bioinfo_dict["assembly_params"] = relecov_bioinfo_metadata["assembly_params"] + bioinfo_dict["variant_calling_software_name"] = relecov_bioinfo_metadata[ + "variant_calling_software_name" + ] + bioinfo_dict["variant_calling_software_version"] = relecov_bioinfo_metadata[ + "variant_calling_software_version" + ] # NO HARCODED + bioinfo_dict["variant_calling_params"] = relecov_bioinfo_metadata[ + "variant_calling_params" + ] + # bioinfo_dict["consensus_sequence_name"]= + # bioinfo_dict["consensus_sequence_name_md5"]= - bioinfo_dict["consensus_sequence_software_name"] = relecov_bioinfo_metadata[ - "consensus_sequence_software_name" - ] - bioinfo_dict[ - "consensus_sequence_software_version" - ] = relecov_bioinfo_metadata["consensus_sequence_software_version"] - bioinfo_dict["if_consensus_other"] = relecov_bioinfo_metadata[ - "if_consensur_other" - ] - bioinfo_dict["consensus_params"] = relecov_bioinfo_metadata[ - "consensus_params" - ] - bioinfo_dict["depth_of_coverage_threshold"] = relecov_bioinfo_metadata[ - "depth_of_coverage_threshold" - ] - bioinfo_dict["depth_of_coverage_threshold"] = relecov_bioinfo_metadata[ - "depth_of_coverage_threshold" - ] - # "number_of_base_pairs_sequenced": "", - # "consensus_genome_length": "", - # "ns_per_100_kbp": "", - # "reference_genome_accession": "", - bioinfo_dict[ - "bioinformatics_protocol_software_name" - ] = relecov_bioinfo_metadata["bioinformatics_protocol_software_name"] - bioinfo_dict[ - "bioinformatics_protocol_software_version" - ] = relecov_bioinfo_metadata["bioinformatics_protocol_software_version"] - bioinfo_dict[ - "if_bioinformatic_protocol_is_other_specify" - ] = relecov_bioinfo_metadata["if_bioinformatic_protocol_is_other_specify"] - bioinfo_dict["commercial_open_source_both"] = relecov_bioinfo_metadata[ - "commercial_open_source_both" - ] - bioinfo_dict["preprocessing_software_name"] = relecov_bioinfo_metadata[ - "preprocessing_software_name" - ] - bioinfo_dict["preprocessing_software_version"] = relecov_bioinfo_metadata[ - "preprocessing_software_version" - ] - bioinfo_dict["if_preprocessing_other"] = relecov_bioinfo_metadata[ - "if_preprocessing_other" - ] - bioinfo_dict["preprocessing_params"] = relecov_bioinfo_metadata[ - "preprocessing_params" - ] - bioinfo_dict["mapping_software_name"] = relecov_bioinfo_metadata[ - "mapping_software_name" - ] - bioinfo_dict["mapping_software_version"] = relecov_bioinfo_metadata[ - "mapping_software_version" - ] - bioinfo_dict["if_mapping_other"] = relecov_bioinfo_metadata[ - "if_mapping_other" - ] - bioinfo_dict["mapping_params"] = relecov_bioinfo_metadata["mapping_params"] - # "lineage_name": "" - bioinfo_dict["lineage_analysis_software_name"] = relecov_bioinfo_metadata[ - "lineage_analysis_software_name" - ] - bioinfo_dict[ - "lineage_analysis_software_version" - ] = relecov_bioinfo_metadata["lineage_analysis_software_version"] - bioinfo_dict["if_lineage_identification_other"] = relecov_bioinfo_metadata[ - "if_lineage_identification_other" - ] - # "variant_designation": "", - # "per_qc_filtered": "", - # "per_reads_host": "", - # "per_reads_virus": "", - # "per_unmapped": "", - # "per_genome _greater_10x": "", - # "median_depth_of_coverage_value": "", - # "per_Ns": "", - # "number_of_variants_AF_greater_75percent": "", - # "number_of_variants_with_effect": "", - bioinfo_dict["long_table_path"] = self.input_folder + bioinfo_dict["consensus_sequence_filepath"] = self.input_folder - print(bioinfo_dict) - import pdb + bioinfo_dict["consensus_sequence_software_name"] = relecov_bioinfo_metadata[ + "consensus_sequence_software_name" + ] + bioinfo_dict["consensus_sequence_software_version"] = relecov_bioinfo_metadata[ + "consensus_sequence_software_version" + ] # NO HARCODED + bioinfo_dict["if_consensus_other"] = relecov_bioinfo_metadata[ + "if_consensur_other" + ] # NO HARCODED + bioinfo_dict["consensus_params"] = relecov_bioinfo_metadata["consensus_params"] + bioinfo_dict["depth_of_coverage_threshold"] = relecov_bioinfo_metadata[ + "depth_of_coverage_threshold" + ] + bioinfo_dict["depth_of_coverage_threshold"] = relecov_bioinfo_metadata[ + "depth_of_coverage_threshold" + ] + # "number_of_base_pairs_sequenced": "", # Input reads summary_variants_metrics_mqc.csv * 2 * read length + # "consensus_genome_length": "", script que cuente el numero de nucleotidos tamaño del fasta + # "ns_per_100_kbp": "", summary_variants_metrics_mqc.csv + # "reference_genome_accession": "", + bioinfo_dict[ + "bioinformatics_protocol_software_name" + ] = relecov_bioinfo_metadata["bioinformatics_protocol_software_name"] + bioinfo_dict[ + "bioinformatics_protocol_software_version" + ] = relecov_bioinfo_metadata[ + "bioinformatics_protocol_software_version" + ] # NO HARCODED + bioinfo_dict[ + "if_bioinformatic_protocol_is_other_specify" + ] = relecov_bioinfo_metadata["if_bioinformatic_protocol_is_other_specify"] + bioinfo_dict["commercial_open_source_both"] = relecov_bioinfo_metadata[ + "commercial_open_source_both" + ] + bioinfo_dict["preprocessing_software_name"] = relecov_bioinfo_metadata[ + "preprocessing_software_name" + ] + bioinfo_dict["preprocessing_software_version"] = relecov_bioinfo_metadata[ + "preprocessing_software_version" + ] # NO HARCODED + bioinfo_dict["if_preprocessing_other"] = relecov_bioinfo_metadata[ + "if_preprocessing_other" + ] + bioinfo_dict["preprocessing_params"] = relecov_bioinfo_metadata[ + "preprocessing_params" + ] + bioinfo_dict["mapping_software_name"] = relecov_bioinfo_metadata[ + "mapping_software_name" + ] + bioinfo_dict["mapping_software_version"] = relecov_bioinfo_metadata[ + "mapping_software_version" + ] # NO HARCODED + bioinfo_dict["if_mapping_other"] = relecov_bioinfo_metadata["if_mapping_other"] + bioinfo_dict["mapping_params"] = relecov_bioinfo_metadata["mapping_params"] + # "lineage_name": "" mapping_illumina + bioinfo_dict["lineage_analysis_software_name"] = relecov_bioinfo_metadata[ + "lineage_analysis_software_name" + ] + bioinfo_dict["lineage_analysis_software_version"] = relecov_bioinfo_metadata[ + "lineage_analysis_software_version" + ] + bioinfo_dict["if_lineage_identification_other"] = relecov_bioinfo_metadata[ + "if_lineage_identification_other" + ] + # "variant_designation": "", pangolin csv parseo + # "per_qc_filtered": "", tabla stats + # "per_reads_host": "", tabla stats + # "per_reads_virus": "", tabla stats + # "per_unmapped": "", tabla stats + # "per_genome _greater_10x": "", tabla stats + # "median_depth_of_coverage_value": "", tabla stats + # "per_Ns": "", tabla stats + # "number_of_variants_AF_greater_75percent": "", tabla stats + # "number_of_variants_with_effect": "", tabla stats + bioinfo_dict["long_table_path"] = self.input_folder + """ + print(bioinfo_dict) + import pdb - pdb.set_trace() + pdb.set_trace() From 2e788c9da941788ff572845ae2cf0647a507e853 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 11 May 2022 17:08:57 +0200 Subject: [PATCH 0443/1454] linting --- relecov_tools/read_bioinfo_metadata.py | 98 +++----------------------- 1 file changed, 11 insertions(+), 87 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 163c6342..e21ac454 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -81,96 +81,20 @@ def bioinfo_parse(self, file_name): for key in relecov_bioinfo_metadata.keys(): bioinfo_dict[key] = relecov_bioinfo_metadata[key] """ - - bioinfo_dict["dehosting_method_software_name"] = relecov_bioinfo_metadata[ - "dehosting_method_software_name" - ] - bioinfo_dict["dehosting_method_software_version"] = relecov_bioinfo_metadata[ - "dehosting_method_software_version" - ] # NO HARCODED - bioinfo_dict["assembly"] = relecov_bioinfo_metadata["assembly"] - bioinfo_dict["if_assembly_other"] = relecov_bioinfo_metadata[ - "if_assembly_other" - ] - bioinfo_dict["assembly_params"] = relecov_bioinfo_metadata["assembly_params"] - bioinfo_dict["variant_calling_software_name"] = relecov_bioinfo_metadata[ - "variant_calling_software_name" - ] - bioinfo_dict["variant_calling_software_version"] = relecov_bioinfo_metadata[ - "variant_calling_software_version" - ] # NO HARCODED - bioinfo_dict["variant_calling_params"] = relecov_bioinfo_metadata[ - "variant_calling_params" - ] - # bioinfo_dict["consensus_sequence_name"]= - # bioinfo_dict["consensus_sequence_name_md5"]= - - bioinfo_dict["consensus_sequence_filepath"] = self.input_folder - - bioinfo_dict["consensus_sequence_software_name"] = relecov_bioinfo_metadata[ - "consensus_sequence_software_name" - ] - bioinfo_dict["consensus_sequence_software_version"] = relecov_bioinfo_metadata[ - "consensus_sequence_software_version" - ] # NO HARCODED - bioinfo_dict["if_consensus_other"] = relecov_bioinfo_metadata[ - "if_consensur_other" - ] # NO HARCODED - bioinfo_dict["consensus_params"] = relecov_bioinfo_metadata["consensus_params"] - bioinfo_dict["depth_of_coverage_threshold"] = relecov_bioinfo_metadata[ - "depth_of_coverage_threshold" - ] - bioinfo_dict["depth_of_coverage_threshold"] = relecov_bioinfo_metadata[ - "depth_of_coverage_threshold" - ] + # "dehosting_method_software_version" # NO HARCODED + # "variant_calling_software_version" # NO HARCODED + # "consensus_sequence_software_version" # NO HARCODED + # "bioinformatics_protocol_software_version" # NO HARCODED + # "preprocessing_software_version"# NO HARCODED + # "mapping_software_version" # NO HARCODED + # "lineage_analysis_software_version" + # "lineage_name": "" mapping_illumina # "number_of_base_pairs_sequenced": "", # Input reads summary_variants_metrics_mqc.csv * 2 * read length # "consensus_genome_length": "", script que cuente el numero de nucleotidos tamaño del fasta # "ns_per_100_kbp": "", summary_variants_metrics_mqc.csv # "reference_genome_accession": "", - bioinfo_dict[ - "bioinformatics_protocol_software_name" - ] = relecov_bioinfo_metadata["bioinformatics_protocol_software_name"] - bioinfo_dict[ - "bioinformatics_protocol_software_version" - ] = relecov_bioinfo_metadata[ - "bioinformatics_protocol_software_version" - ] # NO HARCODED - bioinfo_dict[ - "if_bioinformatic_protocol_is_other_specify" - ] = relecov_bioinfo_metadata["if_bioinformatic_protocol_is_other_specify"] - bioinfo_dict["commercial_open_source_both"] = relecov_bioinfo_metadata[ - "commercial_open_source_both" - ] - bioinfo_dict["preprocessing_software_name"] = relecov_bioinfo_metadata[ - "preprocessing_software_name" - ] - bioinfo_dict["preprocessing_software_version"] = relecov_bioinfo_metadata[ - "preprocessing_software_version" - ] # NO HARCODED - bioinfo_dict["if_preprocessing_other"] = relecov_bioinfo_metadata[ - "if_preprocessing_other" - ] - bioinfo_dict["preprocessing_params"] = relecov_bioinfo_metadata[ - "preprocessing_params" - ] - bioinfo_dict["mapping_software_name"] = relecov_bioinfo_metadata[ - "mapping_software_name" - ] - bioinfo_dict["mapping_software_version"] = relecov_bioinfo_metadata[ - "mapping_software_version" - ] # NO HARCODED - bioinfo_dict["if_mapping_other"] = relecov_bioinfo_metadata["if_mapping_other"] - bioinfo_dict["mapping_params"] = relecov_bioinfo_metadata["mapping_params"] - # "lineage_name": "" mapping_illumina - bioinfo_dict["lineage_analysis_software_name"] = relecov_bioinfo_metadata[ - "lineage_analysis_software_name" - ] - bioinfo_dict["lineage_analysis_software_version"] = relecov_bioinfo_metadata[ - "lineage_analysis_software_version" - ] - bioinfo_dict["if_lineage_identification_other"] = relecov_bioinfo_metadata[ - "if_lineage_identification_other" - ] + # bioinfo_dict["consensus_sequence_name"]= + # bioinfo_dict["consensus_sequence_name_md5"]= # "variant_designation": "", pangolin csv parseo # "per_qc_filtered": "", tabla stats # "per_reads_host": "", tabla stats @@ -180,7 +104,7 @@ def bioinfo_parse(self, file_name): # "median_depth_of_coverage_value": "", tabla stats # "per_Ns": "", tabla stats # "number_of_variants_AF_greater_75percent": "", tabla stats - # "number_of_variants_with_effect": "", tabla stats + # "number_of_variants_with_effect": "", tabla stats bioinfo_dict["long_table_path"] = self.input_folder """ print(bioinfo_dict) From 35190e92d6c79eed1eb0b0ed233d7dd3a32b5285 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 11 May 2022 17:55:42 +0200 Subject: [PATCH 0444/1454] lastest minor changes --- relecov_tools/read_bioinfo_metadata.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index e21ac454..00f5f486 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -80,6 +80,8 @@ def bioinfo_parse(self, file_name): bioinfo_dict["fastq_r2"] = fastq_r2 for key in relecov_bioinfo_metadata.keys(): bioinfo_dict[key] = relecov_bioinfo_metadata[key] + bioinfo_dict["consensus_sequence_filepath"] = self.input_folder + bioinfo_dict["long_table_path"] = self.input_folder """ # "dehosting_method_software_version" # NO HARCODED # "variant_calling_software_version" # NO HARCODED From 9fff32d0940c64f00ffbe879ed96fc36a7158953 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 11 May 2022 21:25:22 +0200 Subject: [PATCH 0445/1454] modify get_reques when no parameter requires to send --- relecov_tools/rest_api.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/relecov_tools/rest_api.py b/relecov_tools/rest_api.py index ee5f579f..1850f58b 100644 --- a/relecov_tools/rest_api.py +++ b/relecov_tools/rest_api.py @@ -22,7 +22,12 @@ def __init__(self, server, url): self.headers = {"content-type": "application/json"} def get_request(self, request_info, parameter, value, safe=True): - url_http = str(self.request_url + request_info + "?" + parameter + "=" + value) + if parameter == "" or parameter is None: + url_http = str(self.request_url + request_info) + else: + url_http = str( + self.request_url + request_info + "?" + parameter + "=" + value + ) try: req = requests.get(url_http, headers=self.headers) if req.status_code != 200: From a2aaacd09c32b839809de94eb69b68a5a48b91d5 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 11 May 2022 21:59:27 +0200 Subject: [PATCH 0446/1454] remove the exit command if get request is not getting valid response --- relecov_tools/rest_api.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/relecov_tools/rest_api.py b/relecov_tools/rest_api.py index 1850f58b..9695ac2f 100644 --- a/relecov_tools/rest_api.py +++ b/relecov_tools/rest_api.py @@ -39,7 +39,6 @@ def get_request(self, request_info, parameter, value, safe=True): stderr.print( "[red] Unable to fetch data. Received error ", req.status_code ) - sys.exit(1) return {"ERROR": req.status_code} return {"DATA": json.loads(req.text)} except requests.ConnectionError: @@ -69,7 +68,6 @@ def post_request(self, data, credentials, url): ) stderr.print(f"[red] Unable to post data because {req.text}") stderr.print(f"[red] Received error {req.status_code}") - # sys.exit(1) return {"ERROR": req.status_code} return {"Success": req.text} except requests.ConnectionError: From f8586426a51e439f0ec8ff3ec1f70f0ad66c53f8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 12 May 2022 10:21:48 +0200 Subject: [PATCH 0447/1454] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e8d42b6c..200bfaad 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![python_lint](https://github.com/BU-ISCIII/relecov-tools/actions/workflows/python_lint.yml/badge.svg)](https://github.com/BU-ISCIII/relecov-tools/actions/workflows/python_lint.yml) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) -> THIS REPO IS IN ACTIVE DEVELOPMENT. +> THIS REPO IS UNDER ACTIVE DEVELOPMENT. relecov-tools is a set of helper tools for the assembly of the different elements in the RELECOV platform (Spanish Network for genomic surveillance of SARS-Cov-2) as data download, processing, validation and upload to public databases, as well as analysis runs and database storage. From ca2bf73f907e469a2d4c3d376e065a53d394c3b5 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 12 May 2022 13:59:41 +0200 Subject: [PATCH 0448/1454] reading fields from files --- relecov_tools/read_bioinfo_metadata.py | 49 ++++++++++++++++++++------ 1 file changed, 38 insertions(+), 11 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 00f5f486..fec67bcb 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -3,6 +3,7 @@ # from geopy.geocoders import Nominatim # import json +from importlib.resources import path import logging # import yaml @@ -10,6 +11,7 @@ # from turtle import pd import rich.console from itertools import islice +import pandas as pd # from openpyxl import Workbook import openpyxl @@ -67,21 +69,51 @@ def bioinfo_parse(self, file_name): relecov_bioinfo_metadata = config_json.get_configuration( "relecov_bioinfo_metadata" ) - + c = 0 for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): # row = ws_metadata_lab[5] + sample_name = row[5] fastq_r1 = row[47] fastq_r2 = row[48] - bioinfo_dict = {} bioinfo_dict["sample_name"] = sample_name bioinfo_dict["fastq_r1"] = fastq_r1 bioinfo_dict["fastq_r2"] = fastq_r2 - for key in relecov_bioinfo_metadata.keys(): - bioinfo_dict[key] = relecov_bioinfo_metadata[key] - bioinfo_dict["consensus_sequence_filepath"] = self.input_folder - bioinfo_dict["long_table_path"] = self.input_folder + for key in relecov_bioinfo_metadata.keys(): + bioinfo_dict[key] = relecov_bioinfo_metadata[key] + bioinfo_dict["consensus_sequence_filepath"] = self.input_folder + bioinfo_dict["long_table_path"] = self.input_folder + path_mapping_illumina_tab = os.path.join( + self.input_folder, "mapping_illumina.tab" + ) + mapping_illumina_tab = pd.read_csv(path_mapping_illumina_tab, sep="\t") + bioinfo_dict["linage_name"] = mapping_illumina_tab["Lineage"][c] + summary_variants_metrics_path = os.path.join( + self.input_folder, "summary_variants_metrics_mqc.csv" + ) + summary_variants_metrics = pd.read_csv( + summary_variants_metrics_path, sep="," + ) + bioinfo_dict["number_of_base_pairs_sequenced"] = ( + summary_variants_metrics["# Input reads"][c] * 2 + ) # REVISAR SI ES ASÍ CON SARA + + c = +1 + import pdb + + pdb.set_trace() + """ + f = open(path_illumina_tab, "r") + lines = f.readlines() + lineages = [] + lineage_index = lines[0].index("Lineage") + for line in range(1, len(lines)): + + line_split = lines.split("\t") + lineages.append(line_split[lineage_index]) + """ + """ # "dehosting_method_software_version" # NO HARCODED # "variant_calling_software_version" # NO HARCODED @@ -89,7 +121,6 @@ def bioinfo_parse(self, file_name): # "bioinformatics_protocol_software_version" # NO HARCODED # "preprocessing_software_version"# NO HARCODED # "mapping_software_version" # NO HARCODED - # "lineage_analysis_software_version" # "lineage_name": "" mapping_illumina # "number_of_base_pairs_sequenced": "", # Input reads summary_variants_metrics_mqc.csv * 2 * read length # "consensus_genome_length": "", script que cuente el numero de nucleotidos tamaño del fasta @@ -109,7 +140,3 @@ def bioinfo_parse(self, file_name): # "number_of_variants_with_effect": "", tabla stats bioinfo_dict["long_table_path"] = self.input_folder """ - print(bioinfo_dict) - import pdb - - pdb.set_trace() From 1a1ef7e072c385f531a334acf3dd4d09af5c0aec Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 12 May 2022 16:07:05 +0200 Subject: [PATCH 0449/1454] added more fields --- relecov_tools/read_bioinfo_metadata.py | 79 +++++++++++++++++++------- 1 file changed, 58 insertions(+), 21 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index fec67bcb..12ae6544 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -5,6 +5,9 @@ # import json from importlib.resources import path import logging +import glob +from operator import contains +import pathlib # import yaml @@ -70,6 +73,18 @@ def bioinfo_parse(self, file_name): "relecov_bioinfo_metadata" ) c = 0 + mapping_illumina_tab_path = os.path.join( + self.input_folder, "mapping_illumina.tab" + ) + summary_variants_metrics_path = os.path.join( + self.input_folder, "summary_variants_metrics_mqc.csv" + ) + variants_long_table_path = os.path.join( + self.input_folder, "variants_long_table.csv" + ) + mapping_illumina_tab = pd.read_csv(mapping_illumina_tab_path, sep="\t") + summary_variants_metrics = pd.read_csv(summary_variants_metrics_path, sep=",") + variants_long_table = pd.read_csv(variants_long_table_path, sep=",") for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): # row = ws_metadata_lab[5] @@ -80,30 +95,60 @@ def bioinfo_parse(self, file_name): bioinfo_dict["sample_name"] = sample_name bioinfo_dict["fastq_r1"] = fastq_r1 bioinfo_dict["fastq_r2"] = fastq_r2 + # inserting all keys from configuration.json relecov_bioinfo_metadata into bioinfo_dict for key in relecov_bioinfo_metadata.keys(): bioinfo_dict[key] = relecov_bioinfo_metadata[key] bioinfo_dict["consensus_sequence_filepath"] = self.input_folder bioinfo_dict["long_table_path"] = self.input_folder - path_mapping_illumina_tab = os.path.join( - self.input_folder, "mapping_illumina.tab" - ) - mapping_illumina_tab = pd.read_csv(path_mapping_illumina_tab, sep="\t") + # fields from mapping_illumina.tab bioinfo_dict["linage_name"] = mapping_illumina_tab["Lineage"][c] - summary_variants_metrics_path = os.path.join( - self.input_folder, "summary_variants_metrics_mqc.csv" - ) - summary_variants_metrics = pd.read_csv( - summary_variants_metrics_path, sep="," - ) + bioinfo_dict["variant_designation"] = mapping_illumina_tab[ + "Variantsinconsensusx10" + ][c] + bioinfo_dict["per_qc_filtered"] = mapping_illumina_tab["Coverage>10x(%)"][c] + # bioinfo_dict["per_reads_host"] = mapping_illumina_tab["%readshost"][c] + # bioinfo_dict["per_reads_virus"] = mapping_illumina_tab["%readsvirus"][c] + # bioinfo_dict["per_unmapped"] = mapping_illumina_tab["%unmapedreads"][c] + bioinfo_dict["per_Ns"] = mapping_illumina_tab["%Ns10x"][c] + bioinfo_dict["median_depth_of_coverage_value"] = mapping_illumina_tab[ + "medianDPcoveragevirus" + ][c] + bioinfo_dict[ + "number_of_variants_AF_greater_75percent" + ] = mapping_illumina_tab["Variantsinconsensusx10"][c] + bioinfo_dict["number_of_variants_with_effect"] = mapping_illumina_tab[ + "MissenseVariants" + ][c] + # fields from summary_variants_metrics_mqc.csv bioinfo_dict["number_of_base_pairs_sequenced"] = ( summary_variants_metrics["# Input reads"][c] * 2 ) # REVISAR SI ES ASÍ CON SARA + bioinfo_dict["ns_per_100_kbp"] = summary_variants_metrics[ + "# Ns per 100kb consensus" + ][c] + # FALTA "consensus_genome_length": "", script que cuente el numero de nucleotidos tamaño del fasta + # fields from variants_long_table.csv + bioinfo_dict["reference_genome_accession"] = variants_long_table["CHROM"][c] + """ + + # bioinfo_dict["consensus_sequence_name"] = str(sample_name)s.join(".consensus.fa") + # files_in_dir = os.listdir() + sample_files = sorted( + pathlib.Path(self.input_folder).glob(str(sample_name) + "*") + ) + for i in sample_files: + if i.endswith(".consensus.fa"): + bioinfo_dict["consensus_sequence_name"] = i + if "R1" in i and i.endswith(".md5"): + bioinfo_dict["consensus_sequence_name_md5"] = i + """ c = +1 import pdb pdb.set_trace() - """ + + """ f = open(path_illumina_tab, "r") lines = f.readlines() lineages = [] @@ -128,15 +173,7 @@ def bioinfo_parse(self, file_name): # "reference_genome_accession": "", # bioinfo_dict["consensus_sequence_name"]= # bioinfo_dict["consensus_sequence_name_md5"]= - # "variant_designation": "", pangolin csv parseo - # "per_qc_filtered": "", tabla stats - # "per_reads_host": "", tabla stats - # "per_reads_virus": "", tabla stats - # "per_unmapped": "", tabla stats - # "per_genome _greater_10x": "", tabla stats - # "median_depth_of_coverage_value": "", tabla stats - # "per_Ns": "", tabla stats - # "number_of_variants_AF_greater_75percent": "", tabla stats - # "number_of_variants_with_effect": "", tabla stats + + bioinfo_dict["long_table_path"] = self.input_folder """ From 4fc6fddfcfcc94d7cc6ceb46853f6f3cd3959717 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 12 May 2022 16:19:52 +0200 Subject: [PATCH 0450/1454] almost done --- relecov_tools/conf/configuration.json | 12 ++++++++++++ relecov_tools/read_bioinfo_metadata.py | 14 +++++--------- 2 files changed, 17 insertions(+), 9 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 967e0d67..d885c7bf 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -97,6 +97,18 @@ "lineage_analysis_software_version": "4.0.6", "if_lineage_identification_other": "None" }, + "mapping_illumina_tab_field_list": [ + "Lineage", + "Variantsinconsensusx10", + "Coverage>10x(%)", + "%readshost", + "%readsvirus", + "%unmapedreads", + "%Ns10x", + "medianDPcoveragevirus", + "Variantsinconsensusx10", + "MissenseVariants" + ], "tool": { "tool_name": "ena-upload-cli", "tool_version": "0.5.3" diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 12ae6544..a669f8c2 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -129,9 +129,13 @@ def bioinfo_parse(self, file_name): # FALTA "consensus_genome_length": "", script que cuente el numero de nucleotidos tamaño del fasta # fields from variants_long_table.csv bioinfo_dict["reference_genome_accession"] = variants_long_table["CHROM"][c] + bioinfo_dict["consensus_sequence_name"] = str(sample_name).join( + ".consensus.fa" + ) + """ - # bioinfo_dict["consensus_sequence_name"] = str(sample_name)s.join(".consensus.fa") + # # files_in_dir = os.listdir() sample_files = sorted( pathlib.Path(self.input_folder).glob(str(sample_name) + "*") @@ -166,14 +170,6 @@ def bioinfo_parse(self, file_name): # "bioinformatics_protocol_software_version" # NO HARCODED # "preprocessing_software_version"# NO HARCODED # "mapping_software_version" # NO HARCODED - # "lineage_name": "" mapping_illumina - # "number_of_base_pairs_sequenced": "", # Input reads summary_variants_metrics_mqc.csv * 2 * read length - # "consensus_genome_length": "", script que cuente el numero de nucleotidos tamaño del fasta - # "ns_per_100_kbp": "", summary_variants_metrics_mqc.csv - # "reference_genome_accession": "", # bioinfo_dict["consensus_sequence_name"]= # bioinfo_dict["consensus_sequence_name_md5"]= - - - bioinfo_dict["long_table_path"] = self.input_folder """ From 019f3c9036b096d865fc39f41560da872ea46205 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 12 May 2022 16:27:46 +0200 Subject: [PATCH 0451/1454] linting --- relecov_tools/read_bioinfo_metadata.py | 47 ++++++-------------------- 1 file changed, 11 insertions(+), 36 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index a669f8c2..a3272dd6 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -1,22 +1,16 @@ #!/usr/bin/env python # from itertools import islice -# from geopy.geocoders import Nominatim -# import json + from importlib.resources import path import logging -import glob -from operator import contains -import pathlib -# import yaml -# from turtle import pd import rich.console from itertools import islice import pandas as pd -# from openpyxl import Workbook + import openpyxl import os import sys @@ -87,7 +81,6 @@ def bioinfo_parse(self, file_name): variants_long_table = pd.read_csv(variants_long_table_path, sep=",") for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): # row = ws_metadata_lab[5] - sample_name = row[5] fastq_r1 = row[47] fastq_r2 = row[48] @@ -132,38 +125,20 @@ def bioinfo_parse(self, file_name): bioinfo_dict["consensus_sequence_name"] = str(sample_name).join( ".consensus.fa" ) - - """ - - # - # files_in_dir = os.listdir() - sample_files = sorted( - pathlib.Path(self.input_folder).glob(str(sample_name) + "*") - ) - - for i in sample_files: - if i.endswith(".consensus.fa"): - bioinfo_dict["consensus_sequence_name"] = i - if "R1" in i and i.endswith(".md5"): - bioinfo_dict["consensus_sequence_name_md5"] = i - """ c = +1 import pdb pdb.set_trace() - """ - f = open(path_illumina_tab, "r") - lines = f.readlines() - lineages = [] - lineage_index = lines[0].index("Lineage") - for line in range(1, len(lines)): - - line_split = lines.split("\t") - lineages.append(line_split[lineage_index]) - """ - - """ + """ + f = open(path_illumina_tab, "r") + lines = f.readlines() + lineages = [] + lineage_index = lines[0].index("Lineage") + for line in range(1, len(lines)): + + line_split = lines.split("\t") + lineages.append(line_split[lineage_index]) # "dehosting_method_software_version" # NO HARCODED # "variant_calling_software_version" # NO HARCODED # "consensus_sequence_software_version" # NO HARCODED From f3061953d2bff40ce856751ff55ec6cd9a4297e7 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 12 May 2022 16:34:49 +0200 Subject: [PATCH 0452/1454] linting2 --- relecov_tools/read_bioinfo_metadata.py | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index a3272dd6..2f5b7add 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -2,7 +2,7 @@ # from itertools import islice -from importlib.resources import path +# from importlib.resources import path import logging @@ -129,16 +129,14 @@ def bioinfo_parse(self, file_name): import pdb pdb.set_trace() - """ - f = open(path_illumina_tab, "r") + f = open(path_illumina_tab, "r") lines = f.readlines() lineages = [] lineage_index = lines[0].index("Lineage") - for line in range(1, len(lines)): - - line_split = lines.split("\t") - lineages.append(line_split[lineage_index]) + for line in range(1, len(lines)) + line_split = lines.split("\t") + lineages.append(line_split[lineage_index]) # "dehosting_method_software_version" # NO HARCODED # "variant_calling_software_version" # NO HARCODED # "consensus_sequence_software_version" # NO HARCODED From c6f5df67fee93a70e7968c72d531caf67838d721 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 12 May 2022 16:35:57 +0200 Subject: [PATCH 0453/1454] linting3 --- relecov_tools/read_bioinfo_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 2f5b7add..fc0a4f3c 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -129,7 +129,7 @@ def bioinfo_parse(self, file_name): import pdb pdb.set_trace() - """ + """ f = open(path_illumina_tab, "r") lines = f.readlines() lineages = [] From e46e49d9a2bbc51e5d65031d23bb9fe4925bf04e Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 12 May 2022 16:37:36 +0200 Subject: [PATCH 0454/1454] linting4 --- relecov_tools/read_bioinfo_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index fc0a4f3c..178f71fa 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -129,7 +129,7 @@ def bioinfo_parse(self, file_name): import pdb pdb.set_trace() - """ + """ f = open(path_illumina_tab, "r") lines = f.readlines() lineages = [] From e963fecb6edb79e89ca5361bea66edf932b50c50 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 13 May 2022 22:16:32 +0200 Subject: [PATCH 0455/1454] Allow to send files in POST request. fix bugs when sending relecov request --- relecov_tools/feed_databases.py | 11 +++++------ relecov_tools/rest_api.py | 17 ++++++++++++----- relecov_tools/test/test_cases.txt | 2 +- 3 files changed, 18 insertions(+), 12 deletions(-) diff --git a/relecov_tools/feed_databases.py b/relecov_tools/feed_databases.py index 949d737a..50dcb028 100644 --- a/relecov_tools/feed_databases.py +++ b/relecov_tools/feed_databases.py @@ -160,9 +160,6 @@ def update_databases(self, sample_fields): try: iskylims_data[label] = sample[value] except KeyError as e: - import pdb - - pdb.set_trace() log.error("Found %s when mapping data for sending to iSkyLIMS") stderr.print(f"[red] {e} not found in mapping") sys.exit(1) @@ -183,8 +180,8 @@ def update_databases(self, sample_fields): # wait 5 sec before resending the request time.sleep(5) result = self.iskylims_rest_api.post_request( - iskylims_data, - {"user": self.user, "passwd": self.passwd}, + json.dumps(iskylims_data), + {"user": self.user, "pass": self.passwd}, self.iskylims_settings["store_samples"], ) if "ERROR" not in result: @@ -210,7 +207,9 @@ def update_databases(self, sample_fields): relecov_data[label] = value result = self.relecov_rest_api.post_request( - relecov_data, {"user": self.user, "passwd": self.passwd} + json.dumps(iskylims_data), + {"user": self.user, "pass": self.passwd}, + self.relecov_settings["store_samples"], ) return diff --git a/relecov_tools/rest_api.py b/relecov_tools/rest_api.py index 9695ac2f..9274e8b6 100644 --- a/relecov_tools/rest_api.py +++ b/relecov_tools/rest_api.py @@ -2,7 +2,6 @@ import logging import json import requests -import sys import rich.console import relecov_tools.utils @@ -55,12 +54,20 @@ def put_request(self, request_info, parameter, value): log.error("Unable to open connection towards %s", self.server) return False - def post_request(self, data, credentials, url): + def post_request(self, data, credentials, url, file=None): if isinstance(credentials, dict): auth = (credentials["user"], credentials["pass"]) url_http = str(self.request_url + url) try: - req = requests.post(url_http, data=data, headers=self.headers, auth=auth) + if file: + files = {"upload_file": open(file, "rb")} + req = requests.post( + url_http, files=files, data=data, headers=self.headers, auth=auth + ) + else: + req = requests.post( + url_http, data=data, headers=self.headers, auth=auth + ) if req.status_code != 201: log.error( "Unable to post parameters. Received error code %s", @@ -71,6 +78,6 @@ def post_request(self, data, credentials, url): return {"ERROR": req.status_code} return {"Success": req.text} except requests.ConnectionError: - log.error("Unable to open connection towards %s", self.server) - stderr.print("[red] Unable to open connection towards ", self.server) + log.error("Unable to open connection towards %s", self.request_url) + stderr.print("[red] Unable to open connection towards ", self.request_url) return {"ERROR": "Server not available"} diff --git a/relecov_tools/test/test_cases.txt b/relecov_tools/test/test_cases.txt index c9b80f05..5b90e570 100644 --- a/relecov_tools/test/test_cases.txt +++ b/relecov_tools/test/test_cases.txt @@ -5,4 +5,4 @@ relecov-tools validate -j relecov_tools/example_data/processed_METADATA_LAB_TEST relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -d ENA -o /tmp relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -d GISAID -o /tmp relecov-tools update-db -i http://iskylims.isciiides.es/wetlab/api -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -relecov-tools update-db -i http://localhost:8001/wetlab/api -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -u admin -p Apple@123 +relecov-tools update-db -i http://localhost:8001/wetlab/api -r http://localhost:8000/api -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -u admin -p Apple@123 From 03f813e8de0bd82f425577765a88fd5fd5659465 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 13 May 2022 22:23:53 +0200 Subject: [PATCH 0456/1454] Change the url for creating samples --- relecov_tools/conf/configuration.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index f80f4c96..08e1c007 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -42,7 +42,7 @@ "relecov": { "server": "http://relecov-platform.isciiides.es", "url": "/api/", - "store_samples": "storeData", + "store_samples": "createSample", "token": "" } }, @@ -81,4 +81,4 @@ "tool_version": "0.5.3" }, "checklist": "ERC000033" -} \ No newline at end of file +} From b16b07222b13bed23cb47be8c1965bbe7068d42d Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 14 May 2022 00:02:15 +0200 Subject: [PATCH 0457/1454] change Put request for sending json data --- relecov_tools/rest_api.py | 23 +++++++++++++++++------ 1 file changed, 17 insertions(+), 6 deletions(-) diff --git a/relecov_tools/rest_api.py b/relecov_tools/rest_api.py index 9274e8b6..b8a765d1 100644 --- a/relecov_tools/rest_api.py +++ b/relecov_tools/rest_api.py @@ -45,14 +45,25 @@ def get_request(self, request_info, parameter, value, safe=True): stderr.print("[red] Unable to open connection towards ", self.server) return {"ERROR": "Server not available"} - def put_request(self, request_info, parameter, value): - url_http = str(self.request_url + request_info + "?" + parameter + "=" + value) + def put_request(self, data, credentials, url): + if isinstance(credentials, dict): + auth = (credentials["user"], credentials["pass"]) + url_http = str(self.request_url + url) try: - requests.get(url_http, headers=self.headers) - return True + req = requests.put(url_http, data=data, headers=self.headers, auth=auth) except requests.ConnectionError: - log.error("Unable to open connection towards %s", self.server) - return False + log.error("Unable to open connection towards %s", self.request_url) + stderr.print("[red] Unable to open connection towards ", self.request_url) + return {"ERROR": "Server not available"} + if req.status_code != 201: + log.error( + "Unable to post parameters. Received error code %s", + req.status_code, + ) + stderr.print(f"[red] Unable to post data because {req.text}") + stderr.print(f"[red] Received error {req.status_code}") + return {"ERROR": req.status_code} + return {"Success": req.text} def post_request(self, data, credentials, url, file=None): if isinstance(credentials, dict): From 2395574666d454cb176422e9fddbc3deae35f6bc Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 15 May 2022 22:30:43 +0200 Subject: [PATCH 0458/1454] adding classification to the ones which not defined --- relecov_tools/schema/relecov_schema.json | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index d71be668..5b81e5a9 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -797,6 +797,7 @@ "examples": [ "79" ], + "classification": "Host information", "label": "Host Age", "fill_mode": "sample" }, @@ -816,6 +817,7 @@ "examples": [ "years [UO:0000036]" ], + "classification": "Host information", "label": "Host Age unit", "fill_mode": "batch" }, @@ -844,6 +846,7 @@ "examples": [ "50 - 59 [GENEPIO:0100054]" ], + "classification": "Host information", "label": "Host Age Bin", "fill_mode": "batch" }, @@ -867,6 +870,7 @@ "examples": [ "Male [NCIT:C46109]" ], + "classification": "Host information", "label": "Host Gender", "fill_mode": "sample" }, @@ -1095,6 +1099,7 @@ "examples": [ "Yes [NCIT:C49488]" ], + "classification": "Sample collection and processing", "label": "Sample collected in quarantine", "fill_mode": "batch" }, @@ -1598,6 +1603,7 @@ "examples": [ "South Africa [GAZ:00001094]" ], + "classification": "Host Information", "label": "Host residence country", "fill_mode": "batch" }, @@ -1630,6 +1636,7 @@ "examples": [ "Indigenous, European" ], + "classification": "Host Information", "label": "Host ethnicity", "fill_mode": "batch" }, @@ -1816,7 +1823,7 @@ "type": "string", "description": "The user-specified identifier for the library prepared for sequencing.", "classification": "Sequencing", - "labe": "Library Id", + "label": "Library Id", "fill_mode": "batch" }, "enrichment_protocol": { @@ -2925,6 +2932,7 @@ "type": "string", "description": "The common name of the organism.", "classification": "Sample collection and processing", + "label":"Common name", "fill_mode": "batch" }, "collector_name": { @@ -3408,4 +3416,4 @@ "fill_mode": "batch" } } -} \ No newline at end of file +} From 7688d740e90a2a07f16c5e4a129543a90ee92b47 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 16 May 2022 00:53:53 +0200 Subject: [PATCH 0459/1454] Deleting properties that are not selected and fixed quite different issues --- relecov_tools/schema/relecov_schema.json | 1240 +++------------------- 1 file changed, 153 insertions(+), 1087 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 5b81e5a9..0c0ebeb5 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -10,7 +10,6 @@ "organism", "isolate_sample_id", "host_scientific_name", - "host_disease", "sequencing_instrument_model", "sequencing_instrument_platform" ], @@ -27,17 +26,6 @@ "label": "Sample ID given by originating laboratory", "fill_mode": "sample" }, - "sample_description": { - "examples": [ - "" - ], - "ontology": "GENEPIO:0001156", - "type": "string", - "description": "Free text description of the sample.", - "classification": "Sample collection and processing", - "label": "Sample Description", - "fill_mode": "batch" - }, "collecting_institution": { "examples": [ "Public Health Agency of Canada" @@ -72,17 +60,6 @@ "label": "Sample Collection Date", "fill_mode": "sample" }, - "host_subject_id": { - "examples": [ - "e.g. #131" - ], - "ontology": "GENEPIO:0001398", - "type": "string", - "description": "a unique identifier by which each subject can be referred to, de-identified.", - "classification": "Host information", - "label": "Host Subject Id", - "fill_mode": "batch" - }, "geo_loc_country": { "Enums": [ "Afghanistan [GAZ:00006882]", @@ -403,66 +380,6 @@ "label": "Organism", "fill_mode": "batch" }, - "symptom_onset_date": { - "examples": [ - "16/03/2020" - ], - "ontology": "GENEPIO:0001399", - "type": "string", - "description": "The date on which the symptoms began or were first noted.", - "format": "date", - "classification": "Host information", - "label": "Symptom onset date", - "fill_mode": "batch" - }, - "host_health_state": { - "Enums": [ - "Asymptomatic [NCIT:C3833]", - "Deceased [NCIT:C28554]", - "Healthy [NCIT:C115935]", - "Recovered [NCIT:C49498]", - "Symptomatic [NCIT:C25269]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001388", - "type": "string", - "description": "Health status of the host at the time of sample collection.", - "examples": [ - "Asymptomatic [NCIT:C3833]" - ], - "classification": "Host information", - "label": "Host health state", - "fill_mode": "batch" - }, - "host_health_status_details": { - "Enums": [ - "Hospitalized [NCIT:C25179]", - "Hospitalized (Non-ICU) [GENEPIO:0100045]", - "Hospitalized (ICU) [GENEPIO:0100046]", - "Mechanical Ventilation [NCIT:C70909]", - "Medically Isolated [GENEPIO:0100047]", - "Medically Isolated (Negative Pressure) [GENEPIO:0100048]", - "Self-quarantining [NCIT:C173768]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001389", - "type": "string", - "description": "Further details pertaining to the health or disease status of the host at time of collection.", - "examples": [ - "Hospitalized (ICU) [GENEPIO:0100046]" - ], - "classification": "Host information", - "label": "Host health status details", - "fill_mode": "batch" - }, "host_scientific_name": { "Enums": [ "Bos taurus [NCBITaxon:9913]", @@ -580,18 +497,7 @@ "label": "Sequencing Instrument Model", "fill_mode": "batch" }, - "sequencing_instrument_platform": { - "examples": [ - "MinIon" - ], - "ontology": "GENEPIO_0000071", - "type": "string", - "description": "The model of the sequencing instrument used.", - "classification": "Sequencing", - "label": "Sequencing Instrument Platform", - "fill_mode": "batch" - }, - "submitting_lab_sequence_id": { + "submitting_lab_sample_id": { "examples": [ "" ], @@ -602,28 +508,6 @@ "label": "Sample ID given by the submitting laboratory", "fill_mode": "sample" }, - "bioproject_umbrella_accession_ENA": { - "examples": [ - "PRJNA623807" - ], - "ontology": "GENEPIO:0001133", - "type": "string", - "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", - "classification": "Database Identifiers", - "label": "Bioproject umbrella accession ENA", - "fill_mode": "batch" - }, - "bioproject_accession_ENA": { - "examples": [ - "PRJNA12345" - ], - "ontology": "GENEPIO:0001136", - "type": "string", - "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", - "classification": "Database Identifiers", - "label": "Bioproject accession ENA", - "fill_mode": "batch" - }, "biosample_accession_ENA": { "examples": [ "SAMN14180202" @@ -635,39 +519,6 @@ "label": "ENA Sample ID", "fill_mode": "sample" }, - "sra_accession": { - "examples": [ - "SRR11177792" - ], - "ontology": "GENEPIO:0001142", - "type": "string", - "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "classification": "Database Identifiers", - "label": "SRA Accession", - "fill_mode": "batch" - }, - "genBank/ENA/DDBJ_accession": { - "examples": [ - "MN908947.3" - ], - "ontology": "GENEPIO_0001145", - "type": "string", - "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", - "classification": "Database Identifiers", - "label": "GenBank/ENA/DDBJ accession", - "fill_mode": "batch" - }, - "GISAID_accession": { - "examples": [ - "EPI_ISL_123456" - ], - "ontology": "GENEPIO:0001147", - "type": "string", - "description": "The GISAID accession number assigned to the sequence.", - "classification": "Database Identifiers", - "label": "GISAID Accession", - "fill_mode": "batch" - }, "virus_name": { "examples": [ "hCoV-19/Canada/prov_rona_99/2020" @@ -735,30 +586,6 @@ "label": "Sample Received Date", "fill_mode": "sample" }, - "shipping_date": { - "examples": [ - "3/20/2020" - ], - "ontology": "0", - "type": "string", - "description": "The date on which the sample was sent.", - "format": "date", - "classification": "Sample collection and processing", - "label": "Shipping Date", - "fill_mode": "batch" - }, - "results_emission_date": { - "examples": [ - "3/23/2020" - ], - "ontology": "NCIT_C142672", - "type": "string", - "description": "The date on which the results were emitted.", - "format": "date", - "classification": "Sample collection and processing", - "label": "Results Emission Date", - "fill_mode": "batch" - }, "sample_storage_conditions": { "examples": [ "24 degrees celsius" @@ -770,26 +597,6 @@ "label": "Biological Sample Storage Condition", "fill_mode": "batch" }, - "culture_collection": { - "ontology": "GENEPIO:0100284", - "type": "string", - "description": "The name of the source collection and unique culture identifier. ", - "examples": [ - "/culture_collection=\"ATCC:26370\"" - ], - "classification": "Sample collection and processing", - "label": "Culture collection", - "fill_mode": "batch" - }, - "treatment": { - "ontology": "OGMS:0000090", - "type": "string", - "description": "Include drug name, dosage", - "examples": [], - "classification": "Sample collection and processing", - "label": "Treatment", - "fill_mode": "batch" - }, "host_age": { "ontology": "GENEPIO:0001392", "type": "string", @@ -801,55 +608,6 @@ "label": "Host Age", "fill_mode": "sample" }, - "host_age_unit": { - "Enums": [ - "months [UO:0000035]", - "years [UO:0000036]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "NCIT:C50400", - "type": "string", - "description": "The units used to measure the host's age.", - "examples": [ - "years [UO:0000036]" - ], - "classification": "Host information", - "label": "Host Age unit", - "fill_mode": "batch" - }, - "host_age_bin": { - "Enums": [ - "0 - 9 [GENEPIO:0100049]", - "10 - 19 [GENEPIO:0100050]", - "20 - 29 [GENEPIO:0100051]", - "30 - 39 [GENEPIO:0100052]", - "40 - 49 [GENEPIO:0100053]", - "50 - 59 [GENEPIO:0100054]", - "60 - 69 [GENEPIO:0100055]", - "70 - 79 [GENEPIO:0100056]", - "80 - 89 [GENEPIO:0100057]", - "90 - 99 [GENEPIO:0100058]", - "100+ [GENEPIO:0100059]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001394", - "type": "string", - "description": "The age category of the host at the time of sampling.", - "examples": [ - "50 - 59 [GENEPIO:0100054]" - ], - "classification": "Host information", - "label": "Host Age Bin", - "fill_mode": "batch" - }, "host_gender": { "Enums": [ "Female [NCIT:C46110]", @@ -967,32 +725,6 @@ "label": "Specimen source", "fill_mode": "batch" }, - "body_product": { - "Enums": [ - "Breast Milk [UBERON:0001913]", - "Feces [UBERON:0001988]", - "Mucus [UBERON:0000912]", - "Semen [UBERON:0006530]", - "Sputum [UBERON:0007311]", - "Sweat [UBERON:0001089]", - "Tear [UBERON:0001827]", - "Urine [UBERON:0001088]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001216", - "type": "string", - "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", - "examples": [ - "Feces [UBERON:0001988]" - ], - "classification": "Sample collection and processing", - "label": "Body product", - "fill_mode": "batch" - }, "environmental_material": { "Enums": [ "Air vent [ENVO:03501208]", @@ -1043,601 +775,132 @@ "classification": "Sample collection and processing", "label": "Environmental Material", "fill_mode": "batch" - }, - "environmental_site": { - "Enums": [ - "Acute care facility [ENVO:03501135]", - "Animal house [ENVO:00003040]", - "Bathroom [ENVO:01000422]", - "Clinical assessment centre [ENVO:03501136]", - "Conference venue [ENVO:03501127]", - "Corridor [ENVO:03501121]", - "Daycare [ENVO:01000927]", - "Emergency room (ER) [ENVO:03501145]", - "Family practice clinic [ENVO:03501186]", - "Group home [ENVO:03501196]", - "Homeless shelter [ENVO:03501133]", - "Hospital [ENVO:00002173]", - "Intensive Care Unit (ICU) [ENVO:03501152]", - "Long Term Care Facility [ENVO:03501194]", - "Patient room [ENVO:03501180]", - "Prison [ENVO:03501204]", - "Production Facility [ENVO:01000536]", - "School [ENVO:03501130]", - "Sewage Plant [ENVO:00003043]", - "Subway train [ENVO:03501109]", - "Wet market [ENVO:03501198]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001232", - "type": "string", - "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", - "examples": [ - "Hospital [ENVO:00002173]" - ], - "classification": "Sample collection and processing", - "label": "Environmental System", - "fill_mode": "batch" - }, - "sample_collected_in_quarantine": { - "Enums": [ - "Yes [NCIT:C49488]", - "No [NCIT:C49487]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0100277", - "type": "string", - "description": "Whether the sample was collected from an individual in quarantine.", - "examples": [ - "Yes [NCIT:C49488]" - ], - "classification": "Sample collection and processing", - "label": "Sample collected in quarantine", - "fill_mode": "batch" - }, - "collection_device": { - "Enums": [ - "Air filter [ENVO:00003968]", - "Blood Collection Tube [OBI:0002859]", - "Bronchoscope [OBI:0002826]", - "Collection Container [OBI:0002088]", - "Collection Cup [GENEPIO:0100026]", - "Fibrobronchoscope Brush [OBI:0002825]", - "Filter [GENEPIO:0100103]", - "Fine Needle [OBI:0002827]", - "Microcapillary tube [OBI:0002858]", - "Micropipette [OBI:0001128]", - "Needle [OBI:0000436]", - "Serum Collection Tube [OBI:0002860]", - "Sputum Collection Tube [OBI:0002861]", - "Suction Catheter [OBI:0002831]", - "Swab [GENEPIO:0100027]", - "Urine Collection Tube [OBI:0002862]", - "Virus Transport Medium [OBI:0002866]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001234", - "type": "string", - "description": "The instrument or container used to collect the sample e.g. swab.", - "examples": [ - "Swab [GENEPIO:0100027]" - ], - "classification": "Sample collection and processing", - "label": "Collection Device", - "fill_mode": "batch" - }, - "collection_method": { - "Enums": [ - "Amniocentesis [NCIT:C52009]", - "Aspiration [NCIT:C15631]", - "Suprapubic Aspiration [GENEPIO:0100028]", - "Tracheal Aspiration [GENEPIO:0100029]", - "Vacuum Aspiration [GENEPIO:0100030]", - "Biopsy [OBI:0002650]", - "Needle Biopsy [OBI:0002651]", - "Filtration [OBI:0302885]", - "Air Filtration [GENEPIO:0100031]", - "Lavage [OBI:0600044]", - "Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]", - "Gastric Lavage [GENEPIO:0100033]", - "Lumbar Puncture [NCIT:C15327]", - "Necropsy [MMO:0000344]", - "Phlebotomy [NCIT:C28221]", - "Rinsing [GENEPIO:0002116]", - "Saline gargle (mouth rinse and gargle) [GENEPIO:0100034]", - "Scraping [GENEPIO:0100035]", - "Swabbing [GENEPIO:0002117]", - "Finger Prick [GENEPIO:0100036]", - "Washout Tear Collection [GENEPIO:0100038]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001241", - "type": "string", - "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", - "examples": [ - "Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]" - ], - "classification": "Sample collection and processing", - "label": "Collection Method", - "fill_mode": "batch" - }, - "collection_protocol": { - "examples": [ - "SC2SamplingProtocol 1.2" - ], - "ontology": "GENEPIO:0001243", - "type": "string", - "description": "The name and version of a particular protocol used for sampling.", - "classification": "Sample collection and processing", - "label": "Collection Protocol", - "fill_mode": "batch" - }, - "specimen_processing": { - "Enums": [ - "Virus Passage [GENEPIO:0100039]", - "RNA Re-Extraction (Post RT-PCR) [GENEPIO:0100040]", - "Specimens Pooled [OBI:0600016]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001253", - "type": "string", - "description": "Any processing applied to the sample during or after receiving the sample. ", - "examples": [ - "Virus Passage [GENEPIO:0100039]" - ], - "classification": "Sample collection and processing", - "label": "Specimen Processing", - "fill_mode": "batch" - }, - "lab_host": { - "Enums": [ - "293/ACE2 Cell Line [GENEPIO:0100041]", - "Caco2 Cell Line [BTO:0000195]", - "Calu3 Cell Line [BTO:0002750]", - "EFK3B Cell Line [GENEPIO:0100042]", - "HEK293T Cell Line [BTO:0002181]", - "HRCE Cell Line [GENEPIO:0100043]", - "Huh7 Cell Line [BTO:0001950]", - "LLCMk2 Cell Line [CLO:0007330]", - "MDBK Cell Line [BTO:0000836]", - "NHBE Cell Line [BTO:0002924]", - "PK-15 Cell Line [BTO:0001865]", - "RK-13 Cell Line [BTO:0002909]", - "U251 Cell Line [BTO:0002035]", - "Vero Cell Line [BTO:0001444]", - "Vero E6 Cell Line [BTO:0004755]", - "Vero E6/TMPRSS2 Cell Line [GENEPIO:0100044]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001255", - "type": "string", - "description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.", - "examples": [ - "Vero E6 Cell Line [BTO:0004755]" - ], - "classification": "Sample collection and processing", - "label": "Lab passage Host", - "fill_mode": "batch" - }, - "passage_number": { - "examples": [ - "3" - ], - "ontology": "GENEPIO:0001261", - "type": "string", - "description": "Number of passages.", - "classification": "Sample collection and processing", - "label": "Passage Number", - "fill_mode": "batch" - }, - "passage_method": { - "examples": [ - "AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain." - ], - "ontology": "GENEPIO:0001264", - "type": "string", - "description": "Description of how organism was passaged.", - "classification": "Sample collection and processing", - "label": "Passage Method", - "fill_mode": "batch" - }, - "tax_id": { - "examples": [ - "probably 2697049 in all cases" - ], - "ontology": "GENEPIO_0001724", - "type": "string", - "description": "The NCBITaxon identifier for the organism being sequenced.", - "classification": "Sample collection and processing", - "label": "Tax ID", - "fill_mode": "batch" - }, - "center_name": { - "examples": [ - " KAROLINSKA INSITUTET" - ], - "ontology": "NCIT_C19983", - "type": "string", - "description": "The name of the institution", - "classification": "Sample collection and processing", - "label": "Center Name", - "fill_mode": "batch" - }, - "host_common_name": { - "Enums": [ - "Human [NCBITaxon:9606]", - "Bat [NCBITaxon:9397]", - "Cat [NCBITaxon:9685]", - "Chicken [NCBITaxon:9031]", - "Civet [NCBITaxon:9673]", - "Cow [NCBITaxon:9913]", - "Dog [NCBITaxon:9615]", - "Lion [NCBITaxon:9689]", - "Mink [NCBITaxon:452646]", - "Pangolin [NCBITaxon:9973]", - "Pig [NCBITaxon:9825]", - "Pigeon [NCBITaxon:8930]", - "Tiger [NCBITaxon:9694]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001386", - "type": "string", - "description": "The commonly used name of the host.", - "examples": [ - "Human [NCBITaxon:9606]" - ], - "classification": "Host information", - "label": "Host", - "fill_mode": "batch" - }, - "host_residence_country": { - "Enums": [ - "Afghanistan [GAZ:00006882]", - "Albania [GAZ:00002953]", - "Algeria [GAZ:00000563]", - "American Samoa [GAZ:00003957]", - "Andorra [GAZ:00002948]", - "Angola [GAZ:00001095]", - "Anguilla [GAZ:00009159]", - "Antarctica [GAZ:00000462]", - "Antigua and Barbuda [GAZ:00006883]", - "Argentina [GAZ:00002928]", - "Armenia [GAZ:00004094]", - "Aruba [GAZ:00004025]", - "Ashmore and Cartier Islands [GAZ:00005901]", - "Australia [GAZ:00000463]", - "Austria [GAZ:00002942]", - "Azerbaijan [GAZ:00004941]", - "Bahamas [GAZ:00002733]", - "Bahrain [GAZ:00005281]", - "Baker Island [GAZ:00007117]", - "Bangladesh [GAZ:00003750]", - "Barbados [GAZ:00001251]", - "Bassas da India [GAZ:00005810]", - "Belarus [GAZ:00006886]", - "Belgium [GAZ:00002938]", - "Belize [GAZ:00002934]", - "Benin [GAZ:00000904]", - "Bermuda [GAZ:00001264]", - "Bhutan [GAZ:00003920]", - "Bolivia [GAZ:00002511]", - "Borneo [GAZ:00025355]", - "Bosnia and Herzegovina [GAZ:00006887]", - "Botswana [GAZ:00001097]", - "Bouvet Island [GAZ:00001453]", - "Brazil [GAZ:00002828]", - "British Virgin Islands [GAZ:00003961]", - "Brunei [GAZ:00003901]", - "Bulgaria [GAZ:00002950]", - "Burkina Faso [GAZ:00000905]", - "Burundi [GAZ:00001090]", - "Cambodia [GAZ:00006888]", - "Cameroon [GAZ:00001093]", - "Canada [GAZ:00002560]", - "Cape Verde [GAZ:00001227]", - "Cayman Islands [GAZ:00003986]", - "Central African Republic [GAZ:00001089]", - "Chad [GAZ:00000586]", - "Chile [GAZ:00002825]", - "China [GAZ:00002845]", - "Christmas Island [GAZ:00005915]", - "Clipperton Island [GAZ:00005838]", - "Cocos Islands [GAZ:00009721]", - "Colombia [GAZ:00002929]", - "Comoros [GAZ:00005820]", - "Cook Islands [GAZ:00053798]", - "Coral Sea Islands [GAZ:00005917]", - "Costa Rica [GAZ:00002901]", - "Cote d'Ivoire [GAZ:00000906]", - "Croatia [GAZ:00002719]", - "Cuba [GAZ:00003762]", - "Curacao [GAZ:00012582]", - "Cyprus [GAZ:00004006]", - "Czech Republic [GAZ:00002954]", - "Democratic Republic of the Congo [GAZ:00001086]", - "Denmark [GAZ:00005852]", - "Djibouti [GAZ:00000582]", - "Dominica [GAZ:00006890]", - "Dominican Republic [GAZ:00003952]", - "Ecuador [GAZ:00002912]", - "Egypt [GAZ:00003934]", - "El Salvador [GAZ:00002935]", - "Equatorial Guinea [GAZ:00001091]", - "Eritrea [GAZ:00000581]", - "Estonia [GAZ:00002959]", - "Eswatini [GAZ:00001099]", - "Ethiopia [GAZ:00000567]", - "Europa Island [GAZ:00005811]", - "Falkland Islands (Islas Malvinas) [GAZ:00001412]", - "Faroe Islands [GAZ:00059206]", - "Fiji [GAZ:00006891]", - "Finland [GAZ:00002937]", - "France [GAZ:00003940]", - "French Guiana [GAZ:00002516]", - "French Polynesia [GAZ:00002918]", - "French Southern and Antarctic Lands [GAZ:00003753]", - "Gabon [GAZ:00001092]", - "Gambia [GAZ:00000907]", - "Gaza Strip [GAZ:00009571]", - "Georgia [GAZ:00004942]", - "Germany [GAZ:00002646]", - "Ghana [GAZ:00000908]", - "Gibraltar [GAZ:00003987]", - "Glorioso Islands [GAZ:00005808]", - "Greece [GAZ:00002945]", - "Greenland [GAZ:00001507]", - "Grenada [GAZ:02000573]", - "Guadeloupe [GAZ:00067142]", - "Guam [GAZ:00003706]", - "Guatemala [GAZ:00002936]", - "Guernsey [GAZ:00001550]", - "Guinea [GAZ:00000909]", - "Guinea-Bissau [GAZ:00000910]", - "Guyana [GAZ:00002522]", - "Haiti [GAZ:00003953]", - "Heard Island and McDonald Islands [GAZ:00009718]", - "Honduras [GAZ:00002894]", - "Hong Kong [GAZ:00003203]", - "Howland Island [GAZ:00007120]", - "Hungary [GAZ:00002952]", - "Iceland [GAZ:00000843]", - "India [GAZ:00002839]", - "Indonesia [GAZ:00003727]", - "Iran [GAZ:00004474]", - "Iraq [GAZ:00004483]", - "Ireland [GAZ:00002943]", - "Isle of Man [GAZ:00052477]", - "Israel [GAZ:00002476]", - "Italy [GAZ:00002650]", - "Jamaica [GAZ:00003781]", - "Jan Mayen [GAZ:00005853]", - "Japan [GAZ:00002747]", - "Jarvis Island [GAZ:00007118]", - "Jersey [GAZ:00001551]", - "Johnston Atoll [GAZ:00007114]", - "Jordan [GAZ:00002473]", - "Juan de Nova Island [GAZ:00005809]", - "Kazakhstan [GAZ:00004999]", - "Kenya [GAZ:00001101]", - "Kerguelen Archipelago [GAZ:00005682]", - "Kingman Reef [GAZ:00007116]", - "Kiribati [GAZ:00006894]", - "Kosovo [GAZ:00011337]", - "Kuwait [GAZ:00005285]", - "Kyrgyzstan [GAZ:00006893]", - "Laos [GAZ:00006889]", - "Latvia [GAZ:00002958]", - "Lebanon [GAZ:00002478]", - "Lesotho [GAZ:00001098]", - "Liberia [GAZ:00000911]", - "Libya [GAZ:00000566]", - "Liechtenstein [GAZ:00003858]", - "Line Islands [GAZ:00007144]", - "Lithuania [GAZ:00002960]", - "Luxembourg [GAZ:00002947]", - "Macau [GAZ:00003202]", - "Madagascar [GAZ:00001108]", - "Malawi [GAZ:00001105]", - "Malaysia [GAZ:00003902]", - "Maldives [GAZ:00006924]", - "Mali [GAZ:00000584]", - "Malta [GAZ:00004017]", - "Marshall Islands [GAZ:00007161]", - "Martinique [GAZ:00067143]", - "Mauritania [GAZ:00000583]", - "Mauritius [GAZ:00003745]", - "Mayotte [GAZ:00003943]", - "Mexico [GAZ:00002852]", - "Micronesia [GAZ:00005862]", - "Midway Islands [GAZ:00007112]", - "Moldova [GAZ:00003897]", - "Monaco [GAZ:00003857]", - "Mongolia [GAZ:00008744]", - "Montenegro [GAZ:00006898]", - "Montserrat [GAZ:00003988]", - "Morocco [GAZ:00000565]", - "Mozambique [GAZ:00001100]", - "Myanmar [GAZ:00006899]", - "Namibia [GAZ:00001096]", - "Nauru [GAZ:00006900]", - "Navassa Island [GAZ:00007119]", - "Nepal [GAZ:00004399]", - "Netherlands [GAZ:00002946]", - "New Caledonia [GAZ:00005206]", - "New Zealand [GAZ:00000469]", - "Nicaragua [GAZ:00002978]", - "Niger [GAZ:00000585]", - "Nigeria [GAZ:00000912]", - "Niue [GAZ:00006902]", - "Norfolk Island [GAZ:00005908]", - "North Korea [GAZ:00002801]", - "North Macedonia [GAZ:00006895]", - "North Sea [GAZ:00002284]", - "Northern Mariana Islands [GAZ:00003958]", - "Norway [GAZ:00002699]", - "Oman [GAZ:00005283]", - "Pakistan [GAZ:00005246]", - "Palau [GAZ:00006905]", - "Panama [GAZ:00002892]", - "Papua New Guinea [GAZ:00003922]", - "Paracel Islands [GAZ:00010832]", - "Paraguay [GAZ:00002933]", - "Peru [GAZ:00002932]", - "Philippines [GAZ:00004525]", - "Pitcairn Islands [GAZ:00005867]", - "Poland [GAZ:00002939]", - "Portugal [GAZ:00004126]", - "Puerto Rico [GAZ:00006935]", - "Qatar [GAZ:00005286]", - "Republic of the Congo [GAZ:00001088]", - "Reunion [GAZ:00003945]", - "Romania [GAZ:00002951]", - "Ross Sea [GAZ:00023304]", - "Russia [GAZ:00002721]", - "Rwanda [GAZ:00001087]", - "Saint Helena [GAZ:00000849]", - "Saint Kitts and Nevis [GAZ:00006906]", - "Saint Lucia [GAZ:00006909]", - "Saint Pierre and Miquelon [GAZ:00003942]", - "Saint Martin [GAZ:00005841]", - "Saint Vincent and the Grenadines [GAZ:02000565]", - "Samoa [GAZ:00006910]", - "San Marino [GAZ:00003102]", - "Sao Tome and Principe [GAZ:00006927]", - "Saudi Arabia [GAZ:00005279]", - "Senegal [GAZ:00000913]", - "Serbia [GAZ:00002957]", - "Seychelles [GAZ:00006922]", - "Sierra Leone [GAZ:00000914]", - "Singapore [GAZ:00003923]", - "Sint Maarten [GAZ:00012579]", - "Slovakia [GAZ:00002956]", - "Slovenia [GAZ:00002955]", - "Solomon Islands [GAZ:00005275]", - "Somalia [GAZ:00001104]", - "South Africa [GAZ:00001094]", - "South Georgia and the South Sandwich Islands [GAZ:00003990]", - "South Korea [GAZ:00002802]", - "South Sudan [GAZ:00233439]", - "Spain [GAZ:00003936]", - "Spratly Islands [GAZ:00010831]", - "Sri Lanka [GAZ:00003924]", - "State of Palestine [GAZ:00002475]", - "Sudan [GAZ:00000560]", - "Suriname [GAZ:00002525]", - "Svalbard [GAZ:00005396]", - "Swaziland [GAZ:00001099]", - "Sweden [GAZ:00002729]", - "Switzerland [GAZ:00002941]", - "Syria [GAZ:00002474]", - "Taiwan [GAZ:00005341]", - "Tajikistan [GAZ:00006912]", - "Tanzania [GAZ:00001103]", - "Thailand [GAZ:00003744]", - "Timor-Leste [GAZ:00006913]", - "Togo [GAZ:00000915]", - "Tokelau [GAZ:00260188]", - "Tonga [GAZ:00006916]", - "Trinidad and Tobago [GAZ:00003767]", - "Tromelin Island [GAZ:00005812]", - "Tunisia [GAZ:00000562]", - "Turkey [GAZ:00000558]", - "Turkmenistan [GAZ:00005018]", - "Turks and Caicos Islands [GAZ:00003955]", - "Tuvalu [GAZ:00009715]", - "USA [GAZ:00002459]", - "Uganda [GAZ:00001102]", - "Ukraine [GAZ:00002724]", - "United Arab Emirates [GAZ:00005282]", - "United Kingdom [GAZ:00002637]", - "Uruguay [GAZ:00002930]", - "Uzbekistan [GAZ:00004979]", - "Vanuatu [GAZ:00006918]", - "Venezuela [GAZ:00002931]", - "Viet Nam [GAZ:00003756]", - "Virgin Islands [GAZ:00003959]", - "Wake Island [GAZ:00007111]", - "Wallis and Futuna [GAZ:00007191]", - "West Bank [GAZ:00009572]", - "Western Sahara [GAZ:00000564]", - "Yemen [GAZ:00005284]", - "Zambia [GAZ:00001107]", - "Zimbabwe [GAZ:00001106]", + }, + "environmental_site": { + "Enums": [ + "Acute care facility [ENVO:03501135]", + "Animal house [ENVO:00003040]", + "Bathroom [ENVO:01000422]", + "Clinical assessment centre [ENVO:03501136]", + "Conference venue [ENVO:03501127]", + "Corridor [ENVO:03501121]", + "Daycare [ENVO:01000927]", + "Emergency room (ER) [ENVO:03501145]", + "Family practice clinic [ENVO:03501186]", + "Group home [ENVO:03501196]", + "Homeless shelter [ENVO:03501133]", + "Hospital [ENVO:00002173]", + "Intensive Care Unit (ICU) [ENVO:03501152]", + "Long Term Care Facility [ENVO:03501194]", + "Patient room [ENVO:03501180]", + "Prison [ENVO:03501204]", + "Production Facility [ENVO:01000536]", + "School [ENVO:03501130]", + "Sewage Plant [ENVO:00003043]", + "Subway train [ENVO:03501109]", + "Wet market [ENVO:03501198]", "Not Applicable [GENEPIO:0001619]", "Not Collected [GENEPIO:0001620]", "Not Provided [GENEPIO:0001668]", "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "GENEPIO:0001396", + "ontology": "GENEPIO:0001232", "type": "string", - "description": "The country where the host resides.", + "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", "examples": [ - "South Africa [GAZ:00001094]" + "Hospital [ENVO:00002173]" + ], + "classification": "Sample collection and processing", + "label": "Environmental System", + "fill_mode": "batch" + }, + "collection_device": { + "Enums": [ + "Air filter [ENVO:00003968]", + "Blood Collection Tube [OBI:0002859]", + "Bronchoscope [OBI:0002826]", + "Collection Container [OBI:0002088]", + "Collection Cup [GENEPIO:0100026]", + "Fibrobronchoscope Brush [OBI:0002825]", + "Filter [GENEPIO:0100103]", + "Fine Needle [OBI:0002827]", + "Microcapillary tube [OBI:0002858]", + "Micropipette [OBI:0001128]", + "Needle [OBI:0000436]", + "Serum Collection Tube [OBI:0002860]", + "Sputum Collection Tube [OBI:0002861]", + "Suction Catheter [OBI:0002831]", + "Swab [GENEPIO:0100027]", + "Urine Collection Tube [OBI:0002862]", + "Virus Transport Medium [OBI:0002866]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001234", + "type": "string", + "description": "The instrument or container used to collect the sample e.g. swab.", + "examples": [ + "Swab [GENEPIO:0100027]" ], - "classification": "Host Information", - "label": "Host residence country", + "classification": "Sample collection and processing", + "label": "Collection Device", "fill_mode": "batch" }, - "outbreak": { + "tax_id": { "examples": [ - "Date, Location e.g. type of gathering, Family cluster, etc." + "probably 2697049 in all cases" ], - "ontology": "GENEPIO:0001417", + "ontology": "GENEPIO_0001724", "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "classification": "Host information", - "label": "Outbreak Exposure Event Location", + "description": "The NCBITaxon identifier for the organism being sequenced.", + "classification": "Sample collection and processing", + "label": "Tax ID", "fill_mode": "batch" }, - "additional_host_information": { + "center_name": { "examples": [ - "e.g. Patient infected while traveling in …." + " KAROLINSKA INSITUTET" ], - "ontology": "GENEPIO_0001268", + "ontology": "NCIT_C19983", "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "classification": "Host information", - "label": "Additional Host Information", + "description": "The name of the institution", + "classification": "Sample collection and processing", + "label": "Center Name", "fill_mode": "batch" }, - "host_ethnicity": { - "ontology": "GECKO:0000061", + "host_common_name": { + "Enums": [ + "Human [NCBITaxon:9606]", + "Bat [NCBITaxon:9397]", + "Cat [NCBITaxon:9685]", + "Chicken [NCBITaxon:9031]", + "Civet [NCBITaxon:9673]", + "Cow [NCBITaxon:9913]", + "Dog [NCBITaxon:9615]", + "Lion [NCBITaxon:9689]", + "Mink [NCBITaxon:452646]", + "Pangolin [NCBITaxon:9973]", + "Pig [NCBITaxon:9825]", + "Pigeon [NCBITaxon:8930]", + "Tiger [NCBITaxon:9694]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001386", "type": "string", - "description": "The self-identified ethnicity(ies) of the host.", + "description": "The commonly used name of the host.", "examples": [ - "Indigenous, European" + "Human [NCBITaxon:9606]" ], - "classification": "Host Information", - "label": "Host ethnicity", + "classification": "Host information", + "label": "Host", "fill_mode": "batch" }, "purpose_of_sequencing": { @@ -1682,7 +945,7 @@ "label": "Purpose of Sequencing", "fill_mode": "batch" }, - "purpose_of_sampling": { + "purpose_sampling": { "Enums": [ "Cluster/Outbreak Investigation [GENEPIO:0100001]", "Diagnostic Testing [GENEPIO:0100002]", @@ -1704,16 +967,6 @@ "label": "Purpose of sampling", "fill_mode": "batch" }, - "purpose_of_sampling_details": { - "ontology": "GENEPIO:0001200", - "type": "string", - "description": "Further details pertaining to the reason the sample was collected.", - "examples": [ - "Screening of bat specimens in museum collections." - ], - "label": "Purpose of sampling details", - "fill_mode": "batch" - }, "sequencing_sample_id": { "examples": [ "" @@ -1725,48 +978,6 @@ "label": "Sample ID given for sequencing", "fill_mode": "sample" }, - "passage_details": { - "examples": [ - "" - ], - "ontology": "0", - "type": [ - "string", - "number" - ], - "description": "If the information is unknown or can not be shared, leave blank.", - "classification": "Database Identifiers", - "label": "Passage Details", - "fill_mode": "batch" - }, - "purpose_of_sequencing_details": { - "Enums": [ - "Screened for S gene target failure (S dropout)", - "Screened for mink variants", - "Screened for B.1.1.7 variant", - "Screened for B.1.135 variant", - "Screened for P.1 variant", - "Screened due to travel history", - "Screened due to close contact with infected individual", - "Assessing public health control measures", - "Determining early introductions and spread", - "Investigating airline-related exposures", - "Investigating temporary foreign worker", - "Investigating remote regions", - "Investigating health care workers", - "Investigating schools/universities", - "Investigating reinfection" - ], - "ontology": "GENEPIO:0001446", - "type": "string", - "description": "The description of why the sample was sequenced providing specific details.", - "examples": [ - "Screened for S gene target failure (S dropout)" - ], - "classification": "Sequencing", - "label": "Purpose Of Sequencing Details", - "fill_mode": "batch" - }, "sequencing_date": { "examples": [ "4/26/2021" @@ -1801,31 +1012,6 @@ "label": "Commercial All-in-one library kit", "fill_mode": "batch" }, - "library_name": { - "examples": [ - "e.g PAIRED" - ], - "ontology": "GENEPIO_0001995", - "type": "string", - "description": "The submitter's name for this library.", - "classification": "Sequencing", - "label": "Library Name", - "table": [ - "experiments" - ], - "fill_mode": "batch" - }, - "library_id": { - "examples": [ - "XYZ_123345" - ], - "ontology": "GENEPIO:0001448", - "type": "string", - "description": "The user-specified identifier for the library prepared for sequencing.", - "classification": "Sequencing", - "label": "Library Id", - "fill_mode": "batch" - }, "enrichment_protocol": { "examples": [ "" @@ -1881,28 +1067,6 @@ "label": "Enrichment panel/assay version", "fill_mode": "batch" }, - "amplicon_size": { - "examples": [ - "300bp" - ], - "ontology": "GENEPIO:0001449", - "type": "string", - "description": "The length of the amplicon generated by PCR amplification.", - "classification": "Sequencing", - "label": "Amplicon Size", - "fill_mode": "batch" - }, - "was_phix_used?": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Sequencing", - "label": "Was Phix Used", - "fill_mode": "batch" - }, "number_of_samples_in_run": { "examples": [ "" @@ -1958,50 +1122,6 @@ "label": "Library Preparation Kit", "fill_mode": "batch" }, - "flow_cell_barcode": { - "examples": [ - "FAB06069" - ], - "ontology": "GENEPIO:0001451", - "type": "string", - "description": "The barcode of the flow cell used for sequencing.", - "classification": "Sequencing", - "label": "Flow Cell Barcode", - "fill_mode": "batch" - }, - "sequencing_protocol_name": { - "examples": [ - "1D_DNA_MinION, ARTIC Network Protocol V3" - ], - "ontology": "GENEPIO:0001453", - "type": "string", - "description": "The name and version number of the sequencing protocol used.", - "classification": "Sequencing", - "label": "Sequencing Protocol Name", - "fill_mode": "batch" - }, - "sequencing_protocol": { - "examples": [ - "Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits." - ], - "ontology": "GENEPIO:0001454", - "type": "string", - "description": "The protocol used to generate the sequence.", - "classification": "Sequencing", - "label": "Sequencing Protocol", - "fill_mode": "batch" - }, - "sequencing_kit_number": { - "examples": [ - "AB456XYZ789" - ], - "ontology": "GENEPIO:0001455", - "type": "string", - "description": "The manufacturer's kit number.", - "classification": "Sequencing", - "label": "Sequencing Kit Number", - "fill_mode": "batch" - }, "amplicon_pcr_primer_scheme": { "examples": [ "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv" @@ -2068,29 +1188,7 @@ "label": "Library Layout", "fill_mode": "batch" }, - "nominal_length ": { - "examples": [ - "350" - ], - "ontology": "GENEPIO_0000076", - "type": "string", - "description": "", - "classification": "Sequencing", - "label": "Nominal Length", - "fill_mode": "batch" - }, - "raw_sequence_data_processing_method": { - "examples": [ - "Porechop 0.2.3" - ], - "ontology": "GENEPIO:0001458", - "type": "string", - "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", - "classification": "Bioinformatics and QC metrics", - "label": "Raw sequence data processin method", - "fill_mode": "batch" - }, - "dehosting_method": { + "dehosting_software_name": { "examples": [ "Nanostripper" ], @@ -2101,15 +1199,15 @@ "label": "Dehosting Method", "fill_mode": "batch" }, - "personal_protective_equipment": { + "dehosting_software_version": { "examples": [ - "mask" + "2.4.1" ], - "ontology": "NCIT:C173748", + "ontology": "0", "type": "string", - "description": "Use of personal protective equipment, such as gloves, gowns, during any type of exposure.", - "classification": "Sample collection and processing", - "label": "Personal protective equipment", + "description": "The method version used to remove host reads from the pathogen sequence.", + "classification": "Bioinformatics and QC metrics", + "label": "Dehosting Method Version", "fill_mode": "batch" }, "assembly": { @@ -2145,7 +1243,7 @@ "label": "Assambly params", "fill_mode": "batch" }, - "variant_calling": { + "variant_calling_software_name": { "examples": [ "" ], @@ -2156,6 +1254,17 @@ "label": "Variant Calling", "fill_mode": "batch" }, + "variant_calling_software_version": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "classification": "Bioinformatics and QC metrics", + "label": "Variant Calling Version", + "fill_mode": "batch" + }, "if_variant_calling_other": { "examples": [ "" @@ -2244,7 +1353,7 @@ "label": "Consensus sequence software version", "fill_mode": "batch" }, - "consensus_criteria": { + "consensus_params": { "examples": [ "" ], @@ -2252,7 +1361,7 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Consensus criteria", + "label": "Consensus Params", "fill_mode": "batch" }, "quality_control_metrics": { @@ -2288,17 +1397,6 @@ "label": "Depth of coverage threshold", "fill_mode": "batch" }, - "file_type": { - "examples": [ - "" - ], - "ontology": "", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "", - "fill_mode": "batch" - }, "sequence_file_R1_fastq": { "examples": [ "ABC123_S1_L001_R1_001.fastq.gz" @@ -2398,18 +1496,7 @@ "label": "Ns per 100 kbp", "fill_mode": "batch" }, - "reference_genome_accession": { - "examples": [ - "NC_045512.2" - ], - "ontology": "GENEPIO:0001485", - "type": "string", - "description": "A persistent, unique identifier of a genome database entry.", - "classification": "Bioinformatics and QC metrics", - "label": "Reference genome accession", - "fill_mode": "batch" - }, - "bioinformatics_protocol": { + "bioinformatics_protocol_software_name": { "examples": [ "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" ], @@ -2431,7 +1518,7 @@ "label": "If bioinformatic protocol Is Other, Specify", "fill_mode": "batch" }, - "bioinformatic_protocol_version": { + "bioinformatics_protocol_software_version": { "examples": [ "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" ], @@ -2442,7 +1529,7 @@ "label": "bioinformatics protocol version", "fill_mode": "batch" }, - "commercial/open-source/both": { + "commercial_open_source_both": { "examples": [ "" ], @@ -2453,25 +1540,26 @@ "label": "Commercial/Open-source/both", "fill_mode": "batch" }, - "sample_plan_name": { - "ontology": "GENEPIO:0100285", - "type": "string", - "description": "The name of the sample plan implemented for sample collection.", + "preprocessing_software_name": { "examples": [ - "CanCOGeN Sampling Strategy 1.0" + "" ], - "label": "Sample plan name", + "ontology": "MS_1002386", + "type": "string", + "description": "", + "classification": "Bioinformatics and QC metrics", + "label": "Preprocessing", "fill_mode": "batch" }, - "preprocessing": { + "preprocessing_software_version": { "examples": [ "" ], - "ontology": "MS_1002386", + "ontology": "0", "type": "string", "description": "", "classification": "Bioinformatics and QC metrics", - "label": "Preprocessing", + "label": "Preprocessing Version", "fill_mode": "batch" }, "if_preprocessing_other": { @@ -2496,7 +1584,7 @@ "label": "Preprocessing params", "fill_mode": "batch" }, - "mapping": { + "mapping_software_name": { "examples": [ "" ], @@ -2507,6 +1595,17 @@ "label": "Mapping", "fill_mode": "batch" }, + "mapping_software_version": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "classification": "Bioinformatics and QC metrics", + "label": "Mapping Version", + "fill_mode": "batch" + }, "if_mapping_other": { "examples": [ "" @@ -2573,17 +1672,6 @@ "label": "Lineage/clade analysis software version", "fill_mode": "batch" }, - "design_description": { - "examples": [ - "" - ], - "ontology": "NCIT:C147139", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "", - "fill_mode": "batch" - }, "isolate_sample_id": { "examples": [ "" @@ -2706,7 +1794,7 @@ "label": "%unmapped", "fill_mode": "batch" }, - "per_genome _greater_10x": { + "per_genome_greater_10x": { "examples": [ "" ], @@ -2717,7 +1805,7 @@ "label": "% genome greater 10x", "fill_mode": "batch" }, - "median_depth_of_coverage_value": { + "mean_depth_of_coverage_value": { "examples": [ "" ], @@ -2761,17 +1849,6 @@ "label": "Number of variants with effect", "fill_mode": "batch" }, - "diagnostic_pcr_protocol_1": { - "examples": [ - "PCREGene 2.0" - ], - "ontology": "GENEPIO:0001508", - "type": "string", - "description": "The name and version number of the protocol used for diagnostic marker amplification.", - "classification": "Pathogen diagnostic testing", - "label": "Diagnostic Pcr Protocol 1", - "fill_mode": "batch" - }, "diagnostic_pcr_Ct_value_1": { "examples": [ "21" @@ -2834,17 +1911,6 @@ "label": "Gene Name 2", "fill_mode": "batch" }, - "diagnostic_pcr_protocol_2": { - "examples": [ - "PCRRdRpGene 3.0" - ], - "ontology": "GENEPIO:0001511", - "type": "string", - "description": "The name and version number of the protocol used for diagnostic marker amplification.", - "classification": "Pathogen diagnostic testing", - "label": "Diagnostic Pcr Protocol 2", - "fill_mode": "batch" - }, "analysis_date": { "examples": [ "e.g 2020-08-07" @@ -2880,7 +1946,7 @@ "label": "Diagnostic Pcr Ct Value-2", "fill_mode": "batch" }, - "analysis_author": { + "analysis_authors": { "examples": [ "" ], From 815bae1f418b64d933ef21951e9703b93ccae43d Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 17 May 2022 16:22:09 +0200 Subject: [PATCH 0460/1454] finished v0 read_bioinfo_metadta --- relecov_tools/conf/configuration.json | 29 ++++--- relecov_tools/read_bioinfo_metadata.py | 100 ++++++++++++++----------- 2 files changed, 75 insertions(+), 54 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index d885c7bf..129c047f 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -97,17 +97,24 @@ "lineage_analysis_software_version": "4.0.6", "if_lineage_identification_other": "None" }, - "mapping_illumina_tab_field_list": [ - "Lineage", - "Variantsinconsensusx10", - "Coverage>10x(%)", - "%readshost", - "%readsvirus", - "%unmapedreads", - "%Ns10x", - "medianDPcoveragevirus", - "Variantsinconsensusx10", - "MissenseVariants" + "mapping_illumina_tab_field_list": { + "lineage_name": "Lineage", + "variant_designation": "Variantsinconsensusx10", + "per_qc_filtered": "Coverage>10x(%)", + "per_reads_host": "%readshost", + "per_reads_virus": "%readsvirus", + "per_unmapped": "%unmapedreads", + "per_Ns": "%Ns10x", + "median_depth_of_coverage_value": "medianDPcoveragevirus", + "number_of_variants_AF_greater_75percent": "Variantsinconsensusx10", + "number_of_variants_with_effect": "MissenseVariants" + }, + "files_read_bioinfo_metadata": [ + "mapping_illumina.tab", + "summary_variants_metrics_mqc.csv", + "variants_long_table.csv", + "consensus_genome_length.csv", + "software_versions.yml" ], "tool": { "tool_name": "ena-upload-cli", diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 178f71fa..6395d06c 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -4,12 +4,13 @@ # from importlib.resources import path import logging +from wsgiref.simple_server import software_version import rich.console from itertools import islice import pandas as pd - +import yaml import openpyxl import os @@ -67,6 +68,10 @@ def bioinfo_parse(self, file_name): "relecov_bioinfo_metadata" ) c = 0 + self.files_read_bioinfo_metadata = config_json.get_configuration( + "files_read_bioinfo_metadata" + ) + mapping_illumina_tab_path = os.path.join( self.input_folder, "mapping_illumina.tab" ) @@ -76,9 +81,31 @@ def bioinfo_parse(self, file_name): variants_long_table_path = os.path.join( self.input_folder, "variants_long_table.csv" ) + consensus_genome_length_path = os.path.join( + self.input_folder, "consensus_genome_length.csv" + ) + software_versions_path = os.path.join( + self.input_folder, "software_versions.yml" + ) + md5_info_path = os.path.join( + self.input_folder, + "md5sum_MiSeq_GEN_267_20220208_ICasas.md5", # como hacer esto general para los servicios + ) + mapping_illumina_tab = pd.read_csv(mapping_illumina_tab_path, sep="\t") summary_variants_metrics = pd.read_csv(summary_variants_metrics_path, sep=",") variants_long_table = pd.read_csv(variants_long_table_path, sep=",") + consensus_genome_length = pd.read_csv( + consensus_genome_length_path, header=None, sep="," + ) + md5_info = pd.read_csv(md5_info_path, header=None, sep=",") + + with open(software_versions_path) as file: + software_versions = yaml.load(file, Loader=yaml.FullLoader) + + self.mapping_illumina_tab_field_list = config_json.get_configuration( + "mapping_illumina_tab_field_list" + ) for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): # row = ws_metadata_lab[5] sample_name = row[5] @@ -94,55 +121,42 @@ def bioinfo_parse(self, file_name): bioinfo_dict["consensus_sequence_filepath"] = self.input_folder bioinfo_dict["long_table_path"] = self.input_folder # fields from mapping_illumina.tab - bioinfo_dict["linage_name"] = mapping_illumina_tab["Lineage"][c] - bioinfo_dict["variant_designation"] = mapping_illumina_tab[ - "Variantsinconsensusx10" - ][c] - bioinfo_dict["per_qc_filtered"] = mapping_illumina_tab["Coverage>10x(%)"][c] - # bioinfo_dict["per_reads_host"] = mapping_illumina_tab["%readshost"][c] - # bioinfo_dict["per_reads_virus"] = mapping_illumina_tab["%readsvirus"][c] - # bioinfo_dict["per_unmapped"] = mapping_illumina_tab["%unmapedreads"][c] - bioinfo_dict["per_Ns"] = mapping_illumina_tab["%Ns10x"][c] - bioinfo_dict["median_depth_of_coverage_value"] = mapping_illumina_tab[ - "medianDPcoveragevirus" - ][c] - bioinfo_dict[ - "number_of_variants_AF_greater_75percent" - ] = mapping_illumina_tab["Variantsinconsensusx10"][c] - bioinfo_dict["number_of_variants_with_effect"] = mapping_illumina_tab[ - "MissenseVariants" - ][c] + for key in self.mapping_illumina_tab_field_list.keys(): + bioinfo_dict[key] = mapping_illumina_tab[ + self.mapping_illumina_tab_field_list[key] + ][c] # fields from summary_variants_metrics_mqc.csv bioinfo_dict["number_of_base_pairs_sequenced"] = ( summary_variants_metrics["# Input reads"][c] * 2 - ) # REVISAR SI ES ASÍ CON SARA + ) bioinfo_dict["ns_per_100_kbp"] = summary_variants_metrics[ "# Ns per 100kb consensus" ][c] - # FALTA "consensus_genome_length": "", script que cuente el numero de nucleotidos tamaño del fasta # fields from variants_long_table.csv bioinfo_dict["reference_genome_accession"] = variants_long_table["CHROM"][c] - bioinfo_dict["consensus_sequence_name"] = str(sample_name).join( - ".consensus.fa" + bioinfo_dict["consensus_genome_length"] = consensus_genome_length.iloc[c, 0] + bioinfo_dict["consensus_sequence_name"] = md5_info.iloc[c, 0][0:32] + bioinfo_dict["consensus_sequence_name_md5"] = md5_info.iloc[c, 0][34:60] + + bioinfo_dict["dehosting_method_software_version"] = list( + software_versions["KRAKEN2_KRAKEN2"].values() + ) + bioinfo_dict["variant_calling_software_version"] = list( + software_versions["IVAR_VARIANTS"].values() + ) + bioinfo_dict["consensus_sequence_software_version"] = list( + software_versions["BCFTOOLS_CONSENSUS"].values() ) - c = +1 - import pdb - pdb.set_trace() - """ - f = open(path_illumina_tab, "r") - lines = f.readlines() - lineages = [] - lineage_index = lines[0].index("Lineage") - for line in range(1, len(lines)) - line_split = lines.split("\t") - lineages.append(line_split[lineage_index]) - # "dehosting_method_software_version" # NO HARCODED - # "variant_calling_software_version" # NO HARCODED - # "consensus_sequence_software_version" # NO HARCODED - # "bioinformatics_protocol_software_version" # NO HARCODED - # "preprocessing_software_version"# NO HARCODED - # "mapping_software_version" # NO HARCODED - # bioinfo_dict["consensus_sequence_name"]= - # bioinfo_dict["consensus_sequence_name_md5"]= - """ + bioinfo_dict[ + "bioinformatics_protocol_software_version" + ] = software_versions["Workflow"]["nf-core/viralrecon"] + + bioinfo_dict["preprocessing_software_version"] = list( + software_versions["FASTP"].values() + ) + bioinfo_dict["mapping_software_version"] = software_versions[ + "BOWTIE2_ALIGN" + ].values() + + c = +1 From 15d1449b04cd184c45be5df0581740412252767f Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 19 May 2022 13:44:53 +0200 Subject: [PATCH 0461/1454] fixing lintin --- relecov_tools/read_bioinfo_metadata.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 6395d06c..9dc7e226 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -4,7 +4,8 @@ # from importlib.resources import path import logging -from wsgiref.simple_server import software_version + +# from wsgiref.simple_server import software_version import rich.console From 2a2744cb32dc8451063d0a4806d0734007a983e3 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 19 May 2022 15:19:16 +0200 Subject: [PATCH 0462/1454] added json dumpt and bioinfo_list --- relecov_tools/read_bioinfo_metadata.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 9dc7e226..5e35209e 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -2,10 +2,8 @@ # from itertools import islice -# from importlib.resources import path import logging - -# from wsgiref.simple_server import software_version +import json import rich.console @@ -107,6 +105,7 @@ def bioinfo_parse(self, file_name): self.mapping_illumina_tab_field_list = config_json.get_configuration( "mapping_illumina_tab_field_list" ) + bioinfo_list = [] for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): # row = ws_metadata_lab[5] sample_name = row[5] @@ -159,5 +158,10 @@ def bioinfo_parse(self, file_name): bioinfo_dict["mapping_software_version"] = software_versions[ "BOWTIE2_ALIGN" ].values() - + bioinfo_list[c] = bioinfo_dict c = +1 + + output_path = os.join(self.output_folder, "bioinfo_metadata.json") + + with open(output_path, "w") as jsonFile: + json.dump(bioinfo_dict, jsonFile) From 0601ad15386e01c1c4936cc8bd6306c277652021 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 19 May 2022 16:49:31 +0200 Subject: [PATCH 0463/1454] changes in excel --- .../example_data/METADATA_LAB_TEST.xlsx | Bin 490183 -> 493368 bytes 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software_versions[ "BOWTIE2_ALIGN" ].values() + bioinfo_dict[""] + bioinfo_list[c] = bioinfo_dict c = +1 output_path = os.join(self.output_folder, "bioinfo_metadata.json") with open(output_path, "w") as jsonFile: - json.dump(bioinfo_dict, jsonFile) + json.dump(bioinfo_list, jsonFile) From 5cc2cc797efb928890d6c96c64bfa9b2be4bc0f9 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 20 May 2022 12:39:03 +0200 Subject: [PATCH 0464/1454] added test cases --- relecov_tools/test/test_cases.txt | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/test/test_cases.txt b/relecov_tools/test/test_cases.txt index 5b90e570..69fb7dbf 100644 --- a/relecov_tools/test/test_cases.txt +++ b/relecov_tools/test/test_cases.txt @@ -6,3 +6,5 @@ relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -d GISAID -o /tmp relecov-tools update-db -i http://iskylims.isciiides.es/wetlab/api -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json relecov-tools update-db -i http://localhost:8001/wetlab/api -r http://localhost:8000/api -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -u admin -p Apple@123 +relecov-tools read-bioinfo-metadata -m /data/UCCT_Relecov/COD-2100-MAD-CNM/20220208/lab_metadata_20220208.xlsx -i /data/UCCT_Relecov/COD-2100-MAD-CNM/20220208/ -o /data/UCCT_Relecov/COD-2100-MAD-CNM/20220208/ +relecov-tools upload-to-ena -u Webin-60330 -p W2b3nENA%2021 -e /home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/example_data/to_ena_2.json -o /home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/test -a add -c ISCIII From 8b25b92909e49048c5d7e77a49736f22d50a2f35 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 20 May 2022 14:41:40 +0200 Subject: [PATCH 0465/1454] =?UTF-8?q?why=20the=20freaking=20json=20does=20?= =?UTF-8?q?not=20dump=3F=C2=BF=20WHYY=3F=C2=BF?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- relecov_tools/read_bioinfo_metadata.py | 43 +++++++++++++++++--------- relecov_tools/test/test_cases.txt | 2 +- 2 files changed, 29 insertions(+), 16 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 337cc170..87d72c2c 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -112,7 +112,7 @@ def bioinfo_parse(self, file_name): fastq_r1 = row[47] fastq_r2 = row[48] bioinfo_dict = {} - bioinfo_dict["sample_name"] = sample_name + bioinfo_dict["sample_name"] = str(sample_name) bioinfo_dict["fastq_r1"] = fastq_r1 bioinfo_dict["fastq_r2"] = fastq_r2 # inserting all keys from configuration.json relecov_bioinfo_metadata into bioinfo_dict @@ -126,17 +126,25 @@ def bioinfo_parse(self, file_name): self.mapping_illumina_tab_field_list[key] ][c] # fields from summary_variants_metrics_mqc.csv - bioinfo_dict["number_of_base_pairs_sequenced"] = ( - summary_variants_metrics["# Input reads"][c] * 2 + bioinfo_dict["number_of_base_pairs_sequenced"] = int( + (summary_variants_metrics["# Input reads"][c] * 2) + ) + bioinfo_dict["ns_per_100_kbp"] = int( + summary_variants_metrics["# Ns per 100kb consensus"][c] ) - bioinfo_dict["ns_per_100_kbp"] = summary_variants_metrics[ - "# Ns per 100kb consensus" - ][c] # fields from variants_long_table.csv bioinfo_dict["reference_genome_accession"] = variants_long_table["CHROM"][c] - bioinfo_dict["consensus_genome_length"] = consensus_genome_length.iloc[c, 0] - bioinfo_dict["consensus_sequence_name"] = md5_info.iloc[c, 0][0:32] - bioinfo_dict["consensus_sequence_name_md5"] = md5_info.iloc[c, 0][34:60] + bioinfo_dict["consensus_genome_length"] = int( + consensus_genome_length.iloc[c, 0] + ) + bioinfo_dict["consensus_sequence_R1_name"] = md5_info.iloc[c * 2, 0][34:60] + bioinfo_dict["consensus_sequence_R2_name"] = md5_info.iloc[c * 2 + 1, 0][ + 34:60 + ] + bioinfo_dict["consensus_sequence_R1_md5"] = md5_info.iloc[c * 2, 0][0:32] + bioinfo_dict["consensus_sequence__R2_md5"] = md5_info.iloc[c * 2 + 1, 0][ + 0:32 + ] bioinfo_dict["dehosting_method_software_version"] = list( software_versions["KRAKEN2_KRAKEN2"].values() @@ -158,12 +166,17 @@ def bioinfo_parse(self, file_name): bioinfo_dict["mapping_software_version"] = software_versions[ "BOWTIE2_ALIGN" ].values() - bioinfo_dict[""] - - bioinfo_list[c] = bioinfo_dict + bioinfo_list.append(bioinfo_dict) c = +1 - output_path = os.join(self.output_folder, "bioinfo_metadata.json") + import pdb - with open(output_path, "w") as jsonFile: - json.dump(bioinfo_list, jsonFile) + pdb.set_trace() + + json_file = "bioinfo_metadata.json" + output_path = os.path.join(self.output_folder, json_file) + + with open(output_path, "w", encoding="utf-8") as fh: + fh.write( + json.dumps(bioinfo_list, indent=4, sort_keys=True, ensure_ascii=False) + ) diff --git a/relecov_tools/test/test_cases.txt b/relecov_tools/test/test_cases.txt index 69fb7dbf..f6f2c56d 100644 --- a/relecov_tools/test/test_cases.txt +++ b/relecov_tools/test/test_cases.txt @@ -1,6 +1,6 @@ relecov-tools -l /tmp/logs.log download -u usuario_test -p U[9[Gpyu3. relecov-tools -l /tmp/logs.log download -f relecov_tools/test/sftp_config.yaml -relecov-tools read-metadata -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -s relecov_tools/example_data/samples_data_COD_test_01_20220422.json -o /tmp +relecov-tools read-lab-metadata -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -s relecov_tools/example_data/samples_data_COD_test_01_20220422.json -o /tmp relecov-tools validate -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -o /tmp relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -d ENA -o /tmp relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -d GISAID -o /tmp From d9c20584c2efeaf42a5377df5f7cfdcfefa0ad07 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 23 May 2022 10:39:14 +0200 Subject: [PATCH 0466/1454] dealing with json dump --- relecov_tools/read_bioinfo_metadata.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 87d72c2c..32cfea96 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -169,10 +169,6 @@ def bioinfo_parse(self, file_name): bioinfo_list.append(bioinfo_dict) c = +1 - import pdb - - pdb.set_trace() - json_file = "bioinfo_metadata.json" output_path = os.path.join(self.output_folder, json_file) From baf078070b3bc9df5a6491672a5ed6fc8b0ad0ce Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 23 May 2022 11:37:36 +0200 Subject: [PATCH 0467/1454] fixed read_bioinfo_metadata bug --- relecov_tools/read_bioinfo_metadata.py | 34 ++++++++++++++++---------- 1 file changed, 21 insertions(+), 13 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 32cfea96..34714d47 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -47,7 +47,7 @@ def __init__(self, metadata_file=None, input_folder=None, output_folder=None): msg="Select the input folder" ) else: - self.input_folder = output_folder + self.input_folder = input_folder if output_folder is None: self.output_folder = relecov_tools.utils.prompt_path( msg="Select the output folder" @@ -105,10 +105,12 @@ def bioinfo_parse(self, file_name): self.mapping_illumina_tab_field_list = config_json.get_configuration( "mapping_illumina_tab_field_list" ) - bioinfo_list = [] + bioinfo_list = {} + for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): # row = ws_metadata_lab[5] sample_name = row[5] + fastq_r1 = row[47] fastq_r2 = row[48] bioinfo_dict = {} @@ -126,15 +128,15 @@ def bioinfo_parse(self, file_name): self.mapping_illumina_tab_field_list[key] ][c] # fields from summary_variants_metrics_mqc.csv - bioinfo_dict["number_of_base_pairs_sequenced"] = int( + bioinfo_dict["number_of_base_pairs_sequenced"] = str( (summary_variants_metrics["# Input reads"][c] * 2) ) - bioinfo_dict["ns_per_100_kbp"] = int( + bioinfo_dict["ns_per_100_kbp"] = str( summary_variants_metrics["# Ns per 100kb consensus"][c] ) # fields from variants_long_table.csv bioinfo_dict["reference_genome_accession"] = variants_long_table["CHROM"][c] - bioinfo_dict["consensus_genome_length"] = int( + bioinfo_dict["consensus_genome_length"] = str( consensus_genome_length.iloc[c, 0] ) bioinfo_dict["consensus_sequence_R1_name"] = md5_info.iloc[c * 2, 0][34:60] @@ -148,13 +150,13 @@ def bioinfo_parse(self, file_name): bioinfo_dict["dehosting_method_software_version"] = list( software_versions["KRAKEN2_KRAKEN2"].values() - ) + )[0] bioinfo_dict["variant_calling_software_version"] = list( software_versions["IVAR_VARIANTS"].values() - ) + )[0] bioinfo_dict["consensus_sequence_software_version"] = list( software_versions["BCFTOOLS_CONSENSUS"].values() - ) + )[0] bioinfo_dict[ "bioinformatics_protocol_software_version" @@ -162,16 +164,22 @@ def bioinfo_parse(self, file_name): bioinfo_dict["preprocessing_software_version"] = list( software_versions["FASTP"].values() - ) - bioinfo_dict["mapping_software_version"] = software_versions[ - "BOWTIE2_ALIGN" - ].values() - bioinfo_list.append(bioinfo_dict) + )[0] + bioinfo_dict["mapping_software_version"] = list( + software_versions["BOWTIE2_ALIGN"].values() + )[0] + # bioinfo_list[str(sample_name)].append(bioinfo_dict) + # bioinfo_list.append(bioinfo_dict) + bioinfo_list[str(sample_name)] = bioinfo_dict c = +1 json_file = "bioinfo_metadata.json" output_path = os.path.join(self.output_folder, json_file) + import pdb + + pdb.set_trace() + with open(output_path, "w", encoding="utf-8") as fh: fh.write( json.dumps(bioinfo_list, indent=4, sort_keys=True, ensure_ascii=False) From 68c91278606645c075d5b12b5d8bdaa5b7b28f15 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 23 May 2022 11:46:46 +0200 Subject: [PATCH 0468/1454] fixed bug in read_bioinfo_metadata --- relecov_tools/read_bioinfo_metadata.py | 75 ++++++++++++++------------ 1 file changed, 40 insertions(+), 35 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 34714d47..104eb507 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -124,9 +124,9 @@ def bioinfo_parse(self, file_name): bioinfo_dict["long_table_path"] = self.input_folder # fields from mapping_illumina.tab for key in self.mapping_illumina_tab_field_list.keys(): - bioinfo_dict[key] = mapping_illumina_tab[ - self.mapping_illumina_tab_field_list[key] - ][c] + bioinfo_dict[key] = str( + mapping_illumina_tab[self.mapping_illumina_tab_field_list[key]][c] + ) # fields from summary_variants_metrics_mqc.csv bioinfo_dict["number_of_base_pairs_sequenced"] = str( (summary_variants_metrics["# Input reads"][c] * 2) @@ -135,41 +135,46 @@ def bioinfo_parse(self, file_name): summary_variants_metrics["# Ns per 100kb consensus"][c] ) # fields from variants_long_table.csv - bioinfo_dict["reference_genome_accession"] = variants_long_table["CHROM"][c] + bioinfo_dict["reference_genome_accession"] = str( + variants_long_table["CHROM"][c] + ) bioinfo_dict["consensus_genome_length"] = str( consensus_genome_length.iloc[c, 0] ) - bioinfo_dict["consensus_sequence_R1_name"] = md5_info.iloc[c * 2, 0][34:60] - bioinfo_dict["consensus_sequence_R2_name"] = md5_info.iloc[c * 2 + 1, 0][ - 34:60 - ] - bioinfo_dict["consensus_sequence_R1_md5"] = md5_info.iloc[c * 2, 0][0:32] - bioinfo_dict["consensus_sequence__R2_md5"] = md5_info.iloc[c * 2 + 1, 0][ - 0:32 - ] - - bioinfo_dict["dehosting_method_software_version"] = list( - software_versions["KRAKEN2_KRAKEN2"].values() - )[0] - bioinfo_dict["variant_calling_software_version"] = list( - software_versions["IVAR_VARIANTS"].values() - )[0] - bioinfo_dict["consensus_sequence_software_version"] = list( - software_versions["BCFTOOLS_CONSENSUS"].values() - )[0] - - bioinfo_dict[ - "bioinformatics_protocol_software_version" - ] = software_versions["Workflow"]["nf-core/viralrecon"] - - bioinfo_dict["preprocessing_software_version"] = list( - software_versions["FASTP"].values() - )[0] - bioinfo_dict["mapping_software_version"] = list( - software_versions["BOWTIE2_ALIGN"].values() - )[0] - # bioinfo_list[str(sample_name)].append(bioinfo_dict) - # bioinfo_list.append(bioinfo_dict) + bioinfo_dict["consensus_sequence_R1_name"] = str( + md5_info.iloc[c * 2, 0][34:60] + ) + bioinfo_dict["consensus_sequence_R2_name"] = str( + md5_info.iloc[c * 2 + 1, 0][34:60] + ) + bioinfo_dict["consensus_sequence_R1_md5"] = str( + md5_info.iloc[c * 2, 0][0:32] + ) + bioinfo_dict["consensus_sequence__R2_md5"] = str( + md5_info.iloc[c * 2 + 1, 0][0:32] + ) + + bioinfo_dict["dehosting_method_software_version"] = str( + list(software_versions["KRAKEN2_KRAKEN2"].values())[0] + ) + bioinfo_dict["variant_calling_software_version"] = str( + list(software_versions["IVAR_VARIANTS"].values())[0] + ) + bioinfo_dict["consensus_sequence_software_version"] = str( + list(software_versions["BCFTOOLS_CONSENSUS"].values())[0] + ) + + bioinfo_dict["bioinformatics_protocol_software_version"] = str( + software_versions["Workflow"]["nf-core/viralrecon"] + ) + + bioinfo_dict["preprocessing_software_version"] = str( + list(software_versions["FASTP"].values())[0] + ) + bioinfo_dict["mapping_software_version"] = str( + list(software_versions["BOWTIE2_ALIGN"].values())[0] + ) + bioinfo_list[str(sample_name)] = bioinfo_dict c = +1 From 12c7301049ab28b9aa093600632cdbcd289399da Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 23 May 2022 12:08:27 +0200 Subject: [PATCH 0469/1454] added to test cases and example data --- .../example_data/consensus_genome_length.csv | 91 + .../example_data/lab_metadata_20220208.xlsx | Bin 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z|IV8iD!%$C{-u_SFL`VmTX4kN%OgAL{+td6Ke@WUtw+S&o=46MIl6UgVnuQ8&!aAd zC%hN`&Ze*bvh%RlTYDe08WlSrb4}3qSFd?pz467d%+xqL)t246I=D<2RP~B?-l~1~ zx313i{%cZ=Fvj0O>9p#z%dL(H!dK^&_`99Gqu?kgl}f>JM%G*JZ8cRF9IwrmrGR*x<2px}!mB4a{=BCIW4saKC}1qv=$?)2DF&F}eAk>|S9t@6J# zpnLI1S3&rqNPs%({<8!ef&Yl$>9d1oj*FbF3!7z?6Z806?~DT{iO_uUOlrZZ3M10x(%) Variantsinconsensusx10 MissenseVariants %Ns10x Lineage +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214821 285604 1545 3090 1,08 281428 98,54 1086 0,380247 287 92,0 19 9 8,44 B.1.177 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214822 306868 97177 194354 63,33 61642 20,09 50872 16,5778 6 41,0 8 3 58,83 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214823 196898 57130 114260 58,03 204 0,1 82434 41,8663 NA NA 0 0 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214824 248 41 82 33,06 138 55,65 28 11,2903 NA NA 0 0 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214825 277306 747 1494 0,54 271052 97,74 4760 1,71652 217 91,0 17 9 9,10 B.1.177 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214826 337052 415 830 0,25 334627 99,28 1595 0,473221 239 92,0 17 9 7,87 B.1.177 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214827 246530 27978 55956 22,70 79361 32,19 111213 45,1113 10 50,0 15 7 49,72 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214828 312802 28396 56792 18,16 218183 69,75 37827 12,093 33 68,0 14 7 32,31 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214829 379598 3419 6838 1,80 370149 97,51 2611 0,687833 249 89,0 20 8 10,65 B.1.177 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214830 354342 25175 50350 14,21 300202 84,72 3790 1,06959 169 88,0 22 10 12,15 B.1.177 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214831 253440 107619 215238 84,93 11221 4,43 26981 10,6459 NA 22,0 3 2 77,51 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214832 5052 1844 3688 73,00 364 7,21 1000 19,7941 NA NA 0 0 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214833 326700 61771 123542 37,82 88067 26,96 115091 35,2283 16 55,00000000000001 12 5 44,94 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214834 384218 36429 72858 18,96 296545 77,18 14815 3,85588 85 83,0 17 8 17,29 B.1.177 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214835 347078 42041 84082 24,23 162912 46,94 100084 28,8362 32 67,0 17 7 32,56 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214836 362840 74483 148966 41,06 115115 31,73 98759 27,2183 9 49,0 8 4 50,53 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214837 400430 56534 113068 28,24 223768 55,88 63594 15,8814 52 75,0 17 7 25,35 B.1.177 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214838 113674 25661 51322 45,15 6240 5,49 56112 49,3622 1 27,0 5 3 73,34 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220338 214610 37082 74164 34,56 106457 49,6 33989 15,8376 28 68,0 35 23 31,88 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220339 310682 6731 13462 4,33 295685 95,17 1535 0,494074 401 91,0 49 35 8,77 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220407 188574 72874 145748 77,29 4001 2,12 38825 20,5887 NA 20,0 9 7 80,18 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220433 69680 7033 14066 20,19 16261 23,34 39353 56,4768 3 36,0 16 13 64,03 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220518 87796 15067 30134 34,32 27222 31,01 30440 34,6713 2 37,0 18 13 63,28 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220529 243588 24320 48640 19,97 192650 79,09 2298 0,943396 86 79,0 42 30 21,15 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220530 258694 20191 40382 15,61 164599 63,63 53713 20,7631 27 67,0 38 27 32,76 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220531 322478 7510 15020 4,66 306896 95,17 562 0,174275 317 90,0 57 44 9,95 BA.1.18 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220532 240540 44711 89422 37,18 145549 60,51 5569 2,31521 29 68,0 35 25 31,52 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220533 146454 67492 134984 92,17 7609 5,2 3861 2,63632 NA 15,0 7 5 85,29 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220534 383046 9624 19248 5,02 361544 94,39 2254 0,588441 505 91,0 58 43 8,91 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220535 372112 59321 118642 31,88 247472 66,5 5998 1,61188 39 72,0 36 25 28,36 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220536 342222 69820 139640 40,80 196456 57,41 6126 1,79007 27 66,0 35 23 33,56 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220537 296640 7817 15634 5,27 278999 94,05 2007 0,676578 171 85,0 51 36 14,74 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220538 316128 28736 57472 18,18 256420 81,11 2236 0,707308 154 84,0 52 38 16,06 BA.1.18 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220539 350584 24002 48004 13,69 295145 84,19 7435 2,12075 50 73,0 36 24 26,76 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220540 349706 131768 263536 75,36 73909 21,13 12261 3,50609 3 33,0 18 13 67,33 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220541 314886 34471 68942 21,89 243456 77,32 2488 0,790127 131 82,0 44 31 18,38 BA.1.1.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220542 290650 24450 48900 16,82 231509 79,65 10241 3,52348 17 56,00000000000001 29 21 43,64 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220543 393188 3174 6348 1,61 386045 98,18 795 0,202193 340 89,0 53 40 11,10 BA.1.1.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220544 301018 16814 33628 11,17 263474 87,53 3916 1,30092 44 72,0 43 33 28,08 BA.1.1.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220545 265640 6396 12792 4,82 240982 90,72 11866 4,46695 50 76,0 38 25 24,27 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220546 257054 17714 35428 13,78 219613 85,43 2013 0,783104 127 81,0 47 33 19,22 BA.1.1.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220599 189680 74903 149806 78,98 23086 12,17 16788 8,8507 6 43,0 19 17 56,97 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220600 245316 110739 221478 90,28 73 0,03 23765 9,68751 NA NA 0 0 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220601 296392 13505 27010 9,11 268212 90,49 1170 0,394747 798 97,0 59 42 2,97 BA.1.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220603 132 9 18 13,64 102 77,27 12 9,09091 NA NA 0 0 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220624 295422 43999 87998 29,79 180473 61,09 26951 9,12288 25 67,0 35 25 33,26 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220625 280118 42654 85308 30,45 183443 65,49 11367 4,05793 19 59,0 30 21 41,39 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220626 284748 4918 9836 3,45 272621 95,74 2291 0,804571 62 76,0 35 22 24,47 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220627 346396 2670 5340 1,54 340102 98,18 954 0,275407 303 90,0 49 33 10,41 BA.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220628 322910 4681 9362 2,90 312419 96,75 1129 0,349633 270 89,0 55 40 11,18 BA.1.15.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220629 415182 46596 93192 22,45 306635 73,86 15355 3,69838 25 65,0 34 25 34,69 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220630 295142 60733 121466 41,16 170297 57,7 3379 1,14487 81 72,0 34 23 28,01 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220631 274184 36346 72692 26,51 199758 72,86 1734 0,632422 122 81,0 47 31 18,92 AY.127 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220633 440478 7179 14358 3,26 422987 96,03 3133 0,711273 168 83,0 43 31 17,17 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220634 373722 60717 121434 32,49 228069 61,03 24219 6,48049 28 65,0 33 23 34,87 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220635 333686 33839 67678 20,28 247874 74,28 18134 5,43445 36 70,0 40 29 29,84 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220636 329688 8956 17912 5,43 246754 74,84 65022 19,7223 29 67,0 37 27 33,48 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220637 412358 5079 10158 2,46 396982 96,27 5218 1,26541 245 86,0 46 32 13,83 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220638 280140 3190 6380 2,28 273014 97,46 746 0,266295 195 85,0 56 38 14,94 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220639 293692 15694 31388 10,69 243186 82,8 19118 6,50954 22 64,0 31 22 35,73 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220640 283734 15102 30204 10,65 242119 85,33 11411 4,02172 41 71,0 35 23 28,83 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220642 287392 53325 106650 37,11 167518 58,29 13224 4,60138 15 57,99999999999999 29 17 42,35 B.1.617.2 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220644 329228 29537 59074 17,94 258356 78,47 11798 3,58353 31 67,0 34 25 33,42 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220646 372318 21905 43810 11,77 322145 86,52 6363 1,70902 64 78,0 38 26 22,36 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220647 433376 8059 16118 3,72 396231 91,43 21027 4,85191 170 86,0 51 36 14,41 BA.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220648 343850 86366 172732 50,23 148232 43,11 22886 6,65581 13 54,0 27 19 45,72 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220649 357146 25733 51466 14,41 298948 83,7 6732 1,88494 31 68,0 39 28 32,12 BA.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220650 345044 10516 21032 6,10 320092 92,77 3920 1,13609 66 73,0 36 26 27,50 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220651 375890 45387 90774 24,15 270823 72,05 14293 3,80244 24 65,0 33 24 34,80 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220652 324144 12938 25876 7,98 293776 90,63 4492 1,3858 44 72,0 39 27 27,86 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220653 281982 61894 123788 43,90 120219 42,63 37975 13,4672 8 48,0 25 19 52,46 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220654 264482 9708 19416 7,34 241570 91,34 3496 1,32183 57 76,0 39 27 23,71 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220655 342522 4194 8388 2,45 332968 97,21 1166 0,340416 144 84,0 50 36 15,92 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220656 342082 71678 143356 41,91 186800 54,61 11926 3,4863 7 45,0 24 17 55,26 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220657 289618 24404 48808 16,85 233722 80,7 7088 2,44736 18 59,0 28 21 41,14 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220658 288798 32526 65052 22,53 217510 75,32 6236 2,15929 26 68,0 36 26 32,35 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220659 325092 7722 15444 4,75 307924 94,72 1724 0,530311 127 81,0 43 30 18,81 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220660 314206 13118 26236 8,35 283672 90,28 4298 1,36789 129 84,0 43 28 16,46 BA.1.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220661 377508 8713 17426 4,62 357815 94,78 2267 0,600517 146 81,0 47 32 18,59 BA.1.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220663 367268 113353 226706 61,73 104983 28,58 35579 9,68748 4 41,0 28 23 58,98 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220664 310374 3372 6744 2,17 302546 97,48 1084 0,349256 230 87,0 51 38 13,50 BA.1.1.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220665 335192 11738 23476 7,00 290215 86,58 21501 6,41453 47 72,0 38 26 28,33 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220666 240438 67516 135032 56,16 92624 38,52 12782 5,31613 4 40,0 21 14 59,96 B.1.617.2 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220667 310152 3164 6328 2,04 302582 97,56 1242 0,400449 127 81,0 49 31 18,87 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220668 259344 33241 66482 25,63 177798 68,56 15064 5,8085 15 57,99999999999999 33 23 42,41 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis 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b/relecov_tools/example_data/software_versions.yml @@ -0,0 +1,89 @@ +ASCIIGENOME: + asciigenome: 1.16.0 + bedtools: 2.30.0 +BCFTOOLS_CONSENSUS: + bcftools: '1.14' +BCFTOOLS_FILTER: + bcftools: '1.14' +BCFTOOLS_QUERY: + bcftools: '1.14' +BCFTOOLS_STATS: + bcftools: '1.14' +BEDTOOLS_MASKFASTA: + bedtools: 2.30.0 +BEDTOOLS_MERGE: + bedtools: 2.30.0 +BOWTIE2_ALIGN: + bowtie2: 2.4.4 + pigz: '2.6' + samtools: '1.14' +BOWTIE2_BUILD: + bowtie2: 2.4.4 +COLLAPSE_PRIMERS: + python: 3.9.5 +CUSTOM_DUMPSOFTWAREVERSIONS: + python: 3.9.5 + yaml: 5.4.1 +CUSTOM_GETCHROMSIZES: + custom: '1.14' +FASTP: + fastp: 0.23.2 +FASTQC_RAW: + fastqc: 0.11.9 +FASTQC_TRIM: + fastqc: 0.11.9 +IVAR_TRIM: + ivar: 1.3.1 +IVAR_VARIANTS: + ivar: 1.3.1 +IVAR_VARIANTS_TO_VCF: + python: 3.9.9 +KRAKEN2_KRAKEN2: + kraken2: 2.1.2 + pigz: '2.6' +MAKE_BED_MASK: + python: 3.9.5 + samtools: '1.14' +MAKE_VARIANTS_LONG_TABLE: + python: 3.9.9 +MOSDEPTH_AMPLICON: + mosdepth: 0.3.3 +MOSDEPTH_GENOME: + mosdepth: 0.3.3 +PICARD_COLLECTMULTIPLEMETRICS: + picard: 2.26.10 +PLOT_BASE_DENSITY: + r-base: 4.0.3 +PLOT_MOSDEPTH_REGIONS_AMPLICON: + r-base: 4.0.3 +PLOT_MOSDEPTH_REGIONS_GENOME: + r-base: 4.0.3 +RENAME_FASTA_HEADER: + sed: '4.7' +SAMPLESHEET_CHECK: + python: 3.9.5 +SAMTOOLS_FLAGSTAT: + samtools: '1.14' +SAMTOOLS_IDXSTATS: + samtools: '1.14' +SAMTOOLS_INDEX: + samtools: '1.14' +SAMTOOLS_SORT: + samtools: '1.14' +SAMTOOLS_STATS: + samtools: '1.14' +SNPEFF_ANN: + snpeff: 5.0e +SNPEFF_BUILD: + snpeff: 5.0e +SNPSIFT_EXTRACTFIELDS: + snpsift: '4.3' +TABIX_BGZIP: + tabix: '1.12' +TABIX_TABIX: + tabix: '1.12' +UNTAR_KRAKEN2_DB: + untar: '1.30' +Workflow: + Nextflow: 21.10.6 + nf-core/viralrecon: 2.4.1 diff --git a/relecov_tools/example_data/variants_long_table.csv b/relecov_tools/example_data/variants_long_table.csv new file mode 100755 index 00000000..90148433 --- /dev/null +++ b/relecov_tools/example_data/variants_long_table.csv @@ -0,0 +1,3341 @@ +SAMPLE,CHROM,POS,REF,ALT,FILTER,DP,REF_DP,ALT_DP,AF,GENE,EFFECT,HGVS_C,HGVS_P,HGVS_P_1LETTER,CALLER,LINEAGE +214821,NC_045512.2,11132,G,T,PASS,366,0,363,0.99,orf1ab,missense_variant,c.10867G>T,p.Ala3623Ser,p.A3623S,ivar,B.1.177 +214821,NC_045512.2,14408,C,T,PASS,333,2,331,0.99,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,B.1.177 +214821,NC_045512.2,16726,C,T,PASS,697,1,695,1.0,orf1ab,synonymous_variant,c.16461C>T,p.Tyr5487Tyr,p.Y5487Y,ivar,B.1.177 +214821,NC_045512.2,17658,G,T,PASS,3710,6,3690,0.99,orf1ab,missense_variant,c.17393G>T,p.Cys5798Phe,p.C5798F,ivar,B.1.177 +214821,NC_045512.2,20132,C,T,PASS,83,0,83,1.0,orf1ab,missense_variant,c.19867C>T,p.Pro6623Ser,p.P6623S,ivar,B.1.177 +214821,NC_045512.2,21255,G,C,PASS,78,0,78,1.0,orf1ab,missense_variant,c.20990G>C,p.Arg6997Pro,p.R6997P,ivar,B.1.177 +214821,NC_045512.2,21786,G,T,PASS,276,0,275,1.0,S,missense_variant,c.224G>T,p.Gly75Val,p.G75V,ivar,B.1.177 +214821,NC_045512.2,23403,A,G,PASS,2590,2,2588,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.177 +214821,NC_045512.2,24138,C,T,PASS,1594,913,679,0.43,S,missense_variant,c.2576C>T,p.Thr859Ile,p.T859I,ivar,B.1.177 +214821,NC_045512.2,26801,C,G,PASS,896,0,892,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,B.1.177 +214821,NC_045512.2,28932,C,T,PASS,242,5,236,0.98,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,B.1.177 +214821,NC_045512.2,29645,G,T,PASS,84,0,82,0.98,ORF10,missense_variant,c.88G>T,p.Val30Leu,p.V30L,ivar,B.1.177 +214821,NC_045512.2,3037,C,T,PASS,330,0,330,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,B.1.177 +214821,NC_045512.2,4230,C,T,PASS,57,0,57,1.0,orf1ab,missense_variant,c.3965C>T,p.Thr1322Ile,p.T1322I,ivar,B.1.177 +214821,NC_045512.2,445,T,C,PASS,8440,24,8415,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,B.1.177 +214821,NC_045512.2,504,CTCATGG,C,PASS,7769,7715,6191,0.8,orf1ab,disruptive_inframe_deletion,c.245_250delGTCATG,p.Gly82_His83del,p.G82_H83del,ivar,B.1.177 +214821,NC_045512.2,541,C,T,PASS,7835,36,7791,0.99,orf1ab,synonymous_variant,c.276C>T,p.Leu92Leu,p.L92L,ivar,B.1.177 +214821,NC_045512.2,5548,C,T,PASS,28,0,27,0.96,orf1ab,synonymous_variant,c.5283C>T,p.Thr1761Thr,p.T1761T,ivar,B.1.177 +214821,NC_045512.2,6842,T,C,ft,13,9,4,0.31,orf1ab,missense_variant,c.6577T>C,p.Ser2193Pro,p.S2193P,ivar,B.1.177 +214821,NC_045512.2,8125,T,G,PASS,3054,5,3048,1.0,orf1ab,synonymous_variant,c.7860T>G,p.Leu2620Leu,p.L2620L,ivar,B.1.177 +214822,NC_045512.2,1199,TG,T,PASS,364,361,97,0.27,orf1ab,frameshift_variant,c.935delG,p.Cys312fs,p.C312fs,ivar,Unassigned +214822,NC_045512.2,13179,G,T,PASS,735,546,189,0.26,orf1ab,missense_variant,c.12914G>T,p.Gly4305Val,p.G4305V,ivar,Unassigned +214822,NC_045512.2,17658,G,T,PASS,2579,0,2575,1.0,orf1ab,missense_variant,c.17393G>T,p.Cys5798Phe,p.C5798F,ivar,Unassigned +214822,NC_045512.2,20132,C,T,PASS,10,0,10,1.0,orf1ab,missense_variant,c.19867C>T,p.Pro6623Ser,p.P6623S,ivar,Unassigned +214822,NC_045512.2,20473,A,C,PASS,423,175,247,0.58,orf1ab,missense_variant,c.20208A>C,p.Lys6736Asn,p.K6736N,ivar,Unassigned +214822,NC_045512.2,2076,G,T,PASS,80,47,33,0.41,orf1ab,missense_variant,c.1811G>T,p.Gly604Val,p.G604V,ivar,Unassigned +214822,NC_045512.2,23403,A,G,PASS,44,0,44,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +214822,NC_045512.2,25217,G,T,PASS,334,113,221,0.66,S,missense_variant,c.3655G>T,p.Gly1219Cys,p.G1219C,ivar,Unassigned +214822,NC_045512.2,25424,G,T,PASS,228,109,119,0.52,ORF3a,missense_variant,c.32G>T,p.Gly11Val,p.G11V,ivar,Unassigned +214822,NC_045512.2,25451,T,C,ft,12,8,4,0.33,ORF3a,missense_variant,c.59T>C,p.Ile20Thr,p.I20T,ivar,Unassigned +214822,NC_045512.2,26801,C,G,PASS,21,0,21,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,Unassigned +214822,NC_045512.2,2748,A,G,PASS,852,534,315,0.37,orf1ab,missense_variant,c.2483A>G,p.Asp828Gly,p.D828G,ivar,Unassigned +214822,NC_045512.2,3514,G,T,PASS,59,40,19,0.32,orf1ab,missense_variant,c.3249G>T,p.Met1083Ile,p.M1083I,ivar,Unassigned +214822,NC_045512.2,445,T,C,PASS,7802,4,7798,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,Unassigned +214822,NC_045512.2,504,CTCATGG,C,PASS,6981,6922,5465,0.78,orf1ab,disruptive_inframe_deletion,c.245_250delGTCATG,p.Gly82_His83del,p.G82_H83del,ivar,Unassigned +214822,NC_045512.2,541,C,T,PASS,7271,38,7229,0.99,orf1ab,synonymous_variant,c.276C>T,p.Leu92Leu,p.L92L,ivar,Unassigned +214822,NC_045512.2,8125,T,G,PASS,13,0,13,1.0,orf1ab,synonymous_variant,c.7860T>G,p.Leu2620Leu,p.L2620L,ivar,Unassigned +214825,NC_045512.2,10845,T,C,ft,16,12,4,0.25,orf1ab,missense_variant,c.10580T>C,p.Met3527Thr,p.M3527T,ivar,B.1.177 +214825,NC_045512.2,11132,G,T,PASS,108,0,108,1.0,orf1ab,missense_variant,c.10867G>T,p.Ala3623Ser,p.A3623S,ivar,B.1.177 +214825,NC_045512.2,14408,C,T,PASS,256,0,256,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,B.1.177 +214825,NC_045512.2,16726,C,T,PASS,500,3,496,0.99,orf1ab,synonymous_variant,c.16461C>T,p.Tyr5487Tyr,p.Y5487Y,ivar,B.1.177 +214825,NC_045512.2,17658,G,T,PASS,4879,1,4849,0.99,orf1ab,missense_variant,c.17393G>T,p.Cys5798Phe,p.C5798F,ivar,B.1.177 +214825,NC_045512.2,20132,C,T,PASS,62,0,62,1.0,orf1ab,missense_variant,c.19867C>T,p.Pro6623Ser,p.P6623S,ivar,B.1.177 +214825,NC_045512.2,21255,G,C,PASS,57,0,57,1.0,orf1ab,missense_variant,c.20990G>C,p.Arg6997Pro,p.R6997P,ivar,B.1.177 +214825,NC_045512.2,21786,G,T,PASS,247,0,247,1.0,S,missense_variant,c.224G>T,p.Gly75Val,p.G75V,ivar,B.1.177 +214825,NC_045512.2,22227,C,T,PASS,17,0,17,1.0,S,missense_variant,c.665C>T,p.Ala222Val,p.A222V,ivar,B.1.177 +214825,NC_045512.2,23403,A,G,PASS,2049,10,2039,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.177 +214825,NC_045512.2,26801,C,G,PASS,241,0,241,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,B.1.177 +214825,NC_045512.2,28932,C,T,PASS,173,0,172,0.99,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,B.1.177 +214825,NC_045512.2,29645,G,T,PASS,21,0,21,1.0,ORF10,missense_variant,c.88G>T,p.Val30Leu,p.V30L,ivar,B.1.177 +214825,NC_045512.2,3037,C,T,PASS,243,3,239,0.98,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,B.1.177 +214825,NC_045512.2,445,T,C,PASS,10199,19,10180,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,B.1.177 +214825,NC_045512.2,541,C,T,PASS,9612,41,9559,0.99,orf1ab,synonymous_variant,c.276C>T,p.Leu92Leu,p.L92L,ivar,B.1.177 +214825,NC_045512.2,5548,C,T,PASS,20,0,20,1.0,orf1ab,synonymous_variant,c.5283C>T,p.Thr1761Thr,p.T1761T,ivar,B.1.177 +214826,NC_045512.2,11132,G,T,PASS,238,0,238,1.0,orf1ab,missense_variant,c.10867G>T,p.Ala3623Ser,p.A3623S,ivar,B.1.177 +214826,NC_045512.2,14408,C,T,PASS,428,2,426,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,B.1.177 +214826,NC_045512.2,16726,C,T,PASS,621,0,621,1.0,orf1ab,synonymous_variant,c.16461C>T,p.Tyr5487Tyr,p.Y5487Y,ivar,B.1.177 +214826,NC_045512.2,17658,G,T,PASS,6934,3,6903,1.0,orf1ab,missense_variant,c.17393G>T,p.Cys5798Phe,p.C5798F,ivar,B.1.177 +214826,NC_045512.2,20132,C,T,PASS,101,0,101,1.0,orf1ab,missense_variant,c.19867C>T,p.Pro6623Ser,p.P6623S,ivar,B.1.177 +214826,NC_045512.2,21255,G,C,PASS,91,0,91,1.0,orf1ab,missense_variant,c.20990G>C,p.Arg6997Pro,p.R6997P,ivar,B.1.177 +214826,NC_045512.2,21786,G,T,PASS,464,4,460,0.99,S,missense_variant,c.224G>T,p.Gly75Val,p.G75V,ivar,B.1.177 +214826,NC_045512.2,22227,C,T,PASS,31,0,31,1.0,S,missense_variant,c.665C>T,p.Ala222Val,p.A222V,ivar,B.1.177 +214826,NC_045512.2,23403,A,G,PASS,1826,2,1824,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.177 +214826,NC_045512.2,26801,C,G,PASS,363,0,362,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,B.1.177 +214826,NC_045512.2,28932,C,T,PASS,196,2,193,0.98,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,B.1.177 +214826,NC_045512.2,29645,G,T,PASS,46,0,46,1.0,ORF10,missense_variant,c.88G>T,p.Val30Leu,p.V30L,ivar,B.1.177 +214826,NC_045512.2,3037,C,T,PASS,154,0,154,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,B.1.177 +214826,NC_045512.2,4158,C,T,PASS,112,81,31,0.28,orf1ab,missense_variant,c.3893C>T,p.Ala1298Val,p.A1298V,ivar,B.1.177 +214826,NC_045512.2,445,T,C,PASS,10150,5,10145,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,B.1.177 +214826,NC_045512.2,541,C,T,PASS,9501,38,9460,1.0,orf1ab,synonymous_variant,c.276C>T,p.Leu92Leu,p.L92L,ivar,B.1.177 +214826,NC_045512.2,5548,C,T,PASS,20,0,20,1.0,orf1ab,synonymous_variant,c.5283C>T,p.Thr1761Thr,p.T1761T,ivar,B.1.177 +214827,NC_045512.2,11132,G,T,PASS,36,0,36,1.0,orf1ab,missense_variant,c.10867G>T,p.Ala3623Ser,p.A3623S,ivar,Unassigned +214827,NC_045512.2,1123,A,T,PASS,161,3,158,0.98,orf1ab,synonymous_variant,c.858A>T,p.Pro286Pro,p.P286P,ivar,Unassigned +214827,NC_045512.2,14408,C,T,PASS,28,0,28,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +214827,NC_045512.2,16726,C,T,PASS,47,0,47,1.0,orf1ab,synonymous_variant,c.16461C>T,p.Tyr5487Tyr,p.Y5487Y,ivar,Unassigned +214827,NC_045512.2,17658,G,T,PASS,6726,0,6694,1.0,orf1ab,missense_variant,c.17393G>T,p.Cys5798Phe,p.C5798F,ivar,Unassigned +214827,NC_045512.2,21786,G,T,PASS,49,0,49,1.0,S,missense_variant,c.224G>T,p.Gly75Val,p.G75V,ivar,Unassigned +214827,NC_045512.2,23403,A,G,PASS,336,0,336,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +214827,NC_045512.2,24368,G,C,PASS,73,23,49,0.67,S,missense_variant,c.2806G>C,p.Asp936His,p.D936H,ivar,Unassigned +214827,NC_045512.2,25112,G,T,PASS,90,10,80,0.89,S,missense_variant,c.3550G>T,p.Asp1184Tyr,p.D1184Y,ivar,Unassigned +214827,NC_045512.2,26297,T,C,PASS,652,476,176,0.27,E,missense_variant,c.53T>C,p.Leu18Pro,p.L18P,ivar,Unassigned +214827,NC_045512.2,26410,T,C,ft,10,6,4,0.4,E,missense_variant,c.166T>C,p.Phe56Leu,p.F56L,ivar,Unassigned +214827,NC_045512.2,26801,C,G,PASS,12,1,11,0.92,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,Unassigned +214827,NC_045512.2,28932,C,T,PASS,80,0,80,1.0,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,Unassigned +214827,NC_045512.2,3037,C,T,PASS,48,0,48,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +214827,NC_045512.2,445,T,C,PASS,3394,8,3386,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,Unassigned +214827,NC_045512.2,541,C,T,PASS,3216,10,3206,1.0,orf1ab,synonymous_variant,c.276C>T,p.Leu92Leu,p.L92L,ivar,Unassigned +214827,NC_045512.2,7521,C,T,PASS,29,3,26,0.9,orf1ab,missense_variant,c.7256C>T,p.Thr2419Ile,p.T2419I,ivar,Unassigned +214827,NC_045512.2,76,T,A,ft,14,10,4,0.29,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +214827,NC_045512.2,78,T,G,ft,15,11,4,0.27,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +214827,NC_045512.2,8302,A,T,PASS,28,17,10,0.36,orf1ab,missense_variant,c.8037A>T,p.Lys2679Asn,p.K2679N,ivar,Unassigned +214828,NC_045512.2,11132,G,T,PASS,47,0,47,1.0,orf1ab,missense_variant,c.10867G>T,p.Ala3623Ser,p.A3623S,ivar,Unassigned +214828,NC_045512.2,14408,C,T,PASS,26,0,26,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +214828,NC_045512.2,14646,T,A,PASS,53,25,28,0.53,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,Unassigned +214828,NC_045512.2,16002,T,G,PASS,34,21,13,0.38,orf1ab,stop_gained,c.15737T>G,p.Leu5246*,p.L5246*,ivar,Unassigned +214828,NC_045512.2,16726,C,T,PASS,38,0,38,1.0,orf1ab,synonymous_variant,c.16461C>T,p.Tyr5487Tyr,p.Y5487Y,ivar,Unassigned +214828,NC_045512.2,17658,G,T,PASS,12609,1,12562,1.0,orf1ab,missense_variant,c.17393G>T,p.Cys5798Phe,p.C5798F,ivar,Unassigned +214828,NC_045512.2,19378,T,C,PASS,42,17,25,0.6,orf1ab,synonymous_variant,c.19113T>C,p.Ile6371Ile,p.I6371I,ivar,Unassigned +214828,NC_045512.2,20132,C,T,PASS,23,0,23,1.0,orf1ab,missense_variant,c.19867C>T,p.Pro6623Ser,p.P6623S,ivar,Unassigned +214828,NC_045512.2,21786,G,T,PASS,24,0,24,1.0,S,missense_variant,c.224G>T,p.Gly75Val,p.G75V,ivar,Unassigned +214828,NC_045512.2,23403,A,G,PASS,611,0,611,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +214828,NC_045512.2,26801,C,G,PASS,178,0,178,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,Unassigned +214828,NC_045512.2,27856,T,A,PASS,53,13,40,0.75,ORF7b,missense_variant,c.101T>A,p.Leu34Gln,p.L34Q,ivar,Unassigned +214828,NC_045512.2,28932,C,T,PASS,210,0,210,1.0,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,Unassigned +214828,NC_045512.2,3037,C,T,PASS,30,0,30,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +214828,NC_045512.2,445,T,C,PASS,14026,6,14017,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,Unassigned +214828,NC_045512.2,541,C,T,PASS,13166,68,13075,0.99,orf1ab,synonymous_variant,c.276C>T,p.Leu92Leu,p.L92L,ivar,Unassigned +214829,NC_045512.2,10833,C,T,PASS,17,0,17,1.0,orf1ab,missense_variant,c.10568C>T,p.Ala3523Val,p.A3523V,ivar,B.1.177 +214829,NC_045512.2,11824,C,T,PASS,73,0,73,1.0,orf1ab,synonymous_variant,c.11559C>T,p.Ile3853Ile,p.I3853I,ivar,B.1.177 +214829,NC_045512.2,14408,C,T,PASS,148,0,148,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,B.1.177 +214829,NC_045512.2,16308,C,T,PASS,433,3,428,0.99,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,B.1.177 +214829,NC_045512.2,21255,G,C,PASS,73,0,73,1.0,orf1ab,missense_variant,c.20990G>C,p.Arg6997Pro,p.R6997P,ivar,B.1.177 +214829,NC_045512.2,222,C,T,PASS,158,1,157,0.99,orf1ab,upstream_gene_variant,c.-44C>T,.,.,ivar,B.1.177 +214829,NC_045512.2,22482,C,T,PASS,39,20,19,0.49,S,missense_variant,c.920C>T,p.Thr307Ile,p.T307I,ivar,B.1.177 +214829,NC_045512.2,23403,A,G,PASS,2780,6,2774,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.177 +214829,NC_045512.2,24370,C,T,PASS,443,4,439,0.99,S,synonymous_variant,c.2808C>T,p.Asp936Asp,p.D936D,ivar,B.1.177 +214829,NC_045512.2,26801,C,G,PASS,694,0,694,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,B.1.177 +214829,NC_045512.2,28093,C,T,PASS,592,1,590,1.0,ORF8,missense_variant,c.200C>T,p.Ser67Phe,p.S67F,ivar,B.1.177 +214829,NC_045512.2,28486,C,T,PASS,493,2,491,1.0,N,synonymous_variant,c.213C>T,p.Gly71Gly,p.G71G,ivar,B.1.177 +214829,NC_045512.2,28932,C,T,PASS,556,1,554,1.0,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,B.1.177 +214829,NC_045512.2,29402,G,T,PASS,5976,2,5958,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,B.1.177 +214829,NC_045512.2,29578,C,T,PASS,99,5,94,0.95,ORF10,synonymous_variant,c.21C>T,p.Phe7Phe,p.F7F,ivar,B.1.177 +214829,NC_045512.2,29645,G,T,PASS,117,0,116,0.99,ORF10,missense_variant,c.88G>T,p.Val30Leu,p.V30L,ivar,B.1.177 +214829,NC_045512.2,3037,C,T,PASS,260,0,260,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,B.1.177 +214829,NC_045512.2,445,T,C,PASS,13196,11,13183,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,B.1.177 +214829,NC_045512.2,527,C,T,PASS,11571,51,11487,0.99,orf1ab,synonymous_variant,c.262C>T,p.Leu88Leu,p.L88L,ivar,B.1.177 +214829,NC_045512.2,5869,C,T,PASS,192,0,192,1.0,orf1ab,synonymous_variant,c.5604C>T,p.Tyr1868Tyr,p.Y1868Y,ivar,B.1.177 +214829,NC_045512.2,8326,C,T,PASS,2135,898,1233,0.58,orf1ab,synonymous_variant,c.8061C>T,p.Asp2687Asp,p.D2687D,ivar,B.1.177 +214830,NC_045512.2,10833,C,T,PASS,17,0,17,1.0,orf1ab,missense_variant,c.10568C>T,p.Ala3523Val,p.A3523V,ivar,B.1.177 +214830,NC_045512.2,11824,C,T,PASS,54,0,54,1.0,orf1ab,synonymous_variant,c.11559C>T,p.Ile3853Ile,p.I3853I,ivar,B.1.177 +214830,NC_045512.2,14408,C,T,PASS,160,2,158,0.99,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,B.1.177 +214830,NC_045512.2,16308,C,T,PASS,487,3,484,0.99,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,B.1.177 +214830,NC_045512.2,21255,G,C,PASS,56,0,56,1.0,orf1ab,missense_variant,c.20990G>C,p.Arg6997Pro,p.R6997P,ivar,B.1.177 +214830,NC_045512.2,222,C,T,PASS,52,0,52,1.0,orf1ab,upstream_gene_variant,c.-44C>T,.,.,ivar,B.1.177 +214830,NC_045512.2,22482,C,T,PASS,31,0,31,1.0,S,missense_variant,c.920C>T,p.Thr307Ile,p.T307I,ivar,B.1.177 +214830,NC_045512.2,23403,A,G,PASS,2950,2,2944,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.177 +214830,NC_045512.2,24370,C,T,PASS,234,1,233,1.0,S,synonymous_variant,c.2808C>T,p.Asp936Asp,p.D936D,ivar,B.1.177 +214830,NC_045512.2,26801,C,G,PASS,442,0,442,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,B.1.177 +214830,NC_045512.2,28093,C,T,PASS,632,8,622,0.98,ORF8,missense_variant,c.200C>T,p.Ser67Phe,p.S67F,ivar,B.1.177 +214830,NC_045512.2,28486,C,T,PASS,414,2,410,0.99,N,synonymous_variant,c.213C>T,p.Gly71Gly,p.G71G,ivar,B.1.177 +214830,NC_045512.2,28932,C,T,PASS,811,1,809,1.0,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,B.1.177 +214830,NC_045512.2,29402,G,T,PASS,7244,1,7211,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,B.1.177 +214830,NC_045512.2,29578,C,T,PASS,101,0,101,1.0,ORF10,synonymous_variant,c.21C>T,p.Phe7Phe,p.F7F,ivar,B.1.177 +214830,NC_045512.2,29645,G,T,PASS,106,0,106,1.0,ORF10,missense_variant,c.88G>T,p.Val30Leu,p.V30L,ivar,B.1.177 +214830,NC_045512.2,3037,C,T,PASS,259,0,259,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,B.1.177 +214830,NC_045512.2,445,T,C,PASS,12135,22,12111,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,B.1.177 +214830,NC_045512.2,5274,C,T,PASS,12,0,12,1.0,orf1ab,missense_variant,c.5009C>T,p.Ala1670Val,p.A1670V,ivar,B.1.177 +214830,NC_045512.2,527,C,T,PASS,11747,79,11647,0.99,orf1ab,synonymous_variant,c.262C>T,p.Leu88Leu,p.L88L,ivar,B.1.177 +214830,NC_045512.2,5869,C,T,PASS,58,2,54,0.93,orf1ab,synonymous_variant,c.5604C>T,p.Tyr1868Tyr,p.Y1868Y,ivar,B.1.177 +214831,NC_045512.2,1009,C,A,ft,12,7,5,0.42,orf1ab,missense_variant,c.744C>A,p.Ser248Arg,p.S248R,ivar,Unassigned +214831,NC_045512.2,13408,T,C,ft,13,9,4,0.31,orf1ab,synonymous_variant,c.13143T>C,p.Cys4381Cys,p.C4381C,ivar,Unassigned +214831,NC_045512.2,14646,T,A,ft,15,9,6,0.4,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,Unassigned +214831,NC_045512.2,14647,A,C,ft,15,9,6,0.4,orf1ab,synonymous_variant,c.14382A>C,p.Leu4794Leu,p.L4794L,ivar,Unassigned +214831,NC_045512.2,14661,T,G,PASS,13,7,6,0.46,orf1ab,missense_variant,c.14396T>G,p.Phe4799Cys,p.F4799C,ivar,Unassigned +214831,NC_045512.2,15604,A,T,ft,11,7,4,0.36,orf1ab,synonymous_variant,c.15339A>T,p.Ala5113Ala,p.A5113A,ivar,Unassigned +214831,NC_045512.2,17375,C,T,PASS,344,195,148,0.43,orf1ab,stop_gained,c.17110C>T,p.Gln5704*,p.Q5704*,ivar,Unassigned +214831,NC_045512.2,17469,G,T,PASS,472,337,127,0.27,orf1ab,missense_variant,c.17204G>T,p.Cys5735Phe,p.C5735F,ivar,Unassigned +214831,NC_045512.2,23333,T,C,PASS,54,30,24,0.44,S,missense_variant,c.1771T>C,p.Ser591Pro,p.S591P,ivar,Unassigned +214831,NC_045512.2,23403,A,G,PASS,59,0,59,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +214831,NC_045512.2,28301,C,A,ft,10,6,4,0.4,N,synonymous_variant,c.28C>A,p.Arg10Arg,p.R10R,ivar,Unassigned +214831,NC_045512.2,29402,G,T,PASS,143,2,141,0.99,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,Unassigned +214831,NC_045512.2,3154,T,A,ft,11,8,3,0.27,orf1ab,synonymous_variant,c.2889T>A,p.Gly963Gly,p.G963G,ivar,Unassigned +214831,NC_045512.2,3443,G,T,PASS,17,9,8,0.47,orf1ab,missense_variant,c.3178G>T,p.Ala1060Ser,p.A1060S,ivar,Unassigned +214831,NC_045512.2,3748,T,C,ft,12,8,4,0.33,orf1ab,synonymous_variant,c.3483T>C,p.Ser1161Ser,p.S1161S,ivar,Unassigned +214831,NC_045512.2,445,T,C,PASS,1048,6,1042,0.99,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,Unassigned +214831,NC_045512.2,527,C,T,PASS,951,313,636,0.67,orf1ab,synonymous_variant,c.262C>T,p.Leu88Leu,p.L88L,ivar,Unassigned +214833,NC_045512.2,14408,C,T,PASS,15,0,15,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +214833,NC_045512.2,14595,T,G,ft,23,17,6,0.26,orf1ab,missense_variant,c.14330T>G,p.Val4777Gly,p.V4777G,ivar,Unassigned +214833,NC_045512.2,16308,C,T,PASS,50,0,50,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,Unassigned +214833,NC_045512.2,17213,C,T,PASS,14,4,10,0.71,orf1ab,synonymous_variant,c.16948C>T,p.Leu5650Leu,p.L5650L,ivar,Unassigned +214833,NC_045512.2,21563,A,G,PASS,36,27,9,0.25,S,start_lost,c.1A>G,p.Met1?,p.M1?,ivar,Unassigned +214833,NC_045512.2,23403,A,G,PASS,171,0,171,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +214833,NC_045512.2,24370,C,T,PASS,15,0,15,1.0,S,synonymous_variant,c.2808C>T,p.Asp936Asp,p.D936D,ivar,Unassigned +214833,NC_045512.2,26114,A,G,ft,15,11,4,0.27,ORF3a,missense_variant,c.722A>G,p.Glu241Gly,p.E241G,ivar,Unassigned +214833,NC_045512.2,26663,T,C,PASS,33,19,14,0.42,M,synonymous_variant,c.141T>C,p.Tyr47Tyr,p.Y47Y,ivar,Unassigned +214833,NC_045512.2,26801,C,G,PASS,50,0,50,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,Unassigned +214833,NC_045512.2,28093,C,T,PASS,54,2,51,0.94,ORF8,missense_variant,c.200C>T,p.Ser67Phe,p.S67F,ivar,Unassigned +214833,NC_045512.2,28932,C,T,PASS,45,0,45,1.0,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,Unassigned +214833,NC_045512.2,29402,G,T,PASS,1250,2,1245,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,Unassigned +214833,NC_045512.2,2966,A,G,PASS,36,23,13,0.36,orf1ab,missense_variant,c.2701A>G,p.Ser901Gly,p.S901G,ivar,Unassigned +214833,NC_045512.2,3037,C,T,PASS,28,0,28,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +214833,NC_045512.2,445,T,C,PASS,5706,6,5700,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,Unassigned +214833,NC_045512.2,5869,C,T,ft,16,12,4,0.25,orf1ab,synonymous_variant,c.5604C>T,p.Tyr1868Tyr,p.Y1868Y,ivar,Unassigned +214833,NC_045512.2,7948,C,T,PASS,109,25,84,0.77,orf1ab,synonymous_variant,c.7683C>T,p.Tyr2561Tyr,p.Y2561Y,ivar,Unassigned +214834,NC_045512.2,11824,C,T,PASS,18,0,18,1.0,orf1ab,synonymous_variant,c.11559C>T,p.Ile3853Ile,p.I3853I,ivar,B.1.177 +214834,NC_045512.2,14408,C,T,PASS,137,0,137,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,B.1.177 +214834,NC_045512.2,16308,C,T,PASS,255,0,255,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,B.1.177 +214834,NC_045512.2,21255,G,C,PASS,44,0,42,0.95,orf1ab,missense_variant,c.20990G>C,p.Arg6997Pro,p.R6997P,ivar,B.1.177 +214834,NC_045512.2,222,C,T,PASS,17,0,17,1.0,orf1ab,upstream_gene_variant,c.-44C>T,.,.,ivar,B.1.177 +214834,NC_045512.2,23403,A,G,PASS,1324,1,1323,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.177 +214834,NC_045512.2,24370,C,T,PASS,87,1,86,0.99,S,synonymous_variant,c.2808C>T,p.Asp936Asp,p.D936D,ivar,B.1.177 +214834,NC_045512.2,26801,C,G,PASS,95,0,95,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,B.1.177 +214834,NC_045512.2,28093,C,T,PASS,232,3,229,0.99,ORF8,missense_variant,c.200C>T,p.Ser67Phe,p.S67F,ivar,B.1.177 +214834,NC_045512.2,28932,C,T,PASS,295,1,294,1.0,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,B.1.177 +214834,NC_045512.2,29402,G,T,PASS,4981,0,4965,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,B.1.177 +214834,NC_045512.2,29578,C,T,PASS,13,0,13,1.0,ORF10,synonymous_variant,c.21C>T,p.Phe7Phe,p.F7F,ivar,B.1.177 +214834,NC_045512.2,29645,G,T,PASS,17,0,17,1.0,ORF10,missense_variant,c.88G>T,p.Val30Leu,p.V30L,ivar,B.1.177 +214834,NC_045512.2,29681,TTA,T,PASS,20,20,12,0.6,S,downstream_gene_variant,c.*4298_*4299delTA,.,.,ivar,B.1.177 +214834,NC_045512.2,3037,C,T,PASS,72,1,71,0.99,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,B.1.177 +214834,NC_045512.2,3092,C,T,PASS,76,16,60,0.79,orf1ab,missense_variant,c.2827C>T,p.Pro943Ser,p.P943S,ivar,B.1.177 +214834,NC_045512.2,445,T,C,PASS,21304,21,21277,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,B.1.177 +214834,NC_045512.2,8807,G,A,ft,10,7,3,0.3,orf1ab,missense_variant,c.8542G>A,p.Asp2848Asn,p.D2848N,ivar,B.1.177 +214835,NC_045512.2,10741,CT,C,PASS,25,25,22,0.88,orf1ab,frameshift_variant,c.10479delT,p.Phe3493fs,p.F3493fs,ivar,Unassigned +214835,NC_045512.2,11808,G,C,ft,12,8,4,0.33,orf1ab,missense_variant,c.11543G>C,p.Gly3848Ala,p.G3848A,ivar,Unassigned +214835,NC_045512.2,11824,C,T,PASS,12,0,12,1.0,orf1ab,synonymous_variant,c.11559C>T,p.Ile3853Ile,p.I3853I,ivar,Unassigned +214835,NC_045512.2,14408,C,T,PASS,62,0,62,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +214835,NC_045512.2,16308,C,T,PASS,142,1,139,0.98,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,Unassigned +214835,NC_045512.2,16988,G,A,PASS,28,18,10,0.36,orf1ab,missense_variant,c.16723G>A,p.Ala5575Thr,p.A5575T,ivar,Unassigned +214835,NC_045512.2,19307,A,G,PASS,32,23,9,0.28,orf1ab,missense_variant,c.19042A>G,p.Asn6348Asp,p.N6348D,ivar,Unassigned +214835,NC_045512.2,21255,G,C,PASS,11,0,11,1.0,orf1ab,missense_variant,c.20990G>C,p.Arg6997Pro,p.R6997P,ivar,Unassigned +214835,NC_045512.2,23403,A,G,PASS,183,0,183,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +214835,NC_045512.2,23826,A,G,ft,15,11,4,0.27,S,missense_variant,c.2264A>G,p.Gln755Arg,p.Q755R,ivar,Unassigned +214835,NC_045512.2,24370,C,T,PASS,36,1,35,0.97,S,synonymous_variant,c.2808C>T,p.Asp936Asp,p.D936D,ivar,Unassigned +214835,NC_045512.2,26239,G,T,PASS,57,27,30,0.53,E,upstream_gene_variant,c.-6G>T,.,.,ivar,Unassigned +214835,NC_045512.2,26801,C,G,PASS,48,0,48,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,Unassigned +214835,NC_045512.2,27518,G,A,PASS,84,60,24,0.29,ORF7a,missense_variant,c.125G>A,p.Gly42Asp,p.G42D,ivar,Unassigned +214835,NC_045512.2,28093,C,T,PASS,31,1,30,0.97,ORF8,missense_variant,c.200C>T,p.Ser67Phe,p.S67F,ivar,Unassigned +214835,NC_045512.2,28932,C,T,PASS,138,1,137,0.99,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,Unassigned +214835,NC_045512.2,29402,G,T,PASS,2177,0,2173,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,Unassigned +214835,NC_045512.2,29578,C,T,PASS,24,0,24,1.0,ORF10,synonymous_variant,c.21C>T,p.Phe7Phe,p.F7F,ivar,Unassigned +214835,NC_045512.2,29645,G,T,PASS,25,0,25,1.0,ORF10,missense_variant,c.88G>T,p.Val30Leu,p.V30L,ivar,Unassigned +214835,NC_045512.2,29681,TTA,T,PASS,22,22,13,0.59,S,downstream_gene_variant,c.*4298_*4299delTA,.,.,ivar,Unassigned +214835,NC_045512.2,3037,C,T,PASS,26,0,26,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +214835,NC_045512.2,3092,C,T,PASS,27,15,12,0.44,orf1ab,missense_variant,c.2827C>T,p.Pro943Ser,p.P943S,ivar,Unassigned +214835,NC_045512.2,4079,AGT,A,PASS,74,74,60,0.81,orf1ab,frameshift_variant,c.3816_3817delTG,p.Ser1272fs,p.S1272fs,ivar,Unassigned +214835,NC_045512.2,445,T,C,PASS,10789,17,10764,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,Unassigned +214835,NC_045512.2,5869,C,T,PASS,51,36,15,0.29,orf1ab,synonymous_variant,c.5604C>T,p.Tyr1868Tyr,p.Y1868Y,ivar,Unassigned +214835,NC_045512.2,7639,C,T,PASS,45,33,12,0.27,orf1ab,synonymous_variant,c.7374C>T,p.Phe2458Phe,p.F2458F,ivar,Unassigned +214835,NC_045512.2,8596,A,T,PASS,238,177,61,0.26,orf1ab,synonymous_variant,c.8331A>T,p.Thr2777Thr,p.T2777T,ivar,Unassigned +214836,NC_045512.2,14408,C,T,PASS,51,0,51,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +214836,NC_045512.2,17017,G,A,PASS,23,15,8,0.35,orf1ab,missense_variant,c.16752G>A,p.Met5584Ile,p.M5584I,ivar,Unassigned +214836,NC_045512.2,18774,A,G,PASS,37,27,10,0.27,orf1ab,missense_variant,c.18509A>G,p.Asn6170Ser,p.N6170S,ivar,Unassigned +214836,NC_045512.2,21747,T,G,PASS,35,23,12,0.34,S,missense_variant,c.185T>G,p.Val62Gly,p.V62G,ivar,Unassigned +214836,NC_045512.2,23403,A,G,PASS,149,0,149,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +214836,NC_045512.2,24370,C,T,PASS,74,1,73,0.99,S,synonymous_variant,c.2808C>T,p.Asp936Asp,p.D936D,ivar,Unassigned +214836,NC_045512.2,26263,G,C,PASS,14,4,10,0.71,E,missense_variant,c.19G>C,p.Glu7Gln,p.E7Q,ivar,Unassigned +214836,NC_045512.2,27767,T,C,ft,11,8,3,0.27,ORF7b,synonymous_variant,c.12T>C,p.Leu4Leu,p.L4L,ivar,Unassigned +214836,NC_045512.2,28093,C,T,PASS,80,0,80,1.0,ORF8,missense_variant,c.200C>T,p.Ser67Phe,p.S67F,ivar,Unassigned +214836,NC_045512.2,28932,C,T,PASS,43,1,42,0.98,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,Unassigned +214836,NC_045512.2,29402,G,T,PASS,4413,0,4393,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,Unassigned +214836,NC_045512.2,3037,C,T,PASS,18,0,18,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +214836,NC_045512.2,3092,C,T,ft,19,14,5,0.26,orf1ab,missense_variant,c.2827C>T,p.Pro943Ser,p.P943S,ivar,Unassigned +214836,NC_045512.2,445,T,C,PASS,3540,3,3537,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,Unassigned +214836,NC_045512.2,8317,A,G,PASS,45,33,12,0.27,orf1ab,synonymous_variant,c.8052A>G,p.Thr2684Thr,p.T2684T,ivar,Unassigned +214837,NC_045512.2,10257,T,C,ft,16,12,4,0.25,orf1ab,missense_variant,c.9992T>C,p.Val3331Ala,p.V3331A,ivar,B.1.177 +214837,NC_045512.2,14408,C,T,PASS,55,0,55,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,B.1.177 +214837,NC_045512.2,14946,T,TG,ft,14,14,4,0.29,orf1ab,frameshift_variant,c.14683dupG,p.Val4895fs,p.V4895fs,ivar,B.1.177 +214837,NC_045512.2,14958,T,A,ft,14,10,4,0.29,orf1ab,stop_gained,c.14693T>A,p.Leu4898*,p.L4898*,ivar,B.1.177 +214837,NC_045512.2,16308,C,T,PASS,75,0,75,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,B.1.177 +214837,NC_045512.2,21255,G,C,PASS,19,0,19,1.0,orf1ab,missense_variant,c.20990G>C,p.Arg6997Pro,p.R6997P,ivar,B.1.177 +214837,NC_045512.2,222,C,T,PASS,35,0,35,1.0,orf1ab,upstream_gene_variant,c.-44C>T,.,.,ivar,B.1.177 +214837,NC_045512.2,23403,A,G,PASS,728,0,728,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.177 +214837,NC_045512.2,24370,C,T,PASS,63,1,62,0.98,S,synonymous_variant,c.2808C>T,p.Asp936Asp,p.D936D,ivar,B.1.177 +214837,NC_045512.2,26801,C,G,PASS,163,0,163,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,B.1.177 +214837,NC_045512.2,28093,C,T,PASS,85,0,85,1.0,ORF8,missense_variant,c.200C>T,p.Ser67Phe,p.S67F,ivar,B.1.177 +214837,NC_045512.2,28486,C,T,PASS,108,19,89,0.82,N,synonymous_variant,c.213C>T,p.Gly71Gly,p.G71G,ivar,B.1.177 +214837,NC_045512.2,28932,C,T,PASS,118,0,118,1.0,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,B.1.177 +214837,NC_045512.2,29402,G,T,PASS,1594,0,1584,0.99,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,B.1.177 +214837,NC_045512.2,29578,C,T,PASS,14,0,14,1.0,ORF10,synonymous_variant,c.21C>T,p.Phe7Phe,p.F7F,ivar,B.1.177 +214837,NC_045512.2,29645,G,T,PASS,17,0,17,1.0,ORF10,missense_variant,c.88G>T,p.Val30Leu,p.V30L,ivar,B.1.177 +214837,NC_045512.2,3037,C,T,PASS,59,0,59,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,B.1.177 +214837,NC_045512.2,3958,A,C,PASS,178,56,122,0.69,orf1ab,missense_variant,c.3693A>C,p.Lys1231Asn,p.K1231N,ivar,B.1.177 +214837,NC_045512.2,3963,A,T,PASS,194,56,138,0.71,orf1ab,missense_variant,c.3698A>T,p.Lys1233Ile,p.K1233I,ivar,B.1.177 +214837,NC_045512.2,4082,G,A,PASS,39,16,23,0.59,orf1ab,missense_variant,c.3817G>A,p.Asp1273Asn,p.D1273N,ivar,B.1.177 +214837,NC_045512.2,445,T,C,PASS,19439,22,19412,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,B.1.177 +214837,NC_045512.2,527,C,T,PASS,17846,3108,14730,0.83,orf1ab,synonymous_variant,c.262C>T,p.Leu88Leu,p.L88L,ivar,B.1.177 +214837,NC_045512.2,5869,C,T,PASS,29,0,29,1.0,orf1ab,synonymous_variant,c.5604C>T,p.Tyr1868Tyr,p.Y1868Y,ivar,B.1.177 +214837,NC_045512.2,76,T,A,ft,14,10,4,0.29,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,B.1.177 +214837,NC_045512.2,78,T,G,ft,14,10,4,0.29,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,B.1.177 +214838,NC_045512.2,16276,T,C,ft,10,6,4,0.4,orf1ab,synonymous_variant,c.16011T>C,p.His5337His,p.H5337H,ivar,Unassigned +214838,NC_045512.2,23403,A,G,PASS,11,0,11,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +214838,NC_045512.2,28932,C,T,PASS,10,0,10,1.0,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,Unassigned +214838,NC_045512.2,28951,A,G,ft,12,9,3,0.25,N,synonymous_variant,c.678A>G,p.Arg226Arg,p.R226R,ivar,Unassigned +214838,NC_045512.2,29402,G,T,PASS,60,0,60,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,Unassigned +214838,NC_045512.2,445,T,C,PASS,256,3,253,0.99,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,Unassigned +214838,NC_045512.2,527,C,T,PASS,197,18,179,0.91,orf1ab,synonymous_variant,c.262C>T,p.Leu88Leu,p.L88L,ivar,Unassigned +214838,NC_045512.2,7948,C,T,ft,10,7,3,0.3,orf1ab,synonymous_variant,c.7683C>T,p.Tyr2561Tyr,p.Y2561Y,ivar,Unassigned +214838,NC_045512.2,9711,CCA,C,PASS,40,40,14,0.35,orf1ab,frameshift_variant,c.9449_9450delCA,p.Thr3150fs,p.T3150fs,ivar,Unassigned +220338,NC_045512.2,10029,C,T,PASS,13,0,13,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,Unassigned +220338,NC_045512.2,10449,C,A,PASS,19,0,19,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220338,NC_045512.2,11282,AGTTTGTCTG,A,PASS,80,79,66,0.82,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220338,NC_045512.2,11537,A,G,PASS,39,0,39,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220338,NC_045512.2,13195,T,C,PASS,727,1,726,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220338,NC_045512.2,14408,C,T,PASS,10,0,10,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220338,NC_045512.2,16744,G,A,PASS,185,0,185,1.0,orf1ab,synonymous_variant,c.16479G>A,p.Leu5493Leu,p.L5493L,ivar,Unassigned +220338,NC_045512.2,21762,C,T,PASS,10,0,10,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220338,NC_045512.2,21764,ATACATG,A,PASS,10,10,10,1.0,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220338,NC_045512.2,21846,C,T,PASS,19,0,19,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220338,NC_045512.2,23403,A,G,PASS,732,2,730,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220338,NC_045512.2,23525,C,T,PASS,709,4,704,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220338,NC_045512.2,23599,T,G,PASS,254,0,254,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220338,NC_045512.2,23604,C,A,PASS,244,0,242,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220338,NC_045512.2,23854,C,A,PASS,10,0,10,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220338,NC_045512.2,23948,G,T,PASS,97,0,96,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220338,NC_045512.2,24130,C,A,PASS,162,0,162,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220338,NC_045512.2,24424,A,T,PASS,75,0,75,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220338,NC_045512.2,24469,T,A,PASS,127,0,127,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220338,NC_045512.2,24503,C,T,PASS,137,1,136,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220338,NC_045512.2,25000,C,T,PASS,12,0,12,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220338,NC_045512.2,25584,C,T,PASS,26,0,25,0.96,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220338,NC_045512.2,26270,C,T,PASS,91,0,91,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220338,NC_045512.2,26530,A,G,PASS,11,0,11,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220338,NC_045512.2,26577,C,G,PASS,11,0,11,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220338,NC_045512.2,27259,A,C,PASS,38,0,38,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220338,NC_045512.2,28271,A,T,PASS,36,0,36,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220338,NC_045512.2,28311,C,T,PASS,39,0,39,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220338,NC_045512.2,2832,A,G,PASS,24,0,24,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220338,NC_045512.2,28361,GGAGAACGCA,G,PASS,32,32,27,0.84,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220338,NC_045512.2,28881,GG,AA,PASS,1617,29,1583,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220338,NC_045512.2,28883,G,C,PASS,1606,0,1604,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220338,NC_045512.2,811,C,T,PASS,21,0,21,1.0,orf1ab,synonymous_variant,c.546C>T,p.Tyr182Tyr,p.Y182Y,ivar,Unassigned +220338,NC_045512.2,8393,G,A,PASS,1157,5,1150,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220339,NC_045512.2,10029,C,T,PASS,72,0,72,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220339,NC_045512.2,10449,C,A,PASS,257,0,257,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220339,NC_045512.2,11282,AGTTTGTCTG,A,PASS,507,502,426,0.84,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220339,NC_045512.2,11537,A,G,PASS,561,0,559,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220339,NC_045512.2,13195,T,C,PASS,3850,4,3846,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220339,NC_045512.2,14408,C,T,PASS,235,0,235,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220339,NC_045512.2,15240,C,T,PASS,83,0,83,1.0,orf1ab,missense_variant,c.14975C>T,p.Thr4992Ile,p.T4992I,ivar,BA.1.17 +220339,NC_045512.2,18163,A,G,PASS,92,0,92,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220339,NC_045512.2,21762,C,T,PASS,187,2,185,0.99,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220339,NC_045512.2,21764,ATACATG,A,PASS,192,189,166,0.86,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220339,NC_045512.2,21846,C,T,PASS,155,0,154,0.99,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220339,NC_045512.2,22578,G,A,PASS,38,0,38,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.17 +220339,NC_045512.2,22673,TC,CT,PASS,20,0,20,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.17 +220339,NC_045512.2,22679,T,C,PASS,23,0,23,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220339,NC_045512.2,22686,C,T,PASS,24,0,24,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220339,NC_045512.2,23075,T,C,PASS,12,0,12,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.17 +220339,NC_045512.2,23202,C,A,PASS,28,0,28,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220339,NC_045512.2,23403,A,G,PASS,2573,5,2568,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220339,NC_045512.2,23525,C,T,PASS,2372,11,2360,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220339,NC_045512.2,23599,T,G,PASS,877,0,877,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220339,NC_045512.2,23604,C,A,PASS,845,0,842,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220339,NC_045512.2,23854,C,A,PASS,175,2,171,0.98,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220339,NC_045512.2,23948,G,T,PASS,1194,2,1189,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220339,NC_045512.2,24130,C,A,PASS,1645,0,1631,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220339,NC_045512.2,24424,A,T,PASS,520,0,514,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220339,NC_045512.2,24469,T,A,PASS,983,2,973,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220339,NC_045512.2,24503,C,T,PASS,1108,16,1091,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220339,NC_045512.2,25000,C,T,PASS,98,1,97,0.99,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220339,NC_045512.2,25584,C,T,PASS,263,0,261,0.99,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220339,NC_045512.2,26270,C,T,PASS,738,4,731,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220339,NC_045512.2,26530,A,G,PASS,278,0,278,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220339,NC_045512.2,26568,C,T,PASS,248,2,245,0.99,M,missense_variant,c.46C>T,p.Leu16Phe,p.L16F,ivar,BA.1.17 +220339,NC_045512.2,26577,C,G,PASS,245,0,245,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220339,NC_045512.2,26709,G,A,PASS,271,0,269,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220339,NC_045512.2,27259,A,C,PASS,717,0,715,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220339,NC_045512.2,27807,C,T,PASS,258,2,256,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220339,NC_045512.2,28271,A,T,PASS,1012,1,1010,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220339,NC_045512.2,28311,C,T,PASS,951,3,944,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220339,NC_045512.2,2832,A,G,PASS,344,0,344,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220339,NC_045512.2,28361,GGAGAACGCA,G,PASS,754,751,516,0.68,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220339,NC_045512.2,28881,GG,AA,PASS,1968,19,1949,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220339,NC_045512.2,28883,G,C,PASS,1960,1,1959,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220339,NC_045512.2,29772,T,C,PASS,160,1,159,0.99,S,downstream_gene_variant,c.*4388T>C,.,.,ivar,BA.1.17 +220339,NC_045512.2,3037,C,T,PASS,42,0,42,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220339,NC_045512.2,5386,T,G,PASS,38,0,38,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.17 +220339,NC_045512.2,5672,C,T,PASS,269,2,267,0.99,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220339,NC_045512.2,5924,G,A,PASS,113,1,112,0.99,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220339,NC_045512.2,76,T,A,PASS,48,36,12,0.25,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1.17 +220339,NC_045512.2,78,T,G,PASS,48,36,12,0.25,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1.17 +220339,NC_045512.2,8393,G,A,PASS,2673,17,2656,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220339,NC_045512.2,8652,T,C,PASS,2561,2,2559,1.0,orf1ab,missense_variant,c.8387T>C,p.Met2796Thr,p.M2796T,ivar,BA.1.17 +220407,NC_045512.2,13195,T,C,PASS,34,0,34,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220407,NC_045512.2,23403,A,G,PASS,51,0,51,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220407,NC_045512.2,23525,C,T,PASS,42,0,42,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220407,NC_045512.2,23599,T,G,PASS,12,0,12,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220407,NC_045512.2,23604,C,A,PASS,10,0,10,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220407,NC_045512.2,28881,GG,AA,PASS,133,1,132,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220407,NC_045512.2,28883,G,C,PASS,133,0,132,0.99,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220407,NC_045512.2,8393,G,A,PASS,27,0,27,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220433,NC_045512.2,13195,T,C,PASS,59,2,57,0.97,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220433,NC_045512.2,1437,C,T,PASS,15,0,15,1.0,orf1ab,missense_variant,c.1172C>T,p.Ser391Phe,p.S391F,ivar,Unassigned +220433,NC_045512.2,1451,A,T,PASS,15,8,7,0.47,orf1ab,missense_variant,c.1186A>T,p.Ile396Phe,p.I396F,ivar,Unassigned +220433,NC_045512.2,21846,C,T,PASS,13,0,13,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220433,NC_045512.2,23403,A,G,PASS,18,0,18,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220433,NC_045512.2,23525,C,T,PASS,11,0,11,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220433,NC_045512.2,23987,C,T,PASS,13,4,9,0.69,S,missense_variant,c.2425C>T,p.Pro809Ser,p.P809S,ivar,Unassigned +220433,NC_045512.2,24123,A,C,PASS,19,8,11,0.58,S,missense_variant,c.2561A>C,p.Lys854Thr,p.K854T,ivar,Unassigned +220433,NC_045512.2,24130,C,A,PASS,18,0,18,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220433,NC_045512.2,24469,T,A,PASS,13,0,13,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220433,NC_045512.2,24503,C,T,PASS,18,0,18,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220433,NC_045512.2,26270,C,T,PASS,234,0,234,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220433,NC_045512.2,26577,C,G,PASS,11,0,11,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220433,NC_045512.2,26862,C,A,ft,13,8,5,0.38,M,missense_variant,c.340C>A,p.Pro114Thr,p.P114T,ivar,Unassigned +220433,NC_045512.2,28271,A,T,PASS,67,0,67,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220433,NC_045512.2,28311,C,T,PASS,83,2,81,0.98,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220433,NC_045512.2,28881,GG,AA,PASS,429,0,425,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220433,NC_045512.2,28883,G,C,PASS,431,0,429,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220433,NC_045512.2,8393,G,A,PASS,366,0,366,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220518,NC_045512.2,12834,AT,A,ft,12,12,5,0.42,orf1ab,frameshift_variant,c.12572delT,p.Leu4191fs,p.L4191fs,ivar,Unassigned +220518,NC_045512.2,13195,T,C,PASS,68,0,68,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220518,NC_045512.2,23403,A,G,PASS,35,0,35,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220518,NC_045512.2,23525,C,T,PASS,51,0,51,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220518,NC_045512.2,23599,T,G,PASS,28,0,28,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220518,NC_045512.2,23604,C,A,PASS,28,0,28,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220518,NC_045512.2,23948,G,T,PASS,17,0,17,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220518,NC_045512.2,24130,C,A,PASS,23,0,23,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220518,NC_045512.2,24469,T,A,PASS,32,0,32,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220518,NC_045512.2,24503,C,T,PASS,46,0,46,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220518,NC_045512.2,26270,C,T,PASS,340,2,336,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220518,NC_045512.2,27259,A,C,PASS,12,0,12,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220518,NC_045512.2,28271,A,T,PASS,92,0,92,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220518,NC_045512.2,28311,C,T,PASS,104,2,102,0.98,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220518,NC_045512.2,28361,GGAGAACGCA,G,PASS,81,81,30,0.37,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220518,NC_045512.2,28881,GG,AA,PASS,569,4,565,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220518,NC_045512.2,28883,G,C,PASS,566,0,565,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220518,NC_045512.2,3183,A,G,PASS,48,22,26,0.54,orf1ab,missense_variant,c.2918A>G,p.Glu973Gly,p.E973G,ivar,Unassigned +220518,NC_045512.2,514,TGTTATG,T,PASS,205,205,169,0.82,orf1ab,conservative_inframe_deletion,c.253_258delATGGTT,p.Met85_Val86del,p.M85_V86del,ivar,Unassigned +220518,NC_045512.2,8393,G,A,PASS,779,2,777,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220529,NC_045512.2,10029,C,T,PASS,13,0,13,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,Unassigned +220529,NC_045512.2,10449,C,A,PASS,44,0,44,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220529,NC_045512.2,11282,AGTTTGTCTG,A,PASS,182,178,164,0.9,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220529,NC_045512.2,11537,A,G,PASS,173,0,173,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220529,NC_045512.2,13195,T,C,PASS,4328,6,4322,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220529,NC_045512.2,14408,C,T,PASS,79,4,75,0.95,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220529,NC_045512.2,16064,A,G,PASS,116,0,116,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220529,NC_045512.2,16308,C,T,PASS,220,0,220,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,Unassigned +220529,NC_045512.2,18163,A,G,PASS,14,0,14,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,Unassigned +220529,NC_045512.2,21762,C,T,PASS,119,0,119,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220529,NC_045512.2,21764,ATACATG,A,PASS,122,119,108,0.89,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220529,NC_045512.2,21846,C,T,PASS,100,2,96,0.96,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220529,NC_045512.2,22578,G,A,PASS,13,0,13,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,Unassigned +220529,NC_045512.2,22599,G,A,PASS,10,0,10,1.0,S,missense_variant,c.1037G>A,p.Arg346Lys,p.R346K,ivar,Unassigned +220529,NC_045512.2,22679,T,C,PASS,11,0,11,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,Unassigned +220529,NC_045512.2,22686,C,T,PASS,11,0,11,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,Unassigned +220529,NC_045512.2,23403,A,G,PASS,2006,2,2004,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220529,NC_045512.2,23525,C,T,PASS,1968,2,1964,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220529,NC_045512.2,23599,T,G,PASS,712,0,712,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220529,NC_045512.2,23604,C,A,PASS,685,0,679,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220529,NC_045512.2,23854,C,A,PASS,25,0,25,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220529,NC_045512.2,23948,G,T,PASS,253,0,253,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220529,NC_045512.2,24130,C,A,PASS,342,0,338,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220529,NC_045512.2,24424,A,T,PASS,97,0,97,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220529,NC_045512.2,24469,T,A,PASS,548,1,547,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220529,NC_045512.2,24503,C,T,PASS,682,21,661,0.97,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220529,NC_045512.2,25000,C,T,PASS,60,0,60,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220529,NC_045512.2,25584,C,T,PASS,38,1,37,0.97,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220529,NC_045512.2,26270,C,T,PASS,138,0,138,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220529,NC_045512.2,26530,A,G,PASS,69,2,67,0.97,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220529,NC_045512.2,26577,C,G,PASS,93,0,93,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220529,NC_045512.2,26709,G,A,PASS,90,2,88,0.98,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220529,NC_045512.2,27259,A,C,PASS,80,0,80,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220529,NC_045512.2,27807,C,T,PASS,52,0,52,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220529,NC_045512.2,28271,A,T,PASS,775,0,775,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220529,NC_045512.2,28311,C,T,PASS,809,5,802,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220529,NC_045512.2,2832,A,G,PASS,42,0,42,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220529,NC_045512.2,28361,GGAGAACGCA,G,PASS,659,657,484,0.73,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220529,NC_045512.2,28881,GG,AA,PASS,2822,28,2789,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220529,NC_045512.2,28883,G,C,PASS,2814,0,2809,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220529,NC_045512.2,3037,C,T,PASS,22,0,22,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220529,NC_045512.2,8393,G,A,PASS,2312,8,2302,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220530,NC_045512.2,10029,C,T,PASS,11,0,11,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,Unassigned +220530,NC_045512.2,10449,C,A,PASS,13,0,13,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220530,NC_045512.2,11282,AGTTTGTCTG,A,PASS,34,34,28,0.82,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220530,NC_045512.2,11537,A,G,PASS,46,0,46,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220530,NC_045512.2,13195,T,C,PASS,1638,0,1638,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220530,NC_045512.2,14408,C,T,PASS,16,0,16,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220530,NC_045512.2,16064,A,G,PASS,11,0,11,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220530,NC_045512.2,16308,C,T,PASS,44,0,44,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,Unassigned +220530,NC_045512.2,21762,C,T,PASS,13,0,13,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220530,NC_045512.2,21764,ATACATG,A,PASS,13,13,13,1.0,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220530,NC_045512.2,21846,C,T,PASS,19,0,19,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220530,NC_045512.2,23403,A,G,PASS,470,2,468,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220530,NC_045512.2,23525,C,T,PASS,495,2,493,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220530,NC_045512.2,23599,T,G,PASS,216,0,216,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220530,NC_045512.2,23604,C,A,PASS,215,0,213,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220530,NC_045512.2,23854,C,A,PASS,12,0,12,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220530,NC_045512.2,23948,G,T,PASS,31,0,31,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220530,NC_045512.2,24130,C,A,PASS,31,0,31,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220530,NC_045512.2,24424,A,T,PASS,39,0,37,0.95,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220530,NC_045512.2,24469,T,A,PASS,158,0,158,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220530,NC_045512.2,24503,C,T,PASS,191,2,189,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220530,NC_045512.2,25000,C,T,PASS,16,0,16,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220530,NC_045512.2,25584,C,T,PASS,26,0,26,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220530,NC_045512.2,26270,C,T,PASS,161,0,161,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220530,NC_045512.2,26530,A,G,PASS,46,0,46,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220530,NC_045512.2,26577,C,G,PASS,80,0,80,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220530,NC_045512.2,26709,G,A,PASS,61,0,61,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220530,NC_045512.2,27259,A,C,PASS,64,0,64,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220530,NC_045512.2,27406,C,T,PASS,65,0,65,1.0,ORF7a,missense_variant,c.13C>T,p.Leu5Phe,p.L5F,ivar,Unassigned +220530,NC_045512.2,27784,A,T,ft,16,11,5,0.31,ORF7b,missense_variant,c.29A>T,p.Tyr10Phe,p.Y10F,ivar,Unassigned +220530,NC_045512.2,27790,G,C,ft,13,8,5,0.38,ORF7b,missense_variant,c.35G>C,p.Cys12Ser,p.C12S,ivar,Unassigned +220530,NC_045512.2,27807,C,T,PASS,12,0,12,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220530,NC_045512.2,28271,A,T,PASS,189,0,188,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220530,NC_045512.2,28311,C,T,PASS,206,0,206,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220530,NC_045512.2,2832,A,G,PASS,78,0,78,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220530,NC_045512.2,28361,GGAGAACGCA,G,PASS,171,171,134,0.78,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220530,NC_045512.2,28403,G,A,PASS,112,78,34,0.3,N,missense_variant,c.130G>A,p.Gly44Ser,p.G44S,ivar,Unassigned +220530,NC_045512.2,2857,C,T,PASS,48,36,12,0.25,orf1ab,synonymous_variant,c.2592C>T,p.Leu864Leu,p.L864L,ivar,Unassigned +220530,NC_045512.2,28881,GG,AA,PASS,3635,36,3594,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220530,NC_045512.2,28883,G,C,PASS,3618,3,3608,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220530,NC_045512.2,4964,A,G,ft,10,6,4,0.4,orf1ab,missense_variant,c.4699A>G,p.Thr1567Ala,p.T1567A,ivar,Unassigned +220530,NC_045512.2,8393,G,A,PASS,1049,2,1046,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220531,NC_045512.2,10029,C,T,PASS,65,0,65,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.18 +220531,NC_045512.2,10449,C,A,PASS,294,0,293,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.18 +220531,NC_045512.2,11282,AGTTTGTCTG,A,PASS,608,606,530,0.87,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.18 +220531,NC_045512.2,11537,A,G,PASS,587,0,587,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.18 +220531,NC_045512.2,13195,T,C,PASS,5269,16,5253,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.18 +220531,NC_045512.2,14408,C,T,PASS,234,1,231,0.99,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.18 +220531,NC_045512.2,15336,T,C,ft,10,5,5,0.5,orf1ab,missense_variant,c.15071T>C,p.Leu5024Ser,p.L5024S,ivar,BA.1.18 +220531,NC_045512.2,15359,G,A,PASS,10,4,6,0.6,orf1ab,missense_variant,c.15094G>A,p.Ala5032Thr,p.A5032T,ivar,BA.1.18 +220531,NC_045512.2,18163,A,G,PASS,46,0,46,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.18 +220531,NC_045512.2,2172,A,G,PASS,3340,15,3325,1.0,orf1ab,missense_variant,c.1907A>G,p.Lys636Arg,p.K636R,ivar,BA.1.18 +220531,NC_045512.2,21762,C,T,PASS,443,0,443,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.18 +220531,NC_045512.2,21764,ATACATG,A,PASS,449,444,403,0.9,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.18 +220531,NC_045512.2,21846,C,T,PASS,384,3,381,0.99,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.18 +220531,NC_045512.2,22578,G,A,PASS,57,0,57,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.18 +220531,NC_045512.2,22673,TC,CT,PASS,39,0,39,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.18 +220531,NC_045512.2,22679,T,C,PASS,46,0,46,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.18 +220531,NC_045512.2,22686,C,T,PASS,45,0,45,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.18 +220531,NC_045512.2,22882,T,G,PASS,13,0,13,1.0,S,missense_variant,c.1320T>G,p.Asn440Lys,p.N440K,ivar,BA.1.18 +220531,NC_045512.2,22898,G,A,PASS,13,0,13,1.0,S,missense_variant,c.1336G>A,p.Gly446Ser,p.G446S,ivar,BA.1.18 +220531,NC_045512.2,22992,G,A,PASS,11,0,11,1.0,S,missense_variant,c.1430G>A,p.Ser477Asn,p.S477N,ivar,BA.1.18 +220531,NC_045512.2,22995,C,A,PASS,11,0,11,1.0,S,missense_variant,c.1433C>A,p.Thr478Lys,p.T478K,ivar,BA.1.18 +220531,NC_045512.2,23013,A,C,PASS,11,0,11,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.18 +220531,NC_045512.2,23040,A,G,PASS,15,0,15,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.18 +220531,NC_045512.2,23048,G,A,PASS,18,0,18,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.18 +220531,NC_045512.2,23055,A,G,PASS,18,0,18,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.18 +220531,NC_045512.2,23063,A,T,PASS,17,0,17,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.18 +220531,NC_045512.2,23075,T,C,PASS,20,0,20,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.18 +220531,NC_045512.2,23202,C,A,PASS,48,0,48,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.18 +220531,NC_045512.2,23403,A,G,PASS,3684,4,3680,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.18 +220531,NC_045512.2,23525,C,T,PASS,3562,10,3542,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.18 +220531,NC_045512.2,23599,T,G,PASS,1310,0,1308,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.18 +220531,NC_045512.2,23604,C,A,PASS,1248,0,1245,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.18 +220531,NC_045512.2,23854,C,A,PASS,153,0,153,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.18 +220531,NC_045512.2,23948,G,T,PASS,1231,0,1229,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.18 +220531,NC_045512.2,24130,C,A,PASS,1843,2,1824,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.18 +220531,NC_045512.2,24424,A,T,PASS,589,0,589,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.18 +220531,NC_045512.2,24469,T,A,PASS,1156,4,1150,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.18 +220531,NC_045512.2,24503,C,T,PASS,1344,14,1330,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.18 +220531,NC_045512.2,25000,C,T,PASS,165,1,164,0.99,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.18 +220531,NC_045512.2,25584,C,T,PASS,263,0,263,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.18 +220531,NC_045512.2,25855,G,T,PASS,263,0,262,1.0,ORF3a,missense_variant,c.463G>T,p.Asp155Tyr,p.D155Y,ivar,BA.1.18 +220531,NC_045512.2,25931,CT,AC,PASS,276,1,275,1.0,ORF3a,missense_variant,c.539_540delCTinsAC,p.Ser180Tyr,p.S180Y,ivar,BA.1.18 +220531,NC_045512.2,26270,C,T,PASS,761,2,759,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.18 +220531,NC_045512.2,26530,A,G,PASS,192,0,192,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.18 +220531,NC_045512.2,26577,C,G,PASS,211,0,211,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.18 +220531,NC_045512.2,26709,G,A,PASS,190,1,189,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.18 +220531,NC_045512.2,27259,A,C,PASS,631,0,624,0.99,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.18 +220531,NC_045512.2,27807,C,T,PASS,247,2,245,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.18 +220531,NC_045512.2,27933,G,A,PASS,448,3,442,0.99,ORF8,missense_variant,c.40G>A,p.Ala14Thr,p.A14T,ivar,BA.1.18 +220531,NC_045512.2,28271,A,T,PASS,1392,0,1390,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.18 +220531,NC_045512.2,28311,C,T,PASS,1393,1,1382,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.18 +220531,NC_045512.2,2832,A,G,PASS,216,0,216,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.18 +220531,NC_045512.2,28361,GGAGAACGCA,G,PASS,1099,1092,795,0.72,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.18 +220531,NC_045512.2,28881,GG,AA,PASS,2048,32,2014,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.18 +220531,NC_045512.2,28883,G,C,PASS,2025,2,2020,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.18 +220531,NC_045512.2,3037,C,T,PASS,58,0,58,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.18 +220531,NC_045512.2,5386,T,G,PASS,34,0,34,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.18 +220531,NC_045512.2,5730,C,T,PASS,289,0,289,1.0,orf1ab,missense_variant,c.5465C>T,p.Thr1822Ile,p.T1822I,ivar,BA.1.18 +220531,NC_045512.2,8393,G,A,PASS,3368,17,3350,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.18 +220532,NC_045512.2,10449,C,A,PASS,26,0,26,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220532,NC_045512.2,11282,AGTTTGTCTG,A,PASS,38,38,33,0.87,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220532,NC_045512.2,11537,A,G,PASS,58,0,58,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220532,NC_045512.2,13195,T,C,PASS,3057,4,3053,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220532,NC_045512.2,14090,A,T,ft,13,9,4,0.31,orf1ab,missense_variant,c.13825A>T,p.Met4609Leu,p.M4609L,ivar,Unassigned +220532,NC_045512.2,14408,C,T,PASS,33,0,32,0.97,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220532,NC_045512.2,15933,C,T,PASS,69,4,65,0.94,orf1ab,missense_variant,c.15668C>T,p.Thr5223Ile,p.T5223I,ivar,Unassigned +220532,NC_045512.2,21762,C,T,PASS,51,0,51,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220532,NC_045512.2,21764,ATACATG,A,PASS,51,51,46,0.9,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220532,NC_045512.2,21846,C,T,PASS,72,0,72,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220532,NC_045512.2,23403,A,G,PASS,753,1,752,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220532,NC_045512.2,23525,C,T,PASS,730,0,730,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220532,NC_045512.2,23599,T,G,PASS,267,0,267,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220532,NC_045512.2,23604,C,A,PASS,263,0,261,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220532,NC_045512.2,23854,C,A,PASS,18,0,18,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220532,NC_045512.2,23948,G,T,PASS,81,0,81,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220532,NC_045512.2,24130,C,A,PASS,131,0,131,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220532,NC_045512.2,24424,A,T,PASS,26,0,26,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220532,NC_045512.2,24469,T,A,PASS,242,0,242,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220532,NC_045512.2,24503,C,T,PASS,289,2,287,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220532,NC_045512.2,25000,C,T,PASS,13,0,13,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220532,NC_045512.2,25584,C,T,PASS,13,0,13,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220532,NC_045512.2,26270,C,T,PASS,33,0,33,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220532,NC_045512.2,26530,A,G,PASS,31,0,31,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220532,NC_045512.2,26577,C,G,PASS,31,0,31,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220532,NC_045512.2,26654,G,GT,PASS,28,28,9,0.32,M,frameshift_variant,c.137dupT,p.Leu46fs,p.L46fs,ivar,Unassigned +220532,NC_045512.2,26709,G,A,PASS,33,0,33,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220532,NC_045512.2,27259,A,C,PASS,40,0,40,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220532,NC_045512.2,27807,C,T,PASS,22,3,19,0.86,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220532,NC_045512.2,28271,A,T,PASS,365,0,365,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220532,NC_045512.2,28311,C,T,PASS,335,0,335,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220532,NC_045512.2,2832,A,G,PASS,31,0,31,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220532,NC_045512.2,28361,GGAGAACGCA,G,PASS,279,279,202,0.72,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220532,NC_045512.2,28512,C,T,PASS,110,79,29,0.26,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,Unassigned +220532,NC_045512.2,28881,GG,AA,PASS,2846,42,2800,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220532,NC_045512.2,28883,G,C,PASS,2820,3,2814,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220532,NC_045512.2,4097,T,TC,PASS,25,25,8,0.32,orf1ab,frameshift_variant,c.3832_3833insC,p.Phe1278fs,p.F1278fs,ivar,Unassigned +220532,NC_045512.2,4101,T,C,PASS,25,17,8,0.32,orf1ab,missense_variant,c.3836T>C,p.Leu1279Ser,p.L1279S,ivar,Unassigned +220532,NC_045512.2,5672,C,T,PASS,11,0,11,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220532,NC_045512.2,8393,G,A,PASS,1208,5,1203,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220533,NC_045512.2,13195,T,C,PASS,35,0,35,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220533,NC_045512.2,23403,A,G,PASS,19,0,19,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220533,NC_045512.2,23525,C,T,PASS,15,0,15,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220533,NC_045512.2,28881,GG,AA,PASS,335,4,331,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220533,NC_045512.2,28883,G,C,PASS,331,0,331,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220533,NC_045512.2,8393,G,A,PASS,102,0,102,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220534,NC_045512.2,10029,C,T,PASS,80,1,79,0.99,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220534,NC_045512.2,10449,C,A,PASS,302,0,300,0.99,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220534,NC_045512.2,11282,AGTTTGTCTG,A,PASS,1212,1193,1059,0.87,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220534,NC_045512.2,11537,A,G,PASS,576,0,576,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220534,NC_045512.2,13195,T,C,PASS,6107,17,6090,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220534,NC_045512.2,14408,C,T,PASS,315,0,315,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220534,NC_045512.2,18163,A,G,PASS,58,0,58,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220534,NC_045512.2,19374,C,T,PASS,426,3,423,0.99,orf1ab,missense_variant,c.19109C>T,p.Ser6370Phe,p.S6370F,ivar,BA.1.17 +220534,NC_045512.2,20743,A,C,PASS,3288,0,3285,1.0,orf1ab,missense_variant,c.20478A>C,p.Lys6826Asn,p.K6826N,ivar,BA.1.17 +220534,NC_045512.2,21762,C,T,PASS,429,4,425,0.99,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220534,NC_045512.2,21764,ATACATG,A,PASS,434,429,398,0.92,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220534,NC_045512.2,21846,C,T,PASS,452,2,450,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220534,NC_045512.2,22193,AATT,A,PASS,19,19,16,0.84,S,disruptive_inframe_deletion,c.632_634delATT,p.Asn211_Leu212delinsIle,p.N211_L212delinsI,ivar,BA.1.17 +220534,NC_045512.2,22204,T,TGAGCCAGAA,PASS,16,16,13,0.81,S,disruptive_inframe_insertion,c.644_645insGCCAGAAGA,p.Arg214_Asp215insGluProGlu,p.R214_D215insEPE,ivar,BA.1.17 +220534,NC_045512.2,22578,G,A,PASS,87,0,87,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.17 +220534,NC_045512.2,22673,TC,CT,PASS,68,0,68,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.17 +220534,NC_045512.2,22679,T,C,PASS,95,0,95,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220534,NC_045512.2,22686,C,T,PASS,94,0,94,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220534,NC_045512.2,22882,T,G,PASS,13,0,13,1.0,S,missense_variant,c.1320T>G,p.Asn440Lys,p.N440K,ivar,BA.1.17 +220534,NC_045512.2,22898,G,A,PASS,11,0,11,1.0,S,missense_variant,c.1336G>A,p.Gly446Ser,p.G446S,ivar,BA.1.17 +220534,NC_045512.2,22992,G,A,PASS,20,0,20,1.0,S,missense_variant,c.1430G>A,p.Ser477Asn,p.S477N,ivar,BA.1.17 +220534,NC_045512.2,22995,C,A,PASS,20,0,20,1.0,S,missense_variant,c.1433C>A,p.Thr478Lys,p.T478K,ivar,BA.1.17 +220534,NC_045512.2,23013,A,C,PASS,24,0,24,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.17 +220534,NC_045512.2,23040,A,G,PASS,33,0,33,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.17 +220534,NC_045512.2,23048,G,A,PASS,33,1,32,0.97,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.17 +220534,NC_045512.2,23055,A,G,PASS,35,0,35,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.17 +220534,NC_045512.2,23063,A,T,PASS,38,0,38,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.17 +220534,NC_045512.2,23075,T,C,PASS,42,0,42,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.17 +220534,NC_045512.2,23202,C,A,PASS,77,0,77,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220534,NC_045512.2,23403,A,G,PASS,3887,4,3880,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220534,NC_045512.2,23525,C,T,PASS,3730,6,3714,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220534,NC_045512.2,23599,T,G,PASS,1409,0,1404,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220534,NC_045512.2,23604,C,A,PASS,1356,0,1350,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220534,NC_045512.2,23854,C,A,PASS,252,1,250,0.99,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220534,NC_045512.2,23948,G,T,PASS,1209,0,1206,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220534,NC_045512.2,24130,C,A,PASS,1902,2,1884,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220534,NC_045512.2,24424,A,T,PASS,860,1,856,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220534,NC_045512.2,24469,T,A,PASS,1573,3,1565,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220534,NC_045512.2,24503,C,T,PASS,1795,32,1760,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220534,NC_045512.2,25000,C,T,PASS,198,0,198,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220534,NC_045512.2,25584,C,T,PASS,452,9,441,0.98,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220534,NC_045512.2,26270,C,T,PASS,1216,6,1208,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220534,NC_045512.2,26530,A,G,PASS,353,0,353,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220534,NC_045512.2,26577,C,G,PASS,356,0,355,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220534,NC_045512.2,26709,G,A,PASS,372,2,369,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220534,NC_045512.2,27259,A,C,PASS,803,0,799,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220534,NC_045512.2,27807,C,T,PASS,288,0,288,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220534,NC_045512.2,28271,A,T,PASS,1664,5,1652,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220534,NC_045512.2,28311,C,T,PASS,1664,11,1651,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220534,NC_045512.2,2832,A,G,PASS,326,0,326,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220534,NC_045512.2,28361,GGAGAACGCA,G,PASS,1461,1458,1071,0.73,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220534,NC_045512.2,28881,GG,AA,PASS,2169,23,2143,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220534,NC_045512.2,28883,G,C,PASS,2150,0,2147,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220534,NC_045512.2,3037,C,T,PASS,104,0,104,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220534,NC_045512.2,5386,T,G,PASS,33,0,33,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.17 +220534,NC_045512.2,5672,C,T,PASS,610,2,608,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220534,NC_045512.2,5924,G,A,PASS,241,0,241,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220534,NC_045512.2,8393,G,A,PASS,3994,13,3975,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220534,NC_045512.2,8715,C,T,PASS,28,20,8,0.29,orf1ab,missense_variant,c.8450C>T,p.Thr2817Ile,p.T2817I,ivar,BA.1.17 +220535,NC_045512.2,10449,C,A,PASS,23,0,23,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220535,NC_045512.2,11282,AGTTTGTCTG,A,PASS,76,76,65,0.86,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220535,NC_045512.2,11537,A,G,PASS,61,0,61,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220535,NC_045512.2,13195,T,C,PASS,2278,1,2277,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220535,NC_045512.2,14408,C,T,PASS,40,0,40,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220535,NC_045512.2,14646,T,A,PASS,41,27,12,0.29,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,Unassigned +220535,NC_045512.2,16064,A,G,PASS,42,0,42,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220535,NC_045512.2,16308,C,T,PASS,133,0,133,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,Unassigned +220535,NC_045512.2,21762,C,T,PASS,42,0,42,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220535,NC_045512.2,21764,ATACATG,A,PASS,43,42,36,0.84,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220535,NC_045512.2,21846,C,T,PASS,55,0,55,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220535,NC_045512.2,23403,A,G,PASS,1687,0,1687,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220535,NC_045512.2,23525,C,T,PASS,1723,4,1719,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220535,NC_045512.2,23599,T,G,PASS,665,0,665,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220535,NC_045512.2,23604,C,A,PASS,648,0,645,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220535,NC_045512.2,23948,G,T,PASS,59,0,59,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220535,NC_045512.2,24130,C,A,PASS,93,0,93,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220535,NC_045512.2,24424,A,T,PASS,39,0,39,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220535,NC_045512.2,24469,T,A,PASS,245,1,244,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220535,NC_045512.2,24503,C,T,PASS,281,1,280,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220535,NC_045512.2,25000,C,T,PASS,19,0,19,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220535,NC_045512.2,25584,C,T,PASS,27,0,27,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220535,NC_045512.2,26270,C,T,PASS,194,0,194,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220535,NC_045512.2,26530,A,G,PASS,114,0,114,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220535,NC_045512.2,26577,C,G,PASS,120,1,119,0.99,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220535,NC_045512.2,26709,G,A,PASS,93,0,93,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220535,NC_045512.2,27259,A,C,PASS,78,0,78,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220535,NC_045512.2,27807,C,T,PASS,42,0,42,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220535,NC_045512.2,28271,A,T,PASS,684,0,684,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220535,NC_045512.2,28311,C,T,PASS,667,16,651,0.98,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220535,NC_045512.2,2832,A,G,PASS,25,0,25,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220535,NC_045512.2,28361,GGAGAACGCA,G,PASS,498,496,337,0.68,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220535,NC_045512.2,28512,C,T,PASS,234,171,62,0.26,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,Unassigned +220535,NC_045512.2,28881,GG,AA,PASS,6177,65,6104,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220535,NC_045512.2,28883,G,C,PASS,6141,2,6131,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220535,NC_045512.2,3037,C,T,PASS,11,0,11,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220535,NC_045512.2,4273,T,A,PASS,31,13,18,0.58,orf1ab,synonymous_variant,c.4008T>A,p.Gly1336Gly,p.G1336G,ivar,Unassigned +220535,NC_045512.2,76,T,A,ft,11,7,4,0.36,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220535,NC_045512.2,78,T,G,ft,11,7,4,0.36,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220535,NC_045512.2,8393,G,A,PASS,2646,16,2630,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220535,NC_045512.2,9572,G,A,PASS,1287,8,1277,0.99,orf1ab,missense_variant,c.9307G>A,p.Gly3103Ser,p.G3103S,ivar,Unassigned +220536,NC_045512.2,10449,C,A,PASS,12,0,12,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220536,NC_045512.2,11282,AGTTTGTCTG,A,PASS,36,35,32,0.89,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220536,NC_045512.2,11537,A,G,PASS,25,0,25,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220536,NC_045512.2,13195,T,C,PASS,1638,4,1634,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220536,NC_045512.2,14408,C,T,PASS,33,0,33,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220536,NC_045512.2,14646,T,A,PASS,43,27,16,0.37,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,Unassigned +220536,NC_045512.2,21595,C,T,PASS,167,0,167,1.0,S,synonymous_variant,c.33C>T,p.Val11Val,p.V11V,ivar,Unassigned +220536,NC_045512.2,21762,C,T,PASS,31,2,29,0.94,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220536,NC_045512.2,21764,ATACATG,A,PASS,32,32,32,1.0,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220536,NC_045512.2,21846,C,T,PASS,34,0,34,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220536,NC_045512.2,21859,C,T,PASS,31,0,31,1.0,S,synonymous_variant,c.297C>T,p.Asn99Asn,p.N99N,ivar,Unassigned +220536,NC_045512.2,23403,A,G,PASS,1494,4,1490,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220536,NC_045512.2,23525,C,T,PASS,1441,16,1425,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220536,NC_045512.2,23599,T,G,PASS,586,0,586,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220536,NC_045512.2,23604,C,A,PASS,571,0,571,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220536,NC_045512.2,23948,G,T,PASS,38,0,38,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220536,NC_045512.2,24130,C,A,PASS,51,0,51,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220536,NC_045512.2,24424,A,T,PASS,23,0,23,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220536,NC_045512.2,24469,T,A,PASS,203,0,203,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220536,NC_045512.2,24503,C,T,PASS,240,0,240,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220536,NC_045512.2,25000,C,T,PASS,17,0,17,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220536,NC_045512.2,25577,T,C,PASS,14,0,14,1.0,ORF3a,missense_variant,c.185T>C,p.Ile62Thr,p.I62T,ivar,Unassigned +220536,NC_045512.2,26270,C,T,PASS,99,0,99,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220536,NC_045512.2,26530,A,G,PASS,36,0,36,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220536,NC_045512.2,26577,C,G,PASS,40,0,40,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220536,NC_045512.2,26709,G,A,PASS,42,0,42,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220536,NC_045512.2,27259,A,C,PASS,29,0,29,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220536,NC_045512.2,27807,C,T,PASS,12,0,12,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220536,NC_045512.2,28271,A,T,PASS,310,2,308,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220536,NC_045512.2,28311,C,T,PASS,327,2,325,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220536,NC_045512.2,2832,A,G,PASS,15,0,15,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220536,NC_045512.2,28361,GGAGAACGCA,G,PASS,223,222,162,0.73,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220536,NC_045512.2,28881,GG,AA,PASS,5160,55,5100,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220536,NC_045512.2,28883,G,C,PASS,5134,3,5127,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220536,NC_045512.2,3037,C,T,PASS,14,0,14,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220536,NC_045512.2,8393,G,A,PASS,2570,9,2558,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220537,NC_045512.2,10029,C,T,PASS,30,0,30,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220537,NC_045512.2,10449,C,A,PASS,81,0,79,0.98,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220537,NC_045512.2,11282,AGTTTGTCTG,A,PASS,360,355,322,0.89,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220537,NC_045512.2,11537,A,G,PASS,303,0,303,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220537,NC_045512.2,13195,T,C,PASS,5220,4,5213,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220537,NC_045512.2,14408,C,T,PASS,123,0,123,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220537,NC_045512.2,18163,A,G,PASS,13,0,13,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220537,NC_045512.2,21762,C,T,PASS,202,1,201,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220537,NC_045512.2,21764,ATACATG,A,PASS,207,202,188,0.91,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220537,NC_045512.2,21846,C,T,PASS,220,0,220,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220537,NC_045512.2,22478,T,C,ft,15,11,4,0.27,S,missense_variant,c.916T>C,p.Phe306Leu,p.F306L,ivar,BA.1.17 +220537,NC_045512.2,22578,G,A,PASS,22,0,22,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.17 +220537,NC_045512.2,22673,TC,CT,PASS,18,0,18,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.17 +220537,NC_045512.2,22679,T,C,PASS,22,0,22,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220537,NC_045512.2,22686,C,T,PASS,22,0,22,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220537,NC_045512.2,23048,G,A,PASS,10,0,10,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.17 +220537,NC_045512.2,23055,A,G,PASS,10,0,10,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.17 +220537,NC_045512.2,23063,A,T,PASS,11,0,11,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.17 +220537,NC_045512.2,23075,T,C,PASS,12,0,12,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.17 +220537,NC_045512.2,23202,C,A,PASS,47,0,47,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220537,NC_045512.2,23403,A,G,PASS,3085,4,3081,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220537,NC_045512.2,23525,C,T,PASS,2906,14,2884,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220537,NC_045512.2,23599,T,G,PASS,1118,0,1116,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220537,NC_045512.2,23604,C,A,PASS,1080,0,1077,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220537,NC_045512.2,23854,C,A,PASS,74,0,74,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220537,NC_045512.2,23948,G,T,PASS,689,2,686,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220537,NC_045512.2,24130,C,A,PASS,1007,0,997,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220537,NC_045512.2,24424,A,T,PASS,270,2,268,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220537,NC_045512.2,24469,T,A,PASS,895,0,888,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220537,NC_045512.2,24503,C,T,PASS,1054,21,1033,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220537,NC_045512.2,25000,C,T,PASS,93,0,93,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220537,NC_045512.2,25584,C,T,PASS,117,0,117,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220537,NC_045512.2,26270,C,T,PASS,578,0,576,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220537,NC_045512.2,26530,A,G,PASS,226,0,226,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220537,NC_045512.2,26577,C,G,PASS,274,0,274,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220537,NC_045512.2,26709,G,A,PASS,253,0,253,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220537,NC_045512.2,27259,A,C,PASS,315,0,315,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220537,NC_045512.2,27384,T,C,PASS,451,0,451,1.0,ORF6,synonymous_variant,c.183T>C,p.Asp61Asp,p.D61D,ivar,BA.1.17 +220537,NC_045512.2,27807,C,T,PASS,91,0,91,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220537,NC_045512.2,28271,A,T,PASS,918,2,913,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220537,NC_045512.2,28311,C,T,PASS,933,0,929,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220537,NC_045512.2,2832,A,G,PASS,97,0,97,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220537,NC_045512.2,28361,GGAGAACGCA,G,PASS,774,770,558,0.72,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220537,NC_045512.2,28881,GG,AA,PASS,3048,38,3005,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220537,NC_045512.2,28883,G,C,PASS,3032,4,3020,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220537,NC_045512.2,3037,C,T,PASS,49,0,49,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220537,NC_045512.2,5386,T,G,PASS,15,0,15,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.17 +220537,NC_045512.2,5672,C,T,PASS,149,0,149,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220537,NC_045512.2,5924,G,A,PASS,77,0,77,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220537,NC_045512.2,635,C,T,PASS,9649,48,9569,0.99,orf1ab,missense_variant,c.370C>T,p.Arg124Cys,p.R124C,ivar,BA.1.17 +220537,NC_045512.2,7984,T,C,PASS,1058,2,1056,1.0,orf1ab,synonymous_variant,c.7719T>C,p.Asp2573Asp,p.D2573D,ivar,BA.1.17 +220537,NC_045512.2,8393,G,A,PASS,2866,7,2859,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220538,NC_045512.2,10029,C,T,PASS,23,0,23,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.18 +220538,NC_045512.2,10449,C,A,PASS,82,0,82,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.18 +220538,NC_045512.2,11282,AGTTTGTCTG,A,PASS,493,491,443,0.9,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.18 +220538,NC_045512.2,11537,A,G,PASS,252,0,252,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.18 +220538,NC_045512.2,13195,T,C,PASS,4749,6,4741,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.18 +220538,NC_045512.2,14408,C,T,PASS,81,0,79,0.98,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.18 +220538,NC_045512.2,18163,A,G,PASS,28,0,28,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.18 +220538,NC_045512.2,2172,A,G,PASS,1213,5,1207,1.0,orf1ab,missense_variant,c.1907A>G,p.Lys636Arg,p.K636R,ivar,BA.1.18 +220538,NC_045512.2,21762,C,T,PASS,158,0,158,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.18 +220538,NC_045512.2,21764,ATACATG,A,PASS,165,160,145,0.88,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.18 +220538,NC_045512.2,21846,C,T,PASS,170,0,170,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.18 +220538,NC_045512.2,22578,G,A,PASS,33,0,33,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.18 +220538,NC_045512.2,22673,TC,CT,PASS,19,1,18,0.95,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.18 +220538,NC_045512.2,22679,T,C,PASS,25,0,25,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.18 +220538,NC_045512.2,22686,C,T,PASS,25,0,25,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.18 +220538,NC_045512.2,23040,A,G,PASS,12,0,12,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.18 +220538,NC_045512.2,23048,G,A,PASS,13,0,13,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.18 +220538,NC_045512.2,23055,A,G,PASS,13,0,13,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.18 +220538,NC_045512.2,23063,A,T,PASS,13,0,13,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.18 +220538,NC_045512.2,23075,T,C,PASS,10,0,10,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.18 +220538,NC_045512.2,23202,C,A,PASS,22,0,22,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.18 +220538,NC_045512.2,23403,A,G,PASS,3286,10,3275,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.18 +220538,NC_045512.2,23525,C,T,PASS,3216,2,3208,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.18 +220538,NC_045512.2,23599,T,G,PASS,1320,1,1317,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.18 +220538,NC_045512.2,23604,C,A,PASS,1275,0,1266,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.18 +220538,NC_045512.2,23854,C,A,PASS,51,0,50,0.98,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.18 +220538,NC_045512.2,23948,G,T,PASS,254,0,253,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.18 +220538,NC_045512.2,24130,C,A,PASS,419,0,417,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.18 +220538,NC_045512.2,24424,A,T,PASS,173,0,171,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.18 +220538,NC_045512.2,24469,T,A,PASS,675,2,669,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.18 +220538,NC_045512.2,24503,C,T,PASS,821,13,808,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.18 +220538,NC_045512.2,25000,C,T,PASS,104,0,104,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.18 +220538,NC_045512.2,25584,C,T,PASS,103,0,103,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.18 +220538,NC_045512.2,25855,G,T,PASS,79,0,79,1.0,ORF3a,missense_variant,c.463G>T,p.Asp155Tyr,p.D155Y,ivar,BA.1.18 +220538,NC_045512.2,25931,CT,AC,PASS,88,0,88,1.0,ORF3a,missense_variant,c.539_540delCTinsAC,p.Ser180Tyr,p.S180Y,ivar,BA.1.18 +220538,NC_045512.2,26270,C,T,PASS,315,0,315,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.18 +220538,NC_045512.2,26530,A,G,PASS,141,0,141,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.18 +220538,NC_045512.2,26577,C,G,PASS,152,0,152,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.18 +220538,NC_045512.2,26709,G,A,PASS,160,0,160,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.18 +220538,NC_045512.2,27259,A,C,PASS,327,0,327,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.18 +220538,NC_045512.2,27519,C,T,PASS,303,0,303,1.0,ORF7a,synonymous_variant,c.126C>T,p.Gly42Gly,p.G42G,ivar,BA.1.18 +220538,NC_045512.2,27807,C,T,PASS,118,0,118,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.18 +220538,NC_045512.2,28271,A,T,PASS,985,4,981,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.18 +220538,NC_045512.2,28311,C,T,PASS,995,6,987,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.18 +220538,NC_045512.2,2832,A,G,PASS,59,0,59,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.18 +220538,NC_045512.2,28361,GGAGAACGCA,G,PASS,847,843,615,0.73,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.18 +220538,NC_045512.2,28881,GG,AA,PASS,2536,35,2498,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.18 +220538,NC_045512.2,28883,G,C,PASS,2511,2,2506,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.18 +220538,NC_045512.2,3037,C,T,PASS,42,0,42,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.18 +220538,NC_045512.2,5386,T,G,PASS,11,0,9,0.82,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.18 +220538,NC_045512.2,5730,C,T,PASS,90,1,89,0.99,orf1ab,missense_variant,c.5465C>T,p.Thr1822Ile,p.T1822I,ivar,BA.1.18 +220538,NC_045512.2,8393,G,A,PASS,3456,17,3437,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.18 +220539,NC_045512.2,10449,C,A,PASS,32,0,32,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220539,NC_045512.2,11282,AGTTTGTCTG,A,PASS,101,100,83,0.82,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220539,NC_045512.2,11455,C,T,PASS,127,0,127,1.0,orf1ab,synonymous_variant,c.11190C>T,p.Ala3730Ala,p.A3730A,ivar,Unassigned +220539,NC_045512.2,11537,A,G,PASS,82,0,82,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220539,NC_045512.2,13195,T,C,PASS,4012,6,4006,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220539,NC_045512.2,14408,C,T,PASS,72,0,72,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220539,NC_045512.2,21762,C,T,PASS,89,0,89,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220539,NC_045512.2,21764,ATACATG,A,PASS,89,89,82,0.92,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220539,NC_045512.2,21846,C,T,PASS,73,0,73,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220539,NC_045512.2,23403,A,G,PASS,1894,4,1890,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220539,NC_045512.2,23525,C,T,PASS,1971,3,1968,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220539,NC_045512.2,23599,T,G,PASS,834,0,834,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220539,NC_045512.2,23604,C,A,PASS,809,0,808,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220539,NC_045512.2,23854,C,A,PASS,14,1,12,0.86,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220539,NC_045512.2,23948,G,T,PASS,146,0,146,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220539,NC_045512.2,23987,C,T,PASS,177,2,175,0.99,S,missense_variant,c.2425C>T,p.Pro809Ser,p.P809S,ivar,Unassigned +220539,NC_045512.2,24130,C,A,PASS,230,0,228,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220539,NC_045512.2,24424,A,T,PASS,57,0,57,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220539,NC_045512.2,24469,T,A,PASS,456,0,456,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220539,NC_045512.2,24503,C,T,PASS,539,6,532,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220539,NC_045512.2,25000,C,T,PASS,35,2,33,0.94,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220539,NC_045512.2,25584,C,T,PASS,37,0,37,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220539,NC_045512.2,26270,C,T,PASS,144,0,144,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220539,NC_045512.2,26530,A,G,PASS,35,0,35,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220539,NC_045512.2,26577,C,G,PASS,49,0,49,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220539,NC_045512.2,26709,G,A,PASS,21,0,21,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220539,NC_045512.2,27259,A,C,PASS,73,0,73,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220539,NC_045512.2,27807,C,T,PASS,37,0,37,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220539,NC_045512.2,2785,T,C,PASS,30,22,8,0.27,orf1ab,synonymous_variant,c.2520T>C,p.Asn840Asn,p.N840N,ivar,Unassigned +220539,NC_045512.2,28271,A,T,PASS,299,0,299,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220539,NC_045512.2,28311,C,T,PASS,288,2,286,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220539,NC_045512.2,2832,A,G,PASS,35,0,35,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220539,NC_045512.2,28361,GGAGAACGCA,G,PASS,204,202,147,0.72,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220539,NC_045512.2,28881,GG,AA,PASS,5835,60,5773,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220539,NC_045512.2,28883,G,C,PASS,5804,4,5791,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220539,NC_045512.2,3037,C,T,PASS,24,0,24,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220539,NC_045512.2,8393,G,A,PASS,3152,5,3147,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220540,NC_045512.2,11282,AGTTTGTCTG,A,PASS,12,12,12,1.0,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220540,NC_045512.2,13195,T,C,PASS,87,0,87,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220540,NC_045512.2,14646,T,A,PASS,12,4,8,0.67,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,Unassigned +220540,NC_045512.2,2010,A,G,ft,10,6,4,0.4,orf1ab,missense_variant,c.1745A>G,p.Asp582Gly,p.D582G,ivar,Unassigned +220540,NC_045512.2,23403,A,G,PASS,282,0,282,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220540,NC_045512.2,23525,C,T,PASS,293,0,293,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220540,NC_045512.2,23599,T,G,PASS,121,0,121,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220540,NC_045512.2,23604,C,A,PASS,117,0,117,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220540,NC_045512.2,24130,C,A,PASS,12,0,12,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220540,NC_045512.2,26270,C,T,PASS,40,0,40,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220540,NC_045512.2,26530,A,G,PASS,12,0,12,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220540,NC_045512.2,26577,C,G,PASS,15,0,15,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220540,NC_045512.2,28271,A,T,PASS,41,2,39,0.95,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220540,NC_045512.2,28311,C,T,PASS,45,0,45,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220540,NC_045512.2,28361,GGAGAACGCA,G,PASS,33,33,25,0.76,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220540,NC_045512.2,28881,GG,AA,PASS,3161,17,3140,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220540,NC_045512.2,28883,G,C,PASS,3153,4,3146,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220540,NC_045512.2,8393,G,A,PASS,606,0,606,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220540,NC_045512.2,9572,G,A,PASS,96,2,94,0.98,orf1ab,missense_variant,c.9307G>A,p.Gly3103Ser,p.G3103S,ivar,Unassigned +220541,NC_045512.2,10029,C,T,PASS,11,0,11,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.1.1 +220541,NC_045512.2,10449,C,A,PASS,83,0,82,0.99,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1.1 +220541,NC_045512.2,11282,AGTTTGTCTG,A,PASS,120,120,116,0.97,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1.1 +220541,NC_045512.2,11537,A,G,PASS,197,0,197,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1.1 +220541,NC_045512.2,13195,T,C,PASS,5495,3,5491,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1.1 +220541,NC_045512.2,14408,C,T,PASS,104,0,104,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1.1 +220541,NC_045512.2,16064,A,G,PASS,228,0,228,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,BA.1.1.1 +220541,NC_045512.2,16308,C,T,PASS,423,1,422,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,BA.1.1.1 +220541,NC_045512.2,18163,A,G,PASS,22,0,22,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.1.1 +220541,NC_045512.2,21762,C,T,PASS,147,0,147,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1.1 +220541,NC_045512.2,21764,ATACATG,A,PASS,147,147,141,0.96,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1.1 +220541,NC_045512.2,21846,C,T,PASS,142,0,142,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1.1 +220541,NC_045512.2,22578,G,A,PASS,12,0,12,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.1.1 +220541,NC_045512.2,22599,G,A,PASS,15,0,15,1.0,S,missense_variant,c.1037G>A,p.Arg346Lys,p.R346K,ivar,BA.1.1.1 +220541,NC_045512.2,22679,T,C,PASS,11,0,11,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.1.1 +220541,NC_045512.2,22686,C,T,PASS,11,0,11,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.1.1 +220541,NC_045512.2,23403,A,G,PASS,2543,1,2541,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1.1 +220541,NC_045512.2,23525,C,T,PASS,2437,14,2421,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1.1 +220541,NC_045512.2,23599,T,G,PASS,936,0,936,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1.1 +220541,NC_045512.2,23604,C,A,PASS,908,2,901,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1.1 +220541,NC_045512.2,23854,C,A,PASS,41,0,41,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1.1 +220541,NC_045512.2,23948,G,T,PASS,581,0,580,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1.1 +220541,NC_045512.2,24130,C,A,PASS,761,0,760,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1.1 +220541,NC_045512.2,24424,A,T,PASS,135,0,135,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1.1 +220541,NC_045512.2,24469,T,A,PASS,759,0,758,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1.1 +220541,NC_045512.2,24503,C,T,PASS,912,18,894,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1.1 +220541,NC_045512.2,25000,C,T,PASS,39,0,39,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1.1 +220541,NC_045512.2,25584,C,T,PASS,60,2,58,0.97,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1.1 +220541,NC_045512.2,26270,C,T,PASS,319,0,317,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1.1 +220541,NC_045512.2,26530,A,G,PASS,157,0,157,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1.1 +220541,NC_045512.2,26577,C,G,PASS,174,0,174,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1.1 +220541,NC_045512.2,26709,G,A,PASS,152,2,150,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1.1 +220541,NC_045512.2,27259,A,C,PASS,165,0,165,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1.1 +220541,NC_045512.2,27807,C,T,PASS,120,0,120,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1.1 +220541,NC_045512.2,28271,A,T,PASS,1013,1,1010,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1.1 +220541,NC_045512.2,28311,C,T,PASS,991,3,987,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1.1 +220541,NC_045512.2,2832,A,G,PASS,41,0,41,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1.1 +220541,NC_045512.2,28361,GGAGAACGCA,G,PASS,729,726,511,0.7,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1.1 +220541,NC_045512.2,28512,C,T,PASS,407,288,106,0.26,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,BA.1.1.1 +220541,NC_045512.2,28881,GG,AA,PASS,3023,30,2990,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1.1 +220541,NC_045512.2,28883,G,C,PASS,3005,0,2998,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1.1 +220541,NC_045512.2,3037,C,T,PASS,33,0,33,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1.1 +220541,NC_045512.2,5386,T,G,PASS,16,0,16,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.1.1 +220541,NC_045512.2,728,G,A,PASS,79,58,20,0.25,orf1ab,missense_variant,c.463G>A,p.Glu155Lys,p.E155K,ivar,BA.1.1.1 +220541,NC_045512.2,8393,G,A,PASS,3521,3,3515,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1.1 +220541,NC_045512.2,9572,G,A,PASS,2527,14,2509,0.99,orf1ab,missense_variant,c.9307G>A,p.Gly3103Ser,p.G3103S,ivar,BA.1.1.1 +220542,NC_045512.2,10449,C,A,PASS,23,0,23,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220542,NC_045512.2,11537,A,G,PASS,83,0,83,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220542,NC_045512.2,13195,T,C,PASS,3374,13,3359,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220542,NC_045512.2,14408,C,T,PASS,61,0,61,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220542,NC_045512.2,16064,A,G,PASS,32,0,32,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220542,NC_045512.2,16308,C,T,PASS,94,0,94,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,Unassigned +220542,NC_045512.2,21762,C,T,PASS,64,0,64,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220542,NC_045512.2,21764,ATACATG,A,PASS,65,64,64,0.98,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220542,NC_045512.2,21846,C,T,PASS,65,0,65,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220542,NC_045512.2,23403,A,G,PASS,1214,0,1214,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220542,NC_045512.2,23525,C,T,PASS,1267,3,1261,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220542,NC_045512.2,23599,T,G,PASS,536,1,534,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220542,NC_045512.2,23604,C,A,PASS,511,0,510,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220542,NC_045512.2,23948,G,T,PASS,34,0,34,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220542,NC_045512.2,24130,C,A,PASS,86,0,86,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220542,NC_045512.2,24469,T,A,PASS,299,0,297,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220542,NC_045512.2,24503,C,T,PASS,373,5,368,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220542,NC_045512.2,26530,A,G,PASS,11,0,11,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220542,NC_045512.2,26577,C,G,PASS,13,0,13,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220542,NC_045512.2,26709,G,A,PASS,17,0,17,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220542,NC_045512.2,27807,C,T,PASS,35,0,35,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220542,NC_045512.2,28271,A,T,PASS,768,0,767,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220542,NC_045512.2,28311,C,T,PASS,724,2,722,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220542,NC_045512.2,28361,GGAGAACGCA,G,PASS,451,450,317,0.7,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220542,NC_045512.2,28512,C,T,PASS,106,64,42,0.4,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,Unassigned +220542,NC_045512.2,28881,GG,AA,PASS,6562,63,6491,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220542,NC_045512.2,28883,G,C,PASS,6525,2,6516,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220542,NC_045512.2,3037,C,T,PASS,13,1,12,0.92,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220542,NC_045512.2,4276,C,T,PASS,40,0,40,1.0,orf1ab,synonymous_variant,c.4011C>T,p.Tyr1337Tyr,p.Y1337Y,ivar,Unassigned +220542,NC_045512.2,8393,G,A,PASS,1787,5,1782,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220543,NC_045512.2,10029,C,T,PASS,66,0,66,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.1.1 +220543,NC_045512.2,10449,C,A,PASS,291,0,290,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1.1 +220543,NC_045512.2,11282,AGTTTGTCTG,A,PASS,357,354,314,0.88,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1.1 +220543,NC_045512.2,11537,A,G,PASS,556,1,554,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1.1 +220543,NC_045512.2,13195,T,C,PASS,7272,15,7253,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1.1 +220543,NC_045512.2,14408,C,T,PASS,487,3,484,0.99,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1.1 +220543,NC_045512.2,15336,T,C,PASS,19,12,7,0.37,orf1ab,missense_variant,c.15071T>C,p.Leu5024Ser,p.L5024S,ivar,BA.1.1.1 +220543,NC_045512.2,15359,G,A,PASS,15,7,8,0.53,orf1ab,missense_variant,c.15094G>A,p.Ala5032Thr,p.A5032T,ivar,BA.1.1.1 +220543,NC_045512.2,16064,A,G,PASS,636,1,635,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,BA.1.1.1 +220543,NC_045512.2,16308,C,T,PASS,1330,1,1329,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,BA.1.1.1 +220543,NC_045512.2,18163,A,G,PASS,43,0,43,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.1.1 +220543,NC_045512.2,21306,C,T,PASS,138,4,134,0.97,orf1ab,missense_variant,c.21041C>T,p.Ala7014Val,p.A7014V,ivar,BA.1.1.1 +220543,NC_045512.2,21762,C,T,PASS,541,1,540,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1.1 +220543,NC_045512.2,21764,ATACATG,A,PASS,555,541,494,0.89,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1.1 +220543,NC_045512.2,21846,C,T,PASS,533,2,531,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1.1 +220543,NC_045512.2,22578,G,A,PASS,17,0,17,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.1.1 +220543,NC_045512.2,22599,G,A,PASS,15,0,15,1.0,S,missense_variant,c.1037G>A,p.Arg346Lys,p.R346K,ivar,BA.1.1.1 +220543,NC_045512.2,22673,TC,CT,PASS,17,0,17,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.1.1 +220543,NC_045512.2,22679,T,C,PASS,27,0,27,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.1.1 +220543,NC_045512.2,22686,C,T,PASS,26,0,26,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.1.1 +220543,NC_045512.2,23013,A,C,PASS,10,0,10,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.1.1 +220543,NC_045512.2,23040,A,G,PASS,10,0,10,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.1.1 +220543,NC_045512.2,23048,G,A,PASS,10,0,10,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.1.1 +220543,NC_045512.2,23055,A,G,PASS,10,0,10,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.1.1 +220543,NC_045512.2,23063,A,T,PASS,10,0,10,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.1.1 +220543,NC_045512.2,23075,T,C,PASS,10,0,10,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.1.1 +220543,NC_045512.2,23202,C,A,PASS,33,0,33,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.1.1 +220543,NC_045512.2,23403,A,G,PASS,5345,6,5339,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1.1 +220543,NC_045512.2,23525,C,T,PASS,5055,8,5044,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1.1 +220543,NC_045512.2,23599,T,G,PASS,1780,0,1780,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1.1 +220543,NC_045512.2,23604,C,A,PASS,1726,0,1719,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1.1 +220543,NC_045512.2,23854,C,A,PASS,106,0,106,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1.1 +220543,NC_045512.2,23948,G,T,PASS,1529,0,1527,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1.1 +220543,NC_045512.2,24130,C,A,PASS,2315,0,2289,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1.1 +220543,NC_045512.2,24424,A,T,PASS,386,0,384,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1.1 +220543,NC_045512.2,24469,T,A,PASS,1576,0,1573,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1.1 +220543,NC_045512.2,24503,C,T,PASS,1890,45,1845,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1.1 +220543,NC_045512.2,25000,C,T,PASS,139,0,139,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1.1 +220543,NC_045512.2,25584,C,T,PASS,235,1,234,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1.1 +220543,NC_045512.2,26270,C,T,PASS,603,4,599,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1.1 +220543,NC_045512.2,26530,A,G,PASS,60,0,60,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1.1 +220543,NC_045512.2,26577,C,G,PASS,65,0,65,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1.1 +220543,NC_045512.2,26709,G,A,PASS,72,0,72,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1.1 +220543,NC_045512.2,27259,A,C,PASS,453,0,451,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1.1 +220543,NC_045512.2,27807,C,T,PASS,142,0,141,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1.1 +220543,NC_045512.2,28271,A,T,PASS,1561,4,1557,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1.1 +220543,NC_045512.2,28311,C,T,PASS,1582,3,1577,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1.1 +220543,NC_045512.2,2832,A,G,PASS,172,1,171,0.99,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1.1 +220543,NC_045512.2,28361,GGAGAACGCA,G,PASS,1130,1128,735,0.65,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1.1 +220543,NC_045512.2,28512,C,T,PASS,615,428,178,0.29,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,BA.1.1.1 +220543,NC_045512.2,28881,GG,AA,PASS,2666,37,2626,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1.1 +220543,NC_045512.2,28883,G,C,PASS,2644,3,2638,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1.1 +220543,NC_045512.2,29451,C,T,PASS,5293,30,5263,0.99,N,missense_variant,c.1178C>T,p.Thr393Ile,p.T393I,ivar,BA.1.1.1 +220543,NC_045512.2,3037,C,T,PASS,78,1,77,0.99,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1.1 +220543,NC_045512.2,5386,T,G,PASS,26,0,26,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.1.1 +220543,NC_045512.2,8393,G,A,PASS,4660,24,4632,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1.1 +220544,NC_045512.2,10449,C,A,PASS,10,0,10,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1.1 +220544,NC_045512.2,11282,AGTTTGTCTG,A,PASS,73,72,66,0.9,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1.1 +220544,NC_045512.2,11537,A,G,PASS,46,0,46,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1.1 +220544,NC_045512.2,13195,T,C,PASS,3335,1,3334,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1.1 +220544,NC_045512.2,14408,C,T,PASS,36,0,36,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1.1 +220544,NC_045512.2,16064,A,G,PASS,57,0,57,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,BA.1.1.1 +220544,NC_045512.2,16308,C,T,PASS,147,0,147,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,BA.1.1.1 +220544,NC_045512.2,206,C,A,PASS,32,18,12,0.38,orf1ab,upstream_gene_variant,c.-60C>A,.,.,ivar,BA.1.1.1 +220544,NC_045512.2,21762,C,T,PASS,78,0,78,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1.1 +220544,NC_045512.2,21764,ATACATG,A,PASS,79,78,66,0.84,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1.1 +220544,NC_045512.2,21846,C,T,PASS,38,0,38,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1.1 +220544,NC_045512.2,23013,A,C,PASS,10,0,10,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.1.1 +220544,NC_045512.2,23030,T,C,ft,10,7,3,0.3,S,missense_variant,c.1468T>C,p.Phe490Leu,p.F490L,ivar,BA.1.1.1 +220544,NC_045512.2,23040,A,G,PASS,10,0,10,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.1.1 +220544,NC_045512.2,23048,G,A,PASS,11,0,11,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.1.1 +220544,NC_045512.2,23055,A,G,PASS,11,0,11,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.1.1 +220544,NC_045512.2,23063,A,T,PASS,13,0,13,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.1.1 +220544,NC_045512.2,23075,T,C,PASS,16,0,16,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.1.1 +220544,NC_045512.2,23202,C,A,PASS,10,0,10,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.1.1 +220544,NC_045512.2,23403,A,G,PASS,1658,2,1655,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1.1 +220544,NC_045512.2,23525,C,T,PASS,1539,5,1533,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1.1 +220544,NC_045512.2,23599,T,G,PASS,601,3,598,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1.1 +220544,NC_045512.2,23604,C,A,PASS,583,0,583,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1.1 +220544,NC_045512.2,23756,A,G,ft,11,8,3,0.27,S,missense_variant,c.2194A>G,p.Thr732Ala,p.T732A,ivar,BA.1.1.1 +220544,NC_045512.2,23854,C,A,PASS,12,0,12,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1.1 +220544,NC_045512.2,23948,G,T,PASS,178,0,178,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1.1 +220544,NC_045512.2,24130,C,A,PASS,282,0,279,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1.1 +220544,NC_045512.2,24424,A,T,PASS,68,0,68,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1.1 +220544,NC_045512.2,24469,T,A,PASS,322,0,322,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1.1 +220544,NC_045512.2,24503,C,T,PASS,381,14,367,0.96,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1.1 +220544,NC_045512.2,25000,C,T,PASS,18,0,18,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1.1 +220544,NC_045512.2,25584,C,T,PASS,27,0,27,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1.1 +220544,NC_045512.2,26270,C,T,PASS,131,0,131,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1.1 +220544,NC_045512.2,26530,A,G,PASS,119,0,119,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1.1 +220544,NC_045512.2,26577,C,G,PASS,123,0,123,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1.1 +220544,NC_045512.2,26709,G,A,PASS,133,2,131,0.98,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1.1 +220544,NC_045512.2,27259,A,C,PASS,73,0,73,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1.1 +220544,NC_045512.2,27807,C,T,PASS,15,0,15,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1.1 +220544,NC_045512.2,2790,C,T,ft,15,11,4,0.27,orf1ab,missense_variant,c.2525C>T,p.Thr842Ile,p.T842I,ivar,BA.1.1.1 +220544,NC_045512.2,28271,A,T,PASS,206,0,206,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1.1 +220544,NC_045512.2,28311,C,T,PASS,200,0,198,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1.1 +220544,NC_045512.2,2832,A,G,PASS,15,0,15,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1.1 +220544,NC_045512.2,28361,GGAGAACGCA,G,PASS,156,154,111,0.71,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1.1 +220544,NC_045512.2,28881,GG,AA,PASS,6341,80,6256,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1.1 +220544,NC_045512.2,28883,G,C,PASS,6310,0,6304,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1.1 +220544,NC_045512.2,8393,G,A,PASS,1458,11,1447,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1.1 +220544,NC_045512.2,9572,G,A,PASS,1323,9,1310,0.99,orf1ab,missense_variant,c.9307G>A,p.Gly3103Ser,p.G3103S,ivar,BA.1.1.1 +220545,NC_045512.2,10029,C,T,PASS,16,0,16,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,Unassigned +220545,NC_045512.2,10449,C,A,PASS,23,0,23,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220545,NC_045512.2,11282,AGTTTGTCTG,A,PASS,94,94,81,0.86,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220545,NC_045512.2,11537,A,G,PASS,99,0,99,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220545,NC_045512.2,11958,T,C,PASS,18,0,18,1.0,orf1ab,missense_variant,c.11693T>C,p.Ile3898Thr,p.I3898T,ivar,Unassigned +220545,NC_045512.2,13195,T,C,PASS,3708,5,3703,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220545,NC_045512.2,14408,C,T,PASS,59,0,59,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220545,NC_045512.2,14774,A,T,ft,13,9,4,0.31,orf1ab,missense_variant,c.14509A>T,p.Met4837Leu,p.M4837L,ivar,Unassigned +220545,NC_045512.2,16064,A,G,PASS,75,0,75,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220545,NC_045512.2,18163,A,G,PASS,10,0,10,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,Unassigned +220545,NC_045512.2,21762,C,T,PASS,106,0,106,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220545,NC_045512.2,21764,ATACATG,A,PASS,109,106,91,0.83,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220545,NC_045512.2,21846,C,T,PASS,81,0,81,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220545,NC_045512.2,23403,A,G,PASS,1153,0,1153,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220545,NC_045512.2,23525,C,T,PASS,1133,2,1131,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220545,NC_045512.2,23599,T,G,PASS,445,0,445,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220545,NC_045512.2,23604,C,A,PASS,432,0,430,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220545,NC_045512.2,23854,C,A,PASS,24,0,24,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220545,NC_045512.2,23948,G,T,PASS,141,0,141,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220545,NC_045512.2,24130,C,A,PASS,177,0,177,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220545,NC_045512.2,24424,A,T,PASS,93,0,93,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220545,NC_045512.2,24469,T,A,PASS,454,0,451,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220545,NC_045512.2,24503,C,T,PASS,534,3,531,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220545,NC_045512.2,25000,C,T,PASS,35,0,35,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220545,NC_045512.2,25584,C,T,PASS,20,0,20,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220545,NC_045512.2,26270,C,T,PASS,77,0,77,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220545,NC_045512.2,26530,A,G,PASS,25,0,25,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220545,NC_045512.2,26577,C,G,PASS,36,0,36,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220545,NC_045512.2,26709,G,A,PASS,42,2,40,0.95,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220545,NC_045512.2,27259,A,C,PASS,62,0,62,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220545,NC_045512.2,27807,C,T,PASS,27,0,27,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220545,NC_045512.2,28238,T,C,PASS,556,0,556,1.0,ORF8,synonymous_variant,c.345T>C,p.Arg115Arg,p.R115R,ivar,Unassigned +220545,NC_045512.2,28271,A,T,PASS,638,4,630,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220545,NC_045512.2,28311,C,T,PASS,637,2,635,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220545,NC_045512.2,28361,GGAGAACGCA,G,PASS,462,461,341,0.74,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220545,NC_045512.2,28881,GG,AA,PASS,4829,76,4753,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220545,NC_045512.2,28883,G,C,PASS,4774,5,4765,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220545,NC_045512.2,3037,C,T,PASS,20,0,20,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220545,NC_045512.2,4835,G,C,PASS,55,35,20,0.36,orf1ab,missense_variant,c.4570G>C,p.Gly1524Arg,p.G1524R,ivar,Unassigned +220545,NC_045512.2,8393,G,A,PASS,1501,4,1495,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220546,NC_045512.2,10029,C,T,PASS,29,0,29,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.1.1 +220546,NC_045512.2,10449,C,A,PASS,74,0,74,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1.1 +220546,NC_045512.2,11282,AGTTTGTCTG,A,PASS,229,225,199,0.87,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1.1 +220546,NC_045512.2,11537,A,G,PASS,132,0,132,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1.1 +220546,NC_045512.2,13195,T,C,PASS,4491,2,4489,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1.1 +220546,NC_045512.2,14408,C,T,PASS,115,0,115,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1.1 +220546,NC_045512.2,16064,A,G,PASS,219,0,219,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,BA.1.1.1 +220546,NC_045512.2,18163,A,G,PASS,14,0,14,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.1.1 +220546,NC_045512.2,21762,C,T,PASS,121,0,121,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1.1 +220546,NC_045512.2,21764,ATACATG,A,PASS,127,121,110,0.87,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1.1 +220546,NC_045512.2,21846,C,T,PASS,121,0,121,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1.1 +220546,NC_045512.2,22679,T,C,PASS,11,0,11,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.1.1 +220546,NC_045512.2,22686,C,T,PASS,10,0,10,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.1.1 +220546,NC_045512.2,23040,A,G,PASS,12,0,12,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.1.1 +220546,NC_045512.2,23048,G,A,PASS,12,0,12,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.1.1 +220546,NC_045512.2,23055,A,G,PASS,12,0,12,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.1.1 +220546,NC_045512.2,23063,A,T,PASS,12,0,12,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.1.1 +220546,NC_045512.2,23075,T,C,PASS,13,0,13,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.1.1 +220546,NC_045512.2,23202,C,A,PASS,30,0,30,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.1.1 +220546,NC_045512.2,23403,A,G,PASS,3367,2,3365,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1.1 +220546,NC_045512.2,23525,C,T,PASS,3050,3,3045,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1.1 +220546,NC_045512.2,23599,T,G,PASS,1142,0,1142,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1.1 +220546,NC_045512.2,23604,C,A,PASS,1100,0,1094,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1.1 +220546,NC_045512.2,23854,C,A,PASS,28,0,28,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1.1 +220546,NC_045512.2,23948,G,T,PASS,349,1,344,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1.1 +220546,NC_045512.2,24130,C,A,PASS,564,0,559,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1.1 +220546,NC_045512.2,24424,A,T,PASS,122,0,122,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1.1 +220546,NC_045512.2,24469,T,A,PASS,553,0,548,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1.1 +220546,NC_045512.2,24503,C,T,PASS,663,14,649,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1.1 +220546,NC_045512.2,25000,C,T,PASS,53,0,53,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1.1 +220546,NC_045512.2,25584,C,T,PASS,61,0,61,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1.1 +220546,NC_045512.2,26270,C,T,PASS,368,2,366,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1.1 +220546,NC_045512.2,26530,A,G,PASS,140,0,140,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1.1 +220546,NC_045512.2,26577,C,G,PASS,173,0,173,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1.1 +220546,NC_045512.2,26709,G,A,PASS,158,1,157,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1.1 +220546,NC_045512.2,27259,A,C,PASS,165,0,165,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1.1 +220546,NC_045512.2,27807,C,T,PASS,79,0,79,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1.1 +220546,NC_045512.2,28238,T,C,PASS,607,0,607,1.0,ORF8,synonymous_variant,c.345T>C,p.Arg115Arg,p.R115R,ivar,BA.1.1.1 +220546,NC_045512.2,28271,A,T,PASS,751,0,749,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1.1 +220546,NC_045512.2,28311,C,T,PASS,709,4,703,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1.1 +220546,NC_045512.2,2832,A,G,PASS,42,0,42,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1.1 +220546,NC_045512.2,28361,GGAGAACGCA,G,PASS,531,529,373,0.7,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1.1 +220546,NC_045512.2,28512,C,T,PASS,385,283,99,0.26,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,BA.1.1.1 +220546,NC_045512.2,28881,GG,AA,PASS,2009,27,1980,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1.1 +220546,NC_045512.2,28883,G,C,PASS,1988,0,1982,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1.1 +220546,NC_045512.2,3037,C,T,PASS,24,0,24,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1.1 +220546,NC_045512.2,5386,T,G,PASS,12,0,12,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.1.1 +220546,NC_045512.2,76,T,A,ft,11,7,4,0.36,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1.1.1 +220546,NC_045512.2,78,T,G,ft,11,7,4,0.36,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1.1.1 +220546,NC_045512.2,8393,G,A,PASS,3173,9,3162,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1.1 +220599,NC_045512.2,11537,A,G,PASS,13,0,13,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220599,NC_045512.2,13195,T,C,PASS,273,2,271,0.99,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220599,NC_045512.2,16064,A,G,PASS,19,0,19,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220599,NC_045512.2,16853,G,T,PASS,16,0,14,0.88,orf1ab,missense_variant,c.16588G>T,p.Val5530Leu,p.V5530L,ivar,Unassigned +220599,NC_045512.2,23403,A,G,PASS,187,0,187,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220599,NC_045512.2,23525,C,T,PASS,144,0,144,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220599,NC_045512.2,23599,T,G,PASS,67,0,67,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220599,NC_045512.2,23604,C,A,PASS,67,0,67,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220599,NC_045512.2,23948,G,T,PASS,20,0,20,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220599,NC_045512.2,24130,C,A,PASS,36,0,36,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220599,NC_045512.2,24424,A,T,PASS,14,0,14,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220599,NC_045512.2,24469,T,A,PASS,30,0,30,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220599,NC_045512.2,24503,C,T,PASS,33,1,32,0.97,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220599,NC_045512.2,28881,GG,AA,PASS,166,5,161,0.97,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220599,NC_045512.2,28883,G,C,PASS,167,2,165,0.99,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220599,NC_045512.2,29400,C,T,PASS,89,0,89,1.0,N,missense_variant,c.1127C>T,p.Ala376Val,p.A376V,ivar,Unassigned +220599,NC_045512.2,3663,G,A,PASS,148,2,146,0.99,orf1ab,missense_variant,c.3398G>A,p.Ser1133Asn,p.S1133N,ivar,Unassigned +220599,NC_045512.2,4266,T,C,ft,11,8,3,0.27,orf1ab,missense_variant,c.4001T>C,p.Leu1334Ser,p.L1334S,ivar,Unassigned +220599,NC_045512.2,4363,A,T,ft,10,6,4,0.4,orf1ab,missense_variant,c.4098A>T,p.Glu1366Asp,p.E1366D,ivar,Unassigned +220599,NC_045512.2,8393,G,A,PASS,197,1,196,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220601,NC_045512.2,10029,C,T,PASS,335,2,333,0.99,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.1 +220601,NC_045512.2,10449,C,A,PASS,827,0,824,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1 +220601,NC_045512.2,11282,AGTTTGTCTG,A,PASS,1412,1400,1185,0.84,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1 +220601,NC_045512.2,11537,A,G,PASS,872,0,872,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1 +220601,NC_045512.2,13195,T,C,PASS,2886,7,2877,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1 +220601,NC_045512.2,14408,C,T,PASS,367,5,362,0.99,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1 +220601,NC_045512.2,15240,C,T,PASS,59,0,59,1.0,orf1ab,missense_variant,c.14975C>T,p.Thr4992Ile,p.T4992I,ivar,BA.1.1 +220601,NC_045512.2,18163,A,G,PASS,241,2,239,0.99,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.1 +220601,NC_045512.2,21762,C,T,PASS,460,2,458,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1 +220601,NC_045512.2,21764,ATACATG,A,PASS,465,463,409,0.88,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1 +220601,NC_045512.2,21846,C,T,PASS,446,6,440,0.99,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1 +220601,NC_045512.2,21986,GGTGTTTATT,G,PASS,15,15,15,1.0,S,disruptive_inframe_deletion,c.425_433delGTGTTTATT,p.Gly142_Tyr145delinsAsp,p.G142_Y145delinsD,ivar,BA.1.1 +220601,NC_045512.2,22193,AATT,A,PASS,25,25,15,0.6,S,disruptive_inframe_deletion,c.632_634delATT,p.Asn211_Leu212delinsIle,p.N211_L212delinsI,ivar,BA.1.1 +220601,NC_045512.2,22204,T,TGAGCCAGAA,ft,14,14,5,0.36,S,disruptive_inframe_insertion,c.644_645insGCCAGAAGA,p.Arg214_Asp215insGluProGlu,p.R214_D215insEPE,ivar,BA.1.1 +220601,NC_045512.2,22578,G,A,PASS,130,2,128,0.98,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.1 +220601,NC_045512.2,22599,G,A,PASS,141,0,141,1.0,S,missense_variant,c.1037G>A,p.Arg346Lys,p.R346K,ivar,BA.1.1 +220601,NC_045512.2,22673,TC,CT,PASS,111,0,111,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.1 +220601,NC_045512.2,22679,T,C,PASS,162,0,162,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.1 +220601,NC_045512.2,22686,C,T,PASS,161,1,160,0.99,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.1 +220601,NC_045512.2,22813,G,T,PASS,20,0,20,1.0,S,missense_variant,c.1251G>T,p.Lys417Asn,p.K417N,ivar,BA.1.1 +220601,NC_045512.2,22882,T,G,PASS,10,0,10,1.0,S,missense_variant,c.1320T>G,p.Asn440Lys,p.N440K,ivar,BA.1.1 +220601,NC_045512.2,22898,G,A,PASS,13,0,13,1.0,S,missense_variant,c.1336G>A,p.Gly446Ser,p.G446S,ivar,BA.1.1 +220601,NC_045512.2,22992,G,A,PASS,38,0,38,1.0,S,missense_variant,c.1430G>A,p.Ser477Asn,p.S477N,ivar,BA.1.1 +220601,NC_045512.2,22995,C,A,PASS,37,0,37,1.0,S,missense_variant,c.1433C>A,p.Thr478Lys,p.T478K,ivar,BA.1.1 +220601,NC_045512.2,23013,A,C,PASS,52,0,52,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.1 +220601,NC_045512.2,23040,A,G,PASS,53,0,53,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.1 +220601,NC_045512.2,23048,G,A,PASS,56,0,56,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.1 +220601,NC_045512.2,23055,A,G,PASS,57,0,57,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.1 +220601,NC_045512.2,23063,A,T,PASS,62,0,62,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.1 +220601,NC_045512.2,23075,T,C,PASS,67,0,67,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.1 +220601,NC_045512.2,23202,C,A,PASS,101,1,99,0.98,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.1 +220601,NC_045512.2,23403,A,G,PASS,2063,4,2059,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1 +220601,NC_045512.2,23525,C,T,PASS,1975,4,1971,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1 +220601,NC_045512.2,23599,T,G,PASS,738,0,738,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1 +220601,NC_045512.2,23604,C,A,PASS,705,2,699,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1 +220601,NC_045512.2,23854,C,A,PASS,538,0,538,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1 +220601,NC_045512.2,23948,G,T,PASS,1237,0,1235,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1 +220601,NC_045512.2,24130,C,A,PASS,1834,0,1827,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1 +220601,NC_045512.2,24424,A,T,PASS,1387,0,1383,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1 +220601,NC_045512.2,24469,T,A,PASS,1593,3,1585,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1 +220601,NC_045512.2,24503,C,T,PASS,1682,21,1660,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1 +220601,NC_045512.2,25000,C,T,PASS,565,1,564,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1 +220601,NC_045512.2,25584,C,T,PASS,769,3,763,0.99,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1 +220601,NC_045512.2,26270,C,T,PASS,1265,4,1260,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1 +220601,NC_045512.2,26530,A,G,PASS,243,0,243,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1 +220601,NC_045512.2,26577,C,G,PASS,223,0,223,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1 +220601,NC_045512.2,26709,G,A,PASS,305,2,303,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1 +220601,NC_045512.2,27259,A,C,PASS,843,0,843,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1 +220601,NC_045512.2,27807,C,T,PASS,419,0,416,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1 +220601,NC_045512.2,28271,A,T,PASS,834,0,833,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1 +220601,NC_045512.2,28311,C,T,PASS,845,3,842,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1 +220601,NC_045512.2,2832,A,G,PASS,1221,6,1215,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1 +220601,NC_045512.2,28361,GGAGAACGCA,G,PASS,695,694,501,0.72,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1 +220601,NC_045512.2,28877,AG,TC,PASS,632,2,629,1.0,N,synonymous_variant,c.604_605delAGinsTC,p.203,p.203,ivar,BA.1.1 +220601,NC_045512.2,28881,GG,AA,PASS,631,2,628,1.0,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1 +220601,NC_045512.2,28883,G,C,PASS,629,0,629,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1 +220601,NC_045512.2,3037,C,T,PASS,124,0,124,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1 +220601,NC_045512.2,5386,T,G,PASS,102,0,102,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.1 +220601,NC_045512.2,6445,C,T,PASS,10,0,10,1.0,orf1ab,synonymous_variant,c.6180C>T,p.Asp2060Asp,p.D2060D,ivar,BA.1.1 +220601,NC_045512.2,6512,AGTT,A,PASS,12,12,10,0.83,orf1ab,disruptive_inframe_deletion,c.6248_6250delGTT,p.Ser2083_Leu2084delinsIle,p.S2083_L2084delinsI,ivar,BA.1.1 +220601,NC_045512.2,8393,G,A,PASS,1980,19,1959,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1 +220624,NC_045512.2,10449,C,A,PASS,11,0,11,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220624,NC_045512.2,11282,AGTTTGTCTG,A,PASS,31,31,28,0.9,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220624,NC_045512.2,11537,A,G,PASS,58,0,58,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220624,NC_045512.2,13195,T,C,PASS,2327,1,2323,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220624,NC_045512.2,14408,C,T,PASS,26,0,26,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220624,NC_045512.2,16925,A,G,ft,24,18,6,0.25,orf1ab,missense_variant,c.16660A>G,p.Ile5554Val,p.I5554V,ivar,Unassigned +220624,NC_045512.2,20371,C,G,ft,23,17,6,0.26,orf1ab,stop_gained,c.20106C>G,p.Tyr6702*,p.Y6702*,ivar,Unassigned +220624,NC_045512.2,2172,A,G,PASS,181,5,176,0.97,orf1ab,missense_variant,c.1907A>G,p.Lys636Arg,p.K636R,ivar,Unassigned +220624,NC_045512.2,21762,C,T,PASS,21,0,21,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220624,NC_045512.2,21764,ATACATG,A,PASS,21,21,20,0.95,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220624,NC_045512.2,21846,C,T,PASS,25,0,25,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220624,NC_045512.2,23403,A,G,PASS,920,0,920,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220624,NC_045512.2,23525,C,T,PASS,910,0,907,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220624,NC_045512.2,23599,T,G,PASS,359,0,359,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220624,NC_045512.2,23604,C,A,PASS,351,0,351,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220624,NC_045512.2,23948,G,T,PASS,35,0,35,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220624,NC_045512.2,24130,C,A,PASS,29,0,29,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220624,NC_045512.2,24424,A,T,PASS,26,0,26,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220624,NC_045512.2,24469,T,A,PASS,145,0,142,0.98,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220624,NC_045512.2,24503,C,T,PASS,171,3,168,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220624,NC_045512.2,25584,C,T,PASS,17,0,17,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220624,NC_045512.2,25855,G,T,PASS,11,0,11,1.0,ORF3a,missense_variant,c.463G>T,p.Asp155Tyr,p.D155Y,ivar,Unassigned +220624,NC_045512.2,26270,C,T,PASS,112,0,112,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220624,NC_045512.2,26530,A,G,PASS,166,0,166,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220624,NC_045512.2,26577,C,G,PASS,175,0,175,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220624,NC_045512.2,26709,G,A,PASS,200,0,200,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220624,NC_045512.2,27259,A,C,PASS,51,0,51,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220624,NC_045512.2,27807,C,T,PASS,52,0,52,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220624,NC_045512.2,27933,G,A,PASS,186,0,186,1.0,ORF8,missense_variant,c.40G>A,p.Ala14Thr,p.A14T,ivar,Unassigned +220624,NC_045512.2,28271,A,T,PASS,345,2,343,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220624,NC_045512.2,28311,C,T,PASS,378,2,376,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220624,NC_045512.2,2832,A,G,PASS,18,0,18,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220624,NC_045512.2,28361,GGAGAACGCA,G,PASS,299,296,209,0.7,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220624,NC_045512.2,28512,C,T,PASS,182,132,46,0.25,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,Unassigned +220624,NC_045512.2,28881,GG,AA,PASS,4288,63,4219,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220624,NC_045512.2,28883,G,C,PASS,4247,4,4241,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220624,NC_045512.2,3037,C,T,PASS,20,0,20,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220624,NC_045512.2,8393,G,A,PASS,2102,5,2097,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220625,NC_045512.2,10449,C,A,PASS,15,0,15,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220625,NC_045512.2,11282,AGTTTGTCTG,A,PASS,47,47,42,0.89,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220625,NC_045512.2,11537,A,G,PASS,14,0,14,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220625,NC_045512.2,13195,T,C,PASS,1350,2,1348,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220625,NC_045512.2,14408,C,T,PASS,19,0,19,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220625,NC_045512.2,21762,C,T,PASS,26,0,26,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220625,NC_045512.2,21764,ATACATG,A,PASS,26,26,22,0.85,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220625,NC_045512.2,21846,C,T,PASS,16,0,16,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220625,NC_045512.2,23403,A,G,PASS,467,0,467,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220625,NC_045512.2,23525,C,T,PASS,551,0,551,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220625,NC_045512.2,23599,T,G,PASS,216,0,216,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220625,NC_045512.2,23604,C,A,PASS,209,0,207,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220625,NC_045512.2,23948,G,T,PASS,33,0,33,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220625,NC_045512.2,24130,C,A,PASS,40,0,40,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220625,NC_045512.2,24424,A,T,PASS,38,0,37,0.97,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220625,NC_045512.2,24469,T,A,PASS,152,2,150,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220625,NC_045512.2,24503,C,T,PASS,165,2,163,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220625,NC_045512.2,25584,C,T,PASS,21,0,21,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220625,NC_045512.2,26270,C,T,PASS,74,0,74,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220625,NC_045512.2,26530,A,G,PASS,194,0,194,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220625,NC_045512.2,26577,C,G,PASS,195,0,195,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220625,NC_045512.2,26709,G,A,PASS,162,2,160,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220625,NC_045512.2,27259,A,C,PASS,40,0,40,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220625,NC_045512.2,27807,C,T,PASS,32,0,32,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220625,NC_045512.2,28271,A,T,PASS,286,3,281,0.98,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220625,NC_045512.2,28311,C,T,PASS,291,2,288,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220625,NC_045512.2,28361,GGAGAACGCA,G,PASS,230,223,167,0.73,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220625,NC_045512.2,28881,GG,AA,PASS,8535,93,8429,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220625,NC_045512.2,28883,G,C,PASS,8481,1,8473,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220625,NC_045512.2,8269,T,A,PASS,183,66,115,0.63,orf1ab,missense_variant,c.8004T>A,p.Asp2668Glu,p.D2668E,ivar,Unassigned +220625,NC_045512.2,8393,G,A,PASS,932,7,925,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220626,NC_045512.2,10449,C,A,PASS,33,0,33,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220626,NC_045512.2,11074,CT,C,PASS,41,41,13,0.32,orf1ab,frameshift_variant,c.10817delT,p.Leu3606fs,p.L3606fs,ivar,Unassigned +220626,NC_045512.2,11282,AGTTTGTCTG,A,PASS,86,85,78,0.91,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220626,NC_045512.2,11537,A,G,PASS,82,0,82,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220626,NC_045512.2,13195,T,C,PASS,2747,4,2743,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220626,NC_045512.2,14408,C,T,PASS,43,0,43,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220626,NC_045512.2,21762,C,T,PASS,56,0,56,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220626,NC_045512.2,21764,ATACATG,A,PASS,57,56,48,0.84,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220626,NC_045512.2,21846,C,T,PASS,51,2,49,0.96,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220626,NC_045512.2,21,C,T,PASS,10,0,10,1.0,orf1ab,upstream_gene_variant,c.-245C>T,.,.,ivar,Unassigned +220626,NC_045512.2,23403,A,G,PASS,878,3,875,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220626,NC_045512.2,23525,C,T,PASS,938,2,934,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220626,NC_045512.2,23599,T,G,PASS,371,0,370,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220626,NC_045512.2,23604,C,A,PASS,357,0,352,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220626,NC_045512.2,23948,G,T,PASS,196,0,195,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220626,NC_045512.2,24130,C,A,PASS,297,0,296,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220626,NC_045512.2,24424,A,T,PASS,52,0,52,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220626,NC_045512.2,24469,T,A,PASS,251,0,249,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220626,NC_045512.2,24503,C,T,PASS,313,2,311,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220626,NC_045512.2,25000,C,T,PASS,21,0,21,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220626,NC_045512.2,25584,C,T,PASS,42,0,42,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220626,NC_045512.2,26270,C,T,PASS,221,0,221,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220626,NC_045512.2,26530,A,G,PASS,111,0,111,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220626,NC_045512.2,26577,C,G,PASS,88,0,88,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220626,NC_045512.2,26709,G,A,PASS,113,0,113,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220626,NC_045512.2,27052,C,T,ft,14,10,4,0.29,M,missense_variant,c.530C>T,p.Ser177Phe,p.S177F,ivar,Unassigned +220626,NC_045512.2,27259,A,C,PASS,184,0,184,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220626,NC_045512.2,27807,C,T,PASS,52,0,52,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220626,NC_045512.2,28271,A,T,PASS,513,0,513,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220626,NC_045512.2,28311,C,T,PASS,534,0,534,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220626,NC_045512.2,2832,A,G,PASS,36,0,36,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220626,NC_045512.2,28361,GGAGAACGCA,G,PASS,424,423,278,0.66,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220626,NC_045512.2,28877,AG,TC,PASS,4416,5,4405,1.0,N,synonymous_variant,c.604_605delAGinsTC,p.203,p.203,ivar,Unassigned +220626,NC_045512.2,28881,GG,AA,PASS,4440,22,4409,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220626,NC_045512.2,28883,G,C,PASS,4441,0,4429,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220626,NC_045512.2,3037,C,T,PASS,30,0,30,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220626,NC_045512.2,76,T,A,ft,13,9,4,0.31,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220626,NC_045512.2,78,T,G,ft,13,9,4,0.31,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220626,NC_045512.2,8393,G,A,PASS,2004,2,2002,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220627,NC_045512.2,10029,C,T,PASS,32,0,32,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1 +220627,NC_045512.2,10449,C,A,PASS,122,0,122,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1 +220627,NC_045512.2,11282,AGTTTGTCTG,A,PASS,385,380,343,0.89,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1 +220627,NC_045512.2,11537,A,G,PASS,480,0,480,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1 +220627,NC_045512.2,13195,T,C,PASS,6218,9,6205,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1 +220627,NC_045512.2,14408,C,T,PASS,260,0,258,0.99,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1 +220627,NC_045512.2,18163,A,G,PASS,37,0,37,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1 +220627,NC_045512.2,21762,C,T,PASS,324,2,319,0.98,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1 +220627,NC_045512.2,21764,ATACATG,A,PASS,333,322,292,0.88,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1 +220627,NC_045512.2,21795,G,A,PASS,361,3,355,0.98,S,missense_variant,c.233G>A,p.Arg78Lys,p.R78K,ivar,BA.1 +220627,NC_045512.2,21846,C,T,PASS,346,0,346,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1 +220627,NC_045512.2,22193,AATT,A,PASS,19,19,18,0.95,S,disruptive_inframe_deletion,c.632_634delATT,p.Asn211_Leu212delinsIle,p.N211_L212delinsI,ivar,BA.1 +220627,NC_045512.2,22204,T,TGAGCCAGAA,PASS,17,17,14,0.82,S,disruptive_inframe_insertion,c.644_645insGCCAGAAGA,p.Arg214_Asp215insGluProGlu,p.R214_D215insEPE,ivar,BA.1 +220627,NC_045512.2,22578,G,A,PASS,36,0,36,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1 +220627,NC_045512.2,22673,TC,CT,PASS,33,0,33,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1 +220627,NC_045512.2,22679,T,C,PASS,42,0,42,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1 +220627,NC_045512.2,22686,C,T,PASS,42,0,42,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1 +220627,NC_045512.2,23063,A,T,PASS,10,0,10,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1 +220627,NC_045512.2,23075,T,C,PASS,12,0,12,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1 +220627,NC_045512.2,23202,C,A,PASS,40,0,39,0.98,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1 +220627,NC_045512.2,23403,A,G,PASS,2548,5,2543,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1 +220627,NC_045512.2,23525,C,T,PASS,2427,2,2416,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1 +220627,NC_045512.2,23599,T,G,PASS,916,0,916,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1 +220627,NC_045512.2,23604,C,A,PASS,885,0,881,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1 +220627,NC_045512.2,23854,C,A,PASS,66,0,64,0.97,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1 +220627,NC_045512.2,23948,G,T,PASS,817,1,810,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1 +220627,NC_045512.2,24130,C,A,PASS,1219,0,1209,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1 +220627,NC_045512.2,24424,A,T,PASS,314,0,312,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1 +220627,NC_045512.2,24469,T,A,PASS,1245,0,1245,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1 +220627,NC_045512.2,24503,C,T,PASS,1525,27,1496,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1 +220627,NC_045512.2,25000,C,T,PASS,110,0,110,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1 +220627,NC_045512.2,25584,C,T,PASS,182,3,179,0.98,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1 +220627,NC_045512.2,26270,C,T,PASS,987,2,984,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1 +220627,NC_045512.2,26530,A,G,PASS,399,0,399,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1 +220627,NC_045512.2,26577,C,G,PASS,422,0,422,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1 +220627,NC_045512.2,26709,G,A,PASS,464,3,461,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1 +220627,NC_045512.2,27259,A,C,PASS,444,0,441,0.99,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1 +220627,NC_045512.2,27807,C,T,PASS,143,0,143,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1 +220627,NC_045512.2,28271,A,T,PASS,3928,8,3914,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1 +220627,NC_045512.2,28311,C,T,PASS,4161,5,4146,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1 +220627,NC_045512.2,2832,A,G,PASS,161,2,159,0.99,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1 +220627,NC_045512.2,28361,GGAGAACGCA,G,PASS,3059,3037,1264,0.41,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1 +220627,NC_045512.2,28881,GG,AA,PASS,2726,36,2687,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1 +220627,NC_045512.2,28883,G,C,PASS,2704,2,2697,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1 +220627,NC_045512.2,29195,G,T,PASS,2958,0,2935,0.99,N,missense_variant,c.922G>T,p.Ala308Ser,p.A308S,ivar,BA.1 +220627,NC_045512.2,3037,C,T,PASS,68,0,68,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1 +220627,NC_045512.2,5386,T,G,PASS,16,0,16,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1 +220627,NC_045512.2,5515,G,T,PASS,26,0,26,1.0,orf1ab,synonymous_variant,c.5250G>T,p.Val1750Val,p.V1750V,ivar,BA.1 +220627,NC_045512.2,7321,C,T,ft,12,8,4,0.33,orf1ab,synonymous_variant,c.7056C>T,p.Ser2352Ser,p.S2352S,ivar,BA.1 +220627,NC_045512.2,8393,G,A,PASS,2820,7,2811,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1 +220628,NC_045512.2,10029,C,T,PASS,42,0,42,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.15.1 +220628,NC_045512.2,10135,T,C,PASS,138,0,138,1.0,orf1ab,synonymous_variant,c.9870T>C,p.Leu3290Leu,p.L3290L,ivar,BA.1.15.1 +220628,NC_045512.2,10449,C,A,PASS,143,0,141,0.99,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.15.1 +220628,NC_045512.2,11282,AGTTTGTCTG,A,PASS,551,550,482,0.87,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.15.1 +220628,NC_045512.2,11537,A,G,PASS,649,0,649,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.15.1 +220628,NC_045512.2,13195,T,C,PASS,5534,17,5515,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.15.1 +220628,NC_045512.2,14408,C,T,PASS,273,0,273,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.15.1 +220628,NC_045512.2,18163,A,G,PASS,26,0,26,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.15.1 +220628,NC_045512.2,21762,C,T,PASS,404,2,402,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.15.1 +220628,NC_045512.2,21764,ATACATG,A,PASS,409,405,357,0.87,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.15.1 +220628,NC_045512.2,21846,C,T,PASS,379,2,375,0.99,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.15.1 +220628,NC_045512.2,21,C,T,PASS,28,0,28,1.0,orf1ab,upstream_gene_variant,c.-245C>T,.,.,ivar,BA.1.15.1 +220628,NC_045512.2,22578,G,A,PASS,37,0,37,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.15.1 +220628,NC_045512.2,22673,TC,CT,PASS,14,0,14,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.15.1 +220628,NC_045512.2,22679,T,C,PASS,21,0,21,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.15.1 +220628,NC_045512.2,22686,C,T,PASS,20,0,20,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.15.1 +220628,NC_045512.2,22992,G,A,PASS,12,0,12,1.0,S,missense_variant,c.1430G>A,p.Ser477Asn,p.S477N,ivar,BA.1.15.1 +220628,NC_045512.2,22995,C,A,PASS,12,0,10,0.83,S,missense_variant,c.1433C>A,p.Thr478Lys,p.T478K,ivar,BA.1.15.1 +220628,NC_045512.2,23013,A,C,PASS,15,0,15,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.15.1 +220628,NC_045512.2,23040,A,G,PASS,16,0,16,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.15.1 +220628,NC_045512.2,23048,G,A,PASS,15,0,15,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.15.1 +220628,NC_045512.2,23055,A,G,PASS,15,0,15,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.15.1 +220628,NC_045512.2,23063,A,T,PASS,16,0,16,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.15.1 +220628,NC_045512.2,23075,T,C,PASS,16,0,16,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.15.1 +220628,NC_045512.2,23202,C,A,PASS,37,0,37,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.15.1 +220628,NC_045512.2,23403,A,G,PASS,3111,5,3106,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.15.1 +220628,NC_045512.2,23525,C,T,PASS,2843,8,2834,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.15.1 +220628,NC_045512.2,23599,T,G,PASS,962,0,962,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.15.1 +220628,NC_045512.2,23604,C,A,PASS,912,0,906,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.15.1 +220628,NC_045512.2,23854,C,A,PASS,88,1,87,0.99,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.15.1 +220628,NC_045512.2,23948,G,T,PASS,794,0,788,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.15.1 +220628,NC_045512.2,24130,C,A,PASS,1286,0,1279,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.15.1 +220628,NC_045512.2,24424,A,T,PASS,354,0,353,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.15.1 +220628,NC_045512.2,24469,T,A,PASS,1256,4,1247,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.15.1 +220628,NC_045512.2,24503,C,T,PASS,1507,30,1473,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.15.1 +220628,NC_045512.2,24803,A,G,PASS,632,0,632,1.0,S,missense_variant,c.3241A>G,p.Ile1081Val,p.I1081V,ivar,BA.1.15.1 +220628,NC_045512.2,25000,C,T,PASS,102,3,99,0.97,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.15.1 +220628,NC_045512.2,25584,C,T,PASS,85,0,85,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.15.1 +220628,NC_045512.2,25708,C,T,PASS,106,0,106,1.0,ORF3a,missense_variant,c.316C>T,p.Leu106Phe,p.L106F,ivar,BA.1.15.1 +220628,NC_045512.2,26270,C,T,PASS,620,0,620,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.15.1 +220628,NC_045512.2,26530,A,G,PASS,288,0,288,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.15.1 +220628,NC_045512.2,26577,C,G,PASS,372,0,372,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.15.1 +220628,NC_045512.2,26709,G,A,PASS,304,2,302,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.15.1 +220628,NC_045512.2,27259,A,C,PASS,303,0,303,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.15.1 +220628,NC_045512.2,27667,G,T,PASS,76,56,20,0.26,ORF7a,stop_gained,c.274G>T,p.Glu92*,p.E92*,ivar,BA.1.15.1 +220628,NC_045512.2,27807,C,T,PASS,93,0,93,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.15.1 +220628,NC_045512.2,28271,A,T,PASS,1719,2,1712,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.15.1 +220628,NC_045512.2,28311,C,T,PASS,1718,5,1712,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.15.1 +220628,NC_045512.2,2832,A,G,PASS,220,0,220,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.15.1 +220628,NC_045512.2,28361,GGAGAACGCA,G,PASS,1218,1209,726,0.6,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.15.1 +220628,NC_045512.2,28363,A,T,PASS,16,12,4,0.25,N,synonymous_variant,c.90A>T,p.Gly30Gly,p.G30G,ivar,BA.1.15.1 +220628,NC_045512.2,28881,GG,AA,PASS,2323,23,2299,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.15.1 +220628,NC_045512.2,28883,G,C,PASS,2314,1,2311,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.15.1 +220628,NC_045512.2,29301,A,G,PASS,3873,8,3862,1.0,N,missense_variant,c.1028A>G,p.Asp343Gly,p.D343G,ivar,BA.1.15.1 +220628,NC_045512.2,3037,C,T,PASS,99,0,99,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.15.1 +220628,NC_045512.2,5386,T,G,PASS,34,0,34,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.15.1 +220628,NC_045512.2,694,T,A,PASS,6454,3969,2458,0.38,orf1ab,missense_variant,c.429T>A,p.Phe143Leu,p.F143L,ivar,BA.1.15.1 +220628,NC_045512.2,728,G,A,PASS,296,218,78,0.26,orf1ab,missense_variant,c.463G>A,p.Glu155Lys,p.E155K,ivar,BA.1.15.1 +220628,NC_045512.2,7488,C,T,PASS,1405,1041,364,0.26,orf1ab,missense_variant,c.7223C>T,p.Thr2408Ile,p.T2408I,ivar,BA.1.15.1 +220628,NC_045512.2,8393,G,A,PASS,3090,10,3074,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.15.1 +220629,NC_045512.2,11282,AGTTTGTCTG,A,PASS,38,38,34,0.89,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220629,NC_045512.2,11537,A,G,PASS,34,0,34,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220629,NC_045512.2,13195,T,C,PASS,1615,3,1612,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220629,NC_045512.2,14408,C,T,PASS,28,0,28,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220629,NC_045512.2,14646,T,A,PASS,36,22,14,0.39,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,Unassigned +220629,NC_045512.2,15738,C,T,PASS,1840,8,1832,1.0,orf1ab,missense_variant,c.15473C>T,p.Ser5158Leu,p.S5158L,ivar,Unassigned +220629,NC_045512.2,21762,C,T,PASS,26,0,26,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220629,NC_045512.2,21764,ATACATG,A,PASS,29,26,26,0.9,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220629,NC_045512.2,21846,C,T,PASS,43,0,43,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220629,NC_045512.2,23403,A,G,PASS,916,0,916,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220629,NC_045512.2,23525,C,T,PASS,950,0,949,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220629,NC_045512.2,23599,T,G,PASS,431,0,431,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220629,NC_045512.2,23604,C,A,PASS,415,0,413,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220629,NC_045512.2,23811,G,A,ft,11,6,5,0.45,S,missense_variant,c.2249G>A,p.Ser750Asn,p.S750N,ivar,Unassigned +220629,NC_045512.2,23853,AC,A,ft,13,13,4,0.31,S,frameshift_variant,c.2293delC,p.Arg765fs,p.R765fs,ivar,Unassigned +220629,NC_045512.2,23948,G,T,PASS,45,0,45,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220629,NC_045512.2,24130,C,A,PASS,85,0,85,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220629,NC_045512.2,24424,A,T,PASS,44,0,44,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220629,NC_045512.2,24469,T,A,PASS,346,0,346,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220629,NC_045512.2,24503,C,T,PASS,398,4,394,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220629,NC_045512.2,25584,C,T,PASS,23,0,23,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220629,NC_045512.2,25893,T,C,ft,16,12,4,0.25,ORF3a,synonymous_variant,c.501T>C,p.Ile167Ile,p.I167I,ivar,Unassigned +220629,NC_045512.2,26270,C,T,PASS,711,0,711,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220629,NC_045512.2,26530,A,G,PASS,243,0,243,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220629,NC_045512.2,26577,C,G,PASS,236,0,236,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220629,NC_045512.2,26709,G,A,PASS,290,2,288,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220629,NC_045512.2,27259,A,C,PASS,76,0,76,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220629,NC_045512.2,27670,G,T,PASS,18,0,18,1.0,ORF7a,missense_variant,c.277G>T,p.Val93Phe,p.V93F,ivar,Unassigned +220629,NC_045512.2,27807,C,T,PASS,22,0,22,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220629,NC_045512.2,28271,A,T,PASS,1156,0,1152,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220629,NC_045512.2,28311,C,T,PASS,1197,0,1193,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220629,NC_045512.2,2832,A,G,PASS,10,0,10,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220629,NC_045512.2,28361,GGAGAACGCA,G,PASS,975,969,682,0.7,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220629,NC_045512.2,28881,GG,AA,PASS,17113,95,17009,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220629,NC_045512.2,28883,G,C,PASS,17089,4,17063,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220629,NC_045512.2,5672,C,T,PASS,18,0,18,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220629,NC_045512.2,5924,G,A,PASS,11,0,11,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220629,NC_045512.2,685,AAAGTCATTT,A,PASS,11104,11008,5619,0.51,orf1ab,conservative_inframe_deletion,c.421_429delAAGTCATTT,p.Lys141_Phe143del,p.K141_F143del,ivar,Unassigned +220629,NC_045512.2,694,T,A,PASS,13,9,4,0.31,orf1ab,missense_variant,c.429T>A,p.Phe143Leu,p.F143L,ivar,Unassigned +220629,NC_045512.2,7690,A,G,PASS,29,21,8,0.28,orf1ab,synonymous_variant,c.7425A>G,p.Leu2475Leu,p.L2475L,ivar,Unassigned +220629,NC_045512.2,76,T,A,PASS,18,6,12,0.67,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220629,NC_045512.2,8393,G,A,PASS,974,1,973,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220630,NC_045512.2,10449,C,A,PASS,35,0,35,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220630,NC_045512.2,11282,AGTTTGTCTG,A,PASS,64,64,58,0.91,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220630,NC_045512.2,11537,A,G,PASS,134,0,134,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220630,NC_045512.2,13195,T,C,PASS,2893,5,2888,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220630,NC_045512.2,13544,T,C,ft,13,9,4,0.31,orf1ab,synonymous_variant,c.13279T>C,p.Leu4427Leu,p.L4427L,ivar,Unassigned +220630,NC_045512.2,14408,C,T,PASS,69,1,68,0.99,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220630,NC_045512.2,14646,T,A,PASS,123,91,32,0.26,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,Unassigned +220630,NC_045512.2,21762,C,T,PASS,121,0,121,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220630,NC_045512.2,21764,ATACATG,A,PASS,122,121,111,0.91,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220630,NC_045512.2,21846,C,T,PASS,117,0,117,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220630,NC_045512.2,23403,A,G,PASS,2458,2,2456,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220630,NC_045512.2,23525,C,T,PASS,2286,6,2280,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220630,NC_045512.2,23599,T,G,PASS,851,0,847,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220630,NC_045512.2,23604,C,A,PASS,823,0,815,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220630,NC_045512.2,23948,G,T,PASS,69,0,69,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220630,NC_045512.2,24130,C,A,PASS,115,0,115,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220630,NC_045512.2,24424,A,T,PASS,20,0,20,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220630,NC_045512.2,24469,T,A,PASS,294,0,291,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220630,NC_045512.2,24503,C,T,PASS,365,7,356,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220630,NC_045512.2,25000,C,T,PASS,28,0,28,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220630,NC_045512.2,25584,C,T,PASS,14,0,14,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220630,NC_045512.2,26270,C,T,PASS,131,2,129,0.98,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220630,NC_045512.2,26530,A,G,PASS,89,0,89,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220630,NC_045512.2,26577,C,G,PASS,75,0,75,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220630,NC_045512.2,26709,G,A,PASS,82,2,80,0.98,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220630,NC_045512.2,27259,A,C,PASS,79,0,79,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220630,NC_045512.2,27670,G,T,PASS,70,0,70,1.0,ORF7a,missense_variant,c.277G>T,p.Val93Phe,p.V93F,ivar,Unassigned +220630,NC_045512.2,27807,C,T,PASS,105,1,104,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220630,NC_045512.2,28271,A,T,PASS,798,0,796,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220630,NC_045512.2,28311,C,T,PASS,837,3,833,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220630,NC_045512.2,2832,A,G,PASS,16,0,16,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220630,NC_045512.2,28361,GGAGAACGCA,G,PASS,631,629,451,0.71,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220630,NC_045512.2,28512,C,T,PASS,400,289,104,0.26,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,Unassigned +220630,NC_045512.2,28881,GG,AA,PASS,2288,23,2261,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220630,NC_045512.2,28883,G,C,PASS,2275,0,2270,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220630,NC_045512.2,3037,C,T,PASS,20,0,20,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220630,NC_045512.2,728,G,A,ft,19,14,5,0.26,orf1ab,missense_variant,c.463G>A,p.Glu155Lys,p.E155K,ivar,Unassigned +220630,NC_045512.2,8393,G,A,PASS,2760,9,2748,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220631,NC_045512.2,10029,C,T,PASS,12,0,12,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,AY.127 +220631,NC_045512.2,11201,A,G,PASS,84,1,83,0.99,orf1ab,missense_variant,c.10936A>G,p.Thr3646Ala,p.T3646A,ivar,AY.127 +220631,NC_045512.2,11332,A,G,PASS,241,0,241,1.0,orf1ab,synonymous_variant,c.11067A>G,p.Val3689Val,p.V3689V,ivar,AY.127 +220631,NC_045512.2,1420,C,T,PASS,228,2,226,0.99,orf1ab,synonymous_variant,c.1155C>T,p.Ala385Ala,p.A385A,ivar,AY.127 +220631,NC_045512.2,14408,C,T,PASS,45,0,45,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,AY.127 +220631,NC_045512.2,14511,G,C,PASS,84,0,84,1.0,orf1ab,missense_variant,c.14246G>C,p.Arg4749Thr,p.R4749T,ivar,AY.127 +220631,NC_045512.2,15535,G,A,ft,16,12,4,0.25,orf1ab,synonymous_variant,c.15270G>A,p.Lys5090Lys,p.K5090K,ivar,AY.127 +220631,NC_045512.2,16466,C,T,PASS,221,0,221,1.0,orf1ab,missense_variant,c.16201C>T,p.His5401Tyr,p.H5401Y,ivar,AY.127 +220631,NC_045512.2,18788,C,T,PASS,1387,2,1385,1.0,orf1ab,stop_gained,c.18523C>T,p.Gln6175*,p.Q6175*,ivar,AY.127 +220631,NC_045512.2,19220,C,T,PASS,387,0,387,1.0,orf1ab,synonymous_variant,c.18955C>T,p.Leu6319Leu,p.L6319L,ivar,AY.127 +220631,NC_045512.2,21057,C,T,PASS,31,1,30,0.97,orf1ab,missense_variant,c.20792C>T,p.Thr6931Ile,p.T6931I,ivar,AY.127 +220631,NC_045512.2,210,G,T,PASS,39,0,39,1.0,orf1ab,upstream_gene_variant,c.-56G>T,.,.,ivar,AY.127 +220631,NC_045512.2,21618,C,G,PASS,390,0,390,1.0,S,missense_variant,c.56C>G,p.Thr19Arg,p.T19R,ivar,AY.127 +220631,NC_045512.2,21846,C,T,PASS,138,0,138,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,AY.127 +220631,NC_045512.2,22917,T,G,PASS,10,0,10,1.0,S,missense_variant,c.1355T>G,p.Leu452Arg,p.L452R,ivar,AY.127 +220631,NC_045512.2,23403,A,G,PASS,2800,7,2793,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,AY.127 +220631,NC_045512.2,23604,C,G,PASS,796,0,794,1.0,S,missense_variant,c.2042C>G,p.Pro681Arg,p.P681R,ivar,AY.127 +220631,NC_045512.2,24410,G,A,PASS,75,0,75,1.0,S,missense_variant,c.2848G>A,p.Asp950Asn,p.D950N,ivar,AY.127 +220631,NC_045512.2,25469,C,T,PASS,43,0,43,1.0,ORF3a,missense_variant,c.77C>T,p.Ser26Leu,p.S26L,ivar,AY.127 +220631,NC_045512.2,25518,T,C,PASS,43,0,43,1.0,ORF3a,synonymous_variant,c.126T>C,p.Pro42Pro,p.P42P,ivar,AY.127 +220631,NC_045512.2,25538,G,T,PASS,45,0,45,1.0,ORF3a,missense_variant,c.146G>T,p.Gly49Val,p.G49V,ivar,AY.127 +220631,NC_045512.2,26054,C,A,PASS,83,0,83,1.0,ORF3a,missense_variant,c.662C>A,p.Thr221Lys,p.T221K,ivar,AY.127 +220631,NC_045512.2,26172,G,T,PASS,94,0,92,0.98,ORF3a,missense_variant,c.780G>T,p.Met260Ile,p.M260I,ivar,AY.127 +220631,NC_045512.2,26767,T,C,PASS,376,0,376,1.0,M,missense_variant,c.245T>C,p.Ile82Thr,p.I82T,ivar,AY.127 +220631,NC_045512.2,27590,C,T,PASS,115,1,114,0.99,ORF7a,missense_variant,c.197C>T,p.Ala66Val,p.A66V,ivar,AY.127 +220631,NC_045512.2,27638,T,C,PASS,107,0,107,1.0,ORF7a,missense_variant,c.245T>C,p.Val82Ala,p.V82A,ivar,AY.127 +220631,NC_045512.2,27722,T,C,PASS,91,0,91,1.0,ORF7a,missense_variant,c.329T>C,p.Ile110Thr,p.I110T,ivar,AY.127 +220631,NC_045512.2,27752,C,T,PASS,109,0,109,1.0,ORF7a,missense_variant,c.359C>T,p.Thr120Ile,p.T120I,ivar,AY.127 +220631,NC_045512.2,27874,C,T,PASS,146,0,146,1.0,ORF7b,missense_variant,c.119C>T,p.Thr40Ile,p.T40I,ivar,AY.127 +220631,NC_045512.2,28247,AGATTTC,A,PASS,974,967,888,0.91,ORF8,conservative_inframe_deletion,c.355_360delGATTTC,p.Asp119_Phe120del,p.D119_F120del,ivar,AY.127 +220631,NC_045512.2,28253,C,A,PASS,105,1,102,0.97,ORF8,missense_variant,c.360C>A,p.Phe120Leu,p.F120L,ivar,AY.127 +220631,NC_045512.2,28270,TA,T,PASS,1218,1212,1147,0.94,N,upstream_gene_variant,c.-3delA,.,.,ivar,AY.127 +220631,NC_045512.2,28378,G,T,PASS,764,0,753,0.99,N,synonymous_variant,c.105G>T,p.Ala35Ala,p.A35A,ivar,AY.127 +220631,NC_045512.2,28461,A,G,PASS,480,0,480,1.0,N,missense_variant,c.188A>G,p.Asp63Gly,p.D63G,ivar,AY.127 +220631,NC_045512.2,28881,G,T,PASS,4129,17,4080,0.99,N,missense_variant,c.608G>T,p.Arg203Met,p.R203M,ivar,AY.127 +220631,NC_045512.2,28916,G,T,PASS,1270,0,1258,0.99,N,missense_variant,c.643G>T,p.Gly215Cys,p.G215C,ivar,AY.127 +220631,NC_045512.2,29402,G,T,PASS,6716,4,6694,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,AY.127 +220631,NC_045512.2,29734,G,A,PASS,113,0,113,1.0,S,downstream_gene_variant,c.*4350G>A,.,.,ivar,AY.127 +220631,NC_045512.2,29742,G,T,PASS,109,0,109,1.0,S,downstream_gene_variant,c.*4358G>T,.,.,ivar,AY.127 +220631,NC_045512.2,29751,G,T,PASS,113,0,111,0.98,S,downstream_gene_variant,c.*4367G>T,.,.,ivar,AY.127 +220631,NC_045512.2,3037,C,T,PASS,420,0,420,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,AY.127 +220631,NC_045512.2,3411,C,T,PASS,995,12,979,0.98,orf1ab,missense_variant,c.3146C>T,p.Ala1049Val,p.A1049V,ivar,AY.127 +220631,NC_045512.2,4181,G,T,PASS,27,0,27,1.0,orf1ab,missense_variant,c.3916G>T,p.Ala1306Ser,p.A1306S,ivar,AY.127 +220631,NC_045512.2,7526,G,A,PASS,1855,12,1843,0.99,orf1ab,missense_variant,c.7261G>A,p.Val2421Ile,p.V2421I,ivar,AY.127 +220631,NC_045512.2,8010,A,G,PASS,1725,54,1670,0.97,orf1ab,missense_variant,c.7745A>G,p.Asp2582Gly,p.D2582G,ivar,AY.127 +220631,NC_045512.2,8986,C,T,PASS,22,0,22,1.0,orf1ab,synonymous_variant,c.8721C>T,p.Asp2907Asp,p.D2907D,ivar,AY.127 +220631,NC_045512.2,9053,G,T,PASS,28,0,28,1.0,orf1ab,missense_variant,c.8788G>T,p.Val2930Leu,p.V2930L,ivar,AY.127 +220633,NC_045512.2,10029,C,T,PASS,30,0,30,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220633,NC_045512.2,10449,C,A,PASS,122,0,122,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220633,NC_045512.2,11282,AGTTTGTCTG,A,PASS,246,246,223,0.91,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220633,NC_045512.2,11537,A,G,PASS,139,0,139,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220633,NC_045512.2,13195,T,C,PASS,7290,16,7274,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220633,NC_045512.2,14408,C,T,PASS,146,0,146,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220633,NC_045512.2,18163,A,G,PASS,30,0,30,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220633,NC_045512.2,21762,C,T,PASS,154,0,154,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220633,NC_045512.2,21764,ATACATG,A,PASS,156,154,140,0.9,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220633,NC_045512.2,21846,C,T,PASS,158,0,158,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220633,NC_045512.2,22578,G,A,PASS,20,0,20,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.17 +220633,NC_045512.2,22673,TC,CT,PASS,11,0,11,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.17 +220633,NC_045512.2,22679,T,C,PASS,13,0,13,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220633,NC_045512.2,22686,C,T,PASS,13,0,13,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220633,NC_045512.2,23403,A,G,PASS,3760,2,3757,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220633,NC_045512.2,23525,C,T,PASS,3604,13,3581,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220633,NC_045512.2,23599,T,G,PASS,1393,0,1391,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220633,NC_045512.2,23604,C,A,PASS,1340,0,1337,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220633,NC_045512.2,23854,C,A,PASS,60,0,60,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220633,NC_045512.2,23948,G,T,PASS,659,0,658,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220633,NC_045512.2,24130,C,A,PASS,1017,1,1009,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220633,NC_045512.2,24424,A,T,PASS,219,1,216,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220633,NC_045512.2,24469,T,A,PASS,888,0,885,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220633,NC_045512.2,24503,C,T,PASS,1069,13,1054,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220633,NC_045512.2,25000,C,T,PASS,103,2,101,0.98,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220633,NC_045512.2,25584,C,T,PASS,173,0,173,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220633,NC_045512.2,26270,C,T,PASS,598,0,597,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220633,NC_045512.2,26530,A,G,PASS,161,0,161,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220633,NC_045512.2,26577,C,G,PASS,181,0,181,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220633,NC_045512.2,26709,G,A,PASS,150,0,150,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220633,NC_045512.2,27259,A,C,PASS,464,0,464,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220633,NC_045512.2,27670,G,T,PASS,112,0,111,0.99,ORF7a,missense_variant,c.277G>T,p.Val93Phe,p.V93F,ivar,BA.1.17 +220633,NC_045512.2,27807,C,T,PASS,123,1,122,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220633,NC_045512.2,28271,A,T,PASS,1502,5,1488,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220633,NC_045512.2,28311,C,T,PASS,1544,2,1540,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220633,NC_045512.2,2832,A,G,PASS,135,0,135,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220633,NC_045512.2,28361,GGAGAACGCA,G,PASS,1103,1083,619,0.56,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220633,NC_045512.2,28881,GG,AA,PASS,5114,72,5038,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220633,NC_045512.2,28883,G,C,PASS,5062,6,5048,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220633,NC_045512.2,3037,C,T,PASS,35,0,35,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220633,NC_045512.2,5672,C,T,PASS,153,0,153,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220633,NC_045512.2,5924,G,A,PASS,66,0,66,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220633,NC_045512.2,8393,G,A,PASS,5806,16,5787,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220634,NC_045512.2,11282,AGTTTGTCTG,A,PASS,61,61,50,0.82,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220634,NC_045512.2,11537,A,G,PASS,27,0,27,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220634,NC_045512.2,13195,T,C,PASS,1103,6,1097,0.99,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220634,NC_045512.2,21762,C,T,PASS,24,0,24,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220634,NC_045512.2,21764,ATACATG,A,PASS,24,24,19,0.79,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220634,NC_045512.2,21846,C,T,PASS,25,0,25,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220634,NC_045512.2,23403,A,G,PASS,955,2,953,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220634,NC_045512.2,23525,C,T,PASS,930,0,928,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220634,NC_045512.2,23599,T,G,PASS,394,0,394,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220634,NC_045512.2,23604,C,A,PASS,379,0,374,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220634,NC_045512.2,23948,G,T,PASS,35,0,35,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220634,NC_045512.2,24130,C,A,PASS,54,0,54,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220634,NC_045512.2,24424,A,T,PASS,41,0,41,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220634,NC_045512.2,24469,T,A,PASS,182,0,182,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220634,NC_045512.2,24503,C,T,PASS,193,4,189,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220634,NC_045512.2,25584,C,T,PASS,20,0,20,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220634,NC_045512.2,26270,C,T,PASS,186,2,184,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220634,NC_045512.2,26465,T,C,ft,11,8,3,0.27,E,missense_variant,c.221T>C,p.Leu74Pro,p.L74P,ivar,Unassigned +220634,NC_045512.2,26530,A,G,PASS,202,0,202,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220634,NC_045512.2,26577,C,G,PASS,209,0,209,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220634,NC_045512.2,26709,G,A,PASS,216,0,216,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220634,NC_045512.2,27259,A,C,PASS,90,0,90,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220634,NC_045512.2,27384,T,C,PASS,72,0,72,1.0,ORF6,synonymous_variant,c.183T>C,p.Asp61Asp,p.D61D,ivar,Unassigned +220634,NC_045512.2,27807,C,T,PASS,34,0,34,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220634,NC_045512.2,28271,A,T,PASS,256,0,254,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220634,NC_045512.2,28311,C,T,PASS,270,0,270,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220634,NC_045512.2,2832,A,G,PASS,23,0,23,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220634,NC_045512.2,28361,GGAGAACGCA,G,PASS,202,201,147,0.73,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220634,NC_045512.2,28881,GG,AA,PASS,7905,96,7806,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220634,NC_045512.2,28883,G,C,PASS,7846,1,7833,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220634,NC_045512.2,5672,C,T,PASS,24,0,24,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220634,NC_045512.2,5924,G,A,PASS,12,0,12,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220634,NC_045512.2,7984,T,C,PASS,214,0,214,1.0,orf1ab,synonymous_variant,c.7719T>C,p.Asp2573Asp,p.D2573D,ivar,Unassigned +220634,NC_045512.2,8393,G,A,PASS,2278,6,2271,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220635,NC_045512.2,10029,C,T,PASS,10,0,10,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,Unassigned +220635,NC_045512.2,10135,T,C,PASS,12,0,12,1.0,orf1ab,synonymous_variant,c.9870T>C,p.Leu3290Leu,p.L3290L,ivar,Unassigned +220635,NC_045512.2,10449,C,A,PASS,28,0,28,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220635,NC_045512.2,11074,CT,C,PASS,32,30,9,0.28,orf1ab,frameshift_variant,c.10817delT,p.Leu3606fs,p.L3606fs,ivar,Unassigned +220635,NC_045512.2,11282,AGTTTGTCTG,A,PASS,114,114,105,0.92,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220635,NC_045512.2,11537,A,G,PASS,25,0,25,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220635,NC_045512.2,12864,A,C,PASS,80,0,78,0.98,orf1ab,missense_variant,c.12599A>C,p.Asp4200Ala,p.D4200A,ivar,Unassigned +220635,NC_045512.2,13195,T,C,PASS,1827,0,1827,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220635,NC_045512.2,14408,C,T,PASS,15,0,15,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220635,NC_045512.2,21762,C,T,PASS,33,0,33,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220635,NC_045512.2,21764,ATACATG,A,PASS,35,35,33,0.94,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220635,NC_045512.2,21846,C,T,PASS,33,0,33,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220635,NC_045512.2,21856,T,C,PASS,30,0,30,1.0,S,synonymous_variant,c.294T>C,p.Ser98Ser,p.S98S,ivar,Unassigned +220635,NC_045512.2,22578,G,A,PASS,15,0,15,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,Unassigned +220635,NC_045512.2,23403,A,G,PASS,713,2,711,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220635,NC_045512.2,23525,C,T,PASS,852,0,848,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220635,NC_045512.2,23599,T,G,PASS,337,0,335,0.99,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220635,NC_045512.2,23604,C,A,PASS,327,0,325,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220635,NC_045512.2,23854,C,A,PASS,10,0,10,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220635,NC_045512.2,23948,G,T,PASS,68,0,65,0.96,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220635,NC_045512.2,24130,C,A,PASS,110,0,110,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220635,NC_045512.2,24424,A,T,PASS,52,0,52,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220635,NC_045512.2,24469,T,A,PASS,197,0,197,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220635,NC_045512.2,24503,C,T,PASS,238,6,232,0.97,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220635,NC_045512.2,25584,C,T,PASS,32,0,32,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220635,NC_045512.2,25708,C,T,PASS,39,0,39,1.0,ORF3a,missense_variant,c.316C>T,p.Leu106Phe,p.L106F,ivar,Unassigned +220635,NC_045512.2,26270,C,T,PASS,278,0,276,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220635,NC_045512.2,26530,A,G,PASS,71,1,70,0.99,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220635,NC_045512.2,26577,C,G,PASS,96,0,96,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220635,NC_045512.2,26709,G,A,PASS,76,0,76,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220635,NC_045512.2,27259,A,C,PASS,122,0,122,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220635,NC_045512.2,27807,C,T,PASS,19,0,19,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220635,NC_045512.2,28271,A,T,PASS,593,0,592,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220635,NC_045512.2,28311,C,T,PASS,617,0,615,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220635,NC_045512.2,2832,A,G,PASS,17,0,17,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220635,NC_045512.2,28361,GGAGAACGCA,G,PASS,483,482,327,0.68,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220635,NC_045512.2,28881,GG,AA,PASS,6445,87,6352,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220635,NC_045512.2,28883,G,C,PASS,6389,4,6374,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220635,NC_045512.2,29301,A,G,PASS,2221,1,2219,1.0,N,missense_variant,c.1028A>G,p.Asp343Gly,p.D343G,ivar,Unassigned +220635,NC_045512.2,3105,A,G,PASS,110,2,108,0.98,orf1ab,missense_variant,c.2840A>G,p.Tyr947Cys,p.Y947C,ivar,Unassigned +220635,NC_045512.2,76,T,A,ft,19,13,6,0.32,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220635,NC_045512.2,78,T,G,ft,19,13,6,0.32,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220635,NC_045512.2,8393,G,A,PASS,2010,9,2001,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220636,NC_045512.2,10449,C,A,PASS,12,0,12,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220636,NC_045512.2,11282,AGTTTGTCTG,A,PASS,40,40,39,0.98,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220636,NC_045512.2,11537,A,G,PASS,38,1,37,0.97,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220636,NC_045512.2,12864,A,C,PASS,59,0,59,1.0,orf1ab,missense_variant,c.12599A>C,p.Asp4200Ala,p.D4200A,ivar,Unassigned +220636,NC_045512.2,13195,T,C,PASS,2304,3,2301,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220636,NC_045512.2,14408,C,T,PASS,18,0,18,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220636,NC_045512.2,18047,A,T,PASS,12,4,8,0.67,orf1ab,missense_variant,c.17782A>T,p.Met5928Leu,p.M5928L,ivar,Unassigned +220636,NC_045512.2,21762,C,T,PASS,21,0,21,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220636,NC_045512.2,21764,ATACATG,A,PASS,24,21,21,0.88,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220636,NC_045512.2,21846,C,T,PASS,36,0,36,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220636,NC_045512.2,21856,T,C,PASS,38,0,38,1.0,S,synonymous_variant,c.294T>C,p.Ser98Ser,p.S98S,ivar,Unassigned +220636,NC_045512.2,23403,A,G,PASS,706,2,704,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220636,NC_045512.2,23525,C,T,PASS,762,0,762,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220636,NC_045512.2,23599,T,G,PASS,299,0,299,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220636,NC_045512.2,23604,C,A,PASS,295,0,295,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220636,NC_045512.2,23948,G,T,PASS,33,0,33,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220636,NC_045512.2,24130,C,A,PASS,39,0,38,0.97,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220636,NC_045512.2,24424,A,T,PASS,21,0,21,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220636,NC_045512.2,24469,T,A,PASS,277,0,277,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220636,NC_045512.2,24503,C,T,PASS,304,1,303,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220636,NC_045512.2,25584,C,T,PASS,23,0,23,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220636,NC_045512.2,25708,C,T,PASS,18,0,18,1.0,ORF3a,missense_variant,c.316C>T,p.Leu106Phe,p.L106F,ivar,Unassigned +220636,NC_045512.2,26270,C,T,PASS,340,2,338,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220636,NC_045512.2,26530,A,G,PASS,121,0,121,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220636,NC_045512.2,26577,C,G,PASS,140,0,140,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220636,NC_045512.2,26709,G,A,PASS,138,0,138,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220636,NC_045512.2,27259,A,C,PASS,28,0,28,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220636,NC_045512.2,2754,T,C,PASS,102,1,101,0.99,orf1ab,missense_variant,c.2489T>C,p.Val830Ala,p.V830A,ivar,Unassigned +220636,NC_045512.2,27711,A,G,ft,13,9,4,0.31,ORF7a,synonymous_variant,c.318A>G,p.Ala106Ala,p.A106A,ivar,Unassigned +220636,NC_045512.2,27807,C,T,PASS,15,1,14,0.93,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220636,NC_045512.2,28271,A,T,PASS,490,1,489,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220636,NC_045512.2,28311,C,T,PASS,483,1,480,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220636,NC_045512.2,2832,A,G,PASS,132,0,132,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220636,NC_045512.2,28361,GGAGAACGCA,G,PASS,377,373,254,0.67,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220636,NC_045512.2,28881,GG,AA,PASS,8195,126,8059,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220636,NC_045512.2,28883,G,C,PASS,8109,0,8105,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220636,NC_045512.2,29301,A,G,PASS,3626,4,3622,1.0,N,missense_variant,c.1028A>G,p.Asp343Gly,p.D343G,ivar,Unassigned +220636,NC_045512.2,3105,A,G,PASS,56,0,56,1.0,orf1ab,missense_variant,c.2840A>G,p.Tyr947Cys,p.Y947C,ivar,Unassigned +220636,NC_045512.2,4097,T,TC,ft,17,17,5,0.29,orf1ab,frameshift_variant,c.3832_3833insC,p.Phe1278fs,p.F1278fs,ivar,Unassigned +220636,NC_045512.2,4101,T,C,ft,18,12,6,0.33,orf1ab,missense_variant,c.3836T>C,p.Leu1279Ser,p.L1279S,ivar,Unassigned +220636,NC_045512.2,4166,A,T,PASS,52,26,26,0.5,orf1ab,missense_variant,c.3901A>T,p.Ile1301Leu,p.I1301L,ivar,Unassigned +220636,NC_045512.2,4171,T,C,PASS,51,25,26,0.51,orf1ab,synonymous_variant,c.3906T>C,p.Pro1302Pro,p.P1302P,ivar,Unassigned +220636,NC_045512.2,728,G,A,ft,11,8,3,0.27,orf1ab,missense_variant,c.463G>A,p.Glu155Lys,p.E155K,ivar,Unassigned +220636,NC_045512.2,76,T,A,PASS,10,3,7,0.7,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220636,NC_045512.2,78,T,G,PASS,10,3,7,0.7,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220636,NC_045512.2,8393,G,A,PASS,1312,23,1286,0.98,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220637,NC_045512.2,10029,C,T,PASS,34,0,34,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220637,NC_045512.2,10449,C,A,PASS,121,0,121,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220637,NC_045512.2,11282,AGTTTGTCTG,A,PASS,312,310,269,0.86,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220637,NC_045512.2,11537,A,G,PASS,289,0,289,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220637,NC_045512.2,13195,T,C,PASS,7412,12,7399,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220637,NC_045512.2,14408,C,T,PASS,177,2,175,0.99,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220637,NC_045512.2,18163,A,G,PASS,30,0,30,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220637,NC_045512.2,21762,C,T,PASS,275,0,275,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220637,NC_045512.2,21764,ATACATG,A,PASS,280,276,255,0.91,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220637,NC_045512.2,21846,C,T,PASS,292,0,292,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220637,NC_045512.2,22578,G,A,PASS,25,0,25,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.17 +220637,NC_045512.2,22673,TC,CT,PASS,23,0,23,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.17 +220637,NC_045512.2,22679,T,C,PASS,29,0,29,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220637,NC_045512.2,22686,C,T,PASS,28,0,28,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220637,NC_045512.2,23202,C,A,PASS,20,0,20,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220637,NC_045512.2,23403,A,G,PASS,3875,6,3869,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220637,NC_045512.2,23525,C,T,PASS,3568,12,3551,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220637,NC_045512.2,23599,T,G,PASS,1289,0,1286,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220637,NC_045512.2,23604,C,A,PASS,1255,0,1246,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220637,NC_045512.2,23854,C,A,PASS,90,0,90,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220637,NC_045512.2,23948,G,T,PASS,810,0,810,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220637,NC_045512.2,24130,C,A,PASS,1321,0,1311,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220637,NC_045512.2,24424,A,T,PASS,329,2,323,0.98,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220637,NC_045512.2,24469,T,A,PASS,1351,1,1347,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220637,NC_045512.2,24503,C,T,PASS,1588,29,1552,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220637,NC_045512.2,25000,C,T,PASS,121,0,121,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220637,NC_045512.2,25584,C,T,PASS,173,0,173,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220637,NC_045512.2,26270,C,T,PASS,1076,2,1070,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220637,NC_045512.2,26530,A,G,PASS,346,2,344,0.99,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220637,NC_045512.2,26577,C,G,PASS,342,0,342,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220637,NC_045512.2,26709,G,A,PASS,373,1,371,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220637,NC_045512.2,27259,A,C,PASS,412,0,412,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220637,NC_045512.2,27807,C,T,PASS,128,0,127,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220637,NC_045512.2,28271,A,T,PASS,1853,2,1851,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220637,NC_045512.2,28311,C,T,PASS,1865,8,1857,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220637,NC_045512.2,2832,A,G,PASS,140,0,140,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220637,NC_045512.2,28361,GGAGAACGCA,G,PASS,1461,1454,930,0.64,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220637,NC_045512.2,28363,A,T,PASS,14,10,4,0.29,N,synonymous_variant,c.90A>T,p.Gly30Gly,p.G30G,ivar,BA.1.17 +220637,NC_045512.2,28881,GG,AA,PASS,3791,57,3732,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220637,NC_045512.2,28883,G,C,PASS,3743,3,3735,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220637,NC_045512.2,29772,T,C,PASS,48,1,47,0.98,S,downstream_gene_variant,c.*4388T>C,.,.,ivar,BA.1.17 +220637,NC_045512.2,3037,C,T,PASS,52,3,49,0.94,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220637,NC_045512.2,5386,T,G,PASS,22,0,22,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.17 +220637,NC_045512.2,5672,C,T,PASS,278,0,278,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220637,NC_045512.2,5924,G,A,PASS,105,0,105,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220637,NC_045512.2,8393,G,A,PASS,3953,20,3931,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220637,NC_045512.2,8652,T,C,PASS,3517,5,3510,1.0,orf1ab,missense_variant,c.8387T>C,p.Met2796Thr,p.M2796T,ivar,BA.1.17 +220638,NC_045512.2,10029,C,T,PASS,19,0,19,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220638,NC_045512.2,10449,C,A,PASS,95,0,95,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220638,NC_045512.2,1051,A,G,PASS,3027,5,3022,1.0,orf1ab,synonymous_variant,c.786A>G,p.Lys262Lys,p.K262K,ivar,BA.1.17 +220638,NC_045512.2,11282,AGTTTGTCTG,A,PASS,254,252,219,0.86,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220638,NC_045512.2,11537,A,G,PASS,215,0,215,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220638,NC_045512.2,13195,T,C,PASS,4423,4,4419,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220638,NC_045512.2,14408,C,T,PASS,120,3,117,0.98,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220638,NC_045512.2,15359,G,A,ft,11,5,5,0.45,orf1ab,missense_variant,c.15094G>A,p.Ala5032Thr,p.A5032T,ivar,BA.1.17 +220638,NC_045512.2,16887,C,T,PASS,704,4,700,0.99,orf1ab,missense_variant,c.16622C>T,p.Thr5541Ile,p.T5541I,ivar,BA.1.17 +220638,NC_045512.2,18163,A,G,PASS,21,0,21,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220638,NC_045512.2,18326,C,T,PASS,7551,39,7508,0.99,orf1ab,synonymous_variant,c.18061C>T,p.Leu6021Leu,p.L6021L,ivar,BA.1.17 +220638,NC_045512.2,21762,C,T,PASS,218,0,218,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220638,NC_045512.2,21764,ATACATG,A,PASS,227,218,201,0.89,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220638,NC_045512.2,21846,C,T,PASS,221,0,219,0.99,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220638,NC_045512.2,22193,AATT,A,PASS,11,11,11,1.0,S,disruptive_inframe_deletion,c.632_634delATT,p.Asn211_Leu212delinsIle,p.N211_L212delinsI,ivar,BA.1.17 +220638,NC_045512.2,22204,T,TGAGCCAGAA,ft,11,11,9,0.82,S,disruptive_inframe_insertion,c.644_645insGCCAGAAGA,p.Arg214_Asp215insGluProGlu,p.R214_D215insEPE,ivar,BA.1.17 +220638,NC_045512.2,22578,G,A,PASS,17,0,17,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.17 +220638,NC_045512.2,22673,T,C,PASS,10,0,10,1.0,S,missense_variant,c.1111T>C,p.Ser371Pro,p.S371P,ivar,BA.1.17 +220638,NC_045512.2,22679,T,C,PASS,18,0,18,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220638,NC_045512.2,22686,C,T,PASS,18,0,18,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220638,NC_045512.2,23013,A,C,PASS,10,0,10,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.17 +220638,NC_045512.2,23040,A,G,PASS,15,0,15,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.17 +220638,NC_045512.2,23048,G,A,PASS,15,0,15,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.17 +220638,NC_045512.2,23055,A,G,PASS,15,0,15,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.17 +220638,NC_045512.2,23063,A,T,PASS,15,0,15,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.17 +220638,NC_045512.2,23075,T,C,PASS,17,0,17,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.17 +220638,NC_045512.2,23202,C,A,PASS,24,0,24,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220638,NC_045512.2,23403,A,G,PASS,3470,2,3468,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220638,NC_045512.2,23525,C,T,PASS,3180,6,3174,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220638,NC_045512.2,23599,T,G,PASS,1176,0,1176,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220638,NC_045512.2,23604,C,A,PASS,1131,2,1124,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220638,NC_045512.2,23854,C,A,PASS,57,0,57,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220638,NC_045512.2,23948,G,T,PASS,760,0,755,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220638,NC_045512.2,24130,C,A,PASS,1140,1,1136,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220638,NC_045512.2,24424,A,T,PASS,228,2,224,0.98,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220638,NC_045512.2,24469,T,A,PASS,848,0,844,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220638,NC_045512.2,24503,C,T,PASS,979,18,961,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220638,NC_045512.2,25000,C,T,PASS,110,2,108,0.98,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220638,NC_045512.2,25584,C,T,PASS,133,0,133,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220638,NC_045512.2,26270,C,T,PASS,779,0,779,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220638,NC_045512.2,26530,A,G,PASS,350,0,350,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220638,NC_045512.2,26577,C,G,PASS,369,0,369,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220638,NC_045512.2,26709,G,A,PASS,422,0,422,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220638,NC_045512.2,27259,A,C,PASS,515,0,515,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220638,NC_045512.2,27384,T,C,PASS,601,0,601,1.0,ORF6,synonymous_variant,c.183T>C,p.Asp61Asp,p.D61D,ivar,BA.1.17 +220638,NC_045512.2,27807,C,T,PASS,135,1,134,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220638,NC_045512.2,28271,A,T,PASS,1839,6,1831,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220638,NC_045512.2,28311,C,T,PASS,1989,8,1976,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220638,NC_045512.2,2832,A,G,PASS,111,2,109,0.98,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220638,NC_045512.2,28361,GGAGAACGCA,G,PASS,1474,1463,704,0.48,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220638,NC_045512.2,28881,GG,AA,PASS,2234,12,2219,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220638,NC_045512.2,28883,G,C,PASS,2229,0,2227,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220638,NC_045512.2,3037,C,T,PASS,41,0,41,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220638,NC_045512.2,5672,C,T,PASS,257,0,257,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220638,NC_045512.2,5924,G,A,PASS,85,0,85,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220638,NC_045512.2,7984,T,C,PASS,1178,0,1178,1.0,orf1ab,synonymous_variant,c.7719T>C,p.Asp2573Asp,p.D2573D,ivar,BA.1.17 +220638,NC_045512.2,8393,G,A,PASS,3255,8,3241,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220638,NC_045512.2,9430,C,T,ft,14,9,5,0.36,orf1ab,synonymous_variant,c.9165C>T,p.Ile3055Ile,p.I3055I,ivar,BA.1.17 +220639,NC_045512.2,10449,C,A,PASS,16,0,16,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220639,NC_045512.2,11282,AGTTTGTCTG,A,PASS,57,57,52,0.91,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220639,NC_045512.2,11537,A,G,PASS,59,0,59,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220639,NC_045512.2,13195,T,C,PASS,3114,3,3110,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220639,NC_045512.2,14408,C,T,PASS,24,0,23,0.96,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220639,NC_045512.2,20337,T,C,ft,10,7,3,0.3,orf1ab,missense_variant,c.20072T>C,p.Ile6691Thr,p.I6691T,ivar,Unassigned +220639,NC_045512.2,21762,C,T,PASS,38,0,38,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220639,NC_045512.2,21764,ATACATG,A,PASS,38,38,36,0.95,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220639,NC_045512.2,21846,C,T,PASS,40,0,40,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220639,NC_045512.2,23403,A,G,PASS,1179,2,1177,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220639,NC_045512.2,23525,C,T,PASS,1112,0,1112,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220639,NC_045512.2,23599,T,G,PASS,414,0,414,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220639,NC_045512.2,23604,C,A,PASS,400,0,399,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220639,NC_045512.2,23948,G,T,PASS,80,0,80,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220639,NC_045512.2,24130,C,A,PASS,119,0,119,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220639,NC_045512.2,24424,A,T,PASS,14,0,14,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220639,NC_045512.2,24469,T,A,PASS,311,2,309,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220639,NC_045512.2,24503,C,T,PASS,388,8,380,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220639,NC_045512.2,25570,T,C,ft,20,14,6,0.3,ORF3a,missense_variant,c.178T>C,p.Ser60Pro,p.S60P,ivar,Unassigned +220639,NC_045512.2,25584,C,T,PASS,20,0,20,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220639,NC_045512.2,26270,C,T,PASS,53,0,53,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220639,NC_045512.2,26709,G,A,PASS,11,0,11,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220639,NC_045512.2,27259,A,C,PASS,35,0,35,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220639,NC_045512.2,27807,C,T,PASS,21,0,21,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220639,NC_045512.2,28271,A,T,PASS,460,2,456,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220639,NC_045512.2,28311,C,T,PASS,473,0,471,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220639,NC_045512.2,2832,A,G,PASS,17,0,17,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220639,NC_045512.2,28361,GGAGAACGCA,G,PASS,321,319,210,0.65,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220639,NC_045512.2,28881,GG,AA,PASS,6361,88,6267,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220639,NC_045512.2,28883,G,C,PASS,6288,3,6278,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220639,NC_045512.2,5672,C,T,PASS,35,0,35,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220639,NC_045512.2,5924,G,A,PASS,10,0,10,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220639,NC_045512.2,685,AAAGTCATTT,A,PASS,11186,11106,5685,0.51,orf1ab,conservative_inframe_deletion,c.421_429delAAGTCATTT,p.Lys141_Phe143del,p.K141_F143del,ivar,Unassigned +220639,NC_045512.2,8393,G,A,PASS,1511,2,1506,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220640,NC_045512.2,10449,C,A,PASS,18,0,18,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220640,NC_045512.2,11282,AGTTTGTCTG,A,PASS,43,43,43,1.0,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220640,NC_045512.2,11537,A,G,PASS,55,0,55,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220640,NC_045512.2,13195,T,C,PASS,2220,3,2217,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220640,NC_045512.2,14408,C,T,PASS,29,0,29,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220640,NC_045512.2,19834,C,T,ft,12,8,4,0.33,orf1ab,synonymous_variant,c.19569C>T,p.Tyr6523Tyr,p.Y6523Y,ivar,Unassigned +220640,NC_045512.2,21762,C,T,PASS,43,0,43,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220640,NC_045512.2,21764,ATACATG,A,PASS,43,43,42,0.98,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220640,NC_045512.2,21846,C,T,PASS,37,0,37,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220640,NC_045512.2,23403,A,G,PASS,1160,1,1159,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220640,NC_045512.2,23525,C,T,PASS,1142,3,1139,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220640,NC_045512.2,23599,T,G,PASS,447,0,447,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220640,NC_045512.2,23604,C,A,PASS,424,0,424,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220640,NC_045512.2,23948,G,T,PASS,99,0,97,0.98,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220640,NC_045512.2,24130,C,A,PASS,179,0,177,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220640,NC_045512.2,24424,A,T,PASS,40,0,40,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220640,NC_045512.2,24469,T,A,PASS,333,0,332,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220640,NC_045512.2,24503,C,T,PASS,408,4,404,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220640,NC_045512.2,25000,C,T,PASS,14,0,14,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220640,NC_045512.2,25584,C,T,PASS,32,0,32,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220640,NC_045512.2,26270,C,T,PASS,220,0,220,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220640,NC_045512.2,26530,A,G,PASS,150,2,148,0.99,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220640,NC_045512.2,26577,C,G,PASS,136,0,136,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220640,NC_045512.2,26709,G,A,PASS,135,0,135,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220640,NC_045512.2,27259,A,C,PASS,62,0,62,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220640,NC_045512.2,27807,C,T,PASS,19,0,19,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220640,NC_045512.2,28271,A,T,PASS,374,0,374,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220640,NC_045512.2,28311,C,T,PASS,386,0,386,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220640,NC_045512.2,2832,A,G,PASS,47,0,47,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220640,NC_045512.2,28361,GGAGAACGCA,G,PASS,306,304,221,0.72,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220640,NC_045512.2,28881,GG,AA,PASS,6266,77,6185,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220640,NC_045512.2,28883,G,C,PASS,6208,1,6194,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220640,NC_045512.2,3037,C,T,PASS,10,0,10,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220640,NC_045512.2,3241,C,T,PASS,261,0,261,1.0,orf1ab,synonymous_variant,c.2976C>T,p.Asp992Asp,p.D992D,ivar,Unassigned +220640,NC_045512.2,5924,G,A,PASS,11,0,11,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220640,NC_045512.2,76,T,A,ft,15,9,6,0.4,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220640,NC_045512.2,78,T,G,ft,15,9,6,0.4,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220640,NC_045512.2,8393,G,A,PASS,1676,2,1671,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220642,NC_045512.2,11072,TTC,T,ft,16,14,4,0.25,orf1ab,frameshift_variant,c.10809_10810delCT,p.Leu3606fs,p.L3606fs,ivar,B.1.617.2 +220642,NC_045512.2,11201,A,G,PASS,11,0,11,1.0,orf1ab,missense_variant,c.10936A>G,p.Thr3646Ala,p.T3646A,ivar,B.1.617.2 +220642,NC_045512.2,11332,A,G,PASS,27,0,26,0.96,orf1ab,synonymous_variant,c.11067A>G,p.Val3689Val,p.V3689V,ivar,B.1.617.2 +220642,NC_045512.2,14646,T,A,ft,23,17,6,0.26,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,B.1.617.2 +220642,NC_045512.2,15952,C,A,PASS,22,0,22,1.0,orf1ab,synonymous_variant,c.15687C>A,p.Ser5229Ser,p.S5229S,ivar,B.1.617.2 +220642,NC_045512.2,16466,C,T,PASS,41,0,41,1.0,orf1ab,missense_variant,c.16201C>T,p.His5401Tyr,p.H5401Y,ivar,B.1.617.2 +220642,NC_045512.2,18744,C,T,PASS,99,1,98,0.99,orf1ab,missense_variant,c.18479C>T,p.Thr6160Met,p.T6160M,ivar,B.1.617.2 +220642,NC_045512.2,19220,C,T,PASS,111,0,110,0.99,orf1ab,synonymous_variant,c.18955C>T,p.Leu6319Leu,p.L6319L,ivar,B.1.617.2 +220642,NC_045512.2,19590,T,C,ft,11,8,3,0.27,orf1ab,missense_variant,c.19325T>C,p.Ile6442Thr,p.I6442T,ivar,B.1.617.2 +220642,NC_045512.2,210,G,T,PASS,18,0,18,1.0,orf1ab,upstream_gene_variant,c.-56G>T,.,.,ivar,B.1.617.2 +220642,NC_045512.2,21618,C,G,PASS,12,0,12,1.0,S,missense_variant,c.56C>G,p.Thr19Arg,p.T19R,ivar,B.1.617.2 +220642,NC_045512.2,21682,C,T,PASS,23,0,23,1.0,S,synonymous_variant,c.120C>T,p.Asp40Asp,p.D40D,ivar,B.1.617.2 +220642,NC_045512.2,23403,A,G,PASS,557,0,557,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.617.2 +220642,NC_045512.2,23604,C,G,PASS,226,0,224,0.99,S,missense_variant,c.2042C>G,p.Pro681Arg,p.P681R,ivar,B.1.617.2 +220642,NC_045512.2,24410,G,A,PASS,21,0,21,1.0,S,missense_variant,c.2848G>A,p.Asp950Asn,p.D950N,ivar,B.1.617.2 +220642,NC_045512.2,26767,T,C,PASS,183,0,183,1.0,M,missense_variant,c.245T>C,p.Ile82Thr,p.I82T,ivar,B.1.617.2 +220642,NC_045512.2,27752,C,T,PASS,10,0,10,1.0,ORF7a,missense_variant,c.359C>T,p.Thr120Ile,p.T120I,ivar,B.1.617.2 +220642,NC_045512.2,27874,C,T,PASS,14,0,14,1.0,ORF7b,missense_variant,c.119C>T,p.Thr40Ile,p.T40I,ivar,B.1.617.2 +220642,NC_045512.2,28179,G,A,PASS,111,79,32,0.29,ORF8,missense_variant,c.286G>A,p.Gly96Ser,p.G96S,ivar,B.1.617.2 +220642,NC_045512.2,28247,AGATTTC,A,PASS,169,163,155,0.92,ORF8,conservative_inframe_deletion,c.355_360delGATTTC,p.Asp119_Phe120del,p.D119_F120del,ivar,B.1.617.2 +220642,NC_045512.2,28253,C,A,PASS,10,0,10,1.0,ORF8,missense_variant,c.360C>A,p.Phe120Leu,p.F120L,ivar,B.1.617.2 +220642,NC_045512.2,28270,TA,T,PASS,245,245,234,0.96,N,upstream_gene_variant,c.-3delA,.,.,ivar,B.1.617.2 +220642,NC_045512.2,28299,A,T,PASS,251,0,250,1.0,N,missense_variant,c.26A>T,p.Gln9Leu,p.Q9L,ivar,B.1.617.2 +220642,NC_045512.2,28326,G,T,PASS,239,1,236,0.99,N,missense_variant,c.53G>T,p.Gly18Val,p.G18V,ivar,B.1.617.2 +220642,NC_045512.2,28461,A,G,PASS,100,0,100,1.0,N,missense_variant,c.188A>G,p.Asp63Gly,p.D63G,ivar,B.1.617.2 +220642,NC_045512.2,28486,C,A,PASS,108,0,108,1.0,N,synonymous_variant,c.213C>A,p.Gly71Gly,p.G71G,ivar,B.1.617.2 +220642,NC_045512.2,28881,G,T,PASS,10522,44,10412,0.99,N,missense_variant,c.608G>T,p.Arg203Met,p.R203M,ivar,B.1.617.2 +220642,NC_045512.2,28916,G,T,PASS,434,0,429,0.99,N,missense_variant,c.643G>T,p.Gly215Cys,p.G215C,ivar,B.1.617.2 +220642,NC_045512.2,29260,G,T,PASS,1390,0,1387,1.0,N,synonymous_variant,c.987G>T,p.Thr329Thr,p.T329T,ivar,B.1.617.2 +220642,NC_045512.2,29402,G,T,PASS,2068,0,2058,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,B.1.617.2 +220642,NC_045512.2,3037,C,T,PASS,21,0,21,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,B.1.617.2 +220642,NC_045512.2,7945,C,T,PASS,279,4,275,0.99,orf1ab,synonymous_variant,c.7680C>T,p.Tyr2560Tyr,p.Y2560Y,ivar,B.1.617.2 +220644,NC_045512.2,11282,AGTTTGTCTG,A,PASS,32,32,29,0.91,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220644,NC_045512.2,11537,A,G,PASS,32,0,32,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220644,NC_045512.2,13195,T,C,PASS,1360,2,1358,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220644,NC_045512.2,14408,C,T,PASS,23,0,23,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220644,NC_045512.2,21762,C,T,PASS,35,0,35,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220644,NC_045512.2,21764,ATACATG,A,PASS,35,35,29,0.83,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220644,NC_045512.2,21846,C,T,PASS,37,4,33,0.89,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220644,NC_045512.2,23403,A,G,PASS,708,0,707,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220644,NC_045512.2,23525,C,T,PASS,716,3,713,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220644,NC_045512.2,23599,T,G,PASS,356,0,356,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220644,NC_045512.2,23604,C,A,PASS,349,0,347,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220644,NC_045512.2,23948,G,T,PASS,71,0,71,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220644,NC_045512.2,24130,C,A,PASS,90,0,90,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220644,NC_045512.2,24263,CA,C,ft,16,16,6,0.38,S,frameshift_variant,c.2704delA,p.Met902fs,p.M902fs,ivar,Unassigned +220644,NC_045512.2,24424,A,T,PASS,16,0,16,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220644,NC_045512.2,24469,T,A,PASS,168,0,168,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220644,NC_045512.2,24503,C,T,PASS,200,4,196,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220644,NC_045512.2,25584,C,T,PASS,24,0,24,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220644,NC_045512.2,26270,C,T,PASS,378,0,378,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220644,NC_045512.2,26530,A,G,PASS,116,2,114,0.98,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220644,NC_045512.2,26577,C,G,PASS,114,0,114,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220644,NC_045512.2,26709,G,A,PASS,135,0,135,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220644,NC_045512.2,27259,A,C,PASS,111,0,111,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220644,NC_045512.2,2754,T,C,PASS,101,13,88,0.87,orf1ab,missense_variant,c.2489T>C,p.Val830Ala,p.V830A,ivar,Unassigned +220644,NC_045512.2,27621,G,C,PASS,11,0,11,1.0,ORF7a,missense_variant,c.228G>C,p.Gln76His,p.Q76H,ivar,Unassigned +220644,NC_045512.2,27628,GC,G,ft,13,13,4,0.31,ORF7a,frameshift_variant,c.237delC,p.Arg80fs,p.R80fs,ivar,Unassigned +220644,NC_045512.2,27807,C,T,PASS,28,0,28,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220644,NC_045512.2,28271,A,T,PASS,550,2,546,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220644,NC_045512.2,28311,C,T,PASS,561,3,558,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220644,NC_045512.2,2832,A,G,PASS,97,0,97,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220644,NC_045512.2,28361,GGAGAACGCA,G,PASS,409,407,262,0.64,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220644,NC_045512.2,28881,GG,AA,PASS,11494,98,11384,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220644,NC_045512.2,28883,G,C,PASS,11443,5,11421,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220644,NC_045512.2,4097,T,TC,PASS,24,24,14,0.58,orf1ab,frameshift_variant,c.3832_3833insC,p.Phe1278fs,p.F1278fs,ivar,Unassigned +220644,NC_045512.2,4101,T,C,PASS,27,10,17,0.63,orf1ab,missense_variant,c.3836T>C,p.Leu1279Ser,p.L1279S,ivar,Unassigned +220644,NC_045512.2,4699,T,C,ft,10,7,3,0.3,orf1ab,synonymous_variant,c.4434T>C,p.Ser1478Ser,p.S1478S,ivar,Unassigned +220644,NC_045512.2,5672,C,T,PASS,13,0,13,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220644,NC_045512.2,5924,G,A,PASS,11,0,11,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220644,NC_045512.2,76,T,A,ft,10,6,4,0.4,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220644,NC_045512.2,78,T,G,ft,10,6,4,0.4,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220644,NC_045512.2,8393,G,A,PASS,1470,0,1470,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220646,NC_045512.2,10029,C,T,PASS,18,0,18,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,Unassigned +220646,NC_045512.2,10449,C,A,PASS,27,0,27,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220646,NC_045512.2,11282,AGTTTGTCTG,A,PASS,84,84,74,0.88,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220646,NC_045512.2,11537,A,G,PASS,69,0,69,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220646,NC_045512.2,13195,T,C,PASS,3077,6,3071,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220646,NC_045512.2,14408,C,T,PASS,48,0,48,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220646,NC_045512.2,16064,A,G,PASS,37,0,37,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220646,NC_045512.2,16950,T,A,PASS,136,98,38,0.28,orf1ab,missense_variant,c.16685T>A,p.Leu5562Gln,p.L5562Q,ivar,Unassigned +220646,NC_045512.2,18163,A,G,PASS,17,0,17,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,Unassigned +220646,NC_045512.2,21762,C,T,PASS,45,0,45,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220646,NC_045512.2,21764,ATACATG,A,PASS,45,45,42,0.93,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220646,NC_045512.2,21846,C,T,PASS,46,0,46,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220646,NC_045512.2,22578,G,A,PASS,10,0,10,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,Unassigned +220646,NC_045512.2,23403,A,G,PASS,773,0,773,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220646,NC_045512.2,23525,C,T,PASS,776,2,774,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220646,NC_045512.2,23599,T,G,PASS,337,0,337,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220646,NC_045512.2,23604,C,A,PASS,326,0,324,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220646,NC_045512.2,23854,C,A,PASS,18,0,17,0.94,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220646,NC_045512.2,23948,G,T,PASS,99,0,99,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220646,NC_045512.2,24130,C,A,PASS,158,0,156,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220646,NC_045512.2,24424,A,T,PASS,114,0,114,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220646,NC_045512.2,24469,T,A,PASS,545,6,539,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220646,NC_045512.2,24503,C,T,PASS,626,7,619,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220646,NC_045512.2,25000,C,T,PASS,31,0,31,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220646,NC_045512.2,25584,C,T,PASS,51,0,51,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220646,NC_045512.2,26270,C,T,PASS,516,2,514,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220646,NC_045512.2,26530,A,G,PASS,515,0,515,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220646,NC_045512.2,26577,C,G,PASS,562,0,562,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220646,NC_045512.2,26709,G,A,PASS,563,2,559,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220646,NC_045512.2,27259,A,C,PASS,166,0,166,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220646,NC_045512.2,27807,C,T,PASS,44,0,44,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220646,NC_045512.2,28271,A,T,PASS,690,0,690,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220646,NC_045512.2,28311,C,T,PASS,717,16,699,0.97,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220646,NC_045512.2,2832,A,G,PASS,37,0,37,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220646,NC_045512.2,28361,GGAGAACGCA,G,PASS,572,566,417,0.73,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220646,NC_045512.2,28881,GG,AA,PASS,8092,117,7963,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220646,NC_045512.2,28883,G,C,PASS,8026,5,8016,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220646,NC_045512.2,3037,C,T,PASS,15,0,15,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220646,NC_045512.2,8393,G,A,PASS,1947,10,1934,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220647,NC_045512.2,10029,C,T,PASS,27,0,27,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1 +220647,NC_045512.2,10449,C,A,PASS,65,0,65,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1 +220647,NC_045512.2,10647,C,T,PASS,55,12,43,0.78,orf1ab,missense_variant,c.10382C>T,p.Thr3461Ile,p.T3461I,ivar,BA.1 +220647,NC_045512.2,11005,C,T,PASS,16,4,12,0.75,orf1ab,synonymous_variant,c.10740C>T,p.His3580His,p.H3580H,ivar,BA.1 +220647,NC_045512.2,11282,AGTTTGTCTG,A,PASS,61,61,57,0.93,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1 +220647,NC_045512.2,11537,A,G,PASS,177,0,177,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1 +220647,NC_045512.2,13195,T,C,PASS,6907,12,6895,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1 +220647,NC_045512.2,14408,C,T,PASS,123,0,123,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1 +220647,NC_045512.2,15240,C,T,PASS,10,0,10,1.0,orf1ab,missense_variant,c.14975C>T,p.Thr4992Ile,p.T4992I,ivar,BA.1 +220647,NC_045512.2,15359,G,A,PASS,10,4,6,0.6,orf1ab,missense_variant,c.15094G>A,p.Ala5032Thr,p.A5032T,ivar,BA.1 +220647,NC_045512.2,16064,A,G,PASS,224,42,182,0.81,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,BA.1 +220647,NC_045512.2,18163,A,G,PASS,20,0,20,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1 +220647,NC_045512.2,21762,C,T,PASS,165,2,161,0.98,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1 +220647,NC_045512.2,21764,ATACATG,A,PASS,167,164,153,0.92,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1 +220647,NC_045512.2,21846,C,T,PASS,158,0,158,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1 +220647,NC_045512.2,21,C,T,PASS,12,0,12,1.0,orf1ab,upstream_gene_variant,c.-245C>T,.,.,ivar,BA.1 +220647,NC_045512.2,22578,G,A,PASS,15,0,15,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1 +220647,NC_045512.2,22599,G,A,PASS,15,4,11,0.73,S,missense_variant,c.1037G>A,p.Arg346Lys,p.R346K,ivar,BA.1 +220647,NC_045512.2,22679,T,C,PASS,16,0,16,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1 +220647,NC_045512.2,22686,C,T,PASS,16,0,16,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1 +220647,NC_045512.2,23013,A,C,PASS,11,0,11,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1 +220647,NC_045512.2,23040,A,G,PASS,11,0,11,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1 +220647,NC_045512.2,23048,G,A,PASS,11,0,11,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1 +220647,NC_045512.2,23055,A,G,PASS,11,0,11,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1 +220647,NC_045512.2,23063,A,T,PASS,11,0,11,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1 +220647,NC_045512.2,23075,T,C,PASS,10,0,10,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1 +220647,NC_045512.2,23403,A,G,PASS,2817,2,2815,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1 +220647,NC_045512.2,23525,C,T,PASS,2713,5,2696,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1 +220647,NC_045512.2,23599,T,G,PASS,1006,0,1005,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1 +220647,NC_045512.2,23604,C,A,PASS,972,0,966,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1 +220647,NC_045512.2,23854,C,A,PASS,58,0,57,0.98,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1 +220647,NC_045512.2,23948,G,T,PASS,380,0,378,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1 +220647,NC_045512.2,24130,C,A,PASS,569,0,567,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1 +220647,NC_045512.2,24424,A,T,PASS,225,0,223,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1 +220647,NC_045512.2,24469,T,A,PASS,865,1,862,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1 +220647,NC_045512.2,24503,C,T,PASS,1063,11,1050,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1 +220647,NC_045512.2,25000,C,T,PASS,78,0,78,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1 +220647,NC_045512.2,25531,A,G,PASS,101,27,74,0.73,ORF3a,missense_variant,c.139A>G,p.Ile47Val,p.I47V,ivar,BA.1 +220647,NC_045512.2,25584,C,T,PASS,104,0,102,0.98,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1 +220647,NC_045512.2,26270,C,T,PASS,714,1,713,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1 +220647,NC_045512.2,26530,A,G,PASS,619,0,619,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1 +220647,NC_045512.2,26577,C,G,PASS,691,2,689,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1 +220647,NC_045512.2,26709,G,A,PASS,724,4,720,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1 +220647,NC_045512.2,27259,A,C,PASS,416,0,415,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1 +220647,NC_045512.2,27807,C,T,PASS,126,0,126,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1 +220647,NC_045512.2,28271,A,T,PASS,1379,0,1377,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1 +220647,NC_045512.2,28311,C,T,PASS,1323,4,1317,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1 +220647,NC_045512.2,2832,A,G,PASS,91,0,91,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1 +220647,NC_045512.2,28361,GGAGAACGCA,G,PASS,976,967,669,0.69,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1 +220647,NC_045512.2,28881,GG,AA,PASS,5179,67,5106,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1 +220647,NC_045512.2,28883,G,C,PASS,5137,2,5122,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1 +220647,NC_045512.2,3037,C,T,PASS,29,0,29,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1 +220647,NC_045512.2,5386,T,G,PASS,18,0,18,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1 +220647,NC_045512.2,8393,G,A,PASS,3724,9,3714,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1 +220648,NC_045512.2,11074,CT,C,ft,15,15,4,0.27,orf1ab,frameshift_variant,c.10817delT,p.Leu3606fs,p.L3606fs,ivar,Unassigned +220648,NC_045512.2,11282,AGTTTGTCTG,A,PASS,60,60,57,0.95,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220648,NC_045512.2,11537,A,G,PASS,20,0,20,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220648,NC_045512.2,13195,T,C,PASS,1619,0,1619,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220648,NC_045512.2,14408,C,T,PASS,14,0,14,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220648,NC_045512.2,14717,A,G,ft,13,9,4,0.31,orf1ab,missense_variant,c.14452A>G,p.Arg4818Gly,p.R4818G,ivar,Unassigned +220648,NC_045512.2,1513,C,T,PASS,51,34,17,0.33,orf1ab,synonymous_variant,c.1248C>T,p.Cys416Cys,p.C416C,ivar,Unassigned +220648,NC_045512.2,21762,C,T,PASS,13,0,13,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220648,NC_045512.2,21764,ATACATG,A,PASS,13,13,11,0.85,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220648,NC_045512.2,23403,A,G,PASS,339,0,339,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220648,NC_045512.2,23525,C,T,PASS,317,0,317,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220648,NC_045512.2,23599,T,G,PASS,160,0,160,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220648,NC_045512.2,23604,C,A,PASS,149,0,148,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220648,NC_045512.2,23948,G,T,PASS,20,0,20,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220648,NC_045512.2,24130,C,A,PASS,45,0,45,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220648,NC_045512.2,24424,A,T,PASS,18,0,18,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220648,NC_045512.2,24469,T,A,PASS,106,0,106,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220648,NC_045512.2,24503,C,T,PASS,131,1,130,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220648,NC_045512.2,25584,C,T,PASS,11,0,11,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220648,NC_045512.2,26270,C,T,PASS,24,2,22,0.92,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220648,NC_045512.2,26530,A,G,PASS,80,0,80,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220648,NC_045512.2,26577,C,G,PASS,68,0,68,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220648,NC_045512.2,26709,G,A,PASS,56,0,56,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220648,NC_045512.2,27259,A,C,PASS,22,0,22,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220648,NC_045512.2,28271,A,T,PASS,75,2,73,0.97,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220648,NC_045512.2,28311,C,T,PASS,78,2,76,0.97,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220648,NC_045512.2,28361,GGAGAACGCA,G,PASS,58,57,37,0.64,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220648,NC_045512.2,28881,GG,AA,PASS,6310,41,6263,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220648,NC_045512.2,28883,G,C,PASS,6308,2,6297,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220648,NC_045512.2,8393,G,A,PASS,930,4,924,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220649,NC_045512.2,11282,AGTTTGTCTG,A,PASS,22,22,21,0.95,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1 +220649,NC_045512.2,11537,A,G,PASS,52,0,52,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1 +220649,NC_045512.2,13195,T,C,PASS,1944,4,1940,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1 +220649,NC_045512.2,14408,C,T,PASS,27,0,27,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1 +220649,NC_045512.2,14646,T,A,PASS,35,21,14,0.4,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,BA.1 +220649,NC_045512.2,19275,T,C,PASS,37,5,32,0.86,orf1ab,missense_variant,c.19010T>C,p.Leu6337Pro,p.L6337P,ivar,BA.1 +220649,NC_045512.2,21762,C,T,PASS,68,0,68,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1 +220649,NC_045512.2,21764,ATACATG,A,PASS,68,68,60,0.88,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1 +220649,NC_045512.2,21846,C,T,PASS,79,0,79,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1 +220649,NC_045512.2,22673,TC,CT,PASS,12,0,12,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1 +220649,NC_045512.2,22679,T,C,PASS,12,0,12,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1 +220649,NC_045512.2,22686,C,T,PASS,11,0,11,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1 +220649,NC_045512.2,23403,A,G,PASS,886,0,886,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1 +220649,NC_045512.2,23525,C,T,PASS,950,4,946,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1 +220649,NC_045512.2,23599,T,G,PASS,385,0,385,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1 +220649,NC_045512.2,23604,C,A,PASS,374,0,374,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1 +220649,NC_045512.2,23854,C,A,PASS,14,0,14,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1 +220649,NC_045512.2,23948,G,T,PASS,159,0,159,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1 +220649,NC_045512.2,24130,C,A,PASS,219,0,217,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1 +220649,NC_045512.2,24424,A,T,PASS,16,0,16,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1 +220649,NC_045512.2,24469,T,A,PASS,253,0,250,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1 +220649,NC_045512.2,24503,C,T,PASS,310,6,304,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1 +220649,NC_045512.2,25000,C,T,PASS,17,0,17,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1 +220649,NC_045512.2,25482,C,T,PASS,30,0,30,1.0,ORF3a,synonymous_variant,c.90C>T,p.Arg30Arg,p.R30R,ivar,BA.1 +220649,NC_045512.2,25584,C,T,PASS,20,0,20,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1 +220649,NC_045512.2,26270,C,T,PASS,293,0,293,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1 +220649,NC_045512.2,26530,A,G,PASS,178,0,178,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1 +220649,NC_045512.2,26577,C,G,PASS,169,0,169,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1 +220649,NC_045512.2,26709,G,A,PASS,149,0,149,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1 +220649,NC_045512.2,27259,A,C,PASS,88,0,88,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1 +220649,NC_045512.2,2754,T,C,PASS,25,13,12,0.48,orf1ab,missense_variant,c.2489T>C,p.Val830Ala,p.V830A,ivar,BA.1 +220649,NC_045512.2,27670,G,T,PASS,18,0,18,1.0,ORF7a,missense_variant,c.277G>T,p.Val93Phe,p.V93F,ivar,BA.1 +220649,NC_045512.2,27807,C,T,PASS,30,0,30,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1 +220649,NC_045512.2,2815,TA,T,PASS,34,34,19,0.56,orf1ab,frameshift_variant,c.2553delA,p.Val852fs,p.V852fs,ivar,BA.1 +220649,NC_045512.2,28271,A,T,PASS,719,1,718,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1 +220649,NC_045512.2,28311,C,T,PASS,808,2,802,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1 +220649,NC_045512.2,2832,A,G,PASS,31,0,31,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1 +220649,NC_045512.2,28361,GGAGAACGCA,G,PASS,558,557,301,0.54,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1 +220649,NC_045512.2,28363,A,T,PASS,23,13,6,0.26,N,synonymous_variant,c.90A>T,p.Gly30Gly,p.G30G,ivar,BA.1 +220649,NC_045512.2,28881,GG,AA,PASS,10996,110,10874,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1 +220649,NC_045512.2,28883,G,C,PASS,10931,9,10905,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1 +220649,NC_045512.2,5672,C,T,PASS,19,0,19,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1 +220649,NC_045512.2,76,T,A,ft,14,8,6,0.43,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1 +220649,NC_045512.2,78,T,G,PASS,12,6,6,0.5,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1 +220649,NC_045512.2,8393,G,A,PASS,2396,9,2383,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1 +220650,NC_045512.2,10449,C,A,PASS,27,0,27,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220650,NC_045512.2,10647,C,T,PASS,14,0,14,1.0,orf1ab,missense_variant,c.10382C>T,p.Thr3461Ile,p.T3461I,ivar,Unassigned +220650,NC_045512.2,11282,AGTTTGTCTG,A,PASS,20,20,18,0.9,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220650,NC_045512.2,11537,A,G,PASS,65,0,65,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220650,NC_045512.2,13195,T,C,PASS,3292,5,3287,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220650,NC_045512.2,14408,C,T,PASS,82,0,82,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220650,NC_045512.2,16064,A,G,PASS,70,0,70,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220650,NC_045512.2,21762,C,T,PASS,63,0,63,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220650,NC_045512.2,21764,ATACATG,A,PASS,63,63,53,0.84,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220650,NC_045512.2,21846,C,T,PASS,94,1,93,0.99,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220650,NC_045512.2,23403,A,G,PASS,993,2,991,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220650,NC_045512.2,23525,C,T,PASS,908,0,908,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220650,NC_045512.2,23599,T,G,PASS,328,0,328,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220650,NC_045512.2,23604,C,A,PASS,312,0,311,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220650,NC_045512.2,23854,C,A,PASS,12,0,12,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220650,NC_045512.2,23948,G,T,PASS,190,0,190,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220650,NC_045512.2,24130,C,A,PASS,240,0,240,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220650,NC_045512.2,24424,A,T,PASS,42,0,42,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220650,NC_045512.2,24469,T,A,PASS,455,0,454,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220650,NC_045512.2,24503,C,T,PASS,551,10,540,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220650,NC_045512.2,25000,C,T,PASS,17,0,17,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220650,NC_045512.2,25531,A,G,PASS,28,0,28,1.0,ORF3a,missense_variant,c.139A>G,p.Ile47Val,p.I47V,ivar,Unassigned +220650,NC_045512.2,25584,C,T,PASS,26,0,26,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220650,NC_045512.2,26270,C,T,PASS,249,0,249,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220650,NC_045512.2,26530,A,G,PASS,144,0,144,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220650,NC_045512.2,26577,C,G,PASS,147,0,147,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220650,NC_045512.2,26709,G,A,PASS,176,1,175,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220650,NC_045512.2,27259,A,C,PASS,126,0,126,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220650,NC_045512.2,27807,C,T,PASS,26,0,26,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220650,NC_045512.2,2785,T,C,PASS,79,51,28,0.35,orf1ab,synonymous_variant,c.2520T>C,p.Asn840Asn,p.N840N,ivar,Unassigned +220650,NC_045512.2,28271,A,T,PASS,795,2,791,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220650,NC_045512.2,28311,C,T,PASS,801,2,799,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220650,NC_045512.2,2832,A,G,PASS,88,0,88,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220650,NC_045512.2,28361,GGAGAACGCA,G,PASS,589,587,367,0.62,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220650,NC_045512.2,28881,GG,AA,PASS,6879,67,6807,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220650,NC_045512.2,28883,G,C,PASS,6840,2,6824,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220650,NC_045512.2,76,T,A,PASS,21,13,8,0.38,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220650,NC_045512.2,78,T,G,PASS,21,13,8,0.38,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220650,NC_045512.2,8393,G,A,PASS,2169,2,2167,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220651,NC_045512.2,10323,A,G,PASS,11,0,11,1.0,orf1ab,missense_variant,c.10058A>G,p.Lys3353Arg,p.K3353R,ivar,Unassigned +220651,NC_045512.2,10333,A,G,ft,11,8,3,0.27,orf1ab,synonymous_variant,c.10068A>G,p.Thr3356Thr,p.T3356T,ivar,Unassigned +220651,NC_045512.2,10449,C,A,PASS,22,0,22,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220651,NC_045512.2,11282,AGTTTGTCTG,A,PASS,34,33,26,0.76,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220651,NC_045512.2,11537,A,G,PASS,32,0,32,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220651,NC_045512.2,13195,T,C,PASS,1396,7,1389,0.99,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220651,NC_045512.2,14408,C,T,PASS,20,0,20,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220651,NC_045512.2,21740,T,G,PASS,27,15,12,0.44,S,missense_variant,c.178T>G,p.Ser60Ala,p.S60A,ivar,Unassigned +220651,NC_045512.2,21762,C,T,PASS,24,2,22,0.92,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220651,NC_045512.2,21764,ATACATG,A,PASS,24,24,24,1.0,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220651,NC_045512.2,21843,C,A,PASS,31,19,12,0.39,S,missense_variant,c.281C>A,p.Ser94Tyr,p.S94Y,ivar,Unassigned +220651,NC_045512.2,21846,C,T,PASS,31,0,31,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220651,NC_045512.2,23403,A,G,PASS,827,0,827,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220651,NC_045512.2,23525,C,T,PASS,880,1,878,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220651,NC_045512.2,23599,T,G,PASS,393,0,393,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220651,NC_045512.2,23604,C,A,PASS,380,1,378,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220651,NC_045512.2,23948,G,T,PASS,26,0,26,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220651,NC_045512.2,24130,C,A,PASS,44,0,44,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220651,NC_045512.2,24424,A,T,PASS,22,0,22,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220651,NC_045512.2,24469,T,A,PASS,263,0,262,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220651,NC_045512.2,24503,C,T,PASS,300,4,296,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220651,NC_045512.2,25584,C,T,PASS,17,0,17,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220651,NC_045512.2,2592,C,A,PASS,24,16,8,0.33,orf1ab,missense_variant,c.2327C>A,p.Ala776Asp,p.A776D,ivar,Unassigned +220651,NC_045512.2,26270,C,T,PASS,295,0,295,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220651,NC_045512.2,26530,A,G,PASS,223,0,223,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220651,NC_045512.2,26577,C,G,PASS,230,0,230,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220651,NC_045512.2,26709,G,A,PASS,234,0,234,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220651,NC_045512.2,27259,A,C,PASS,73,0,71,0.97,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220651,NC_045512.2,27807,C,T,PASS,24,0,24,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220651,NC_045512.2,28271,A,T,PASS,194,1,193,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220651,NC_045512.2,28311,C,T,PASS,223,2,221,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220651,NC_045512.2,2832,A,G,PASS,28,0,28,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220651,NC_045512.2,28361,GGAGAACGCA,G,PASS,186,186,128,0.69,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220651,NC_045512.2,28881,GG,AA,PASS,11290,87,11197,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220651,NC_045512.2,28883,G,C,PASS,11251,5,11237,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220651,NC_045512.2,4301,C,T,ft,12,8,4,0.33,orf1ab,missense_variant,c.4036C>T,p.Leu1346Phe,p.L1346F,ivar,Unassigned +220651,NC_045512.2,5672,C,T,PASS,16,0,16,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220651,NC_045512.2,7680,A,G,PASS,44,31,13,0.3,orf1ab,missense_variant,c.7415A>G,p.Asp2472Gly,p.D2472G,ivar,Unassigned +220651,NC_045512.2,76,T,A,ft,16,12,4,0.25,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220651,NC_045512.2,78,T,G,ft,16,12,4,0.25,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220651,NC_045512.2,8393,G,A,PASS,1490,7,1483,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220652,NC_045512.2,10135,T,C,PASS,11,0,11,1.0,orf1ab,synonymous_variant,c.9870T>C,p.Leu3290Leu,p.L3290L,ivar,Unassigned +220652,NC_045512.2,10449,C,A,PASS,21,0,21,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220652,NC_045512.2,11282,AGTTTGTCTG,A,PASS,58,58,53,0.91,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220652,NC_045512.2,113,A,G,PASS,33,20,13,0.39,orf1ab,upstream_gene_variant,c.-153A>G,.,.,ivar,Unassigned +220652,NC_045512.2,11537,A,G,PASS,41,0,41,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220652,NC_045512.2,116,G,A,PASS,36,23,13,0.36,orf1ab,upstream_gene_variant,c.-150G>A,.,.,ivar,Unassigned +220652,NC_045512.2,13195,T,C,PASS,2217,3,2214,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220652,NC_045512.2,14408,C,T,PASS,19,0,19,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220652,NC_045512.2,14646,T,A,PASS,49,35,14,0.29,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,Unassigned +220652,NC_045512.2,21762,C,T,PASS,48,0,48,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220652,NC_045512.2,21764,ATACATG,A,PASS,49,48,45,0.92,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220652,NC_045512.2,21846,C,T,PASS,62,0,62,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220652,NC_045512.2,23403,A,G,PASS,858,0,858,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220652,NC_045512.2,23525,C,T,PASS,930,0,930,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220652,NC_045512.2,23599,T,G,PASS,413,0,413,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220652,NC_045512.2,23604,C,A,PASS,403,1,400,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220652,NC_045512.2,23854,C,A,PASS,14,0,14,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220652,NC_045512.2,23948,G,T,PASS,181,2,179,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220652,NC_045512.2,24130,C,A,PASS,220,0,219,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220652,NC_045512.2,24424,A,T,PASS,78,0,77,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220652,NC_045512.2,24469,T,A,PASS,425,0,425,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220652,NC_045512.2,24503,C,T,PASS,509,17,492,0.97,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220652,NC_045512.2,24803,A,G,PASS,190,0,190,1.0,S,missense_variant,c.3241A>G,p.Ile1081Val,p.I1081V,ivar,Unassigned +220652,NC_045512.2,25000,C,T,PASS,14,0,14,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220652,NC_045512.2,25584,C,T,PASS,19,0,19,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220652,NC_045512.2,25708,C,T,PASS,19,2,17,0.89,ORF3a,missense_variant,c.316C>T,p.Leu106Phe,p.L106F,ivar,Unassigned +220652,NC_045512.2,26270,C,T,PASS,493,0,493,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220652,NC_045512.2,26530,A,G,PASS,207,0,207,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220652,NC_045512.2,26577,C,G,PASS,193,0,193,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220652,NC_045512.2,26709,G,A,PASS,201,1,199,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220652,NC_045512.2,27259,A,C,PASS,95,0,95,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220652,NC_045512.2,2755,G,A,PASS,92,69,23,0.25,orf1ab,synonymous_variant,c.2490G>A,p.Val830Val,p.V830V,ivar,Unassigned +220652,NC_045512.2,27807,C,T,PASS,31,0,31,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220652,NC_045512.2,28271,A,T,PASS,646,0,644,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220652,NC_045512.2,28311,C,T,PASS,720,2,718,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220652,NC_045512.2,2832,A,G,PASS,95,0,95,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220652,NC_045512.2,28361,GGAGAACGCA,G,PASS,559,554,308,0.55,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220652,NC_045512.2,28881,GG,AA,PASS,9059,70,8983,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220652,NC_045512.2,28883,G,C,PASS,9032,4,9012,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220652,NC_045512.2,29301,A,G,PASS,3790,4,3786,1.0,N,missense_variant,c.1028A>G,p.Asp343Gly,p.D343G,ivar,Unassigned +220652,NC_045512.2,3037,C,T,PASS,11,0,11,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220652,NC_045512.2,7488,C,T,PASS,228,0,228,1.0,orf1ab,missense_variant,c.7223C>T,p.Thr2408Ile,p.T2408I,ivar,Unassigned +220652,NC_045512.2,76,T,A,ft,16,12,4,0.25,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220652,NC_045512.2,8393,G,A,PASS,2474,4,2469,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220653,NC_045512.2,11282,AGTTTGTCTG,A,ft,10,10,9,0.9,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220653,NC_045512.2,11537,A,G,PASS,10,0,10,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220653,NC_045512.2,13195,T,C,PASS,387,0,387,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220653,NC_045512.2,14560,T,A,ft,10,7,3,0.3,orf1ab,stop_gained,c.14295T>A,p.Cys4765*,p.C4765*,ivar,Unassigned +220653,NC_045512.2,23403,A,G,PASS,311,0,311,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220653,NC_045512.2,23525,C,T,PASS,312,2,310,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220653,NC_045512.2,23599,T,G,PASS,157,0,157,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220653,NC_045512.2,23604,C,A,PASS,154,0,154,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220653,NC_045512.2,23948,G,T,PASS,31,0,31,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220653,NC_045512.2,24130,C,A,PASS,25,0,25,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220653,NC_045512.2,24469,T,A,PASS,63,0,61,0.97,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220653,NC_045512.2,24503,C,T,PASS,71,0,71,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220653,NC_045512.2,26270,C,T,PASS,393,0,393,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220653,NC_045512.2,2633,T,A,PASS,11,5,6,0.55,orf1ab,missense_variant,c.2368T>A,p.Leu790Met,p.L790M,ivar,Unassigned +220653,NC_045512.2,26530,A,G,PASS,113,0,113,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220653,NC_045512.2,26577,C,G,PASS,115,0,113,0.98,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220653,NC_045512.2,26709,G,A,PASS,95,0,95,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220653,NC_045512.2,2702,T,C,ft,11,8,3,0.27,orf1ab,missense_variant,c.2437T>C,p.Phe813Leu,p.F813L,ivar,Unassigned +220653,NC_045512.2,27259,A,C,PASS,30,0,30,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220653,NC_045512.2,27807,C,T,PASS,17,0,17,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220653,NC_045512.2,28271,A,T,PASS,184,0,184,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220653,NC_045512.2,28311,C,T,PASS,212,1,211,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220653,NC_045512.2,2832,A,G,PASS,14,0,14,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220653,NC_045512.2,28361,GGAGAACGCA,G,PASS,166,166,120,0.72,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220653,NC_045512.2,28881,GG,AA,PASS,6955,64,6886,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220653,NC_045512.2,28883,G,C,PASS,6937,2,6917,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220653,NC_045512.2,5672,C,T,PASS,14,0,14,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220653,NC_045512.2,685,AAAGTCATTT,A,PASS,4513,4475,2142,0.47,orf1ab,conservative_inframe_deletion,c.421_429delAAGTCATTT,p.Lys141_Phe143del,p.K141_F143del,ivar,Unassigned +220653,NC_045512.2,694,T,A,PASS,14,9,5,0.36,orf1ab,missense_variant,c.429T>A,p.Phe143Leu,p.F143L,ivar,Unassigned +220653,NC_045512.2,76,T,A,PASS,10,4,6,0.6,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220653,NC_045512.2,8393,G,A,PASS,618,0,618,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220654,NC_045512.2,10029,C,T,PASS,14,0,14,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,Unassigned +220654,NC_045512.2,10449,C,A,PASS,29,0,29,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220654,NC_045512.2,11282,AGTTTGTCTG,A,PASS,106,106,97,0.92,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220654,NC_045512.2,11537,A,G,PASS,65,0,65,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220654,NC_045512.2,13195,T,C,PASS,2838,1,2837,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220654,NC_045512.2,14408,C,T,PASS,21,0,21,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220654,NC_045512.2,18163,A,G,PASS,15,0,15,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,Unassigned +220654,NC_045512.2,21762,C,T,PASS,35,0,35,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220654,NC_045512.2,21764,ATACATG,A,PASS,37,35,33,0.89,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220654,NC_045512.2,21846,C,T,PASS,62,0,62,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220654,NC_045512.2,22578,G,A,PASS,10,0,10,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,Unassigned +220654,NC_045512.2,23403,A,G,PASS,780,0,780,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220654,NC_045512.2,23525,C,T,PASS,754,0,754,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220654,NC_045512.2,23599,T,G,PASS,331,0,331,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220654,NC_045512.2,23604,C,A,PASS,321,0,317,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220654,NC_045512.2,23854,C,A,PASS,26,0,26,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220654,NC_045512.2,23948,G,T,PASS,258,2,255,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220654,NC_045512.2,24130,C,A,PASS,310,0,308,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220654,NC_045512.2,24424,A,T,PASS,93,0,93,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220654,NC_045512.2,24469,T,A,PASS,384,0,384,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220654,NC_045512.2,24503,C,T,PASS,439,6,433,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220654,NC_045512.2,25000,C,T,PASS,26,0,26,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220654,NC_045512.2,25584,C,T,PASS,32,0,32,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220654,NC_045512.2,26270,C,T,PASS,591,3,588,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220654,NC_045512.2,26530,A,G,PASS,261,0,261,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220654,NC_045512.2,26577,C,G,PASS,241,0,241,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220654,NC_045512.2,26709,G,A,PASS,269,2,267,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220654,NC_045512.2,27259,A,C,PASS,227,0,225,0.99,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220654,NC_045512.2,27807,C,T,PASS,44,0,44,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220654,NC_045512.2,28271,A,T,PASS,695,0,693,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220654,NC_045512.2,28311,C,T,PASS,714,0,712,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220654,NC_045512.2,2832,A,G,PASS,19,0,19,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220654,NC_045512.2,28361,GGAGAACGCA,G,PASS,538,535,345,0.64,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220654,NC_045512.2,28881,GG,AA,PASS,5172,63,5108,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220654,NC_045512.2,28883,G,C,PASS,5131,0,5124,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220654,NC_045512.2,3037,C,T,PASS,17,0,17,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220654,NC_045512.2,5672,C,T,PASS,73,0,73,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220654,NC_045512.2,5924,G,A,PASS,24,0,24,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220654,NC_045512.2,76,T,A,PASS,21,13,8,0.38,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220654,NC_045512.2,78,T,G,PASS,21,13,8,0.38,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220654,NC_045512.2,8393,G,A,PASS,1798,4,1792,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220655,NC_045512.2,10029,C,T,PASS,13,0,13,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220655,NC_045512.2,10449,C,A,PASS,66,0,66,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220655,NC_045512.2,11282,AGTTTGTCTG,A,PASS,124,124,112,0.9,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220655,NC_045512.2,11537,A,G,PASS,249,2,247,0.99,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220655,NC_045512.2,13195,T,C,PASS,6068,4,6064,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220655,NC_045512.2,14408,C,T,PASS,167,2,164,0.98,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220655,NC_045512.2,17797,G,T,PASS,11,5,6,0.55,orf1ab,synonymous_variant,c.17532G>T,p.Leu5844Leu,p.L5844L,ivar,BA.1.17 +220655,NC_045512.2,18163,A,G,PASS,13,0,13,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220655,NC_045512.2,21762,C,T,PASS,224,0,224,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220655,NC_045512.2,21764,ATACATG,A,PASS,226,224,213,0.94,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220655,NC_045512.2,21846,C,T,PASS,271,0,271,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220655,NC_045512.2,21,C,T,PASS,14,0,14,1.0,orf1ab,upstream_gene_variant,c.-245C>T,.,.,ivar,BA.1.17 +220655,NC_045512.2,2270,A,G,PASS,22,0,22,1.0,orf1ab,missense_variant,c.2005A>G,p.Lys669Glu,p.K669E,ivar,BA.1.17 +220655,NC_045512.2,23013,A,C,PASS,13,0,13,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.17 +220655,NC_045512.2,23040,A,G,PASS,11,0,11,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.17 +220655,NC_045512.2,23048,G,A,PASS,11,0,11,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.17 +220655,NC_045512.2,23055,A,G,PASS,12,0,12,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.17 +220655,NC_045512.2,23063,A,T,PASS,11,2,9,0.82,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.17 +220655,NC_045512.2,23075,T,C,PASS,18,0,18,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.17 +220655,NC_045512.2,23202,C,A,PASS,23,0,23,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220655,NC_045512.2,23403,A,G,PASS,1843,2,1841,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220655,NC_045512.2,23525,C,T,PASS,1813,2,1808,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220655,NC_045512.2,23599,T,G,PASS,652,0,652,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220655,NC_045512.2,23604,C,A,PASS,630,0,620,0.98,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220655,NC_045512.2,23854,C,A,PASS,31,0,31,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220655,NC_045512.2,23948,G,T,PASS,445,0,445,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220655,NC_045512.2,24130,C,A,PASS,779,0,777,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220655,NC_045512.2,24424,A,T,PASS,137,0,136,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220655,NC_045512.2,24469,T,A,PASS,827,0,825,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220655,NC_045512.2,24503,C,T,PASS,960,7,950,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220655,NC_045512.2,25000,C,T,PASS,48,0,48,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220655,NC_045512.2,25584,C,T,PASS,85,0,85,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220655,NC_045512.2,25855,G,A,PASS,101,0,101,1.0,ORF3a,missense_variant,c.463G>A,p.Asp155Asn,p.D155N,ivar,BA.1.17 +220655,NC_045512.2,26270,C,T,PASS,450,2,448,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220655,NC_045512.2,26530,A,G,PASS,478,1,477,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220655,NC_045512.2,26577,C,G,PASS,554,0,554,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220655,NC_045512.2,26709,G,A,PASS,578,4,571,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220655,NC_045512.2,27259,A,C,PASS,283,0,281,0.99,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220655,NC_045512.2,27807,C,T,PASS,164,1,163,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220655,NC_045512.2,28271,A,T,PASS,2207,4,2199,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220655,NC_045512.2,28311,C,T,PASS,2296,7,2282,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220655,NC_045512.2,2832,A,G,PASS,60,0,60,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220655,NC_045512.2,28361,GGAGAACGCA,G,PASS,1753,1743,1191,0.68,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220655,NC_045512.2,28881,GG,AA,PASS,5261,74,5183,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220655,NC_045512.2,28883,G,C,PASS,5202,6,5186,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220655,NC_045512.2,29772,T,C,PASS,24,0,24,1.0,S,downstream_gene_variant,c.*4388T>C,.,.,ivar,BA.1.17 +220655,NC_045512.2,3037,C,T,PASS,24,0,24,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220655,NC_045512.2,5672,C,T,PASS,76,1,75,0.99,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220655,NC_045512.2,5924,G,A,PASS,36,0,36,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220655,NC_045512.2,76,T,A,ft,24,18,6,0.25,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1.17 +220655,NC_045512.2,78,T,G,ft,24,18,6,0.25,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1.17 +220655,NC_045512.2,8393,G,A,PASS,2376,3,2367,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220655,NC_045512.2,8652,T,C,PASS,2140,8,2132,1.0,orf1ab,missense_variant,c.8387T>C,p.Met2796Thr,p.M2796T,ivar,BA.1.17 +220656,NC_045512.2,11537,A,G,PASS,16,0,16,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220656,NC_045512.2,13195,T,C,PASS,831,0,831,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220656,NC_045512.2,13975,G,A,ft,11,8,3,0.27,orf1ab,stop_retained_variant,c.13710G>A,p.Ter4570Ter,p.*4570*,ivar,Unassigned +220656,NC_045512.2,14408,C,T,PASS,19,0,19,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220656,NC_045512.2,16409,C,T,PASS,31,22,9,0.29,orf1ab,stop_gained,c.16144C>T,p.Gln5382*,p.Q5382*,ivar,Unassigned +220656,NC_045512.2,21762,C,T,PASS,19,0,19,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220656,NC_045512.2,21764,ATACATG,A,PASS,19,19,17,0.89,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220656,NC_045512.2,21846,C,T,PASS,27,0,27,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220656,NC_045512.2,23403,A,G,PASS,428,0,428,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220656,NC_045512.2,23525,C,T,PASS,502,4,498,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220656,NC_045512.2,23599,T,G,PASS,215,0,215,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220656,NC_045512.2,23604,C,A,PASS,206,0,204,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220656,NC_045512.2,23948,G,T,PASS,45,0,45,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220656,NC_045512.2,24130,C,A,PASS,50,0,50,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220656,NC_045512.2,24469,T,A,PASS,80,0,80,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220656,NC_045512.2,24503,C,T,PASS,87,1,86,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220656,NC_045512.2,26577,C,G,PASS,16,0,16,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220656,NC_045512.2,26598,T,C,ft,14,10,4,0.29,M,missense_variant,c.76T>C,p.Phe26Leu,p.F26L,ivar,Unassigned +220656,NC_045512.2,26709,G,A,PASS,15,0,15,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220656,NC_045512.2,26712,T,C,PASS,15,5,10,0.67,M,missense_variant,c.190T>C,p.Cys64Arg,p.C64R,ivar,Unassigned +220656,NC_045512.2,27259,A,C,PASS,13,0,13,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220656,NC_045512.2,28271,A,T,PASS,136,0,134,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220656,NC_045512.2,28311,C,T,PASS,133,0,132,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220656,NC_045512.2,28361,GGAGAACGCA,G,PASS,98,97,63,0.64,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220656,NC_045512.2,28877,AG,TC,PASS,7768,7,7718,0.99,N,synonymous_variant,c.604_605delAGinsTC,p.203,p.203,ivar,Unassigned +220656,NC_045512.2,28881,GG,AA,PASS,7783,17,7748,1.0,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220656,NC_045512.2,28883,G,C,PASS,7807,2,7798,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220656,NC_045512.2,4920,C,T,ft,12,9,3,0.25,orf1ab,missense_variant,c.4655C>T,p.Thr1552Ile,p.T1552I,ivar,Unassigned +220656,NC_045512.2,8393,G,A,PASS,610,3,607,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220657,NC_045512.2,10647,C,T,PASS,19,0,19,1.0,orf1ab,missense_variant,c.10382C>T,p.Thr3461Ile,p.T3461I,ivar,Unassigned +220657,NC_045512.2,11537,A,G,PASS,34,0,34,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220657,NC_045512.2,13195,T,C,PASS,1613,0,1613,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220657,NC_045512.2,14408,C,T,PASS,22,0,22,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220657,NC_045512.2,15966,T,C,PASS,20,12,8,0.4,orf1ab,missense_variant,c.15701T>C,p.Val5234Ala,p.V5234A,ivar,Unassigned +220657,NC_045512.2,16064,A,G,PASS,14,0,14,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220657,NC_045512.2,21762,C,T,PASS,37,0,37,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220657,NC_045512.2,21764,ATACATG,A,PASS,38,37,30,0.79,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220657,NC_045512.2,21846,C,T,PASS,36,0,36,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220657,NC_045512.2,23403,A,G,PASS,510,2,508,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220657,NC_045512.2,23525,C,T,PASS,541,0,541,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220657,NC_045512.2,23599,T,G,PASS,264,0,264,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220657,NC_045512.2,23604,C,A,PASS,253,0,249,0.98,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220657,NC_045512.2,23948,G,T,PASS,44,0,44,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220657,NC_045512.2,24130,C,A,PASS,53,0,53,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220657,NC_045512.2,24424,A,T,PASS,26,0,26,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220657,NC_045512.2,24469,T,A,PASS,149,0,146,0.98,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220657,NC_045512.2,24503,C,T,PASS,170,4,166,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220657,NC_045512.2,26270,C,T,PASS,139,0,139,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220657,NC_045512.2,26577,C,G,PASS,11,0,11,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220657,NC_045512.2,26709,G,A,PASS,10,0,10,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220657,NC_045512.2,27259,A,C,PASS,44,0,43,0.98,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220657,NC_045512.2,27807,C,T,PASS,10,0,10,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220657,NC_045512.2,28271,A,T,PASS,737,0,737,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220657,NC_045512.2,28311,C,T,PASS,713,2,711,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220657,NC_045512.2,28361,GGAGAACGCA,G,PASS,527,525,343,0.65,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220657,NC_045512.2,28425,C,T,PASS,95,70,25,0.26,N,missense_variant,c.152C>T,p.Ser51Phe,p.S51F,ivar,Unassigned +220657,NC_045512.2,28881,GG,AA,PASS,9546,60,9475,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220657,NC_045512.2,28883,G,C,PASS,9546,3,9522,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220657,NC_045512.2,8393,G,A,PASS,1051,5,1046,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220658,NC_045512.2,11282,AGTTTGTCTG,A,PASS,20,20,18,0.9,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220658,NC_045512.2,11454,C,T,PASS,29,0,27,0.93,orf1ab,missense_variant,c.11189C>T,p.Ala3730Val,p.A3730V,ivar,Unassigned +220658,NC_045512.2,11537,A,G,PASS,22,0,22,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220658,NC_045512.2,13195,T,C,PASS,1324,7,1317,0.99,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220658,NC_045512.2,20936,C,T,ft,15,11,4,0.27,orf1ab,missense_variant,c.20671C>T,p.Arg6891Cys,p.R6891C,ivar,Unassigned +220658,NC_045512.2,21266,A,G,ft,12,8,4,0.33,orf1ab,missense_variant,c.21001A>G,p.Lys7001Glu,p.K7001E,ivar,Unassigned +220658,NC_045512.2,21762,C,T,PASS,27,0,27,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220658,NC_045512.2,21764,ATACATG,A,PASS,27,27,24,0.89,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220658,NC_045512.2,21846,C,T,PASS,19,0,19,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220658,NC_045512.2,22679,T,C,PASS,12,0,12,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,Unassigned +220658,NC_045512.2,22686,C,T,PASS,11,0,11,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,Unassigned +220658,NC_045512.2,23403,A,G,PASS,786,0,786,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220658,NC_045512.2,23525,C,T,PASS,772,0,772,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220658,NC_045512.2,23599,T,G,PASS,327,0,327,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220658,NC_045512.2,23604,C,A,PASS,323,0,323,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220658,NC_045512.2,23854,C,A,PASS,11,0,11,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220658,NC_045512.2,23948,G,T,PASS,89,0,89,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220658,NC_045512.2,24130,C,A,PASS,118,0,118,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220658,NC_045512.2,24424,A,T,PASS,36,0,36,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220658,NC_045512.2,24469,T,A,PASS,233,0,232,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220658,NC_045512.2,24503,C,T,PASS,264,11,253,0.96,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220658,NC_045512.2,25584,C,T,PASS,23,0,23,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220658,NC_045512.2,26270,C,T,PASS,231,2,229,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220658,NC_045512.2,26530,A,G,PASS,217,0,217,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220658,NC_045512.2,26577,C,G,PASS,261,0,261,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220658,NC_045512.2,26709,G,A,PASS,244,0,244,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220658,NC_045512.2,27259,A,C,PASS,60,0,60,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220658,NC_045512.2,27807,C,T,PASS,31,0,31,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220658,NC_045512.2,28271,A,T,PASS,725,0,723,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220658,NC_045512.2,28311,C,T,PASS,708,0,707,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220658,NC_045512.2,2832,A,G,PASS,13,0,13,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220658,NC_045512.2,28361,GGAGAACGCA,G,PASS,566,561,435,0.77,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220658,NC_045512.2,28881,GG,AA,PASS,10102,94,9997,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220658,NC_045512.2,28883,G,C,PASS,10039,10,10008,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220658,NC_045512.2,3037,C,T,PASS,19,0,19,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220658,NC_045512.2,5672,C,T,PASS,11,0,11,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220658,NC_045512.2,8393,G,A,PASS,885,0,885,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220659,NC_045512.2,10449,C,A,PASS,67,0,67,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220659,NC_045512.2,11282,AGTTTGTCTG,A,PASS,147,147,129,0.88,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220659,NC_045512.2,11537,A,G,PASS,153,0,153,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220659,NC_045512.2,13195,T,C,PASS,5113,5,5106,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220659,NC_045512.2,14408,C,T,PASS,87,0,87,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220659,NC_045512.2,18163,A,G,PASS,26,0,26,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220659,NC_045512.2,21762,C,T,PASS,130,2,128,0.98,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220659,NC_045512.2,21764,ATACATG,A,PASS,132,132,117,0.89,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220659,NC_045512.2,21846,C,T,PASS,126,0,126,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220659,NC_045512.2,22679,T,C,PASS,12,0,12,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220659,NC_045512.2,22686,C,T,PASS,12,0,12,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220659,NC_045512.2,23202,C,A,PASS,12,0,12,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220659,NC_045512.2,23403,A,G,PASS,3188,6,3182,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220659,NC_045512.2,23525,C,T,PASS,3075,2,3067,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220659,NC_045512.2,23599,T,G,PASS,1225,0,1223,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220659,NC_045512.2,23604,C,A,PASS,1183,1,1178,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220659,NC_045512.2,23854,C,A,PASS,44,0,44,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220659,NC_045512.2,23948,G,T,PASS,575,0,574,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220659,NC_045512.2,24130,C,A,PASS,852,0,845,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220659,NC_045512.2,24424,A,T,PASS,87,1,85,0.98,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220659,NC_045512.2,24469,T,A,PASS,624,1,618,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220659,NC_045512.2,24503,C,T,PASS,757,12,745,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220659,NC_045512.2,25000,C,T,PASS,40,1,39,0.98,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220659,NC_045512.2,25584,C,T,PASS,88,0,88,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220659,NC_045512.2,26270,C,T,PASS,546,1,545,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220659,NC_045512.2,26530,A,G,PASS,449,2,447,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220659,NC_045512.2,26577,C,G,PASS,432,0,432,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220659,NC_045512.2,26709,G,A,PASS,479,2,477,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220659,NC_045512.2,27259,A,C,PASS,294,0,294,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220659,NC_045512.2,27807,C,T,PASS,180,1,179,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220659,NC_045512.2,27970,C,T,PASS,696,19,675,0.97,ORF8,missense_variant,c.77C>T,p.Thr26Ile,p.T26I,ivar,BA.1.17 +220659,NC_045512.2,28271,A,T,PASS,1877,3,1872,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220659,NC_045512.2,28311,C,T,PASS,1989,8,1980,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220659,NC_045512.2,2832,A,G,PASS,68,0,68,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220659,NC_045512.2,28361,GGAGAACGCA,G,PASS,1571,1561,969,0.62,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220659,NC_045512.2,28881,GG,AA,PASS,3757,52,3700,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220659,NC_045512.2,28883,G,C,PASS,3725,2,3716,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220659,NC_045512.2,3037,C,T,PASS,23,0,23,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220659,NC_045512.2,5672,C,T,PASS,91,0,91,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220659,NC_045512.2,5924,G,A,PASS,34,0,34,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220659,NC_045512.2,76,T,A,PASS,24,10,14,0.58,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1.17 +220659,NC_045512.2,78,T,G,PASS,23,9,14,0.61,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1.17 +220659,NC_045512.2,7984,T,C,PASS,934,1,933,1.0,orf1ab,synonymous_variant,c.7719T>C,p.Asp2573Asp,p.D2573D,ivar,BA.1.17 +220659,NC_045512.2,8393,G,A,PASS,3572,10,3552,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220659,NC_045512.2,999,C,T,PASS,2162,22,2138,0.99,orf1ab,missense_variant,c.734C>T,p.Ser245Phe,p.S245F,ivar,BA.1.17 +220660,NC_045512.2,10029,C,T,PASS,15,0,15,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.1 +220660,NC_045512.2,10449,C,A,PASS,59,0,59,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1 +220660,NC_045512.2,11282,AGTTTGTCTG,A,PASS,155,151,132,0.85,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1 +220660,NC_045512.2,11537,A,G,PASS,138,0,138,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1 +220660,NC_045512.2,13195,T,C,PASS,4902,11,4891,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1 +220660,NC_045512.2,13750,T,A,ft,15,11,4,0.27,orf1ab,missense_variant,c.13485T>A,p.Ser4495Arg,p.S4495R,ivar,BA.1.1 +220660,NC_045512.2,14408,C,T,PASS,103,0,103,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1 +220660,NC_045512.2,15336,T,C,PASS,11,2,9,0.82,orf1ab,missense_variant,c.15071T>C,p.Leu5024Ser,p.L5024S,ivar,BA.1.1 +220660,NC_045512.2,15359,G,A,PASS,14,7,7,0.5,orf1ab,missense_variant,c.15094G>A,p.Ala5032Thr,p.A5032T,ivar,BA.1.1 +220660,NC_045512.2,16744,G,A,PASS,344,0,344,1.0,orf1ab,synonymous_variant,c.16479G>A,p.Leu5493Leu,p.L5493L,ivar,BA.1.1 +220660,NC_045512.2,18163,A,G,PASS,20,0,20,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.1 +220660,NC_045512.2,21762,C,T,PASS,186,0,186,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1 +220660,NC_045512.2,21764,ATACATG,A,PASS,190,187,174,0.92,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1 +220660,NC_045512.2,21846,C,T,PASS,164,0,164,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1 +220660,NC_045512.2,22578,G,A,PASS,13,0,13,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.1 +220660,NC_045512.2,23202,C,A,PASS,11,0,11,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.1 +220660,NC_045512.2,23403,A,G,PASS,3655,3,3650,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1 +220660,NC_045512.2,23525,C,T,PASS,3613,12,3596,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1 +220660,NC_045512.2,23599,T,G,PASS,1227,0,1225,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1 +220660,NC_045512.2,23604,C,A,PASS,1189,2,1175,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1 +220660,NC_045512.2,23854,C,A,PASS,22,0,22,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1 +220660,NC_045512.2,23948,G,T,PASS,242,0,239,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1 +220660,NC_045512.2,24130,C,A,PASS,408,0,407,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1 +220660,NC_045512.2,24424,A,T,PASS,95,0,95,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1 +220660,NC_045512.2,24469,T,A,PASS,525,0,521,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1 +220660,NC_045512.2,24503,C,T,PASS,600,6,592,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1 +220660,NC_045512.2,25000,C,T,PASS,48,0,48,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1 +220660,NC_045512.2,2500,A,G,PASS,21,0,21,1.0,orf1ab,synonymous_variant,c.2235A>G,p.Glu745Glu,p.E745E,ivar,BA.1.1 +220660,NC_045512.2,25584,C,T,PASS,60,0,60,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1 +220660,NC_045512.2,26270,C,T,PASS,318,1,317,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1 +220660,NC_045512.2,26530,A,G,PASS,309,0,309,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1 +220660,NC_045512.2,26577,C,G,PASS,350,0,350,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1 +220660,NC_045512.2,26709,G,A,PASS,356,3,353,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1 +220660,NC_045512.2,27259,A,C,PASS,249,0,249,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1 +220660,NC_045512.2,27807,C,T,PASS,129,1,128,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1 +220660,NC_045512.2,28271,A,T,PASS,1073,0,1070,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1 +220660,NC_045512.2,28311,C,T,PASS,1105,5,1097,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1 +220660,NC_045512.2,2832,A,G,PASS,32,0,32,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1 +220660,NC_045512.2,28361,GGAGAACGCA,G,PASS,776,768,491,0.63,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1 +220660,NC_045512.2,28881,GG,AA,PASS,3182,53,3121,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1 +220660,NC_045512.2,28883,G,C,PASS,3146,1,3138,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1 +220660,NC_045512.2,3037,C,T,PASS,27,0,27,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1 +220660,NC_045512.2,3264,C,T,PASS,1132,6,1125,0.99,orf1ab,missense_variant,c.2999C>T,p.Thr1000Ile,p.T1000I,ivar,BA.1.1 +220660,NC_045512.2,5386,T,G,PASS,10,0,10,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.1 +220660,NC_045512.2,5512,C,T,ft,15,11,4,0.27,orf1ab,synonymous_variant,c.5247C>T,p.Asn1749Asn,p.N1749N,ivar,BA.1.1 +220660,NC_045512.2,76,T,A,PASS,36,24,12,0.33,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1.1 +220660,NC_045512.2,78,T,G,PASS,36,24,12,0.33,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1.1 +220660,NC_045512.2,8393,G,A,PASS,3635,10,3623,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1 +220661,NC_045512.2,10029,C,T,PASS,28,2,26,0.93,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.1 +220661,NC_045512.2,10449,C,A,PASS,83,0,83,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1 +220661,NC_045512.2,11282,AGTTTGTCTG,A,PASS,268,262,243,0.91,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1 +220661,NC_045512.2,11537,A,G,PASS,203,0,203,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1 +220661,NC_045512.2,13195,T,C,PASS,7311,6,7305,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1 +220661,NC_045512.2,13678,T,C,PASS,10,0,10,1.0,orf1ab,synonymous_variant,c.13413T>C,p.Thr4471Thr,p.T4471T,ivar,BA.1.1 +220661,NC_045512.2,14408,C,T,PASS,157,0,157,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1 +220661,NC_045512.2,18163,A,G,PASS,14,1,13,0.93,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.1 +220661,NC_045512.2,20081,C,T,ft,11,7,4,0.36,orf1ab,synonymous_variant,c.19816C>T,p.Leu6606Leu,p.L6606L,ivar,BA.1.1 +220661,NC_045512.2,20085,AG,A,ft,12,12,4,0.33,orf1ab,frameshift_variant,c.19822delG,p.Val6608fs,p.V6608fs,ivar,BA.1.1 +220661,NC_045512.2,21595,C,T,PASS,626,3,621,0.99,S,synonymous_variant,c.33C>T,p.Val11Val,p.V11V,ivar,BA.1.1 +220661,NC_045512.2,21762,C,T,PASS,151,2,149,0.99,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1 +220661,NC_045512.2,21764,ATACATG,A,PASS,152,151,145,0.95,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1 +220661,NC_045512.2,21846,C,T,PASS,232,1,231,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1 +220661,NC_045512.2,22992,G,A,PASS,13,0,13,1.0,S,missense_variant,c.1430G>A,p.Ser477Asn,p.S477N,ivar,BA.1.1 +220661,NC_045512.2,22995,C,A,PASS,13,0,13,1.0,S,missense_variant,c.1433C>A,p.Thr478Lys,p.T478K,ivar,BA.1.1 +220661,NC_045512.2,23013,A,C,PASS,11,0,11,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.1 +220661,NC_045512.2,23040,A,G,PASS,11,0,11,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.1 +220661,NC_045512.2,23048,G,A,PASS,11,0,11,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.1 +220661,NC_045512.2,23055,A,G,PASS,11,0,11,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.1 +220661,NC_045512.2,23063,A,T,PASS,11,0,11,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.1 +220661,NC_045512.2,23202,C,A,PASS,23,0,23,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.1 +220661,NC_045512.2,23403,A,G,PASS,3174,1,3172,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1 +220661,NC_045512.2,23525,C,T,PASS,3000,2,2995,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1 +220661,NC_045512.2,23599,T,G,PASS,1121,0,1121,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1 +220661,NC_045512.2,23604,C,A,PASS,1072,0,1066,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1 +220661,NC_045512.2,23854,C,A,PASS,29,0,29,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1 +220661,NC_045512.2,23948,G,T,PASS,427,0,427,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1 +220661,NC_045512.2,24130,C,A,PASS,638,0,636,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1 +220661,NC_045512.2,24424,A,T,PASS,151,2,149,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1 +220661,NC_045512.2,24469,T,A,PASS,857,0,855,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1 +220661,NC_045512.2,24503,C,T,PASS,1013,12,1001,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1 +220661,NC_045512.2,2470,C,T,PASS,13,0,13,1.0,orf1ab,synonymous_variant,c.2205C>T,p.Ala735Ala,p.A735A,ivar,BA.1.1 +220661,NC_045512.2,25000,C,T,PASS,59,2,57,0.97,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1 +220661,NC_045512.2,25584,C,T,PASS,70,0,70,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1 +220661,NC_045512.2,26270,C,T,PASS,516,0,516,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1 +220661,NC_045512.2,26530,A,G,PASS,322,0,322,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1 +220661,NC_045512.2,26577,C,G,PASS,284,0,283,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1 +220661,NC_045512.2,26709,G,A,PASS,337,7,330,0.98,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1 +220661,NC_045512.2,27259,A,C,PASS,178,0,178,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1 +220661,NC_045512.2,27807,C,T,PASS,70,0,70,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1 +220661,NC_045512.2,28271,A,T,PASS,1288,0,1287,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1 +220661,NC_045512.2,28311,C,T,PASS,1327,5,1322,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1 +220661,NC_045512.2,2832,A,G,PASS,29,0,29,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1 +220661,NC_045512.2,28361,GGAGAACGCA,G,PASS,988,984,611,0.62,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1 +220661,NC_045512.2,28881,GG,AA,PASS,4858,62,4792,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1 +220661,NC_045512.2,28883,G,C,PASS,4828,1,4820,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1 +220661,NC_045512.2,3037,C,T,PASS,31,0,31,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1 +220661,NC_045512.2,8393,G,A,PASS,2995,5,2985,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1 +220663,NC_045512.2,11537,A,G,PASS,11,0,11,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220663,NC_045512.2,12864,A,C,PASS,17,0,17,1.0,orf1ab,missense_variant,c.12599A>C,p.Asp4200Ala,p.D4200A,ivar,Unassigned +220663,NC_045512.2,1312,G,T,PASS,475,0,473,1.0,orf1ab,missense_variant,c.1047G>T,p.Leu349Phe,p.L349F,ivar,Unassigned +220663,NC_045512.2,13195,T,C,PASS,259,0,259,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220663,NC_045512.2,18622,A,G,ft,16,11,5,0.31,orf1ab,synonymous_variant,c.18357A>G,p.Leu6119Leu,p.L6119L,ivar,Unassigned +220663,NC_045512.2,22578,G,A,PASS,10,0,10,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,Unassigned +220663,NC_045512.2,23403,A,G,PASS,89,0,89,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220663,NC_045512.2,23525,C,T,PASS,106,0,106,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220663,NC_045512.2,23599,T,G,PASS,65,0,65,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220663,NC_045512.2,23604,C,A,PASS,61,0,61,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220663,NC_045512.2,23948,G,T,PASS,13,0,13,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220663,NC_045512.2,24130,C,A,PASS,37,0,37,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220663,NC_045512.2,24424,A,T,PASS,61,0,61,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220663,NC_045512.2,24469,T,A,PASS,139,0,139,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220663,NC_045512.2,24503,C,T,PASS,158,0,158,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220663,NC_045512.2,26270,C,T,PASS,479,2,477,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220663,NC_045512.2,26530,A,G,PASS,156,0,156,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220663,NC_045512.2,26577,C,G,PASS,120,0,120,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220663,NC_045512.2,26709,G,A,PASS,166,2,163,0.98,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220663,NC_045512.2,27259,A,C,PASS,23,0,23,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220663,NC_045512.2,27274,T,A,PASS,24,17,7,0.29,ORF6,missense_variant,c.73T>A,p.Ser25Thr,p.S25T,ivar,Unassigned +220663,NC_045512.2,27476,C,T,PASS,147,21,126,0.86,ORF7a,missense_variant,c.83C>T,p.Thr28Ile,p.T28I,ivar,Unassigned +220663,NC_045512.2,28271,A,T,PASS,150,0,150,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220663,NC_045512.2,28311,C,T,PASS,159,2,157,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220663,NC_045512.2,28361,GGAGAACGCA,G,PASS,171,171,136,0.8,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220663,NC_045512.2,28881,GG,AA,PASS,9147,39,9102,1.0,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220663,NC_045512.2,28883,G,C,PASS,9138,1,9105,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220663,NC_045512.2,29301,A,G,PASS,1729,4,1725,1.0,N,missense_variant,c.1028A>G,p.Asp343Gly,p.D343G,ivar,Unassigned +220663,NC_045512.2,3760,T,A,PASS,316,215,97,0.31,orf1ab,stop_gained,c.3495T>A,p.Cys1165*,p.C1165*,ivar,Unassigned +220663,NC_045512.2,8393,G,A,PASS,223,0,223,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220664,NC_045512.2,10029,C,T,PASS,25,0,25,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.1.1 +220664,NC_045512.2,10449,C,A,PASS,112,0,112,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1.1 +220664,NC_045512.2,11282,AGTTTGTCTG,A,PASS,302,300,269,0.89,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1.1 +220664,NC_045512.2,11537,A,G,PASS,300,0,300,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1.1 +220664,NC_045512.2,13195,T,C,PASS,5521,11,5501,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1.1 +220664,NC_045512.2,14408,C,T,PASS,214,4,210,0.98,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1.1 +220664,NC_045512.2,15336,T,C,PASS,11,5,6,0.55,orf1ab,missense_variant,c.15071T>C,p.Leu5024Ser,p.L5024S,ivar,BA.1.1.1 +220664,NC_045512.2,15359,G,A,PASS,13,6,7,0.54,orf1ab,missense_variant,c.15094G>A,p.Ala5032Thr,p.A5032T,ivar,BA.1.1.1 +220664,NC_045512.2,16064,A,G,PASS,251,1,250,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,BA.1.1.1 +220664,NC_045512.2,18163,A,G,PASS,24,0,24,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.1.1 +220664,NC_045512.2,21762,C,T,PASS,261,0,261,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1.1 +220664,NC_045512.2,21764,ATACATG,A,PASS,266,261,232,0.87,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1.1 +220664,NC_045512.2,21846,C,T,PASS,297,0,297,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1.1 +220664,NC_045512.2,22578,G,A,PASS,12,0,12,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.1.1 +220664,NC_045512.2,22599,G,A,PASS,13,0,13,1.0,S,missense_variant,c.1037G>A,p.Arg346Lys,p.R346K,ivar,BA.1.1.1 +220664,NC_045512.2,22673,TC,CT,PASS,11,0,11,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.1.1 +220664,NC_045512.2,22679,T,C,PASS,14,0,14,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.1.1 +220664,NC_045512.2,22686,C,T,PASS,12,0,12,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.1.1 +220664,NC_045512.2,22992,G,A,PASS,10,0,10,1.0,S,missense_variant,c.1430G>A,p.Ser477Asn,p.S477N,ivar,BA.1.1.1 +220664,NC_045512.2,23013,A,C,PASS,10,0,10,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.1.1 +220664,NC_045512.2,23040,A,G,PASS,11,0,11,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.1.1 +220664,NC_045512.2,23048,G,A,PASS,15,0,15,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.1.1 +220664,NC_045512.2,23055,A,G,PASS,15,0,15,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.1.1 +220664,NC_045512.2,23063,A,T,PASS,16,0,14,0.88,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.1.1 +220664,NC_045512.2,23075,T,C,PASS,17,0,17,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.1.1 +220664,NC_045512.2,23202,C,A,PASS,25,0,25,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.1.1 +220664,NC_045512.2,23403,A,G,PASS,2654,0,2654,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1.1 +220664,NC_045512.2,23525,C,T,PASS,2542,8,2530,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1.1 +220664,NC_045512.2,23599,T,G,PASS,936,0,935,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1.1 +220664,NC_045512.2,23604,C,A,PASS,896,0,889,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1.1 +220664,NC_045512.2,23854,C,A,PASS,55,0,54,0.98,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1.1 +220664,NC_045512.2,23948,G,T,PASS,895,0,891,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1.1 +220664,NC_045512.2,24130,C,A,PASS,1211,0,1198,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1.1 +220664,NC_045512.2,24424,A,T,PASS,268,0,268,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1.1 +220664,NC_045512.2,24469,T,A,PASS,1053,0,1053,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1.1 +220664,NC_045512.2,24503,C,T,PASS,1182,13,1169,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1.1 +220664,NC_045512.2,25000,C,T,PASS,80,0,80,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1.1 +220664,NC_045512.2,25584,C,T,PASS,152,0,152,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1.1 +220664,NC_045512.2,26270,C,T,PASS,636,2,634,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1.1 +220664,NC_045512.2,26530,A,G,PASS,177,0,177,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1.1 +220664,NC_045512.2,26577,C,G,PASS,203,0,203,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1.1 +220664,NC_045512.2,26709,G,A,PASS,205,0,205,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1.1 +220664,NC_045512.2,27259,A,C,PASS,346,0,340,0.98,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1.1 +220664,NC_045512.2,27807,C,T,PASS,64,0,64,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1.1 +220664,NC_045512.2,28271,A,T,PASS,1831,9,1819,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1.1 +220664,NC_045512.2,28311,C,T,PASS,1835,8,1827,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1.1 +220664,NC_045512.2,2832,A,G,PASS,167,1,166,0.99,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1.1 +220664,NC_045512.2,28361,GGAGAACGCA,G,PASS,1291,1282,743,0.58,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1.1 +220664,NC_045512.2,28881,GG,AA,PASS,2695,46,2646,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1.1 +220664,NC_045512.2,28883,G,C,PASS,2663,6,2655,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1.1 +220664,NC_045512.2,3037,C,T,PASS,50,0,50,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1.1 +220664,NC_045512.2,5386,T,G,PASS,15,0,15,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.1.1 +220664,NC_045512.2,8393,G,A,PASS,2721,8,2712,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1.1 +220665,NC_045512.2,10449,C,A,PASS,14,0,14,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220665,NC_045512.2,11074,CT,C,ft,15,15,4,0.27,orf1ab,frameshift_variant,c.10817delT,p.Leu3606fs,p.L3606fs,ivar,BA.1.17 +220665,NC_045512.2,11186,T,C,PASS,26,18,8,0.31,orf1ab,synonymous_variant,c.10921T>C,p.Leu3641Leu,p.L3641L,ivar,BA.1.17 +220665,NC_045512.2,11282,AGTTTGTCTG,A,PASS,49,49,41,0.84,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220665,NC_045512.2,11537,A,G,PASS,41,0,41,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220665,NC_045512.2,13195,T,C,PASS,2411,5,2405,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220665,NC_045512.2,14408,C,T,PASS,27,0,27,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220665,NC_045512.2,19162,G,T,PASS,872,0,868,1.0,orf1ab,synonymous_variant,c.18897G>T,p.Leu6299Leu,p.L6299L,ivar,BA.1.17 +220665,NC_045512.2,21762,C,T,PASS,52,0,52,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220665,NC_045512.2,21764,ATACATG,A,PASS,52,52,47,0.9,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220665,NC_045512.2,21846,C,T,PASS,44,0,44,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220665,NC_045512.2,23202,C,A,PASS,16,0,16,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220665,NC_045512.2,23235,A,G,PASS,19,12,7,0.37,S,missense_variant,c.1673A>G,p.Lys558Arg,p.K558R,ivar,BA.1.17 +220665,NC_045512.2,23403,A,G,PASS,1508,0,1508,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220665,NC_045512.2,23525,C,T,PASS,1423,6,1417,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220665,NC_045512.2,23599,T,G,PASS,648,0,648,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220665,NC_045512.2,23604,C,A,PASS,624,0,621,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220665,NC_045512.2,23948,G,T,PASS,71,0,71,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220665,NC_045512.2,24130,C,A,PASS,140,0,140,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220665,NC_045512.2,24424,A,T,PASS,37,0,37,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220665,NC_045512.2,24469,T,A,PASS,384,0,383,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220665,NC_045512.2,24503,C,T,PASS,449,11,438,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220665,NC_045512.2,25000,C,T,PASS,17,0,17,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220665,NC_045512.2,25584,C,T,PASS,35,0,35,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220665,NC_045512.2,26270,C,T,PASS,646,0,646,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220665,NC_045512.2,26530,A,G,PASS,242,0,242,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220665,NC_045512.2,26577,C,G,PASS,271,0,269,0.99,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220665,NC_045512.2,26709,G,A,PASS,262,1,261,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220665,NC_045512.2,27259,A,C,PASS,149,0,149,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220665,NC_045512.2,27670,G,T,PASS,32,0,32,1.0,ORF7a,missense_variant,c.277G>T,p.Val93Phe,p.V93F,ivar,BA.1.17 +220665,NC_045512.2,27676,G,C,PASS,31,23,8,0.26,ORF7a,missense_variant,c.283G>C,p.Glu95Gln,p.E95Q,ivar,BA.1.17 +220665,NC_045512.2,27807,C,T,PASS,55,0,55,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220665,NC_045512.2,28271,A,T,PASS,837,0,837,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220665,NC_045512.2,28311,C,T,PASS,921,0,919,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220665,NC_045512.2,2832,A,G,PASS,88,0,88,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220665,NC_045512.2,28361,GGAGAACGCA,G,PASS,702,694,428,0.61,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220665,NC_045512.2,28881,GG,AA,PASS,8854,85,8762,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220665,NC_045512.2,28883,G,C,PASS,8819,2,8808,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220665,NC_045512.2,3037,C,T,PASS,11,0,11,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220665,NC_045512.2,4087,T,C,ft,15,11,4,0.27,orf1ab,synonymous_variant,c.3822T>C,p.Ile1274Ile,p.I1274I,ivar,BA.1.17 +220665,NC_045512.2,5672,C,T,PASS,49,0,49,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220665,NC_045512.2,5924,G,A,PASS,20,0,20,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220665,NC_045512.2,76,T,A,PASS,17,5,12,0.71,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1.17 +220665,NC_045512.2,78,T,G,PASS,17,5,12,0.71,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1.17 +220665,NC_045512.2,8393,G,A,PASS,2963,3,2957,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220666,NC_045512.2,11267,GAT,G,PASS,28,24,10,0.36,orf1ab,frameshift_variant,c.11005_11006delAT,p.Met3669fs,p.M3669fs,ivar,B.1.617.2 +220666,NC_045512.2,11332,A,G,PASS,31,0,31,1.0,orf1ab,synonymous_variant,c.11067A>G,p.Val3689Val,p.V3689V,ivar,B.1.617.2 +220666,NC_045512.2,11387,G,A,ft,14,10,4,0.29,orf1ab,missense_variant,c.11122G>A,p.Val3708Met,p.V3708M,ivar,B.1.617.2 +220666,NC_045512.2,13432,C,T,PASS,486,0,486,1.0,orf1ab,synonymous_variant,c.13167C>T,p.Pro4389Pro,p.P4389P,ivar,B.1.617.2 +220666,NC_045512.2,21456,A,G,ft,10,7,3,0.3,orf1ab,missense_variant,c.21191A>G,p.Lys7064Arg,p.K7064R,ivar,B.1.617.2 +220666,NC_045512.2,21618,C,G,PASS,18,0,18,1.0,S,missense_variant,c.56C>G,p.Thr19Arg,p.T19R,ivar,B.1.617.2 +220666,NC_045512.2,23403,A,G,PASS,319,0,319,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.617.2 +220666,NC_045512.2,23604,C,G,PASS,103,0,103,1.0,S,missense_variant,c.2042C>G,p.Pro681Arg,p.P681R,ivar,B.1.617.2 +220666,NC_045512.2,26767,T,C,PASS,24,0,24,1.0,M,missense_variant,c.245T>C,p.Ile82Thr,p.I82T,ivar,B.1.617.2 +220666,NC_045512.2,27874,C,T,PASS,13,0,13,1.0,ORF7b,missense_variant,c.119C>T,p.Thr40Ile,p.T40I,ivar,B.1.617.2 +220666,NC_045512.2,27916,G,A,PASS,12,0,12,1.0,ORF8,missense_variant,c.23G>A,p.Gly8Glu,p.G8E,ivar,B.1.617.2 +220666,NC_045512.2,27943,A,G,PASS,10,3,7,0.7,ORF8,missense_variant,c.50A>G,p.His17Arg,p.H17R,ivar,B.1.617.2 +220666,NC_045512.2,28055,A,G,PASS,15,8,7,0.47,ORF8,synonymous_variant,c.162A>G,p.Ser54Ser,p.S54S,ivar,B.1.617.2 +220666,NC_045512.2,28089,GGTTCTA,G,PASS,12,12,12,1.0,ORF8,disruptive_inframe_deletion,c.197_202delGTTCTA,p.Gly66_Lys68delinsGlu,p.G66_K68delinsE,ivar,B.1.617.2 +220666,NC_045512.2,28179,G,T,PASS,18,0,18,1.0,ORF8,missense_variant,c.286G>T,p.Gly96Cys,p.G96C,ivar,B.1.617.2 +220666,NC_045512.2,28247,AGATTTC,A,PASS,90,90,86,0.96,ORF8,conservative_inframe_deletion,c.355_360delGATTTC,p.Asp119_Phe120del,p.D119_F120del,ivar,B.1.617.2 +220666,NC_045512.2,28270,TA,T,PASS,118,118,105,0.89,N,upstream_gene_variant,c.-3delA,.,.,ivar,B.1.617.2 +220666,NC_045512.2,28367,C,T,PASS,96,0,96,1.0,N,missense_variant,c.94C>T,p.Arg32Cys,p.R32C,ivar,B.1.617.2 +220666,NC_045512.2,28378,G,T,PASS,78,0,78,1.0,N,synonymous_variant,c.105G>T,p.Ala35Ala,p.A35A,ivar,B.1.617.2 +220666,NC_045512.2,28461,A,G,PASS,16,0,16,1.0,N,missense_variant,c.188A>G,p.Asp63Gly,p.D63G,ivar,B.1.617.2 +220666,NC_045512.2,28881,G,T,PASS,5069,16,5029,0.99,N,missense_variant,c.608G>T,p.Arg203Met,p.R203M,ivar,B.1.617.2 +220666,NC_045512.2,28916,G,T,PASS,56,0,56,1.0,N,missense_variant,c.643G>T,p.Gly215Cys,p.G215C,ivar,B.1.617.2 +220666,NC_045512.2,29402,G,T,PASS,1865,0,1860,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,B.1.617.2 +220666,NC_045512.2,3903,C,T,PASS,82,0,82,1.0,orf1ab,missense_variant,c.3638C>T,p.Pro1213Leu,p.P1213L,ivar,B.1.617.2 +220666,NC_045512.2,3987,C,T,PASS,90,0,90,1.0,orf1ab,missense_variant,c.3722C>T,p.Thr1241Ile,p.T1241I,ivar,B.1.617.2 +220667,NC_045512.2,10029,C,T,PASS,30,0,30,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220667,NC_045512.2,10449,C,A,PASS,76,0,74,0.97,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220667,NC_045512.2,11282,AGTTTGTCTG,A,PASS,206,202,182,0.88,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220667,NC_045512.2,11537,A,G,PASS,96,0,96,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220667,NC_045512.2,13195,T,C,PASS,3626,4,3622,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220667,NC_045512.2,14408,C,T,PASS,117,0,117,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220667,NC_045512.2,18163,A,G,PASS,13,0,13,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220667,NC_045512.2,21762,C,T,PASS,157,2,155,0.99,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220667,NC_045512.2,21764,ATACATG,A,PASS,159,157,139,0.87,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220667,NC_045512.2,21846,C,T,PASS,153,1,152,0.99,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220667,NC_045512.2,21,C,T,PASS,10,0,10,1.0,orf1ab,upstream_gene_variant,c.-245C>T,.,.,ivar,BA.1.17 +220667,NC_045512.2,22578,G,A,PASS,18,0,18,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.17 +220667,NC_045512.2,22673,TC,CT,PASS,10,0,10,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.17 +220667,NC_045512.2,22679,T,C,PASS,20,0,20,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220667,NC_045512.2,22686,C,T,PASS,20,0,20,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220667,NC_045512.2,23202,C,A,PASS,16,0,16,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220667,NC_045512.2,23403,A,G,PASS,3381,6,3375,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220667,NC_045512.2,23525,C,T,PASS,3427,9,3416,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220667,NC_045512.2,23599,T,G,PASS,1504,0,1502,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220667,NC_045512.2,23604,C,A,PASS,1436,0,1431,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220667,NC_045512.2,23854,C,A,PASS,19,0,19,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220667,NC_045512.2,23948,G,T,PASS,846,0,845,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220667,NC_045512.2,24130,C,A,PASS,1170,0,1164,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220667,NC_045512.2,24424,A,T,PASS,128,2,124,0.97,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220667,NC_045512.2,24469,T,A,PASS,798,2,795,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220667,NC_045512.2,24503,C,T,PASS,930,23,905,0.97,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220667,NC_045512.2,25000,C,T,PASS,67,0,67,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220667,NC_045512.2,25584,C,T,PASS,100,2,98,0.98,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220667,NC_045512.2,26270,C,T,PASS,1358,2,1355,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220667,NC_045512.2,26361,G,A,ft,11,8,3,0.27,E,synonymous_variant,c.117G>A,p.Leu39Leu,p.L39L,ivar,BA.1.17 +220667,NC_045512.2,26530,A,G,PASS,438,0,436,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220667,NC_045512.2,26577,C,G,PASS,513,0,513,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220667,NC_045512.2,26709,G,A,PASS,473,1,472,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220667,NC_045512.2,27259,A,C,PASS,618,0,618,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220667,NC_045512.2,27384,T,C,PASS,764,0,764,1.0,ORF6,synonymous_variant,c.183T>C,p.Asp61Asp,p.D61D,ivar,BA.1.17 +220667,NC_045512.2,27807,C,T,PASS,112,0,112,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220667,NC_045512.2,28271,A,T,PASS,1976,8,1963,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220667,NC_045512.2,28311,C,T,PASS,2173,5,2164,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220667,NC_045512.2,2832,A,G,PASS,80,0,80,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220667,NC_045512.2,28361,GGAGAACGCA,G,PASS,1572,1560,679,0.43,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220667,NC_045512.2,28881,GG,AA,PASS,3593,32,3558,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220667,NC_045512.2,28883,G,C,PASS,3570,4,3559,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220667,NC_045512.2,3037,C,T,PASS,19,0,19,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220667,NC_045512.2,3040,C,T,PASS,19,0,19,1.0,orf1ab,synonymous_variant,c.2775C>T,p.Tyr925Tyr,p.Y925Y,ivar,BA.1.17 +220667,NC_045512.2,5672,C,T,PASS,165,0,165,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220667,NC_045512.2,5924,G,A,PASS,77,0,77,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220667,NC_045512.2,76,T,A,PASS,45,9,36,0.8,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1.17 +220667,NC_045512.2,78,T,G,PASS,45,9,36,0.8,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1.17 +220667,NC_045512.2,7984,T,C,PASS,627,0,627,1.0,orf1ab,synonymous_variant,c.7719T>C,p.Asp2573Asp,p.D2573D,ivar,BA.1.17 +220667,NC_045512.2,8393,G,A,PASS,4302,15,4285,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220668,NC_045512.2,10449,C,A,PASS,11,0,11,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220668,NC_045512.2,11282,AGTTTGTCTG,A,PASS,33,33,29,0.88,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220668,NC_045512.2,13195,T,C,PASS,418,0,418,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220668,NC_045512.2,206,C,A,PASS,20,13,7,0.35,orf1ab,upstream_gene_variant,c.-60C>A,.,.,ivar,Unassigned +220668,NC_045512.2,21762,C,T,PASS,11,0,11,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220668,NC_045512.2,21764,ATACATG,A,ft,11,11,7,0.64,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220668,NC_045512.2,21846,C,T,PASS,16,0,16,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220668,NC_045512.2,23403,A,G,PASS,734,0,734,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220668,NC_045512.2,23525,C,T,PASS,748,0,748,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220668,NC_045512.2,23599,T,G,PASS,379,0,377,0.99,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220668,NC_045512.2,23604,C,A,PASS,358,0,358,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220668,NC_045512.2,23948,G,T,PASS,25,0,25,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220668,NC_045512.2,24130,C,A,PASS,19,0,19,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220668,NC_045512.2,24424,A,T,PASS,30,0,30,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220668,NC_045512.2,24469,T,A,PASS,94,0,94,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220668,NC_045512.2,24503,C,T,PASS,95,0,95,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220668,NC_045512.2,25000,C,T,PASS,17,0,17,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220668,NC_045512.2,25584,C,T,PASS,28,0,28,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220668,NC_045512.2,26270,C,T,PASS,475,2,473,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220668,NC_045512.2,26530,A,G,PASS,90,0,90,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220668,NC_045512.2,26577,C,G,PASS,87,0,87,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220668,NC_045512.2,26709,G,A,PASS,96,0,96,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220668,NC_045512.2,27259,A,C,PASS,68,0,68,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220668,NC_045512.2,27384,T,C,PASS,82,0,82,1.0,ORF6,synonymous_variant,c.183T>C,p.Asp61Asp,p.D61D,ivar,Unassigned +220668,NC_045512.2,27807,C,T,PASS,11,0,11,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220668,NC_045512.2,28271,A,T,PASS,260,2,258,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220668,NC_045512.2,28311,C,T,PASS,297,0,297,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220668,NC_045512.2,2832,A,G,PASS,10,0,10,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220668,NC_045512.2,28361,GGAGAACGCA,G,PASS,176,176,105,0.6,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220668,NC_045512.2,28881,GG,AA,PASS,8461,46,8410,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220668,NC_045512.2,28883,G,C,PASS,8448,1,8431,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220668,NC_045512.2,5672,C,T,PASS,10,0,10,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220668,NC_045512.2,5924,G,A,PASS,10,0,10,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220668,NC_045512.2,76,T,A,PASS,18,6,12,0.67,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220668,NC_045512.2,78,T,G,PASS,18,6,12,0.67,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220668,NC_045512.2,7984,T,C,PASS,85,0,85,1.0,orf1ab,synonymous_variant,c.7719T>C,p.Asp2573Asp,p.D2573D,ivar,Unassigned +220668,NC_045512.2,8393,G,A,PASS,1330,2,1325,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220669,NC_045512.2,10449,C,A,PASS,19,0,19,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220669,NC_045512.2,11282,AGTTTGTCTG,A,PASS,35,35,33,0.94,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220669,NC_045512.2,11537,A,G,PASS,38,0,38,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220669,NC_045512.2,13195,T,C,PASS,1499,4,1495,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220669,NC_045512.2,14408,C,T,PASS,27,0,27,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220669,NC_045512.2,14466,T,C,PASS,28,20,8,0.29,orf1ab,missense_variant,c.14201T>C,p.Phe4734Ser,p.F4734S,ivar,Unassigned +220669,NC_045512.2,14533,A,G,ft,16,12,4,0.25,orf1ab,synonymous_variant,c.14268A>G,p.Leu4756Leu,p.L4756L,ivar,Unassigned +220669,NC_045512.2,15572,A,G,PASS,2032,731,1301,0.64,orf1ab,missense_variant,c.15307A>G,p.Met5103Val,p.M5103V,ivar,Unassigned +220669,NC_045512.2,21762,C,T,PASS,37,0,37,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220669,NC_045512.2,21764,ATACATG,A,PASS,38,37,29,0.76,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220669,NC_045512.2,21846,C,T,PASS,45,0,45,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220669,NC_045512.2,22578,G,A,PASS,12,0,12,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,Unassigned +220669,NC_045512.2,23403,A,G,PASS,1002,0,1002,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220669,NC_045512.2,23525,C,T,PASS,1030,4,1026,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220669,NC_045512.2,23599,T,G,PASS,490,0,488,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220669,NC_045512.2,23604,C,A,PASS,473,0,471,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220669,NC_045512.2,23948,G,T,PASS,113,0,113,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220669,NC_045512.2,24130,C,A,PASS,208,0,204,0.98,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220669,NC_045512.2,24424,A,T,PASS,42,0,40,0.95,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220669,NC_045512.2,24469,T,A,PASS,239,0,239,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220669,NC_045512.2,24503,C,T,PASS,281,6,275,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220669,NC_045512.2,25000,C,T,PASS,27,0,27,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220669,NC_045512.2,25584,C,T,PASS,26,0,26,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220669,NC_045512.2,26270,C,T,PASS,1060,2,1056,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220669,NC_045512.2,26530,A,G,PASS,516,0,516,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220669,NC_045512.2,26577,C,G,PASS,508,1,505,0.99,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220669,NC_045512.2,26709,G,A,PASS,474,1,472,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220669,NC_045512.2,27259,A,C,PASS,247,0,247,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220669,NC_045512.2,27807,C,T,PASS,93,0,92,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220669,NC_045512.2,28271,A,T,PASS,1304,1,1302,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220669,NC_045512.2,28311,C,T,PASS,1395,0,1393,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220669,NC_045512.2,2832,A,G,PASS,11,0,11,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220669,NC_045512.2,28361,GGAGAACGCA,G,PASS,1092,1088,734,0.67,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220669,NC_045512.2,28363,A,T,PASS,16,10,6,0.38,N,synonymous_variant,c.90A>T,p.Gly30Gly,p.G30G,ivar,Unassigned +220669,NC_045512.2,28881,GG,AA,PASS,10404,75,10319,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220669,NC_045512.2,28883,G,C,PASS,10380,2,10364,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220669,NC_045512.2,5672,C,T,PASS,37,2,35,0.95,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220669,NC_045512.2,5924,G,A,PASS,19,0,19,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220669,NC_045512.2,76,T,A,PASS,44,7,37,0.84,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220669,NC_045512.2,8393,G,A,PASS,2083,5,2078,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220670,NC_045512.2,10449,C,A,PASS,39,0,38,0.97,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220670,NC_045512.2,11282,AGTTTGTCTG,A,PASS,101,101,83,0.82,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220670,NC_045512.2,11537,A,G,PASS,81,0,81,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220670,NC_045512.2,13195,T,C,PASS,4671,5,4664,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220670,NC_045512.2,14408,C,T,PASS,72,0,72,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220670,NC_045512.2,21762,C,T,PASS,121,0,121,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220670,NC_045512.2,21764,ATACATG,A,PASS,121,121,114,0.94,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220670,NC_045512.2,21846,C,T,PASS,117,0,117,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220670,NC_045512.2,22673,TC,CT,PASS,11,0,11,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.17 +220670,NC_045512.2,22679,T,C,PASS,11,0,11,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220670,NC_045512.2,22686,C,T,PASS,11,0,11,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220670,NC_045512.2,23202,C,A,PASS,14,0,14,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220670,NC_045512.2,23403,A,G,PASS,2094,0,2093,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220670,NC_045512.2,23525,C,T,PASS,2060,6,2053,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220670,NC_045512.2,23599,T,G,PASS,847,0,845,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220670,NC_045512.2,23604,C,A,PASS,817,0,815,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220670,NC_045512.2,23854,C,A,PASS,25,0,25,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220670,NC_045512.2,23948,G,T,PASS,328,0,327,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220670,NC_045512.2,24130,C,A,PASS,478,0,477,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220670,NC_045512.2,24424,A,T,PASS,93,0,93,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220670,NC_045512.2,24469,T,A,PASS,520,0,518,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220670,NC_045512.2,24503,C,T,PASS,628,4,624,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220670,NC_045512.2,25000,C,T,PASS,33,0,33,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220670,NC_045512.2,25584,C,T,PASS,58,0,58,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220670,NC_045512.2,26270,C,T,PASS,372,2,370,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220670,NC_045512.2,26530,A,G,PASS,296,0,296,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220670,NC_045512.2,26577,C,G,PASS,354,0,354,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220670,NC_045512.2,26709,G,A,PASS,361,0,361,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220670,NC_045512.2,27259,A,C,PASS,268,0,268,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220670,NC_045512.2,27632,G,A,PASS,42,28,14,0.33,ORF7a,missense_variant,c.239G>A,p.Arg80Lys,p.R80K,ivar,BA.1.17 +220670,NC_045512.2,27807,C,T,PASS,65,0,65,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220670,NC_045512.2,28253,CA,C,PASS,482,480,479,0.99,ORF8,frameshift_variant,c.361delA,p.Ile121fs,p.I121fs,ivar,BA.1.17 +220670,NC_045512.2,28271,A,T,PASS,569,0,566,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220670,NC_045512.2,28311,C,T,PASS,572,4,568,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220670,NC_045512.2,2832,A,G,PASS,78,0,78,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220670,NC_045512.2,28361,GGAGAACGCA,G,PASS,386,382,243,0.63,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220670,NC_045512.2,28881,GG,AA,PASS,7323,72,7246,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220670,NC_045512.2,28883,G,C,PASS,7288,2,7274,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220670,NC_045512.2,29399,G,T,PASS,4164,2,4135,0.99,N,missense_variant,c.1126G>T,p.Ala376Ser,p.A376S,ivar,BA.1.17 +220670,NC_045512.2,3037,C,T,PASS,14,0,14,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220670,NC_045512.2,5672,C,T,PASS,57,2,55,0.96,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220670,NC_045512.2,5924,G,A,PASS,19,0,19,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220670,NC_045512.2,8393,G,A,PASS,3256,13,3242,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220670,NC_045512.2,8652,T,C,PASS,2794,8,2786,1.0,orf1ab,missense_variant,c.8387T>C,p.Met2796Thr,p.M2796T,ivar,BA.1.17 +220671,NC_045512.2,10029,C,T,PASS,28,0,28,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220671,NC_045512.2,10449,C,A,PASS,72,0,72,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220671,NC_045512.2,11282,AGTTTGTCTG,A,PASS,205,204,183,0.89,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220671,NC_045512.2,11537,A,G,PASS,98,0,98,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220671,NC_045512.2,12008,C,T,PASS,232,1,230,0.99,orf1ab,missense_variant,c.11743C>T,p.Leu3915Phe,p.L3915F,ivar,BA.1.17 +220671,NC_045512.2,13195,T,C,PASS,3794,10,3783,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220671,NC_045512.2,14408,C,T,PASS,62,1,61,0.98,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220671,NC_045512.2,18163,A,G,PASS,15,0,15,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220671,NC_045512.2,21762,C,T,PASS,95,0,95,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220671,NC_045512.2,21764,ATACATG,A,PASS,97,95,87,0.9,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220671,NC_045512.2,21846,C,T,PASS,108,0,108,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220671,NC_045512.2,22578,G,A,PASS,23,0,23,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.17 +220671,NC_045512.2,22673,TC,CT,PASS,12,0,12,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.17 +220671,NC_045512.2,22679,T,C,PASS,20,0,20,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220671,NC_045512.2,22686,C,T,PASS,20,0,20,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220671,NC_045512.2,23202,C,A,PASS,22,0,20,0.91,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220671,NC_045512.2,23403,A,G,PASS,2394,0,2394,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220671,NC_045512.2,23525,C,T,PASS,2316,2,2309,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220671,NC_045512.2,23599,T,G,PASS,848,0,848,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220671,NC_045512.2,23604,C,A,PASS,798,0,798,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220671,NC_045512.2,23854,C,A,PASS,59,0,59,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220671,NC_045512.2,23948,G,T,PASS,554,0,553,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220671,NC_045512.2,24130,C,A,PASS,893,0,890,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220671,NC_045512.2,24424,A,T,PASS,239,0,239,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220671,NC_045512.2,24469,T,A,PASS,691,0,687,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220671,NC_045512.2,24503,C,T,PASS,756,12,744,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220671,NC_045512.2,25000,C,T,PASS,56,0,56,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220671,NC_045512.2,25584,C,T,PASS,115,1,113,0.98,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220671,NC_045512.2,26270,C,T,PASS,1039,7,1032,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220671,NC_045512.2,26530,A,G,PASS,611,1,610,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220671,NC_045512.2,26577,C,G,PASS,638,0,637,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220671,NC_045512.2,26709,G,A,PASS,596,5,588,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220671,NC_045512.2,27259,A,C,PASS,630,0,630,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220671,NC_045512.2,27670,G,T,PASS,211,0,211,1.0,ORF7a,missense_variant,c.277G>T,p.Val93Phe,p.V93F,ivar,BA.1.17 +220671,NC_045512.2,27807,C,T,PASS,253,4,248,0.98,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220671,NC_045512.2,28271,A,T,PASS,1608,3,1605,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220671,NC_045512.2,28311,C,T,PASS,1682,3,1673,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220671,NC_045512.2,2832,A,G,PASS,92,0,92,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220671,NC_045512.2,28361,GGAGAACGCA,G,PASS,1336,1327,801,0.6,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220671,NC_045512.2,28881,GG,AA,PASS,2721,26,2694,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220671,NC_045512.2,28883,G,C,PASS,2714,2,2706,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220671,NC_045512.2,3037,C,T,PASS,31,1,30,0.97,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220671,NC_045512.2,5672,C,T,PASS,183,0,183,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220671,NC_045512.2,5924,G,A,PASS,61,0,61,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220671,NC_045512.2,76,T,A,PASS,44,27,17,0.39,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1.17 +220671,NC_045512.2,78,T,G,PASS,44,27,17,0.39,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1.17 +220671,NC_045512.2,8393,G,A,PASS,3239,22,3215,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220672,NC_045512.2,10029,C,T,PASS,15,0,15,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,Unassigned +220672,NC_045512.2,11282,AGTTTGTCTG,A,PASS,48,48,44,0.92,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220672,NC_045512.2,11537,A,G,PASS,64,0,64,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220672,NC_045512.2,13195,T,C,PASS,1572,4,1568,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220672,NC_045512.2,14408,C,T,PASS,61,0,61,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220672,NC_045512.2,20776,A,G,PASS,29,0,29,1.0,orf1ab,synonymous_variant,c.20511A>G,p.Ala6837Ala,p.A6837A,ivar,Unassigned +220672,NC_045512.2,21762,C,T,PASS,41,0,41,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220672,NC_045512.2,21764,ATACATG,A,PASS,41,41,37,0.9,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220672,NC_045512.2,21846,C,T,PASS,53,0,53,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220672,NC_045512.2,21,C,T,PASS,10,0,10,1.0,orf1ab,upstream_gene_variant,c.-245C>T,.,.,ivar,Unassigned +220672,NC_045512.2,23323,T,C,PASS,173,2,171,0.99,S,synonymous_variant,c.1761T>C,p.Ile587Ile,p.I587I,ivar,Unassigned +220672,NC_045512.2,23403,A,G,PASS,197,0,197,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220672,NC_045512.2,23525,C,T,PASS,191,0,191,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220672,NC_045512.2,23599,T,G,PASS,81,0,81,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220672,NC_045512.2,23604,C,A,PASS,79,0,79,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220672,NC_045512.2,23948,G,T,PASS,46,0,46,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220672,NC_045512.2,24130,C,A,PASS,60,0,60,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220672,NC_045512.2,24424,A,T,PASS,82,0,82,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220672,NC_045512.2,24469,T,A,PASS,575,2,571,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220672,NC_045512.2,24503,C,T,PASS,689,5,684,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220672,NC_045512.2,25000,C,T,PASS,31,0,31,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220672,NC_045512.2,25584,C,T,PASS,27,2,25,0.93,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220672,NC_045512.2,26270,C,T,PASS,1197,0,1197,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220672,NC_045512.2,26530,A,G,PASS,248,0,248,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220672,NC_045512.2,26577,C,G,PASS,225,0,225,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220672,NC_045512.2,26709,G,A,PASS,228,0,228,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220672,NC_045512.2,27259,A,C,PASS,103,0,103,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220672,NC_045512.2,27807,C,T,PASS,18,0,18,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220672,NC_045512.2,28271,A,T,PASS,1324,4,1318,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220672,NC_045512.2,28311,C,T,PASS,1356,0,1352,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220672,NC_045512.2,2832,A,G,PASS,19,0,19,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220672,NC_045512.2,28361,GGAGAACGCA,G,PASS,932,929,481,0.52,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220672,NC_045512.2,28881,GG,AA,PASS,9896,69,9823,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220672,NC_045512.2,28883,G,C,PASS,9878,3,9869,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220672,NC_045512.2,3800,G,A,PASS,80,2,78,0.98,orf1ab,missense_variant,c.3535G>A,p.Asp1179Asn,p.D1179N,ivar,Unassigned +220672,NC_045512.2,514,TGTTATG,T,PASS,11985,11766,9796,0.82,orf1ab,conservative_inframe_deletion,c.253_258delATGGTT,p.Met85_Val86del,p.M85_V86del,ivar,Unassigned +220672,NC_045512.2,520,G,C,PASS,87,44,43,0.49,orf1ab,missense_variant,c.255G>C,p.Met85Ile,p.M85I,ivar,Unassigned +220672,NC_045512.2,76,T,A,PASS,11,3,8,0.73,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220672,NC_045512.2,78,T,G,PASS,11,3,8,0.73,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220672,NC_045512.2,8393,G,A,PASS,544,2,541,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220675,NC_045512.2,11537,A,G,PASS,17,0,17,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220675,NC_045512.2,13195,T,C,PASS,553,0,553,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220675,NC_045512.2,13908,T,C,ft,10,6,4,0.4,orf1ab,missense_variant,c.13643T>C,p.Ile4548Thr,p.I4548T,ivar,Unassigned +220675,NC_045512.2,14408,C,T,PASS,13,0,13,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220675,NC_045512.2,21762,C,T,PASS,16,0,16,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220675,NC_045512.2,21764,ATACATG,A,PASS,16,16,16,1.0,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220675,NC_045512.2,21846,C,T,PASS,30,0,30,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220675,NC_045512.2,23403,A,G,PASS,214,0,214,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220675,NC_045512.2,23525,C,T,PASS,221,3,218,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220675,NC_045512.2,23599,T,G,PASS,105,0,105,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220675,NC_045512.2,23604,C,A,PASS,103,0,103,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220675,NC_045512.2,23948,G,T,PASS,25,0,25,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220675,NC_045512.2,24130,C,A,PASS,50,0,50,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220675,NC_045512.2,24424,A,T,PASS,24,0,24,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220675,NC_045512.2,24469,T,A,PASS,131,1,130,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220675,NC_045512.2,24503,C,T,PASS,140,7,133,0.95,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220675,NC_045512.2,25000,C,T,PASS,12,0,12,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220675,NC_045512.2,25057,T,C,ft,13,8,5,0.38,S,synonymous_variant,c.3495T>C,p.Asp1165Asp,p.D1165D,ivar,Unassigned +220675,NC_045512.2,25584,C,T,PASS,24,2,22,0.92,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220675,NC_045512.2,26270,C,T,PASS,221,0,221,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220675,NC_045512.2,26530,A,G,PASS,72,0,72,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220675,NC_045512.2,26577,C,G,PASS,67,0,67,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220675,NC_045512.2,26709,G,A,PASS,75,2,73,0.97,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220675,NC_045512.2,27259,A,C,PASS,48,0,48,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220675,NC_045512.2,28271,A,T,PASS,187,0,187,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220675,NC_045512.2,28311,C,T,PASS,213,2,211,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220675,NC_045512.2,28361,GGAGAACGCA,G,PASS,185,185,129,0.7,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220675,NC_045512.2,28881,GG,AA,PASS,12043,60,11972,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220675,NC_045512.2,28883,G,C,PASS,12008,2,11991,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220675,NC_045512.2,5672,C,T,PASS,40,2,38,0.95,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220675,NC_045512.2,8393,G,A,PASS,307,0,307,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220675,NC_045512.2,8652,T,C,PASS,198,0,198,1.0,orf1ab,missense_variant,c.8387T>C,p.Met2796Thr,p.M2796T,ivar,Unassigned +220677,NC_045512.2,10449,C,A,PASS,19,0,19,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220677,NC_045512.2,10947,G,A,ft,10,7,3,0.3,orf1ab,missense_variant,c.10682G>A,p.Arg3561Lys,p.R3561K,ivar,Unassigned +220677,NC_045512.2,11282,AGTTTGTCTG,A,PASS,27,27,25,0.93,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220677,NC_045512.2,11537,A,G,PASS,43,0,43,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220677,NC_045512.2,12053,C,T,PASS,154,0,154,1.0,orf1ab,missense_variant,c.11788C>T,p.Leu3930Phe,p.L3930F,ivar,Unassigned +220677,NC_045512.2,13195,T,C,PASS,2302,4,2298,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220677,NC_045512.2,14408,C,T,PASS,27,0,27,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220677,NC_045512.2,21762,C,T,PASS,44,0,44,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220677,NC_045512.2,21764,ATACATG,A,PASS,44,44,39,0.89,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220677,NC_045512.2,21846,C,T,PASS,43,0,43,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220677,NC_045512.2,23403,A,G,PASS,1670,8,1662,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220677,NC_045512.2,23525,C,T,PASS,1615,3,1609,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220677,NC_045512.2,23599,T,G,PASS,575,0,575,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220677,NC_045512.2,23604,C,A,PASS,558,0,551,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220677,NC_045512.2,23948,G,T,PASS,147,0,147,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220677,NC_045512.2,24130,C,A,PASS,220,0,218,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220677,NC_045512.2,24424,A,T,PASS,24,0,24,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220677,NC_045512.2,24469,T,A,PASS,305,0,302,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220677,NC_045512.2,24503,C,T,PASS,348,7,341,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220677,NC_045512.2,25000,C,T,PASS,16,0,16,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220677,NC_045512.2,25032,A,G,ft,15,11,4,0.27,S,missense_variant,c.3470A>G,p.Lys1157Arg,p.K1157R,ivar,Unassigned +220677,NC_045512.2,25584,C,T,PASS,26,0,26,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220677,NC_045512.2,26270,C,T,PASS,328,2,326,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220677,NC_045512.2,26530,A,G,PASS,216,0,216,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220677,NC_045512.2,26577,C,G,PASS,231,0,230,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220677,NC_045512.2,26612,A,G,PASS,182,0,182,1.0,M,synonymous_variant,c.90A>G,p.Thr30Thr,p.T30T,ivar,Unassigned +220677,NC_045512.2,26709,G,A,PASS,223,0,223,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220677,NC_045512.2,27259,A,C,PASS,134,0,134,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220677,NC_045512.2,27670,G,T,PASS,60,0,60,1.0,ORF7a,missense_variant,c.277G>T,p.Val93Phe,p.V93F,ivar,Unassigned +220677,NC_045512.2,27807,C,T,PASS,87,0,87,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220677,NC_045512.2,28271,A,T,PASS,979,3,974,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220677,NC_045512.2,28311,C,T,PASS,971,0,967,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220677,NC_045512.2,2832,A,G,PASS,10,0,10,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220677,NC_045512.2,28361,GGAGAACGCA,G,PASS,710,708,439,0.62,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220677,NC_045512.2,28512,C,T,PASS,190,135,50,0.26,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,Unassigned +220677,NC_045512.2,28881,GG,AA,PASS,6996,77,6913,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220677,NC_045512.2,28883,G,C,PASS,6957,1,6945,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220677,NC_045512.2,3037,C,T,PASS,21,0,21,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220677,NC_045512.2,5672,C,T,PASS,18,0,18,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220677,NC_045512.2,5924,G,A,PASS,13,0,13,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220677,NC_045512.2,8393,G,A,PASS,2925,8,2915,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220678,NC_045512.2,10449,C,A,PASS,42,0,42,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1.1 +220678,NC_045512.2,11282,AGTTTGTCTG,A,PASS,99,99,86,0.87,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1.1 +220678,NC_045512.2,11537,A,G,PASS,164,0,164,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1.1 +220678,NC_045512.2,13195,T,C,PASS,5198,9,5188,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1.1 +220678,NC_045512.2,14408,C,T,PASS,150,0,150,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1.1 +220678,NC_045512.2,16064,A,G,PASS,125,0,125,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,BA.1.1.1 +220678,NC_045512.2,21762,C,T,PASS,162,0,162,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1.1 +220678,NC_045512.2,21764,ATACATG,A,PASS,164,160,140,0.85,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1.1 +220678,NC_045512.2,21846,C,T,PASS,187,0,187,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1.1 +220678,NC_045512.2,22578,G,A,PASS,14,0,14,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.1.1 +220678,NC_045512.2,22599,G,A,PASS,16,0,16,1.0,S,missense_variant,c.1037G>A,p.Arg346Lys,p.R346K,ivar,BA.1.1.1 +220678,NC_045512.2,22673,TC,CT,PASS,14,0,14,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.1.1 +220678,NC_045512.2,22679,T,C,PASS,16,0,16,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.1.1 +220678,NC_045512.2,22686,C,T,PASS,15,0,15,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.1.1 +220678,NC_045512.2,23202,C,A,PASS,21,0,21,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.1.1 +220678,NC_045512.2,23403,A,G,PASS,2029,0,2029,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1.1 +220678,NC_045512.2,23525,C,T,PASS,1991,10,1981,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1.1 +220678,NC_045512.2,23599,T,G,PASS,763,2,761,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1.1 +220678,NC_045512.2,23604,C,A,PASS,732,0,724,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1.1 +220678,NC_045512.2,23854,C,A,PASS,21,0,21,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1.1 +220678,NC_045512.2,23948,G,T,PASS,280,0,278,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1.1 +220678,NC_045512.2,24130,C,A,PASS,345,0,343,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1.1 +220678,NC_045512.2,24424,A,T,PASS,95,0,95,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1.1 +220678,NC_045512.2,24469,T,A,PASS,708,0,708,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1.1 +220678,NC_045512.2,24503,C,T,PASS,855,8,845,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1.1 +220678,NC_045512.2,25000,C,T,PASS,37,0,37,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1.1 +220678,NC_045512.2,25584,C,T,PASS,45,0,45,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1.1 +220678,NC_045512.2,26270,C,T,PASS,305,0,305,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1.1 +220678,NC_045512.2,26530,A,G,PASS,272,0,272,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1.1 +220678,NC_045512.2,26577,C,G,PASS,290,0,290,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1.1 +220678,NC_045512.2,26709,G,A,PASS,255,4,251,0.98,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1.1 +220678,NC_045512.2,27259,A,C,PASS,129,0,129,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1.1 +220678,NC_045512.2,27807,C,T,PASS,51,0,51,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1.1 +220678,NC_045512.2,28271,A,T,PASS,1166,5,1159,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1.1 +220678,NC_045512.2,28311,C,T,PASS,1184,7,1171,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1.1 +220678,NC_045512.2,2832,A,G,PASS,89,0,89,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1.1 +220678,NC_045512.2,28361,GGAGAACGCA,G,PASS,910,906,488,0.54,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1.1 +220678,NC_045512.2,28881,GG,AA,PASS,5630,77,5551,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1.1 +220678,NC_045512.2,28883,G,C,PASS,5585,3,5569,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1.1 +220678,NC_045512.2,3037,C,T,PASS,18,0,18,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1.1 +220678,NC_045512.2,8014,T,C,PASS,492,17,475,0.97,orf1ab,synonymous_variant,c.7749T>C,p.Ser2583Ser,p.S2583S,ivar,BA.1.1.1 +220678,NC_045512.2,8393,G,A,PASS,2422,5,2413,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1.1 +220679,NC_045512.2,10449,C,A,PASS,14,0,14,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220679,NC_045512.2,11282,AGTTTGTCTG,A,PASS,72,69,59,0.82,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220679,NC_045512.2,11537,A,G,PASS,42,0,42,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220679,NC_045512.2,13195,T,C,PASS,2959,4,2953,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220679,NC_045512.2,14408,C,T,PASS,35,0,35,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220679,NC_045512.2,19374,C,T,PASS,103,0,103,1.0,orf1ab,missense_variant,c.19109C>T,p.Ser6370Phe,p.S6370F,ivar,Unassigned +220679,NC_045512.2,20743,A,C,PASS,1266,0,1263,1.0,orf1ab,missense_variant,c.20478A>C,p.Lys6826Asn,p.K6826N,ivar,Unassigned +220679,NC_045512.2,21274,T,C,PASS,28,0,28,1.0,orf1ab,synonymous_variant,c.21009T>C,p.Phe7003Phe,p.F7003F,ivar,Unassigned +220679,NC_045512.2,21762,C,T,PASS,72,0,72,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220679,NC_045512.2,21764,ATACATG,A,PASS,72,72,63,0.88,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220679,NC_045512.2,21846,C,T,PASS,74,0,74,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220679,NC_045512.2,21,C,T,PASS,10,0,10,1.0,orf1ab,upstream_gene_variant,c.-245C>T,.,.,ivar,Unassigned +220679,NC_045512.2,23403,A,G,PASS,1977,2,1975,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220679,NC_045512.2,23525,C,T,PASS,1792,2,1789,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220679,NC_045512.2,23599,T,G,PASS,744,0,744,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220679,NC_045512.2,23604,C,A,PASS,722,0,719,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220679,NC_045512.2,23854,C,A,PASS,19,0,19,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220679,NC_045512.2,23948,G,T,PASS,98,0,96,0.98,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220679,NC_045512.2,24130,C,A,PASS,142,0,141,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220679,NC_045512.2,24424,A,T,PASS,60,0,60,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220679,NC_045512.2,24469,T,A,PASS,275,0,275,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220679,NC_045512.2,24503,C,T,PASS,350,4,346,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220679,NC_045512.2,25000,C,T,PASS,26,0,26,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220679,NC_045512.2,25584,C,T,PASS,71,0,71,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220679,NC_045512.2,2610,C,A,ft,14,10,4,0.29,orf1ab,missense_variant,c.2345C>A,p.Pro782Gln,p.P782Q,ivar,Unassigned +220679,NC_045512.2,26270,C,T,PASS,438,1,437,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220679,NC_045512.2,26530,A,G,PASS,320,0,320,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220679,NC_045512.2,26577,C,G,PASS,362,0,362,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220679,NC_045512.2,26709,G,A,PASS,358,0,358,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220679,NC_045512.2,27259,A,C,PASS,167,0,167,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220679,NC_045512.2,27807,C,T,PASS,55,0,55,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220679,NC_045512.2,28271,A,T,PASS,559,2,557,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220679,NC_045512.2,28311,C,T,PASS,631,3,626,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220679,NC_045512.2,2832,A,G,PASS,20,0,20,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220679,NC_045512.2,28361,GGAGAACGCA,G,PASS,514,508,361,0.7,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220679,NC_045512.2,28881,GG,AA,PASS,4183,51,4127,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220679,NC_045512.2,28883,G,C,PASS,4145,1,4137,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220679,NC_045512.2,3037,C,T,PASS,18,0,18,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220679,NC_045512.2,5672,C,T,PASS,40,0,40,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220679,NC_045512.2,5924,G,A,PASS,17,0,17,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220679,NC_045512.2,76,T,A,PASS,26,16,8,0.31,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220679,NC_045512.2,78,T,G,PASS,26,18,8,0.31,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220679,NC_045512.2,8393,G,A,PASS,2826,4,2818,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220680,NC_045512.2,11537,A,G,PASS,19,0,19,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220680,NC_045512.2,12368,A,G,ft,17,12,5,0.29,orf1ab,missense_variant,c.12103A>G,p.Thr4035Ala,p.T4035A,ivar,Unassigned +220680,NC_045512.2,12749,G,T,PASS,36,21,15,0.42,orf1ab,missense_variant,c.12484G>T,p.Ala4162Ser,p.A4162S,ivar,Unassigned +220680,NC_045512.2,13195,T,C,PASS,665,2,663,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220680,NC_045512.2,21762,C,T,PASS,14,0,14,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220680,NC_045512.2,21764,ATACATG,A,ft,14,14,8,0.57,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220680,NC_045512.2,21846,C,T,PASS,18,0,18,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220680,NC_045512.2,23403,A,G,PASS,246,0,246,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220680,NC_045512.2,23525,C,T,PASS,216,0,216,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220680,NC_045512.2,23599,T,G,PASS,95,0,95,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220680,NC_045512.2,23604,C,A,PASS,90,0,90,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220680,NC_045512.2,23948,G,T,PASS,13,0,13,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220680,NC_045512.2,24130,C,A,PASS,22,2,20,0.91,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220680,NC_045512.2,24469,T,A,PASS,67,0,65,0.97,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220680,NC_045512.2,24503,C,T,PASS,76,0,76,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220680,NC_045512.2,26270,C,T,PASS,259,0,259,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220680,NC_045512.2,26530,A,G,PASS,39,0,39,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220680,NC_045512.2,26577,C,G,PASS,46,0,46,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220680,NC_045512.2,26709,G,A,PASS,38,0,38,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220680,NC_045512.2,27259,A,C,PASS,33,0,33,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220680,NC_045512.2,28253,CA,C,PASS,575,575,572,0.99,ORF8,frameshift_variant,c.361delA,p.Ile121fs,p.I121fs,ivar,Unassigned +220680,NC_045512.2,28271,A,T,PASS,728,2,724,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220680,NC_045512.2,28311,C,T,PASS,721,2,713,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220680,NC_045512.2,28361,GGAGAACGCA,G,PASS,501,498,352,0.7,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220680,NC_045512.2,28881,GG,AA,PASS,4386,36,4344,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220680,NC_045512.2,28883,G,C,PASS,4380,2,4371,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220680,NC_045512.2,29399,G,T,PASS,2419,4,2405,0.99,N,missense_variant,c.1126G>T,p.Ala376Ser,p.A376S,ivar,Unassigned +220680,NC_045512.2,4221,A,G,ft,16,12,4,0.25,orf1ab,missense_variant,c.3956A>G,p.Lys1319Arg,p.K1319R,ivar,Unassigned +220680,NC_045512.2,8256,A,G,PASS,77,53,24,0.31,orf1ab,missense_variant,c.7991A>G,p.Glu2664Gly,p.E2664G,ivar,Unassigned +220680,NC_045512.2,8393,G,A,PASS,606,2,604,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220680,NC_045512.2,8652,T,C,PASS,427,1,426,1.0,orf1ab,missense_variant,c.8387T>C,p.Met2796Thr,p.M2796T,ivar,Unassigned +220684,NC_045512.2,10449,C,A,PASS,23,0,23,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220684,NC_045512.2,11282,AGTTTGTCTG,A,PASS,71,71,67,0.94,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220684,NC_045512.2,11537,A,G,PASS,25,0,25,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220684,NC_045512.2,13195,T,C,PASS,4647,1,4644,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220684,NC_045512.2,14408,C,T,PASS,61,3,58,0.95,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220684,NC_045512.2,16064,A,G,PASS,80,2,78,0.98,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220684,NC_045512.2,19937,A,G,ft,14,10,4,0.29,orf1ab,missense_variant,c.19672A>G,p.Thr6558Ala,p.T6558A,ivar,Unassigned +220684,NC_045512.2,21458,T,C,PASS,263,0,263,1.0,orf1ab,missense_variant,c.21193T>C,p.Ser7065Pro,p.S7065P,ivar,Unassigned +220684,NC_045512.2,21762,C,T,PASS,70,0,70,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220684,NC_045512.2,21764,ATACATG,A,PASS,70,69,63,0.9,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220684,NC_045512.2,21846,C,T,PASS,72,0,72,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220684,NC_045512.2,23403,A,G,PASS,1549,3,1546,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220684,NC_045512.2,23525,C,T,PASS,1462,0,1461,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220684,NC_045512.2,23599,T,G,PASS,609,0,609,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220684,NC_045512.2,23604,C,A,PASS,592,0,592,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220684,NC_045512.2,23854,C,A,PASS,23,0,23,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220684,NC_045512.2,23948,G,T,PASS,255,0,255,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220684,NC_045512.2,24130,C,A,PASS,379,0,379,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220684,NC_045512.2,24424,A,T,PASS,47,0,46,0.98,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220684,NC_045512.2,24469,T,A,PASS,463,0,460,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220684,NC_045512.2,24503,C,T,PASS,595,9,586,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220684,NC_045512.2,25000,C,T,PASS,14,0,14,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220684,NC_045512.2,25584,C,T,PASS,65,0,65,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220684,NC_045512.2,26270,C,T,PASS,205,0,205,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220684,NC_045512.2,26530,A,G,PASS,60,0,60,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220684,NC_045512.2,26577,C,G,PASS,68,0,68,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220684,NC_045512.2,26709,G,A,PASS,70,0,70,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220684,NC_045512.2,27259,A,C,PASS,120,0,119,0.99,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220684,NC_045512.2,27807,C,T,PASS,30,0,30,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220684,NC_045512.2,28271,A,T,PASS,400,0,399,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220684,NC_045512.2,28311,C,T,PASS,415,1,412,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220684,NC_045512.2,2832,A,G,PASS,133,0,133,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220684,NC_045512.2,28361,GGAGAACGCA,G,PASS,319,317,227,0.71,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220684,NC_045512.2,28881,GG,AA,PASS,5519,59,5456,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220684,NC_045512.2,28883,G,C,PASS,5487,2,5473,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220684,NC_045512.2,8393,G,A,PASS,2672,20,2646,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220685,NC_045512.2,10449,C,A,PASS,20,0,20,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1.1 +220685,NC_045512.2,11282,AGTTTGTCTG,A,PASS,110,109,100,0.91,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1.1 +220685,NC_045512.2,11537,A,G,PASS,62,0,62,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1.1 +220685,NC_045512.2,13195,T,C,PASS,3349,12,3337,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1.1 +220685,NC_045512.2,14408,C,T,PASS,64,0,64,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1.1 +220685,NC_045512.2,16064,A,G,PASS,72,2,70,0.97,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,BA.1.1.1 +220685,NC_045512.2,21762,C,T,PASS,47,0,47,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1.1 +220685,NC_045512.2,21764,ATACATG,A,PASS,47,47,43,0.91,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1.1 +220685,NC_045512.2,21846,C,T,PASS,42,0,42,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1.1 +220685,NC_045512.2,22578,G,A,PASS,12,0,12,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.1.1 +220685,NC_045512.2,22599,G,A,PASS,14,0,14,1.0,S,missense_variant,c.1037G>A,p.Arg346Lys,p.R346K,ivar,BA.1.1.1 +220685,NC_045512.2,22673,TC,CT,PASS,10,0,10,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.1.1 +220685,NC_045512.2,22679,T,C,PASS,14,0,14,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.1.1 +220685,NC_045512.2,22686,C,T,PASS,14,0,14,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.1.1 +220685,NC_045512.2,23403,A,G,PASS,1274,2,1272,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1.1 +220685,NC_045512.2,23525,C,T,PASS,1276,1,1275,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1.1 +220685,NC_045512.2,23599,T,G,PASS,519,0,519,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1.1 +220685,NC_045512.2,23604,C,A,PASS,510,0,508,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1.1 +220685,NC_045512.2,23854,C,A,PASS,29,0,29,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1.1 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+220685,NC_045512.2,28361,GGAGAACGCA,G,PASS,258,256,188,0.73,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1.1 +220685,NC_045512.2,28512,C,T,PASS,186,124,56,0.3,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,BA.1.1.1 +220685,NC_045512.2,28881,GG,AA,PASS,3917,51,3864,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1.1 +220685,NC_045512.2,28883,G,C,PASS,3900,4,3892,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1.1 +220685,NC_045512.2,3037,C,T,PASS,13,0,13,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1.1 +220685,NC_045512.2,4710,C,A,ft,12,7,5,0.42,orf1ab,missense_variant,c.4445C>A,p.Ala1482Asp,p.A1482D,ivar,BA.1.1.1 +220685,NC_045512.2,8393,G,A,PASS,2105,5,2100,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1.1 diff --git a/relecov_tools/test/test_cases.txt b/relecov_tools/test/test_cases.txt index f6f2c56d..c7e14a0e 100644 --- a/relecov_tools/test/test_cases.txt +++ b/relecov_tools/test/test_cases.txt @@ -6,5 +6,5 @@ relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -d GISAID -o /tmp relecov-tools update-db -i http://iskylims.isciiides.es/wetlab/api -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json relecov-tools update-db -i http://localhost:8001/wetlab/api -r http://localhost:8000/api -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -u admin -p Apple@123 -relecov-tools read-bioinfo-metadata -m /data/UCCT_Relecov/COD-2100-MAD-CNM/20220208/lab_metadata_20220208.xlsx -i /data/UCCT_Relecov/COD-2100-MAD-CNM/20220208/ -o /data/UCCT_Relecov/COD-2100-MAD-CNM/20220208/ -relecov-tools upload-to-ena -u Webin-60330 -p W2b3nENA%2021 -e /home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/example_data/to_ena_2.json -o /home/erika.kvalem/Documents/Relecov/relecov-tools/relecov_tools/test -a add -c ISCIII +relecov-tools read-bioinfo-metadata -m relecov_tools/example_data/lab_metadata_20220208.xlsx -i /relecov_tools/example_data -o relecov_tools/example_data +relecov-tools upload-to-ena -u Webin-60330 -p W2b3nENA%2021 -e relecov_tools/example_data/to_ena_2.json -o relecov_tools/test -a add -c ISCIII From 050e90096f6db6e7866ee68927877bc46babf574 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 23 May 2022 12:10:23 +0200 Subject: [PATCH 0470/1454] added to test cases --- .../example_data/lab_metadata_20220208.xlsx | Bin 403681 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100755 relecov_tools/example_data/lab_metadata_20220208.xlsx diff --git a/relecov_tools/example_data/lab_metadata_20220208.xlsx b/relecov_tools/example_data/lab_metadata_20220208.xlsx deleted file mode 100755 index c14b3b92fdbbae225c5e168ca500ab1725dd8d33..0000000000000000000000000000000000000000 GIT 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z*QP6NFUFmpFlR`+CGp!Qscu{vpPiq3ZAV3AMOqU)djgXM2zC16(V2J{YlX&(Ig!2j-M-zMFdFT)^b05Obku~S9oBO`twe|3>+zRvA;?lk?vwhaIS@hYTuKjX* z|IV8iD!%$C{-u_SFL`VmTX4kN%OgAL{+td6Ke@WUtw+S&o=46MIl6UgVnuQ8&!aAd zC%hN`&Ze*bvh%RlTYDe08WlSrb4}3qSFd?pz467d%+xqL)t246I=D<2RP~B?-l~1~ zx313i{%cZ=Fvj0O>9p#z%dL(H!dK^&_`99Gqu?kgl}f>JM%G*JZ8cRF9IwrmrGR*x<2px}!mB4a{=BCIW4saKC}1qv=$?)2DF&F}eAk>|S9t@6J# zpnLI1S3&rqNPs%({<8!ef&Yl$>9d1oj*FbF3!7z?6Z806?~DT{iO_uUOlrZZ3M Date: Mon, 23 May 2022 12:43:23 +0200 Subject: [PATCH 0471/1454] added to testcases --- relecov_tools/test/test_cases.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/test/test_cases.txt b/relecov_tools/test/test_cases.txt index c7e14a0e..b13c4cf0 100644 --- a/relecov_tools/test/test_cases.txt +++ b/relecov_tools/test/test_cases.txt @@ -7,4 +7,4 @@ relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json relecov-tools update-db -i http://iskylims.isciiides.es/wetlab/api -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json relecov-tools update-db -i http://localhost:8001/wetlab/api -r http://localhost:8000/api -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -u admin -p Apple@123 relecov-tools read-bioinfo-metadata -m relecov_tools/example_data/lab_metadata_20220208.xlsx -i /relecov_tools/example_data -o relecov_tools/example_data -relecov-tools upload-to-ena -u Webin-60330 -p W2b3nENA%2021 -e relecov_tools/example_data/to_ena_2.json -o relecov_tools/test -a add -c ISCIII +relecov-tools upload-to-ena -u XXXXXXXX -p XXXXXXXXX -e relecov_tools/example_data/to_ena_2.json -o relecov_tools/test -a add -c ISCIII From 2c4be1febb0a8d248cc28435b0ed70b7d21dee41 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 23 May 2022 23:20:29 +0200 Subject: [PATCH 0472/1454] fixing mergin conflict in schema --- relecov_tools/schema/relecov_schema.json | 18 ------------------ setup.py | 2 +- 2 files changed, 1 insertion(+), 19 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 61598073..8332a00a 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1496,8 +1496,6 @@ "label": "Ns per 100 kbp", "fill_mode": "batch" }, -<<<<<<< HEAD -======= "reference_genome_accession": { "examples": [ "NC_045512.2" @@ -1509,7 +1507,6 @@ "label": "Reference genome accession", "fill_mode": "batch" }, ->>>>>>> 9d13b1cfaeb342bdc1b234b294fa7835845035ab "bioinformatics_protocol_software_name": { "examples": [ "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" @@ -1565,21 +1562,6 @@ "label": "Preprocessing", "fill_mode": "batch" }, -<<<<<<< HEAD - "preprocessing_software_version": { -======= - "preprocessing_software_name": { ->>>>>>> 9d13b1cfaeb342bdc1b234b294fa7835845035ab - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "Preprocessing Version", - "fill_mode": "batch" - }, "preprocessing_software_version": { "examples": [ "" diff --git a/setup.py b/setup.py index 5f081b36..8636af99 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import setup, find_packages -version = "0.0.2" +version = "0.0.3" with open("README.md") as f: readme = f.read() From 5cd3b06b064542eaa6cf60dc7008d16b80f81db8 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 25 May 2022 11:21:40 +0200 Subject: [PATCH 0473/1454] latest changes in counter --- relecov_tools/conf/configuration.json | 29 +++++++++++++------------- relecov_tools/read_bioinfo_metadata.py | 12 +++++------ 2 files changed, 21 insertions(+), 20 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 54e6b5d8..51641900 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -42,7 +42,7 @@ "relecov": { "server": "http://relecov-platform.isciiides.es", "url": "/api/", - "store_samples": "createSample", + "store_samples": "storeData", "token": "" } }, @@ -68,15 +68,15 @@ "sequencing_date" ], "relecov_bioinfo_metadata": { - "dehosting_method_software_name": "kraken2", + "dehosting_method_software_name": "KRAKEN2_KRAKEN2", "dehosting_method_software_version": "2.1.2", "assembly": "None", "if_assembly_other": "None", "assembly_params": "None", - "variant_calling_software_name": "ivar_variants", + "variant_calling_software_name": "IVAR_VARIANTS", "variant_calling_software_version": "1.3.1", "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", - "consensus_sequence_software_name": "bcftools_consensus", + "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "consensus_sequence_software_version": "1.14", "if_consensur_other": "None", "consensus_params": "-p vcf -f", @@ -85,11 +85,11 @@ "bioinformatics_protocol_software_version": "2.4.1", "if_bioinformatic_protocol_is_other_specify": "None", "commercial_open_source_both": "open-source", - "preprocessing_software_name": "fastp", + "preprocessing_software_name": "FASTP", "preprocessing_software_version": "0.23.2", "if_preprocessing_other": "None", "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", - "mapping_software_name": "bowtie2", + "mapping_software_name": "BOWTIE2_ALIGN", "mapping_software_version": "2.4.4", "if_mapping_other": "None", "mapping_params": "--seed 1", @@ -109,16 +109,17 @@ "number_of_variants_AF_greater_75percent": "Variantsinconsensusx10", "number_of_variants_with_effect": "MissenseVariants" }, - "files_read_bioinfo_metadata": [ - "mapping_illumina.tab", - "summary_variants_metrics_mqc.csv", - "variants_long_table.csv", - "consensus_genome_length.csv", - "software_versions.yml" - ], + "files_read_bioinfo_metadata": { + "mapping_illumina.tab": "mapping_illumina_tab_path", + "summary_variants_metrics_mqc.csv": "summary_variants_metrics_path ", + "variants_long_table.csv": "variants_long_table_path", + "consensus_genome_length.csv": "consensus_genome_length_path", + "software_versions.yml": "software_versions_path" + }, "tool": { "tool_name": "ena-upload-cli", "tool_version": "0.5.3" }, + "md5_file_name": "md5sum_MiSeq_GEN_267_20220208_ICasas_removed_samples.md5", "checklist": "ERC000033" -} +} \ No newline at end of file diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 104eb507..ab856402 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -86,9 +86,10 @@ def bioinfo_parse(self, file_name): software_versions_path = os.path.join( self.input_folder, "software_versions.yml" ) + self.md5_file_name = config_json.get_configuration("md5_file_name") md5_info_path = os.path.join( self.input_folder, - "md5sum_MiSeq_GEN_267_20220208_ICasas.md5", # como hacer esto general para los servicios + self.md5_file_name, # como hacer esto general para los servicios ) mapping_illumina_tab = pd.read_csv(mapping_illumina_tab_path, sep="\t") @@ -123,10 +124,13 @@ def bioinfo_parse(self, file_name): bioinfo_dict["consensus_sequence_filepath"] = self.input_folder bioinfo_dict["long_table_path"] = self.input_folder # fields from mapping_illumina.tab + for key in self.mapping_illumina_tab_field_list.keys(): + bioinfo_dict[key] = str( mapping_illumina_tab[self.mapping_illumina_tab_field_list[key]][c] ) + # fields from summary_variants_metrics_mqc.csv bioinfo_dict["number_of_base_pairs_sequenced"] = str( (summary_variants_metrics["# Input reads"][c] * 2) @@ -176,15 +180,11 @@ def bioinfo_parse(self, file_name): ) bioinfo_list[str(sample_name)] = bioinfo_dict - c = +1 + c = c + 1 json_file = "bioinfo_metadata.json" output_path = os.path.join(self.output_folder, json_file) - import pdb - - pdb.set_trace() - with open(output_path, "w", encoding="utf-8") as fh: fh.write( json.dumps(bioinfo_list, indent=4, sort_keys=True, ensure_ascii=False) From cdcc47cb583b5da343750e65a1135fba8963cd2e Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 26 May 2022 10:37:16 +0200 Subject: [PATCH 0474/1454] latest changes --- relecov_tools/conf/configuration.json | 2 +- relecov_tools/schema/relecov_schema.json | 22 ++-------------------- 2 files changed, 3 insertions(+), 21 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 51641900..cc37ab32 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -6,7 +6,7 @@ }, "sftp_connection": { "sftp_server": "sftprelecov.isciii.es", - "sftp_port": "50122" + "sftp_port": "22" }, "abort_if_md5_mismatch": "False", "storage_local_folder": "/tmp/relecov", diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 61598073..d8a421ef 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1496,8 +1496,6 @@ "label": "Ns per 100 kbp", "fill_mode": "batch" }, -<<<<<<< HEAD -======= "reference_genome_accession": { "examples": [ "NC_045512.2" @@ -1509,7 +1507,6 @@ "label": "Reference genome accession", "fill_mode": "batch" }, ->>>>>>> 9d13b1cfaeb342bdc1b234b294fa7835845035ab "bioinformatics_protocol_software_name": { "examples": [ "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" @@ -1565,21 +1562,6 @@ "label": "Preprocessing", "fill_mode": "batch" }, -<<<<<<< HEAD - "preprocessing_software_version": { -======= - "preprocessing_software_name": { ->>>>>>> 9d13b1cfaeb342bdc1b234b294fa7835845035ab - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics", - "label": "Preprocessing Version", - "fill_mode": "batch" - }, "preprocessing_software_version": { "examples": [ "" @@ -2027,7 +2009,7 @@ "type": "string", "description": "The common name of the organism.", "classification": "Sample collection and processing", - "label":"Common name", + "label": "Common name", "fill_mode": "batch" }, "collector_name": { @@ -2511,4 +2493,4 @@ "fill_mode": "batch" } } -} +} \ No newline at end of file From c6b90400124dc9d5d48c6a864435d4ef7ab421f3 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 26 May 2022 23:12:35 +0200 Subject: [PATCH 0475/1454] missing Classification to purpose_sampling property --- relecov_tools/schema/relecov_schema.json | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 8332a00a..040294af 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -964,6 +964,7 @@ "examples": [ "Diagnostic Testing [GENEPIO:0100002]" ], + "classification": "Sample collection and processing", "label": "Purpose of sampling", "fill_mode": "batch" }, From 1d895d39ebd040570f274c3bb313fe531f0b88ee Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 27 May 2022 11:18:53 +0200 Subject: [PATCH 0476/1454] trying the modules --- relecov_tools/conf/geo_loc_cities.json | 7 ++++++- relecov_tools/conf/laboratory_address.json | 10 +++++++++- relecov_tools/read_lab_metadata.py | 1 + relecov_tools/schema/relecov_schema.json | 10 +++++----- 4 files changed, 21 insertions(+), 7 deletions(-) diff --git a/relecov_tools/conf/geo_loc_cities.json b/relecov_tools/conf/geo_loc_cities.json index dbd0fc2e..873f9406 100644 --- a/relecov_tools/conf/geo_loc_cities.json +++ b/relecov_tools/conf/geo_loc_cities.json @@ -369,6 +369,11 @@ "geo_loc_latitude": "35.8867", "geo_loc_longitude": "-5.3000" }, + { + "geo_loc_city": "Ciudad de Melilla", + "geo_loc_latitude": "35.2919", + "geo_loc_longitude": "-2.93848" + }, { "geo_loc_city": "Torrente", "geo_loc_latitude": "39.4365", @@ -12214,4 +12219,4 @@ "geo_loc_latitude": "41.7667", "geo_loc_longitude": "-2.4667" } -] +] \ No newline at end of file diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 0b0f7045..b1bdecf5 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -190,6 +190,14 @@ "geo_loc_city": "Ceuta", "geo_loc_country": "Spain" }, + { + "collecting_institution": "Hospital Comarcal de Melilla", + "collecting_institution_address": "Remonta, 2", + "collecting_institution_email": "", + "geo_loc_state": "Melilla", + "geo_loc_city": "Melilla", + "geo_loc_country": "Spain" + }, { "collecting_institution": "Hospital de Mostoles", "collecting_institution_address": "C. Dr. Luis Montes, S/N ", @@ -214,4 +222,4 @@ "geo_loc_city": "Donostia", "geo_loc_country": "Spain" } -] +] \ No newline at end of file diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 47439689..7d5b48f6 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -94,6 +94,7 @@ def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): log.error("Found empti Originating Laboratory") return data for lab in lab_json: + if lab_name == lab["collecting_institution"]: for key, value in lab.items(): data[key] = value diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index d8a421ef..393a1817 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1646,7 +1646,7 @@ "ontology": "GENEPIO:0001500", "type": "string", "description": "The name of the lineage or clade.", - "classification": "Bioinformatics and QC metrics", + "classification": "Lineage fields", "label": "Lineage/clade name", "fill_mode": "batch" }, @@ -1657,7 +1657,7 @@ "ontology": "GENEPIO:0001501", "type": "string", "description": "The name of the software used to determine the lineage/clade.", - "classification": "Bioinformatics and QC metrics", + "classification": "Lineage fields", "label": "lineage/clade analysis software name", "fill_mode": "batch" }, @@ -1668,7 +1668,7 @@ "ontology": "0", "type": "string", "description": "The name of the software used to determine the lineage/clade.", - "classification": "Bioinformatics and QC metrics", + "classification": "Lineage fields", "label": "If lineage identification Is Other, Specify", "fill_mode": "batch" }, @@ -1679,7 +1679,7 @@ "ontology": "GENEPIO:0001502", "type": "string", "description": "The version of the software used to determine the lineage/clade.", - "classification": "Bioinformatics and QC metrics", + "classification": "Lineage fields", "label": "Lineage/clade analysis software version", "fill_mode": "batch" }, @@ -1942,7 +1942,7 @@ "type": "string", "format": "date", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Lineage fields", "label": "Lineage identification date", "fill_mode": "batch" }, From 6d8a8f7ca5fab3aaa4b676321b765dba21d06064 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 27 May 2022 13:52:32 +0200 Subject: [PATCH 0477/1454] minor changes --- relecov_tools/map_schema.py | 3 ++- relecov_tools/read_lab_metadata.py | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 3755ff4f..f96de788 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -153,6 +153,7 @@ def additional_formating(self, mapped_json_data): """ if self.destination_schema == "ENA": for idx in range(len(self.json_data)): + mapped_json_data[idx]["fastq_r1_md5"] = self.json_data[idx][ "fastq_r1_md5" ] @@ -190,7 +191,7 @@ def additional_formating(self, mapped_json_data): "collecting_lab_sample_id" ] mapped_json_data[idx]["study_type"] = self.json_data[idx][ - "purpose_of_sampling" + "purpose_sampling" ] mapped_json_data[idx]["study_abstract"] = self.json_data[idx][ "study_title" diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 7d5b48f6..b7af0a19 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -180,6 +180,7 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): for key, value in samples_json[ row_sample["collecting_lab_sample_id"] ].items(): + row_sample[key] = value except KeyError: pass From fd10f506b559e747f7dd5c8843a951b703b22853 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 27 May 2022 21:27:24 +0200 Subject: [PATCH 0478/1454] Fix the issue that when sample name starts with 0 this character was removed to convert to integer --- relecov_tools/conf/configuration.json | 2 +- relecov_tools/conf/laboratory_address.json | 8 ++++++++ relecov_tools/read_lab_metadata.py | 7 +++++-- relecov_tools/sftp_handle.py | 8 ++++---- 4 files changed, 18 insertions(+), 7 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index cc37ab32..ff6bb646 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -122,4 +122,4 @@ }, "md5_file_name": "md5sum_MiSeq_GEN_267_20220208_ICasas_removed_samples.md5", "checklist": "ERC000033" -} \ No newline at end of file +} diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 0b0f7045..07bc97bf 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -213,5 +213,13 @@ "geo_loc_state": "País Vasco", "geo_loc_city": "Donostia", "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Comarcal de Melilla", + "collecting_institution_address": "C. Remonta, 2", + "collecting_institution_email": "", + "geo_loc_state": "Melilla", + "geo_loc_city": "Melilla", + "geo_loc_country": "Spain" } ] diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 47439689..890e16d9 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -180,8 +180,11 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): row_sample["collecting_lab_sample_id"] ].items(): row_sample[key] = value - except KeyError: - pass + except KeyError as e: + stderr.print( + "[red] ERROR MD5 information not found in sample json. ", e + ) + """ Fetch the information related to the laboratory. Info is stored in lab_data, to prevent to call get_laboratory_data each time for each sample that belongs to the same lab diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index e3b8b90f..7fc902d6 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -240,7 +240,6 @@ def create_tmp_files_with_metadata_info( stderr.print("[red] Unable to copy Metadata file") return False data = copy.deepcopy(file_list) - for s_name, values in file_list.items(): for f_type, f_name in values.items(): if not f_name.endswith(tuple(self.allowed_sample_ext)): @@ -252,7 +251,6 @@ def create_tmp_files_with_metadata_info( data[s_name]["r2_fastq_filepath"] = md5_data[f_name][0] data[s_name]["fastq_r2_md5"] = md5_data[f_name][1] else: - # reserved for future develoment pass with open(sample_data_path, "w", encoding="utf-8") as fh: fh.write(json.dumps(data, indent=4, sort_keys=True, ensure_ascii=False)) @@ -298,11 +296,13 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): if row[2] is not None: try: - s_name = str(int(row[2])) - except ValueError: s_name = str(row[2]) + except ValueError as e: + stderr.print("[red] Unable to convert to string. ", e) if s_name not in sample_file_list: sample_file_list[s_name] = {} + else: + print("Found duplicated sample ", s_name) if row[index_fastq_r1] is not None: sample_file_list[s_name]["sequence_file_R1_fastq"] = row[ index_fastq_r1 From 8934254ddd51117bd380766d0e26dd78eba7c19c Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 30 May 2022 18:08:59 +0200 Subject: [PATCH 0479/1454] created long_table_parse module --- relecov_tools/__main__.py | 21 ++++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 664f8f7d..0371ed1c 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -16,6 +16,7 @@ import relecov_tools.map_schema import relecov_tools.feed_databases import relecov_tools.read_bioinfo_metadata +import relecov_tools.long_table_parse log = logging.getLogger() @@ -305,7 +306,7 @@ def update_db(user, password, json, schema, iskylims, relecov): # read metadata bioinformatics -@relecov_tools_cli.command(help_priority=3) +@relecov_tools_cli.command(help_priority=10) @click.option( "-m", "--metadata_file", @@ -328,5 +329,23 @@ def read_bioinfo_metadata(metadata_file, input_folder, metadata_out): new_bioinfo_metadata.bioinfo_parse(metadata_file) +# read metadata bioinformatics +@relecov_tools_cli.command(help_priority=11) +@click.option( + "-l", + "--longtable_file", + type=click.Path(), + help="file containing long table ", +) +@click.option( + "-o", "--output", type=click.Path(), help="Path to save json output") +def long_table_parse(longtable_file, output): + """Create Json file from long table """ + new_json_parse = relecov_tools.long_table_parse.LongTableParse( + longtable_file, output + ) + new_json_parse.parsing_csv() + + if __name__ == "__main__": run_relecov_tools() From 63a368038a19ee922d29be192a0e5857a0511044 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 30 May 2022 18:12:29 +0200 Subject: [PATCH 0480/1454] created long_table_parse module --- relecov_tools/__main__.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 0371ed1c..70600ac1 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -337,10 +337,9 @@ def read_bioinfo_metadata(metadata_file, input_folder, metadata_out): type=click.Path(), help="file containing long table ", ) -@click.option( - "-o", "--output", type=click.Path(), help="Path to save json output") +@click.option("-o", "--output", type=click.Path(), help="Path to save json output") def long_table_parse(longtable_file, output): - """Create Json file from long table """ + """Create Json file from long table""" new_json_parse = relecov_tools.long_table_parse.LongTableParse( longtable_file, output ) From 2eec5449935ae399265df0f2c24801ad0d495591 Mon Sep 17 00:00:00 2001 From: birbi Date: Tue, 31 May 2022 12:04:04 +0200 Subject: [PATCH 0481/1454] added long_table_parse.py --- relecov_tools/long_table_parse.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 relecov_tools/long_table_parse.py diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py new file mode 100644 index 00000000..e69de29b From 1b9153e7e6088c8d82891488e5518145291b1db4 Mon Sep 17 00:00:00 2001 From: birbi Date: Tue, 31 May 2022 13:19:26 +0200 Subject: [PATCH 0482/1454] added code to long_table_parse.py, saving files OK --- relecov_tools/long_table_parse.py | 63 +++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index e69de29b..e9c7bfed 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -0,0 +1,63 @@ +from datetime import datetime +import json +from relecov_tools.rest_api import RestApi + + +class LongTableParse: + def __init__(self, file_path, output_directory): + self.file_path = file_path + self.output_directory = output_directory + + def parsing_csv(self): + list_of_dictionaries = [] + + with open(self.file_path) as fh: + lines = fh.readlines() + + for line in lines[1:]: + data_dict_from_long_table = {} + data_list = line.strip().split(",") + + data_dict_from_long_table["Chromosome"] = {"chromosome": data_list[1]} + + data_dict_from_long_table["Position"] = { + "pos": data_list[2], + "nucleotide": data_list[4], + } + + data_dict_from_long_table["Filter"] = {"filter": data_list[5]} + + data_dict_from_long_table["VariantInSample"] = { + "dp": data_list[6], + "ref_dp": data_list[7], + "alt_dp": data_list[8], + "af": data_list[9], + } + + data_dict_from_long_table["Gene"] = {"gene": data_list[10]} + + data_dict_from_long_table["Effect"] = { + "effect": data_list[11], + "hgvs_c": data_list[12], + "hgvs_p": data_list[13], + "hgvs_p_1_letter": data_list[14], + } + + data_dict_from_long_table["Variant"] = {"ref": data_list[3]} + + data_dict_from_long_table["Sample"] = {"sample": data_list[0]} + + list_of_dictionaries.append(data_dict_from_long_table) + + generated_json = json.dumps(list_of_dictionaries) + + date_now = datetime.now() + + file_to_save = open( + self.output_directory + "long_table_JSON_" + str(date_now) + ".txt", "xt" + ) + file_to_save.write(generated_json) + + file_to_save.close() + + return generated_json From 917531a490e49aed46d5d80c18ae6c8c65a0aec1 Mon Sep 17 00:00:00 2001 From: birbi Date: Tue, 31 May 2022 13:24:48 +0200 Subject: [PATCH 0483/1454] added code to long_table_parse.py, saving files OK, flake OK --- relecov_tools/long_table_parse.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index e9c7bfed..241c7770 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -1,6 +1,7 @@ from datetime import datetime import json -from relecov_tools.rest_api import RestApi + +# from relecov_tools.rest_api import RestApi class LongTableParse: From c37de13e3213e445de6be195e1f105af53210ecd Mon Sep 17 00:00:00 2001 From: birbi Date: Tue, 31 May 2022 15:55:01 +0200 Subject: [PATCH 0484/1454] modified long_table_parse.py,functionality split in 2 function --- ..._table_JSON_2022-05-31 14:26:13.286679.txt | 0 ..._table_JSON_2022-05-31 14:27:49.199936.txt | 0 ..._table_JSON_2022-05-31 14:31:06.062731.txt | 0 ..._table_JSON_2022-05-31 14:33:09.319141.txt | 1 + ..._table_JSON_2022-05-31 14:35:11.067577.txt | 1 + ..._table_JSON_2022-05-31 14:52:03.933969.txt | 1 + relecov_tools/long_table_parse.py | 89 +++++++++++-------- 7 files changed, 53 insertions(+), 39 deletions(-) create mode 100644 long_table_JSON_2022-05-31 14:26:13.286679.txt create mode 100644 long_table_JSON_2022-05-31 14:27:49.199936.txt create mode 100644 long_table_JSON_2022-05-31 14:31:06.062731.txt create mode 100644 long_table_JSON_2022-05-31 14:33:09.319141.txt create mode 100644 long_table_JSON_2022-05-31 14:35:11.067577.txt create mode 100644 long_table_JSON_2022-05-31 14:52:03.933969.txt diff --git a/long_table_JSON_2022-05-31 14:26:13.286679.txt b/long_table_JSON_2022-05-31 14:26:13.286679.txt new file mode 100644 index 00000000..e69de29b diff --git a/long_table_JSON_2022-05-31 14:27:49.199936.txt b/long_table_JSON_2022-05-31 14:27:49.199936.txt new file mode 100644 index 00000000..e69de29b diff --git a/long_table_JSON_2022-05-31 14:31:06.062731.txt b/long_table_JSON_2022-05-31 14:31:06.062731.txt new file mode 100644 index 00000000..e69de29b diff --git a/long_table_JSON_2022-05-31 14:33:09.319141.txt b/long_table_JSON_2022-05-31 14:33:09.319141.txt new file mode 100644 index 00000000..7dbc6e36 --- /dev/null +++ b/long_table_JSON_2022-05-31 14:33:09.319141.txt @@ -0,0 +1 @@ +[{"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "11132", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "366", "ref_dp": "0", "alt_dp": "363", "af": "0.99"}, "Gene": {"gene": "orf1ab"}, "Effect": 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{"chromosome": "NC_045512.2"}, "Position": {"pos": "23604", "nucleotide": "A"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "510", "ref_dp": "0", "alt_dp": "508", "af": "1.0"}, "Gene": {"gene": "S"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.2042C>A", "hgvs_p": "p.Pro681His", "hgvs_p_1_letter": "p.P681H"}, "Variant": {"ref": "C"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "23854", "nucleotide": "A"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "29", "ref_dp": "0", "alt_dp": "29", "af": "1.0"}, "Gene": {"gene": "S"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.2292C>A", "hgvs_p": "p.Asn764Lys", "hgvs_p_1_letter": "p.N764K"}, "Variant": {"ref": "C"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "23948", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "169", "ref_dp": "0", "alt_dp": "169", "af": "1.0"}, "Gene": {"gene": "S"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.2386G>T", "hgvs_p": "p.Asp796Tyr", "hgvs_p_1_letter": "p.D796Y"}, "Variant": {"ref": "G"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "24130", "nucleotide": "A"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "171", "ref_dp": "0", "alt_dp": "171", "af": "1.0"}, "Gene": {"gene": "S"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.2568C>A", "hgvs_p": "p.Asn856Lys", "hgvs_p_1_letter": "p.N856K"}, "Variant": {"ref": "C"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "24424", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "101", "ref_dp": "3", "alt_dp": "98", "af": "0.97"}, "Gene": {"gene": "S"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.2862A>T", "hgvs_p": "p.Gln954His", "hgvs_p_1_letter": "p.Q954H"}, "Variant": {"ref": "A"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "24469", "nucleotide": "A"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "402", "ref_dp": "1", "alt_dp": "400", "af": "1.0"}, "Gene": {"gene": "S"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.2907T>A", "hgvs_p": "p.Asn969Lys", "hgvs_p_1_letter": "p.N969K"}, "Variant": {"ref": "T"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "24503", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "469", "ref_dp": "11", "alt_dp": "458", "af": "0.98"}, "Gene": {"gene": "S"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.2941C>T", "hgvs_p": "p.Leu981Phe", "hgvs_p_1_letter": "p.L981F"}, "Variant": {"ref": "C"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "25000", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "19", "ref_dp": "0", "alt_dp": "19", "af": "1.0"}, "Gene": {"gene": "S"}, "Effect": {"effect": "synonymous_variant", "hgvs_c": "c.3438C>T", "hgvs_p": "p.Asp1146Asp", "hgvs_p_1_letter": "p.D1146D"}, "Variant": {"ref": "C"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "25584", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "50", "ref_dp": "0", "alt_dp": "50", "af": "1.0"}, "Gene": {"gene": "ORF3a"}, "Effect": {"effect": "synonymous_variant", "hgvs_c": "c.192C>T", "hgvs_p": "p.Thr64Thr", "hgvs_p_1_letter": "p.T64T"}, "Variant": {"ref": "C"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "26270", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "114", "ref_dp": "0", "alt_dp": "114", "af": "1.0"}, "Gene": {"gene": "E"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.26C>T", "hgvs_p": "p.Thr9Ile", "hgvs_p_1_letter": "p.T9I"}, "Variant": {"ref": "C"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "26530", "nucleotide": "G"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "48", "ref_dp": "0", "alt_dp": "48", "af": "1.0"}, "Gene": {"gene": "M"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.8A>G", "hgvs_p": "p.Asp3Gly", "hgvs_p_1_letter": "p.D3G"}, "Variant": {"ref": "A"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "26577", "nucleotide": "G"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "36", "ref_dp": "0", "alt_dp": "36", "af": "1.0"}, "Gene": {"gene": "M"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.55C>G", "hgvs_p": "p.Gln19Glu", "hgvs_p_1_letter": "p.Q19E"}, "Variant": {"ref": "C"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "26709", "nucleotide": "A"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "37", "ref_dp": "0", "alt_dp": "37", "af": "1.0"}, "Gene": {"gene": "M"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.187G>A", "hgvs_p": "p.Ala63Thr", "hgvs_p_1_letter": "p.A63T"}, "Variant": {"ref": "G"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "27259", "nucleotide": "C"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "82", "ref_dp": "0", "alt_dp": "82", "af": "1.0"}, "Gene": {"gene": "ORF6"}, "Effect": {"effect": "synonymous_variant", "hgvs_c": "c.58A>C", "hgvs_p": "p.Arg20Arg", "hgvs_p_1_letter": "p.R20R"}, "Variant": {"ref": "A"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "27807", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "23", "ref_dp": "0", "alt_dp": "23", "af": "1.0"}, "Gene": {"gene": "ORF7b"}, "Effect": {"effect": "synonymous_variant", "hgvs_c": "c.52C>T", "hgvs_p": "p.Leu18Leu", "hgvs_p_1_letter": "p.L18L"}, "Variant": {"ref": "C"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "28271", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "315", "ref_dp": "0", "alt_dp": "313", "af": "0.99"}, "Gene": {"gene": "N"}, "Effect": {"effect": "upstream_gene_variant", "hgvs_c": "c.-3A>T", "hgvs_p": ".", "hgvs_p_1_letter": "."}, "Variant": {"ref": "A"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "28311", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "318", "ref_dp": "8", "alt_dp": "308", "af": "0.97"}, "Gene": {"gene": "N"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.38C>T", "hgvs_p": "p.Pro13Leu", "hgvs_p_1_letter": "p.P13L"}, "Variant": {"ref": "C"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "2832", "nucleotide": "G"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "19", "ref_dp": "0", "alt_dp": "19", "af": "1.0"}, "Gene": {"gene": "orf1ab"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.2567A>G", "hgvs_p": "p.Lys856Arg", "hgvs_p_1_letter": "p.K856R"}, "Variant": {"ref": "A"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "28333", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "307", "ref_dp": "4", "alt_dp": "303", "af": "0.99"}, "Gene": {"gene": "N"}, "Effect": {"effect": "synonymous_variant", "hgvs_c": "c.60C>T", "hgvs_p": "p.Pro20Pro", "hgvs_p_1_letter": "p.P20P"}, "Variant": {"ref": "C"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "28361", "nucleotide": "G"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "258", "ref_dp": "256", "alt_dp": "188", "af": "0.73"}, "Gene": {"gene": "N"}, "Effect": {"effect": "disruptive_inframe_deletion", "hgvs_c": "c.90_98delAGAACGCAG", "hgvs_p": "p.Glu31_Ser33del", "hgvs_p_1_letter": "p.E31_S33del"}, "Variant": {"ref": "GGAGAACGCA"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "28512", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "186", "ref_dp": "124", "alt_dp": "56", "af": "0.3"}, "Gene": {"gene": "N"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.239C>T", "hgvs_p": "p.Pro80Leu", "hgvs_p_1_letter": "p.P80L"}, "Variant": {"ref": "C"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "28881", "nucleotide": "AA"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "3917", "ref_dp": "51", "alt_dp": "3864", "af": "0.99"}, "Gene": {"gene": "N"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.608_609delGGinsAA", "hgvs_p": "p.Arg203Lys", "hgvs_p_1_letter": "p.R203K"}, "Variant": {"ref": "GG"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "28883", "nucleotide": "C"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "3900", "ref_dp": "4", "alt_dp": "3892", "af": "1.0"}, "Gene": {"gene": "N"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.610G>C", "hgvs_p": "p.Gly204Arg", "hgvs_p_1_letter": "p.G204R"}, "Variant": {"ref": "G"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "3037", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "13", "ref_dp": "0", "alt_dp": "13", "af": "1.0"}, "Gene": {"gene": "orf1ab"}, "Effect": {"effect": "synonymous_variant", "hgvs_c": "c.2772C>T", "hgvs_p": "p.Phe924Phe", "hgvs_p_1_letter": "p.F924F"}, "Variant": {"ref": "C"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "4710", "nucleotide": "A"}, "Filter": {"filter": "ft"}, "VariantInSample": {"dp": "12", "ref_dp": "7", "alt_dp": "5", "af": "0.42"}, "Gene": {"gene": "orf1ab"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.4445C>A", "hgvs_p": "p.Ala1482Asp", "hgvs_p_1_letter": "p.A1482D"}, "Variant": {"ref": "C"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "8393", "nucleotide": "A"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "2105", "ref_dp": "5", "alt_dp": "2100", "af": "1.0"}, "Gene": {"gene": "orf1ab"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.8128G>A", "hgvs_p": "p.Ala2710Thr", "hgvs_p_1_letter": "p.A2710T"}, "Variant": {"ref": "G"}, "Sample": {"sample": "220685"}}] \ No newline at end of file diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index 241c7770..34ad8034 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -1,5 +1,7 @@ +from asyncore import write from datetime import datetime import json +import os.path # from relecov_tools.rest_api import RestApi @@ -9,56 +11,65 @@ def __init__(self, file_path, output_directory): self.file_path = file_path self.output_directory = output_directory - def parsing_csv(self): - list_of_dictionaries = [] - - with open(self.file_path) as fh: - lines = fh.readlines() + def saving_file(self, generated_JSON, output_dir): + if os.path.exists(output_dir): + date_now = datetime.now() + file_name = "long_table_JSON_" + str(date_now) + ".txt" + os.path.join(output_dir, file_name) - for line in lines[1:]: - data_dict_from_long_table = {} - data_list = line.strip().split(",") + with open(file_name, "xt") as file: + file.write(generated_JSON) + else: + print("Sorry the directory we're looking for... doesn't exist") + exit() - data_dict_from_long_table["Chromosome"] = {"chromosome": data_list[1]} - - data_dict_from_long_table["Position"] = { - "pos": data_list[2], - "nucleotide": data_list[4], - } + def parsing_csv(self): + list_of_dictionaries = [] + try: + with open(self.file_path) as fh: + lines = fh.readlines() - data_dict_from_long_table["Filter"] = {"filter": data_list[5]} + for line in lines[1:]: + data_dict_from_long_table = {} + data_list = line.strip().split(",") - data_dict_from_long_table["VariantInSample"] = { - "dp": data_list[6], - "ref_dp": data_list[7], - "alt_dp": data_list[8], - "af": data_list[9], - } + data_dict_from_long_table["Chromosome"] = {"chromosome": data_list[1]} - data_dict_from_long_table["Gene"] = {"gene": data_list[10]} + data_dict_from_long_table["Position"] = { + "pos": data_list[2], + "nucleotide": data_list[4], + } - data_dict_from_long_table["Effect"] = { - "effect": data_list[11], - "hgvs_c": data_list[12], - "hgvs_p": data_list[13], - "hgvs_p_1_letter": data_list[14], - } + data_dict_from_long_table["Filter"] = {"filter": data_list[5]} - data_dict_from_long_table["Variant"] = {"ref": data_list[3]} + data_dict_from_long_table["VariantInSample"] = { + "dp": data_list[6], + "ref_dp": data_list[7], + "alt_dp": data_list[8], + "af": data_list[9], + } - data_dict_from_long_table["Sample"] = {"sample": data_list[0]} + data_dict_from_long_table["Gene"] = {"gene": data_list[10]} - list_of_dictionaries.append(data_dict_from_long_table) + data_dict_from_long_table["Effect"] = { + "effect": data_list[11], + "hgvs_c": data_list[12], + "hgvs_p": data_list[13], + "hgvs_p_1_letter": data_list[14], + } - generated_json = json.dumps(list_of_dictionaries) + data_dict_from_long_table["Variant"] = {"ref": data_list[3]} - date_now = datetime.now() + data_dict_from_long_table["Sample"] = {"sample": data_list[0]} - file_to_save = open( - self.output_directory + "long_table_JSON_" + str(date_now) + ".txt", "xt" - ) - file_to_save.write(generated_json) + list_of_dictionaries.append(data_dict_from_long_table) - file_to_save.close() + generated_json = json.dumps(list_of_dictionaries) - return generated_json + self.saving_file( + generated_JSON=generated_json, output_dir=self.output_directory + ) + except FileNotFoundError: + print("Sorry the file we're looking for... doesn't exist") + exit() + # return generated_json From 0ab67f46537968471d1d32e1aeca26f9c660a161 Mon Sep 17 00:00:00 2001 From: birbi Date: Tue, 31 May 2022 15:57:03 +0200 Subject: [PATCH 0485/1454] modified long_table_parse.py,functionality split in 2 function, flakeOK --- relecov_tools/long_table_parse.py | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index 34ad8034..87acf9f0 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -1,4 +1,3 @@ -from asyncore import write from datetime import datetime import json import os.path From f80f589bed808bbb01ce9b49f6b04f7dc0e85ca6 Mon Sep 17 00:00:00 2001 From: birbi Date: Tue, 31 May 2022 16:26:44 +0200 Subject: [PATCH 0486/1454] modified long_table_parse.py,functionality split in 2 function... now correct --- long_table_JSON_2022-05-31 14:26:13.286679.txt | 0 long_table_JSON_2022-05-31 14:27:49.199936.txt | 0 long_table_JSON_2022-05-31 14:31:06.062731.txt | 0 long_table_JSON_2022-05-31 14:33:09.319141.txt | 1 - long_table_JSON_2022-05-31 14:35:11.067577.txt | 1 - long_table_JSON_2022-05-31 14:52:03.933969.txt | 1 - relecov_tools/long_table_parse.py | 9 +++++---- 7 files changed, 5 insertions(+), 7 deletions(-) delete mode 100644 long_table_JSON_2022-05-31 14:26:13.286679.txt delete mode 100644 long_table_JSON_2022-05-31 14:27:49.199936.txt delete mode 100644 long_table_JSON_2022-05-31 14:31:06.062731.txt delete mode 100644 long_table_JSON_2022-05-31 14:33:09.319141.txt delete mode 100644 long_table_JSON_2022-05-31 14:35:11.067577.txt delete mode 100644 long_table_JSON_2022-05-31 14:52:03.933969.txt diff --git a/long_table_JSON_2022-05-31 14:26:13.286679.txt b/long_table_JSON_2022-05-31 14:26:13.286679.txt deleted file mode 100644 index e69de29b..00000000 diff --git a/long_table_JSON_2022-05-31 14:27:49.199936.txt b/long_table_JSON_2022-05-31 14:27:49.199936.txt deleted file mode 100644 index e69de29b..00000000 diff --git a/long_table_JSON_2022-05-31 14:31:06.062731.txt b/long_table_JSON_2022-05-31 14:31:06.062731.txt deleted file mode 100644 index e69de29b..00000000 diff --git a/long_table_JSON_2022-05-31 14:33:09.319141.txt b/long_table_JSON_2022-05-31 14:33:09.319141.txt deleted file mode 100644 index 7dbc6e36..00000000 --- a/long_table_JSON_2022-05-31 14:33:09.319141.txt +++ /dev/null @@ -1 +0,0 @@ -[{"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "11132", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "366", "ref_dp": "0", "alt_dp": "363", "af": "0.99"}, "Gene": {"gene": "orf1ab"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.10867G>T", "hgvs_p": "p.Ala3623Ser", "hgvs_p_1_letter": "p.A3623S"}, "Variant": {"ref": "G"}, "Sample": {"sample": "214821"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "14408", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "333", "ref_dp": "2", "alt_dp": "331", "af": "0.99"}, "Gene": {"gene": "orf1ab"}, "Effect": {"effect": "synonymous_variant", "hgvs_c": "c.14143C>T", "hgvs_p": "p.Leu4715Leu", "hgvs_p_1_letter": "p.L4715L"}, "Variant": {"ref": "C"}, "Sample": {"sample": "214821"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "16726", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "697", "ref_dp": "1", "alt_dp": "695", "af": "1.0"}, "Gene": {"gene": "orf1ab"}, "Effect": {"effect": "synonymous_variant", "hgvs_c": "c.16461C>T", "hgvs_p": "p.Tyr5487Tyr", "hgvs_p_1_letter": "p.Y5487Y"}, "Variant": {"ref": "C"}, "Sample": {"sample": "214821"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "17658", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "3710", "ref_dp": "6", "alt_dp": "3690", "af": "0.99"}, "Gene": {"gene": "orf1ab"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.17393G>T", "hgvs_p": "p.Cys5798Phe", "hgvs_p_1_letter": "p.C5798F"}, 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"28883", "nucleotide": "C"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "3900", "ref_dp": "4", "alt_dp": "3892", "af": "1.0"}, "Gene": {"gene": "N"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.610G>C", "hgvs_p": "p.Gly204Arg", "hgvs_p_1_letter": "p.G204R"}, "Variant": {"ref": "G"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "3037", "nucleotide": "T"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "13", "ref_dp": "0", "alt_dp": "13", "af": "1.0"}, "Gene": {"gene": "orf1ab"}, "Effect": {"effect": "synonymous_variant", "hgvs_c": "c.2772C>T", "hgvs_p": "p.Phe924Phe", "hgvs_p_1_letter": "p.F924F"}, "Variant": {"ref": "C"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "4710", "nucleotide": "A"}, "Filter": {"filter": "ft"}, "VariantInSample": {"dp": "12", "ref_dp": "7", "alt_dp": "5", "af": "0.42"}, "Gene": {"gene": "orf1ab"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.4445C>A", "hgvs_p": "p.Ala1482Asp", "hgvs_p_1_letter": "p.A1482D"}, "Variant": {"ref": "C"}, "Sample": {"sample": "220685"}}, {"Chromosome": {"chromosome": "NC_045512.2"}, "Position": {"pos": "8393", "nucleotide": "A"}, "Filter": {"filter": "PASS"}, "VariantInSample": {"dp": "2105", "ref_dp": "5", "alt_dp": "2100", "af": "1.0"}, "Gene": {"gene": "orf1ab"}, "Effect": {"effect": "missense_variant", "hgvs_c": "c.8128G>A", "hgvs_p": "p.Ala2710Thr", "hgvs_p_1_letter": "p.A2710T"}, "Variant": {"ref": "G"}, "Sample": {"sample": "220685"}}] \ No newline at end of file diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index 87acf9f0..732fe901 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -14,17 +14,18 @@ def saving_file(self, generated_JSON, output_dir): if os.path.exists(output_dir): date_now = datetime.now() file_name = "long_table_JSON_" + str(date_now) + ".txt" - os.path.join(output_dir, file_name) - - with open(file_name, "xt") as file: + complete_path = os.path.join(output_dir, file_name) + with open(complete_path, "xt") as file: file.write(generated_JSON) + else: print("Sorry the directory we're looking for... doesn't exist") exit() def parsing_csv(self): - list_of_dictionaries = [] + try: + list_of_dictionaries = [] with open(self.file_path) as fh: lines = fh.readlines() From bd49455fba3773a1c386955583d9f6a5300a3f9a Mon Sep 17 00:00:00 2001 From: birbi Date: Tue, 31 May 2022 17:33:41 +0200 Subject: [PATCH 0487/1454] modified long_table_parse.py, new function check_if_dir_exits() --- relecov_tools/long_table_parse.py | 40 ++++++++++++++++++++++++------- 1 file changed, 31 insertions(+), 9 deletions(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index 732fe901..68cecb3f 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -1,6 +1,8 @@ from datetime import datetime import json import os.path +import sys +from pathlib import Path # from relecov_tools.rest_api import RestApi @@ -10,25 +12,49 @@ def __init__(self, file_path, output_directory): self.file_path = file_path self.output_directory = output_directory + def check_if_dir_exits(self, output_dir): + dir_exits = False + if not os.path.exists(output_dir): + Path(output_dir).mkdir(parents=True, exist_ok=True) + dir_exits = True + else: + dir_exits = True + return dir_exits + def saving_file(self, generated_JSON, output_dir): - if os.path.exists(output_dir): + if self.check_if_dir_exits(output_dir): date_now = datetime.now() file_name = "long_table_JSON_" + str(date_now) + ".txt" complete_path = os.path.join(output_dir, file_name) with open(complete_path, "xt") as file: file.write(generated_JSON) - + """ + if not os.path.exists(output_dir): + Path(output_dir).mkdir(parents=True, exist_ok=True) + elif os.path.exists(output_dir): + date_now = datetime.now() + file_name = "long_table_JSON_" + str(date_now) + ".txt" + complete_path = os.path.join(output_dir, file_name) + with open(complete_path, "xt") as file: + file.write(generated_JSON) + """ + """ else: print("Sorry the directory we're looking for... doesn't exist") - exit() + sys.exit(1) + """ def parsing_csv(self): - try: - list_of_dictionaries = [] with open(self.file_path) as fh: lines = fh.readlines() + except FileNotFoundError: + print("Sorry the file we're looking for... doesn't exist") + sys.exit(1) + + else: + list_of_dictionaries = [] for line in lines[1:]: data_dict_from_long_table = {} data_list = line.strip().split(",") @@ -69,7 +95,3 @@ def parsing_csv(self): self.saving_file( generated_JSON=generated_json, output_dir=self.output_directory ) - except FileNotFoundError: - print("Sorry the file we're looking for... doesn't exist") - exit() - # return generated_json From 2385c2f9411a2f40ec35912c7dfe53931c861c1c Mon Sep 17 00:00:00 2001 From: birbi Date: Tue, 31 May 2022 22:02:34 +0200 Subject: [PATCH 0488/1454] file long_table_parse.py -> class LongTableParse -> add fuction create_dir_if_not_exists --- relecov_tools/long_table_parse.py | 44 +++++++++++-------------------- 1 file changed, 16 insertions(+), 28 deletions(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index 68cecb3f..b4b4c778 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -12,37 +12,25 @@ def __init__(self, file_path, output_directory): self.file_path = file_path self.output_directory = output_directory - def check_if_dir_exits(self, output_dir): - dir_exits = False + def check_if_dir_exists(self, output_dir): + dir_exists = False if not os.path.exists(output_dir): - Path(output_dir).mkdir(parents=True, exist_ok=True) - dir_exits = True - else: - dir_exits = True - return dir_exits + dir_exists = False + + return dir_exists + + def create_dir_if_not_exists(self, output_dir): + Path(output_dir).mkdir(parents=True, exist_ok=True) def saving_file(self, generated_JSON, output_dir): - if self.check_if_dir_exits(output_dir): - date_now = datetime.now() - file_name = "long_table_JSON_" + str(date_now) + ".txt" - complete_path = os.path.join(output_dir, file_name) - with open(complete_path, "xt") as file: - file.write(generated_JSON) - """ - if not os.path.exists(output_dir): - Path(output_dir).mkdir(parents=True, exist_ok=True) - elif os.path.exists(output_dir): - date_now = datetime.now() - file_name = "long_table_JSON_" + str(date_now) + ".txt" - complete_path = os.path.join(output_dir, file_name) - with open(complete_path, "xt") as file: - file.write(generated_JSON) - """ - """ - else: - print("Sorry the directory we're looking for... doesn't exist") - sys.exit(1) - """ + if not self.check_if_dir_exists(output_dir): + self.create_dir_if_not_exists(output_dir) + + date_now = datetime.now() + file_name = "long_table_JSON_" + str(date_now) + ".txt" + complete_path = os.path.join(output_dir, file_name) + with open(complete_path, "xt") as file: + file.write(generated_JSON) def parsing_csv(self): try: From 4e95b13b9020a7804bcf99439961c41ea5d24b4d Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 1 Jun 2022 00:20:03 +0200 Subject: [PATCH 0489/1454] successful get info from iSkyLIMS. Working on mapping json to variables to send iSkyLIMS --- relecov_tools/__main__.py | 66 +++---- relecov_tools/conf/configuration.json | 15 +- .../{feed_databases.py => feed_database.py} | 179 ++++++++++++------ 3 files changed, 165 insertions(+), 95 deletions(-) rename relecov_tools/{feed_databases.py => feed_database.py} (54%) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 70600ac1..b9eac18e 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -14,7 +14,7 @@ import relecov_tools.ena_upload import relecov_tools.json_validation import relecov_tools.map_schema -import relecov_tools.feed_databases +import relecov_tools.feed_database import relecov_tools.read_bioinfo_metadata import relecov_tools.long_table_parse @@ -129,28 +129,6 @@ def relecov_tools_cli(verbose, log_file): log.addHandler(log_fh) -# @relecov_tools_cli.command(help_priority=1) -# @click.argument("keywords", required=False, nargs=-1, metavar="") -# @click.option( -# "-s", -# "--sort", -# type=click.Choice(["release", "pulled", "name", "stars"]), -# default="release", -# help="How to sort listed pipelines", -# ) -# @click.option("--json", is_flag=True, default=False, help="Print full output as JSON") -# @click.option( -# "--show-archived", is_flag=True, default=False, help="Print archived workflows" -# ) -# def list(keywords, sort, json, show_archived): -# """ -# List available bu-isciii workflows used for relecov. -# Checks the web for a list of nf-core pipelines with their latest releases. -# Shows which nf-core pipelines you have pulled locally and whether they are up to date. -# """ -# pass - - # sftp @relecov_tools_cli.command(help_priority=2) @click.option("-u", "--user", help="User name for login to sftp server") @@ -283,6 +261,7 @@ def upload_to_gisaid(user, password, gisaid_json, output_path): pass +# launch @relecov_tools_cli.command(help_priority=8) @click.option("-u", "--user", help="user name for connecting to the server") def launch(user): @@ -290,19 +269,42 @@ def launch(user): pass +# update_db @relecov_tools_cli.command(help_priority=9) -@click.option("-u", "--user", help="user name for login") -@click.option("-p", "--password", help="password for the user to login") @click.option("-j", "--json", help="data in json format") @click.option("-s", "--schema", help="json schema if relecov is not used") -@click.option("-i", "--iskylims", help="url for sending request to iSkyLIMs") -@click.option("-r", "--relecov", help="url for sending request to Relecov Platform") -def update_db(user, password, json, schema, iskylims, relecov): - """feed database with metadata jsons""" - feed_databases = relecov_tools.feed_databases.FeedDatabases( - user, password, json, schema, iskylims, relecov +@click.option( + "-t", + "--type", + type=click.Choice( + [ + "sample", + "analysis" + ] + ), + multiple=False, + help="Select the type of information to upload to database" +) +@click.option( + "-d", + "databaseServer", + type=click.Choice( + [ + "iskylims", + "relecov", + ] + ), + multiple=False, + help="name of the server which information is defined in config file" +) +@click.option("-u", "--user", help="user name for login") +@click.option("-p", "--password", help="password for the user to login") +def update_db(user, password, json, schema, type, databaseServer): + """feed database with json""" + feed_database = relecov_tools.feed_database.FeedDatabase( + user, password, json, schema, type, databaseServer ) - feed_databases.store_data() + feed_database.store_data() # read metadata bioinformatics diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index ff6bb646..8e009e17 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -32,11 +32,13 @@ }, "external_url": { "iskylims": { - "server": "http://relecov-iskylims.isciiides.es", + "server": "http://relecov-iskylims.isciiides.es:8001", "url": "/wetlab/api/", "store_samples": "createSampleData", "url_project_fields": "sampleProjectFields", - "project_name": "Relecov", + "url_sample_fields": "samplefields", + "param_sample_project": "project", + "project_name": "relecov", "token": "" }, "relecov": { @@ -46,15 +48,8 @@ "token": "" } }, - "iskylims_sample_fields": { - "sampleName": "collecting_lab_sample_id", - "labRequest": "collecting_institution", - "sampleType": "anatomical_material", - "species": "host_common_name", - "sampleEntryDate": "sample_received_date", - "collectionSampleDate": "sample_collection_date" - }, "iskylims_fixed_values": { + "patient": "", "sampleProject": "Relecov", "onlyRecorded": "Yes", "sampleLocation": "Not defined" diff --git a/relecov_tools/feed_databases.py b/relecov_tools/feed_database.py similarity index 54% rename from relecov_tools/feed_databases.py rename to relecov_tools/feed_database.py index 50dcb028..2f9e7bc5 100644 --- a/relecov_tools/feed_databases.py +++ b/relecov_tools/feed_database.py @@ -23,24 +23,24 @@ ) -class FeedDatabases: +class FeedDatabase: def __init__( self, user=None, passwd=None, json_file=None, schema=None, - iskylims_url=None, - relecov_url=None, + type_of_info=None, + database_server=None, ): if user is None: user = relecov_tools.utils.prompt_text( - msg="Enter username for iskylims and relecov_plaform" + msg="Enter username for upload data to server" ) self.user = user if passwd is None: passwd = relecov_tools.utils.prompt_text( - msg="Enter credential password for iskylims and relecov_plaform" + msg="Enter credential password" ) self.passwd = passwd self.config_json = ConfigJson() @@ -74,11 +74,33 @@ def __init__( stderr.print("[red] Schema does not fulfil Draft 202012 Validation") sys.exit(1) self.schema = rel_schema_json + if type_of_info is None: + type_of_info = relecov_tools.utils.prompt_selection( + "Select:", + ["sample", "analysis"], + ) + self.type_of_info = type_of_info - # Get iSkyLIMS settings - self.iskylims_settings = self.config_json.get_topic_data( - "external_url", "iskylims" - ) + if database_server is None: + database_server = relecov_tools.utils.prompt_selection( + "Select:", + ["iskylims", "relecov"], + ) + self.server_type = database_server + # Get database settings + try: + self.database_settings = self.config_json.get_topic_data( + "external_url", database_server + ) + except KeyError: + log.error("Unable to get parameters for dataserver") + stderr.print( + f"[red] Unable to fetch parameters data for {database_server}" + ) + sys.exit(1) + self.database_server = self.database_settings["server"] + self.database_url = self.database_settings["url"] + """ self.iskylims_server = self.iskylims_settings["server"] self.iskylims_url = self.iskylims_settings["url"] if iskylims_url: @@ -97,63 +119,107 @@ def __init__( self.relecov_url = "/".join(split[1:]) self.iskylims_rest_api = RestApi(self.iskylims_server, self.iskylims_url) - self.relecov_rest_api = RestApi(self.relecov_server, self.relecov_url) + """ + self.database_rest_api = RestApi(self.database_server, self.database_url) - def mapping_sample_project_fields(self, s_project_fields): - """Map the label defined in the sample project fields with the name + def get_schema_ontology_values(self): + """Read the schema and extract the values of ontology with the label""" + ontology_dict = {} + for prop, values in self.schema["properties"].items(): + if "ontology" in values and values["ontology"] != "": + ontology_dict[values["ontology"]] = prop + return ontology_dict + + def map_sample_fields_values(self, sample_fields, s_project_fields): + """Map the values to the properties send to dtabasee in json schema based on label """ - label_prop_dict = {} - map_list = {} # key is the label, value the property - for prop, values in self.schema["properties"].items(): - try: - label_prop_dict[values["label"]] = prop - except KeyError: - continue - for field in s_project_fields: - try: - map_list[field] = label_prop_dict[field] - except KeyError as e: - log.error("Unable to map in the schema the label %s", e) - stderr.print("[red] Unable to map in the schema the label ", e) - sys.exit(1) - return map_list + sample_list = [] + s_fields = list(sample_fields.keys()) + for row in self.json_data: + s_dict = {} + for key, value in row.items: + if key in s_project_fields: + s_dict[key] = value + elif key in s_fields: + s_dict[sample_list[key]] = value + else: + import pdb; pdb.set_trace() + # include the fix value + if self.server_type == "iskylims": + for prop, val in self.config_json["iskylims_fixed_values"].items(): + s_dict[prop] = val + sample_list.append(s_dict) + + import pdb; pdb.set_trace() + return sample_list def get_fields_sample(self): - """Get from configuration file the mandatory fields for Sample""" + """2 requests are sent to iSkyLIMS. One for getting the sample fields + These fields are mapped using the ontology. + The second request is for getting the sample project fields. These are + mapped using the label value. + """ sample_fields = {} - sample_fields["iskylims_s_fields"] = self.config_json.get_configuration( - "iskylims_sample_fields" - ) - sample_fields["relecov_fields"] = self.config_json.get_configuration( - "relecov_fields" - ) + s_project_fields = [] + # get the ontology values for mapping values in sample fields + ontology_dict = self.get_schema_ontology_values() + sample_url = self.database_settings["url_sample_fields"] + try: + sample_fields_raw = self.database_rest_api.get_request(sample_url, "", "") + except AttributeError: + log.error("Unable to connect to server %s", self.database_server) + stderr.print( + f"[red] Unable to connect to server {self.database_server}" + ) + sys.exit(1) + if "ERROR" in sample_fields_raw: + log.error( + "Unable to get parameters. Received error code %s", sample_fields_raw["ERROR"] + ) + stderr.print( + f"[red] Unable to fetch data. Received error {sample_fields_raw['ERROR']}" + ) + sys.exit(1) - s_project = self.iskylims_rest_api.get_request( - self.iskylims_settings["url_project_fields"], - "project", - self.iskylims_settings["project_name"], - ) - if "ERROR" in s_project: + for key, values in sample_fields_raw["DATA"].items(): + if "ontology" in values: + try: + property = ontology_dict[values["ontology"]] + # sample_fields has a key the label in metadata and value + # the field name for sample + sample_fields[property] = key + except KeyError as e: + stderr.print(f"[red]Error in map ontology {e}") + else: + # for the ones that do no have ontologuy label is the sample field + # and the value is empty + sample_fields[key] = "" + # fetch label for sample Project + s_project_url = self.database_settings["url_project_fields"] + param = self.database_settings["param_sample_project"] + p_name = self.database_settings["project_name"] + s_project_fields_raw = self.database_rest_api.get_request(s_project_url, param, p_name) + if "ERROR" in s_project_fields_raw: log.error( - "Unable to get parameters. Received error code %s", s_project["ERROR"] + "Unable to get parameters. Received error code %s", s_project_fields_raw["ERROR"] ) stderr.print( - "[red] Unable to fetch data. Received error ", s_project["ERROR"] + f"[red] Unable to fetch data. Received error {s_project_fields_raw['ERROR']}" ) sys.exit(1) - s_project_fields = [x["sampleProjectFieldName"] for x in s_project["DATA"]] + for field in s_project_fields_raw["DATA"]: + s_project_fields.append(field["sampleProjectFieldName"]) - sample_fields["iskylims_s_fields"].update( - self.mapping_sample_project_fields(s_project_fields) + sample_fields["relecov_fields"] = self.config_json.get_configuration( + "relecov_fields" ) + return [sample_fields, s_project_fields] - return sample_fields - - def update_databases(self, sample_fields): - """Split the information in the input json to populate iSkyLIMS and - Relecov platform - """ + def update_database(self, field_values): + """Send the request to update database""" + for chunk in field_values: + pass for sample in self.json_data: iskylims_data = {} for label, value in sample_fields["iskylims_s_fields"].items(): @@ -168,11 +234,13 @@ def update_databases(self, sample_fields): iskylims_data["sampleLocation"] = "" iskylims_data["onlyRecorded"] = "Yes" iskylims_data["sampleProject"] = self.iskylims_settings["project_name"] + import pdb; pdb.set_trace() result = self.iskylims_rest_api.post_request( json.dumps(iskylims_data), {"user": self.user, "pass": self.passwd}, self.iskylims_settings["store_samples"], ) + import pdb; pdb.set_trace() if "ERROR" in result: if result["ERROR"] == "Server not available": # retry to connect to server @@ -217,5 +285,10 @@ def store_data(self): """Collect data from json file and split them to store data in iSkyLIMS amd in Relecov Platform """ - sample_fields = self.get_fields_sample() - self.update_databases(sample_fields) + if self.type_of_info == "sample": + if self.server_type == "iskylims": + sample_fields, s_project_fields = self.get_fields_sample() + map_fields = self.map_sample_fields_values(sample_fields, s_project_fields) + else: + pass + self.update_databases(map_fields) From 1c45377a264a2f186b331e181769bdda5af4a72e Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Wed, 1 Jun 2022 10:40:19 +0200 Subject: [PATCH 0490/1454] LongTableParse -> added Header --- relecov_tools/long_table_parse.py | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index b4b4c778..5e4504f3 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -1,3 +1,28 @@ +""" +============================================================= +HEADER +============================================================= +INSTITUTION: BU-ISCIII +AUTHOR: Luis D. Aranda Lillo +MAIL: laranda@isciii.es +VERSION: 0 +CREATED: 31-5-2022 +REVISED: 31-5-2022 +REVISED BY: Luis Chapado +DESCRIPTION: + + Parse a csv file and save the results in a file + +REQUIREMENTS: + -Python + +TO DO: + +================================================================ +END_OF_HEADER +================================================================ +""" + from datetime import datetime import json import os.path From 13e1366baa98b5e7939e56f210305dd7aa3246e8 Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Wed, 1 Jun 2022 14:24:45 +0200 Subject: [PATCH 0491/1454] modified long_table_parse.py --- relecov_tools/conf/configuration.json | 9 +- relecov_tools/long_table_parse.py | 132 ++++++++++++++++---------- 2 files changed, 90 insertions(+), 51 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index ff6bb646..059c6f5d 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -121,5 +121,12 @@ "tool_version": "0.5.3" }, "md5_file_name": "md5sum_MiSeq_GEN_267_20220208_ICasas_removed_samples.md5", - "checklist": "ERC000033" + "checklist": "ERC000033", + "long_table_heading": [ + "SAMPLE", "CHROM", "POS", "REF", + "ALT", "FILTER", "DP", "REF_DP", "ALT_DP", + "AF", "GENE", "EFFECT", "HGVS_C", "HGVS_P", + "HGVS_P_1LETTER", "CALLER", "LINEAGE" + + ] } diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index 5e4504f3..11f44b10 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -25,86 +25,118 @@ from datetime import datetime import json +import logging import os.path import sys from pathlib import Path +import rich +import relecov_tools +from relecov_tools.config_json import ConfigJson + # from relecov_tools.rest_api import RestApi +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + class LongTableParse: - def __init__(self, file_path, output_directory): - self.file_path = file_path - self.output_directory = output_directory + def __init__(self, file_path=None, output_directory=None): + if file_path is None: + self.file_path = relecov_tools.utils.prompt_path( + msg="Select the csv file which contains metadata" + ) + else: + self.file_path = file_path - def check_if_dir_exists(self, output_dir): - dir_exists = False - if not os.path.exists(output_dir): - dir_exists = False + if not os.path.exists(self.file_path): + log.error("Metadata file %s does not exist ", self.file_path) + stderr.print("[red] Metadata file " + self.file_path + " does not exist") + sys.exit(1) - return dir_exists + if not self.file_path.endswith(".csv"): + log.error("Metadata file %s is not a csv file ", self.file_path) + stderr.print( + "[red] Metadata file " + self.file_path + " must be a csv file" + ) + sys.exit(1) - def create_dir_if_not_exists(self, output_dir): - Path(output_dir).mkdir(parents=True, exist_ok=True) + if output_directory is None: + self.output_directory = relecov_tools.utils.prompt_path( + msg="Select the output folder" + ) + else: + self.output_directory = output_directory + Path(self.output_directory).mkdir(parents=True, exist_ok=True) - def saving_file(self, generated_JSON, output_dir): - if not self.check_if_dir_exists(output_dir): - self.create_dir_if_not_exists(output_dir) + config_json = ConfigJson() + self.long_table_heading = config_json.get_configuration("long_table_heading") + def saving_file(self, generated_JSON): date_now = datetime.now() - file_name = "long_table_JSON_" + str(date_now) + ".txt" - complete_path = os.path.join(output_dir, file_name) - with open(complete_path, "xt") as file: - file.write(generated_JSON) + file_name = "long_table_JSON_" + str(date_now) + ".json" + complete_path = os.path.join(self.output_directory, file_name) + with open(complete_path, "w") as fh: + fh.write(generated_JSON) - def parsing_csv(self): + def parse_a_list_of_dictionaries(self): try: with open(self.file_path) as fh: lines = fh.readlines() except FileNotFoundError: - print("Sorry the file we're looking for... doesn't exist") + print("The file we're looking for... doesn't exist") sys.exit(1) - else: - list_of_dictionaries = [] - for line in lines[1:]: - data_dict_from_long_table = {} - data_list = line.strip().split(",") + list_of_dictionaries = [] + headings_from_csv = lines[0].strip().split(",") + dict_index_of_heading = {} - data_dict_from_long_table["Chromosome"] = {"chromosome": data_list[1]} + for heading in self.long_table_heading: + dict_index_of_heading[heading] = headings_from_csv.index(heading) - data_dict_from_long_table["Position"] = { - "pos": data_list[2], - "nucleotide": data_list[4], - } + for line in lines[1:]: + data_dict_from_long_table = {} + data_list = line.strip().split(",") - data_dict_from_long_table["Filter"] = {"filter": data_list[5]} + data_dict_from_long_table["Chromosome"] = {"chromosome": data_list[1]} - data_dict_from_long_table["VariantInSample"] = { - "dp": data_list[6], - "ref_dp": data_list[7], - "alt_dp": data_list[8], - "af": data_list[9], - } + data_dict_from_long_table["Position"] = { + "pos": data_list[2], + "nucleotide": data_list[4], + } - data_dict_from_long_table["Gene"] = {"gene": data_list[10]} + data_dict_from_long_table["Filter"] = {"filter": data_list[5]} - data_dict_from_long_table["Effect"] = { - "effect": data_list[11], - "hgvs_c": data_list[12], - "hgvs_p": data_list[13], - "hgvs_p_1_letter": data_list[14], - } + data_dict_from_long_table["VariantInSample"] = { + "dp": data_list[6], + "ref_dp": data_list[7], + "alt_dp": data_list[8], + "af": data_list[9], + } - data_dict_from_long_table["Variant"] = {"ref": data_list[3]} + data_dict_from_long_table["Gene"] = {"gene": data_list[10]} - data_dict_from_long_table["Sample"] = {"sample": data_list[0]} + data_dict_from_long_table["Effect"] = { + "effect": data_list[11], + "hgvs_c": data_list[12], + "hgvs_p": data_list[13], + "hgvs_p_1_letter": data_list[14], + } - list_of_dictionaries.append(data_dict_from_long_table) + data_dict_from_long_table["Variant"] = {"ref": data_list[3]} - generated_json = json.dumps(list_of_dictionaries) + data_dict_from_long_table["Sample"] = {"sample": data_list[0]} - self.saving_file( - generated_JSON=generated_json, output_dir=self.output_directory - ) + list_of_dictionaries.append(data_dict_from_long_table) + + return json.dumps(list_of_dictionaries, indent=4) + + def parsing_csv(self): + generated_json = self.parse_a_list_of_dictionaries() + self.saving_file(generated_JSON=generated_json) From 5a902903c2826c6d481d97fbcf8325a696448dc4 Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Wed, 1 Jun 2022 16:05:20 +0200 Subject: [PATCH 0492/1454] long_table_parse.py -> function parse_a_list_of_dictionaries(), check number of fields are correct --- relecov_tools/long_table_parse.py | 44 ++++++++++++++++++++++++++++++- 1 file changed, 43 insertions(+), 1 deletion(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index 11f44b10..4ce605ef 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -98,8 +98,49 @@ def parse_a_list_of_dictionaries(self): dict_index_of_heading = {} for heading in self.long_table_heading: - dict_index_of_heading[heading] = headings_from_csv.index(heading) + dict_index_of_heading[heading] = self.long_table_heading.index(heading) + if len(self.long_table_heading) is len(headings_from_csv): + for line in lines[1:]: + data_dict_from_long_table = {} + data_list = line.strip().split(",") + + data_dict_from_long_table["Chromosome"] = {"chromosome": data_list[1]} + + data_dict_from_long_table["Position"] = { + "pos": data_list[2], + "nucleotide": data_list[4], + } + + data_dict_from_long_table["Filter"] = {"filter": data_list[5]} + + data_dict_from_long_table["VariantInSample"] = { + "dp": data_list[6], + "ref_dp": data_list[7], + "alt_dp": data_list[8], + "af": data_list[9], + } + + data_dict_from_long_table["Gene"] = {"gene": data_list[10]} + + data_dict_from_long_table["Effect"] = { + "effect": data_list[11], + "hgvs_c": data_list[12], + "hgvs_p": data_list[13], + "hgvs_p_1_letter": data_list[14], + } + + data_dict_from_long_table["Variant"] = {"ref": data_list[3]} + + data_dict_from_long_table["Sample"] = {"sample": data_list[0]} + + list_of_dictionaries.append(data_dict_from_long_table) + + return json.dumps(list_of_dictionaries, indent=4) + else: + print("Incorrect format") + sys.exit(1) + """ for line in lines[1:]: data_dict_from_long_table = {} data_list = line.strip().split(",") @@ -136,6 +177,7 @@ def parse_a_list_of_dictionaries(self): list_of_dictionaries.append(data_dict_from_long_table) return json.dumps(list_of_dictionaries, indent=4) + """ def parsing_csv(self): generated_json = self.parse_a_list_of_dictionaries() From 6df1a6f7e4bcaeb4c054eca08d4f7daca325c022 Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Wed, 1 Jun 2022 16:53:42 +0200 Subject: [PATCH 0493/1454] long_table_parse.py -> function parse_a_list_of_dictionaries(), check if the names of fields are the same --- relecov_tools/long_table_parse.py | 91 ++++++++++--------------------- 1 file changed, 29 insertions(+), 62 deletions(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index 4ce605ef..de6d8bf0 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -100,84 +100,51 @@ def parse_a_list_of_dictionaries(self): for heading in self.long_table_heading: dict_index_of_heading[heading] = self.long_table_heading.index(heading) + for heading_csv in headings_from_csv: + if heading_csv not in dict_index_of_heading: + print("incorrect Format, fields don't match") + sys.exit(1) + if len(self.long_table_heading) is len(headings_from_csv): for line in lines[1:]: data_dict_from_long_table = {} - data_list = line.strip().split(",") + data_list = line.strip().split(",") - data_dict_from_long_table["Chromosome"] = {"chromosome": data_list[1]} + data_dict_from_long_table["Chromosome"] = {"chromosome": data_list[1]} - data_dict_from_long_table["Position"] = { - "pos": data_list[2], - "nucleotide": data_list[4], - } + data_dict_from_long_table["Position"] = { + "pos": data_list[2], + "nucleotide": data_list[4], + } - data_dict_from_long_table["Filter"] = {"filter": data_list[5]} + data_dict_from_long_table["Filter"] = {"filter": data_list[5]} - data_dict_from_long_table["VariantInSample"] = { - "dp": data_list[6], - "ref_dp": data_list[7], - "alt_dp": data_list[8], - "af": data_list[9], - } + data_dict_from_long_table["VariantInSample"] = { + "dp": data_list[6], + "ref_dp": data_list[7], + "alt_dp": data_list[8], + "af": data_list[9], + } - data_dict_from_long_table["Gene"] = {"gene": data_list[10]} + data_dict_from_long_table["Gene"] = {"gene": data_list[10]} - data_dict_from_long_table["Effect"] = { - "effect": data_list[11], - "hgvs_c": data_list[12], - "hgvs_p": data_list[13], - "hgvs_p_1_letter": data_list[14], - } + data_dict_from_long_table["Effect"] = { + "effect": data_list[11], + "hgvs_c": data_list[12], + "hgvs_p": data_list[13], + "hgvs_p_1_letter": data_list[14], + } - data_dict_from_long_table["Variant"] = {"ref": data_list[3]} + data_dict_from_long_table["Variant"] = {"ref": data_list[3]} - data_dict_from_long_table["Sample"] = {"sample": data_list[0]} + data_dict_from_long_table["Sample"] = {"sample": data_list[0]} - list_of_dictionaries.append(data_dict_from_long_table) + list_of_dictionaries.append(data_dict_from_long_table) return json.dumps(list_of_dictionaries, indent=4) else: - print("Incorrect format") + print("Incorrect format, the headers do not have the same number of fields") sys.exit(1) - """ - for line in lines[1:]: - data_dict_from_long_table = {} - data_list = line.strip().split(",") - - data_dict_from_long_table["Chromosome"] = {"chromosome": data_list[1]} - - data_dict_from_long_table["Position"] = { - "pos": data_list[2], - "nucleotide": data_list[4], - } - - data_dict_from_long_table["Filter"] = {"filter": data_list[5]} - - data_dict_from_long_table["VariantInSample"] = { - "dp": data_list[6], - "ref_dp": data_list[7], - "alt_dp": data_list[8], - "af": data_list[9], - } - - data_dict_from_long_table["Gene"] = {"gene": data_list[10]} - - data_dict_from_long_table["Effect"] = { - "effect": data_list[11], - "hgvs_c": data_list[12], - "hgvs_p": data_list[13], - "hgvs_p_1_letter": data_list[14], - } - - data_dict_from_long_table["Variant"] = {"ref": data_list[3]} - - data_dict_from_long_table["Sample"] = {"sample": data_list[0]} - - list_of_dictionaries.append(data_dict_from_long_table) - - return json.dumps(list_of_dictionaries, indent=4) - """ def parsing_csv(self): generated_json = self.parse_a_list_of_dictionaries() From 967ac644cd6f73f616f779ea876a750bb5e07e7d Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 2 Jun 2022 00:18:39 +0200 Subject: [PATCH 0494/1454] wrong onotology value for collector_name --- relecov_tools/schema/relecov_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index a3eb1718..af526fa6 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2017,7 +2017,7 @@ "examples": [ "John Smith" ], - "ontology": "GENEPIO:0001153", + "ontology": "GENEPIO:0001797", "type": "string", "description": "Name of the person who collected the specimen", "classification": "Sample collection and processing", @@ -2494,4 +2494,4 @@ "fill_mode": "batch" } } -} \ No newline at end of file +} From 2f684a5f989ecbdb52ac1d6b6b5f2d2a08df38ef Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 2 Jun 2022 09:12:51 +0200 Subject: [PATCH 0495/1454] Tested upload samples to iSkyLIMS --- relecov_tools/conf/configuration.json | 2 +- relecov_tools/feed_database.py | 70 +++++++++++---------------- 2 files changed, 30 insertions(+), 42 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 8e009e17..85fd60d5 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -49,7 +49,7 @@ } }, "iskylims_fixed_values": { - "patient": "", + "patientCore": "", "sampleProject": "Relecov", "onlyRecorded": "Yes", "sampleLocation": "Not defined" diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 2f9e7bc5..d9271ec2 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -39,9 +39,7 @@ def __init__( ) self.user = user if passwd is None: - passwd = relecov_tools.utils.prompt_text( - msg="Enter credential password" - ) + passwd = relecov_tools.utils.prompt_text(msg="Enter credential password") self.passwd = passwd self.config_json = ConfigJson() if json_file is None: @@ -94,9 +92,7 @@ def __init__( ) except KeyError: log.error("Unable to get parameters for dataserver") - stderr.print( - f"[red] Unable to fetch parameters data for {database_server}" - ) + stderr.print(f"[red] Unable to fetch parameters data for {database_server}") sys.exit(1) self.database_server = self.database_settings["server"] self.database_url = self.database_settings["url"] @@ -138,20 +134,23 @@ def map_sample_fields_values(self, sample_fields, s_project_fields): s_fields = list(sample_fields.keys()) for row in self.json_data: s_dict = {} - for key, value in row.items: + + for key, value in row.items(): if key in s_project_fields: s_dict[key] = value elif key in s_fields: - s_dict[sample_list[key]] = value + s_dict[sample_fields[key]] = value else: - import pdb; pdb.set_trace() + print("not key in iSkyLIMS", key) # include the fix value if self.server_type == "iskylims": - for prop, val in self.config_json["iskylims_fixed_values"].items(): + fixed_value = self.config_json.get_configuration( + "iskylims_fixed_values" + ) + for prop, val in fixed_value.items(): s_dict[prop] = val sample_list.append(s_dict) - import pdb; pdb.set_trace() return sample_list def get_fields_sample(self): @@ -169,13 +168,12 @@ def get_fields_sample(self): sample_fields_raw = self.database_rest_api.get_request(sample_url, "", "") except AttributeError: log.error("Unable to connect to server %s", self.database_server) - stderr.print( - f"[red] Unable to connect to server {self.database_server}" - ) + stderr.print(f"[red] Unable to connect to server {self.database_server}") sys.exit(1) if "ERROR" in sample_fields_raw: log.error( - "Unable to get parameters. Received error code %s", sample_fields_raw["ERROR"] + "Unable to get parameters. Received error code %s", + sample_fields_raw["ERROR"], ) stderr.print( f"[red] Unable to fetch data. Received error {sample_fields_raw['ERROR']}" @@ -188,21 +186,26 @@ def get_fields_sample(self): property = ontology_dict[values["ontology"]] # sample_fields has a key the label in metadata and value # the field name for sample - sample_fields[property] = key + sample_fields[property] = values["field_name"] except KeyError as e: stderr.print(f"[red]Error in map ontology {e}") else: # for the ones that do no have ontologuy label is the sample field # and the value is empty - sample_fields[key] = "" + # sample_fields[key] = "" + print(values["field_name"]) + # fetch label for sample Project s_project_url = self.database_settings["url_project_fields"] param = self.database_settings["param_sample_project"] p_name = self.database_settings["project_name"] - s_project_fields_raw = self.database_rest_api.get_request(s_project_url, param, p_name) + s_project_fields_raw = self.database_rest_api.get_request( + s_project_url, param, p_name + ) if "ERROR" in s_project_fields_raw: log.error( - "Unable to get parameters. Received error code %s", s_project_fields_raw["ERROR"] + "Unable to get parameters. Received error code %s", + s_project_fields_raw["ERROR"], ) stderr.print( f"[red] Unable to fetch data. Received error {s_project_fields_raw['ERROR']}" @@ -219,28 +222,11 @@ def get_fields_sample(self): def update_database(self, field_values): """Send the request to update database""" for chunk in field_values: - pass - for sample in self.json_data: - iskylims_data = {} - for label, value in sample_fields["iskylims_s_fields"].items(): - try: - iskylims_data[label] = sample[value] - except KeyError as e: - log.error("Found %s when mapping data for sending to iSkyLIMS") - stderr.print(f"[red] {e} not found in mapping") - sys.exit(1) - # add fxxed valuurs before sending request - iskylims_data["patientCore"] = "" - iskylims_data["sampleLocation"] = "" - iskylims_data["onlyRecorded"] = "Yes" - iskylims_data["sampleProject"] = self.iskylims_settings["project_name"] - import pdb; pdb.set_trace() - result = self.iskylims_rest_api.post_request( - json.dumps(iskylims_data), + result = self.database_rest_api.post_request( + json.dumps(chunk), {"user": self.user, "pass": self.passwd}, - self.iskylims_settings["store_samples"], + self.database_settings["store_samples"], ) - import pdb; pdb.set_trace() if "ERROR" in result: if result["ERROR"] == "Server not available": # retry to connect to server @@ -288,7 +274,9 @@ def store_data(self): if self.type_of_info == "sample": if self.server_type == "iskylims": sample_fields, s_project_fields = self.get_fields_sample() - map_fields = self.map_sample_fields_values(sample_fields, s_project_fields) + map_fields = self.map_sample_fields_values( + sample_fields, s_project_fields + ) else: pass - self.update_databases(map_fields) + self.update_database(map_fields) From d23ffd166c5812bf28bf7b54438a6da9e326e70e Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 2 Jun 2022 09:13:19 +0200 Subject: [PATCH 0496/1454] Tested upload samples to iSkyLIMS --- relecov_tools/conf/configuration.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 85fd60d5..7be4dbb4 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -32,7 +32,7 @@ }, "external_url": { "iskylims": { - "server": "http://relecov-iskylims.isciiides.es:8001", + "server": "http://relecov-iskylims.isciiides.es:", "url": "/wetlab/api/", "store_samples": "createSampleData", "url_project_fields": "sampleProjectFields", From 745f2d58837617a367fba16fed006de22cb5b86c Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 2 Jun 2022 09:22:12 +0200 Subject: [PATCH 0497/1454] Tested upload samples to iSkyLIMS --- relecov_tools/feed_database.py | 15 ++------------- 1 file changed, 2 insertions(+), 13 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index d9271ec2..74272fb6 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -234,7 +234,7 @@ def update_database(self, field_values): # wait 5 sec before resending the request time.sleep(5) result = self.iskylims_rest_api.post_request( - json.dumps(iskylims_data), + json.dumps(chunk), {"user": self.user, "pass": self.passwd}, self.iskylims_settings["store_samples"], ) @@ -252,18 +252,7 @@ def update_database(self, field_values): sys.exit(1) log.info( - "stored data in iskylims for sample %s", iskylims_data["sampleName"] - ) - # send request to releco-platform - relecov_data = {} - for label, value in sample.items(): - if label not in sample_fields["iskylims_s_fields"]: - relecov_data[label] = value - - result = self.relecov_rest_api.post_request( - json.dumps(iskylims_data), - {"user": self.user, "pass": self.passwd}, - self.relecov_settings["store_samples"], + "stored data in iskylims for sample %s", chunk["sampleName"] ) return From 79e4ce908b5b866f466558e2ccee94b253012973 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 2 Jun 2022 09:25:11 +0200 Subject: [PATCH 0498/1454] Reformat the main options for feed-database --- relecov_tools/__main__.py | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index b9eac18e..203a80cc 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -276,14 +276,9 @@ def launch(user): @click.option( "-t", "--type", - type=click.Choice( - [ - "sample", - "analysis" - ] - ), + type=click.Choice(["sample", "analysis"]), multiple=False, - help="Select the type of information to upload to database" + help="Select the type of information to upload to database", ) @click.option( "-d", @@ -295,7 +290,7 @@ def launch(user): ] ), multiple=False, - help="name of the server which information is defined in config file" + help="name of the server which information is defined in config file", ) @click.option("-u", "--user", help="user name for login") @click.option("-p", "--password", help="password for the user to login") From 730acc21364ad1bff999482cf2dfd46898f584e1 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 2 Jun 2022 09:30:48 +0200 Subject: [PATCH 0499/1454] Tested upload samples to iSkyLIMS --- relecov_tools/feed_database.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 74272fb6..7ef602cc 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -251,9 +251,7 @@ def update_database(self, field_values): ) sys.exit(1) - log.info( - "stored data in iskylims for sample %s", chunk["sampleName"] - ) + log.info("stored data in iskylims for sample %s", chunk["sampleName"]) return def store_data(self): From d86e08af870cb6fbaae50a9ba7f7539ab1681548 Mon Sep 17 00:00:00 2001 From: birbi Date: Thu, 2 Jun 2022 09:56:57 +0200 Subject: [PATCH 0500/1454] long_table_parse.py -> check if the headers of both files have the same order --- relecov_tools/long_table_parse.py | 19 ++++++++++++++++--- 1 file changed, 16 insertions(+), 3 deletions(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index de6d8bf0..59d1dda7 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -90,7 +90,7 @@ def parse_a_list_of_dictionaries(self): lines = fh.readlines() except FileNotFoundError: - print("The file we're looking for... doesn't exist") + stderr.print("[red]The file we're looking for... doesn't exist") sys.exit(1) list_of_dictionaries = [] @@ -100,12 +100,23 @@ def parse_a_list_of_dictionaries(self): for heading in self.long_table_heading: dict_index_of_heading[heading] = self.long_table_heading.index(heading) + # check if the headers of both files are the same for heading_csv in headings_from_csv: if heading_csv not in dict_index_of_heading: - print("incorrect Format, fields don't match") + stderr.print("[red]Incorrect Format, fields don't match") sys.exit(1) + # check if both files contain the same number of fields if len(self.long_table_heading) is len(headings_from_csv): + + # check if the headers of both files have the same order + for idx in range(len(self.long_table_heading)): + if self.long_table_heading[idx] != headings_from_csv[idx]: + stderr.print( + "[red]Incorrect Format, fields don't have the same order" + ) + sys.exit(1) + for line in lines[1:]: data_dict_from_long_table = {} data_list = line.strip().split(",") @@ -143,7 +154,9 @@ def parse_a_list_of_dictionaries(self): return json.dumps(list_of_dictionaries, indent=4) else: - print("Incorrect format, the headers do not have the same number of fields") + print( + "[red]Incorrect format, the headers do not have the same number of fields" + ) sys.exit(1) def parsing_csv(self): From 437f7b2826ec55f0cc8501ce3cb50e540c33fe54 Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Thu, 2 Jun 2022 11:26:41 +0200 Subject: [PATCH 0501/1454] ordered fields if csv file is disordered --- relecov_tools/long_table_parse.py | 70 ++++++++++++++++++++++++++++--- 1 file changed, 65 insertions(+), 5 deletions(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index 59d1dda7..b63eff17 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -106,17 +106,77 @@ def parse_a_list_of_dictionaries(self): stderr.print("[red]Incorrect Format, fields don't match") sys.exit(1) + dict_aux = {} # check if both files contain the same number of fields if len(self.long_table_heading) is len(headings_from_csv): # check if the headers of both files have the same order for idx in range(len(self.long_table_heading)): if self.long_table_heading[idx] != headings_from_csv[idx]: - stderr.print( - "[red]Incorrect Format, fields don't have the same order" - ) - sys.exit(1) + + for heading in headings_from_csv: + dict_aux[heading] = headings_from_csv.index(heading) + + print(dict_index_of_heading) + print(dict_aux) + dict_index_of_heading.clear() + dict_index_of_heading = dict_aux + print(dict_index_of_heading) + """ + stderr.print( + "[red]Incorrect Format, fields don't have the same order" + ) + sys.exit(1) + """ + for line in lines[1:]: + data_dict_from_long_table = {} + data_list = line.strip().split(",") + + data_dict_from_long_table["Chromosome"] = { + "chromosome": data_list[dict_index_of_heading["CHROM"]] + } + + data_dict_from_long_table["Position"] = { + "pos": data_list[dict_index_of_heading["POS"]], + "nucleotide": data_list[dict_index_of_heading["ALT"]], + } + + data_dict_from_long_table["Filter"] = { + "filter": data_list[dict_index_of_heading["FILTER"]] + } + + data_dict_from_long_table["VariantInSample"] = { + "dp": data_list[dict_index_of_heading["DP"]], + "ref_dp": data_list[dict_index_of_heading["REF_DP"]], + "alt_dp": data_list[dict_index_of_heading["ALT_DP"]], + "af": data_list[dict_index_of_heading["AF"]], + } + + data_dict_from_long_table["Gene"] = { + "gene": data_list[dict_index_of_heading["GENE"]] + } + + data_dict_from_long_table["Effect"] = { + "effect": data_list[dict_index_of_heading["EFFECT"]], + "hgvs_c": data_list[dict_index_of_heading["HGVS_C"]], + "hgvs_p": data_list[dict_index_of_heading["HGVS_P"]], + "hgvs_p_1_letter": data_list[ + dict_index_of_heading["HGVS_P_1LETTER"] + ], + } + + data_dict_from_long_table["Variant"] = { + "ref": data_list[dict_index_of_heading["REF"]] + } + + data_dict_from_long_table["Sample"] = { + "sample": data_list[dict_index_of_heading["SAMPLE"]] + } + + list_of_dictionaries.append(data_dict_from_long_table) + + """ for line in lines[1:]: data_dict_from_long_table = {} data_list = line.strip().split(",") @@ -151,7 +211,7 @@ def parse_a_list_of_dictionaries(self): data_dict_from_long_table["Sample"] = {"sample": data_list[0]} list_of_dictionaries.append(data_dict_from_long_table) - + """ return json.dumps(list_of_dictionaries, indent=4) else: print( From ab7eea097deba7b8795ee41acca86ad414ce854b Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 2 Jun 2022 12:19:54 +0200 Subject: [PATCH 0502/1454] added changes to schema --- relecov_tools/conf/configuration.json | 4 +- relecov_tools/read_bioinfo_metadata.py | 2 + relecov_tools/schema/relecov_schema.json | 62 ++++++++++++------------ 3 files changed, 35 insertions(+), 33 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index ff6bb646..c7f8d058 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -120,6 +120,6 @@ "tool_name": "ena-upload-cli", "tool_version": "0.5.3" }, - "md5_file_name": "md5sum_MiSeq_GEN_267_20220208_ICasas_removed_samples.md5", + "md5_file_name": "md5sum_MiSeq_GEN_267_20220208_ICasas.md5", "checklist": "ERC000033" -} +} \ No newline at end of file diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index ab856402..e754f444 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -2,6 +2,7 @@ # from itertools import islice +from bdb import set_trace import logging import json @@ -142,6 +143,7 @@ def bioinfo_parse(self, file_name): bioinfo_dict["reference_genome_accession"] = str( variants_long_table["CHROM"][c] ) + bioinfo_dict["consensus_genome_length"] = str( consensus_genome_length.iloc[c, 0] ) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index a3eb1718..58448e8a 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1196,7 +1196,7 @@ "ontology": "GENEPIO:0001459", "type": "string", "description": "The method used to remove host reads from the pathogen sequence.", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Dehosting Method", "fill_mode": "batch" }, @@ -1207,7 +1207,7 @@ "ontology": "0", "type": "string", "description": "The method version used to remove host reads from the pathogen sequence.", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Dehosting Method Version", "fill_mode": "batch" }, @@ -1218,7 +1218,7 @@ "ontology": "NCIT_C63548", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Assembly", "fill_mode": "batch" }, @@ -1229,7 +1229,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "If assembly Is Other, Specify", "fill_mode": "batch" }, @@ -1240,7 +1240,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Assambly params", "fill_mode": "batch" }, @@ -1251,7 +1251,7 @@ "ontology": "operation_3227", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Variants", "label": "Variant Calling", "fill_mode": "batch" }, @@ -1262,7 +1262,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Variants", "label": "Variant Calling Version", "fill_mode": "batch" }, @@ -1273,7 +1273,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Variants", "label": "If variant calling Is Other, Specify", "fill_mode": "batch" }, @@ -1284,7 +1284,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Variants", "label": "Variant Calling params", "fill_mode": "batch" }, @@ -1295,7 +1295,7 @@ "examples": [ "ncov123assembly3" ], - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Consensus sequence name", "fill_mode": "batch" }, @@ -1306,7 +1306,7 @@ "examples": [ "ncov123assembly3" ], - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Consensus sequence name md5", "fill_mode": "batch" }, @@ -1317,7 +1317,7 @@ "ontology": "GENEPIO:0001462", "type": "string", "description": "The filepath of the consesnsus sequence file.", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Consensus sequence filepath", "fill_mode": "batch" }, @@ -1328,7 +1328,7 @@ "ontology": "GENEPIO:0001463", "type": "string", "description": "The name of software used to generate the consensus sequence.", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Consensus sequence software name", "fill_mode": "batch" }, @@ -1339,7 +1339,7 @@ "ontology": "0", "type": "string", "description": "The version of the software used to generate the consensus sequence.", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "If consensus Is Other, Specify", "fill_mode": "batch" }, @@ -1350,7 +1350,7 @@ "ontology": "GENEPIO:0001469", "type": "string", "description": "The version of the software used to generate the consensus sequence.", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Consensus sequence software version", "fill_mode": "batch" }, @@ -1361,7 +1361,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Consensus Params", "fill_mode": "batch" }, @@ -1515,7 +1515,7 @@ "ontology": "GENEPIO:0001489", "type": "string", "description": "The name of the bioinformatics protocol used.", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Bioinformatics protocol", "fill_mode": "batch" }, @@ -1526,7 +1526,7 @@ "ontology": "0", "type": "string", "description": "The name of the bioinformatics protocol used.", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "If bioinformatic protocol Is Other, Specify", "fill_mode": "batch" }, @@ -1537,7 +1537,7 @@ "ontology": "NCIT:C93490", "type": "string", "description": "The version number of the bioinformatics protocol used.", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "bioinformatics protocol version", "fill_mode": "batch" }, @@ -1548,7 +1548,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Commercial/Open-source/both", "fill_mode": "batch" }, @@ -1559,7 +1559,7 @@ "ontology": "MS_1002386", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Preprocessing", "fill_mode": "batch" }, @@ -1570,7 +1570,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Preprocessing Version", "fill_mode": "batch" }, @@ -1581,7 +1581,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "If preprocessing Is Other, Specify", "fill_mode": "batch" }, @@ -1592,7 +1592,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Preprocessing params", "fill_mode": "batch" }, @@ -1603,7 +1603,7 @@ "ontology": "topic:0102", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Mapping", "fill_mode": "batch" }, @@ -1614,7 +1614,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Mapping Version", "fill_mode": "batch" }, @@ -1625,7 +1625,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "If mapping Is Other, Specify", "fill_mode": "batch" }, @@ -1636,7 +1636,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Analysis", "label": "Mapping params", "fill_mode": "batch" }, @@ -1707,7 +1707,7 @@ "examples": [ "Variant of Concern (VOC) [GENEPIO:0100083]" ], - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Variants", "label": "Variant designation", "fill_mode": "batch" }, @@ -1846,7 +1846,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Variants", "label": "Number of variants (AF greater 75%)", "fill_mode": "batch" }, @@ -1857,7 +1857,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatic Variants", "label": "Number of variants with effect", "fill_mode": "batch" }, From a44c8a7b8a2b4ea8b3884e16c075e63ca6de427e Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 2 Jun 2022 13:08:19 +0200 Subject: [PATCH 0503/1454] change python version --- .github/workflows/python_lint.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml index 12d3beb8..deeaf672 100644 --- a/.github/workflows/python_lint.yml +++ b/.github/workflows/python_lint.yml @@ -15,7 +15,7 @@ jobs: - name: Setup Python uses: actions/setup-python@v1 with: - python-version: 3.9.12 + python-version: 3.9.x architecture: x64 - name: Checkout PyTorch uses: actions/checkout@master From 7683298bd60c78cd8f8b754083e01280a8d42cc3 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 2 Jun 2022 13:13:28 +0200 Subject: [PATCH 0504/1454] update file for updating the python version in actions --- relecov_tools/feed_database.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 7ef602cc..8d8b0dce 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -266,4 +266,6 @@ def store_data(self): ) else: pass + else: + pass self.update_database(map_fields) From b81ab1a5d74a28cf210c8338d45ea780b90c8ee0 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 2 Jun 2022 13:20:15 +0200 Subject: [PATCH 0505/1454] small change --- relecov_tools/schema/relecov_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 63362d4e..f71af1f2 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1180,7 +1180,7 @@ }, "library_layout": { "examples": [ - "PAIRED" + "PAIRED end" ], "ontology": "NCIT:C175894", "type": "string", @@ -2494,4 +2494,4 @@ "fill_mode": "batch" } } -} +} \ No newline at end of file From 8430e581a948f264fc0100deaca526bc178ae351 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 2 Jun 2022 13:31:39 +0200 Subject: [PATCH 0506/1454] fix linting --- relecov_tools/read_bioinfo_metadata.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index e754f444..aa9f052c 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -1,8 +1,6 @@ #!/usr/bin/env python # from itertools import islice - -from bdb import set_trace import logging import json From 28671c05122cbacc0d44ffab6479fceb35ec26fe Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Thu, 2 Jun 2022 14:01:05 +0200 Subject: [PATCH 0507/1454] finalized long-table-parse.py function, added DocString --- relecov_tools/long_table_parse.py | 83 ++++++++++--------------------- 1 file changed, 27 insertions(+), 56 deletions(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index b63eff17..b14128f6 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -46,6 +46,15 @@ class LongTableParse: + """ + + - parse_a_list_of_dictionaries() : returns generated_JSON + - saving_file(generated_JSON) + - parsing_csv() : It manages all this proccess: + - calling first to parse_a_list_of_dictionaries() and then calling to saving_file() + + """ + def __init__(self, file_path=None, output_directory=None): if file_path is None: self.file_path = relecov_tools.utils.prompt_path( @@ -78,6 +87,13 @@ def __init__(self, file_path=None, output_directory=None): self.long_table_heading = config_json.get_configuration("long_table_heading") def saving_file(self, generated_JSON): + """ + Save the list of dictionaries, generated by the parse_a_list_of_dictionaries() function , + to a json file, naming as "long_table_JSON_" + "current date" + ".json" + + Args: + generated_JSON (a list of dictionaries) + """ date_now = datetime.now() file_name = "long_table_JSON_" + str(date_now) + ".json" complete_path = os.path.join(self.output_directory, file_name) @@ -85,6 +101,14 @@ def saving_file(self, generated_JSON): fh.write(generated_JSON) def parse_a_list_of_dictionaries(self): + """_summary_ + This function generates a json file from the csv file entered by the user (long_table.csv). + - It checks if the headers of both files are the same + - It checks if both files contain the same number of fields + Returns: + A list of dictionaries in json format. + """ + try: with open(self.file_path) as fh: lines = fh.readlines() @@ -106,29 +130,9 @@ def parse_a_list_of_dictionaries(self): stderr.print("[red]Incorrect Format, fields don't match") sys.exit(1) - dict_aux = {} # check if both files contain the same number of fields if len(self.long_table_heading) is len(headings_from_csv): - # check if the headers of both files have the same order - for idx in range(len(self.long_table_heading)): - if self.long_table_heading[idx] != headings_from_csv[idx]: - - for heading in headings_from_csv: - dict_aux[heading] = headings_from_csv.index(heading) - - print(dict_index_of_heading) - print(dict_aux) - dict_index_of_heading.clear() - dict_index_of_heading = dict_aux - print(dict_index_of_heading) - """ - stderr.print( - "[red]Incorrect Format, fields don't have the same order" - ) - sys.exit(1) - """ - for line in lines[1:]: data_dict_from_long_table = {} data_list = line.strip().split(",") @@ -176,42 +180,6 @@ def parse_a_list_of_dictionaries(self): list_of_dictionaries.append(data_dict_from_long_table) - """ - for line in lines[1:]: - data_dict_from_long_table = {} - data_list = line.strip().split(",") - - data_dict_from_long_table["Chromosome"] = {"chromosome": data_list[1]} - - data_dict_from_long_table["Position"] = { - "pos": data_list[2], - "nucleotide": data_list[4], - } - - data_dict_from_long_table["Filter"] = {"filter": data_list[5]} - - data_dict_from_long_table["VariantInSample"] = { - "dp": data_list[6], - "ref_dp": data_list[7], - "alt_dp": data_list[8], - "af": data_list[9], - } - - data_dict_from_long_table["Gene"] = {"gene": data_list[10]} - - data_dict_from_long_table["Effect"] = { - "effect": data_list[11], - "hgvs_c": data_list[12], - "hgvs_p": data_list[13], - "hgvs_p_1_letter": data_list[14], - } - - data_dict_from_long_table["Variant"] = {"ref": data_list[3]} - - data_dict_from_long_table["Sample"] = {"sample": data_list[0]} - - list_of_dictionaries.append(data_dict_from_long_table) - """ return json.dumps(list_of_dictionaries, indent=4) else: print( @@ -220,5 +188,8 @@ def parse_a_list_of_dictionaries(self): sys.exit(1) def parsing_csv(self): + """ + function called when using the relecov-tools long-table-parse function. + """ generated_json = self.parse_a_list_of_dictionaries() self.saving_file(generated_JSON=generated_json) From 97b9eef68c1d855b10b4a502c74fdd0d24eeebfe Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 2 Jun 2022 15:14:12 +0200 Subject: [PATCH 0508/1454] added field text in classification for those that must be loaded in the BionifoProcessFields --- relecov_tools/schema/relecov_schema.json | 82 ++++++++++++------------ 1 file changed, 41 insertions(+), 41 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index f71af1f2..34376b5b 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1196,7 +1196,7 @@ "ontology": "GENEPIO:0001459", "type": "string", "description": "The method used to remove host reads from the pathogen sequence.", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Dehosting Method", "fill_mode": "batch" }, @@ -1207,7 +1207,7 @@ "ontology": "0", "type": "string", "description": "The method version used to remove host reads from the pathogen sequence.", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Dehosting Method Version", "fill_mode": "batch" }, @@ -1218,7 +1218,7 @@ "ontology": "NCIT_C63548", "type": "string", "description": "", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Assembly", "fill_mode": "batch" }, @@ -1229,7 +1229,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "If assembly Is Other, Specify", "fill_mode": "batch" }, @@ -1240,7 +1240,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Assambly params", "fill_mode": "batch" }, @@ -1295,7 +1295,7 @@ "examples": [ "ncov123assembly3" ], - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence name", "fill_mode": "batch" }, @@ -1306,7 +1306,7 @@ "examples": [ "ncov123assembly3" ], - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence name md5", "fill_mode": "batch" }, @@ -1317,7 +1317,7 @@ "ontology": "GENEPIO:0001462", "type": "string", "description": "The filepath of the consesnsus sequence file.", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence filepath", "fill_mode": "batch" }, @@ -1328,7 +1328,7 @@ "ontology": "GENEPIO:0001463", "type": "string", "description": "The name of software used to generate the consensus sequence.", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence software name", "fill_mode": "batch" }, @@ -1339,7 +1339,7 @@ "ontology": "0", "type": "string", "description": "The version of the software used to generate the consensus sequence.", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "If consensus Is Other, Specify", "fill_mode": "batch" }, @@ -1350,7 +1350,7 @@ "ontology": "GENEPIO:0001469", "type": "string", "description": "The version of the software used to generate the consensus sequence.", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence software version", "fill_mode": "batch" }, @@ -1361,7 +1361,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Consensus Params", "fill_mode": "batch" }, @@ -1372,7 +1372,7 @@ "ontology": "data_3914", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics fields", "label": "Quality control metrics ", "fill_mode": "batch" }, @@ -1383,7 +1383,7 @@ "ontology": "GENEPIO:0001474", "type": "string", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics fields", "label": "Depth of coverage value ", "fill_mode": "batch" }, @@ -1394,7 +1394,7 @@ "ontology": "GENEPIO:0001475", "type": "string", "description": "The threshold used as a cut-off for the depth of coverage.", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics fields", "label": "Depth of coverage threshold", "fill_mode": "batch" }, @@ -1471,7 +1471,7 @@ "ontology": "GENEPIO:0001482", "type": "string", "description": "The number of total base pairs generated by the sequencing process.", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics fields", "label": "Number of base pairs sequenced ", "fill_mode": "batch" }, @@ -1482,7 +1482,7 @@ "ontology": "GENEPIO:0001483", "type": "string", "description": "Size of the assembled genome described as the number of base pairs.", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics fields", "label": "Consensus genome length", "fill_mode": "batch" }, @@ -1493,7 +1493,7 @@ "ontology": "GENEPIO:0001484", "type": "string", "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics fields", "label": "Ns per 100 kbp", "fill_mode": "batch" }, @@ -1504,7 +1504,7 @@ "ontology": "GENEPIO:0001485", "type": "string", "description": "A persistent, unique identifier of a genome database entry.", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics fields", "label": "Reference genome accession", "fill_mode": "batch" }, @@ -1515,7 +1515,7 @@ "ontology": "GENEPIO:0001489", "type": "string", "description": "The name of the bioinformatics protocol used.", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Bioinformatics protocol", "fill_mode": "batch" }, @@ -1526,7 +1526,7 @@ "ontology": "0", "type": "string", "description": "The name of the bioinformatics protocol used.", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "If bioinformatic protocol Is Other, Specify", "fill_mode": "batch" }, @@ -1537,7 +1537,7 @@ "ontology": "NCIT:C93490", "type": "string", "description": "The version number of the bioinformatics protocol used.", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "bioinformatics protocol version", "fill_mode": "batch" }, @@ -1548,7 +1548,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Commercial/Open-source/both", "fill_mode": "batch" }, @@ -1559,7 +1559,7 @@ "ontology": "MS_1002386", "type": "string", "description": "", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Preprocessing", "fill_mode": "batch" }, @@ -1570,7 +1570,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Preprocessing Version", "fill_mode": "batch" }, @@ -1581,7 +1581,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "If preprocessing Is Other, Specify", "fill_mode": "batch" }, @@ -1592,7 +1592,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Preprocessing params", "fill_mode": "batch" }, @@ -1603,7 +1603,7 @@ "ontology": "topic:0102", "type": "string", "description": "", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Mapping", "fill_mode": "batch" }, @@ -1614,7 +1614,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Mapping Version", "fill_mode": "batch" }, @@ -1625,7 +1625,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "If mapping Is Other, Specify", "fill_mode": "batch" }, @@ -1636,7 +1636,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatic Analysis", + "classification": "Bioinformatic Analysis fields", "label": "Mapping params", "fill_mode": "batch" }, @@ -1758,7 +1758,7 @@ "examples": [ "E gene (orf4) [GENEPIO:0100151]" ], - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics fields", "label": "Gene Name 1", "fill_mode": "batch" }, @@ -1769,7 +1769,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics fields", "label": "%qc filtered", "fill_mode": "batch" }, @@ -1780,7 +1780,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics fields", "label": "%reads host", "fill_mode": "batch" }, @@ -1791,7 +1791,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics fields", "label": "%reads virus", "fill_mode": "batch" }, @@ -1802,7 +1802,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics fields", "label": "%unmapped", "fill_mode": "batch" }, @@ -1813,7 +1813,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics fields", "label": "% genome greater 10x", "fill_mode": "batch" }, @@ -1824,7 +1824,7 @@ "ontology": "NCIT:C167285", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics fields", "label": "mean depth of coverage value", "fill_mode": "batch" }, @@ -1835,7 +1835,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics fields", "label": "%Ns", "fill_mode": "batch" }, @@ -1931,7 +1931,7 @@ "type": "string", "format": "date", "description": "", - "classification": "Bioinformatics and QC metrics", + "classification": "Bioinformatics and QC metrics fields", "label": "Analysis date", "fill_mode": "batch" }, @@ -2494,4 +2494,4 @@ "fill_mode": "batch" } } -} \ No newline at end of file +} From 7a13179458612f4a5f49a3adee55ce93bb436fe8 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 2 Jun 2022 23:08:11 +0200 Subject: [PATCH 0509/1454] added classification fro GISAID_ID that was empty --- relecov_tools/schema/relecov_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 34376b5b..2679e30b 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1986,8 +1986,8 @@ ], "ontology": "NCIT:C54269", "type": "string", - "description": "", - "classification": "enter your GISAID-Username", + "description": "enter your GISAID-Username", + "classification": "Database Identifiers", "label": "GISAID id", "fill_mode": "sample" }, From bbee369a005b4e2bb6fcfc89ff625a8b9c6cf60f Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 2 Jun 2022 23:29:02 +0200 Subject: [PATCH 0510/1454] solved merge conflict --- relecov_tools/conf/configuration.json | 7 ------- 1 file changed, 7 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 5c557ada..776e20ab 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -115,19 +115,12 @@ "tool_name": "ena-upload-cli", "tool_version": "0.5.3" }, -<<<<<<< HEAD "md5_file_name": "md5sum_MiSeq_GEN_267_20220208_ICasas.md5", - "checklist": "ERC000033" -} -======= - "md5_file_name": "md5sum_MiSeq_GEN_267_20220208_ICasas_removed_samples.md5", "checklist": "ERC000033", "long_table_heading": [ "SAMPLE", "CHROM", "POS", "REF", "ALT", "FILTER", "DP", "REF_DP", "ALT_DP", "AF", "GENE", "EFFECT", "HGVS_C", "HGVS_P", "HGVS_P_1LETTER", "CALLER", "LINEAGE" - ] } ->>>>>>> 82754d6fcd1927a7202635005b4822e1bffba4c2 From 891b4dffafbf6ddfc49154b6ff68743955f5169f Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 3 Jun 2022 10:03:22 +0200 Subject: [PATCH 0511/1454] removed softwares versions from config --- relecov_tools/conf/configuration.json | 36 +++++++++++++-------------- 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 5c557ada..b921f142 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -64,28 +64,22 @@ ], "relecov_bioinfo_metadata": { "dehosting_method_software_name": "KRAKEN2_KRAKEN2", - "dehosting_method_software_version": "2.1.2", "assembly": "None", "if_assembly_other": "None", "assembly_params": "None", "variant_calling_software_name": "IVAR_VARIANTS", - "variant_calling_software_version": "1.3.1", "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", - "consensus_sequence_software_version": "1.14", "if_consensur_other": "None", "consensus_params": "-p vcf -f", "depth_of_coverage_threshold": ">10x", "bioinformatics_protocol_software_name": "nf-core/viralrecon", - "bioinformatics_protocol_software_version": "2.4.1", "if_bioinformatic_protocol_is_other_specify": "None", "commercial_open_source_both": "open-source", "preprocessing_software_name": "FASTP", - "preprocessing_software_version": "0.23.2", "if_preprocessing_other": "None", "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", "mapping_software_name": "BOWTIE2_ALIGN", - "mapping_software_version": "2.4.4", "if_mapping_other": "None", "mapping_params": "--seed 1", "lineage_analysis_software_name": "pangolin", @@ -115,19 +109,25 @@ "tool_name": "ena-upload-cli", "tool_version": "0.5.3" }, -<<<<<<< HEAD "md5_file_name": "md5sum_MiSeq_GEN_267_20220208_ICasas.md5", - "checklist": "ERC000033" -} -======= - "md5_file_name": "md5sum_MiSeq_GEN_267_20220208_ICasas_removed_samples.md5", "checklist": "ERC000033", "long_table_heading": [ - "SAMPLE", "CHROM", "POS", "REF", - "ALT", "FILTER", "DP", "REF_DP", "ALT_DP", - "AF", "GENE", "EFFECT", "HGVS_C", "HGVS_P", - "HGVS_P_1LETTER", "CALLER", "LINEAGE" - + "SAMPLE", + "CHROM", + "POS", + "REF", + "ALT", + "FILTER", + "DP", + "REF_DP", + "ALT_DP", + "AF", + "GENE", + "EFFECT", + "HGVS_C", + "HGVS_P", + "HGVS_P_1LETTER", + "CALLER", + "LINEAGE" ] -} ->>>>>>> 82754d6fcd1927a7202635005b4822e1bffba4c2 +} \ No newline at end of file From a482c63ab92f7f4417c80a1b59fab7337d369b64 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 6 Jun 2022 16:58:21 +0200 Subject: [PATCH 0512/1454] fixing read biifoo medtadata --- relecov_tools/read_bioinfo_metadata.py | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index aa9f052c..7600cc10 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -141,7 +141,6 @@ def bioinfo_parse(self, file_name): bioinfo_dict["reference_genome_accession"] = str( variants_long_table["CHROM"][c] ) - bioinfo_dict["consensus_genome_length"] = str( consensus_genome_length.iloc[c, 0] ) From 5f346a5b47f616ca2509cc2dbe4eb1fbba5841b8 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 6 Jun 2022 23:08:59 +0200 Subject: [PATCH 0513/1454] added functionality to send sample data to relecov-platform --- relecov_tools/conf/configuration.json | 16 +++++----- relecov_tools/feed_database.py | 46 +++++++++++---------------- relecov_tools/test/test_cases.txt | 5 ++- 3 files changed, 29 insertions(+), 38 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 776e20ab..2292007e 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -32,7 +32,7 @@ }, "external_url": { "iskylims": { - "server": "http://relecov-iskylims.isciiides.es:", + "server": "http://relecov-iskylims.isciiides.es", "url": "/wetlab/api/", "store_samples": "createSampleData", "url_project_fields": "sampleProjectFields", @@ -54,13 +54,13 @@ "onlyRecorded": "Yes", "sampleLocation": "Not defined" }, - "relecov_metadata": [ - "collecting_lab_sample_id", - "sequencing_sample_id", - "biosample_accession_ENA", - "virus_name", - "gisaid_id", - "sequencing_date" + "relecov_sample_metadata": [ + "bioproject_accession_ENA" , "bioproject_umbrella_accession_ENA", + "biosample_accession_ENA", "GenBank_ENA_DDBJ_accession", + "GISAID_accession", "gisaid_id", "host_specimen_voucher", + "isolate_sample_id", "microbiology_lab_sample_id", + "sequencing_sample_id", "SRA_accession", "submitting_lab_sample_id", + "virus_name" ], "relecov_bioinfo_metadata": { "dehosting_method_software_name": "KRAKEN2_KRAKEN2", diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 8d8b0dce..317ba98d 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -96,26 +96,7 @@ def __init__( sys.exit(1) self.database_server = self.database_settings["server"] self.database_url = self.database_settings["url"] - """ - self.iskylims_server = self.iskylims_settings["server"] - self.iskylims_url = self.iskylims_settings["url"] - if iskylims_url: - split = iskylims_url.split("/") - self.iskylims_server = split[0] + "/" - self.iskylims_url = "/".join(split[1:]) + "/" - - self.relecov_settings = self.config_json.get_topic_data( - "external_url", "relecov" - ) - self.relecov_server = self.relecov_settings["server"] - self.relecov_url = self.relecov_settings["url"] - if relecov_url: - split = relecov_url.split("/") - self.relecov_server = split[0] + "/" - self.relecov_url = "/".join(split[1:]) - self.iskylims_rest_api = RestApi(self.iskylims_server, self.iskylims_url) - """ self.database_rest_api = RestApi(self.database_server, self.database_url) def get_schema_ontology_values(self): @@ -126,7 +107,7 @@ def get_schema_ontology_values(self): ontology_dict[values["ontology"]] = prop return ontology_dict - def map_sample_fields_values(self, sample_fields, s_project_fields): + def map_iskylims_sample_fields_values(self, sample_fields, s_project_fields): """Map the values to the properties send to dtabasee in json schema based on label """ @@ -153,7 +134,7 @@ def map_sample_fields_values(self, sample_fields, s_project_fields): return sample_list - def get_fields_sample(self): + def get_iskylims_fields_sample(self): """2 requests are sent to iSkyLIMS. One for getting the sample fields These fields are mapped using the ontology. The second request is for getting the sample project fields. These are @@ -214,11 +195,22 @@ def get_fields_sample(self): for field in s_project_fields_raw["DATA"]: s_project_fields.append(field["sampleProjectFieldName"]) - sample_fields["relecov_fields"] = self.config_json.get_configuration( - "relecov_fields" - ) return [sample_fields, s_project_fields] + def map_relecov_sample_data(self): + """Select the values from self.json_data""" + field_values = [] + r_fields = self.config_json.get_configuration("relecov_sample_metadata") + for row in self.json_data: + s_dict = {} + for r_field in r_fields: + if r_field in row: + s_dict[r_field] = row[r_field] + else: + s_dict[r_field] = None + field_values.append(s_dict) + return field_values + def update_database(self, field_values): """Send the request to update database""" for chunk in field_values: @@ -260,12 +252,12 @@ def store_data(self): """ if self.type_of_info == "sample": if self.server_type == "iskylims": - sample_fields, s_project_fields = self.get_fields_sample() - map_fields = self.map_sample_fields_values( + sample_fields, s_project_fields = self.get_iskylims_fields_sample() + map_fields = self.map_iskylims_sample_fields_values( sample_fields, s_project_fields ) else: - pass + map_fields = self.map_relecov_sample_data() else: pass self.update_database(map_fields) diff --git a/relecov_tools/test/test_cases.txt b/relecov_tools/test/test_cases.txt index b13c4cf0..430ae49a 100644 --- a/relecov_tools/test/test_cases.txt +++ b/relecov_tools/test/test_cases.txt @@ -4,7 +4,6 @@ relecov-tools read-lab-metadata -m relecov_tools/example_data/METADATA_LAB_TEST. relecov-tools validate -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -o /tmp relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -d ENA -o /tmp relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -d GISAID -o /tmp -relecov-tools update-db -i http://iskylims.isciiides.es/wetlab/api -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -relecov-tools update-db -i http://localhost:8001/wetlab/api -r http://localhost:8000/api -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -u admin -p Apple@123 +relecov-tools update-db -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json relecov-tools read-bioinfo-metadata -m relecov_tools/example_data/lab_metadata_20220208.xlsx -i /relecov_tools/example_data -o relecov_tools/example_data -relecov-tools upload-to-ena -u XXXXXXXX -p XXXXXXXXX -e relecov_tools/example_data/to_ena_2.json -o relecov_tools/test -a add -c ISCIII +relecov-tools upload-to-ena -e relecov_tools/example_data/to_ena_2.json -o relecov_tools/test -a add -c ISCIII From 4d42f8be009f705142db369ec9560c3c0c02ca29 Mon Sep 17 00:00:00 2001 From: Alema91 Date: Tue, 7 Jun 2022 12:06:09 +0200 Subject: [PATCH 0514/1454] Pangolin version table: 1 --- .../example_data/lab_metadata_20220208.xlsx | Bin 0 -> 403686 bytes 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+[ + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_material": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123456", + "collecting_institution": "HU Virgen de la Arrixaca", + "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", + "collecting_institution_email": "", + "collecting_lab_sample_id": "1197860", + "collection_device": "Swab", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "diagnostic_pcr_Ct_value_1": "45", + "diagnostic_pcr_Ct_value_2": "34", + "enrichment_protocol": "Amplicon", + "environmental_material": "Other", + "environmental_site": "Earth surface", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "f2facbd1d6c7e0972074ced31ccbfd8e", + "fastq_r2_md5": "fd9948be8da7a38b0f80659dfc21aeea", + "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", + "gene_name_1": "ORF 1ab", + "gene_name_2": "S", + "geo_loc_city": "Murcia", + "geo_loc_country": "Spain", + "geo_loc_latitude": "37.9861", + "geo_loc_longitude": "-1.1303", + "geo_loc_state": "Murcia", + "gisaid_id": "EPI_ISL_11222687", + "host_age": "55", + "host_common_name": "Human", + "host_disease": "COVID-19", + "host_gender": "Female", + "host_scientific_name": "Homo Sapiens", + "if_amplicon_protocol_if_other_especify": "", + "if_enrichment_protocol_is_other_specify": "", + "isolate_sample_id": "1197860", + "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_layout": "SINGLE", + "library_preparation_kit": "Truseq Nano", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "microbiology_lab_sample_id": "220407", + "number_of_samples_in_run": "96", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "2022CEU01394", + "purpose_of_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2021-04-13", + "sample_description": "Sample for surveillance", + "sample_received_date": "2021-05-13", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_001.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_001.fastq.gz", + "sequencing_date": "2022-02-22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 214824, + "study_alias": "RELECOV", + "study_id": "ERP137164", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202201751", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2022" + }, + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_material": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123457", + "collecting_institution": "HU Virgen de la Arrixaca", + "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", + "collecting_institution_email": "", + "collecting_lab_sample_id": "1197824", + "collection_device": "Swab", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "diagnostic_pcr_Ct_value_1": "12", + "diagnostic_pcr_Ct_value_2": "16", + "enrichment_protocol": "Amplicon", + "environmental_material": "Other", + "environmental_site": "Earth surface", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "9a460a812086516536c1a1023ab5f7fe", + "fastq_r2_md5": "41cd79b8a167d85eb06309207fd120cf", + "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", + "gene_name_1": "ORF 1ab", + "gene_name_2": "S", + "geo_loc_city": "Murcia", + "geo_loc_country": "Spain", + "geo_loc_latitude": "37.9861", + "geo_loc_longitude": "-1.1303", + "geo_loc_state": "Murcia", + "gisaid_id": "EPI_ISL_11222688", + "host_age": "59", + "host_common_name": "Human", + "host_disease": "COVID-19", + "host_gender": "Male", + "host_scientific_name": "Homo Sapiens", + "if_amplicon_protocol_if_other_especify": "", + "if_enrichment_protocol_is_other_specify": "", + "isolate_sample_id": "1197824", + "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_layout": "SINGLE", + "library_preparation_kit": "Truseq Nano", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "microbiology_lab_sample_id": "220433", + "number_of_samples_in_run": "96", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "2022CEU01469", + "purpose_of_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2021-03-31", + "sample_description": "Sample for surveillance", + "sample_received_date": "2021-05-13", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_002.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_002.fastq.gz", + "sequencing_date": "2022-02-22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 214832, + "study_alias": "RELECOV", + "study_id": "ERP137164", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202201678", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2023" + }, + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_material": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123458", + "collecting_institution": "HU Virgen de la Arrixaca", + "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", + "collecting_institution_email": "", + "collecting_lab_sample_id": "1197767", + "collection_device": "Swab", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "diagnostic_pcr_Ct_value_1": "45", + "diagnostic_pcr_Ct_value_2": "41", + "enrichment_protocol": "Amplicon", + "environmental_material": "Other", + "environmental_site": "Earth surface", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "c78fcb585a0f44734ce8c2aebf3eff33", + "fastq_r2_md5": "8361d5a6b50279fbc8c93226ecc3568a", + "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", + "gene_name_1": "ORF 1ab", + "gene_name_2": "S", + "geo_loc_city": "Murcia", + "geo_loc_country": "Spain", + "geo_loc_latitude": "37.9861", + "geo_loc_longitude": "-1.1303", + "geo_loc_state": "Murcia", + "gisaid_id": "EPI_ISL_11222689", + "host_age": "8", + "host_common_name": "Human", + "host_disease": "COVID-19", + "host_gender": "Female", + "host_scientific_name": "Homo Sapiens", + "if_amplicon_protocol_if_other_especify": "", + "if_enrichment_protocol_is_other_specify": "", + "isolate_sample_id": "1197767", + "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_layout": "SINGLE", + "library_preparation_kit": "Truseq Nano", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "microbiology_lab_sample_id": "220435", + "number_of_samples_in_run": "96", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "2022CEU03926", + "purpose_of_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2022-01-13", + "sample_description": "Sample for surveillance", + "sample_received_date": "2022-01-18", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_003.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_003.fastq.gz", + "sequencing_date": "2022-02-22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 220338, + "study_alias": "RELECOV", + "study_id": "ERP137164", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202201853", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2024" + }, + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_material": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123459", + "collecting_institution": "HU Virgen de la Arrixaca", + "collecting_institution_address": "Ctra. 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"Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123465", + "collecting_institution": "HU de Donostia", + "collecting_institution_address": "Begiristain Doktorea Pasealekua, s/n", + "collecting_institution_email": "", + "collecting_lab_sample_id": "1197685", + "collection_device": "Swab", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "diagnostic_pcr_Ct_value_1": "32", + "diagnostic_pcr_Ct_value_2": "32", + "enrichment_protocol": "Amplicon", + "environmental_material": "Other", + "environmental_site": "Earth surface", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "a86f4fa0c92d76df34fd000a29d1cdd3", + "fastq_r2_md5": "8c4309dc00d725496c48bee6da0e4bbf", + "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", + "gene_name_1": "ORF 1ab", + "gene_name_2": "S", + "geo_loc_city": "Donostia", + "geo_loc_country": "Spain", + "geo_loc_latitude": "43.3200", + "geo_loc_longitude": "-1.9800", + "geo_loc_state": "País Vasco", + "gisaid_id": "EPI_ISL_11222696", + "host_age": "96", + "host_common_name": "Human", + "host_disease": "COVID-19", + "host_gender": "Female", + "host_scientific_name": "Homo Sapiens", + "if_amplicon_protocol_if_other_especify": "", + "if_enrichment_protocol_is_other_specify": "", + "isolate_sample_id": "1197685", + "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_layout": "SINGLE", + "library_preparation_kit": "Truseq Nano", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "microbiology_lab_sample_id": "220639", + "number_of_samples_in_run": "96", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "2022CEU04223", + "purpose_of_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2022-01-19", + "sample_description": "Sample for surveillance", + "sample_received_date": "2022-01-26", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_0010.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_0010.fastq.gz", + "sequencing_date": "2022-02-22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 220639, + "study_alias": "RELECOV", + "study_id": "ERP137164", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202203166", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2031" + } +] From 908977eec15c6483ae0b2549d58975a81bfddb11 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Adri=C3=A1n=20Mu=C3=B1oz=20Barrera?= Date: Wed, 29 Jun 2022 13:51:25 +0100 Subject: [PATCH 0570/1454] New JSON schema for ITER institution. --- .../institution_schemas/HUNSC-ITER.json | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 relecov_tools/schema/institution_schemas/HUNSC-ITER.json diff --git a/relecov_tools/schema/institution_schemas/HUNSC-ITER.json b/relecov_tools/schema/institution_schemas/HUNSC-ITER.json new file mode 100644 index 00000000..93827e6d --- /dev/null +++ b/relecov_tools/schema/institution_schemas/HUNSC-ITER.json @@ -0,0 +1,22 @@ +{ + "equivalence": + {"Sample ID given by originating laboratory": "Sample ID given by originating laboratory", + "Sample ID given by the submitting laboratory": "Sample ID given by the submitting laboratory", + "Originating Laboratory": "Originating lab", + "Submitting Institution": "Submitting lab", + "Sample Collection Date": "Collection date", + "Specimen source": "Specimen source", + "Host": "Host", + "Host Age": "Patient age", + "Host Gender": "Gender", + "Sequencing Instrument Model": "Sequencing technology", + "Analysis Authors": "Authors", + "Author Submitter": "Submitter", + "Authors": "Authors"}, + "constants": + {"Biological Sample Storage Condition": "-80ºC", + "Collection Device": "Swab", + "Source material": "VIRAL RNA"}, + "empty": [], + "outer": {} +} \ No newline at end of file From 54f5536ca29eb8c7125822b9683cff5383029d0d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Adri=C3=A1n=20Mu=C3=B1oz=20Barrera?= Date: Wed, 29 Jun 2022 14:03:05 +0100 Subject: [PATCH 0571/1454] Add ITER to institution_to_schema.json file --- relecov_tools/schema/institution_to_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/institution_to_schema.json b/relecov_tools/schema/institution_to_schema.json index 43535fd5..95c5ed3c 100644 --- a/relecov_tools/schema/institution_to_schema.json +++ b/relecov_tools/schema/institution_to_schema.json @@ -1,5 +1,5 @@ { - "ITER" : "1.json", - "0001" : "1.json", + "ITER" : "HUNSC-ITER.json", + "HUNSC-ITER" : "HUNSC-ITER.json", "ISCIII" : "ISCIII.json" } \ No newline at end of file From afe7e3afc39146cf21ddcbdcb09ec32b1f0c2d2c Mon Sep 17 00:00:00 2001 From: mlarjim Date: Wed, 29 Jun 2022 15:17:57 +0200 Subject: [PATCH 0572/1454] Modified gisaid_schema.json 2 --- relecov_tools/schema/gisaid_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/gisaid_schema.json b/relecov_tools/schema/gisaid_schema.json index 797eb590..1192a129 100644 --- a/relecov_tools/schema/gisaid_schema.json +++ b/relecov_tools/schema/gisaid_schema.json @@ -222,7 +222,7 @@ "clasification": "Bioinformatics and QC metrics", "label": "Depth of coverage value " }, - "fasta_filename": { + "covv_fasta_filename": { "examples": [ "" ], From ea5cf901ab0ef1d001ed4e7b33342cb6c4136b80 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 29 Jun 2022 15:30:24 +0200 Subject: [PATCH 0573/1454] linting --- relecov_tools/metadata_homogeneizer.py | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 3b389da0..48275f16 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -5,16 +5,16 @@ import json import pandas as pd -# functions def check_extension(instring, extensions): for extension in extensions: if instring.endswith(extension): return True - -# Homogeneizer object + class Homogeneizer: + """Homogeneizer object""" + def __init__(filename, self): self.filename = filename self.dictionary = None @@ -38,18 +38,18 @@ def associate_dict(self): detected = [] institution_dict = json.load(path_to_institution_json) - + for key in institution_dict.keys(): if key in self.filename: detected.append(institution_dict[key]) - + if len(set(detected)) != 1: - print("some problems arised!!!") # change this to an elegant form - sys.exit() # maybe check which ones are being mixed or when none is being found + print("some problems arised!!!") # change this to an elegant form + sys.exit() # maybe check which ones are being mixed or when none is being found else: - print("works fine") # delete this after testing - self.dictionary = detected[0] # first item, they are all equal - + print("works fine") # delete this after testing + self.dictionary = detected[0] # first item, they are all equal + return def load_dataframe(self): @@ -76,7 +76,7 @@ def load_dataframe(self): def load_dictionary(self): """Load the corresponding dictionary""" - + path_to_tools = "" dict_path = path_to_tools + "/schema/institution_schemas" + self.filename self.dictionary = json.load(dict_path) @@ -84,6 +84,7 @@ def load_dictionary(self): def translate_dataframe(self): """Use the corresponding dictionary to translate the df""" + # if dictionary is "none" or similar, do nothing pass return @@ -92,4 +93,3 @@ def verify_translated_dataframe(self): pass return - From 8f69ead8c89d927067b1a5651244554d6d1661d2 Mon Sep 17 00:00:00 2001 From: Wanamalauasha Date: Wed, 29 Jun 2022 15:50:49 +0200 Subject: [PATCH 0574/1454] Added HUGTiP.json --- .../schema/institution_schemas/HUGTiP.json | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 relecov_tools/schema/institution_schemas/HUGTiP.json diff --git a/relecov_tools/schema/institution_schemas/HUGTiP.json b/relecov_tools/schema/institution_schemas/HUGTiP.json new file mode 100644 index 00000000..7b2f4637 --- /dev/null +++ b/relecov_tools/schema/institution_schemas/HUGTiP.json @@ -0,0 +1,54 @@ + +{ + "equivalences" : { + "Sample ID given by the submitting laboratory": "sample_id", + "Sample ID given in the microbiology lab": "sample_id", + "Sample ID given for sequencing": "sample_id", + "Sample Collection Date": "collection_date", + "Originating Laboratory": "OriginatingLab", + "Purpose of sampling": "sequencing_strategy", + "Specimen source": "source", + "Host": "host", + "Host Age": "age", + "Host Gender": "gender", + "Authors": "OriginatingLabAuthors" + }, + "constants" : { + "Public Health sample id (SIVIES)": "", + "Sample ID given if multiple rna-extraction or passages": "", + "ENA Sample ID": "", + "GISAID Virus Name": "", + "GISAID id": "", + "Submitting Institution": "HUGTiP", + "Sample Received Date": "", + "Biological Sample Storage Condition": "-80ºC", + "Environmental Material": "", + "Environmental System": "", + "Collection Device": "", + "Sequencing Date": "", + "Rna Extraction Protocol": "Seegene", + "Commercial All-in-one library kit": "", + "Library Preparation Kit": "", + "Enrichment Protocol": "", + "If Enrichment Protocol. If Other,Specify": "", + "Enrichment panel/assay": "", + "Number Of Samples In Run": "", + "Runid": "", + "Sequencing Instrument Model": "", + "Flowcell Kit": "", + "Source material": "", + "Capture method": "", + "Sequencing technique": "", + "Library Layout": "", + "Gene Name 1": "", + "Diagnostic Pcr Ct Value 1": "", + "Gene Name 2": "", + "Diagnostic Pcr Ct Value-2": "", + "Analysis Authors":"Marc Noguera-Julian", + "Author Submitter": "Elisa Martró", + "Sequence file R1 fastq": "", + "Sequence file R2 fastq": "" + }, + "empty" : {}, + "outer" : {} +} From 73e840377d037f169e060a6cc3599d5744fbe66e Mon Sep 17 00:00:00 2001 From: Wanamalauasha Date: Wed, 29 Jun 2022 15:55:16 +0200 Subject: [PATCH 0575/1454] Modified institution_to_schema.json --- relecov_tools/schema/institution_to_schema.json | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/institution_to_schema.json b/relecov_tools/schema/institution_to_schema.json index 95c5ed3c..eb0ff59c 100644 --- a/relecov_tools/schema/institution_to_schema.json +++ b/relecov_tools/schema/institution_to_schema.json @@ -1,5 +1,6 @@ { "ITER" : "HUNSC-ITER.json", "HUNSC-ITER" : "HUNSC-ITER.json", - "ISCIII" : "ISCIII.json" -} \ No newline at end of file + "ISCIII" : "ISCIII.json", + "HUGTiP" : "HUGTiP.json" +} From 1c560f931eefc57f9bcb3be8dac3263b2a5de868 Mon Sep 17 00:00:00 2001 From: Ivan Bloise Date: Wed, 29 Jun 2022 16:38:03 +0200 Subject: [PATCH 0576/1454] add new table headers --- relecov_tools/conf/configuration.json | 52 ++++++++++++++++++++++++++- 1 file changed, 51 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 2d7e5741..2a170b0a 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -1,4 +1,54 @@ -{ +{ + "new_table_headers" : [ + "Public Health sample id (SIVIES)", + "Sample ID given by originating laboratory", + "Sample ID given by the submitting laboratory", + "Sample ID given in the microbiology lab", + "Sample ID given if multiple rna-extraction or passages", + "Sample ID given for sequencing", + "ENA Sample ID", + "GISAID Virus Name", + "GISAID id", + "Originating Laboratory", + "Submitting Institution", + "Sample Collection Date", + "Sample Received Date", + "Purpose of sampling", + "Biological Sample Storage Condition ", + "Specimen source", + "Environmental Material", + "Environmental System", + "Collection Device", + "Host", + "Host Age", + "Host Gender", + "Sequencing Date", + "Rna Extraction Protocol", + "Commercial All-in-one library kit", + "Library Preparation Kit", + "Enrichment Protocol", + "If Enrichment Protocol. If Other,Specify", + "Enrichment panel/assay", + "If Enrichment panel/assay. If Other, Specify", + "Enrichment panel/assay version", + "Number Of Samples In Run", + "Runid", + "Sequencing Instrument Model", + "Flowcell Kit", + "Source material", + "Capture method", + "Sequencing technique", + "Library Layout", + "Gene Name 1", + "Diagnostic Pcr Ct Value 1", + "Gene Name 2", + "Diagnostic Pcr Ct Value-2", + "Analysis Authors", + "Author Submitter", + "Authors", + "Sequence file R1 fastq", + "Sequence file R2 fastq" +], "json_schemas": { "relecov_schema": "relecov_schema.json", "ena_schema": "ena_schema.json", From 538bce5efcc4d20742039671c398178cd3330eff Mon Sep 17 00:00:00 2001 From: mlarjim Date: Wed, 29 Jun 2022 17:36:19 +0200 Subject: [PATCH 0577/1454] Added first steps gisaid_upload --- relecov_tools/gisaid_upload.py | 126 +++++++++++++++++++++++++++++++++ 1 file changed, 126 insertions(+) create mode 100644 relecov_tools/gisaid_upload.py diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py new file mode 100644 index 00000000..8c8fd13f --- /dev/null +++ b/relecov_tools/gisaid_upload.py @@ -0,0 +1,126 @@ +import logging + +# from pyparsing import col +import rich.console +import json + + +import pandas as pd +import sys +import os + +import ftplib +import relecov_tools.utils +from relecov_tools.config_json import ConfigJson + + +import site + + +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + + +class GisaidUpload: + def __init__( + self, + user=None, + passwd=None, + source_json=None, + customized_project=None, + action=None, + output_path=None, + metadata=None, + ): + if user is None: + self.user = relecov_tools.utils.prompt_text( + msg="Enter your username defined in ENA" + ) + else: + self.user = user + if passwd is None: + self.passwd = relecov_tools.utils.prompt_password( + msg="Enter your password to ENA" + ) + else: + self.passwd = passwd + if center is None: + self.center = relecov_tools.utils.prompt_text( + msg="Enter your center name") + else: + self.center = center + if source_json is None: + self.source_json_file = relecov_tools.utils.prompt_path( + msg="Select the ENA json file to upload" + ) + else: + self.source_json_file = source_json + if dev is None: + self.dev = relecov_tools.utils.prompt_yn_question( + msg="Do you want to test upload data?" + ) + else: + self.dev = dev + + if customized_project is None: + self.customized_project = None + else: + self.customized_project = customized_project + if action is None: + self.action = relecov_tools.utils.prompt_selection( + msg="Select the action to upload to ENA", + choices=["add", "modify", "cancel", "release"], + ) + else: + self.action = action.upper() + if output_path is None: + self.output_path = relecov_tools.utils.prompt_path( + msg="Select the folder to store the xml files" + ) + else: + self.output_path = output_path + if metadata is None: + self.metadata = relecov_tools.utils.prompt_path( + msg="Select metadata json file" + ) + else: + self.metadata = metadata + if not os.path.isfile(self.source_json_file): + log.error("json data file %s does not exist ", + self.source_json_file) + stderr.print( + f"[red]json data file {self.source_json_file} does not exist") + sys.exit(1) + with open(self.source_json_file, "r") as fh: + self.json_data = json.loads(fh.read()) + + def convert_input_json_to_ena(self): + """Split the input ena json, in samples and runs json""" + pass + + ####################################### + ## Metadatos + def metadata_to_csv(self): + data= relecov_utils.tools.read_json_file(self.metadata) + df_data= pd.DataFrame(data) + df_data.to_csv("meta_gisaid.csv") + + + ## Sequences + # Unificar en multifasta + # Cambiar headers/id + + + ## Upload + # Subir con cli3 + + + def upload(self): + """Create the required files and upload to ENA""" + self.convert_input_json_to_ena() + self.create_structure_to_ena() From ad49f5de7413922ec8b277c2fd3a92cf69afae4b Mon Sep 17 00:00:00 2001 From: Ivan Bloise Date: Wed, 29 Jun 2022 17:40:48 +0200 Subject: [PATCH 0578/1454] started dataframe translation. Fix json load throught function --- relecov_tools/metadata_homogeneizer.py | 21 +++++++++++++++------ 1 file changed, 15 insertions(+), 6 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 48275f16..ca05cf61 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -11,6 +11,10 @@ def check_extension(instring, extensions): if instring.endswith(extension): return True +def open_json(json_path): + with open(json_path) as file: + json_dict = json.load(file) + return json_dict class Homogeneizer: """Homogeneizer object""" @@ -20,9 +24,8 @@ def __init__(filename, self): self.dictionary = None self.centre = None self.dataframe = None - self.translated_dataframe = None - - pass + header_path = "" + self.translated_dataframe = pd.DataFrame(columns=open_json(header_path)["new_table_headers"]) return def associate_dict(self): @@ -37,7 +40,7 @@ def associate_dict(self): path_to_institution_json = "" detected = [] - institution_dict = json.load(path_to_institution_json) + institution_dict = open_json(path_to_institution_json) for key in institution_dict.keys(): if key in self.filename: @@ -79,13 +82,19 @@ def load_dictionary(self): path_to_tools = "" dict_path = path_to_tools + "/schema/institution_schemas" + self.filename - self.dictionary = json.load(dict_path) + self.dictionary = open_json(dict_path) return def translate_dataframe(self): """Use the corresponding dictionary to translate the df""" # if dictionary is "none" or similar, do nothing - pass + + for key, value in self.dictionary["equivalence"].items(): + self.translate_dataframe[key] = self.dataframe[value] + + for key, value in self.dictionary["constants"].items(): + self.translate_dataframe[key] = value + return def verify_translated_dataframe(self): From 2f8004a66b36a7138efc9b7924341fc70c202ff2 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 29 Jun 2022 21:05:08 +0200 Subject: [PATCH 0579/1454] updated docstrings and notes --- relecov_tools/metadata_homogeneizer.py | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index ca05cf61..d38c0c25 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -1,17 +1,21 @@ #!/usr/bin/env python # Imports +import os import sys import json import pandas as pd def check_extension(instring, extensions): + """Given a file as a string and a list of possible extensions, + returns true if the extension can be found in the file""" for extension in extensions: if instring.endswith(extension): return True def open_json(json_path): + """Load the json file""" with open(json_path) as file: json_dict = json.load(file) return json_dict @@ -24,6 +28,10 @@ def __init__(filename, self): self.dictionary = None self.centre = None self.dataframe = None + + # To Do: replace string with local file system for testing + # Header path can be found in conf/configuration.json + header_path = "" self.translated_dataframe = pd.DataFrame(columns=open_json(header_path)["new_table_headers"]) return @@ -56,9 +64,8 @@ def associate_dict(self): return def load_dataframe(self): - """Read the metadata file""" - # check possible extensions - # load with pandas + """Detect possible extensions for the metadata file + Open it into a dataframe""" excel_extensions = [".xlsx", ".xls", ".xlsm", ".xlsb"] odf_extension = [".odf"] @@ -80,6 +87,7 @@ def load_dataframe(self): def load_dictionary(self): """Load the corresponding dictionary""" + # To Do: replace string with local file system for testing path_to_tools = "" dict_path = path_to_tools + "/schema/institution_schemas" + self.filename self.dictionary = open_json(dict_path) From d510430e527467a3e5d78e9266543436807e86b5 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 29 Jun 2022 21:05:21 +0200 Subject: [PATCH 0580/1454] prettified schemas --- .../schema/institution_schemas/HUNSC-ITER.json | 14 ++++++++------ .../schema/institution_schemas/ISCIII.json | 11 ++++++----- 2 files changed, 14 insertions(+), 11 deletions(-) diff --git a/relecov_tools/schema/institution_schemas/HUNSC-ITER.json b/relecov_tools/schema/institution_schemas/HUNSC-ITER.json index 93827e6d..0ac43269 100644 --- a/relecov_tools/schema/institution_schemas/HUNSC-ITER.json +++ b/relecov_tools/schema/institution_schemas/HUNSC-ITER.json @@ -1,6 +1,6 @@ { - "equivalence": - {"Sample ID given by originating laboratory": "Sample ID given by originating laboratory", + "equivalence": { + "Sample ID given by originating laboratory": "Sample ID given by originating laboratory", "Sample ID given by the submitting laboratory": "Sample ID given by the submitting laboratory", "Originating Laboratory": "Originating lab", "Submitting Institution": "Submitting lab", @@ -12,11 +12,13 @@ "Sequencing Instrument Model": "Sequencing technology", "Analysis Authors": "Authors", "Author Submitter": "Submitter", - "Authors": "Authors"}, - "constants": - {"Biological Sample Storage Condition": "-80ºC", + "Authors": "Authors" + }, + "constants": { + "Biological Sample Storage Condition": "-80ºC", "Collection Device": "Swab", - "Source material": "VIRAL RNA"}, + "Source material": "VIRAL RNA" + }, "empty": [], "outer": {} } \ No newline at end of file diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 33d6dbc2..d60ba3f0 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -1,6 +1,6 @@ { - "equivalence": - {"Public Health sample id": "Código SiViEs", + "equivalence": { + "Public Health sample id": "Código SiViEs", "Sample ID given by originating laboratory": "Ref Hospital", "Sample ID given by the submitting laboratory": "ID CNM", "Sample ID given in the microbiology lab": "ID VI-VRP", @@ -13,7 +13,8 @@ "Host Age": "Grupo edad", "Diagnostic Pcr Ct Value 1": "PCR genE", "Sequencing Date": "Fecha de secuenciación", - "Rna Extraction Protocol": ""}, - "constants": {}, - "outer": {} + "Rna Extraction Protocol": "" + }, + "constants": {}, + "outer": {} } \ No newline at end of file From 77da3c07c765ede9143dca1d9861ebdf8898f038 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 29 Jun 2022 21:09:41 +0200 Subject: [PATCH 0581/1454] removed the "empty" category --- relecov_tools/schema/institution_schemas/HUGTiP.json | 1 - relecov_tools/schema/institution_schemas/HUNSC-ITER.json | 1 - 2 files changed, 2 deletions(-) diff --git a/relecov_tools/schema/institution_schemas/HUGTiP.json b/relecov_tools/schema/institution_schemas/HUGTiP.json index 7b2f4637..b83a10cc 100644 --- a/relecov_tools/schema/institution_schemas/HUGTiP.json +++ b/relecov_tools/schema/institution_schemas/HUGTiP.json @@ -49,6 +49,5 @@ "Sequence file R1 fastq": "", "Sequence file R2 fastq": "" }, - "empty" : {}, "outer" : {} } diff --git a/relecov_tools/schema/institution_schemas/HUNSC-ITER.json b/relecov_tools/schema/institution_schemas/HUNSC-ITER.json index 0ac43269..e25d36aa 100644 --- a/relecov_tools/schema/institution_schemas/HUNSC-ITER.json +++ b/relecov_tools/schema/institution_schemas/HUNSC-ITER.json @@ -19,6 +19,5 @@ "Collection Device": "Swab", "Source material": "VIRAL RNA" }, - "empty": [], "outer": {} } \ No newline at end of file From d8aebdf18ccc4256b70dd03f482eab053dee61c8 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 29 Jun 2022 21:16:32 +0200 Subject: [PATCH 0582/1454] linted script! --- relecov_tools/metadata_homogeneizer.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index d38c0c25..e42edef1 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -1,25 +1,27 @@ #!/usr/bin/env python # Imports -import os +# import os import sys import json import pandas as pd def check_extension(instring, extensions): - """Given a file as a string and a list of possible extensions, + """Given a file as a string and a list of possible extensions, returns true if the extension can be found in the file""" for extension in extensions: if instring.endswith(extension): return True + def open_json(json_path): """Load the json file""" with open(json_path) as file: json_dict = json.load(file) return json_dict + class Homogeneizer: """Homogeneizer object""" @@ -33,7 +35,9 @@ def __init__(filename, self): # Header path can be found in conf/configuration.json header_path = "" - self.translated_dataframe = pd.DataFrame(columns=open_json(header_path)["new_table_headers"]) + self.translated_dataframe = pd.DataFrame( + columns=open_json(header_path)["new_table_headers"] + ) return def associate_dict(self): @@ -102,7 +106,7 @@ def translate_dataframe(self): for key, value in self.dictionary["constants"].items(): self.translate_dataframe[key] = value - + return def verify_translated_dataframe(self): From 7e10f8951d1af31ec1f9ea2a4b8ba10f1e96be85 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 08:59:05 +0200 Subject: [PATCH 0583/1454] added cap-insensitive search --- relecov_tools/metadata_homogeneizer.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index e42edef1..79043027 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -55,7 +55,7 @@ def associate_dict(self): institution_dict = open_json(path_to_institution_json) for key in institution_dict.keys(): - if key in self.filename: + if key.lower() in self.filename.lower(): detected.append(institution_dict[key]) if len(set(detected)) != 1: From 4be30f25bbb1d0931c670974d65ac14ce9b3be4b Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 08:59:15 +0200 Subject: [PATCH 0584/1454] update --- relecov_tools/metadata_homogeneizer.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 79043027..54361ddc 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -55,6 +55,7 @@ def associate_dict(self): institution_dict = open_json(path_to_institution_json) for key in institution_dict.keys(): + # cap insensitive if key.lower() in self.filename.lower(): detected.append(institution_dict[key]) From 990f8cd342cb28680a3efa692d16048834e0d0cf Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 10:14:13 +0200 Subject: [PATCH 0585/1454] updated ISCIII schema (just so it works) --- .../schema/institution_schemas/ISCIII.json | 42 +++++++++++++++++-- 1 file changed, 39 insertions(+), 3 deletions(-) diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index d60ba3f0..9bea8246 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -1,6 +1,6 @@ { "equivalence": { - "Public Health sample id": "Código SiViEs", + "Public Health sample id (SIVIES)": "Código SiViEs", "Sample ID given by originating laboratory": "Ref Hospital", "Sample ID given by the submitting laboratory": "ID CNM", "Sample ID given in the microbiology lab": "ID VI-VRP", @@ -15,6 +15,42 @@ "Sequencing Date": "Fecha de secuenciación", "Rna Extraction Protocol": "" }, - "constants": {}, + "constants": { + "ENA Sample ID": "", + "GISAID Virus Name": "", + "GISAID id": "", + "Submitting Institution": "", + "Purpose of sampling": "", + "Specimen source": "", + "Environmental Material": "", + "Environmental System": "", + "Collection Device": "", + "Host": "", + "Host Gender": "", + "Commercial All-in-one library kit": "", + "Library Preparation Kit": "", + "Enrichment Protocol": "", + "If Enrichment Protocol. If Other,Specify": "", + "Enrichment panel/assay": "", + "If Enrichment panel/assay. If Other, Specify": "", + "Enrichment panel/assay version": "", + "Number Of Samples In Run": "", + "Runid": "", + "Sequencing Instrument Model": "", + "Flowcell Kit": "", + "Source material": "", + "Capture method": "", + "Sequencing technique": "", + "Library Layout": "", + "Gene Name 1": "", + "Diagnostic Pcr Ct Value 1": "", + "Gene Name 2": "", + "Diagnostic Pcr Ct Value-2": "", + "Analysis Authors": "", + "Author Submitter": "", + "Authors": "", + "Sequence file R1 fastq": "", + "Sequence file R2 fastq": "" + }, "outer": {} -} \ No newline at end of file +} From e457dce0968309ab3f94a0884258ca6018111084 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 10:15:46 +0200 Subject: [PATCH 0586/1454] new function to update --- relecov_tools/metadata_homogeneizer.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 54361ddc..0ffcc95a 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -115,3 +115,7 @@ def verify_translated_dataframe(self): pass return + + def export_translated_dataframe(self): + pass + return \ No newline at end of file From 27e1e058878b5987cbc258e0a42aa8ac5e039aab Mon Sep 17 00:00:00 2001 From: mlarjim Date: Thu, 30 Jun 2022 11:15:21 +0200 Subject: [PATCH 0587/1454] lintin 1 --- relecov_tools/gisaid_upload.py | 47 ++++++++++++---------------------- 1 file changed, 16 insertions(+), 31 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 8c8fd13f..3df434e0 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -9,12 +9,12 @@ import sys import os -import ftplib +#import ftplib import relecov_tools.utils -from relecov_tools.config_json import ConfigJson +#from relecov_tools.config_json import ConfigJson -import site +#import site log = logging.getLogger(__name__) @@ -49,24 +49,12 @@ def __init__( ) else: self.passwd = passwd - if center is None: - self.center = relecov_tools.utils.prompt_text( - msg="Enter your center name") - else: - self.center = center if source_json is None: self.source_json_file = relecov_tools.utils.prompt_path( msg="Select the ENA json file to upload" ) else: self.source_json_file = source_json - if dev is None: - self.dev = relecov_tools.utils.prompt_yn_question( - msg="Do you want to test upload data?" - ) - else: - self.dev = dev - if customized_project is None: self.customized_project = None else: @@ -103,24 +91,21 @@ def convert_input_json_to_ena(self): """Split the input ena json, in samples and runs json""" pass - ####################################### - ## Metadatos + # Metadatos + def metadata_to_csv(self): - data= relecov_utils.tools.read_json_file(self.metadata) - df_data= pd.DataFrame(data) - df_data.to_csv("meta_gisaid.csv") - - - ## Sequences + data = relecov_tools.utils.read_json_file(self.metadata) + df_data = pd.DataFrame(data) + df_data.to_csv("meta_gisaid.csv") + + # Sequences # Unificar en multifasta # Cambiar headers/id - - - ## Upload + + # Upload # Subir con cli3 - - def upload(self): - """Create the required files and upload to ENA""" - self.convert_input_json_to_ena() - self.create_structure_to_ena() + # def upload(self): + #"""Create the required files and upload to ENA""" + # self.convert_input_json_to_ena() + # self.create_structure_to_ena() From 20020372f7837fe2fde3036bbc305e78ff6b290d Mon Sep 17 00:00:00 2001 From: mlarjim Date: Thu, 30 Jun 2022 11:25:50 +0200 Subject: [PATCH 0588/1454] lintin 2 --- relecov_tools/gisaid_upload.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 3df434e0..3b59a418 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -9,12 +9,12 @@ import sys import os -#import ftplib +# import ftplib import relecov_tools.utils -#from relecov_tools.config_json import ConfigJson +# from relecov_tools.config_json import ConfigJson -#import site +# import site log = logging.getLogger(__name__) @@ -106,6 +106,6 @@ def metadata_to_csv(self): # Subir con cli3 # def upload(self): - #"""Create the required files and upload to ENA""" + # """Create the required files and upload to ENA""" # self.convert_input_json_to_ena() # self.create_structure_to_ena() From 1358db2099ff2660b4b9bd441f785498c6fdaf22 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Adri=C3=A1n=20Mu=C3=B1oz=20Barrera?= Date: Thu, 30 Jun 2022 10:28:55 +0100 Subject: [PATCH 0589/1454] HUNSC-ITER.json and laboratory_address.json updates --- relecov_tools/conf/laboratory_address.json | 8 +++++ .../institution_schemas/HUNSC-ITER.json | 34 ++++++++++++++++++- 2 files changed, 41 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 8fe15224..5c1d2ea2 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -71,6 +71,14 @@ "geo_loc_city": "Santa Cruz de Tenerife", "geo_loc_country": "Spain" }, + { + "collecting_institution": "Instituto Tecnológico y de Energías Renovables", + "collecting_institution_address": "Polígono Industrial de Granadilla, s/n", + "collecting_institution_email": "genomica@iter.es", + "geo_loc_state": "Canarias", + "geo_loc_city": "Santa Cruz de Tenerife", + "geo_loc_country": "Spain" + }, { "collecting_institution": "Hospital Universitario de Gran Canaria", "collecting_institution_address": "Bco. de la Ballena s/n", diff --git a/relecov_tools/schema/institution_schemas/HUNSC-ITER.json b/relecov_tools/schema/institution_schemas/HUNSC-ITER.json index e25d36aa..209615fc 100644 --- a/relecov_tools/schema/institution_schemas/HUNSC-ITER.json +++ b/relecov_tools/schema/institution_schemas/HUNSC-ITER.json @@ -9,15 +9,47 @@ "Host": "Host", "Host Age": "Patient age", "Host Gender": "Gender", + "Library Preparation Kit": "Assembly method", "Sequencing Instrument Model": "Sequencing technology", "Analysis Authors": "Authors", "Author Submitter": "Submitter", "Authors": "Authors" }, "constants": { + "Public Health sample id (SIVIES)": "NA", + "Sample ID given in the microbiology lab": "NA", + "Sample ID given if multiple rna-extraction or passages": "NA", + "Sample ID given for sequencing": "NA", + "ENA Sample ID": "NA", + "GISAID Virus Name": "NA", + "GISAID id": "NA", + "Sample Received Date": "NA", + "Purpose of sampling": "NA", "Biological Sample Storage Condition": "-80ºC", + "Environmental Material": "NA", + "Environmental System": "NA", "Collection Device": "Swab", - "Source material": "VIRAL RNA" + "Sequencing Date": "NA", + "Rna Extraction Protocol": "NA", + "Commercial All-in-one library kit": "NA", + "Enrichment Protocol": "NA", + "If Enrichment Protocol. If Other,Specify": "NA", + "Enrichment panel/assay": "NA", + "If Enrichment panel/assay. If Other, Specify": "NA", + "Enrichment panel/assay version": "NA", + "Number Of Samples In Run": "NA", + "Runid": "NA", + "Flowcell Kit": "NA", + "Source material": "VIRAL RNA", + "Capture method": "NA", + "Sequencing technique": "NA", + "Library Layout": "NA", + "Gene Name 1": "NA", + "Diagnostic Pcr Ct Value 1": "NA", + "Gene Name 2": "NA", + "Diagnostic Pcr Ct Value-2": "NA", + "Sequence file R1 fastq": "NA", + "Sequence file R2 fastq": "NA" }, "outer": {} } \ No newline at end of file From d87d33505d9ffd31393ae673a635da916b2684b3 Mon Sep 17 00:00:00 2001 From: mlarjim Date: Thu, 30 Jun 2022 11:33:17 +0200 Subject: [PATCH 0590/1454] lintin 3 --- relecov_tools/gisaid_upload.py | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 3b59a418..bbf86e2d 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -11,6 +11,7 @@ # import ftplib import relecov_tools.utils + # from relecov_tools.config_json import ConfigJson @@ -79,10 +80,8 @@ def __init__( else: self.metadata = metadata if not os.path.isfile(self.source_json_file): - log.error("json data file %s does not exist ", - self.source_json_file) - stderr.print( - f"[red]json data file {self.source_json_file} does not exist") + log.error("json data file %s does not exist ", self.source_json_file) + stderr.print(f"[red]json data file {self.source_json_file} does not exist") sys.exit(1) with open(self.source_json_file, "r") as fh: self.json_data = json.loads(fh.read()) @@ -106,6 +105,6 @@ def metadata_to_csv(self): # Subir con cli3 # def upload(self): - # """Create the required files and upload to ENA""" - # self.convert_input_json_to_ena() - # self.create_structure_to_ena() + # """Create the required files and upload to ENA""" + # self.convert_input_json_to_ena() + # self.create_structure_to_ena() From 971db563022f4b0b1d5cbec4cdd12d072c876671 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 12:10:35 +0200 Subject: [PATCH 0591/1454] update on ISCIII schema --- relecov_tools/schema/institution_schemas/ISCIII.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 9bea8246..823f98b8 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -13,9 +13,10 @@ "Host Age": "Grupo edad", "Diagnostic Pcr Ct Value 1": "PCR genE", "Sequencing Date": "Fecha de secuenciación", - "Rna Extraction Protocol": "" + }, "constants": { + "Rna Extraction Protocol": "", "ENA Sample ID": "", "GISAID Virus Name": "", "GISAID id": "", From a68464b01dc097984686ca8cc43cafe09a4f4df9 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 12:10:51 +0200 Subject: [PATCH 0592/1454] bug fixing! --- relecov_tools/metadata_homogeneizer.py | 49 ++++++++++++++++++-------- 1 file changed, 34 insertions(+), 15 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 0ffcc95a..1c54fad1 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -14,7 +14,6 @@ def check_extension(instring, extensions): if instring.endswith(extension): return True - def open_json(json_path): """Load the json file""" with open(json_path) as file: @@ -25,16 +24,17 @@ def open_json(json_path): class Homogeneizer: """Homogeneizer object""" - def __init__(filename, self): + def __init__(self, filename): self.filename = filename - self.dictionary = None + self.dictionary_path = None + self.dicionary = None self.centre = None self.dataframe = None # To Do: replace string with local file system for testing # Header path can be found in conf/configuration.json - header_path = "" + header_path = "Schemas/configuration.json" self.translated_dataframe = pd.DataFrame( columns=open_json(header_path)["new_table_headers"] ) @@ -49,22 +49,26 @@ def associate_dict(self): # raise error when in doubt # must check on schema/institution_schemas - path_to_institution_json = "" + path_to_institution_json = "Schemas/institution_to_schema.json" detected = [] institution_dict = open_json(path_to_institution_json) for key in institution_dict.keys(): # cap insensitive - if key.lower() in self.filename.lower(): + print(self.filename.split("/")[-1].lower()) + if key.lower() in self.filename.split("/")[-1].lower(): detected.append(institution_dict[key]) - if len(set(detected)) != 1: + if len(set(detected)) == 0: + print(f"No file could be found matching with the '{self.filename}' filename given.") + + elif len(set(detected)) > 1: print("some problems arised!!!") # change this to an elegant form sys.exit() # maybe check which ones are being mixed or when none is being found else: - print("works fine") # delete this after testing - self.dictionary = detected[0] # first item, they are all equal + self.dictionary_path = detected[0] # first item, they are all equal + print(f"JSON file found successfully: {self.dictionary_path}") # delete this after testing return @@ -94,7 +98,7 @@ def load_dictionary(self): # To Do: replace string with local file system for testing path_to_tools = "" - dict_path = path_to_tools + "/schema/institution_schemas" + self.filename + dict_path = path_to_tools + "Schemas/" + self.dictionary_path self.dictionary = open_json(dict_path) return @@ -103,19 +107,34 @@ def translate_dataframe(self): # if dictionary is "none" or similar, do nothing for key, value in self.dictionary["equivalence"].items(): - self.translate_dataframe[key] = self.dataframe[value] + if len(value) == 0: + print(f"Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'") + elif value in self.dataframe.columns: + self.translated_dataframe[key] = self.dataframe[value] + else: + print(f"Column '{value}' indicated in the '{self.dictionary_path}' schema could not be found.") for key, value in self.dictionary["constants"].items(): - self.translate_dataframe[key] = value + if key in self.translated_dataframe.columns: + self.translated_dataframe[key] = value + else: + print(f"Value '{key}' in schema not found in the resulting dataframe") + return def verify_translated_dataframe(self): """Checks if the dataframe holds all the needed values for the relecov tools suite""" - + + if self.dataframe.shape[0] != self.translated_dataframe.shape[0]: + print("Different number of rows after translation") + else: + print("Same number of rows after translation") + pass return - def export_translated_dataframe(self): + def export_translated_dataframe(self): pass - return \ No newline at end of file + return + \ No newline at end of file From 642467fed16f38d91e6ad70cc6d54c6cf9c35fdc Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 12:16:57 +0200 Subject: [PATCH 0593/1454] linting --- relecov_tools/metadata_homogeneizer.py | 27 ++++++++++++++++---------- 1 file changed, 17 insertions(+), 10 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 1c54fad1..20190dfc 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -14,6 +14,7 @@ def check_extension(instring, extensions): if instring.endswith(extension): return True + def open_json(json_path): """Load the json file""" with open(json_path) as file: @@ -61,14 +62,18 @@ def associate_dict(self): detected.append(institution_dict[key]) if len(set(detected)) == 0: - print(f"No file could be found matching with the '{self.filename}' filename given.") - + print( + f"No file could be found matching with the '{self.filename}' filename given." + ) + elif len(set(detected)) > 1: print("some problems arised!!!") # change this to an elegant form sys.exit() # maybe check which ones are being mixed or when none is being found else: self.dictionary_path = detected[0] # first item, they are all equal - print(f"JSON file found successfully: {self.dictionary_path}") # delete this after testing + print( + f"JSON file found successfully: {self.dictionary_path}" + ) # delete this after testing return @@ -108,33 +113,35 @@ def translate_dataframe(self): for key, value in self.dictionary["equivalence"].items(): if len(value) == 0: - print(f"Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'") + print( + f"Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'" + ) elif value in self.dataframe.columns: self.translated_dataframe[key] = self.dataframe[value] else: - print(f"Column '{value}' indicated in the '{self.dictionary_path}' schema could not be found.") + print( + f"Column '{value}' indicated in the '{self.dictionary_path}' schema could not be found." + ) for key, value in self.dictionary["constants"].items(): if key in self.translated_dataframe.columns: self.translated_dataframe[key] = value else: print(f"Value '{key}' in schema not found in the resulting dataframe") - return def verify_translated_dataframe(self): """Checks if the dataframe holds all the needed values for the relecov tools suite""" - + if self.dataframe.shape[0] != self.translated_dataframe.shape[0]: print("Different number of rows after translation") else: print("Same number of rows after translation") - + pass return - def export_translated_dataframe(self): + def export_translated_dataframe(self): pass return - \ No newline at end of file From 8e56f82474a8e4938e7104bcb187f0d584d13650 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 12:40:16 +0200 Subject: [PATCH 0594/1454] removed testing print --- relecov_tools/metadata_homogeneizer.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 20190dfc..9d7eeff2 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -57,7 +57,6 @@ def associate_dict(self): for key in institution_dict.keys(): # cap insensitive - print(self.filename.split("/")[-1].lower()) if key.lower() in self.filename.split("/")[-1].lower(): detected.append(institution_dict[key]) @@ -95,6 +94,8 @@ def load_dataframe(self): self.dataframe = pd.read_csv(self.filename, sep=",", header=0) elif check_extension(self.filename, tsv_extensions): self.dataframe = pd.read_csv(self.filename, sep="\t", header=0) + else: + print(f"The extension of the file '{self.filename}' could not be identified. My bad there.") return @@ -127,7 +128,7 @@ def translate_dataframe(self): if key in self.translated_dataframe.columns: self.translated_dataframe[key] = value else: - print(f"Value '{key}' in schema not found in the resulting dataframe") + print(f"Value '{key}' in the '{self.dictionary_path}' schema not found in the resulting dataframe") return @@ -137,7 +138,9 @@ def verify_translated_dataframe(self): if self.dataframe.shape[0] != self.translated_dataframe.shape[0]: print("Different number of rows after translation") else: - print("Same number of rows after translation") + print("Number of rows: OK") + + if pass return From c0297d0b416a63c2a5833263bb8a87c16f960c37 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 12:41:25 +0200 Subject: [PATCH 0595/1454] removed unnecessary if --- relecov_tools/metadata_homogeneizer.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 9d7eeff2..69b046c2 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -139,8 +139,6 @@ def verify_translated_dataframe(self): print("Different number of rows after translation") else: print("Number of rows: OK") - - if pass return From 30fd37604bc3c1e09a2cc341b605d4785fcb5ca2 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 13:01:10 +0200 Subject: [PATCH 0596/1454] linting --- relecov_tools/metadata_homogeneizer.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 69b046c2..df320b74 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -95,7 +95,9 @@ def load_dataframe(self): elif check_extension(self.filename, tsv_extensions): self.dataframe = pd.read_csv(self.filename, sep="\t", header=0) else: - print(f"The extension of the file '{self.filename}' could not be identified. My bad there.") + print( + f"The extension of the file '{self.filename}' could not be identified. My bad there." + ) return @@ -128,7 +130,9 @@ def translate_dataframe(self): if key in self.translated_dataframe.columns: self.translated_dataframe[key] = value else: - print(f"Value '{key}' in the '{self.dictionary_path}' schema not found in the resulting dataframe") + print( + f"Value '{key}' in the '{self.dictionary_path}' schema not found in the resulting dataframe" + ) return From f30e2c0fc812f406b35956877c9b15b9f7dc36cd Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 30 Jun 2022 13:31:59 +0200 Subject: [PATCH 0597/1454] new organization example_data --- .../example_data/ENA_TEST1_V1.R1.fastq.gz | Bin 4221 -> 0 bytes .../example_data/METADATA_LAB_TEST.xlsx | Bin 493368 -> 0 bytes ...B_TEST_2022_04_25_00_03_GISAID_mapped.json | 0 ..._LAB_TEST_2022_04_28_21_05_ENA_mapped.json | 0 .../invalid_METADATA_LAB_TEST.json | 136 - .../long_table_2022_06_13_22_34_59.json | 100657 --------------- .../metadata_lab_COD_test_01_20220422.xlsx | Bin 490767 -> 0 bytes .../processed_METADATA_LAB_TEST.json | 782 - .../bioinfo_metadata.json | 0 .../consensus_genome_length.csv | 0 .../lab_metadata_20220208.xlsx | Bin .../mapping_illumina.tab | 0 .../md5sum_MiSeq_GEN_267_20220208_ICasas.md5 | 0 .../software_versions.yml | 0 .../summary_variants_metrics_mqc.csv | 97 + .../variants_long_table.csv | 0 .../lab_metadata_20220208.xlsx | Bin 0 -> 403686 bytes .../samples_data_COD_test_01_20220422.json | 82 - relecov_tools/example_data/to_ena_2.json | 51 - 19 files changed, 97 insertions(+), 101708 deletions(-) delete mode 100644 relecov_tools/example_data/ENA_TEST1_V1.R1.fastq.gz delete mode 100644 relecov_tools/example_data/METADATA_LAB_TEST.xlsx rename relecov_tools/example_data/{ => ena_upload_module}/processed_METADATA_LAB_TEST_2022_04_25_00_03_GISAID_mapped.json (100%) rename relecov_tools/example_data/{ => ena_upload_module}/processed_METADATA_LAB_TEST_2022_04_28_21_05_ENA_mapped.json (100%) delete mode 100644 relecov_tools/example_data/invalid_METADATA_LAB_TEST.json delete mode 100644 relecov_tools/example_data/long_table_2022_06_13_22_34_59.json delete mode 100644 relecov_tools/example_data/metadata_lab_COD_test_01_20220422.xlsx delete mode 100644 relecov_tools/example_data/processed_METADATA_LAB_TEST.json rename relecov_tools/example_data/{ => read_bioinfo_metadata}/bioinfo_metadata.json (100%) rename relecov_tools/example_data/{ => read_bioinfo_metadata}/consensus_genome_length.csv (100%) rename relecov_tools/example_data/{ => read_bioinfo_metadata}/lab_metadata_20220208.xlsx (100%) rename relecov_tools/example_data/{ => read_bioinfo_metadata}/mapping_illumina.tab (100%) rename relecov_tools/example_data/{ => read_bioinfo_metadata}/md5sum_MiSeq_GEN_267_20220208_ICasas.md5 (100%) rename relecov_tools/example_data/{ => read_bioinfo_metadata}/software_versions.yml (100%) create mode 100755 relecov_tools/example_data/read_bioinfo_metadata/summary_variants_metrics_mqc.csv rename 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diff --git a/relecov_tools/example_data/bioinfo_metadata.json b/relecov_tools/example_data/read_bioinfo_metadata/bioinfo_metadata.json similarity index 100% rename from relecov_tools/example_data/bioinfo_metadata.json rename to relecov_tools/example_data/read_bioinfo_metadata/bioinfo_metadata.json diff --git a/relecov_tools/example_data/consensus_genome_length.csv b/relecov_tools/example_data/read_bioinfo_metadata/consensus_genome_length.csv similarity index 100% rename from relecov_tools/example_data/consensus_genome_length.csv rename to relecov_tools/example_data/read_bioinfo_metadata/consensus_genome_length.csv diff --git a/relecov_tools/example_data/lab_metadata_20220208.xlsx b/relecov_tools/example_data/read_bioinfo_metadata/lab_metadata_20220208.xlsx similarity index 100% rename from relecov_tools/example_data/lab_metadata_20220208.xlsx rename to relecov_tools/example_data/read_bioinfo_metadata/lab_metadata_20220208.xlsx diff --git a/relecov_tools/example_data/mapping_illumina.tab b/relecov_tools/example_data/read_bioinfo_metadata/mapping_illumina.tab similarity index 100% rename from relecov_tools/example_data/mapping_illumina.tab rename to relecov_tools/example_data/read_bioinfo_metadata/mapping_illumina.tab diff --git a/relecov_tools/example_data/md5sum_MiSeq_GEN_267_20220208_ICasas.md5 b/relecov_tools/example_data/read_bioinfo_metadata/md5sum_MiSeq_GEN_267_20220208_ICasas.md5 similarity index 100% rename from relecov_tools/example_data/md5sum_MiSeq_GEN_267_20220208_ICasas.md5 rename to relecov_tools/example_data/read_bioinfo_metadata/md5sum_MiSeq_GEN_267_20220208_ICasas.md5 diff --git a/relecov_tools/example_data/software_versions.yml b/relecov_tools/example_data/read_bioinfo_metadata/software_versions.yml similarity index 100% rename from relecov_tools/example_data/software_versions.yml rename to relecov_tools/example_data/read_bioinfo_metadata/software_versions.yml diff --git a/relecov_tools/example_data/read_bioinfo_metadata/summary_variants_metrics_mqc.csv b/relecov_tools/example_data/read_bioinfo_metadata/summary_variants_metrics_mqc.csv new file mode 100755 index 00000000..2edeb8d9 --- /dev/null +++ b/relecov_tools/example_data/read_bioinfo_metadata/summary_variants_metrics_mqc.csv @@ -0,0 +1,97 @@ +Sample,# Input reads,# Trimmed reads (fastp),% Non-host reads (Kraken 2),% Mapped reads,# Mapped reads,# Trimmed reads (iVar),Coverage median,% Coverage > 1x,% Coverage > 10x,# SNPs,# INDELs,# Missense variants,# Ns per 100kb consensus,Pangolin lineage,Nextclade clade +214821,316942,285604,98.9180823797986,98.54,281428,281038,287,98.0,92.0,20,1,12,8442.32,NA,NA +214822,382722,306868,36.6652762751411,20.09,61642,61447,6,67.0,41.0,16,2,12,58831.99,NA,NA +214823,298848,196898,41.969953986327944,0.1,204,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +214824,364,248,66.93548387096774,55.65,138,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA 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zE^oK7G_X8Xn&qi4NoG|uW}nlroh;CH&*(U-dlLX)k6@KlY# z&%5x!F|qNp^)XUI*BLcqpTZ0sG2Fez(2y2#w*(K$7zSchXmIq`n5U?H9|9l9E zAb-rvsnPoB<6@%?kuxME8G7a2h;fi)8FoQk{R4unryxu>P8$<#jEeD{W{lQLEhOb$ zv->wNED@i0y2kM7zSV|Ljf#>QU77h(!Xk|9)LamrsWCdaw;)U&Zj6l8N5)2skB`#F zOp*FP$lSSoUp^}cosTvXp0DwNkiL)f7c*0@kBz}r;I9EvU(vnVWPHvML2%O6{>nL5 zr{Arh`d40*`pUVmTOWFVDhMM!bFC#y-bu-?^q2aIwR_8{oel{?mTzrYMkY8*$)c6| zO74|WPR2!o@WYQyYss>8XcMWgydd?J?N^WZHoG7Q%lFon<&6W9U-6Ur%KE0R!w&a> zo$qk2CCj$;E>g1elln@M*MGuFCJMsllG Date: Thu, 30 Jun 2022 13:40:55 +0200 Subject: [PATCH 0598/1454] Update ISCIII.json --- .../schema/institution_schemas/ISCIII.json | 29 ++++++++++--------- 1 file changed, 15 insertions(+), 14 deletions(-) diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 823f98b8..1fc1e3e0 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -16,39 +16,40 @@ }, "constants": { - "Rna Extraction Protocol": "", + "Biological Sample Storage Condition": "-80 C", + "Rna Extraction Protocol": "RT-PCR", "ENA Sample ID": "", "GISAID Virus Name": "", "GISAID id": "", "Submitting Institution": "", - "Purpose of sampling": "", - "Specimen source": "", + "Purpose of sampling": "Surveillance", + "Specimen source": "Nasopharyngeal exudate", "Environmental Material": "", - "Environmental System": "", + "Environmental System": "Swab", "Collection Device": "", - "Host": "", + "Host": "Human", "Host Gender": "", "Commercial All-in-one library kit": "", - "Library Preparation Kit": "", - "Enrichment Protocol": "", + "Library Preparation Kit": "Illumina DNA Prep", + "Enrichment Protocol": "Amplicon", "If Enrichment Protocol. If Other,Specify": "", - "Enrichment panel/assay": "", + "Enrichment panel/assay": "ARTIC", "If Enrichment panel/assay. If Other, Specify": "", "Enrichment panel/assay version": "", "Number Of Samples In Run": "", "Runid": "", "Sequencing Instrument Model": "", "Flowcell Kit": "", - "Source material": "", - "Capture method": "", - "Sequencing technique": "", - "Library Layout": "", - "Gene Name 1": "", + "Source material": "Viral RNA", + "Capture method": "PCR", + "Sequencing technique": "Amplicon", + "Library Layout": "Paired", + "Gene Name 1": "ORF E", "Diagnostic Pcr Ct Value 1": "", "Gene Name 2": "", "Diagnostic Pcr Ct Value-2": "", "Analysis Authors": "", - "Author Submitter": "", + "Author Submitter": "A. Monzón; F. Casas; I. Jiménez; M. Camarero; P. Zaballos; ROMAN SOTO; S. Cuesta, I.; S. Iglesias-Caballero; S. Pozo; S. Varona; SERGIO; Sandonís; V. Vázquez-Morón", "Authors": "", "Sequence file R1 fastq": "", "Sequence file R2 fastq": "" From 50f4e6e11b25a5765cdb0fd4ec3854327b735158 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 30 Jun 2022 13:59:12 +0200 Subject: [PATCH 0599/1454] reorder examples_data and READMEs --- .../ENA_TEST1_V1.R1.fastq.gz | Bin .../example_data/0.download_module/README | 3 + .../1.read_lab_metadata_module/README | 5 + .../lab_metadata_20220208.xlsx | Bin 0 -> 403686 bytes .../2.validate_module/METADATA_LAB_TEST.xlsx | Bin 0 -> 493368 bytes .../example_data/2.validate_module/README | 6 + .../processed_METADATA_LAB_TEST.json | 782 ++++ .../example_data/3.map_module/README | 6 + .../example_data/4.ena_upload_module/README | 8 + ...B_TEST_2022_04_25_00_03_GISAID_mapped.json | 152 + ..._LAB_TEST_2022_04_28_21_05_ENA_mapped.json | 452 +++ .../bioinfo_metadata.json | 46 + .../consensus_genome_length.csv | 91 + .../lab_metadata_20220208.xlsx | Bin 0 -> 403686 bytes .../mapping_illumina.tab | 97 + .../md5sum_MiSeq_GEN_267_20220208_ICasas.md5 | 192 + .../software_versions.yml | 89 + .../summary_variants_metrics_mqc.csv | 97 + .../variants_long_table.csv | 3341 +++++++++++++++++ 19 files changed, 5367 insertions(+) rename relecov_tools/example_data/{download_module => 0.download_module}/ENA_TEST1_V1.R1.fastq.gz (100%) create mode 100644 relecov_tools/example_data/0.download_module/README create mode 100644 relecov_tools/example_data/1.read_lab_metadata_module/README create mode 100755 relecov_tools/example_data/1.read_lab_metadata_module/lab_metadata_20220208.xlsx create mode 100644 relecov_tools/example_data/2.validate_module/METADATA_LAB_TEST.xlsx create mode 100644 relecov_tools/example_data/2.validate_module/README create mode 100644 relecov_tools/example_data/2.validate_module/processed_METADATA_LAB_TEST.json create mode 100644 relecov_tools/example_data/3.map_module/README create mode 100644 relecov_tools/example_data/4.ena_upload_module/README create mode 100644 relecov_tools/example_data/4.ena_upload_module/processed_METADATA_LAB_TEST_2022_04_25_00_03_GISAID_mapped.json create mode 100644 relecov_tools/example_data/4.ena_upload_module/processed_METADATA_LAB_TEST_2022_04_28_21_05_ENA_mapped.json create mode 100644 relecov_tools/example_data/5.read_bioinfo_metadata/bioinfo_metadata.json create mode 100755 relecov_tools/example_data/5.read_bioinfo_metadata/consensus_genome_length.csv create mode 100755 relecov_tools/example_data/5.read_bioinfo_metadata/lab_metadata_20220208.xlsx create mode 100755 relecov_tools/example_data/5.read_bioinfo_metadata/mapping_illumina.tab create mode 100755 relecov_tools/example_data/5.read_bioinfo_metadata/md5sum_MiSeq_GEN_267_20220208_ICasas.md5 create mode 100755 relecov_tools/example_data/5.read_bioinfo_metadata/software_versions.yml create mode 100755 relecov_tools/example_data/5.read_bioinfo_metadata/summary_variants_metrics_mqc.csv create mode 100755 relecov_tools/example_data/5.read_bioinfo_metadata/variants_long_table.csv diff --git a/relecov_tools/example_data/download_module/ENA_TEST1_V1.R1.fastq.gz b/relecov_tools/example_data/0.download_module/ENA_TEST1_V1.R1.fastq.gz similarity index 100% rename from relecov_tools/example_data/download_module/ENA_TEST1_V1.R1.fastq.gz rename to relecov_tools/example_data/0.download_module/ENA_TEST1_V1.R1.fastq.gz diff --git a/relecov_tools/example_data/0.download_module/README b/relecov_tools/example_data/0.download_module/README new file mode 100644 index 00000000..263e66ca --- /dev/null +++ b/relecov_tools/example_data/0.download_module/README @@ -0,0 +1,3 @@ +Para usar este modulo se necesita: +usuario del sftp asociado al centro +contraseña asociada al usuario diff --git a/relecov_tools/example_data/1.read_lab_metadata_module/README b/relecov_tools/example_data/1.read_lab_metadata_module/README new file mode 100644 index 00000000..7ddb82c4 --- /dev/null +++ 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-0,0 +1,782 @@ +[ + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_material": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123456", + "collecting_institution": "HU Virgen de la Arrixaca", + "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", + "collecting_institution_email": "", + "collecting_lab_sample_id": "1197860", + "collection_device": "Swab", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "diagnostic_pcr_Ct_value_1": "45", + "diagnostic_pcr_Ct_value_2": "34", + "enrichment_protocol": "Amplicon", + "environmental_material": "Other", + "environmental_site": "Earth surface", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "f2facbd1d6c7e0972074ced31ccbfd8e", + "fastq_r2_md5": "fd9948be8da7a38b0f80659dfc21aeea", + "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", + "gene_name_1": "ORF 1ab", + "gene_name_2": "S", + "geo_loc_city": "Murcia", + "geo_loc_country": "Spain", + "geo_loc_latitude": "37.9861", + "geo_loc_longitude": "-1.1303", + "geo_loc_state": "Murcia", + "gisaid_id": "EPI_ISL_11222687", + "host_age": "55", + "host_common_name": "Human", + "host_disease": "COVID-19", + "host_gender": "Female", + "host_scientific_name": "Homo Sapiens", + "if_amplicon_protocol_if_other_especify": "", + "if_enrichment_protocol_is_other_specify": "", + "isolate_sample_id": "1197860", + "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_layout": "SINGLE", + "library_preparation_kit": "Truseq Nano", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "microbiology_lab_sample_id": "220407", + "number_of_samples_in_run": "96", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "2022CEU01394", + "purpose_of_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2021-04-13", + "sample_description": "Sample for surveillance", + "sample_received_date": "2021-05-13", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_001.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_001.fastq.gz", + "sequencing_date": "2022-02-22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 214824, + "study_alias": "RELECOV", + "study_id": "ERP137164", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202201751", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2022" + }, + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_material": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123457", + "collecting_institution": "HU Virgen de la Arrixaca", + "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", + "collecting_institution_email": "", + "collecting_lab_sample_id": "1197824", + "collection_device": "Swab", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "diagnostic_pcr_Ct_value_1": "12", + "diagnostic_pcr_Ct_value_2": "16", + "enrichment_protocol": "Amplicon", + "environmental_material": "Other", + "environmental_site": "Earth surface", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "9a460a812086516536c1a1023ab5f7fe", + "fastq_r2_md5": "41cd79b8a167d85eb06309207fd120cf", + "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", + "gene_name_1": "ORF 1ab", + "gene_name_2": "S", + "geo_loc_city": "Murcia", + "geo_loc_country": "Spain", + "geo_loc_latitude": "37.9861", + "geo_loc_longitude": "-1.1303", + "geo_loc_state": "Murcia", + "gisaid_id": "EPI_ISL_11222688", + "host_age": "59", + "host_common_name": "Human", + "host_disease": "COVID-19", + "host_gender": "Male", + "host_scientific_name": "Homo Sapiens", + "if_amplicon_protocol_if_other_especify": "", + "if_enrichment_protocol_is_other_specify": "", + "isolate_sample_id": "1197824", + "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_layout": "SINGLE", + "library_preparation_kit": "Truseq Nano", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "microbiology_lab_sample_id": "220433", + "number_of_samples_in_run": "96", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "2022CEU01469", + "purpose_of_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2021-03-31", + "sample_description": "Sample for surveillance", + "sample_received_date": "2021-05-13", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_002.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_002.fastq.gz", + "sequencing_date": "2022-02-22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 214832, + "study_alias": "RELECOV", + "study_id": "ERP137164", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202201678", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2023" + }, + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_material": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123458", + "collecting_institution": "HU Virgen de la Arrixaca", + "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", + "collecting_institution_email": "", + "collecting_lab_sample_id": "1197767", + "collection_device": "Swab", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "diagnostic_pcr_Ct_value_1": "45", + "diagnostic_pcr_Ct_value_2": "41", + "enrichment_protocol": "Amplicon", + "environmental_material": "Other", + "environmental_site": "Earth surface", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "c78fcb585a0f44734ce8c2aebf3eff33", + "fastq_r2_md5": "8361d5a6b50279fbc8c93226ecc3568a", + "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", + "gene_name_1": "ORF 1ab", + "gene_name_2": "S", + "geo_loc_city": "Murcia", + "geo_loc_country": "Spain", + "geo_loc_latitude": "37.9861", + "geo_loc_longitude": "-1.1303", + "geo_loc_state": "Murcia", + "gisaid_id": "EPI_ISL_11222689", + "host_age": "8", + "host_common_name": "Human", + "host_disease": "COVID-19", + "host_gender": "Female", + "host_scientific_name": "Homo Sapiens", + "if_amplicon_protocol_if_other_especify": "", + "if_enrichment_protocol_is_other_specify": "", + "isolate_sample_id": "1197767", + "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_layout": "SINGLE", + "library_preparation_kit": "Truseq Nano", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "microbiology_lab_sample_id": "220435", + "number_of_samples_in_run": "96", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "2022CEU03926", + "purpose_of_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2022-01-13", + "sample_description": "Sample for surveillance", + "sample_received_date": "2022-01-18", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_003.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_003.fastq.gz", + "sequencing_date": "2022-02-22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 220338, + "study_alias": "RELECOV", + "study_id": "ERP137164", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202201853", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2024" + }, + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "v.4", + "analysis_author": "Inmaculada Casas", + "anatomical_material": "Nasopharynx aspirate", + "author_submitter": "Maria de la Montaña", + "authors": "Inmaculada Casas,Maria de la Montaña", + "biosample_accession_ENA": "ERS123459", + "collecting_institution": "HU Virgen de la Arrixaca", + "collecting_institution_address": "Ctra. 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"/tmp/relecov/COD_test_01/20220422", + "rna_extraction_protocol": "In-house method for Opetrons robots", + "runID": "MiSeq_GEN_267_20220208_ICasas", + "run_alias": "", + "sample_collection_date": "2022-01-19", + "sample_description": "Sample for surveillance", + "sample_received_date": "2022-01-26", + "sample_storage_conditions": " -80ºC", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_0010.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_0010.fastq.gz", + "sequencing_date": "2022-02-22", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": 220639, + "study_alias": "RELECOV", + "study_id": "ERP137164", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", + "submitting_institution": "Instituto de Salud Carlos III ", + "submitting_lab_sequence_id": "202203166", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2031" + } +] diff --git a/relecov_tools/example_data/3.map_module/README b/relecov_tools/example_data/3.map_module/README new file mode 100644 index 00000000..f4936fdb --- /dev/null +++ b/relecov_tools/example_data/3.map_module/README @@ -0,0 +1,6 @@ +This module will map the metadata_lab.json to the selected DB (ENA or GISAID) +This moduleinput is: +-j processed_metadata_lab.json +- d ENA or GISAID +-o output folder where json file will be generated +- diff --git a/relecov_tools/example_data/4.ena_upload_module/README b/relecov_tools/example_data/4.ena_upload_module/README new file mode 100644 index 00000000..bf9201b4 --- /dev/null +++ b/relecov_tools/example_data/4.ena_upload_module/README @@ -0,0 +1,8 @@ +This module will upload fastq.gz and metadata associated to ENA +This module input: +- e processed_metadata_mapped_ENA.json +- u ENA Webin user +- p ENA Webin passsword (if special charcters add % in front of the special character) +- c center name (e.g Instituto de Salud Carlos III) +- o output folder where accession xml files will begenerated +--dev (This option for development server TESTS) diff --git a/relecov_tools/example_data/4.ena_upload_module/processed_METADATA_LAB_TEST_2022_04_25_00_03_GISAID_mapped.json b/relecov_tools/example_data/4.ena_upload_module/processed_METADATA_LAB_TEST_2022_04_25_00_03_GISAID_mapped.json new file mode 100644 index 00000000..edf69533 --- /dev/null +++ b/relecov_tools/example_data/4.ena_upload_module/processed_METADATA_LAB_TEST_2022_04_25_00_03_GISAID_mapped.json @@ -0,0 +1,152 @@ +[ + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "P.º Isabel la Católica, 1-3", + "collection_date": "2021/04/13", + "gender": "Mujer", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 55, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222687", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2022" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "P.º Isabel la Católica, 1-3", + "collection_date": "2021/03/31", + "gender": "Hombre", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 59, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222688", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2023" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "P.º Isabel la Católica, 1-3", + "collection_date": "2022/01/13", + "gender": "Mujer", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 8, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222689", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2024" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "P.º Isabel la Católica, 1-3", + "collection_date": "2022/01/11", + "gender": "Mujer", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 9, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222690", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2025" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "P.º Isabel la Católica, 1-3", + "collection_date": "2022/01/10", + "gender": "Hombre", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 31, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222691", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2026" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "P.º Isabel la Católica, 1-3", + "collection_date": "2022/01/12", + "gender": "Mujer", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 27, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222692", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2027" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "S. Juan Bosco, 15", + "collection_date": "2022/01/02", + "gender": "Mujer", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 42, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222693", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2028" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "S. Juan Bosco, 15", + "collection_date": "2022/01/23", + "gender": "Hombre", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 40, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222694", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2029" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "S. Juan Bosco, 15", + "collection_date": "2022/01/18", + "gender": "Hombre", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 53, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222695", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2030" + }, + { + "authors": "Inmaculada Casas,Maria de la Montaña", + "collecting_address": "S. Juan Bosco, 15", + "collection_date": "2022/01/19", + "gender": "Male", + "host": "Homo Sapiens", + "location": "Spain", + "patient_age": 96, + "sequencing_technology": "Illumina MiSeq", + "specimen_source": "Nasopharynx aspirate", + "submitter": "EPI_ISL_11222696", + "submitting_lab": "Instituto de Salud Carlos III ", + "type": "betacoronavirus", + "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2031" + } +] \ No newline at end of file diff --git a/relecov_tools/example_data/4.ena_upload_module/processed_METADATA_LAB_TEST_2022_04_28_21_05_ENA_mapped.json b/relecov_tools/example_data/4.ena_upload_module/processed_METADATA_LAB_TEST_2022_04_28_21_05_ENA_mapped.json new file mode 100644 index 00000000..684be7bc --- /dev/null +++ b/relecov_tools/example_data/4.ena_upload_module/processed_METADATA_LAB_TEST_2022_04_28_21_05_ENA_mapped.json @@ -0,0 +1,452 @@ +[ + { + "collecting_institution": "HU Virgen de la Arrixaca", + "collection_date": "2021-04-13", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "f2facbd1d6c7e0972074ced31ccbfd8e", + "fastq_r2_md5": "fd9948be8da7a38b0f80659dfc21aeea", + "file_type": "fastq", + "geographic location (latitude)": "37.9861", + "geographic location (longitude)": "-1.1303", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_scientific_name": "Homo Sapiens", + "host_sex": "Female", + "instrument_model": "Illumina MiSeq", + "isolate": "1197860", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "SINGLE", + "library_name": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "platform": "Illumina", + "purpose_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_001.fastq.gz", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_001.fastq.gz", + "receipt_date": "2021-05-13", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197860", + "sample_storage_conditions": " -80ºC", + "sample_title": "1197860", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_001.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_001.fastq.gz", + "study_abstract": "RELECOV Spanish Network for genomics surveillance", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "Whole Genome Sequencing", + "taxon_id": "2697049" + }, + { + "collecting_institution": "HU Virgen de la Arrixaca", + "collection_date": "2021-03-31", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "9a460a812086516536c1a1023ab5f7fe", + "fastq_r2_md5": "41cd79b8a167d85eb06309207fd120cf", + "file_type": "fastq", + "geographic location (latitude)": "37.9861", + "geographic location (longitude)": "-1.1303", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_scientific_name": "Homo Sapiens", + "host_sex": "Male", + "instrument_model": "Illumina MiSeq", + "isolate": "1197824", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "SINGLE", + "library_name": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "platform": "Illumina", + "purpose_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_002.fastq.gz", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_002.fastq.gz", + "receipt_date": "2021-05-13", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197824", + "sample_storage_conditions": " -80ºC", + "sample_title": "1197824", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_002.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_002.fastq.gz", + "study_abstract": "RELECOV Spanish Network for genomics surveillance", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "Whole Genome Sequencing", + "taxon_id": "2697049" + }, + { + "collecting_institution": "HU Virgen de la Arrixaca", + "collection_date": "2022-01-13", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "c78fcb585a0f44734ce8c2aebf3eff33", + "fastq_r2_md5": "8361d5a6b50279fbc8c93226ecc3568a", + "file_type": "fastq", + "geographic location (latitude)": "37.9861", + "geographic location (longitude)": "-1.1303", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_scientific_name": "Homo Sapiens", + "host_sex": "Female", + "instrument_model": "Illumina MiSeq", + "isolate": "1197767", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "SINGLE", + "library_name": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "platform": "Illumina", + "purpose_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_003.fastq.gz", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_003.fastq.gz", + "receipt_date": "2022-01-18", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197767", + "sample_storage_conditions": " -80ºC", + "sample_title": "1197767", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_003.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_003.fastq.gz", + "study_abstract": "RELECOV Spanish Network for genomics surveillance", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "Whole Genome Sequencing", + "taxon_id": "2697049" + }, + { + "collecting_institution": "HU Virgen de la Arrixaca", + "collection_date": "2022-01-11", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "aa557fc40d3a9e16f470ac595fb5eb3e", + "fastq_r2_md5": "a2dd5e08b75815dab892e392cb8468fc", + "file_type": "fastq", + "geographic location (latitude)": "37.9861", + "geographic location (longitude)": "-1.1303", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_scientific_name": "Homo Sapiens", + "host_sex": "Male", + "instrument_model": "Illumina MiSeq", + "isolate": "8328199", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "SINGLE", + "library_name": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "platform": "Illumina", + "purpose_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_004.fastq.gz", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_004.fastq.gz", + "receipt_date": "2022-01-20", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "8328199", + "sample_storage_conditions": " -80ºC", + "sample_title": "8328199", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_004.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_004.fastq.gz", + "study_abstract": "RELECOV Spanish Network for genomics surveillance", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "Whole Genome Sequencing", + "taxon_id": "2697049" + }, + { + "collecting_institution": "HU de Donostia", + "collection_date": "2022-01-10", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "b0a13671031ef5aa7e0e6559a925a688", + "fastq_r2_md5": "8c420a603c81823e68436003825b1e1f", + "file_type": "fastq", + "geographic location (latitude)": "43.3200", + "geographic location (longitude)": "-1.9800", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_scientific_name": "Homo Sapiens", + "host_sex": "Male", + "instrument_model": "Illumina MiSeq", + "isolate": "1197677", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "SINGLE", + "library_name": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS", + "platform": "Illumina", + "purpose_sampling": "Whole Genome Sequencing", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_005.fastq.gz", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_005.fastq.gz", + "receipt_date": "2022-01-20", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197677", + "sample_storage_conditions": " -80ºC", + "sample_title": "1197677", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_005.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_005.fastq.gz", + "study_abstract": "RELECOV Spanish Network for genomics surveillance", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "Whole Genome Sequencing", + "taxon_id": "2697049" + }, + { + "collecting_institution": "HU de Donostia", + "collection_date": "2022-01-12", + "collector_name": "Maria de la Montaña", + "common_name": "PEPITO", + "design_description": "Design Description", + 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Analysis NC_045512.2 214824 248 41 82 33,06 138 55,65 28 11,2903 NA NA 0 0 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214825 277306 747 1494 0,54 271052 97,74 4760 1,71652 217 91,0 17 9 9,10 B.1.177 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214826 337052 415 830 0,25 334627 99,28 1595 0,473221 239 92,0 17 9 7,87 B.1.177 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214827 246530 27978 55956 22,70 79361 32,19 111213 45,1113 10 50,0 15 7 49,72 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214828 312802 28396 56792 18,16 218183 69,75 37827 12,093 33 68,0 14 7 32,31 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214829 379598 3419 6838 1,80 370149 97,51 2611 0,687833 249 89,0 20 8 10,65 B.1.177 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214830 354342 25175 50350 14,21 300202 84,72 3790 1,06959 169 88,0 22 10 12,15 B.1.177 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214831 253440 107619 215238 84,93 11221 4,43 26981 10,6459 NA 22,0 3 2 77,51 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214832 5052 1844 3688 73,00 364 7,21 1000 19,7941 NA NA 0 0 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214833 326700 61771 123542 37,82 88067 26,96 115091 35,2283 16 55,00000000000001 12 5 44,94 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214834 384218 36429 72858 18,96 296545 77,18 14815 3,85588 85 83,0 17 8 17,29 B.1.177 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214835 347078 42041 84082 24,23 162912 46,94 100084 28,8362 32 67,0 17 7 32,56 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214836 362840 74483 148966 41,06 115115 31,73 98759 27,2183 9 49,0 8 4 50,53 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214837 400430 56534 113068 28,24 223768 55,88 63594 15,8814 52 75,0 17 7 25,35 B.1.177 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 214838 113674 25661 51322 45,15 6240 5,49 56112 49,3622 1 27,0 5 3 73,34 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220338 214610 37082 74164 34,56 106457 49,6 33989 15,8376 28 68,0 35 23 31,88 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220339 310682 6731 13462 4,33 295685 95,17 1535 0,494074 401 91,0 49 35 8,77 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220407 188574 72874 145748 77,29 4001 2,12 38825 20,5887 NA 20,0 9 7 80,18 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220433 69680 7033 14066 20,19 16261 23,34 39353 56,4768 3 36,0 16 13 64,03 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220518 87796 15067 30134 34,32 27222 31,01 30440 34,6713 2 37,0 18 13 63,28 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220529 243588 24320 48640 19,97 192650 79,09 2298 0,943396 86 79,0 42 30 21,15 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220530 258694 20191 40382 15,61 164599 63,63 53713 20,7631 27 67,0 38 27 32,76 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220531 322478 7510 15020 4,66 306896 95,17 562 0,174275 317 90,0 57 44 9,95 BA.1.18 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220532 240540 44711 89422 37,18 145549 60,51 5569 2,31521 29 68,0 35 25 31,52 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220533 146454 67492 134984 92,17 7609 5,2 3861 2,63632 NA 15,0 7 5 85,29 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220534 383046 9624 19248 5,02 361544 94,39 2254 0,588441 505 91,0 58 43 8,91 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220535 372112 59321 118642 31,88 247472 66,5 5998 1,61188 39 72,0 36 25 28,36 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220536 342222 69820 139640 40,80 196456 57,41 6126 1,79007 27 66,0 35 23 33,56 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220537 296640 7817 15634 5,27 278999 94,05 2007 0,676578 171 85,0 51 36 14,74 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220538 316128 28736 57472 18,18 256420 81,11 2236 0,707308 154 84,0 52 38 16,06 BA.1.18 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220539 350584 24002 48004 13,69 295145 84,19 7435 2,12075 50 73,0 36 24 26,76 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220540 349706 131768 263536 75,36 73909 21,13 12261 3,50609 3 33,0 18 13 67,33 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220541 314886 34471 68942 21,89 243456 77,32 2488 0,790127 131 82,0 44 31 18,38 BA.1.1.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220542 290650 24450 48900 16,82 231509 79,65 10241 3,52348 17 56,00000000000001 29 21 43,64 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220543 393188 3174 6348 1,61 386045 98,18 795 0,202193 340 89,0 53 40 11,10 BA.1.1.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220544 301018 16814 33628 11,17 263474 87,53 3916 1,30092 44 72,0 43 33 28,08 BA.1.1.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220545 265640 6396 12792 4,82 240982 90,72 11866 4,46695 50 76,0 38 25 24,27 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220546 257054 17714 35428 13,78 219613 85,43 2013 0,783104 127 81,0 47 33 19,22 BA.1.1.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220599 189680 74903 149806 78,98 23086 12,17 16788 8,8507 6 43,0 19 17 56,97 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220600 245316 110739 221478 90,28 73 0,03 23765 9,68751 NA NA 0 0 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220601 296392 13505 27010 9,11 268212 90,49 1170 0,394747 798 97,0 59 42 2,97 BA.1.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220603 132 9 18 13,64 102 77,27 12 9,09091 NA NA 0 0 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220624 295422 43999 87998 29,79 180473 61,09 26951 9,12288 25 67,0 35 25 33,26 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220625 280118 42654 85308 30,45 183443 65,49 11367 4,05793 19 59,0 30 21 41,39 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220626 284748 4918 9836 3,45 272621 95,74 2291 0,804571 62 76,0 35 22 24,47 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220627 346396 2670 5340 1,54 340102 98,18 954 0,275407 303 90,0 49 33 10,41 BA.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220628 322910 4681 9362 2,90 312419 96,75 1129 0,349633 270 89,0 55 40 11,18 BA.1.15.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220629 415182 46596 93192 22,45 306635 73,86 15355 3,69838 25 65,0 34 25 34,69 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220630 295142 60733 121466 41,16 170297 57,7 3379 1,14487 81 72,0 34 23 28,01 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220631 274184 36346 72692 26,51 199758 72,86 1734 0,632422 122 81,0 47 31 18,92 AY.127 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220633 440478 7179 14358 3,26 422987 96,03 3133 0,711273 168 83,0 43 31 17,17 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220634 373722 60717 121434 32,49 228069 61,03 24219 6,48049 28 65,0 33 23 34,87 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220635 333686 33839 67678 20,28 247874 74,28 18134 5,43445 36 70,0 40 29 29,84 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220636 329688 8956 17912 5,43 246754 74,84 65022 19,7223 29 67,0 37 27 33,48 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220637 412358 5079 10158 2,46 396982 96,27 5218 1,26541 245 86,0 46 32 13,83 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220638 280140 3190 6380 2,28 273014 97,46 746 0,266295 195 85,0 56 38 14,94 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220639 293692 15694 31388 10,69 243186 82,8 19118 6,50954 22 64,0 31 22 35,73 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220640 283734 15102 30204 10,65 242119 85,33 11411 4,02172 41 71,0 35 23 28,83 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220642 287392 53325 106650 37,11 167518 58,29 13224 4,60138 15 57,99999999999999 29 17 42,35 B.1.617.2 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220644 329228 29537 59074 17,94 258356 78,47 11798 3,58353 31 67,0 34 25 33,42 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220646 372318 21905 43810 11,77 322145 86,52 6363 1,70902 64 78,0 38 26 22,36 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220647 433376 8059 16118 3,72 396231 91,43 21027 4,85191 170 86,0 51 36 14,41 BA.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220648 343850 86366 172732 50,23 148232 43,11 22886 6,65581 13 54,0 27 19 45,72 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220649 357146 25733 51466 14,41 298948 83,7 6732 1,88494 31 68,0 39 28 32,12 BA.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220650 345044 10516 21032 6,10 320092 92,77 3920 1,13609 66 73,0 36 26 27,50 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220651 375890 45387 90774 24,15 270823 72,05 14293 3,80244 24 65,0 33 24 34,80 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220652 324144 12938 25876 7,98 293776 90,63 4492 1,3858 44 72,0 39 27 27,86 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220653 281982 61894 123788 43,90 120219 42,63 37975 13,4672 8 48,0 25 19 52,46 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220654 264482 9708 19416 7,34 241570 91,34 3496 1,32183 57 76,0 39 27 23,71 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220655 342522 4194 8388 2,45 332968 97,21 1166 0,340416 144 84,0 50 36 15,92 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220656 342082 71678 143356 41,91 186800 54,61 11926 3,4863 7 45,0 24 17 55,26 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220657 289618 24404 48808 16,85 233722 80,7 7088 2,44736 18 59,0 28 21 41,14 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220658 288798 32526 65052 22,53 217510 75,32 6236 2,15929 26 68,0 36 26 32,35 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220659 325092 7722 15444 4,75 307924 94,72 1724 0,530311 127 81,0 43 30 18,81 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220660 314206 13118 26236 8,35 283672 90,28 4298 1,36789 129 84,0 43 28 16,46 BA.1.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220661 377508 8713 17426 4,62 357815 94,78 2267 0,600517 146 81,0 47 32 18,59 BA.1.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220663 367268 113353 226706 61,73 104983 28,58 35579 9,68748 4 41,0 28 23 58,98 Unassigned +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220664 310374 3372 6744 2,17 302546 97,48 1084 0,349256 230 87,0 51 38 13,50 BA.1.1.1 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220665 335192 11738 23476 7,00 290215 86,58 21501 6,41453 47 72,0 38 26 28,33 BA.1.17 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220666 240438 67516 135032 56,16 92624 38,52 12782 5,31613 4 40,0 21 14 59,96 B.1.617.2 +MiSeq_GEN_267_20220208_ICasas virology Analysis NC_045512.2 220667 310152 3164 6328 2,04 302582 97,56 1242 0,400449 127 81,0 49 31 18,87 BA.1.17 +MiSeq_GEN_267_20220208_ICasas 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0.11.9 +FASTQC_TRIM: + fastqc: 0.11.9 +IVAR_TRIM: + ivar: 1.3.1 +IVAR_VARIANTS: + ivar: 1.3.1 +IVAR_VARIANTS_TO_VCF: + python: 3.9.9 +KRAKEN2_KRAKEN2: + kraken2: 2.1.2 + pigz: '2.6' +MAKE_BED_MASK: + python: 3.9.5 + samtools: '1.14' +MAKE_VARIANTS_LONG_TABLE: + python: 3.9.9 +MOSDEPTH_AMPLICON: + mosdepth: 0.3.3 +MOSDEPTH_GENOME: + mosdepth: 0.3.3 +PICARD_COLLECTMULTIPLEMETRICS: + picard: 2.26.10 +PLOT_BASE_DENSITY: + r-base: 4.0.3 +PLOT_MOSDEPTH_REGIONS_AMPLICON: + r-base: 4.0.3 +PLOT_MOSDEPTH_REGIONS_GENOME: + r-base: 4.0.3 +RENAME_FASTA_HEADER: + sed: '4.7' +SAMPLESHEET_CHECK: + python: 3.9.5 +SAMTOOLS_FLAGSTAT: + samtools: '1.14' +SAMTOOLS_IDXSTATS: + samtools: '1.14' +SAMTOOLS_INDEX: + samtools: '1.14' +SAMTOOLS_SORT: + samtools: '1.14' +SAMTOOLS_STATS: + samtools: '1.14' +SNPEFF_ANN: + snpeff: 5.0e +SNPEFF_BUILD: + snpeff: 5.0e +SNPSIFT_EXTRACTFIELDS: + snpsift: '4.3' +TABIX_BGZIP: + tabix: '1.12' +TABIX_TABIX: + tabix: '1.12' +UNTAR_KRAKEN2_DB: + untar: '1.30' +Workflow: + 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+220667,356530,310152,97.95971007763936,97.56,302582,301989,127,94.0,81.0,46,3,29,18867.1,NA,NA +220668,322372,259344,74.36532173483867,68.56,177798,177421,15,80.0,57.99999999999999,34,3,22,42413.19,NA,NA +220669,377304,310808,83.75395742709325,81.76,254109,253502,32,89.0,68.0,37,3,26,32002.81,NA,NA +220670,466540,410196,89.57961559839687,88.29,362154,361638,90,94.0,78.0,39,4,30,21514.37,NA,NA +220671,335280,281328,96.59401126087698,96.0,270074,269588,161,97.0,83.0,43,3,31,17224.3,NA,NA +220672,344566,286140,88.36513594743832,84.1,240636,240096,35,87.0,70.0,36,4,23,30192.09,NA,NA +220675,378180,310914,66.55924146226931,60.25,187328,186944,12,78.0,54.0,30,2,22,46409.34,NA,NA +220677,357032,305936,88.044558338999,86.75,265405,264932,47,91.0,71.0,38,3,28,29038.41,NA,NA +220678,407204,346738,94.27463964145839,93.41,323905,323270,98,95.0,81.0,38,3,28,19021.01,NA,NA +220679,316188,276880,87.93484542039873,84.28,233349,232957,63,91.0,75.0,40,3,27,24712.26,NA,NA +220680,444904,363996,43.487291069132624,38.03,138444,138242,11,78.0,51.0,28,3,24,49070.3,NA,NA +220684,378006,327920,90.79470602585997,89.28,292768,292274,63,93.0,75.0,33,3,25,25046.84,NA,NA +220685,319610,276336,86.64379595854322,84.52,233558,233170,56,91.0,75.0,39,3,29,25488.49,NA,NA diff --git a/relecov_tools/example_data/5.read_bioinfo_metadata/variants_long_table.csv b/relecov_tools/example_data/5.read_bioinfo_metadata/variants_long_table.csv new file mode 100755 index 00000000..90148433 --- /dev/null +++ b/relecov_tools/example_data/5.read_bioinfo_metadata/variants_long_table.csv @@ -0,0 +1,3341 @@ +SAMPLE,CHROM,POS,REF,ALT,FILTER,DP,REF_DP,ALT_DP,AF,GENE,EFFECT,HGVS_C,HGVS_P,HGVS_P_1LETTER,CALLER,LINEAGE +214821,NC_045512.2,11132,G,T,PASS,366,0,363,0.99,orf1ab,missense_variant,c.10867G>T,p.Ala3623Ser,p.A3623S,ivar,B.1.177 +214821,NC_045512.2,14408,C,T,PASS,333,2,331,0.99,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,B.1.177 +214821,NC_045512.2,16726,C,T,PASS,697,1,695,1.0,orf1ab,synonymous_variant,c.16461C>T,p.Tyr5487Tyr,p.Y5487Y,ivar,B.1.177 +214821,NC_045512.2,17658,G,T,PASS,3710,6,3690,0.99,orf1ab,missense_variant,c.17393G>T,p.Cys5798Phe,p.C5798F,ivar,B.1.177 +214821,NC_045512.2,20132,C,T,PASS,83,0,83,1.0,orf1ab,missense_variant,c.19867C>T,p.Pro6623Ser,p.P6623S,ivar,B.1.177 +214821,NC_045512.2,21255,G,C,PASS,78,0,78,1.0,orf1ab,missense_variant,c.20990G>C,p.Arg6997Pro,p.R6997P,ivar,B.1.177 +214821,NC_045512.2,21786,G,T,PASS,276,0,275,1.0,S,missense_variant,c.224G>T,p.Gly75Val,p.G75V,ivar,B.1.177 +214821,NC_045512.2,23403,A,G,PASS,2590,2,2588,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.177 +214821,NC_045512.2,24138,C,T,PASS,1594,913,679,0.43,S,missense_variant,c.2576C>T,p.Thr859Ile,p.T859I,ivar,B.1.177 +214821,NC_045512.2,26801,C,G,PASS,896,0,892,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,B.1.177 +214821,NC_045512.2,28932,C,T,PASS,242,5,236,0.98,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,B.1.177 +214821,NC_045512.2,29645,G,T,PASS,84,0,82,0.98,ORF10,missense_variant,c.88G>T,p.Val30Leu,p.V30L,ivar,B.1.177 +214821,NC_045512.2,3037,C,T,PASS,330,0,330,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,B.1.177 +214821,NC_045512.2,4230,C,T,PASS,57,0,57,1.0,orf1ab,missense_variant,c.3965C>T,p.Thr1322Ile,p.T1322I,ivar,B.1.177 +214821,NC_045512.2,445,T,C,PASS,8440,24,8415,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,B.1.177 +214821,NC_045512.2,504,CTCATGG,C,PASS,7769,7715,6191,0.8,orf1ab,disruptive_inframe_deletion,c.245_250delGTCATG,p.Gly82_His83del,p.G82_H83del,ivar,B.1.177 +214821,NC_045512.2,541,C,T,PASS,7835,36,7791,0.99,orf1ab,synonymous_variant,c.276C>T,p.Leu92Leu,p.L92L,ivar,B.1.177 +214821,NC_045512.2,5548,C,T,PASS,28,0,27,0.96,orf1ab,synonymous_variant,c.5283C>T,p.Thr1761Thr,p.T1761T,ivar,B.1.177 +214821,NC_045512.2,6842,T,C,ft,13,9,4,0.31,orf1ab,missense_variant,c.6577T>C,p.Ser2193Pro,p.S2193P,ivar,B.1.177 +214821,NC_045512.2,8125,T,G,PASS,3054,5,3048,1.0,orf1ab,synonymous_variant,c.7860T>G,p.Leu2620Leu,p.L2620L,ivar,B.1.177 +214822,NC_045512.2,1199,TG,T,PASS,364,361,97,0.27,orf1ab,frameshift_variant,c.935delG,p.Cys312fs,p.C312fs,ivar,Unassigned +214822,NC_045512.2,13179,G,T,PASS,735,546,189,0.26,orf1ab,missense_variant,c.12914G>T,p.Gly4305Val,p.G4305V,ivar,Unassigned +214822,NC_045512.2,17658,G,T,PASS,2579,0,2575,1.0,orf1ab,missense_variant,c.17393G>T,p.Cys5798Phe,p.C5798F,ivar,Unassigned +214822,NC_045512.2,20132,C,T,PASS,10,0,10,1.0,orf1ab,missense_variant,c.19867C>T,p.Pro6623Ser,p.P6623S,ivar,Unassigned +214822,NC_045512.2,20473,A,C,PASS,423,175,247,0.58,orf1ab,missense_variant,c.20208A>C,p.Lys6736Asn,p.K6736N,ivar,Unassigned +214822,NC_045512.2,2076,G,T,PASS,80,47,33,0.41,orf1ab,missense_variant,c.1811G>T,p.Gly604Val,p.G604V,ivar,Unassigned +214822,NC_045512.2,23403,A,G,PASS,44,0,44,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +214822,NC_045512.2,25217,G,T,PASS,334,113,221,0.66,S,missense_variant,c.3655G>T,p.Gly1219Cys,p.G1219C,ivar,Unassigned +214822,NC_045512.2,25424,G,T,PASS,228,109,119,0.52,ORF3a,missense_variant,c.32G>T,p.Gly11Val,p.G11V,ivar,Unassigned +214822,NC_045512.2,25451,T,C,ft,12,8,4,0.33,ORF3a,missense_variant,c.59T>C,p.Ile20Thr,p.I20T,ivar,Unassigned +214822,NC_045512.2,26801,C,G,PASS,21,0,21,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,Unassigned +214822,NC_045512.2,2748,A,G,PASS,852,534,315,0.37,orf1ab,missense_variant,c.2483A>G,p.Asp828Gly,p.D828G,ivar,Unassigned +214822,NC_045512.2,3514,G,T,PASS,59,40,19,0.32,orf1ab,missense_variant,c.3249G>T,p.Met1083Ile,p.M1083I,ivar,Unassigned +214822,NC_045512.2,445,T,C,PASS,7802,4,7798,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,Unassigned +214822,NC_045512.2,504,CTCATGG,C,PASS,6981,6922,5465,0.78,orf1ab,disruptive_inframe_deletion,c.245_250delGTCATG,p.Gly82_His83del,p.G82_H83del,ivar,Unassigned +214822,NC_045512.2,541,C,T,PASS,7271,38,7229,0.99,orf1ab,synonymous_variant,c.276C>T,p.Leu92Leu,p.L92L,ivar,Unassigned +214822,NC_045512.2,8125,T,G,PASS,13,0,13,1.0,orf1ab,synonymous_variant,c.7860T>G,p.Leu2620Leu,p.L2620L,ivar,Unassigned +214825,NC_045512.2,10845,T,C,ft,16,12,4,0.25,orf1ab,missense_variant,c.10580T>C,p.Met3527Thr,p.M3527T,ivar,B.1.177 +214825,NC_045512.2,11132,G,T,PASS,108,0,108,1.0,orf1ab,missense_variant,c.10867G>T,p.Ala3623Ser,p.A3623S,ivar,B.1.177 +214825,NC_045512.2,14408,C,T,PASS,256,0,256,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,B.1.177 +214825,NC_045512.2,16726,C,T,PASS,500,3,496,0.99,orf1ab,synonymous_variant,c.16461C>T,p.Tyr5487Tyr,p.Y5487Y,ivar,B.1.177 +214825,NC_045512.2,17658,G,T,PASS,4879,1,4849,0.99,orf1ab,missense_variant,c.17393G>T,p.Cys5798Phe,p.C5798F,ivar,B.1.177 +214825,NC_045512.2,20132,C,T,PASS,62,0,62,1.0,orf1ab,missense_variant,c.19867C>T,p.Pro6623Ser,p.P6623S,ivar,B.1.177 +214825,NC_045512.2,21255,G,C,PASS,57,0,57,1.0,orf1ab,missense_variant,c.20990G>C,p.Arg6997Pro,p.R6997P,ivar,B.1.177 +214825,NC_045512.2,21786,G,T,PASS,247,0,247,1.0,S,missense_variant,c.224G>T,p.Gly75Val,p.G75V,ivar,B.1.177 +214825,NC_045512.2,22227,C,T,PASS,17,0,17,1.0,S,missense_variant,c.665C>T,p.Ala222Val,p.A222V,ivar,B.1.177 +214825,NC_045512.2,23403,A,G,PASS,2049,10,2039,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.177 +214825,NC_045512.2,26801,C,G,PASS,241,0,241,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,B.1.177 +214825,NC_045512.2,28932,C,T,PASS,173,0,172,0.99,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,B.1.177 +214825,NC_045512.2,29645,G,T,PASS,21,0,21,1.0,ORF10,missense_variant,c.88G>T,p.Val30Leu,p.V30L,ivar,B.1.177 +214825,NC_045512.2,3037,C,T,PASS,243,3,239,0.98,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,B.1.177 +214825,NC_045512.2,445,T,C,PASS,10199,19,10180,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,B.1.177 +214825,NC_045512.2,541,C,T,PASS,9612,41,9559,0.99,orf1ab,synonymous_variant,c.276C>T,p.Leu92Leu,p.L92L,ivar,B.1.177 +214825,NC_045512.2,5548,C,T,PASS,20,0,20,1.0,orf1ab,synonymous_variant,c.5283C>T,p.Thr1761Thr,p.T1761T,ivar,B.1.177 +214826,NC_045512.2,11132,G,T,PASS,238,0,238,1.0,orf1ab,missense_variant,c.10867G>T,p.Ala3623Ser,p.A3623S,ivar,B.1.177 +214826,NC_045512.2,14408,C,T,PASS,428,2,426,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,B.1.177 +214826,NC_045512.2,16726,C,T,PASS,621,0,621,1.0,orf1ab,synonymous_variant,c.16461C>T,p.Tyr5487Tyr,p.Y5487Y,ivar,B.1.177 +214826,NC_045512.2,17658,G,T,PASS,6934,3,6903,1.0,orf1ab,missense_variant,c.17393G>T,p.Cys5798Phe,p.C5798F,ivar,B.1.177 +214826,NC_045512.2,20132,C,T,PASS,101,0,101,1.0,orf1ab,missense_variant,c.19867C>T,p.Pro6623Ser,p.P6623S,ivar,B.1.177 +214826,NC_045512.2,21255,G,C,PASS,91,0,91,1.0,orf1ab,missense_variant,c.20990G>C,p.Arg6997Pro,p.R6997P,ivar,B.1.177 +214826,NC_045512.2,21786,G,T,PASS,464,4,460,0.99,S,missense_variant,c.224G>T,p.Gly75Val,p.G75V,ivar,B.1.177 +214826,NC_045512.2,22227,C,T,PASS,31,0,31,1.0,S,missense_variant,c.665C>T,p.Ala222Val,p.A222V,ivar,B.1.177 +214826,NC_045512.2,23403,A,G,PASS,1826,2,1824,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.177 +214826,NC_045512.2,26801,C,G,PASS,363,0,362,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,B.1.177 +214826,NC_045512.2,28932,C,T,PASS,196,2,193,0.98,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,B.1.177 +214826,NC_045512.2,29645,G,T,PASS,46,0,46,1.0,ORF10,missense_variant,c.88G>T,p.Val30Leu,p.V30L,ivar,B.1.177 +214826,NC_045512.2,3037,C,T,PASS,154,0,154,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,B.1.177 +214826,NC_045512.2,4158,C,T,PASS,112,81,31,0.28,orf1ab,missense_variant,c.3893C>T,p.Ala1298Val,p.A1298V,ivar,B.1.177 +214826,NC_045512.2,445,T,C,PASS,10150,5,10145,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,B.1.177 +214826,NC_045512.2,541,C,T,PASS,9501,38,9460,1.0,orf1ab,synonymous_variant,c.276C>T,p.Leu92Leu,p.L92L,ivar,B.1.177 +214826,NC_045512.2,5548,C,T,PASS,20,0,20,1.0,orf1ab,synonymous_variant,c.5283C>T,p.Thr1761Thr,p.T1761T,ivar,B.1.177 +214827,NC_045512.2,11132,G,T,PASS,36,0,36,1.0,orf1ab,missense_variant,c.10867G>T,p.Ala3623Ser,p.A3623S,ivar,Unassigned +214827,NC_045512.2,1123,A,T,PASS,161,3,158,0.98,orf1ab,synonymous_variant,c.858A>T,p.Pro286Pro,p.P286P,ivar,Unassigned +214827,NC_045512.2,14408,C,T,PASS,28,0,28,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +214827,NC_045512.2,16726,C,T,PASS,47,0,47,1.0,orf1ab,synonymous_variant,c.16461C>T,p.Tyr5487Tyr,p.Y5487Y,ivar,Unassigned +214827,NC_045512.2,17658,G,T,PASS,6726,0,6694,1.0,orf1ab,missense_variant,c.17393G>T,p.Cys5798Phe,p.C5798F,ivar,Unassigned +214827,NC_045512.2,21786,G,T,PASS,49,0,49,1.0,S,missense_variant,c.224G>T,p.Gly75Val,p.G75V,ivar,Unassigned +214827,NC_045512.2,23403,A,G,PASS,336,0,336,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +214827,NC_045512.2,24368,G,C,PASS,73,23,49,0.67,S,missense_variant,c.2806G>C,p.Asp936His,p.D936H,ivar,Unassigned +214827,NC_045512.2,25112,G,T,PASS,90,10,80,0.89,S,missense_variant,c.3550G>T,p.Asp1184Tyr,p.D1184Y,ivar,Unassigned +214827,NC_045512.2,26297,T,C,PASS,652,476,176,0.27,E,missense_variant,c.53T>C,p.Leu18Pro,p.L18P,ivar,Unassigned +214827,NC_045512.2,26410,T,C,ft,10,6,4,0.4,E,missense_variant,c.166T>C,p.Phe56Leu,p.F56L,ivar,Unassigned +214827,NC_045512.2,26801,C,G,PASS,12,1,11,0.92,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,Unassigned +214827,NC_045512.2,28932,C,T,PASS,80,0,80,1.0,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,Unassigned +214827,NC_045512.2,3037,C,T,PASS,48,0,48,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +214827,NC_045512.2,445,T,C,PASS,3394,8,3386,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,Unassigned +214827,NC_045512.2,541,C,T,PASS,3216,10,3206,1.0,orf1ab,synonymous_variant,c.276C>T,p.Leu92Leu,p.L92L,ivar,Unassigned +214827,NC_045512.2,7521,C,T,PASS,29,3,26,0.9,orf1ab,missense_variant,c.7256C>T,p.Thr2419Ile,p.T2419I,ivar,Unassigned +214827,NC_045512.2,76,T,A,ft,14,10,4,0.29,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +214827,NC_045512.2,78,T,G,ft,15,11,4,0.27,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +214827,NC_045512.2,8302,A,T,PASS,28,17,10,0.36,orf1ab,missense_variant,c.8037A>T,p.Lys2679Asn,p.K2679N,ivar,Unassigned +214828,NC_045512.2,11132,G,T,PASS,47,0,47,1.0,orf1ab,missense_variant,c.10867G>T,p.Ala3623Ser,p.A3623S,ivar,Unassigned +214828,NC_045512.2,14408,C,T,PASS,26,0,26,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +214828,NC_045512.2,14646,T,A,PASS,53,25,28,0.53,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,Unassigned +214828,NC_045512.2,16002,T,G,PASS,34,21,13,0.38,orf1ab,stop_gained,c.15737T>G,p.Leu5246*,p.L5246*,ivar,Unassigned +214828,NC_045512.2,16726,C,T,PASS,38,0,38,1.0,orf1ab,synonymous_variant,c.16461C>T,p.Tyr5487Tyr,p.Y5487Y,ivar,Unassigned +214828,NC_045512.2,17658,G,T,PASS,12609,1,12562,1.0,orf1ab,missense_variant,c.17393G>T,p.Cys5798Phe,p.C5798F,ivar,Unassigned +214828,NC_045512.2,19378,T,C,PASS,42,17,25,0.6,orf1ab,synonymous_variant,c.19113T>C,p.Ile6371Ile,p.I6371I,ivar,Unassigned +214828,NC_045512.2,20132,C,T,PASS,23,0,23,1.0,orf1ab,missense_variant,c.19867C>T,p.Pro6623Ser,p.P6623S,ivar,Unassigned +214828,NC_045512.2,21786,G,T,PASS,24,0,24,1.0,S,missense_variant,c.224G>T,p.Gly75Val,p.G75V,ivar,Unassigned +214828,NC_045512.2,23403,A,G,PASS,611,0,611,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +214828,NC_045512.2,26801,C,G,PASS,178,0,178,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,Unassigned +214828,NC_045512.2,27856,T,A,PASS,53,13,40,0.75,ORF7b,missense_variant,c.101T>A,p.Leu34Gln,p.L34Q,ivar,Unassigned +214828,NC_045512.2,28932,C,T,PASS,210,0,210,1.0,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,Unassigned +214828,NC_045512.2,3037,C,T,PASS,30,0,30,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +214828,NC_045512.2,445,T,C,PASS,14026,6,14017,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,Unassigned +214828,NC_045512.2,541,C,T,PASS,13166,68,13075,0.99,orf1ab,synonymous_variant,c.276C>T,p.Leu92Leu,p.L92L,ivar,Unassigned +214829,NC_045512.2,10833,C,T,PASS,17,0,17,1.0,orf1ab,missense_variant,c.10568C>T,p.Ala3523Val,p.A3523V,ivar,B.1.177 +214829,NC_045512.2,11824,C,T,PASS,73,0,73,1.0,orf1ab,synonymous_variant,c.11559C>T,p.Ile3853Ile,p.I3853I,ivar,B.1.177 +214829,NC_045512.2,14408,C,T,PASS,148,0,148,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,B.1.177 +214829,NC_045512.2,16308,C,T,PASS,433,3,428,0.99,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,B.1.177 +214829,NC_045512.2,21255,G,C,PASS,73,0,73,1.0,orf1ab,missense_variant,c.20990G>C,p.Arg6997Pro,p.R6997P,ivar,B.1.177 +214829,NC_045512.2,222,C,T,PASS,158,1,157,0.99,orf1ab,upstream_gene_variant,c.-44C>T,.,.,ivar,B.1.177 +214829,NC_045512.2,22482,C,T,PASS,39,20,19,0.49,S,missense_variant,c.920C>T,p.Thr307Ile,p.T307I,ivar,B.1.177 +214829,NC_045512.2,23403,A,G,PASS,2780,6,2774,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.177 +214829,NC_045512.2,24370,C,T,PASS,443,4,439,0.99,S,synonymous_variant,c.2808C>T,p.Asp936Asp,p.D936D,ivar,B.1.177 +214829,NC_045512.2,26801,C,G,PASS,694,0,694,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,B.1.177 +214829,NC_045512.2,28093,C,T,PASS,592,1,590,1.0,ORF8,missense_variant,c.200C>T,p.Ser67Phe,p.S67F,ivar,B.1.177 +214829,NC_045512.2,28486,C,T,PASS,493,2,491,1.0,N,synonymous_variant,c.213C>T,p.Gly71Gly,p.G71G,ivar,B.1.177 +214829,NC_045512.2,28932,C,T,PASS,556,1,554,1.0,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,B.1.177 +214829,NC_045512.2,29402,G,T,PASS,5976,2,5958,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,B.1.177 +214829,NC_045512.2,29578,C,T,PASS,99,5,94,0.95,ORF10,synonymous_variant,c.21C>T,p.Phe7Phe,p.F7F,ivar,B.1.177 +214829,NC_045512.2,29645,G,T,PASS,117,0,116,0.99,ORF10,missense_variant,c.88G>T,p.Val30Leu,p.V30L,ivar,B.1.177 +214829,NC_045512.2,3037,C,T,PASS,260,0,260,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,B.1.177 +214829,NC_045512.2,445,T,C,PASS,13196,11,13183,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,B.1.177 +214829,NC_045512.2,527,C,T,PASS,11571,51,11487,0.99,orf1ab,synonymous_variant,c.262C>T,p.Leu88Leu,p.L88L,ivar,B.1.177 +214829,NC_045512.2,5869,C,T,PASS,192,0,192,1.0,orf1ab,synonymous_variant,c.5604C>T,p.Tyr1868Tyr,p.Y1868Y,ivar,B.1.177 +214829,NC_045512.2,8326,C,T,PASS,2135,898,1233,0.58,orf1ab,synonymous_variant,c.8061C>T,p.Asp2687Asp,p.D2687D,ivar,B.1.177 +214830,NC_045512.2,10833,C,T,PASS,17,0,17,1.0,orf1ab,missense_variant,c.10568C>T,p.Ala3523Val,p.A3523V,ivar,B.1.177 +214830,NC_045512.2,11824,C,T,PASS,54,0,54,1.0,orf1ab,synonymous_variant,c.11559C>T,p.Ile3853Ile,p.I3853I,ivar,B.1.177 +214830,NC_045512.2,14408,C,T,PASS,160,2,158,0.99,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,B.1.177 +214830,NC_045512.2,16308,C,T,PASS,487,3,484,0.99,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,B.1.177 +214830,NC_045512.2,21255,G,C,PASS,56,0,56,1.0,orf1ab,missense_variant,c.20990G>C,p.Arg6997Pro,p.R6997P,ivar,B.1.177 +214830,NC_045512.2,222,C,T,PASS,52,0,52,1.0,orf1ab,upstream_gene_variant,c.-44C>T,.,.,ivar,B.1.177 +214830,NC_045512.2,22482,C,T,PASS,31,0,31,1.0,S,missense_variant,c.920C>T,p.Thr307Ile,p.T307I,ivar,B.1.177 +214830,NC_045512.2,23403,A,G,PASS,2950,2,2944,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.177 +214830,NC_045512.2,24370,C,T,PASS,234,1,233,1.0,S,synonymous_variant,c.2808C>T,p.Asp936Asp,p.D936D,ivar,B.1.177 +214830,NC_045512.2,26801,C,G,PASS,442,0,442,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,B.1.177 +214830,NC_045512.2,28093,C,T,PASS,632,8,622,0.98,ORF8,missense_variant,c.200C>T,p.Ser67Phe,p.S67F,ivar,B.1.177 +214830,NC_045512.2,28486,C,T,PASS,414,2,410,0.99,N,synonymous_variant,c.213C>T,p.Gly71Gly,p.G71G,ivar,B.1.177 +214830,NC_045512.2,28932,C,T,PASS,811,1,809,1.0,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,B.1.177 +214830,NC_045512.2,29402,G,T,PASS,7244,1,7211,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,B.1.177 +214830,NC_045512.2,29578,C,T,PASS,101,0,101,1.0,ORF10,synonymous_variant,c.21C>T,p.Phe7Phe,p.F7F,ivar,B.1.177 +214830,NC_045512.2,29645,G,T,PASS,106,0,106,1.0,ORF10,missense_variant,c.88G>T,p.Val30Leu,p.V30L,ivar,B.1.177 +214830,NC_045512.2,3037,C,T,PASS,259,0,259,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,B.1.177 +214830,NC_045512.2,445,T,C,PASS,12135,22,12111,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,B.1.177 +214830,NC_045512.2,5274,C,T,PASS,12,0,12,1.0,orf1ab,missense_variant,c.5009C>T,p.Ala1670Val,p.A1670V,ivar,B.1.177 +214830,NC_045512.2,527,C,T,PASS,11747,79,11647,0.99,orf1ab,synonymous_variant,c.262C>T,p.Leu88Leu,p.L88L,ivar,B.1.177 +214830,NC_045512.2,5869,C,T,PASS,58,2,54,0.93,orf1ab,synonymous_variant,c.5604C>T,p.Tyr1868Tyr,p.Y1868Y,ivar,B.1.177 +214831,NC_045512.2,1009,C,A,ft,12,7,5,0.42,orf1ab,missense_variant,c.744C>A,p.Ser248Arg,p.S248R,ivar,Unassigned +214831,NC_045512.2,13408,T,C,ft,13,9,4,0.31,orf1ab,synonymous_variant,c.13143T>C,p.Cys4381Cys,p.C4381C,ivar,Unassigned +214831,NC_045512.2,14646,T,A,ft,15,9,6,0.4,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,Unassigned +214831,NC_045512.2,14647,A,C,ft,15,9,6,0.4,orf1ab,synonymous_variant,c.14382A>C,p.Leu4794Leu,p.L4794L,ivar,Unassigned +214831,NC_045512.2,14661,T,G,PASS,13,7,6,0.46,orf1ab,missense_variant,c.14396T>G,p.Phe4799Cys,p.F4799C,ivar,Unassigned +214831,NC_045512.2,15604,A,T,ft,11,7,4,0.36,orf1ab,synonymous_variant,c.15339A>T,p.Ala5113Ala,p.A5113A,ivar,Unassigned +214831,NC_045512.2,17375,C,T,PASS,344,195,148,0.43,orf1ab,stop_gained,c.17110C>T,p.Gln5704*,p.Q5704*,ivar,Unassigned +214831,NC_045512.2,17469,G,T,PASS,472,337,127,0.27,orf1ab,missense_variant,c.17204G>T,p.Cys5735Phe,p.C5735F,ivar,Unassigned +214831,NC_045512.2,23333,T,C,PASS,54,30,24,0.44,S,missense_variant,c.1771T>C,p.Ser591Pro,p.S591P,ivar,Unassigned +214831,NC_045512.2,23403,A,G,PASS,59,0,59,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +214831,NC_045512.2,28301,C,A,ft,10,6,4,0.4,N,synonymous_variant,c.28C>A,p.Arg10Arg,p.R10R,ivar,Unassigned +214831,NC_045512.2,29402,G,T,PASS,143,2,141,0.99,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,Unassigned +214831,NC_045512.2,3154,T,A,ft,11,8,3,0.27,orf1ab,synonymous_variant,c.2889T>A,p.Gly963Gly,p.G963G,ivar,Unassigned +214831,NC_045512.2,3443,G,T,PASS,17,9,8,0.47,orf1ab,missense_variant,c.3178G>T,p.Ala1060Ser,p.A1060S,ivar,Unassigned +214831,NC_045512.2,3748,T,C,ft,12,8,4,0.33,orf1ab,synonymous_variant,c.3483T>C,p.Ser1161Ser,p.S1161S,ivar,Unassigned +214831,NC_045512.2,445,T,C,PASS,1048,6,1042,0.99,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,Unassigned +214831,NC_045512.2,527,C,T,PASS,951,313,636,0.67,orf1ab,synonymous_variant,c.262C>T,p.Leu88Leu,p.L88L,ivar,Unassigned +214833,NC_045512.2,14408,C,T,PASS,15,0,15,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +214833,NC_045512.2,14595,T,G,ft,23,17,6,0.26,orf1ab,missense_variant,c.14330T>G,p.Val4777Gly,p.V4777G,ivar,Unassigned +214833,NC_045512.2,16308,C,T,PASS,50,0,50,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,Unassigned +214833,NC_045512.2,17213,C,T,PASS,14,4,10,0.71,orf1ab,synonymous_variant,c.16948C>T,p.Leu5650Leu,p.L5650L,ivar,Unassigned +214833,NC_045512.2,21563,A,G,PASS,36,27,9,0.25,S,start_lost,c.1A>G,p.Met1?,p.M1?,ivar,Unassigned +214833,NC_045512.2,23403,A,G,PASS,171,0,171,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +214833,NC_045512.2,24370,C,T,PASS,15,0,15,1.0,S,synonymous_variant,c.2808C>T,p.Asp936Asp,p.D936D,ivar,Unassigned +214833,NC_045512.2,26114,A,G,ft,15,11,4,0.27,ORF3a,missense_variant,c.722A>G,p.Glu241Gly,p.E241G,ivar,Unassigned +214833,NC_045512.2,26663,T,C,PASS,33,19,14,0.42,M,synonymous_variant,c.141T>C,p.Tyr47Tyr,p.Y47Y,ivar,Unassigned +214833,NC_045512.2,26801,C,G,PASS,50,0,50,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,Unassigned +214833,NC_045512.2,28093,C,T,PASS,54,2,51,0.94,ORF8,missense_variant,c.200C>T,p.Ser67Phe,p.S67F,ivar,Unassigned +214833,NC_045512.2,28932,C,T,PASS,45,0,45,1.0,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,Unassigned +214833,NC_045512.2,29402,G,T,PASS,1250,2,1245,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,Unassigned +214833,NC_045512.2,2966,A,G,PASS,36,23,13,0.36,orf1ab,missense_variant,c.2701A>G,p.Ser901Gly,p.S901G,ivar,Unassigned +214833,NC_045512.2,3037,C,T,PASS,28,0,28,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +214833,NC_045512.2,445,T,C,PASS,5706,6,5700,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,Unassigned +214833,NC_045512.2,5869,C,T,ft,16,12,4,0.25,orf1ab,synonymous_variant,c.5604C>T,p.Tyr1868Tyr,p.Y1868Y,ivar,Unassigned +214833,NC_045512.2,7948,C,T,PASS,109,25,84,0.77,orf1ab,synonymous_variant,c.7683C>T,p.Tyr2561Tyr,p.Y2561Y,ivar,Unassigned +214834,NC_045512.2,11824,C,T,PASS,18,0,18,1.0,orf1ab,synonymous_variant,c.11559C>T,p.Ile3853Ile,p.I3853I,ivar,B.1.177 +214834,NC_045512.2,14408,C,T,PASS,137,0,137,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,B.1.177 +214834,NC_045512.2,16308,C,T,PASS,255,0,255,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,B.1.177 +214834,NC_045512.2,21255,G,C,PASS,44,0,42,0.95,orf1ab,missense_variant,c.20990G>C,p.Arg6997Pro,p.R6997P,ivar,B.1.177 +214834,NC_045512.2,222,C,T,PASS,17,0,17,1.0,orf1ab,upstream_gene_variant,c.-44C>T,.,.,ivar,B.1.177 +214834,NC_045512.2,23403,A,G,PASS,1324,1,1323,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.177 +214834,NC_045512.2,24370,C,T,PASS,87,1,86,0.99,S,synonymous_variant,c.2808C>T,p.Asp936Asp,p.D936D,ivar,B.1.177 +214834,NC_045512.2,26801,C,G,PASS,95,0,95,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,B.1.177 +214834,NC_045512.2,28093,C,T,PASS,232,3,229,0.99,ORF8,missense_variant,c.200C>T,p.Ser67Phe,p.S67F,ivar,B.1.177 +214834,NC_045512.2,28932,C,T,PASS,295,1,294,1.0,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,B.1.177 +214834,NC_045512.2,29402,G,T,PASS,4981,0,4965,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,B.1.177 +214834,NC_045512.2,29578,C,T,PASS,13,0,13,1.0,ORF10,synonymous_variant,c.21C>T,p.Phe7Phe,p.F7F,ivar,B.1.177 +214834,NC_045512.2,29645,G,T,PASS,17,0,17,1.0,ORF10,missense_variant,c.88G>T,p.Val30Leu,p.V30L,ivar,B.1.177 +214834,NC_045512.2,29681,TTA,T,PASS,20,20,12,0.6,S,downstream_gene_variant,c.*4298_*4299delTA,.,.,ivar,B.1.177 +214834,NC_045512.2,3037,C,T,PASS,72,1,71,0.99,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,B.1.177 +214834,NC_045512.2,3092,C,T,PASS,76,16,60,0.79,orf1ab,missense_variant,c.2827C>T,p.Pro943Ser,p.P943S,ivar,B.1.177 +214834,NC_045512.2,445,T,C,PASS,21304,21,21277,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,B.1.177 +214834,NC_045512.2,8807,G,A,ft,10,7,3,0.3,orf1ab,missense_variant,c.8542G>A,p.Asp2848Asn,p.D2848N,ivar,B.1.177 +214835,NC_045512.2,10741,CT,C,PASS,25,25,22,0.88,orf1ab,frameshift_variant,c.10479delT,p.Phe3493fs,p.F3493fs,ivar,Unassigned +214835,NC_045512.2,11808,G,C,ft,12,8,4,0.33,orf1ab,missense_variant,c.11543G>C,p.Gly3848Ala,p.G3848A,ivar,Unassigned +214835,NC_045512.2,11824,C,T,PASS,12,0,12,1.0,orf1ab,synonymous_variant,c.11559C>T,p.Ile3853Ile,p.I3853I,ivar,Unassigned +214835,NC_045512.2,14408,C,T,PASS,62,0,62,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +214835,NC_045512.2,16308,C,T,PASS,142,1,139,0.98,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,Unassigned +214835,NC_045512.2,16988,G,A,PASS,28,18,10,0.36,orf1ab,missense_variant,c.16723G>A,p.Ala5575Thr,p.A5575T,ivar,Unassigned +214835,NC_045512.2,19307,A,G,PASS,32,23,9,0.28,orf1ab,missense_variant,c.19042A>G,p.Asn6348Asp,p.N6348D,ivar,Unassigned +214835,NC_045512.2,21255,G,C,PASS,11,0,11,1.0,orf1ab,missense_variant,c.20990G>C,p.Arg6997Pro,p.R6997P,ivar,Unassigned +214835,NC_045512.2,23403,A,G,PASS,183,0,183,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +214835,NC_045512.2,23826,A,G,ft,15,11,4,0.27,S,missense_variant,c.2264A>G,p.Gln755Arg,p.Q755R,ivar,Unassigned +214835,NC_045512.2,24370,C,T,PASS,36,1,35,0.97,S,synonymous_variant,c.2808C>T,p.Asp936Asp,p.D936D,ivar,Unassigned +214835,NC_045512.2,26239,G,T,PASS,57,27,30,0.53,E,upstream_gene_variant,c.-6G>T,.,.,ivar,Unassigned +214835,NC_045512.2,26801,C,G,PASS,48,0,48,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,Unassigned +214835,NC_045512.2,27518,G,A,PASS,84,60,24,0.29,ORF7a,missense_variant,c.125G>A,p.Gly42Asp,p.G42D,ivar,Unassigned +214835,NC_045512.2,28093,C,T,PASS,31,1,30,0.97,ORF8,missense_variant,c.200C>T,p.Ser67Phe,p.S67F,ivar,Unassigned +214835,NC_045512.2,28932,C,T,PASS,138,1,137,0.99,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,Unassigned +214835,NC_045512.2,29402,G,T,PASS,2177,0,2173,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,Unassigned +214835,NC_045512.2,29578,C,T,PASS,24,0,24,1.0,ORF10,synonymous_variant,c.21C>T,p.Phe7Phe,p.F7F,ivar,Unassigned +214835,NC_045512.2,29645,G,T,PASS,25,0,25,1.0,ORF10,missense_variant,c.88G>T,p.Val30Leu,p.V30L,ivar,Unassigned +214835,NC_045512.2,29681,TTA,T,PASS,22,22,13,0.59,S,downstream_gene_variant,c.*4298_*4299delTA,.,.,ivar,Unassigned +214835,NC_045512.2,3037,C,T,PASS,26,0,26,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +214835,NC_045512.2,3092,C,T,PASS,27,15,12,0.44,orf1ab,missense_variant,c.2827C>T,p.Pro943Ser,p.P943S,ivar,Unassigned +214835,NC_045512.2,4079,AGT,A,PASS,74,74,60,0.81,orf1ab,frameshift_variant,c.3816_3817delTG,p.Ser1272fs,p.S1272fs,ivar,Unassigned +214835,NC_045512.2,445,T,C,PASS,10789,17,10764,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,Unassigned +214835,NC_045512.2,5869,C,T,PASS,51,36,15,0.29,orf1ab,synonymous_variant,c.5604C>T,p.Tyr1868Tyr,p.Y1868Y,ivar,Unassigned +214835,NC_045512.2,7639,C,T,PASS,45,33,12,0.27,orf1ab,synonymous_variant,c.7374C>T,p.Phe2458Phe,p.F2458F,ivar,Unassigned +214835,NC_045512.2,8596,A,T,PASS,238,177,61,0.26,orf1ab,synonymous_variant,c.8331A>T,p.Thr2777Thr,p.T2777T,ivar,Unassigned +214836,NC_045512.2,14408,C,T,PASS,51,0,51,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +214836,NC_045512.2,17017,G,A,PASS,23,15,8,0.35,orf1ab,missense_variant,c.16752G>A,p.Met5584Ile,p.M5584I,ivar,Unassigned +214836,NC_045512.2,18774,A,G,PASS,37,27,10,0.27,orf1ab,missense_variant,c.18509A>G,p.Asn6170Ser,p.N6170S,ivar,Unassigned +214836,NC_045512.2,21747,T,G,PASS,35,23,12,0.34,S,missense_variant,c.185T>G,p.Val62Gly,p.V62G,ivar,Unassigned +214836,NC_045512.2,23403,A,G,PASS,149,0,149,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +214836,NC_045512.2,24370,C,T,PASS,74,1,73,0.99,S,synonymous_variant,c.2808C>T,p.Asp936Asp,p.D936D,ivar,Unassigned +214836,NC_045512.2,26263,G,C,PASS,14,4,10,0.71,E,missense_variant,c.19G>C,p.Glu7Gln,p.E7Q,ivar,Unassigned +214836,NC_045512.2,27767,T,C,ft,11,8,3,0.27,ORF7b,synonymous_variant,c.12T>C,p.Leu4Leu,p.L4L,ivar,Unassigned +214836,NC_045512.2,28093,C,T,PASS,80,0,80,1.0,ORF8,missense_variant,c.200C>T,p.Ser67Phe,p.S67F,ivar,Unassigned +214836,NC_045512.2,28932,C,T,PASS,43,1,42,0.98,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,Unassigned +214836,NC_045512.2,29402,G,T,PASS,4413,0,4393,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,Unassigned +214836,NC_045512.2,3037,C,T,PASS,18,0,18,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +214836,NC_045512.2,3092,C,T,ft,19,14,5,0.26,orf1ab,missense_variant,c.2827C>T,p.Pro943Ser,p.P943S,ivar,Unassigned +214836,NC_045512.2,445,T,C,PASS,3540,3,3537,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,Unassigned +214836,NC_045512.2,8317,A,G,PASS,45,33,12,0.27,orf1ab,synonymous_variant,c.8052A>G,p.Thr2684Thr,p.T2684T,ivar,Unassigned +214837,NC_045512.2,10257,T,C,ft,16,12,4,0.25,orf1ab,missense_variant,c.9992T>C,p.Val3331Ala,p.V3331A,ivar,B.1.177 +214837,NC_045512.2,14408,C,T,PASS,55,0,55,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,B.1.177 +214837,NC_045512.2,14946,T,TG,ft,14,14,4,0.29,orf1ab,frameshift_variant,c.14683dupG,p.Val4895fs,p.V4895fs,ivar,B.1.177 +214837,NC_045512.2,14958,T,A,ft,14,10,4,0.29,orf1ab,stop_gained,c.14693T>A,p.Leu4898*,p.L4898*,ivar,B.1.177 +214837,NC_045512.2,16308,C,T,PASS,75,0,75,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,B.1.177 +214837,NC_045512.2,21255,G,C,PASS,19,0,19,1.0,orf1ab,missense_variant,c.20990G>C,p.Arg6997Pro,p.R6997P,ivar,B.1.177 +214837,NC_045512.2,222,C,T,PASS,35,0,35,1.0,orf1ab,upstream_gene_variant,c.-44C>T,.,.,ivar,B.1.177 +214837,NC_045512.2,23403,A,G,PASS,728,0,728,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.177 +214837,NC_045512.2,24370,C,T,PASS,63,1,62,0.98,S,synonymous_variant,c.2808C>T,p.Asp936Asp,p.D936D,ivar,B.1.177 +214837,NC_045512.2,26801,C,G,PASS,163,0,163,1.0,M,synonymous_variant,c.279C>G,p.Leu93Leu,p.L93L,ivar,B.1.177 +214837,NC_045512.2,28093,C,T,PASS,85,0,85,1.0,ORF8,missense_variant,c.200C>T,p.Ser67Phe,p.S67F,ivar,B.1.177 +214837,NC_045512.2,28486,C,T,PASS,108,19,89,0.82,N,synonymous_variant,c.213C>T,p.Gly71Gly,p.G71G,ivar,B.1.177 +214837,NC_045512.2,28932,C,T,PASS,118,0,118,1.0,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,B.1.177 +214837,NC_045512.2,29402,G,T,PASS,1594,0,1584,0.99,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,B.1.177 +214837,NC_045512.2,29578,C,T,PASS,14,0,14,1.0,ORF10,synonymous_variant,c.21C>T,p.Phe7Phe,p.F7F,ivar,B.1.177 +214837,NC_045512.2,29645,G,T,PASS,17,0,17,1.0,ORF10,missense_variant,c.88G>T,p.Val30Leu,p.V30L,ivar,B.1.177 +214837,NC_045512.2,3037,C,T,PASS,59,0,59,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,B.1.177 +214837,NC_045512.2,3958,A,C,PASS,178,56,122,0.69,orf1ab,missense_variant,c.3693A>C,p.Lys1231Asn,p.K1231N,ivar,B.1.177 +214837,NC_045512.2,3963,A,T,PASS,194,56,138,0.71,orf1ab,missense_variant,c.3698A>T,p.Lys1233Ile,p.K1233I,ivar,B.1.177 +214837,NC_045512.2,4082,G,A,PASS,39,16,23,0.59,orf1ab,missense_variant,c.3817G>A,p.Asp1273Asn,p.D1273N,ivar,B.1.177 +214837,NC_045512.2,445,T,C,PASS,19439,22,19412,1.0,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,B.1.177 +214837,NC_045512.2,527,C,T,PASS,17846,3108,14730,0.83,orf1ab,synonymous_variant,c.262C>T,p.Leu88Leu,p.L88L,ivar,B.1.177 +214837,NC_045512.2,5869,C,T,PASS,29,0,29,1.0,orf1ab,synonymous_variant,c.5604C>T,p.Tyr1868Tyr,p.Y1868Y,ivar,B.1.177 +214837,NC_045512.2,76,T,A,ft,14,10,4,0.29,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,B.1.177 +214837,NC_045512.2,78,T,G,ft,14,10,4,0.29,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,B.1.177 +214838,NC_045512.2,16276,T,C,ft,10,6,4,0.4,orf1ab,synonymous_variant,c.16011T>C,p.His5337His,p.H5337H,ivar,Unassigned +214838,NC_045512.2,23403,A,G,PASS,11,0,11,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +214838,NC_045512.2,28932,C,T,PASS,10,0,10,1.0,N,missense_variant,c.659C>T,p.Ala220Val,p.A220V,ivar,Unassigned +214838,NC_045512.2,28951,A,G,ft,12,9,3,0.25,N,synonymous_variant,c.678A>G,p.Arg226Arg,p.R226R,ivar,Unassigned +214838,NC_045512.2,29402,G,T,PASS,60,0,60,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,Unassigned +214838,NC_045512.2,445,T,C,PASS,256,3,253,0.99,orf1ab,synonymous_variant,c.180T>C,p.Val60Val,p.V60V,ivar,Unassigned +214838,NC_045512.2,527,C,T,PASS,197,18,179,0.91,orf1ab,synonymous_variant,c.262C>T,p.Leu88Leu,p.L88L,ivar,Unassigned +214838,NC_045512.2,7948,C,T,ft,10,7,3,0.3,orf1ab,synonymous_variant,c.7683C>T,p.Tyr2561Tyr,p.Y2561Y,ivar,Unassigned +214838,NC_045512.2,9711,CCA,C,PASS,40,40,14,0.35,orf1ab,frameshift_variant,c.9449_9450delCA,p.Thr3150fs,p.T3150fs,ivar,Unassigned +220338,NC_045512.2,10029,C,T,PASS,13,0,13,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,Unassigned +220338,NC_045512.2,10449,C,A,PASS,19,0,19,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220338,NC_045512.2,11282,AGTTTGTCTG,A,PASS,80,79,66,0.82,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220338,NC_045512.2,11537,A,G,PASS,39,0,39,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220338,NC_045512.2,13195,T,C,PASS,727,1,726,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220338,NC_045512.2,14408,C,T,PASS,10,0,10,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220338,NC_045512.2,16744,G,A,PASS,185,0,185,1.0,orf1ab,synonymous_variant,c.16479G>A,p.Leu5493Leu,p.L5493L,ivar,Unassigned +220338,NC_045512.2,21762,C,T,PASS,10,0,10,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220338,NC_045512.2,21764,ATACATG,A,PASS,10,10,10,1.0,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220338,NC_045512.2,21846,C,T,PASS,19,0,19,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220338,NC_045512.2,23403,A,G,PASS,732,2,730,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220338,NC_045512.2,23525,C,T,PASS,709,4,704,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220338,NC_045512.2,23599,T,G,PASS,254,0,254,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220338,NC_045512.2,23604,C,A,PASS,244,0,242,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220338,NC_045512.2,23854,C,A,PASS,10,0,10,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220338,NC_045512.2,23948,G,T,PASS,97,0,96,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220338,NC_045512.2,24130,C,A,PASS,162,0,162,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220338,NC_045512.2,24424,A,T,PASS,75,0,75,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220338,NC_045512.2,24469,T,A,PASS,127,0,127,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220338,NC_045512.2,24503,C,T,PASS,137,1,136,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220338,NC_045512.2,25000,C,T,PASS,12,0,12,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220338,NC_045512.2,25584,C,T,PASS,26,0,25,0.96,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220338,NC_045512.2,26270,C,T,PASS,91,0,91,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220338,NC_045512.2,26530,A,G,PASS,11,0,11,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220338,NC_045512.2,26577,C,G,PASS,11,0,11,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220338,NC_045512.2,27259,A,C,PASS,38,0,38,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220338,NC_045512.2,28271,A,T,PASS,36,0,36,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220338,NC_045512.2,28311,C,T,PASS,39,0,39,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220338,NC_045512.2,2832,A,G,PASS,24,0,24,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220338,NC_045512.2,28361,GGAGAACGCA,G,PASS,32,32,27,0.84,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220338,NC_045512.2,28881,GG,AA,PASS,1617,29,1583,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220338,NC_045512.2,28883,G,C,PASS,1606,0,1604,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220338,NC_045512.2,811,C,T,PASS,21,0,21,1.0,orf1ab,synonymous_variant,c.546C>T,p.Tyr182Tyr,p.Y182Y,ivar,Unassigned +220338,NC_045512.2,8393,G,A,PASS,1157,5,1150,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220339,NC_045512.2,10029,C,T,PASS,72,0,72,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220339,NC_045512.2,10449,C,A,PASS,257,0,257,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220339,NC_045512.2,11282,AGTTTGTCTG,A,PASS,507,502,426,0.84,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220339,NC_045512.2,11537,A,G,PASS,561,0,559,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220339,NC_045512.2,13195,T,C,PASS,3850,4,3846,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220339,NC_045512.2,14408,C,T,PASS,235,0,235,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220339,NC_045512.2,15240,C,T,PASS,83,0,83,1.0,orf1ab,missense_variant,c.14975C>T,p.Thr4992Ile,p.T4992I,ivar,BA.1.17 +220339,NC_045512.2,18163,A,G,PASS,92,0,92,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220339,NC_045512.2,21762,C,T,PASS,187,2,185,0.99,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220339,NC_045512.2,21764,ATACATG,A,PASS,192,189,166,0.86,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220339,NC_045512.2,21846,C,T,PASS,155,0,154,0.99,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220339,NC_045512.2,22578,G,A,PASS,38,0,38,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.17 +220339,NC_045512.2,22673,TC,CT,PASS,20,0,20,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.17 +220339,NC_045512.2,22679,T,C,PASS,23,0,23,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220339,NC_045512.2,22686,C,T,PASS,24,0,24,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220339,NC_045512.2,23075,T,C,PASS,12,0,12,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.17 +220339,NC_045512.2,23202,C,A,PASS,28,0,28,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220339,NC_045512.2,23403,A,G,PASS,2573,5,2568,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220339,NC_045512.2,23525,C,T,PASS,2372,11,2360,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220339,NC_045512.2,23599,T,G,PASS,877,0,877,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220339,NC_045512.2,23604,C,A,PASS,845,0,842,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220339,NC_045512.2,23854,C,A,PASS,175,2,171,0.98,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220339,NC_045512.2,23948,G,T,PASS,1194,2,1189,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220339,NC_045512.2,24130,C,A,PASS,1645,0,1631,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220339,NC_045512.2,24424,A,T,PASS,520,0,514,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220339,NC_045512.2,24469,T,A,PASS,983,2,973,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220339,NC_045512.2,24503,C,T,PASS,1108,16,1091,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220339,NC_045512.2,25000,C,T,PASS,98,1,97,0.99,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220339,NC_045512.2,25584,C,T,PASS,263,0,261,0.99,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220339,NC_045512.2,26270,C,T,PASS,738,4,731,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220339,NC_045512.2,26530,A,G,PASS,278,0,278,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220339,NC_045512.2,26568,C,T,PASS,248,2,245,0.99,M,missense_variant,c.46C>T,p.Leu16Phe,p.L16F,ivar,BA.1.17 +220339,NC_045512.2,26577,C,G,PASS,245,0,245,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220339,NC_045512.2,26709,G,A,PASS,271,0,269,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220339,NC_045512.2,27259,A,C,PASS,717,0,715,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220339,NC_045512.2,27807,C,T,PASS,258,2,256,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220339,NC_045512.2,28271,A,T,PASS,1012,1,1010,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220339,NC_045512.2,28311,C,T,PASS,951,3,944,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220339,NC_045512.2,2832,A,G,PASS,344,0,344,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220339,NC_045512.2,28361,GGAGAACGCA,G,PASS,754,751,516,0.68,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220339,NC_045512.2,28881,GG,AA,PASS,1968,19,1949,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220339,NC_045512.2,28883,G,C,PASS,1960,1,1959,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220339,NC_045512.2,29772,T,C,PASS,160,1,159,0.99,S,downstream_gene_variant,c.*4388T>C,.,.,ivar,BA.1.17 +220339,NC_045512.2,3037,C,T,PASS,42,0,42,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220339,NC_045512.2,5386,T,G,PASS,38,0,38,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.17 +220339,NC_045512.2,5672,C,T,PASS,269,2,267,0.99,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220339,NC_045512.2,5924,G,A,PASS,113,1,112,0.99,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220339,NC_045512.2,76,T,A,PASS,48,36,12,0.25,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1.17 +220339,NC_045512.2,78,T,G,PASS,48,36,12,0.25,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1.17 +220339,NC_045512.2,8393,G,A,PASS,2673,17,2656,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220339,NC_045512.2,8652,T,C,PASS,2561,2,2559,1.0,orf1ab,missense_variant,c.8387T>C,p.Met2796Thr,p.M2796T,ivar,BA.1.17 +220407,NC_045512.2,13195,T,C,PASS,34,0,34,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220407,NC_045512.2,23403,A,G,PASS,51,0,51,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220407,NC_045512.2,23525,C,T,PASS,42,0,42,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220407,NC_045512.2,23599,T,G,PASS,12,0,12,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220407,NC_045512.2,23604,C,A,PASS,10,0,10,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220407,NC_045512.2,28881,GG,AA,PASS,133,1,132,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220407,NC_045512.2,28883,G,C,PASS,133,0,132,0.99,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220407,NC_045512.2,8393,G,A,PASS,27,0,27,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220433,NC_045512.2,13195,T,C,PASS,59,2,57,0.97,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220433,NC_045512.2,1437,C,T,PASS,15,0,15,1.0,orf1ab,missense_variant,c.1172C>T,p.Ser391Phe,p.S391F,ivar,Unassigned +220433,NC_045512.2,1451,A,T,PASS,15,8,7,0.47,orf1ab,missense_variant,c.1186A>T,p.Ile396Phe,p.I396F,ivar,Unassigned +220433,NC_045512.2,21846,C,T,PASS,13,0,13,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220433,NC_045512.2,23403,A,G,PASS,18,0,18,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220433,NC_045512.2,23525,C,T,PASS,11,0,11,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220433,NC_045512.2,23987,C,T,PASS,13,4,9,0.69,S,missense_variant,c.2425C>T,p.Pro809Ser,p.P809S,ivar,Unassigned +220433,NC_045512.2,24123,A,C,PASS,19,8,11,0.58,S,missense_variant,c.2561A>C,p.Lys854Thr,p.K854T,ivar,Unassigned +220433,NC_045512.2,24130,C,A,PASS,18,0,18,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220433,NC_045512.2,24469,T,A,PASS,13,0,13,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220433,NC_045512.2,24503,C,T,PASS,18,0,18,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220433,NC_045512.2,26270,C,T,PASS,234,0,234,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220433,NC_045512.2,26577,C,G,PASS,11,0,11,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220433,NC_045512.2,26862,C,A,ft,13,8,5,0.38,M,missense_variant,c.340C>A,p.Pro114Thr,p.P114T,ivar,Unassigned +220433,NC_045512.2,28271,A,T,PASS,67,0,67,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220433,NC_045512.2,28311,C,T,PASS,83,2,81,0.98,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220433,NC_045512.2,28881,GG,AA,PASS,429,0,425,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220433,NC_045512.2,28883,G,C,PASS,431,0,429,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220433,NC_045512.2,8393,G,A,PASS,366,0,366,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220518,NC_045512.2,12834,AT,A,ft,12,12,5,0.42,orf1ab,frameshift_variant,c.12572delT,p.Leu4191fs,p.L4191fs,ivar,Unassigned +220518,NC_045512.2,13195,T,C,PASS,68,0,68,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220518,NC_045512.2,23403,A,G,PASS,35,0,35,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220518,NC_045512.2,23525,C,T,PASS,51,0,51,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220518,NC_045512.2,23599,T,G,PASS,28,0,28,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220518,NC_045512.2,23604,C,A,PASS,28,0,28,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220518,NC_045512.2,23948,G,T,PASS,17,0,17,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220518,NC_045512.2,24130,C,A,PASS,23,0,23,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220518,NC_045512.2,24469,T,A,PASS,32,0,32,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220518,NC_045512.2,24503,C,T,PASS,46,0,46,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220518,NC_045512.2,26270,C,T,PASS,340,2,336,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220518,NC_045512.2,27259,A,C,PASS,12,0,12,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220518,NC_045512.2,28271,A,T,PASS,92,0,92,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220518,NC_045512.2,28311,C,T,PASS,104,2,102,0.98,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220518,NC_045512.2,28361,GGAGAACGCA,G,PASS,81,81,30,0.37,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220518,NC_045512.2,28881,GG,AA,PASS,569,4,565,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220518,NC_045512.2,28883,G,C,PASS,566,0,565,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220518,NC_045512.2,3183,A,G,PASS,48,22,26,0.54,orf1ab,missense_variant,c.2918A>G,p.Glu973Gly,p.E973G,ivar,Unassigned +220518,NC_045512.2,514,TGTTATG,T,PASS,205,205,169,0.82,orf1ab,conservative_inframe_deletion,c.253_258delATGGTT,p.Met85_Val86del,p.M85_V86del,ivar,Unassigned +220518,NC_045512.2,8393,G,A,PASS,779,2,777,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220529,NC_045512.2,10029,C,T,PASS,13,0,13,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,Unassigned +220529,NC_045512.2,10449,C,A,PASS,44,0,44,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220529,NC_045512.2,11282,AGTTTGTCTG,A,PASS,182,178,164,0.9,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220529,NC_045512.2,11537,A,G,PASS,173,0,173,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220529,NC_045512.2,13195,T,C,PASS,4328,6,4322,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220529,NC_045512.2,14408,C,T,PASS,79,4,75,0.95,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220529,NC_045512.2,16064,A,G,PASS,116,0,116,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220529,NC_045512.2,16308,C,T,PASS,220,0,220,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,Unassigned +220529,NC_045512.2,18163,A,G,PASS,14,0,14,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,Unassigned +220529,NC_045512.2,21762,C,T,PASS,119,0,119,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220529,NC_045512.2,21764,ATACATG,A,PASS,122,119,108,0.89,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220529,NC_045512.2,21846,C,T,PASS,100,2,96,0.96,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220529,NC_045512.2,22578,G,A,PASS,13,0,13,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,Unassigned +220529,NC_045512.2,22599,G,A,PASS,10,0,10,1.0,S,missense_variant,c.1037G>A,p.Arg346Lys,p.R346K,ivar,Unassigned +220529,NC_045512.2,22679,T,C,PASS,11,0,11,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,Unassigned +220529,NC_045512.2,22686,C,T,PASS,11,0,11,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,Unassigned +220529,NC_045512.2,23403,A,G,PASS,2006,2,2004,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220529,NC_045512.2,23525,C,T,PASS,1968,2,1964,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220529,NC_045512.2,23599,T,G,PASS,712,0,712,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220529,NC_045512.2,23604,C,A,PASS,685,0,679,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220529,NC_045512.2,23854,C,A,PASS,25,0,25,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220529,NC_045512.2,23948,G,T,PASS,253,0,253,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220529,NC_045512.2,24130,C,A,PASS,342,0,338,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220529,NC_045512.2,24424,A,T,PASS,97,0,97,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220529,NC_045512.2,24469,T,A,PASS,548,1,547,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220529,NC_045512.2,24503,C,T,PASS,682,21,661,0.97,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220529,NC_045512.2,25000,C,T,PASS,60,0,60,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220529,NC_045512.2,25584,C,T,PASS,38,1,37,0.97,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220529,NC_045512.2,26270,C,T,PASS,138,0,138,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220529,NC_045512.2,26530,A,G,PASS,69,2,67,0.97,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220529,NC_045512.2,26577,C,G,PASS,93,0,93,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220529,NC_045512.2,26709,G,A,PASS,90,2,88,0.98,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220529,NC_045512.2,27259,A,C,PASS,80,0,80,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220529,NC_045512.2,27807,C,T,PASS,52,0,52,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220529,NC_045512.2,28271,A,T,PASS,775,0,775,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220529,NC_045512.2,28311,C,T,PASS,809,5,802,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220529,NC_045512.2,2832,A,G,PASS,42,0,42,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220529,NC_045512.2,28361,GGAGAACGCA,G,PASS,659,657,484,0.73,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220529,NC_045512.2,28881,GG,AA,PASS,2822,28,2789,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220529,NC_045512.2,28883,G,C,PASS,2814,0,2809,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220529,NC_045512.2,3037,C,T,PASS,22,0,22,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220529,NC_045512.2,8393,G,A,PASS,2312,8,2302,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220530,NC_045512.2,10029,C,T,PASS,11,0,11,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,Unassigned +220530,NC_045512.2,10449,C,A,PASS,13,0,13,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220530,NC_045512.2,11282,AGTTTGTCTG,A,PASS,34,34,28,0.82,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220530,NC_045512.2,11537,A,G,PASS,46,0,46,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220530,NC_045512.2,13195,T,C,PASS,1638,0,1638,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220530,NC_045512.2,14408,C,T,PASS,16,0,16,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220530,NC_045512.2,16064,A,G,PASS,11,0,11,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220530,NC_045512.2,16308,C,T,PASS,44,0,44,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,Unassigned +220530,NC_045512.2,21762,C,T,PASS,13,0,13,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220530,NC_045512.2,21764,ATACATG,A,PASS,13,13,13,1.0,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220530,NC_045512.2,21846,C,T,PASS,19,0,19,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220530,NC_045512.2,23403,A,G,PASS,470,2,468,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220530,NC_045512.2,23525,C,T,PASS,495,2,493,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220530,NC_045512.2,23599,T,G,PASS,216,0,216,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220530,NC_045512.2,23604,C,A,PASS,215,0,213,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220530,NC_045512.2,23854,C,A,PASS,12,0,12,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220530,NC_045512.2,23948,G,T,PASS,31,0,31,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220530,NC_045512.2,24130,C,A,PASS,31,0,31,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220530,NC_045512.2,24424,A,T,PASS,39,0,37,0.95,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220530,NC_045512.2,24469,T,A,PASS,158,0,158,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220530,NC_045512.2,24503,C,T,PASS,191,2,189,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220530,NC_045512.2,25000,C,T,PASS,16,0,16,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220530,NC_045512.2,25584,C,T,PASS,26,0,26,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220530,NC_045512.2,26270,C,T,PASS,161,0,161,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220530,NC_045512.2,26530,A,G,PASS,46,0,46,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220530,NC_045512.2,26577,C,G,PASS,80,0,80,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220530,NC_045512.2,26709,G,A,PASS,61,0,61,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220530,NC_045512.2,27259,A,C,PASS,64,0,64,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220530,NC_045512.2,27406,C,T,PASS,65,0,65,1.0,ORF7a,missense_variant,c.13C>T,p.Leu5Phe,p.L5F,ivar,Unassigned +220530,NC_045512.2,27784,A,T,ft,16,11,5,0.31,ORF7b,missense_variant,c.29A>T,p.Tyr10Phe,p.Y10F,ivar,Unassigned +220530,NC_045512.2,27790,G,C,ft,13,8,5,0.38,ORF7b,missense_variant,c.35G>C,p.Cys12Ser,p.C12S,ivar,Unassigned +220530,NC_045512.2,27807,C,T,PASS,12,0,12,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220530,NC_045512.2,28271,A,T,PASS,189,0,188,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220530,NC_045512.2,28311,C,T,PASS,206,0,206,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220530,NC_045512.2,2832,A,G,PASS,78,0,78,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220530,NC_045512.2,28361,GGAGAACGCA,G,PASS,171,171,134,0.78,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220530,NC_045512.2,28403,G,A,PASS,112,78,34,0.3,N,missense_variant,c.130G>A,p.Gly44Ser,p.G44S,ivar,Unassigned +220530,NC_045512.2,2857,C,T,PASS,48,36,12,0.25,orf1ab,synonymous_variant,c.2592C>T,p.Leu864Leu,p.L864L,ivar,Unassigned +220530,NC_045512.2,28881,GG,AA,PASS,3635,36,3594,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220530,NC_045512.2,28883,G,C,PASS,3618,3,3608,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220530,NC_045512.2,4964,A,G,ft,10,6,4,0.4,orf1ab,missense_variant,c.4699A>G,p.Thr1567Ala,p.T1567A,ivar,Unassigned +220530,NC_045512.2,8393,G,A,PASS,1049,2,1046,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220531,NC_045512.2,10029,C,T,PASS,65,0,65,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.18 +220531,NC_045512.2,10449,C,A,PASS,294,0,293,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.18 +220531,NC_045512.2,11282,AGTTTGTCTG,A,PASS,608,606,530,0.87,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.18 +220531,NC_045512.2,11537,A,G,PASS,587,0,587,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.18 +220531,NC_045512.2,13195,T,C,PASS,5269,16,5253,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.18 +220531,NC_045512.2,14408,C,T,PASS,234,1,231,0.99,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.18 +220531,NC_045512.2,15336,T,C,ft,10,5,5,0.5,orf1ab,missense_variant,c.15071T>C,p.Leu5024Ser,p.L5024S,ivar,BA.1.18 +220531,NC_045512.2,15359,G,A,PASS,10,4,6,0.6,orf1ab,missense_variant,c.15094G>A,p.Ala5032Thr,p.A5032T,ivar,BA.1.18 +220531,NC_045512.2,18163,A,G,PASS,46,0,46,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.18 +220531,NC_045512.2,2172,A,G,PASS,3340,15,3325,1.0,orf1ab,missense_variant,c.1907A>G,p.Lys636Arg,p.K636R,ivar,BA.1.18 +220531,NC_045512.2,21762,C,T,PASS,443,0,443,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.18 +220531,NC_045512.2,21764,ATACATG,A,PASS,449,444,403,0.9,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.18 +220531,NC_045512.2,21846,C,T,PASS,384,3,381,0.99,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.18 +220531,NC_045512.2,22578,G,A,PASS,57,0,57,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.18 +220531,NC_045512.2,22673,TC,CT,PASS,39,0,39,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.18 +220531,NC_045512.2,22679,T,C,PASS,46,0,46,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.18 +220531,NC_045512.2,22686,C,T,PASS,45,0,45,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.18 +220531,NC_045512.2,22882,T,G,PASS,13,0,13,1.0,S,missense_variant,c.1320T>G,p.Asn440Lys,p.N440K,ivar,BA.1.18 +220531,NC_045512.2,22898,G,A,PASS,13,0,13,1.0,S,missense_variant,c.1336G>A,p.Gly446Ser,p.G446S,ivar,BA.1.18 +220531,NC_045512.2,22992,G,A,PASS,11,0,11,1.0,S,missense_variant,c.1430G>A,p.Ser477Asn,p.S477N,ivar,BA.1.18 +220531,NC_045512.2,22995,C,A,PASS,11,0,11,1.0,S,missense_variant,c.1433C>A,p.Thr478Lys,p.T478K,ivar,BA.1.18 +220531,NC_045512.2,23013,A,C,PASS,11,0,11,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.18 +220531,NC_045512.2,23040,A,G,PASS,15,0,15,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.18 +220531,NC_045512.2,23048,G,A,PASS,18,0,18,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.18 +220531,NC_045512.2,23055,A,G,PASS,18,0,18,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.18 +220531,NC_045512.2,23063,A,T,PASS,17,0,17,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.18 +220531,NC_045512.2,23075,T,C,PASS,20,0,20,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.18 +220531,NC_045512.2,23202,C,A,PASS,48,0,48,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.18 +220531,NC_045512.2,23403,A,G,PASS,3684,4,3680,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.18 +220531,NC_045512.2,23525,C,T,PASS,3562,10,3542,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.18 +220531,NC_045512.2,23599,T,G,PASS,1310,0,1308,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.18 +220531,NC_045512.2,23604,C,A,PASS,1248,0,1245,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.18 +220531,NC_045512.2,23854,C,A,PASS,153,0,153,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.18 +220531,NC_045512.2,23948,G,T,PASS,1231,0,1229,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.18 +220531,NC_045512.2,24130,C,A,PASS,1843,2,1824,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.18 +220531,NC_045512.2,24424,A,T,PASS,589,0,589,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.18 +220531,NC_045512.2,24469,T,A,PASS,1156,4,1150,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.18 +220531,NC_045512.2,24503,C,T,PASS,1344,14,1330,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.18 +220531,NC_045512.2,25000,C,T,PASS,165,1,164,0.99,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.18 +220531,NC_045512.2,25584,C,T,PASS,263,0,263,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.18 +220531,NC_045512.2,25855,G,T,PASS,263,0,262,1.0,ORF3a,missense_variant,c.463G>T,p.Asp155Tyr,p.D155Y,ivar,BA.1.18 +220531,NC_045512.2,25931,CT,AC,PASS,276,1,275,1.0,ORF3a,missense_variant,c.539_540delCTinsAC,p.Ser180Tyr,p.S180Y,ivar,BA.1.18 +220531,NC_045512.2,26270,C,T,PASS,761,2,759,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.18 +220531,NC_045512.2,26530,A,G,PASS,192,0,192,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.18 +220531,NC_045512.2,26577,C,G,PASS,211,0,211,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.18 +220531,NC_045512.2,26709,G,A,PASS,190,1,189,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.18 +220531,NC_045512.2,27259,A,C,PASS,631,0,624,0.99,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.18 +220531,NC_045512.2,27807,C,T,PASS,247,2,245,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.18 +220531,NC_045512.2,27933,G,A,PASS,448,3,442,0.99,ORF8,missense_variant,c.40G>A,p.Ala14Thr,p.A14T,ivar,BA.1.18 +220531,NC_045512.2,28271,A,T,PASS,1392,0,1390,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.18 +220531,NC_045512.2,28311,C,T,PASS,1393,1,1382,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.18 +220531,NC_045512.2,2832,A,G,PASS,216,0,216,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.18 +220531,NC_045512.2,28361,GGAGAACGCA,G,PASS,1099,1092,795,0.72,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.18 +220531,NC_045512.2,28881,GG,AA,PASS,2048,32,2014,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.18 +220531,NC_045512.2,28883,G,C,PASS,2025,2,2020,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.18 +220531,NC_045512.2,3037,C,T,PASS,58,0,58,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.18 +220531,NC_045512.2,5386,T,G,PASS,34,0,34,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.18 +220531,NC_045512.2,5730,C,T,PASS,289,0,289,1.0,orf1ab,missense_variant,c.5465C>T,p.Thr1822Ile,p.T1822I,ivar,BA.1.18 +220531,NC_045512.2,8393,G,A,PASS,3368,17,3350,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.18 +220532,NC_045512.2,10449,C,A,PASS,26,0,26,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220532,NC_045512.2,11282,AGTTTGTCTG,A,PASS,38,38,33,0.87,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220532,NC_045512.2,11537,A,G,PASS,58,0,58,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220532,NC_045512.2,13195,T,C,PASS,3057,4,3053,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220532,NC_045512.2,14090,A,T,ft,13,9,4,0.31,orf1ab,missense_variant,c.13825A>T,p.Met4609Leu,p.M4609L,ivar,Unassigned +220532,NC_045512.2,14408,C,T,PASS,33,0,32,0.97,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220532,NC_045512.2,15933,C,T,PASS,69,4,65,0.94,orf1ab,missense_variant,c.15668C>T,p.Thr5223Ile,p.T5223I,ivar,Unassigned +220532,NC_045512.2,21762,C,T,PASS,51,0,51,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220532,NC_045512.2,21764,ATACATG,A,PASS,51,51,46,0.9,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220532,NC_045512.2,21846,C,T,PASS,72,0,72,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220532,NC_045512.2,23403,A,G,PASS,753,1,752,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220532,NC_045512.2,23525,C,T,PASS,730,0,730,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220532,NC_045512.2,23599,T,G,PASS,267,0,267,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220532,NC_045512.2,23604,C,A,PASS,263,0,261,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220532,NC_045512.2,23854,C,A,PASS,18,0,18,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220532,NC_045512.2,23948,G,T,PASS,81,0,81,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220532,NC_045512.2,24130,C,A,PASS,131,0,131,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220532,NC_045512.2,24424,A,T,PASS,26,0,26,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220532,NC_045512.2,24469,T,A,PASS,242,0,242,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220532,NC_045512.2,24503,C,T,PASS,289,2,287,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220532,NC_045512.2,25000,C,T,PASS,13,0,13,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220532,NC_045512.2,25584,C,T,PASS,13,0,13,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220532,NC_045512.2,26270,C,T,PASS,33,0,33,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220532,NC_045512.2,26530,A,G,PASS,31,0,31,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220532,NC_045512.2,26577,C,G,PASS,31,0,31,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220532,NC_045512.2,26654,G,GT,PASS,28,28,9,0.32,M,frameshift_variant,c.137dupT,p.Leu46fs,p.L46fs,ivar,Unassigned +220532,NC_045512.2,26709,G,A,PASS,33,0,33,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220532,NC_045512.2,27259,A,C,PASS,40,0,40,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220532,NC_045512.2,27807,C,T,PASS,22,3,19,0.86,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220532,NC_045512.2,28271,A,T,PASS,365,0,365,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220532,NC_045512.2,28311,C,T,PASS,335,0,335,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220532,NC_045512.2,2832,A,G,PASS,31,0,31,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220532,NC_045512.2,28361,GGAGAACGCA,G,PASS,279,279,202,0.72,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220532,NC_045512.2,28512,C,T,PASS,110,79,29,0.26,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,Unassigned +220532,NC_045512.2,28881,GG,AA,PASS,2846,42,2800,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220532,NC_045512.2,28883,G,C,PASS,2820,3,2814,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220532,NC_045512.2,4097,T,TC,PASS,25,25,8,0.32,orf1ab,frameshift_variant,c.3832_3833insC,p.Phe1278fs,p.F1278fs,ivar,Unassigned +220532,NC_045512.2,4101,T,C,PASS,25,17,8,0.32,orf1ab,missense_variant,c.3836T>C,p.Leu1279Ser,p.L1279S,ivar,Unassigned +220532,NC_045512.2,5672,C,T,PASS,11,0,11,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220532,NC_045512.2,8393,G,A,PASS,1208,5,1203,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220533,NC_045512.2,13195,T,C,PASS,35,0,35,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220533,NC_045512.2,23403,A,G,PASS,19,0,19,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220533,NC_045512.2,23525,C,T,PASS,15,0,15,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220533,NC_045512.2,28881,GG,AA,PASS,335,4,331,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220533,NC_045512.2,28883,G,C,PASS,331,0,331,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220533,NC_045512.2,8393,G,A,PASS,102,0,102,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220534,NC_045512.2,10029,C,T,PASS,80,1,79,0.99,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220534,NC_045512.2,10449,C,A,PASS,302,0,300,0.99,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220534,NC_045512.2,11282,AGTTTGTCTG,A,PASS,1212,1193,1059,0.87,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220534,NC_045512.2,11537,A,G,PASS,576,0,576,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220534,NC_045512.2,13195,T,C,PASS,6107,17,6090,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220534,NC_045512.2,14408,C,T,PASS,315,0,315,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220534,NC_045512.2,18163,A,G,PASS,58,0,58,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220534,NC_045512.2,19374,C,T,PASS,426,3,423,0.99,orf1ab,missense_variant,c.19109C>T,p.Ser6370Phe,p.S6370F,ivar,BA.1.17 +220534,NC_045512.2,20743,A,C,PASS,3288,0,3285,1.0,orf1ab,missense_variant,c.20478A>C,p.Lys6826Asn,p.K6826N,ivar,BA.1.17 +220534,NC_045512.2,21762,C,T,PASS,429,4,425,0.99,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220534,NC_045512.2,21764,ATACATG,A,PASS,434,429,398,0.92,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220534,NC_045512.2,21846,C,T,PASS,452,2,450,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220534,NC_045512.2,22193,AATT,A,PASS,19,19,16,0.84,S,disruptive_inframe_deletion,c.632_634delATT,p.Asn211_Leu212delinsIle,p.N211_L212delinsI,ivar,BA.1.17 +220534,NC_045512.2,22204,T,TGAGCCAGAA,PASS,16,16,13,0.81,S,disruptive_inframe_insertion,c.644_645insGCCAGAAGA,p.Arg214_Asp215insGluProGlu,p.R214_D215insEPE,ivar,BA.1.17 +220534,NC_045512.2,22578,G,A,PASS,87,0,87,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.17 +220534,NC_045512.2,22673,TC,CT,PASS,68,0,68,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.17 +220534,NC_045512.2,22679,T,C,PASS,95,0,95,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220534,NC_045512.2,22686,C,T,PASS,94,0,94,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220534,NC_045512.2,22882,T,G,PASS,13,0,13,1.0,S,missense_variant,c.1320T>G,p.Asn440Lys,p.N440K,ivar,BA.1.17 +220534,NC_045512.2,22898,G,A,PASS,11,0,11,1.0,S,missense_variant,c.1336G>A,p.Gly446Ser,p.G446S,ivar,BA.1.17 +220534,NC_045512.2,22992,G,A,PASS,20,0,20,1.0,S,missense_variant,c.1430G>A,p.Ser477Asn,p.S477N,ivar,BA.1.17 +220534,NC_045512.2,22995,C,A,PASS,20,0,20,1.0,S,missense_variant,c.1433C>A,p.Thr478Lys,p.T478K,ivar,BA.1.17 +220534,NC_045512.2,23013,A,C,PASS,24,0,24,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.17 +220534,NC_045512.2,23040,A,G,PASS,33,0,33,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.17 +220534,NC_045512.2,23048,G,A,PASS,33,1,32,0.97,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.17 +220534,NC_045512.2,23055,A,G,PASS,35,0,35,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.17 +220534,NC_045512.2,23063,A,T,PASS,38,0,38,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.17 +220534,NC_045512.2,23075,T,C,PASS,42,0,42,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.17 +220534,NC_045512.2,23202,C,A,PASS,77,0,77,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220534,NC_045512.2,23403,A,G,PASS,3887,4,3880,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220534,NC_045512.2,23525,C,T,PASS,3730,6,3714,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220534,NC_045512.2,23599,T,G,PASS,1409,0,1404,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220534,NC_045512.2,23604,C,A,PASS,1356,0,1350,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220534,NC_045512.2,23854,C,A,PASS,252,1,250,0.99,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220534,NC_045512.2,23948,G,T,PASS,1209,0,1206,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220534,NC_045512.2,24130,C,A,PASS,1902,2,1884,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220534,NC_045512.2,24424,A,T,PASS,860,1,856,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220534,NC_045512.2,24469,T,A,PASS,1573,3,1565,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220534,NC_045512.2,24503,C,T,PASS,1795,32,1760,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220534,NC_045512.2,25000,C,T,PASS,198,0,198,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220534,NC_045512.2,25584,C,T,PASS,452,9,441,0.98,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220534,NC_045512.2,26270,C,T,PASS,1216,6,1208,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220534,NC_045512.2,26530,A,G,PASS,353,0,353,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220534,NC_045512.2,26577,C,G,PASS,356,0,355,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220534,NC_045512.2,26709,G,A,PASS,372,2,369,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220534,NC_045512.2,27259,A,C,PASS,803,0,799,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220534,NC_045512.2,27807,C,T,PASS,288,0,288,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220534,NC_045512.2,28271,A,T,PASS,1664,5,1652,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220534,NC_045512.2,28311,C,T,PASS,1664,11,1651,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220534,NC_045512.2,2832,A,G,PASS,326,0,326,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220534,NC_045512.2,28361,GGAGAACGCA,G,PASS,1461,1458,1071,0.73,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220534,NC_045512.2,28881,GG,AA,PASS,2169,23,2143,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220534,NC_045512.2,28883,G,C,PASS,2150,0,2147,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220534,NC_045512.2,3037,C,T,PASS,104,0,104,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220534,NC_045512.2,5386,T,G,PASS,33,0,33,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.17 +220534,NC_045512.2,5672,C,T,PASS,610,2,608,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220534,NC_045512.2,5924,G,A,PASS,241,0,241,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220534,NC_045512.2,8393,G,A,PASS,3994,13,3975,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220534,NC_045512.2,8715,C,T,PASS,28,20,8,0.29,orf1ab,missense_variant,c.8450C>T,p.Thr2817Ile,p.T2817I,ivar,BA.1.17 +220535,NC_045512.2,10449,C,A,PASS,23,0,23,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220535,NC_045512.2,11282,AGTTTGTCTG,A,PASS,76,76,65,0.86,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220535,NC_045512.2,11537,A,G,PASS,61,0,61,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220535,NC_045512.2,13195,T,C,PASS,2278,1,2277,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220535,NC_045512.2,14408,C,T,PASS,40,0,40,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220535,NC_045512.2,14646,T,A,PASS,41,27,12,0.29,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,Unassigned +220535,NC_045512.2,16064,A,G,PASS,42,0,42,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220535,NC_045512.2,16308,C,T,PASS,133,0,133,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,Unassigned +220535,NC_045512.2,21762,C,T,PASS,42,0,42,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220535,NC_045512.2,21764,ATACATG,A,PASS,43,42,36,0.84,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220535,NC_045512.2,21846,C,T,PASS,55,0,55,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220535,NC_045512.2,23403,A,G,PASS,1687,0,1687,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220535,NC_045512.2,23525,C,T,PASS,1723,4,1719,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220535,NC_045512.2,23599,T,G,PASS,665,0,665,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220535,NC_045512.2,23604,C,A,PASS,648,0,645,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220535,NC_045512.2,23948,G,T,PASS,59,0,59,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220535,NC_045512.2,24130,C,A,PASS,93,0,93,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220535,NC_045512.2,24424,A,T,PASS,39,0,39,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220535,NC_045512.2,24469,T,A,PASS,245,1,244,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220535,NC_045512.2,24503,C,T,PASS,281,1,280,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220535,NC_045512.2,25000,C,T,PASS,19,0,19,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220535,NC_045512.2,25584,C,T,PASS,27,0,27,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220535,NC_045512.2,26270,C,T,PASS,194,0,194,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220535,NC_045512.2,26530,A,G,PASS,114,0,114,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220535,NC_045512.2,26577,C,G,PASS,120,1,119,0.99,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220535,NC_045512.2,26709,G,A,PASS,93,0,93,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220535,NC_045512.2,27259,A,C,PASS,78,0,78,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220535,NC_045512.2,27807,C,T,PASS,42,0,42,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220535,NC_045512.2,28271,A,T,PASS,684,0,684,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220535,NC_045512.2,28311,C,T,PASS,667,16,651,0.98,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220535,NC_045512.2,2832,A,G,PASS,25,0,25,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220535,NC_045512.2,28361,GGAGAACGCA,G,PASS,498,496,337,0.68,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220535,NC_045512.2,28512,C,T,PASS,234,171,62,0.26,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,Unassigned +220535,NC_045512.2,28881,GG,AA,PASS,6177,65,6104,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220535,NC_045512.2,28883,G,C,PASS,6141,2,6131,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220535,NC_045512.2,3037,C,T,PASS,11,0,11,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220535,NC_045512.2,4273,T,A,PASS,31,13,18,0.58,orf1ab,synonymous_variant,c.4008T>A,p.Gly1336Gly,p.G1336G,ivar,Unassigned +220535,NC_045512.2,76,T,A,ft,11,7,4,0.36,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220535,NC_045512.2,78,T,G,ft,11,7,4,0.36,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220535,NC_045512.2,8393,G,A,PASS,2646,16,2630,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220535,NC_045512.2,9572,G,A,PASS,1287,8,1277,0.99,orf1ab,missense_variant,c.9307G>A,p.Gly3103Ser,p.G3103S,ivar,Unassigned +220536,NC_045512.2,10449,C,A,PASS,12,0,12,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220536,NC_045512.2,11282,AGTTTGTCTG,A,PASS,36,35,32,0.89,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220536,NC_045512.2,11537,A,G,PASS,25,0,25,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220536,NC_045512.2,13195,T,C,PASS,1638,4,1634,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220536,NC_045512.2,14408,C,T,PASS,33,0,33,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220536,NC_045512.2,14646,T,A,PASS,43,27,16,0.37,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,Unassigned +220536,NC_045512.2,21595,C,T,PASS,167,0,167,1.0,S,synonymous_variant,c.33C>T,p.Val11Val,p.V11V,ivar,Unassigned +220536,NC_045512.2,21762,C,T,PASS,31,2,29,0.94,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220536,NC_045512.2,21764,ATACATG,A,PASS,32,32,32,1.0,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220536,NC_045512.2,21846,C,T,PASS,34,0,34,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220536,NC_045512.2,21859,C,T,PASS,31,0,31,1.0,S,synonymous_variant,c.297C>T,p.Asn99Asn,p.N99N,ivar,Unassigned +220536,NC_045512.2,23403,A,G,PASS,1494,4,1490,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220536,NC_045512.2,23525,C,T,PASS,1441,16,1425,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220536,NC_045512.2,23599,T,G,PASS,586,0,586,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220536,NC_045512.2,23604,C,A,PASS,571,0,571,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220536,NC_045512.2,23948,G,T,PASS,38,0,38,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220536,NC_045512.2,24130,C,A,PASS,51,0,51,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220536,NC_045512.2,24424,A,T,PASS,23,0,23,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220536,NC_045512.2,24469,T,A,PASS,203,0,203,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220536,NC_045512.2,24503,C,T,PASS,240,0,240,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220536,NC_045512.2,25000,C,T,PASS,17,0,17,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220536,NC_045512.2,25577,T,C,PASS,14,0,14,1.0,ORF3a,missense_variant,c.185T>C,p.Ile62Thr,p.I62T,ivar,Unassigned +220536,NC_045512.2,26270,C,T,PASS,99,0,99,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220536,NC_045512.2,26530,A,G,PASS,36,0,36,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220536,NC_045512.2,26577,C,G,PASS,40,0,40,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220536,NC_045512.2,26709,G,A,PASS,42,0,42,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220536,NC_045512.2,27259,A,C,PASS,29,0,29,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220536,NC_045512.2,27807,C,T,PASS,12,0,12,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220536,NC_045512.2,28271,A,T,PASS,310,2,308,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220536,NC_045512.2,28311,C,T,PASS,327,2,325,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220536,NC_045512.2,2832,A,G,PASS,15,0,15,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220536,NC_045512.2,28361,GGAGAACGCA,G,PASS,223,222,162,0.73,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220536,NC_045512.2,28881,GG,AA,PASS,5160,55,5100,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220536,NC_045512.2,28883,G,C,PASS,5134,3,5127,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220536,NC_045512.2,3037,C,T,PASS,14,0,14,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220536,NC_045512.2,8393,G,A,PASS,2570,9,2558,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220537,NC_045512.2,10029,C,T,PASS,30,0,30,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220537,NC_045512.2,10449,C,A,PASS,81,0,79,0.98,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220537,NC_045512.2,11282,AGTTTGTCTG,A,PASS,360,355,322,0.89,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220537,NC_045512.2,11537,A,G,PASS,303,0,303,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220537,NC_045512.2,13195,T,C,PASS,5220,4,5213,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220537,NC_045512.2,14408,C,T,PASS,123,0,123,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220537,NC_045512.2,18163,A,G,PASS,13,0,13,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220537,NC_045512.2,21762,C,T,PASS,202,1,201,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220537,NC_045512.2,21764,ATACATG,A,PASS,207,202,188,0.91,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220537,NC_045512.2,21846,C,T,PASS,220,0,220,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220537,NC_045512.2,22478,T,C,ft,15,11,4,0.27,S,missense_variant,c.916T>C,p.Phe306Leu,p.F306L,ivar,BA.1.17 +220537,NC_045512.2,22578,G,A,PASS,22,0,22,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.17 +220537,NC_045512.2,22673,TC,CT,PASS,18,0,18,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.17 +220537,NC_045512.2,22679,T,C,PASS,22,0,22,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220537,NC_045512.2,22686,C,T,PASS,22,0,22,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220537,NC_045512.2,23048,G,A,PASS,10,0,10,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.17 +220537,NC_045512.2,23055,A,G,PASS,10,0,10,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.17 +220537,NC_045512.2,23063,A,T,PASS,11,0,11,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.17 +220537,NC_045512.2,23075,T,C,PASS,12,0,12,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.17 +220537,NC_045512.2,23202,C,A,PASS,47,0,47,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220537,NC_045512.2,23403,A,G,PASS,3085,4,3081,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220537,NC_045512.2,23525,C,T,PASS,2906,14,2884,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220537,NC_045512.2,23599,T,G,PASS,1118,0,1116,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220537,NC_045512.2,23604,C,A,PASS,1080,0,1077,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220537,NC_045512.2,23854,C,A,PASS,74,0,74,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220537,NC_045512.2,23948,G,T,PASS,689,2,686,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220537,NC_045512.2,24130,C,A,PASS,1007,0,997,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220537,NC_045512.2,24424,A,T,PASS,270,2,268,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220537,NC_045512.2,24469,T,A,PASS,895,0,888,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220537,NC_045512.2,24503,C,T,PASS,1054,21,1033,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220537,NC_045512.2,25000,C,T,PASS,93,0,93,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220537,NC_045512.2,25584,C,T,PASS,117,0,117,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220537,NC_045512.2,26270,C,T,PASS,578,0,576,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220537,NC_045512.2,26530,A,G,PASS,226,0,226,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220537,NC_045512.2,26577,C,G,PASS,274,0,274,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220537,NC_045512.2,26709,G,A,PASS,253,0,253,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220537,NC_045512.2,27259,A,C,PASS,315,0,315,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220537,NC_045512.2,27384,T,C,PASS,451,0,451,1.0,ORF6,synonymous_variant,c.183T>C,p.Asp61Asp,p.D61D,ivar,BA.1.17 +220537,NC_045512.2,27807,C,T,PASS,91,0,91,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220537,NC_045512.2,28271,A,T,PASS,918,2,913,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220537,NC_045512.2,28311,C,T,PASS,933,0,929,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220537,NC_045512.2,2832,A,G,PASS,97,0,97,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220537,NC_045512.2,28361,GGAGAACGCA,G,PASS,774,770,558,0.72,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220537,NC_045512.2,28881,GG,AA,PASS,3048,38,3005,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220537,NC_045512.2,28883,G,C,PASS,3032,4,3020,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220537,NC_045512.2,3037,C,T,PASS,49,0,49,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220537,NC_045512.2,5386,T,G,PASS,15,0,15,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.17 +220537,NC_045512.2,5672,C,T,PASS,149,0,149,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220537,NC_045512.2,5924,G,A,PASS,77,0,77,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220537,NC_045512.2,635,C,T,PASS,9649,48,9569,0.99,orf1ab,missense_variant,c.370C>T,p.Arg124Cys,p.R124C,ivar,BA.1.17 +220537,NC_045512.2,7984,T,C,PASS,1058,2,1056,1.0,orf1ab,synonymous_variant,c.7719T>C,p.Asp2573Asp,p.D2573D,ivar,BA.1.17 +220537,NC_045512.2,8393,G,A,PASS,2866,7,2859,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220538,NC_045512.2,10029,C,T,PASS,23,0,23,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.18 +220538,NC_045512.2,10449,C,A,PASS,82,0,82,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.18 +220538,NC_045512.2,11282,AGTTTGTCTG,A,PASS,493,491,443,0.9,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.18 +220538,NC_045512.2,11537,A,G,PASS,252,0,252,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.18 +220538,NC_045512.2,13195,T,C,PASS,4749,6,4741,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.18 +220538,NC_045512.2,14408,C,T,PASS,81,0,79,0.98,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.18 +220538,NC_045512.2,18163,A,G,PASS,28,0,28,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.18 +220538,NC_045512.2,2172,A,G,PASS,1213,5,1207,1.0,orf1ab,missense_variant,c.1907A>G,p.Lys636Arg,p.K636R,ivar,BA.1.18 +220538,NC_045512.2,21762,C,T,PASS,158,0,158,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.18 +220538,NC_045512.2,21764,ATACATG,A,PASS,165,160,145,0.88,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.18 +220538,NC_045512.2,21846,C,T,PASS,170,0,170,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.18 +220538,NC_045512.2,22578,G,A,PASS,33,0,33,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.18 +220538,NC_045512.2,22673,TC,CT,PASS,19,1,18,0.95,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.18 +220538,NC_045512.2,22679,T,C,PASS,25,0,25,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.18 +220538,NC_045512.2,22686,C,T,PASS,25,0,25,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.18 +220538,NC_045512.2,23040,A,G,PASS,12,0,12,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.18 +220538,NC_045512.2,23048,G,A,PASS,13,0,13,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.18 +220538,NC_045512.2,23055,A,G,PASS,13,0,13,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.18 +220538,NC_045512.2,23063,A,T,PASS,13,0,13,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.18 +220538,NC_045512.2,23075,T,C,PASS,10,0,10,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.18 +220538,NC_045512.2,23202,C,A,PASS,22,0,22,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.18 +220538,NC_045512.2,23403,A,G,PASS,3286,10,3275,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.18 +220538,NC_045512.2,23525,C,T,PASS,3216,2,3208,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.18 +220538,NC_045512.2,23599,T,G,PASS,1320,1,1317,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.18 +220538,NC_045512.2,23604,C,A,PASS,1275,0,1266,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.18 +220538,NC_045512.2,23854,C,A,PASS,51,0,50,0.98,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.18 +220538,NC_045512.2,23948,G,T,PASS,254,0,253,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.18 +220538,NC_045512.2,24130,C,A,PASS,419,0,417,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.18 +220538,NC_045512.2,24424,A,T,PASS,173,0,171,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.18 +220538,NC_045512.2,24469,T,A,PASS,675,2,669,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.18 +220538,NC_045512.2,24503,C,T,PASS,821,13,808,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.18 +220538,NC_045512.2,25000,C,T,PASS,104,0,104,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.18 +220538,NC_045512.2,25584,C,T,PASS,103,0,103,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.18 +220538,NC_045512.2,25855,G,T,PASS,79,0,79,1.0,ORF3a,missense_variant,c.463G>T,p.Asp155Tyr,p.D155Y,ivar,BA.1.18 +220538,NC_045512.2,25931,CT,AC,PASS,88,0,88,1.0,ORF3a,missense_variant,c.539_540delCTinsAC,p.Ser180Tyr,p.S180Y,ivar,BA.1.18 +220538,NC_045512.2,26270,C,T,PASS,315,0,315,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.18 +220538,NC_045512.2,26530,A,G,PASS,141,0,141,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.18 +220538,NC_045512.2,26577,C,G,PASS,152,0,152,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.18 +220538,NC_045512.2,26709,G,A,PASS,160,0,160,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.18 +220538,NC_045512.2,27259,A,C,PASS,327,0,327,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.18 +220538,NC_045512.2,27519,C,T,PASS,303,0,303,1.0,ORF7a,synonymous_variant,c.126C>T,p.Gly42Gly,p.G42G,ivar,BA.1.18 +220538,NC_045512.2,27807,C,T,PASS,118,0,118,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.18 +220538,NC_045512.2,28271,A,T,PASS,985,4,981,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.18 +220538,NC_045512.2,28311,C,T,PASS,995,6,987,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.18 +220538,NC_045512.2,2832,A,G,PASS,59,0,59,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.18 +220538,NC_045512.2,28361,GGAGAACGCA,G,PASS,847,843,615,0.73,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.18 +220538,NC_045512.2,28881,GG,AA,PASS,2536,35,2498,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.18 +220538,NC_045512.2,28883,G,C,PASS,2511,2,2506,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.18 +220538,NC_045512.2,3037,C,T,PASS,42,0,42,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.18 +220538,NC_045512.2,5386,T,G,PASS,11,0,9,0.82,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.18 +220538,NC_045512.2,5730,C,T,PASS,90,1,89,0.99,orf1ab,missense_variant,c.5465C>T,p.Thr1822Ile,p.T1822I,ivar,BA.1.18 +220538,NC_045512.2,8393,G,A,PASS,3456,17,3437,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.18 +220539,NC_045512.2,10449,C,A,PASS,32,0,32,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220539,NC_045512.2,11282,AGTTTGTCTG,A,PASS,101,100,83,0.82,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220539,NC_045512.2,11455,C,T,PASS,127,0,127,1.0,orf1ab,synonymous_variant,c.11190C>T,p.Ala3730Ala,p.A3730A,ivar,Unassigned +220539,NC_045512.2,11537,A,G,PASS,82,0,82,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220539,NC_045512.2,13195,T,C,PASS,4012,6,4006,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220539,NC_045512.2,14408,C,T,PASS,72,0,72,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220539,NC_045512.2,21762,C,T,PASS,89,0,89,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220539,NC_045512.2,21764,ATACATG,A,PASS,89,89,82,0.92,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220539,NC_045512.2,21846,C,T,PASS,73,0,73,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220539,NC_045512.2,23403,A,G,PASS,1894,4,1890,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220539,NC_045512.2,23525,C,T,PASS,1971,3,1968,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220539,NC_045512.2,23599,T,G,PASS,834,0,834,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220539,NC_045512.2,23604,C,A,PASS,809,0,808,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220539,NC_045512.2,23854,C,A,PASS,14,1,12,0.86,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220539,NC_045512.2,23948,G,T,PASS,146,0,146,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220539,NC_045512.2,23987,C,T,PASS,177,2,175,0.99,S,missense_variant,c.2425C>T,p.Pro809Ser,p.P809S,ivar,Unassigned +220539,NC_045512.2,24130,C,A,PASS,230,0,228,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220539,NC_045512.2,24424,A,T,PASS,57,0,57,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220539,NC_045512.2,24469,T,A,PASS,456,0,456,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220539,NC_045512.2,24503,C,T,PASS,539,6,532,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220539,NC_045512.2,25000,C,T,PASS,35,2,33,0.94,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220539,NC_045512.2,25584,C,T,PASS,37,0,37,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220539,NC_045512.2,26270,C,T,PASS,144,0,144,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220539,NC_045512.2,26530,A,G,PASS,35,0,35,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220539,NC_045512.2,26577,C,G,PASS,49,0,49,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220539,NC_045512.2,26709,G,A,PASS,21,0,21,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220539,NC_045512.2,27259,A,C,PASS,73,0,73,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220539,NC_045512.2,27807,C,T,PASS,37,0,37,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220539,NC_045512.2,2785,T,C,PASS,30,22,8,0.27,orf1ab,synonymous_variant,c.2520T>C,p.Asn840Asn,p.N840N,ivar,Unassigned +220539,NC_045512.2,28271,A,T,PASS,299,0,299,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220539,NC_045512.2,28311,C,T,PASS,288,2,286,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220539,NC_045512.2,2832,A,G,PASS,35,0,35,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220539,NC_045512.2,28361,GGAGAACGCA,G,PASS,204,202,147,0.72,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220539,NC_045512.2,28881,GG,AA,PASS,5835,60,5773,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220539,NC_045512.2,28883,G,C,PASS,5804,4,5791,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220539,NC_045512.2,3037,C,T,PASS,24,0,24,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220539,NC_045512.2,8393,G,A,PASS,3152,5,3147,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220540,NC_045512.2,11282,AGTTTGTCTG,A,PASS,12,12,12,1.0,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220540,NC_045512.2,13195,T,C,PASS,87,0,87,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220540,NC_045512.2,14646,T,A,PASS,12,4,8,0.67,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,Unassigned +220540,NC_045512.2,2010,A,G,ft,10,6,4,0.4,orf1ab,missense_variant,c.1745A>G,p.Asp582Gly,p.D582G,ivar,Unassigned +220540,NC_045512.2,23403,A,G,PASS,282,0,282,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220540,NC_045512.2,23525,C,T,PASS,293,0,293,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220540,NC_045512.2,23599,T,G,PASS,121,0,121,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220540,NC_045512.2,23604,C,A,PASS,117,0,117,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220540,NC_045512.2,24130,C,A,PASS,12,0,12,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220540,NC_045512.2,26270,C,T,PASS,40,0,40,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220540,NC_045512.2,26530,A,G,PASS,12,0,12,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220540,NC_045512.2,26577,C,G,PASS,15,0,15,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220540,NC_045512.2,28271,A,T,PASS,41,2,39,0.95,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220540,NC_045512.2,28311,C,T,PASS,45,0,45,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220540,NC_045512.2,28361,GGAGAACGCA,G,PASS,33,33,25,0.76,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220540,NC_045512.2,28881,GG,AA,PASS,3161,17,3140,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220540,NC_045512.2,28883,G,C,PASS,3153,4,3146,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220540,NC_045512.2,8393,G,A,PASS,606,0,606,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220540,NC_045512.2,9572,G,A,PASS,96,2,94,0.98,orf1ab,missense_variant,c.9307G>A,p.Gly3103Ser,p.G3103S,ivar,Unassigned +220541,NC_045512.2,10029,C,T,PASS,11,0,11,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.1.1 +220541,NC_045512.2,10449,C,A,PASS,83,0,82,0.99,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1.1 +220541,NC_045512.2,11282,AGTTTGTCTG,A,PASS,120,120,116,0.97,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1.1 +220541,NC_045512.2,11537,A,G,PASS,197,0,197,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1.1 +220541,NC_045512.2,13195,T,C,PASS,5495,3,5491,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1.1 +220541,NC_045512.2,14408,C,T,PASS,104,0,104,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1.1 +220541,NC_045512.2,16064,A,G,PASS,228,0,228,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,BA.1.1.1 +220541,NC_045512.2,16308,C,T,PASS,423,1,422,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,BA.1.1.1 +220541,NC_045512.2,18163,A,G,PASS,22,0,22,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.1.1 +220541,NC_045512.2,21762,C,T,PASS,147,0,147,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1.1 +220541,NC_045512.2,21764,ATACATG,A,PASS,147,147,141,0.96,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1.1 +220541,NC_045512.2,21846,C,T,PASS,142,0,142,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1.1 +220541,NC_045512.2,22578,G,A,PASS,12,0,12,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.1.1 +220541,NC_045512.2,22599,G,A,PASS,15,0,15,1.0,S,missense_variant,c.1037G>A,p.Arg346Lys,p.R346K,ivar,BA.1.1.1 +220541,NC_045512.2,22679,T,C,PASS,11,0,11,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.1.1 +220541,NC_045512.2,22686,C,T,PASS,11,0,11,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.1.1 +220541,NC_045512.2,23403,A,G,PASS,2543,1,2541,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1.1 +220541,NC_045512.2,23525,C,T,PASS,2437,14,2421,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1.1 +220541,NC_045512.2,23599,T,G,PASS,936,0,936,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1.1 +220541,NC_045512.2,23604,C,A,PASS,908,2,901,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1.1 +220541,NC_045512.2,23854,C,A,PASS,41,0,41,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1.1 +220541,NC_045512.2,23948,G,T,PASS,581,0,580,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1.1 +220541,NC_045512.2,24130,C,A,PASS,761,0,760,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1.1 +220541,NC_045512.2,24424,A,T,PASS,135,0,135,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1.1 +220541,NC_045512.2,24469,T,A,PASS,759,0,758,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1.1 +220541,NC_045512.2,24503,C,T,PASS,912,18,894,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1.1 +220541,NC_045512.2,25000,C,T,PASS,39,0,39,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1.1 +220541,NC_045512.2,25584,C,T,PASS,60,2,58,0.97,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1.1 +220541,NC_045512.2,26270,C,T,PASS,319,0,317,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1.1 +220541,NC_045512.2,26530,A,G,PASS,157,0,157,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1.1 +220541,NC_045512.2,26577,C,G,PASS,174,0,174,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1.1 +220541,NC_045512.2,26709,G,A,PASS,152,2,150,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1.1 +220541,NC_045512.2,27259,A,C,PASS,165,0,165,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1.1 +220541,NC_045512.2,27807,C,T,PASS,120,0,120,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1.1 +220541,NC_045512.2,28271,A,T,PASS,1013,1,1010,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1.1 +220541,NC_045512.2,28311,C,T,PASS,991,3,987,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1.1 +220541,NC_045512.2,2832,A,G,PASS,41,0,41,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1.1 +220541,NC_045512.2,28361,GGAGAACGCA,G,PASS,729,726,511,0.7,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1.1 +220541,NC_045512.2,28512,C,T,PASS,407,288,106,0.26,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,BA.1.1.1 +220541,NC_045512.2,28881,GG,AA,PASS,3023,30,2990,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1.1 +220541,NC_045512.2,28883,G,C,PASS,3005,0,2998,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1.1 +220541,NC_045512.2,3037,C,T,PASS,33,0,33,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1.1 +220541,NC_045512.2,5386,T,G,PASS,16,0,16,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.1.1 +220541,NC_045512.2,728,G,A,PASS,79,58,20,0.25,orf1ab,missense_variant,c.463G>A,p.Glu155Lys,p.E155K,ivar,BA.1.1.1 +220541,NC_045512.2,8393,G,A,PASS,3521,3,3515,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1.1 +220541,NC_045512.2,9572,G,A,PASS,2527,14,2509,0.99,orf1ab,missense_variant,c.9307G>A,p.Gly3103Ser,p.G3103S,ivar,BA.1.1.1 +220542,NC_045512.2,10449,C,A,PASS,23,0,23,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220542,NC_045512.2,11537,A,G,PASS,83,0,83,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220542,NC_045512.2,13195,T,C,PASS,3374,13,3359,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220542,NC_045512.2,14408,C,T,PASS,61,0,61,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220542,NC_045512.2,16064,A,G,PASS,32,0,32,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220542,NC_045512.2,16308,C,T,PASS,94,0,94,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,Unassigned +220542,NC_045512.2,21762,C,T,PASS,64,0,64,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220542,NC_045512.2,21764,ATACATG,A,PASS,65,64,64,0.98,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220542,NC_045512.2,21846,C,T,PASS,65,0,65,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220542,NC_045512.2,23403,A,G,PASS,1214,0,1214,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220542,NC_045512.2,23525,C,T,PASS,1267,3,1261,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220542,NC_045512.2,23599,T,G,PASS,536,1,534,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220542,NC_045512.2,23604,C,A,PASS,511,0,510,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220542,NC_045512.2,23948,G,T,PASS,34,0,34,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220542,NC_045512.2,24130,C,A,PASS,86,0,86,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220542,NC_045512.2,24469,T,A,PASS,299,0,297,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220542,NC_045512.2,24503,C,T,PASS,373,5,368,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220542,NC_045512.2,26530,A,G,PASS,11,0,11,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220542,NC_045512.2,26577,C,G,PASS,13,0,13,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220542,NC_045512.2,26709,G,A,PASS,17,0,17,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220542,NC_045512.2,27807,C,T,PASS,35,0,35,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220542,NC_045512.2,28271,A,T,PASS,768,0,767,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220542,NC_045512.2,28311,C,T,PASS,724,2,722,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220542,NC_045512.2,28361,GGAGAACGCA,G,PASS,451,450,317,0.7,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220542,NC_045512.2,28512,C,T,PASS,106,64,42,0.4,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,Unassigned +220542,NC_045512.2,28881,GG,AA,PASS,6562,63,6491,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220542,NC_045512.2,28883,G,C,PASS,6525,2,6516,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220542,NC_045512.2,3037,C,T,PASS,13,1,12,0.92,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220542,NC_045512.2,4276,C,T,PASS,40,0,40,1.0,orf1ab,synonymous_variant,c.4011C>T,p.Tyr1337Tyr,p.Y1337Y,ivar,Unassigned +220542,NC_045512.2,8393,G,A,PASS,1787,5,1782,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220543,NC_045512.2,10029,C,T,PASS,66,0,66,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.1.1 +220543,NC_045512.2,10449,C,A,PASS,291,0,290,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1.1 +220543,NC_045512.2,11282,AGTTTGTCTG,A,PASS,357,354,314,0.88,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1.1 +220543,NC_045512.2,11537,A,G,PASS,556,1,554,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1.1 +220543,NC_045512.2,13195,T,C,PASS,7272,15,7253,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1.1 +220543,NC_045512.2,14408,C,T,PASS,487,3,484,0.99,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1.1 +220543,NC_045512.2,15336,T,C,PASS,19,12,7,0.37,orf1ab,missense_variant,c.15071T>C,p.Leu5024Ser,p.L5024S,ivar,BA.1.1.1 +220543,NC_045512.2,15359,G,A,PASS,15,7,8,0.53,orf1ab,missense_variant,c.15094G>A,p.Ala5032Thr,p.A5032T,ivar,BA.1.1.1 +220543,NC_045512.2,16064,A,G,PASS,636,1,635,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,BA.1.1.1 +220543,NC_045512.2,16308,C,T,PASS,1330,1,1329,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,BA.1.1.1 +220543,NC_045512.2,18163,A,G,PASS,43,0,43,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.1.1 +220543,NC_045512.2,21306,C,T,PASS,138,4,134,0.97,orf1ab,missense_variant,c.21041C>T,p.Ala7014Val,p.A7014V,ivar,BA.1.1.1 +220543,NC_045512.2,21762,C,T,PASS,541,1,540,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1.1 +220543,NC_045512.2,21764,ATACATG,A,PASS,555,541,494,0.89,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1.1 +220543,NC_045512.2,21846,C,T,PASS,533,2,531,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1.1 +220543,NC_045512.2,22578,G,A,PASS,17,0,17,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.1.1 +220543,NC_045512.2,22599,G,A,PASS,15,0,15,1.0,S,missense_variant,c.1037G>A,p.Arg346Lys,p.R346K,ivar,BA.1.1.1 +220543,NC_045512.2,22673,TC,CT,PASS,17,0,17,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.1.1 +220543,NC_045512.2,22679,T,C,PASS,27,0,27,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.1.1 +220543,NC_045512.2,22686,C,T,PASS,26,0,26,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.1.1 +220543,NC_045512.2,23013,A,C,PASS,10,0,10,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.1.1 +220543,NC_045512.2,23040,A,G,PASS,10,0,10,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.1.1 +220543,NC_045512.2,23048,G,A,PASS,10,0,10,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.1.1 +220543,NC_045512.2,23055,A,G,PASS,10,0,10,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.1.1 +220543,NC_045512.2,23063,A,T,PASS,10,0,10,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.1.1 +220543,NC_045512.2,23075,T,C,PASS,10,0,10,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.1.1 +220543,NC_045512.2,23202,C,A,PASS,33,0,33,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.1.1 +220543,NC_045512.2,23403,A,G,PASS,5345,6,5339,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1.1 +220543,NC_045512.2,23525,C,T,PASS,5055,8,5044,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1.1 +220543,NC_045512.2,23599,T,G,PASS,1780,0,1780,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1.1 +220543,NC_045512.2,23604,C,A,PASS,1726,0,1719,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1.1 +220543,NC_045512.2,23854,C,A,PASS,106,0,106,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1.1 +220543,NC_045512.2,23948,G,T,PASS,1529,0,1527,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1.1 +220543,NC_045512.2,24130,C,A,PASS,2315,0,2289,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1.1 +220543,NC_045512.2,24424,A,T,PASS,386,0,384,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1.1 +220543,NC_045512.2,24469,T,A,PASS,1576,0,1573,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1.1 +220543,NC_045512.2,24503,C,T,PASS,1890,45,1845,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1.1 +220543,NC_045512.2,25000,C,T,PASS,139,0,139,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1.1 +220543,NC_045512.2,25584,C,T,PASS,235,1,234,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1.1 +220543,NC_045512.2,26270,C,T,PASS,603,4,599,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1.1 +220543,NC_045512.2,26530,A,G,PASS,60,0,60,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1.1 +220543,NC_045512.2,26577,C,G,PASS,65,0,65,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1.1 +220543,NC_045512.2,26709,G,A,PASS,72,0,72,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1.1 +220543,NC_045512.2,27259,A,C,PASS,453,0,451,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1.1 +220543,NC_045512.2,27807,C,T,PASS,142,0,141,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1.1 +220543,NC_045512.2,28271,A,T,PASS,1561,4,1557,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1.1 +220543,NC_045512.2,28311,C,T,PASS,1582,3,1577,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1.1 +220543,NC_045512.2,2832,A,G,PASS,172,1,171,0.99,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1.1 +220543,NC_045512.2,28361,GGAGAACGCA,G,PASS,1130,1128,735,0.65,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1.1 +220543,NC_045512.2,28512,C,T,PASS,615,428,178,0.29,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,BA.1.1.1 +220543,NC_045512.2,28881,GG,AA,PASS,2666,37,2626,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1.1 +220543,NC_045512.2,28883,G,C,PASS,2644,3,2638,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1.1 +220543,NC_045512.2,29451,C,T,PASS,5293,30,5263,0.99,N,missense_variant,c.1178C>T,p.Thr393Ile,p.T393I,ivar,BA.1.1.1 +220543,NC_045512.2,3037,C,T,PASS,78,1,77,0.99,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1.1 +220543,NC_045512.2,5386,T,G,PASS,26,0,26,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.1.1 +220543,NC_045512.2,8393,G,A,PASS,4660,24,4632,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1.1 +220544,NC_045512.2,10449,C,A,PASS,10,0,10,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1.1 +220544,NC_045512.2,11282,AGTTTGTCTG,A,PASS,73,72,66,0.9,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1.1 +220544,NC_045512.2,11537,A,G,PASS,46,0,46,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1.1 +220544,NC_045512.2,13195,T,C,PASS,3335,1,3334,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1.1 +220544,NC_045512.2,14408,C,T,PASS,36,0,36,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1.1 +220544,NC_045512.2,16064,A,G,PASS,57,0,57,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,BA.1.1.1 +220544,NC_045512.2,16308,C,T,PASS,147,0,147,1.0,orf1ab,missense_variant,c.16043C>T,p.Ser5348Phe,p.S5348F,ivar,BA.1.1.1 +220544,NC_045512.2,206,C,A,PASS,32,18,12,0.38,orf1ab,upstream_gene_variant,c.-60C>A,.,.,ivar,BA.1.1.1 +220544,NC_045512.2,21762,C,T,PASS,78,0,78,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1.1 +220544,NC_045512.2,21764,ATACATG,A,PASS,79,78,66,0.84,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1.1 +220544,NC_045512.2,21846,C,T,PASS,38,0,38,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1.1 +220544,NC_045512.2,23013,A,C,PASS,10,0,10,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.1.1 +220544,NC_045512.2,23030,T,C,ft,10,7,3,0.3,S,missense_variant,c.1468T>C,p.Phe490Leu,p.F490L,ivar,BA.1.1.1 +220544,NC_045512.2,23040,A,G,PASS,10,0,10,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.1.1 +220544,NC_045512.2,23048,G,A,PASS,11,0,11,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.1.1 +220544,NC_045512.2,23055,A,G,PASS,11,0,11,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.1.1 +220544,NC_045512.2,23063,A,T,PASS,13,0,13,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.1.1 +220544,NC_045512.2,23075,T,C,PASS,16,0,16,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.1.1 +220544,NC_045512.2,23202,C,A,PASS,10,0,10,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.1.1 +220544,NC_045512.2,23403,A,G,PASS,1658,2,1655,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1.1 +220544,NC_045512.2,23525,C,T,PASS,1539,5,1533,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1.1 +220544,NC_045512.2,23599,T,G,PASS,601,3,598,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1.1 +220544,NC_045512.2,23604,C,A,PASS,583,0,583,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1.1 +220544,NC_045512.2,23756,A,G,ft,11,8,3,0.27,S,missense_variant,c.2194A>G,p.Thr732Ala,p.T732A,ivar,BA.1.1.1 +220544,NC_045512.2,23854,C,A,PASS,12,0,12,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1.1 +220544,NC_045512.2,23948,G,T,PASS,178,0,178,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1.1 +220544,NC_045512.2,24130,C,A,PASS,282,0,279,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1.1 +220544,NC_045512.2,24424,A,T,PASS,68,0,68,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1.1 +220544,NC_045512.2,24469,T,A,PASS,322,0,322,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1.1 +220544,NC_045512.2,24503,C,T,PASS,381,14,367,0.96,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1.1 +220544,NC_045512.2,25000,C,T,PASS,18,0,18,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1.1 +220544,NC_045512.2,25584,C,T,PASS,27,0,27,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1.1 +220544,NC_045512.2,26270,C,T,PASS,131,0,131,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1.1 +220544,NC_045512.2,26530,A,G,PASS,119,0,119,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1.1 +220544,NC_045512.2,26577,C,G,PASS,123,0,123,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1.1 +220544,NC_045512.2,26709,G,A,PASS,133,2,131,0.98,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1.1 +220544,NC_045512.2,27259,A,C,PASS,73,0,73,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1.1 +220544,NC_045512.2,27807,C,T,PASS,15,0,15,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1.1 +220544,NC_045512.2,2790,C,T,ft,15,11,4,0.27,orf1ab,missense_variant,c.2525C>T,p.Thr842Ile,p.T842I,ivar,BA.1.1.1 +220544,NC_045512.2,28271,A,T,PASS,206,0,206,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1.1 +220544,NC_045512.2,28311,C,T,PASS,200,0,198,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1.1 +220544,NC_045512.2,2832,A,G,PASS,15,0,15,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1.1 +220544,NC_045512.2,28361,GGAGAACGCA,G,PASS,156,154,111,0.71,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1.1 +220544,NC_045512.2,28881,GG,AA,PASS,6341,80,6256,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1.1 +220544,NC_045512.2,28883,G,C,PASS,6310,0,6304,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1.1 +220544,NC_045512.2,8393,G,A,PASS,1458,11,1447,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1.1 +220544,NC_045512.2,9572,G,A,PASS,1323,9,1310,0.99,orf1ab,missense_variant,c.9307G>A,p.Gly3103Ser,p.G3103S,ivar,BA.1.1.1 +220545,NC_045512.2,10029,C,T,PASS,16,0,16,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,Unassigned +220545,NC_045512.2,10449,C,A,PASS,23,0,23,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220545,NC_045512.2,11282,AGTTTGTCTG,A,PASS,94,94,81,0.86,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220545,NC_045512.2,11537,A,G,PASS,99,0,99,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220545,NC_045512.2,11958,T,C,PASS,18,0,18,1.0,orf1ab,missense_variant,c.11693T>C,p.Ile3898Thr,p.I3898T,ivar,Unassigned +220545,NC_045512.2,13195,T,C,PASS,3708,5,3703,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220545,NC_045512.2,14408,C,T,PASS,59,0,59,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220545,NC_045512.2,14774,A,T,ft,13,9,4,0.31,orf1ab,missense_variant,c.14509A>T,p.Met4837Leu,p.M4837L,ivar,Unassigned +220545,NC_045512.2,16064,A,G,PASS,75,0,75,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220545,NC_045512.2,18163,A,G,PASS,10,0,10,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,Unassigned +220545,NC_045512.2,21762,C,T,PASS,106,0,106,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220545,NC_045512.2,21764,ATACATG,A,PASS,109,106,91,0.83,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220545,NC_045512.2,21846,C,T,PASS,81,0,81,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220545,NC_045512.2,23403,A,G,PASS,1153,0,1153,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220545,NC_045512.2,23525,C,T,PASS,1133,2,1131,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220545,NC_045512.2,23599,T,G,PASS,445,0,445,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220545,NC_045512.2,23604,C,A,PASS,432,0,430,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220545,NC_045512.2,23854,C,A,PASS,24,0,24,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220545,NC_045512.2,23948,G,T,PASS,141,0,141,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220545,NC_045512.2,24130,C,A,PASS,177,0,177,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220545,NC_045512.2,24424,A,T,PASS,93,0,93,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220545,NC_045512.2,24469,T,A,PASS,454,0,451,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220545,NC_045512.2,24503,C,T,PASS,534,3,531,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220545,NC_045512.2,25000,C,T,PASS,35,0,35,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220545,NC_045512.2,25584,C,T,PASS,20,0,20,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220545,NC_045512.2,26270,C,T,PASS,77,0,77,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220545,NC_045512.2,26530,A,G,PASS,25,0,25,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220545,NC_045512.2,26577,C,G,PASS,36,0,36,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220545,NC_045512.2,26709,G,A,PASS,42,2,40,0.95,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220545,NC_045512.2,27259,A,C,PASS,62,0,62,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220545,NC_045512.2,27807,C,T,PASS,27,0,27,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220545,NC_045512.2,28238,T,C,PASS,556,0,556,1.0,ORF8,synonymous_variant,c.345T>C,p.Arg115Arg,p.R115R,ivar,Unassigned +220545,NC_045512.2,28271,A,T,PASS,638,4,630,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220545,NC_045512.2,28311,C,T,PASS,637,2,635,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220545,NC_045512.2,28361,GGAGAACGCA,G,PASS,462,461,341,0.74,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220545,NC_045512.2,28881,GG,AA,PASS,4829,76,4753,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220545,NC_045512.2,28883,G,C,PASS,4774,5,4765,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220545,NC_045512.2,3037,C,T,PASS,20,0,20,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220545,NC_045512.2,4835,G,C,PASS,55,35,20,0.36,orf1ab,missense_variant,c.4570G>C,p.Gly1524Arg,p.G1524R,ivar,Unassigned +220545,NC_045512.2,8393,G,A,PASS,1501,4,1495,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220546,NC_045512.2,10029,C,T,PASS,29,0,29,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.1.1 +220546,NC_045512.2,10449,C,A,PASS,74,0,74,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1.1 +220546,NC_045512.2,11282,AGTTTGTCTG,A,PASS,229,225,199,0.87,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1.1 +220546,NC_045512.2,11537,A,G,PASS,132,0,132,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1.1 +220546,NC_045512.2,13195,T,C,PASS,4491,2,4489,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1.1 +220546,NC_045512.2,14408,C,T,PASS,115,0,115,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1.1 +220546,NC_045512.2,16064,A,G,PASS,219,0,219,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,BA.1.1.1 +220546,NC_045512.2,18163,A,G,PASS,14,0,14,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.1.1 +220546,NC_045512.2,21762,C,T,PASS,121,0,121,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1.1 +220546,NC_045512.2,21764,ATACATG,A,PASS,127,121,110,0.87,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1.1 +220546,NC_045512.2,21846,C,T,PASS,121,0,121,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1.1 +220546,NC_045512.2,22679,T,C,PASS,11,0,11,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.1.1 +220546,NC_045512.2,22686,C,T,PASS,10,0,10,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.1.1 +220546,NC_045512.2,23040,A,G,PASS,12,0,12,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.1.1 +220546,NC_045512.2,23048,G,A,PASS,12,0,12,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.1.1 +220546,NC_045512.2,23055,A,G,PASS,12,0,12,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.1.1 +220546,NC_045512.2,23063,A,T,PASS,12,0,12,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.1.1 +220546,NC_045512.2,23075,T,C,PASS,13,0,13,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.1.1 +220546,NC_045512.2,23202,C,A,PASS,30,0,30,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.1.1 +220546,NC_045512.2,23403,A,G,PASS,3367,2,3365,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1.1 +220546,NC_045512.2,23525,C,T,PASS,3050,3,3045,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1.1 +220546,NC_045512.2,23599,T,G,PASS,1142,0,1142,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1.1 +220546,NC_045512.2,23604,C,A,PASS,1100,0,1094,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1.1 +220546,NC_045512.2,23854,C,A,PASS,28,0,28,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1.1 +220546,NC_045512.2,23948,G,T,PASS,349,1,344,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1.1 +220546,NC_045512.2,24130,C,A,PASS,564,0,559,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1.1 +220546,NC_045512.2,24424,A,T,PASS,122,0,122,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1.1 +220546,NC_045512.2,24469,T,A,PASS,553,0,548,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1.1 +220546,NC_045512.2,24503,C,T,PASS,663,14,649,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1.1 +220546,NC_045512.2,25000,C,T,PASS,53,0,53,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1.1 +220546,NC_045512.2,25584,C,T,PASS,61,0,61,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1.1 +220546,NC_045512.2,26270,C,T,PASS,368,2,366,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1.1 +220546,NC_045512.2,26530,A,G,PASS,140,0,140,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1.1 +220546,NC_045512.2,26577,C,G,PASS,173,0,173,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1.1 +220546,NC_045512.2,26709,G,A,PASS,158,1,157,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1.1 +220546,NC_045512.2,27259,A,C,PASS,165,0,165,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1.1 +220546,NC_045512.2,27807,C,T,PASS,79,0,79,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1.1 +220546,NC_045512.2,28238,T,C,PASS,607,0,607,1.0,ORF8,synonymous_variant,c.345T>C,p.Arg115Arg,p.R115R,ivar,BA.1.1.1 +220546,NC_045512.2,28271,A,T,PASS,751,0,749,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1.1 +220546,NC_045512.2,28311,C,T,PASS,709,4,703,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1.1 +220546,NC_045512.2,2832,A,G,PASS,42,0,42,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1.1 +220546,NC_045512.2,28361,GGAGAACGCA,G,PASS,531,529,373,0.7,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1.1 +220546,NC_045512.2,28512,C,T,PASS,385,283,99,0.26,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,BA.1.1.1 +220546,NC_045512.2,28881,GG,AA,PASS,2009,27,1980,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1.1 +220546,NC_045512.2,28883,G,C,PASS,1988,0,1982,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1.1 +220546,NC_045512.2,3037,C,T,PASS,24,0,24,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1.1 +220546,NC_045512.2,5386,T,G,PASS,12,0,12,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.1.1 +220546,NC_045512.2,76,T,A,ft,11,7,4,0.36,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1.1.1 +220546,NC_045512.2,78,T,G,ft,11,7,4,0.36,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1.1.1 +220546,NC_045512.2,8393,G,A,PASS,3173,9,3162,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1.1 +220599,NC_045512.2,11537,A,G,PASS,13,0,13,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220599,NC_045512.2,13195,T,C,PASS,273,2,271,0.99,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220599,NC_045512.2,16064,A,G,PASS,19,0,19,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220599,NC_045512.2,16853,G,T,PASS,16,0,14,0.88,orf1ab,missense_variant,c.16588G>T,p.Val5530Leu,p.V5530L,ivar,Unassigned +220599,NC_045512.2,23403,A,G,PASS,187,0,187,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220599,NC_045512.2,23525,C,T,PASS,144,0,144,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220599,NC_045512.2,23599,T,G,PASS,67,0,67,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220599,NC_045512.2,23604,C,A,PASS,67,0,67,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220599,NC_045512.2,23948,G,T,PASS,20,0,20,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220599,NC_045512.2,24130,C,A,PASS,36,0,36,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220599,NC_045512.2,24424,A,T,PASS,14,0,14,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220599,NC_045512.2,24469,T,A,PASS,30,0,30,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220599,NC_045512.2,24503,C,T,PASS,33,1,32,0.97,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220599,NC_045512.2,28881,GG,AA,PASS,166,5,161,0.97,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220599,NC_045512.2,28883,G,C,PASS,167,2,165,0.99,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220599,NC_045512.2,29400,C,T,PASS,89,0,89,1.0,N,missense_variant,c.1127C>T,p.Ala376Val,p.A376V,ivar,Unassigned +220599,NC_045512.2,3663,G,A,PASS,148,2,146,0.99,orf1ab,missense_variant,c.3398G>A,p.Ser1133Asn,p.S1133N,ivar,Unassigned +220599,NC_045512.2,4266,T,C,ft,11,8,3,0.27,orf1ab,missense_variant,c.4001T>C,p.Leu1334Ser,p.L1334S,ivar,Unassigned +220599,NC_045512.2,4363,A,T,ft,10,6,4,0.4,orf1ab,missense_variant,c.4098A>T,p.Glu1366Asp,p.E1366D,ivar,Unassigned +220599,NC_045512.2,8393,G,A,PASS,197,1,196,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220601,NC_045512.2,10029,C,T,PASS,335,2,333,0.99,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.1 +220601,NC_045512.2,10449,C,A,PASS,827,0,824,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1 +220601,NC_045512.2,11282,AGTTTGTCTG,A,PASS,1412,1400,1185,0.84,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1 +220601,NC_045512.2,11537,A,G,PASS,872,0,872,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1 +220601,NC_045512.2,13195,T,C,PASS,2886,7,2877,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1 +220601,NC_045512.2,14408,C,T,PASS,367,5,362,0.99,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1 +220601,NC_045512.2,15240,C,T,PASS,59,0,59,1.0,orf1ab,missense_variant,c.14975C>T,p.Thr4992Ile,p.T4992I,ivar,BA.1.1 +220601,NC_045512.2,18163,A,G,PASS,241,2,239,0.99,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.1 +220601,NC_045512.2,21762,C,T,PASS,460,2,458,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1 +220601,NC_045512.2,21764,ATACATG,A,PASS,465,463,409,0.88,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1 +220601,NC_045512.2,21846,C,T,PASS,446,6,440,0.99,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1 +220601,NC_045512.2,21986,GGTGTTTATT,G,PASS,15,15,15,1.0,S,disruptive_inframe_deletion,c.425_433delGTGTTTATT,p.Gly142_Tyr145delinsAsp,p.G142_Y145delinsD,ivar,BA.1.1 +220601,NC_045512.2,22193,AATT,A,PASS,25,25,15,0.6,S,disruptive_inframe_deletion,c.632_634delATT,p.Asn211_Leu212delinsIle,p.N211_L212delinsI,ivar,BA.1.1 +220601,NC_045512.2,22204,T,TGAGCCAGAA,ft,14,14,5,0.36,S,disruptive_inframe_insertion,c.644_645insGCCAGAAGA,p.Arg214_Asp215insGluProGlu,p.R214_D215insEPE,ivar,BA.1.1 +220601,NC_045512.2,22578,G,A,PASS,130,2,128,0.98,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.1 +220601,NC_045512.2,22599,G,A,PASS,141,0,141,1.0,S,missense_variant,c.1037G>A,p.Arg346Lys,p.R346K,ivar,BA.1.1 +220601,NC_045512.2,22673,TC,CT,PASS,111,0,111,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.1 +220601,NC_045512.2,22679,T,C,PASS,162,0,162,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.1 +220601,NC_045512.2,22686,C,T,PASS,161,1,160,0.99,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.1 +220601,NC_045512.2,22813,G,T,PASS,20,0,20,1.0,S,missense_variant,c.1251G>T,p.Lys417Asn,p.K417N,ivar,BA.1.1 +220601,NC_045512.2,22882,T,G,PASS,10,0,10,1.0,S,missense_variant,c.1320T>G,p.Asn440Lys,p.N440K,ivar,BA.1.1 +220601,NC_045512.2,22898,G,A,PASS,13,0,13,1.0,S,missense_variant,c.1336G>A,p.Gly446Ser,p.G446S,ivar,BA.1.1 +220601,NC_045512.2,22992,G,A,PASS,38,0,38,1.0,S,missense_variant,c.1430G>A,p.Ser477Asn,p.S477N,ivar,BA.1.1 +220601,NC_045512.2,22995,C,A,PASS,37,0,37,1.0,S,missense_variant,c.1433C>A,p.Thr478Lys,p.T478K,ivar,BA.1.1 +220601,NC_045512.2,23013,A,C,PASS,52,0,52,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.1 +220601,NC_045512.2,23040,A,G,PASS,53,0,53,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.1 +220601,NC_045512.2,23048,G,A,PASS,56,0,56,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.1 +220601,NC_045512.2,23055,A,G,PASS,57,0,57,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.1 +220601,NC_045512.2,23063,A,T,PASS,62,0,62,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.1 +220601,NC_045512.2,23075,T,C,PASS,67,0,67,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.1 +220601,NC_045512.2,23202,C,A,PASS,101,1,99,0.98,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.1 +220601,NC_045512.2,23403,A,G,PASS,2063,4,2059,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1 +220601,NC_045512.2,23525,C,T,PASS,1975,4,1971,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1 +220601,NC_045512.2,23599,T,G,PASS,738,0,738,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1 +220601,NC_045512.2,23604,C,A,PASS,705,2,699,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1 +220601,NC_045512.2,23854,C,A,PASS,538,0,538,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1 +220601,NC_045512.2,23948,G,T,PASS,1237,0,1235,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1 +220601,NC_045512.2,24130,C,A,PASS,1834,0,1827,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1 +220601,NC_045512.2,24424,A,T,PASS,1387,0,1383,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1 +220601,NC_045512.2,24469,T,A,PASS,1593,3,1585,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1 +220601,NC_045512.2,24503,C,T,PASS,1682,21,1660,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1 +220601,NC_045512.2,25000,C,T,PASS,565,1,564,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1 +220601,NC_045512.2,25584,C,T,PASS,769,3,763,0.99,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1 +220601,NC_045512.2,26270,C,T,PASS,1265,4,1260,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1 +220601,NC_045512.2,26530,A,G,PASS,243,0,243,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1 +220601,NC_045512.2,26577,C,G,PASS,223,0,223,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1 +220601,NC_045512.2,26709,G,A,PASS,305,2,303,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1 +220601,NC_045512.2,27259,A,C,PASS,843,0,843,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1 +220601,NC_045512.2,27807,C,T,PASS,419,0,416,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1 +220601,NC_045512.2,28271,A,T,PASS,834,0,833,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1 +220601,NC_045512.2,28311,C,T,PASS,845,3,842,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1 +220601,NC_045512.2,2832,A,G,PASS,1221,6,1215,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1 +220601,NC_045512.2,28361,GGAGAACGCA,G,PASS,695,694,501,0.72,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1 +220601,NC_045512.2,28877,AG,TC,PASS,632,2,629,1.0,N,synonymous_variant,c.604_605delAGinsTC,p.203,p.203,ivar,BA.1.1 +220601,NC_045512.2,28881,GG,AA,PASS,631,2,628,1.0,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1 +220601,NC_045512.2,28883,G,C,PASS,629,0,629,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1 +220601,NC_045512.2,3037,C,T,PASS,124,0,124,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1 +220601,NC_045512.2,5386,T,G,PASS,102,0,102,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.1 +220601,NC_045512.2,6445,C,T,PASS,10,0,10,1.0,orf1ab,synonymous_variant,c.6180C>T,p.Asp2060Asp,p.D2060D,ivar,BA.1.1 +220601,NC_045512.2,6512,AGTT,A,PASS,12,12,10,0.83,orf1ab,disruptive_inframe_deletion,c.6248_6250delGTT,p.Ser2083_Leu2084delinsIle,p.S2083_L2084delinsI,ivar,BA.1.1 +220601,NC_045512.2,8393,G,A,PASS,1980,19,1959,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1 +220624,NC_045512.2,10449,C,A,PASS,11,0,11,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220624,NC_045512.2,11282,AGTTTGTCTG,A,PASS,31,31,28,0.9,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220624,NC_045512.2,11537,A,G,PASS,58,0,58,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220624,NC_045512.2,13195,T,C,PASS,2327,1,2323,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220624,NC_045512.2,14408,C,T,PASS,26,0,26,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220624,NC_045512.2,16925,A,G,ft,24,18,6,0.25,orf1ab,missense_variant,c.16660A>G,p.Ile5554Val,p.I5554V,ivar,Unassigned +220624,NC_045512.2,20371,C,G,ft,23,17,6,0.26,orf1ab,stop_gained,c.20106C>G,p.Tyr6702*,p.Y6702*,ivar,Unassigned +220624,NC_045512.2,2172,A,G,PASS,181,5,176,0.97,orf1ab,missense_variant,c.1907A>G,p.Lys636Arg,p.K636R,ivar,Unassigned +220624,NC_045512.2,21762,C,T,PASS,21,0,21,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220624,NC_045512.2,21764,ATACATG,A,PASS,21,21,20,0.95,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220624,NC_045512.2,21846,C,T,PASS,25,0,25,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220624,NC_045512.2,23403,A,G,PASS,920,0,920,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220624,NC_045512.2,23525,C,T,PASS,910,0,907,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220624,NC_045512.2,23599,T,G,PASS,359,0,359,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220624,NC_045512.2,23604,C,A,PASS,351,0,351,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220624,NC_045512.2,23948,G,T,PASS,35,0,35,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220624,NC_045512.2,24130,C,A,PASS,29,0,29,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220624,NC_045512.2,24424,A,T,PASS,26,0,26,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220624,NC_045512.2,24469,T,A,PASS,145,0,142,0.98,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220624,NC_045512.2,24503,C,T,PASS,171,3,168,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220624,NC_045512.2,25584,C,T,PASS,17,0,17,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220624,NC_045512.2,25855,G,T,PASS,11,0,11,1.0,ORF3a,missense_variant,c.463G>T,p.Asp155Tyr,p.D155Y,ivar,Unassigned +220624,NC_045512.2,26270,C,T,PASS,112,0,112,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220624,NC_045512.2,26530,A,G,PASS,166,0,166,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220624,NC_045512.2,26577,C,G,PASS,175,0,175,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220624,NC_045512.2,26709,G,A,PASS,200,0,200,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220624,NC_045512.2,27259,A,C,PASS,51,0,51,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220624,NC_045512.2,27807,C,T,PASS,52,0,52,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220624,NC_045512.2,27933,G,A,PASS,186,0,186,1.0,ORF8,missense_variant,c.40G>A,p.Ala14Thr,p.A14T,ivar,Unassigned +220624,NC_045512.2,28271,A,T,PASS,345,2,343,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220624,NC_045512.2,28311,C,T,PASS,378,2,376,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220624,NC_045512.2,2832,A,G,PASS,18,0,18,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220624,NC_045512.2,28361,GGAGAACGCA,G,PASS,299,296,209,0.7,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220624,NC_045512.2,28512,C,T,PASS,182,132,46,0.25,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,Unassigned +220624,NC_045512.2,28881,GG,AA,PASS,4288,63,4219,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220624,NC_045512.2,28883,G,C,PASS,4247,4,4241,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220624,NC_045512.2,3037,C,T,PASS,20,0,20,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220624,NC_045512.2,8393,G,A,PASS,2102,5,2097,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220625,NC_045512.2,10449,C,A,PASS,15,0,15,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220625,NC_045512.2,11282,AGTTTGTCTG,A,PASS,47,47,42,0.89,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220625,NC_045512.2,11537,A,G,PASS,14,0,14,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220625,NC_045512.2,13195,T,C,PASS,1350,2,1348,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220625,NC_045512.2,14408,C,T,PASS,19,0,19,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220625,NC_045512.2,21762,C,T,PASS,26,0,26,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220625,NC_045512.2,21764,ATACATG,A,PASS,26,26,22,0.85,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220625,NC_045512.2,21846,C,T,PASS,16,0,16,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220625,NC_045512.2,23403,A,G,PASS,467,0,467,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220625,NC_045512.2,23525,C,T,PASS,551,0,551,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220625,NC_045512.2,23599,T,G,PASS,216,0,216,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220625,NC_045512.2,23604,C,A,PASS,209,0,207,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220625,NC_045512.2,23948,G,T,PASS,33,0,33,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220625,NC_045512.2,24130,C,A,PASS,40,0,40,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220625,NC_045512.2,24424,A,T,PASS,38,0,37,0.97,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220625,NC_045512.2,24469,T,A,PASS,152,2,150,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220625,NC_045512.2,24503,C,T,PASS,165,2,163,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220625,NC_045512.2,25584,C,T,PASS,21,0,21,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220625,NC_045512.2,26270,C,T,PASS,74,0,74,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220625,NC_045512.2,26530,A,G,PASS,194,0,194,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220625,NC_045512.2,26577,C,G,PASS,195,0,195,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220625,NC_045512.2,26709,G,A,PASS,162,2,160,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220625,NC_045512.2,27259,A,C,PASS,40,0,40,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220625,NC_045512.2,27807,C,T,PASS,32,0,32,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220625,NC_045512.2,28271,A,T,PASS,286,3,281,0.98,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220625,NC_045512.2,28311,C,T,PASS,291,2,288,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220625,NC_045512.2,28361,GGAGAACGCA,G,PASS,230,223,167,0.73,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220625,NC_045512.2,28881,GG,AA,PASS,8535,93,8429,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220625,NC_045512.2,28883,G,C,PASS,8481,1,8473,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220625,NC_045512.2,8269,T,A,PASS,183,66,115,0.63,orf1ab,missense_variant,c.8004T>A,p.Asp2668Glu,p.D2668E,ivar,Unassigned +220625,NC_045512.2,8393,G,A,PASS,932,7,925,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220626,NC_045512.2,10449,C,A,PASS,33,0,33,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220626,NC_045512.2,11074,CT,C,PASS,41,41,13,0.32,orf1ab,frameshift_variant,c.10817delT,p.Leu3606fs,p.L3606fs,ivar,Unassigned +220626,NC_045512.2,11282,AGTTTGTCTG,A,PASS,86,85,78,0.91,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220626,NC_045512.2,11537,A,G,PASS,82,0,82,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220626,NC_045512.2,13195,T,C,PASS,2747,4,2743,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220626,NC_045512.2,14408,C,T,PASS,43,0,43,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220626,NC_045512.2,21762,C,T,PASS,56,0,56,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220626,NC_045512.2,21764,ATACATG,A,PASS,57,56,48,0.84,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220626,NC_045512.2,21846,C,T,PASS,51,2,49,0.96,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220626,NC_045512.2,21,C,T,PASS,10,0,10,1.0,orf1ab,upstream_gene_variant,c.-245C>T,.,.,ivar,Unassigned +220626,NC_045512.2,23403,A,G,PASS,878,3,875,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220626,NC_045512.2,23525,C,T,PASS,938,2,934,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220626,NC_045512.2,23599,T,G,PASS,371,0,370,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220626,NC_045512.2,23604,C,A,PASS,357,0,352,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220626,NC_045512.2,23948,G,T,PASS,196,0,195,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220626,NC_045512.2,24130,C,A,PASS,297,0,296,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220626,NC_045512.2,24424,A,T,PASS,52,0,52,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220626,NC_045512.2,24469,T,A,PASS,251,0,249,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220626,NC_045512.2,24503,C,T,PASS,313,2,311,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220626,NC_045512.2,25000,C,T,PASS,21,0,21,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220626,NC_045512.2,25584,C,T,PASS,42,0,42,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220626,NC_045512.2,26270,C,T,PASS,221,0,221,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220626,NC_045512.2,26530,A,G,PASS,111,0,111,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220626,NC_045512.2,26577,C,G,PASS,88,0,88,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220626,NC_045512.2,26709,G,A,PASS,113,0,113,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220626,NC_045512.2,27052,C,T,ft,14,10,4,0.29,M,missense_variant,c.530C>T,p.Ser177Phe,p.S177F,ivar,Unassigned +220626,NC_045512.2,27259,A,C,PASS,184,0,184,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220626,NC_045512.2,27807,C,T,PASS,52,0,52,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220626,NC_045512.2,28271,A,T,PASS,513,0,513,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220626,NC_045512.2,28311,C,T,PASS,534,0,534,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220626,NC_045512.2,2832,A,G,PASS,36,0,36,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220626,NC_045512.2,28361,GGAGAACGCA,G,PASS,424,423,278,0.66,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220626,NC_045512.2,28877,AG,TC,PASS,4416,5,4405,1.0,N,synonymous_variant,c.604_605delAGinsTC,p.203,p.203,ivar,Unassigned +220626,NC_045512.2,28881,GG,AA,PASS,4440,22,4409,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220626,NC_045512.2,28883,G,C,PASS,4441,0,4429,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220626,NC_045512.2,3037,C,T,PASS,30,0,30,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220626,NC_045512.2,76,T,A,ft,13,9,4,0.31,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220626,NC_045512.2,78,T,G,ft,13,9,4,0.31,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220626,NC_045512.2,8393,G,A,PASS,2004,2,2002,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220627,NC_045512.2,10029,C,T,PASS,32,0,32,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1 +220627,NC_045512.2,10449,C,A,PASS,122,0,122,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1 +220627,NC_045512.2,11282,AGTTTGTCTG,A,PASS,385,380,343,0.89,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1 +220627,NC_045512.2,11537,A,G,PASS,480,0,480,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1 +220627,NC_045512.2,13195,T,C,PASS,6218,9,6205,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1 +220627,NC_045512.2,14408,C,T,PASS,260,0,258,0.99,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1 +220627,NC_045512.2,18163,A,G,PASS,37,0,37,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1 +220627,NC_045512.2,21762,C,T,PASS,324,2,319,0.98,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1 +220627,NC_045512.2,21764,ATACATG,A,PASS,333,322,292,0.88,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1 +220627,NC_045512.2,21795,G,A,PASS,361,3,355,0.98,S,missense_variant,c.233G>A,p.Arg78Lys,p.R78K,ivar,BA.1 +220627,NC_045512.2,21846,C,T,PASS,346,0,346,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1 +220627,NC_045512.2,22193,AATT,A,PASS,19,19,18,0.95,S,disruptive_inframe_deletion,c.632_634delATT,p.Asn211_Leu212delinsIle,p.N211_L212delinsI,ivar,BA.1 +220627,NC_045512.2,22204,T,TGAGCCAGAA,PASS,17,17,14,0.82,S,disruptive_inframe_insertion,c.644_645insGCCAGAAGA,p.Arg214_Asp215insGluProGlu,p.R214_D215insEPE,ivar,BA.1 +220627,NC_045512.2,22578,G,A,PASS,36,0,36,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1 +220627,NC_045512.2,22673,TC,CT,PASS,33,0,33,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1 +220627,NC_045512.2,22679,T,C,PASS,42,0,42,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1 +220627,NC_045512.2,22686,C,T,PASS,42,0,42,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1 +220627,NC_045512.2,23063,A,T,PASS,10,0,10,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1 +220627,NC_045512.2,23075,T,C,PASS,12,0,12,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1 +220627,NC_045512.2,23202,C,A,PASS,40,0,39,0.98,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1 +220627,NC_045512.2,23403,A,G,PASS,2548,5,2543,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1 +220627,NC_045512.2,23525,C,T,PASS,2427,2,2416,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1 +220627,NC_045512.2,23599,T,G,PASS,916,0,916,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1 +220627,NC_045512.2,23604,C,A,PASS,885,0,881,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1 +220627,NC_045512.2,23854,C,A,PASS,66,0,64,0.97,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1 +220627,NC_045512.2,23948,G,T,PASS,817,1,810,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1 +220627,NC_045512.2,24130,C,A,PASS,1219,0,1209,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1 +220627,NC_045512.2,24424,A,T,PASS,314,0,312,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1 +220627,NC_045512.2,24469,T,A,PASS,1245,0,1245,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1 +220627,NC_045512.2,24503,C,T,PASS,1525,27,1496,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1 +220627,NC_045512.2,25000,C,T,PASS,110,0,110,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1 +220627,NC_045512.2,25584,C,T,PASS,182,3,179,0.98,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1 +220627,NC_045512.2,26270,C,T,PASS,987,2,984,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1 +220627,NC_045512.2,26530,A,G,PASS,399,0,399,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1 +220627,NC_045512.2,26577,C,G,PASS,422,0,422,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1 +220627,NC_045512.2,26709,G,A,PASS,464,3,461,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1 +220627,NC_045512.2,27259,A,C,PASS,444,0,441,0.99,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1 +220627,NC_045512.2,27807,C,T,PASS,143,0,143,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1 +220627,NC_045512.2,28271,A,T,PASS,3928,8,3914,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1 +220627,NC_045512.2,28311,C,T,PASS,4161,5,4146,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1 +220627,NC_045512.2,2832,A,G,PASS,161,2,159,0.99,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1 +220627,NC_045512.2,28361,GGAGAACGCA,G,PASS,3059,3037,1264,0.41,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1 +220627,NC_045512.2,28881,GG,AA,PASS,2726,36,2687,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1 +220627,NC_045512.2,28883,G,C,PASS,2704,2,2697,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1 +220627,NC_045512.2,29195,G,T,PASS,2958,0,2935,0.99,N,missense_variant,c.922G>T,p.Ala308Ser,p.A308S,ivar,BA.1 +220627,NC_045512.2,3037,C,T,PASS,68,0,68,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1 +220627,NC_045512.2,5386,T,G,PASS,16,0,16,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1 +220627,NC_045512.2,5515,G,T,PASS,26,0,26,1.0,orf1ab,synonymous_variant,c.5250G>T,p.Val1750Val,p.V1750V,ivar,BA.1 +220627,NC_045512.2,7321,C,T,ft,12,8,4,0.33,orf1ab,synonymous_variant,c.7056C>T,p.Ser2352Ser,p.S2352S,ivar,BA.1 +220627,NC_045512.2,8393,G,A,PASS,2820,7,2811,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1 +220628,NC_045512.2,10029,C,T,PASS,42,0,42,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.15.1 +220628,NC_045512.2,10135,T,C,PASS,138,0,138,1.0,orf1ab,synonymous_variant,c.9870T>C,p.Leu3290Leu,p.L3290L,ivar,BA.1.15.1 +220628,NC_045512.2,10449,C,A,PASS,143,0,141,0.99,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.15.1 +220628,NC_045512.2,11282,AGTTTGTCTG,A,PASS,551,550,482,0.87,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.15.1 +220628,NC_045512.2,11537,A,G,PASS,649,0,649,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.15.1 +220628,NC_045512.2,13195,T,C,PASS,5534,17,5515,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.15.1 +220628,NC_045512.2,14408,C,T,PASS,273,0,273,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.15.1 +220628,NC_045512.2,18163,A,G,PASS,26,0,26,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.15.1 +220628,NC_045512.2,21762,C,T,PASS,404,2,402,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.15.1 +220628,NC_045512.2,21764,ATACATG,A,PASS,409,405,357,0.87,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.15.1 +220628,NC_045512.2,21846,C,T,PASS,379,2,375,0.99,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.15.1 +220628,NC_045512.2,21,C,T,PASS,28,0,28,1.0,orf1ab,upstream_gene_variant,c.-245C>T,.,.,ivar,BA.1.15.1 +220628,NC_045512.2,22578,G,A,PASS,37,0,37,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.15.1 +220628,NC_045512.2,22673,TC,CT,PASS,14,0,14,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.15.1 +220628,NC_045512.2,22679,T,C,PASS,21,0,21,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.15.1 +220628,NC_045512.2,22686,C,T,PASS,20,0,20,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.15.1 +220628,NC_045512.2,22992,G,A,PASS,12,0,12,1.0,S,missense_variant,c.1430G>A,p.Ser477Asn,p.S477N,ivar,BA.1.15.1 +220628,NC_045512.2,22995,C,A,PASS,12,0,10,0.83,S,missense_variant,c.1433C>A,p.Thr478Lys,p.T478K,ivar,BA.1.15.1 +220628,NC_045512.2,23013,A,C,PASS,15,0,15,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.15.1 +220628,NC_045512.2,23040,A,G,PASS,16,0,16,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.15.1 +220628,NC_045512.2,23048,G,A,PASS,15,0,15,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.15.1 +220628,NC_045512.2,23055,A,G,PASS,15,0,15,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.15.1 +220628,NC_045512.2,23063,A,T,PASS,16,0,16,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.15.1 +220628,NC_045512.2,23075,T,C,PASS,16,0,16,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.15.1 +220628,NC_045512.2,23202,C,A,PASS,37,0,37,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.15.1 +220628,NC_045512.2,23403,A,G,PASS,3111,5,3106,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.15.1 +220628,NC_045512.2,23525,C,T,PASS,2843,8,2834,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.15.1 +220628,NC_045512.2,23599,T,G,PASS,962,0,962,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.15.1 +220628,NC_045512.2,23604,C,A,PASS,912,0,906,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.15.1 +220628,NC_045512.2,23854,C,A,PASS,88,1,87,0.99,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.15.1 +220628,NC_045512.2,23948,G,T,PASS,794,0,788,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.15.1 +220628,NC_045512.2,24130,C,A,PASS,1286,0,1279,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.15.1 +220628,NC_045512.2,24424,A,T,PASS,354,0,353,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.15.1 +220628,NC_045512.2,24469,T,A,PASS,1256,4,1247,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.15.1 +220628,NC_045512.2,24503,C,T,PASS,1507,30,1473,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.15.1 +220628,NC_045512.2,24803,A,G,PASS,632,0,632,1.0,S,missense_variant,c.3241A>G,p.Ile1081Val,p.I1081V,ivar,BA.1.15.1 +220628,NC_045512.2,25000,C,T,PASS,102,3,99,0.97,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.15.1 +220628,NC_045512.2,25584,C,T,PASS,85,0,85,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.15.1 +220628,NC_045512.2,25708,C,T,PASS,106,0,106,1.0,ORF3a,missense_variant,c.316C>T,p.Leu106Phe,p.L106F,ivar,BA.1.15.1 +220628,NC_045512.2,26270,C,T,PASS,620,0,620,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.15.1 +220628,NC_045512.2,26530,A,G,PASS,288,0,288,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.15.1 +220628,NC_045512.2,26577,C,G,PASS,372,0,372,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.15.1 +220628,NC_045512.2,26709,G,A,PASS,304,2,302,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.15.1 +220628,NC_045512.2,27259,A,C,PASS,303,0,303,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.15.1 +220628,NC_045512.2,27667,G,T,PASS,76,56,20,0.26,ORF7a,stop_gained,c.274G>T,p.Glu92*,p.E92*,ivar,BA.1.15.1 +220628,NC_045512.2,27807,C,T,PASS,93,0,93,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.15.1 +220628,NC_045512.2,28271,A,T,PASS,1719,2,1712,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.15.1 +220628,NC_045512.2,28311,C,T,PASS,1718,5,1712,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.15.1 +220628,NC_045512.2,2832,A,G,PASS,220,0,220,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.15.1 +220628,NC_045512.2,28361,GGAGAACGCA,G,PASS,1218,1209,726,0.6,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.15.1 +220628,NC_045512.2,28363,A,T,PASS,16,12,4,0.25,N,synonymous_variant,c.90A>T,p.Gly30Gly,p.G30G,ivar,BA.1.15.1 +220628,NC_045512.2,28881,GG,AA,PASS,2323,23,2299,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.15.1 +220628,NC_045512.2,28883,G,C,PASS,2314,1,2311,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.15.1 +220628,NC_045512.2,29301,A,G,PASS,3873,8,3862,1.0,N,missense_variant,c.1028A>G,p.Asp343Gly,p.D343G,ivar,BA.1.15.1 +220628,NC_045512.2,3037,C,T,PASS,99,0,99,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.15.1 +220628,NC_045512.2,5386,T,G,PASS,34,0,34,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.15.1 +220628,NC_045512.2,694,T,A,PASS,6454,3969,2458,0.38,orf1ab,missense_variant,c.429T>A,p.Phe143Leu,p.F143L,ivar,BA.1.15.1 +220628,NC_045512.2,728,G,A,PASS,296,218,78,0.26,orf1ab,missense_variant,c.463G>A,p.Glu155Lys,p.E155K,ivar,BA.1.15.1 +220628,NC_045512.2,7488,C,T,PASS,1405,1041,364,0.26,orf1ab,missense_variant,c.7223C>T,p.Thr2408Ile,p.T2408I,ivar,BA.1.15.1 +220628,NC_045512.2,8393,G,A,PASS,3090,10,3074,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.15.1 +220629,NC_045512.2,11282,AGTTTGTCTG,A,PASS,38,38,34,0.89,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220629,NC_045512.2,11537,A,G,PASS,34,0,34,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220629,NC_045512.2,13195,T,C,PASS,1615,3,1612,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220629,NC_045512.2,14408,C,T,PASS,28,0,28,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220629,NC_045512.2,14646,T,A,PASS,36,22,14,0.39,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,Unassigned +220629,NC_045512.2,15738,C,T,PASS,1840,8,1832,1.0,orf1ab,missense_variant,c.15473C>T,p.Ser5158Leu,p.S5158L,ivar,Unassigned +220629,NC_045512.2,21762,C,T,PASS,26,0,26,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220629,NC_045512.2,21764,ATACATG,A,PASS,29,26,26,0.9,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220629,NC_045512.2,21846,C,T,PASS,43,0,43,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220629,NC_045512.2,23403,A,G,PASS,916,0,916,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220629,NC_045512.2,23525,C,T,PASS,950,0,949,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220629,NC_045512.2,23599,T,G,PASS,431,0,431,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220629,NC_045512.2,23604,C,A,PASS,415,0,413,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220629,NC_045512.2,23811,G,A,ft,11,6,5,0.45,S,missense_variant,c.2249G>A,p.Ser750Asn,p.S750N,ivar,Unassigned +220629,NC_045512.2,23853,AC,A,ft,13,13,4,0.31,S,frameshift_variant,c.2293delC,p.Arg765fs,p.R765fs,ivar,Unassigned +220629,NC_045512.2,23948,G,T,PASS,45,0,45,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220629,NC_045512.2,24130,C,A,PASS,85,0,85,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220629,NC_045512.2,24424,A,T,PASS,44,0,44,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220629,NC_045512.2,24469,T,A,PASS,346,0,346,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220629,NC_045512.2,24503,C,T,PASS,398,4,394,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220629,NC_045512.2,25584,C,T,PASS,23,0,23,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220629,NC_045512.2,25893,T,C,ft,16,12,4,0.25,ORF3a,synonymous_variant,c.501T>C,p.Ile167Ile,p.I167I,ivar,Unassigned +220629,NC_045512.2,26270,C,T,PASS,711,0,711,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220629,NC_045512.2,26530,A,G,PASS,243,0,243,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220629,NC_045512.2,26577,C,G,PASS,236,0,236,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220629,NC_045512.2,26709,G,A,PASS,290,2,288,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220629,NC_045512.2,27259,A,C,PASS,76,0,76,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220629,NC_045512.2,27670,G,T,PASS,18,0,18,1.0,ORF7a,missense_variant,c.277G>T,p.Val93Phe,p.V93F,ivar,Unassigned +220629,NC_045512.2,27807,C,T,PASS,22,0,22,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220629,NC_045512.2,28271,A,T,PASS,1156,0,1152,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220629,NC_045512.2,28311,C,T,PASS,1197,0,1193,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220629,NC_045512.2,2832,A,G,PASS,10,0,10,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220629,NC_045512.2,28361,GGAGAACGCA,G,PASS,975,969,682,0.7,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220629,NC_045512.2,28881,GG,AA,PASS,17113,95,17009,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220629,NC_045512.2,28883,G,C,PASS,17089,4,17063,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220629,NC_045512.2,5672,C,T,PASS,18,0,18,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220629,NC_045512.2,5924,G,A,PASS,11,0,11,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220629,NC_045512.2,685,AAAGTCATTT,A,PASS,11104,11008,5619,0.51,orf1ab,conservative_inframe_deletion,c.421_429delAAGTCATTT,p.Lys141_Phe143del,p.K141_F143del,ivar,Unassigned +220629,NC_045512.2,694,T,A,PASS,13,9,4,0.31,orf1ab,missense_variant,c.429T>A,p.Phe143Leu,p.F143L,ivar,Unassigned +220629,NC_045512.2,7690,A,G,PASS,29,21,8,0.28,orf1ab,synonymous_variant,c.7425A>G,p.Leu2475Leu,p.L2475L,ivar,Unassigned +220629,NC_045512.2,76,T,A,PASS,18,6,12,0.67,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220629,NC_045512.2,8393,G,A,PASS,974,1,973,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220630,NC_045512.2,10449,C,A,PASS,35,0,35,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220630,NC_045512.2,11282,AGTTTGTCTG,A,PASS,64,64,58,0.91,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220630,NC_045512.2,11537,A,G,PASS,134,0,134,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220630,NC_045512.2,13195,T,C,PASS,2893,5,2888,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220630,NC_045512.2,13544,T,C,ft,13,9,4,0.31,orf1ab,synonymous_variant,c.13279T>C,p.Leu4427Leu,p.L4427L,ivar,Unassigned +220630,NC_045512.2,14408,C,T,PASS,69,1,68,0.99,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220630,NC_045512.2,14646,T,A,PASS,123,91,32,0.26,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,Unassigned +220630,NC_045512.2,21762,C,T,PASS,121,0,121,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220630,NC_045512.2,21764,ATACATG,A,PASS,122,121,111,0.91,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220630,NC_045512.2,21846,C,T,PASS,117,0,117,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220630,NC_045512.2,23403,A,G,PASS,2458,2,2456,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220630,NC_045512.2,23525,C,T,PASS,2286,6,2280,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220630,NC_045512.2,23599,T,G,PASS,851,0,847,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220630,NC_045512.2,23604,C,A,PASS,823,0,815,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220630,NC_045512.2,23948,G,T,PASS,69,0,69,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220630,NC_045512.2,24130,C,A,PASS,115,0,115,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220630,NC_045512.2,24424,A,T,PASS,20,0,20,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220630,NC_045512.2,24469,T,A,PASS,294,0,291,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220630,NC_045512.2,24503,C,T,PASS,365,7,356,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220630,NC_045512.2,25000,C,T,PASS,28,0,28,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220630,NC_045512.2,25584,C,T,PASS,14,0,14,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220630,NC_045512.2,26270,C,T,PASS,131,2,129,0.98,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220630,NC_045512.2,26530,A,G,PASS,89,0,89,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220630,NC_045512.2,26577,C,G,PASS,75,0,75,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220630,NC_045512.2,26709,G,A,PASS,82,2,80,0.98,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220630,NC_045512.2,27259,A,C,PASS,79,0,79,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220630,NC_045512.2,27670,G,T,PASS,70,0,70,1.0,ORF7a,missense_variant,c.277G>T,p.Val93Phe,p.V93F,ivar,Unassigned +220630,NC_045512.2,27807,C,T,PASS,105,1,104,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220630,NC_045512.2,28271,A,T,PASS,798,0,796,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220630,NC_045512.2,28311,C,T,PASS,837,3,833,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220630,NC_045512.2,2832,A,G,PASS,16,0,16,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220630,NC_045512.2,28361,GGAGAACGCA,G,PASS,631,629,451,0.71,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220630,NC_045512.2,28512,C,T,PASS,400,289,104,0.26,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,Unassigned +220630,NC_045512.2,28881,GG,AA,PASS,2288,23,2261,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220630,NC_045512.2,28883,G,C,PASS,2275,0,2270,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220630,NC_045512.2,3037,C,T,PASS,20,0,20,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220630,NC_045512.2,728,G,A,ft,19,14,5,0.26,orf1ab,missense_variant,c.463G>A,p.Glu155Lys,p.E155K,ivar,Unassigned +220630,NC_045512.2,8393,G,A,PASS,2760,9,2748,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220631,NC_045512.2,10029,C,T,PASS,12,0,12,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,AY.127 +220631,NC_045512.2,11201,A,G,PASS,84,1,83,0.99,orf1ab,missense_variant,c.10936A>G,p.Thr3646Ala,p.T3646A,ivar,AY.127 +220631,NC_045512.2,11332,A,G,PASS,241,0,241,1.0,orf1ab,synonymous_variant,c.11067A>G,p.Val3689Val,p.V3689V,ivar,AY.127 +220631,NC_045512.2,1420,C,T,PASS,228,2,226,0.99,orf1ab,synonymous_variant,c.1155C>T,p.Ala385Ala,p.A385A,ivar,AY.127 +220631,NC_045512.2,14408,C,T,PASS,45,0,45,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,AY.127 +220631,NC_045512.2,14511,G,C,PASS,84,0,84,1.0,orf1ab,missense_variant,c.14246G>C,p.Arg4749Thr,p.R4749T,ivar,AY.127 +220631,NC_045512.2,15535,G,A,ft,16,12,4,0.25,orf1ab,synonymous_variant,c.15270G>A,p.Lys5090Lys,p.K5090K,ivar,AY.127 +220631,NC_045512.2,16466,C,T,PASS,221,0,221,1.0,orf1ab,missense_variant,c.16201C>T,p.His5401Tyr,p.H5401Y,ivar,AY.127 +220631,NC_045512.2,18788,C,T,PASS,1387,2,1385,1.0,orf1ab,stop_gained,c.18523C>T,p.Gln6175*,p.Q6175*,ivar,AY.127 +220631,NC_045512.2,19220,C,T,PASS,387,0,387,1.0,orf1ab,synonymous_variant,c.18955C>T,p.Leu6319Leu,p.L6319L,ivar,AY.127 +220631,NC_045512.2,21057,C,T,PASS,31,1,30,0.97,orf1ab,missense_variant,c.20792C>T,p.Thr6931Ile,p.T6931I,ivar,AY.127 +220631,NC_045512.2,210,G,T,PASS,39,0,39,1.0,orf1ab,upstream_gene_variant,c.-56G>T,.,.,ivar,AY.127 +220631,NC_045512.2,21618,C,G,PASS,390,0,390,1.0,S,missense_variant,c.56C>G,p.Thr19Arg,p.T19R,ivar,AY.127 +220631,NC_045512.2,21846,C,T,PASS,138,0,138,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,AY.127 +220631,NC_045512.2,22917,T,G,PASS,10,0,10,1.0,S,missense_variant,c.1355T>G,p.Leu452Arg,p.L452R,ivar,AY.127 +220631,NC_045512.2,23403,A,G,PASS,2800,7,2793,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,AY.127 +220631,NC_045512.2,23604,C,G,PASS,796,0,794,1.0,S,missense_variant,c.2042C>G,p.Pro681Arg,p.P681R,ivar,AY.127 +220631,NC_045512.2,24410,G,A,PASS,75,0,75,1.0,S,missense_variant,c.2848G>A,p.Asp950Asn,p.D950N,ivar,AY.127 +220631,NC_045512.2,25469,C,T,PASS,43,0,43,1.0,ORF3a,missense_variant,c.77C>T,p.Ser26Leu,p.S26L,ivar,AY.127 +220631,NC_045512.2,25518,T,C,PASS,43,0,43,1.0,ORF3a,synonymous_variant,c.126T>C,p.Pro42Pro,p.P42P,ivar,AY.127 +220631,NC_045512.2,25538,G,T,PASS,45,0,45,1.0,ORF3a,missense_variant,c.146G>T,p.Gly49Val,p.G49V,ivar,AY.127 +220631,NC_045512.2,26054,C,A,PASS,83,0,83,1.0,ORF3a,missense_variant,c.662C>A,p.Thr221Lys,p.T221K,ivar,AY.127 +220631,NC_045512.2,26172,G,T,PASS,94,0,92,0.98,ORF3a,missense_variant,c.780G>T,p.Met260Ile,p.M260I,ivar,AY.127 +220631,NC_045512.2,26767,T,C,PASS,376,0,376,1.0,M,missense_variant,c.245T>C,p.Ile82Thr,p.I82T,ivar,AY.127 +220631,NC_045512.2,27590,C,T,PASS,115,1,114,0.99,ORF7a,missense_variant,c.197C>T,p.Ala66Val,p.A66V,ivar,AY.127 +220631,NC_045512.2,27638,T,C,PASS,107,0,107,1.0,ORF7a,missense_variant,c.245T>C,p.Val82Ala,p.V82A,ivar,AY.127 +220631,NC_045512.2,27722,T,C,PASS,91,0,91,1.0,ORF7a,missense_variant,c.329T>C,p.Ile110Thr,p.I110T,ivar,AY.127 +220631,NC_045512.2,27752,C,T,PASS,109,0,109,1.0,ORF7a,missense_variant,c.359C>T,p.Thr120Ile,p.T120I,ivar,AY.127 +220631,NC_045512.2,27874,C,T,PASS,146,0,146,1.0,ORF7b,missense_variant,c.119C>T,p.Thr40Ile,p.T40I,ivar,AY.127 +220631,NC_045512.2,28247,AGATTTC,A,PASS,974,967,888,0.91,ORF8,conservative_inframe_deletion,c.355_360delGATTTC,p.Asp119_Phe120del,p.D119_F120del,ivar,AY.127 +220631,NC_045512.2,28253,C,A,PASS,105,1,102,0.97,ORF8,missense_variant,c.360C>A,p.Phe120Leu,p.F120L,ivar,AY.127 +220631,NC_045512.2,28270,TA,T,PASS,1218,1212,1147,0.94,N,upstream_gene_variant,c.-3delA,.,.,ivar,AY.127 +220631,NC_045512.2,28378,G,T,PASS,764,0,753,0.99,N,synonymous_variant,c.105G>T,p.Ala35Ala,p.A35A,ivar,AY.127 +220631,NC_045512.2,28461,A,G,PASS,480,0,480,1.0,N,missense_variant,c.188A>G,p.Asp63Gly,p.D63G,ivar,AY.127 +220631,NC_045512.2,28881,G,T,PASS,4129,17,4080,0.99,N,missense_variant,c.608G>T,p.Arg203Met,p.R203M,ivar,AY.127 +220631,NC_045512.2,28916,G,T,PASS,1270,0,1258,0.99,N,missense_variant,c.643G>T,p.Gly215Cys,p.G215C,ivar,AY.127 +220631,NC_045512.2,29402,G,T,PASS,6716,4,6694,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,AY.127 +220631,NC_045512.2,29734,G,A,PASS,113,0,113,1.0,S,downstream_gene_variant,c.*4350G>A,.,.,ivar,AY.127 +220631,NC_045512.2,29742,G,T,PASS,109,0,109,1.0,S,downstream_gene_variant,c.*4358G>T,.,.,ivar,AY.127 +220631,NC_045512.2,29751,G,T,PASS,113,0,111,0.98,S,downstream_gene_variant,c.*4367G>T,.,.,ivar,AY.127 +220631,NC_045512.2,3037,C,T,PASS,420,0,420,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,AY.127 +220631,NC_045512.2,3411,C,T,PASS,995,12,979,0.98,orf1ab,missense_variant,c.3146C>T,p.Ala1049Val,p.A1049V,ivar,AY.127 +220631,NC_045512.2,4181,G,T,PASS,27,0,27,1.0,orf1ab,missense_variant,c.3916G>T,p.Ala1306Ser,p.A1306S,ivar,AY.127 +220631,NC_045512.2,7526,G,A,PASS,1855,12,1843,0.99,orf1ab,missense_variant,c.7261G>A,p.Val2421Ile,p.V2421I,ivar,AY.127 +220631,NC_045512.2,8010,A,G,PASS,1725,54,1670,0.97,orf1ab,missense_variant,c.7745A>G,p.Asp2582Gly,p.D2582G,ivar,AY.127 +220631,NC_045512.2,8986,C,T,PASS,22,0,22,1.0,orf1ab,synonymous_variant,c.8721C>T,p.Asp2907Asp,p.D2907D,ivar,AY.127 +220631,NC_045512.2,9053,G,T,PASS,28,0,28,1.0,orf1ab,missense_variant,c.8788G>T,p.Val2930Leu,p.V2930L,ivar,AY.127 +220633,NC_045512.2,10029,C,T,PASS,30,0,30,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220633,NC_045512.2,10449,C,A,PASS,122,0,122,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220633,NC_045512.2,11282,AGTTTGTCTG,A,PASS,246,246,223,0.91,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220633,NC_045512.2,11537,A,G,PASS,139,0,139,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220633,NC_045512.2,13195,T,C,PASS,7290,16,7274,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220633,NC_045512.2,14408,C,T,PASS,146,0,146,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220633,NC_045512.2,18163,A,G,PASS,30,0,30,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220633,NC_045512.2,21762,C,T,PASS,154,0,154,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220633,NC_045512.2,21764,ATACATG,A,PASS,156,154,140,0.9,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220633,NC_045512.2,21846,C,T,PASS,158,0,158,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220633,NC_045512.2,22578,G,A,PASS,20,0,20,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.17 +220633,NC_045512.2,22673,TC,CT,PASS,11,0,11,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.17 +220633,NC_045512.2,22679,T,C,PASS,13,0,13,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220633,NC_045512.2,22686,C,T,PASS,13,0,13,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220633,NC_045512.2,23403,A,G,PASS,3760,2,3757,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220633,NC_045512.2,23525,C,T,PASS,3604,13,3581,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220633,NC_045512.2,23599,T,G,PASS,1393,0,1391,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220633,NC_045512.2,23604,C,A,PASS,1340,0,1337,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220633,NC_045512.2,23854,C,A,PASS,60,0,60,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220633,NC_045512.2,23948,G,T,PASS,659,0,658,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220633,NC_045512.2,24130,C,A,PASS,1017,1,1009,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220633,NC_045512.2,24424,A,T,PASS,219,1,216,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220633,NC_045512.2,24469,T,A,PASS,888,0,885,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220633,NC_045512.2,24503,C,T,PASS,1069,13,1054,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220633,NC_045512.2,25000,C,T,PASS,103,2,101,0.98,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220633,NC_045512.2,25584,C,T,PASS,173,0,173,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220633,NC_045512.2,26270,C,T,PASS,598,0,597,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220633,NC_045512.2,26530,A,G,PASS,161,0,161,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220633,NC_045512.2,26577,C,G,PASS,181,0,181,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220633,NC_045512.2,26709,G,A,PASS,150,0,150,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220633,NC_045512.2,27259,A,C,PASS,464,0,464,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220633,NC_045512.2,27670,G,T,PASS,112,0,111,0.99,ORF7a,missense_variant,c.277G>T,p.Val93Phe,p.V93F,ivar,BA.1.17 +220633,NC_045512.2,27807,C,T,PASS,123,1,122,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220633,NC_045512.2,28271,A,T,PASS,1502,5,1488,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220633,NC_045512.2,28311,C,T,PASS,1544,2,1540,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220633,NC_045512.2,2832,A,G,PASS,135,0,135,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220633,NC_045512.2,28361,GGAGAACGCA,G,PASS,1103,1083,619,0.56,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220633,NC_045512.2,28881,GG,AA,PASS,5114,72,5038,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220633,NC_045512.2,28883,G,C,PASS,5062,6,5048,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220633,NC_045512.2,3037,C,T,PASS,35,0,35,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220633,NC_045512.2,5672,C,T,PASS,153,0,153,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220633,NC_045512.2,5924,G,A,PASS,66,0,66,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220633,NC_045512.2,8393,G,A,PASS,5806,16,5787,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220634,NC_045512.2,11282,AGTTTGTCTG,A,PASS,61,61,50,0.82,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220634,NC_045512.2,11537,A,G,PASS,27,0,27,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220634,NC_045512.2,13195,T,C,PASS,1103,6,1097,0.99,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220634,NC_045512.2,21762,C,T,PASS,24,0,24,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220634,NC_045512.2,21764,ATACATG,A,PASS,24,24,19,0.79,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220634,NC_045512.2,21846,C,T,PASS,25,0,25,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220634,NC_045512.2,23403,A,G,PASS,955,2,953,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220634,NC_045512.2,23525,C,T,PASS,930,0,928,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220634,NC_045512.2,23599,T,G,PASS,394,0,394,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220634,NC_045512.2,23604,C,A,PASS,379,0,374,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220634,NC_045512.2,23948,G,T,PASS,35,0,35,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220634,NC_045512.2,24130,C,A,PASS,54,0,54,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220634,NC_045512.2,24424,A,T,PASS,41,0,41,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220634,NC_045512.2,24469,T,A,PASS,182,0,182,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220634,NC_045512.2,24503,C,T,PASS,193,4,189,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220634,NC_045512.2,25584,C,T,PASS,20,0,20,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220634,NC_045512.2,26270,C,T,PASS,186,2,184,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220634,NC_045512.2,26465,T,C,ft,11,8,3,0.27,E,missense_variant,c.221T>C,p.Leu74Pro,p.L74P,ivar,Unassigned +220634,NC_045512.2,26530,A,G,PASS,202,0,202,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220634,NC_045512.2,26577,C,G,PASS,209,0,209,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220634,NC_045512.2,26709,G,A,PASS,216,0,216,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220634,NC_045512.2,27259,A,C,PASS,90,0,90,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220634,NC_045512.2,27384,T,C,PASS,72,0,72,1.0,ORF6,synonymous_variant,c.183T>C,p.Asp61Asp,p.D61D,ivar,Unassigned +220634,NC_045512.2,27807,C,T,PASS,34,0,34,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220634,NC_045512.2,28271,A,T,PASS,256,0,254,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220634,NC_045512.2,28311,C,T,PASS,270,0,270,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220634,NC_045512.2,2832,A,G,PASS,23,0,23,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220634,NC_045512.2,28361,GGAGAACGCA,G,PASS,202,201,147,0.73,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220634,NC_045512.2,28881,GG,AA,PASS,7905,96,7806,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220634,NC_045512.2,28883,G,C,PASS,7846,1,7833,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220634,NC_045512.2,5672,C,T,PASS,24,0,24,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220634,NC_045512.2,5924,G,A,PASS,12,0,12,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220634,NC_045512.2,7984,T,C,PASS,214,0,214,1.0,orf1ab,synonymous_variant,c.7719T>C,p.Asp2573Asp,p.D2573D,ivar,Unassigned +220634,NC_045512.2,8393,G,A,PASS,2278,6,2271,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220635,NC_045512.2,10029,C,T,PASS,10,0,10,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,Unassigned +220635,NC_045512.2,10135,T,C,PASS,12,0,12,1.0,orf1ab,synonymous_variant,c.9870T>C,p.Leu3290Leu,p.L3290L,ivar,Unassigned +220635,NC_045512.2,10449,C,A,PASS,28,0,28,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220635,NC_045512.2,11074,CT,C,PASS,32,30,9,0.28,orf1ab,frameshift_variant,c.10817delT,p.Leu3606fs,p.L3606fs,ivar,Unassigned +220635,NC_045512.2,11282,AGTTTGTCTG,A,PASS,114,114,105,0.92,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220635,NC_045512.2,11537,A,G,PASS,25,0,25,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220635,NC_045512.2,12864,A,C,PASS,80,0,78,0.98,orf1ab,missense_variant,c.12599A>C,p.Asp4200Ala,p.D4200A,ivar,Unassigned +220635,NC_045512.2,13195,T,C,PASS,1827,0,1827,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220635,NC_045512.2,14408,C,T,PASS,15,0,15,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220635,NC_045512.2,21762,C,T,PASS,33,0,33,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220635,NC_045512.2,21764,ATACATG,A,PASS,35,35,33,0.94,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220635,NC_045512.2,21846,C,T,PASS,33,0,33,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220635,NC_045512.2,21856,T,C,PASS,30,0,30,1.0,S,synonymous_variant,c.294T>C,p.Ser98Ser,p.S98S,ivar,Unassigned +220635,NC_045512.2,22578,G,A,PASS,15,0,15,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,Unassigned +220635,NC_045512.2,23403,A,G,PASS,713,2,711,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220635,NC_045512.2,23525,C,T,PASS,852,0,848,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220635,NC_045512.2,23599,T,G,PASS,337,0,335,0.99,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220635,NC_045512.2,23604,C,A,PASS,327,0,325,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220635,NC_045512.2,23854,C,A,PASS,10,0,10,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220635,NC_045512.2,23948,G,T,PASS,68,0,65,0.96,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220635,NC_045512.2,24130,C,A,PASS,110,0,110,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220635,NC_045512.2,24424,A,T,PASS,52,0,52,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220635,NC_045512.2,24469,T,A,PASS,197,0,197,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220635,NC_045512.2,24503,C,T,PASS,238,6,232,0.97,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220635,NC_045512.2,25584,C,T,PASS,32,0,32,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220635,NC_045512.2,25708,C,T,PASS,39,0,39,1.0,ORF3a,missense_variant,c.316C>T,p.Leu106Phe,p.L106F,ivar,Unassigned +220635,NC_045512.2,26270,C,T,PASS,278,0,276,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220635,NC_045512.2,26530,A,G,PASS,71,1,70,0.99,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220635,NC_045512.2,26577,C,G,PASS,96,0,96,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220635,NC_045512.2,26709,G,A,PASS,76,0,76,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220635,NC_045512.2,27259,A,C,PASS,122,0,122,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220635,NC_045512.2,27807,C,T,PASS,19,0,19,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220635,NC_045512.2,28271,A,T,PASS,593,0,592,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220635,NC_045512.2,28311,C,T,PASS,617,0,615,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220635,NC_045512.2,2832,A,G,PASS,17,0,17,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220635,NC_045512.2,28361,GGAGAACGCA,G,PASS,483,482,327,0.68,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220635,NC_045512.2,28881,GG,AA,PASS,6445,87,6352,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220635,NC_045512.2,28883,G,C,PASS,6389,4,6374,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220635,NC_045512.2,29301,A,G,PASS,2221,1,2219,1.0,N,missense_variant,c.1028A>G,p.Asp343Gly,p.D343G,ivar,Unassigned +220635,NC_045512.2,3105,A,G,PASS,110,2,108,0.98,orf1ab,missense_variant,c.2840A>G,p.Tyr947Cys,p.Y947C,ivar,Unassigned +220635,NC_045512.2,76,T,A,ft,19,13,6,0.32,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220635,NC_045512.2,78,T,G,ft,19,13,6,0.32,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220635,NC_045512.2,8393,G,A,PASS,2010,9,2001,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220636,NC_045512.2,10449,C,A,PASS,12,0,12,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220636,NC_045512.2,11282,AGTTTGTCTG,A,PASS,40,40,39,0.98,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220636,NC_045512.2,11537,A,G,PASS,38,1,37,0.97,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220636,NC_045512.2,12864,A,C,PASS,59,0,59,1.0,orf1ab,missense_variant,c.12599A>C,p.Asp4200Ala,p.D4200A,ivar,Unassigned +220636,NC_045512.2,13195,T,C,PASS,2304,3,2301,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220636,NC_045512.2,14408,C,T,PASS,18,0,18,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220636,NC_045512.2,18047,A,T,PASS,12,4,8,0.67,orf1ab,missense_variant,c.17782A>T,p.Met5928Leu,p.M5928L,ivar,Unassigned +220636,NC_045512.2,21762,C,T,PASS,21,0,21,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220636,NC_045512.2,21764,ATACATG,A,PASS,24,21,21,0.88,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220636,NC_045512.2,21846,C,T,PASS,36,0,36,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220636,NC_045512.2,21856,T,C,PASS,38,0,38,1.0,S,synonymous_variant,c.294T>C,p.Ser98Ser,p.S98S,ivar,Unassigned +220636,NC_045512.2,23403,A,G,PASS,706,2,704,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220636,NC_045512.2,23525,C,T,PASS,762,0,762,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220636,NC_045512.2,23599,T,G,PASS,299,0,299,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220636,NC_045512.2,23604,C,A,PASS,295,0,295,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220636,NC_045512.2,23948,G,T,PASS,33,0,33,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220636,NC_045512.2,24130,C,A,PASS,39,0,38,0.97,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220636,NC_045512.2,24424,A,T,PASS,21,0,21,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220636,NC_045512.2,24469,T,A,PASS,277,0,277,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220636,NC_045512.2,24503,C,T,PASS,304,1,303,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220636,NC_045512.2,25584,C,T,PASS,23,0,23,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220636,NC_045512.2,25708,C,T,PASS,18,0,18,1.0,ORF3a,missense_variant,c.316C>T,p.Leu106Phe,p.L106F,ivar,Unassigned +220636,NC_045512.2,26270,C,T,PASS,340,2,338,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220636,NC_045512.2,26530,A,G,PASS,121,0,121,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220636,NC_045512.2,26577,C,G,PASS,140,0,140,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220636,NC_045512.2,26709,G,A,PASS,138,0,138,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220636,NC_045512.2,27259,A,C,PASS,28,0,28,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220636,NC_045512.2,2754,T,C,PASS,102,1,101,0.99,orf1ab,missense_variant,c.2489T>C,p.Val830Ala,p.V830A,ivar,Unassigned +220636,NC_045512.2,27711,A,G,ft,13,9,4,0.31,ORF7a,synonymous_variant,c.318A>G,p.Ala106Ala,p.A106A,ivar,Unassigned +220636,NC_045512.2,27807,C,T,PASS,15,1,14,0.93,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220636,NC_045512.2,28271,A,T,PASS,490,1,489,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220636,NC_045512.2,28311,C,T,PASS,483,1,480,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220636,NC_045512.2,2832,A,G,PASS,132,0,132,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220636,NC_045512.2,28361,GGAGAACGCA,G,PASS,377,373,254,0.67,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220636,NC_045512.2,28881,GG,AA,PASS,8195,126,8059,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220636,NC_045512.2,28883,G,C,PASS,8109,0,8105,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220636,NC_045512.2,29301,A,G,PASS,3626,4,3622,1.0,N,missense_variant,c.1028A>G,p.Asp343Gly,p.D343G,ivar,Unassigned +220636,NC_045512.2,3105,A,G,PASS,56,0,56,1.0,orf1ab,missense_variant,c.2840A>G,p.Tyr947Cys,p.Y947C,ivar,Unassigned +220636,NC_045512.2,4097,T,TC,ft,17,17,5,0.29,orf1ab,frameshift_variant,c.3832_3833insC,p.Phe1278fs,p.F1278fs,ivar,Unassigned +220636,NC_045512.2,4101,T,C,ft,18,12,6,0.33,orf1ab,missense_variant,c.3836T>C,p.Leu1279Ser,p.L1279S,ivar,Unassigned +220636,NC_045512.2,4166,A,T,PASS,52,26,26,0.5,orf1ab,missense_variant,c.3901A>T,p.Ile1301Leu,p.I1301L,ivar,Unassigned +220636,NC_045512.2,4171,T,C,PASS,51,25,26,0.51,orf1ab,synonymous_variant,c.3906T>C,p.Pro1302Pro,p.P1302P,ivar,Unassigned +220636,NC_045512.2,728,G,A,ft,11,8,3,0.27,orf1ab,missense_variant,c.463G>A,p.Glu155Lys,p.E155K,ivar,Unassigned +220636,NC_045512.2,76,T,A,PASS,10,3,7,0.7,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220636,NC_045512.2,78,T,G,PASS,10,3,7,0.7,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220636,NC_045512.2,8393,G,A,PASS,1312,23,1286,0.98,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220637,NC_045512.2,10029,C,T,PASS,34,0,34,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220637,NC_045512.2,10449,C,A,PASS,121,0,121,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220637,NC_045512.2,11282,AGTTTGTCTG,A,PASS,312,310,269,0.86,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220637,NC_045512.2,11537,A,G,PASS,289,0,289,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220637,NC_045512.2,13195,T,C,PASS,7412,12,7399,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220637,NC_045512.2,14408,C,T,PASS,177,2,175,0.99,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220637,NC_045512.2,18163,A,G,PASS,30,0,30,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220637,NC_045512.2,21762,C,T,PASS,275,0,275,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220637,NC_045512.2,21764,ATACATG,A,PASS,280,276,255,0.91,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220637,NC_045512.2,21846,C,T,PASS,292,0,292,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220637,NC_045512.2,22578,G,A,PASS,25,0,25,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.17 +220637,NC_045512.2,22673,TC,CT,PASS,23,0,23,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.17 +220637,NC_045512.2,22679,T,C,PASS,29,0,29,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220637,NC_045512.2,22686,C,T,PASS,28,0,28,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220637,NC_045512.2,23202,C,A,PASS,20,0,20,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220637,NC_045512.2,23403,A,G,PASS,3875,6,3869,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220637,NC_045512.2,23525,C,T,PASS,3568,12,3551,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220637,NC_045512.2,23599,T,G,PASS,1289,0,1286,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220637,NC_045512.2,23604,C,A,PASS,1255,0,1246,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220637,NC_045512.2,23854,C,A,PASS,90,0,90,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220637,NC_045512.2,23948,G,T,PASS,810,0,810,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220637,NC_045512.2,24130,C,A,PASS,1321,0,1311,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220637,NC_045512.2,24424,A,T,PASS,329,2,323,0.98,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220637,NC_045512.2,24469,T,A,PASS,1351,1,1347,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220637,NC_045512.2,24503,C,T,PASS,1588,29,1552,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220637,NC_045512.2,25000,C,T,PASS,121,0,121,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220637,NC_045512.2,25584,C,T,PASS,173,0,173,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220637,NC_045512.2,26270,C,T,PASS,1076,2,1070,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220637,NC_045512.2,26530,A,G,PASS,346,2,344,0.99,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220637,NC_045512.2,26577,C,G,PASS,342,0,342,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220637,NC_045512.2,26709,G,A,PASS,373,1,371,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220637,NC_045512.2,27259,A,C,PASS,412,0,412,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220637,NC_045512.2,27807,C,T,PASS,128,0,127,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220637,NC_045512.2,28271,A,T,PASS,1853,2,1851,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220637,NC_045512.2,28311,C,T,PASS,1865,8,1857,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220637,NC_045512.2,2832,A,G,PASS,140,0,140,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220637,NC_045512.2,28361,GGAGAACGCA,G,PASS,1461,1454,930,0.64,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220637,NC_045512.2,28363,A,T,PASS,14,10,4,0.29,N,synonymous_variant,c.90A>T,p.Gly30Gly,p.G30G,ivar,BA.1.17 +220637,NC_045512.2,28881,GG,AA,PASS,3791,57,3732,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220637,NC_045512.2,28883,G,C,PASS,3743,3,3735,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220637,NC_045512.2,29772,T,C,PASS,48,1,47,0.98,S,downstream_gene_variant,c.*4388T>C,.,.,ivar,BA.1.17 +220637,NC_045512.2,3037,C,T,PASS,52,3,49,0.94,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220637,NC_045512.2,5386,T,G,PASS,22,0,22,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.17 +220637,NC_045512.2,5672,C,T,PASS,278,0,278,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220637,NC_045512.2,5924,G,A,PASS,105,0,105,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220637,NC_045512.2,8393,G,A,PASS,3953,20,3931,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220637,NC_045512.2,8652,T,C,PASS,3517,5,3510,1.0,orf1ab,missense_variant,c.8387T>C,p.Met2796Thr,p.M2796T,ivar,BA.1.17 +220638,NC_045512.2,10029,C,T,PASS,19,0,19,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220638,NC_045512.2,10449,C,A,PASS,95,0,95,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220638,NC_045512.2,1051,A,G,PASS,3027,5,3022,1.0,orf1ab,synonymous_variant,c.786A>G,p.Lys262Lys,p.K262K,ivar,BA.1.17 +220638,NC_045512.2,11282,AGTTTGTCTG,A,PASS,254,252,219,0.86,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220638,NC_045512.2,11537,A,G,PASS,215,0,215,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220638,NC_045512.2,13195,T,C,PASS,4423,4,4419,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220638,NC_045512.2,14408,C,T,PASS,120,3,117,0.98,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220638,NC_045512.2,15359,G,A,ft,11,5,5,0.45,orf1ab,missense_variant,c.15094G>A,p.Ala5032Thr,p.A5032T,ivar,BA.1.17 +220638,NC_045512.2,16887,C,T,PASS,704,4,700,0.99,orf1ab,missense_variant,c.16622C>T,p.Thr5541Ile,p.T5541I,ivar,BA.1.17 +220638,NC_045512.2,18163,A,G,PASS,21,0,21,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220638,NC_045512.2,18326,C,T,PASS,7551,39,7508,0.99,orf1ab,synonymous_variant,c.18061C>T,p.Leu6021Leu,p.L6021L,ivar,BA.1.17 +220638,NC_045512.2,21762,C,T,PASS,218,0,218,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220638,NC_045512.2,21764,ATACATG,A,PASS,227,218,201,0.89,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220638,NC_045512.2,21846,C,T,PASS,221,0,219,0.99,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220638,NC_045512.2,22193,AATT,A,PASS,11,11,11,1.0,S,disruptive_inframe_deletion,c.632_634delATT,p.Asn211_Leu212delinsIle,p.N211_L212delinsI,ivar,BA.1.17 +220638,NC_045512.2,22204,T,TGAGCCAGAA,ft,11,11,9,0.82,S,disruptive_inframe_insertion,c.644_645insGCCAGAAGA,p.Arg214_Asp215insGluProGlu,p.R214_D215insEPE,ivar,BA.1.17 +220638,NC_045512.2,22578,G,A,PASS,17,0,17,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.17 +220638,NC_045512.2,22673,T,C,PASS,10,0,10,1.0,S,missense_variant,c.1111T>C,p.Ser371Pro,p.S371P,ivar,BA.1.17 +220638,NC_045512.2,22679,T,C,PASS,18,0,18,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220638,NC_045512.2,22686,C,T,PASS,18,0,18,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220638,NC_045512.2,23013,A,C,PASS,10,0,10,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.17 +220638,NC_045512.2,23040,A,G,PASS,15,0,15,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.17 +220638,NC_045512.2,23048,G,A,PASS,15,0,15,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.17 +220638,NC_045512.2,23055,A,G,PASS,15,0,15,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.17 +220638,NC_045512.2,23063,A,T,PASS,15,0,15,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.17 +220638,NC_045512.2,23075,T,C,PASS,17,0,17,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.17 +220638,NC_045512.2,23202,C,A,PASS,24,0,24,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220638,NC_045512.2,23403,A,G,PASS,3470,2,3468,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220638,NC_045512.2,23525,C,T,PASS,3180,6,3174,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220638,NC_045512.2,23599,T,G,PASS,1176,0,1176,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220638,NC_045512.2,23604,C,A,PASS,1131,2,1124,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220638,NC_045512.2,23854,C,A,PASS,57,0,57,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220638,NC_045512.2,23948,G,T,PASS,760,0,755,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220638,NC_045512.2,24130,C,A,PASS,1140,1,1136,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220638,NC_045512.2,24424,A,T,PASS,228,2,224,0.98,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220638,NC_045512.2,24469,T,A,PASS,848,0,844,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220638,NC_045512.2,24503,C,T,PASS,979,18,961,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220638,NC_045512.2,25000,C,T,PASS,110,2,108,0.98,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220638,NC_045512.2,25584,C,T,PASS,133,0,133,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220638,NC_045512.2,26270,C,T,PASS,779,0,779,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220638,NC_045512.2,26530,A,G,PASS,350,0,350,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220638,NC_045512.2,26577,C,G,PASS,369,0,369,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220638,NC_045512.2,26709,G,A,PASS,422,0,422,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220638,NC_045512.2,27259,A,C,PASS,515,0,515,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220638,NC_045512.2,27384,T,C,PASS,601,0,601,1.0,ORF6,synonymous_variant,c.183T>C,p.Asp61Asp,p.D61D,ivar,BA.1.17 +220638,NC_045512.2,27807,C,T,PASS,135,1,134,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220638,NC_045512.2,28271,A,T,PASS,1839,6,1831,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220638,NC_045512.2,28311,C,T,PASS,1989,8,1976,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220638,NC_045512.2,2832,A,G,PASS,111,2,109,0.98,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220638,NC_045512.2,28361,GGAGAACGCA,G,PASS,1474,1463,704,0.48,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220638,NC_045512.2,28881,GG,AA,PASS,2234,12,2219,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220638,NC_045512.2,28883,G,C,PASS,2229,0,2227,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220638,NC_045512.2,3037,C,T,PASS,41,0,41,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220638,NC_045512.2,5672,C,T,PASS,257,0,257,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220638,NC_045512.2,5924,G,A,PASS,85,0,85,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220638,NC_045512.2,7984,T,C,PASS,1178,0,1178,1.0,orf1ab,synonymous_variant,c.7719T>C,p.Asp2573Asp,p.D2573D,ivar,BA.1.17 +220638,NC_045512.2,8393,G,A,PASS,3255,8,3241,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220638,NC_045512.2,9430,C,T,ft,14,9,5,0.36,orf1ab,synonymous_variant,c.9165C>T,p.Ile3055Ile,p.I3055I,ivar,BA.1.17 +220639,NC_045512.2,10449,C,A,PASS,16,0,16,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220639,NC_045512.2,11282,AGTTTGTCTG,A,PASS,57,57,52,0.91,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220639,NC_045512.2,11537,A,G,PASS,59,0,59,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220639,NC_045512.2,13195,T,C,PASS,3114,3,3110,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220639,NC_045512.2,14408,C,T,PASS,24,0,23,0.96,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220639,NC_045512.2,20337,T,C,ft,10,7,3,0.3,orf1ab,missense_variant,c.20072T>C,p.Ile6691Thr,p.I6691T,ivar,Unassigned +220639,NC_045512.2,21762,C,T,PASS,38,0,38,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220639,NC_045512.2,21764,ATACATG,A,PASS,38,38,36,0.95,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220639,NC_045512.2,21846,C,T,PASS,40,0,40,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220639,NC_045512.2,23403,A,G,PASS,1179,2,1177,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220639,NC_045512.2,23525,C,T,PASS,1112,0,1112,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220639,NC_045512.2,23599,T,G,PASS,414,0,414,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220639,NC_045512.2,23604,C,A,PASS,400,0,399,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220639,NC_045512.2,23948,G,T,PASS,80,0,80,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220639,NC_045512.2,24130,C,A,PASS,119,0,119,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220639,NC_045512.2,24424,A,T,PASS,14,0,14,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220639,NC_045512.2,24469,T,A,PASS,311,2,309,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220639,NC_045512.2,24503,C,T,PASS,388,8,380,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220639,NC_045512.2,25570,T,C,ft,20,14,6,0.3,ORF3a,missense_variant,c.178T>C,p.Ser60Pro,p.S60P,ivar,Unassigned +220639,NC_045512.2,25584,C,T,PASS,20,0,20,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220639,NC_045512.2,26270,C,T,PASS,53,0,53,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220639,NC_045512.2,26709,G,A,PASS,11,0,11,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220639,NC_045512.2,27259,A,C,PASS,35,0,35,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220639,NC_045512.2,27807,C,T,PASS,21,0,21,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220639,NC_045512.2,28271,A,T,PASS,460,2,456,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220639,NC_045512.2,28311,C,T,PASS,473,0,471,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220639,NC_045512.2,2832,A,G,PASS,17,0,17,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220639,NC_045512.2,28361,GGAGAACGCA,G,PASS,321,319,210,0.65,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220639,NC_045512.2,28881,GG,AA,PASS,6361,88,6267,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220639,NC_045512.2,28883,G,C,PASS,6288,3,6278,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220639,NC_045512.2,5672,C,T,PASS,35,0,35,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220639,NC_045512.2,5924,G,A,PASS,10,0,10,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220639,NC_045512.2,685,AAAGTCATTT,A,PASS,11186,11106,5685,0.51,orf1ab,conservative_inframe_deletion,c.421_429delAAGTCATTT,p.Lys141_Phe143del,p.K141_F143del,ivar,Unassigned +220639,NC_045512.2,8393,G,A,PASS,1511,2,1506,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220640,NC_045512.2,10449,C,A,PASS,18,0,18,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220640,NC_045512.2,11282,AGTTTGTCTG,A,PASS,43,43,43,1.0,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220640,NC_045512.2,11537,A,G,PASS,55,0,55,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220640,NC_045512.2,13195,T,C,PASS,2220,3,2217,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220640,NC_045512.2,14408,C,T,PASS,29,0,29,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220640,NC_045512.2,19834,C,T,ft,12,8,4,0.33,orf1ab,synonymous_variant,c.19569C>T,p.Tyr6523Tyr,p.Y6523Y,ivar,Unassigned +220640,NC_045512.2,21762,C,T,PASS,43,0,43,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220640,NC_045512.2,21764,ATACATG,A,PASS,43,43,42,0.98,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220640,NC_045512.2,21846,C,T,PASS,37,0,37,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220640,NC_045512.2,23403,A,G,PASS,1160,1,1159,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220640,NC_045512.2,23525,C,T,PASS,1142,3,1139,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220640,NC_045512.2,23599,T,G,PASS,447,0,447,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220640,NC_045512.2,23604,C,A,PASS,424,0,424,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220640,NC_045512.2,23948,G,T,PASS,99,0,97,0.98,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220640,NC_045512.2,24130,C,A,PASS,179,0,177,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220640,NC_045512.2,24424,A,T,PASS,40,0,40,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220640,NC_045512.2,24469,T,A,PASS,333,0,332,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220640,NC_045512.2,24503,C,T,PASS,408,4,404,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220640,NC_045512.2,25000,C,T,PASS,14,0,14,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220640,NC_045512.2,25584,C,T,PASS,32,0,32,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220640,NC_045512.2,26270,C,T,PASS,220,0,220,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220640,NC_045512.2,26530,A,G,PASS,150,2,148,0.99,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220640,NC_045512.2,26577,C,G,PASS,136,0,136,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220640,NC_045512.2,26709,G,A,PASS,135,0,135,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220640,NC_045512.2,27259,A,C,PASS,62,0,62,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220640,NC_045512.2,27807,C,T,PASS,19,0,19,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220640,NC_045512.2,28271,A,T,PASS,374,0,374,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220640,NC_045512.2,28311,C,T,PASS,386,0,386,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220640,NC_045512.2,2832,A,G,PASS,47,0,47,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220640,NC_045512.2,28361,GGAGAACGCA,G,PASS,306,304,221,0.72,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220640,NC_045512.2,28881,GG,AA,PASS,6266,77,6185,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220640,NC_045512.2,28883,G,C,PASS,6208,1,6194,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220640,NC_045512.2,3037,C,T,PASS,10,0,10,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220640,NC_045512.2,3241,C,T,PASS,261,0,261,1.0,orf1ab,synonymous_variant,c.2976C>T,p.Asp992Asp,p.D992D,ivar,Unassigned +220640,NC_045512.2,5924,G,A,PASS,11,0,11,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220640,NC_045512.2,76,T,A,ft,15,9,6,0.4,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220640,NC_045512.2,78,T,G,ft,15,9,6,0.4,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220640,NC_045512.2,8393,G,A,PASS,1676,2,1671,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220642,NC_045512.2,11072,TTC,T,ft,16,14,4,0.25,orf1ab,frameshift_variant,c.10809_10810delCT,p.Leu3606fs,p.L3606fs,ivar,B.1.617.2 +220642,NC_045512.2,11201,A,G,PASS,11,0,11,1.0,orf1ab,missense_variant,c.10936A>G,p.Thr3646Ala,p.T3646A,ivar,B.1.617.2 +220642,NC_045512.2,11332,A,G,PASS,27,0,26,0.96,orf1ab,synonymous_variant,c.11067A>G,p.Val3689Val,p.V3689V,ivar,B.1.617.2 +220642,NC_045512.2,14646,T,A,ft,23,17,6,0.26,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,B.1.617.2 +220642,NC_045512.2,15952,C,A,PASS,22,0,22,1.0,orf1ab,synonymous_variant,c.15687C>A,p.Ser5229Ser,p.S5229S,ivar,B.1.617.2 +220642,NC_045512.2,16466,C,T,PASS,41,0,41,1.0,orf1ab,missense_variant,c.16201C>T,p.His5401Tyr,p.H5401Y,ivar,B.1.617.2 +220642,NC_045512.2,18744,C,T,PASS,99,1,98,0.99,orf1ab,missense_variant,c.18479C>T,p.Thr6160Met,p.T6160M,ivar,B.1.617.2 +220642,NC_045512.2,19220,C,T,PASS,111,0,110,0.99,orf1ab,synonymous_variant,c.18955C>T,p.Leu6319Leu,p.L6319L,ivar,B.1.617.2 +220642,NC_045512.2,19590,T,C,ft,11,8,3,0.27,orf1ab,missense_variant,c.19325T>C,p.Ile6442Thr,p.I6442T,ivar,B.1.617.2 +220642,NC_045512.2,210,G,T,PASS,18,0,18,1.0,orf1ab,upstream_gene_variant,c.-56G>T,.,.,ivar,B.1.617.2 +220642,NC_045512.2,21618,C,G,PASS,12,0,12,1.0,S,missense_variant,c.56C>G,p.Thr19Arg,p.T19R,ivar,B.1.617.2 +220642,NC_045512.2,21682,C,T,PASS,23,0,23,1.0,S,synonymous_variant,c.120C>T,p.Asp40Asp,p.D40D,ivar,B.1.617.2 +220642,NC_045512.2,23403,A,G,PASS,557,0,557,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.617.2 +220642,NC_045512.2,23604,C,G,PASS,226,0,224,0.99,S,missense_variant,c.2042C>G,p.Pro681Arg,p.P681R,ivar,B.1.617.2 +220642,NC_045512.2,24410,G,A,PASS,21,0,21,1.0,S,missense_variant,c.2848G>A,p.Asp950Asn,p.D950N,ivar,B.1.617.2 +220642,NC_045512.2,26767,T,C,PASS,183,0,183,1.0,M,missense_variant,c.245T>C,p.Ile82Thr,p.I82T,ivar,B.1.617.2 +220642,NC_045512.2,27752,C,T,PASS,10,0,10,1.0,ORF7a,missense_variant,c.359C>T,p.Thr120Ile,p.T120I,ivar,B.1.617.2 +220642,NC_045512.2,27874,C,T,PASS,14,0,14,1.0,ORF7b,missense_variant,c.119C>T,p.Thr40Ile,p.T40I,ivar,B.1.617.2 +220642,NC_045512.2,28179,G,A,PASS,111,79,32,0.29,ORF8,missense_variant,c.286G>A,p.Gly96Ser,p.G96S,ivar,B.1.617.2 +220642,NC_045512.2,28247,AGATTTC,A,PASS,169,163,155,0.92,ORF8,conservative_inframe_deletion,c.355_360delGATTTC,p.Asp119_Phe120del,p.D119_F120del,ivar,B.1.617.2 +220642,NC_045512.2,28253,C,A,PASS,10,0,10,1.0,ORF8,missense_variant,c.360C>A,p.Phe120Leu,p.F120L,ivar,B.1.617.2 +220642,NC_045512.2,28270,TA,T,PASS,245,245,234,0.96,N,upstream_gene_variant,c.-3delA,.,.,ivar,B.1.617.2 +220642,NC_045512.2,28299,A,T,PASS,251,0,250,1.0,N,missense_variant,c.26A>T,p.Gln9Leu,p.Q9L,ivar,B.1.617.2 +220642,NC_045512.2,28326,G,T,PASS,239,1,236,0.99,N,missense_variant,c.53G>T,p.Gly18Val,p.G18V,ivar,B.1.617.2 +220642,NC_045512.2,28461,A,G,PASS,100,0,100,1.0,N,missense_variant,c.188A>G,p.Asp63Gly,p.D63G,ivar,B.1.617.2 +220642,NC_045512.2,28486,C,A,PASS,108,0,108,1.0,N,synonymous_variant,c.213C>A,p.Gly71Gly,p.G71G,ivar,B.1.617.2 +220642,NC_045512.2,28881,G,T,PASS,10522,44,10412,0.99,N,missense_variant,c.608G>T,p.Arg203Met,p.R203M,ivar,B.1.617.2 +220642,NC_045512.2,28916,G,T,PASS,434,0,429,0.99,N,missense_variant,c.643G>T,p.Gly215Cys,p.G215C,ivar,B.1.617.2 +220642,NC_045512.2,29260,G,T,PASS,1390,0,1387,1.0,N,synonymous_variant,c.987G>T,p.Thr329Thr,p.T329T,ivar,B.1.617.2 +220642,NC_045512.2,29402,G,T,PASS,2068,0,2058,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,B.1.617.2 +220642,NC_045512.2,3037,C,T,PASS,21,0,21,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,B.1.617.2 +220642,NC_045512.2,7945,C,T,PASS,279,4,275,0.99,orf1ab,synonymous_variant,c.7680C>T,p.Tyr2560Tyr,p.Y2560Y,ivar,B.1.617.2 +220644,NC_045512.2,11282,AGTTTGTCTG,A,PASS,32,32,29,0.91,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220644,NC_045512.2,11537,A,G,PASS,32,0,32,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220644,NC_045512.2,13195,T,C,PASS,1360,2,1358,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220644,NC_045512.2,14408,C,T,PASS,23,0,23,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220644,NC_045512.2,21762,C,T,PASS,35,0,35,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220644,NC_045512.2,21764,ATACATG,A,PASS,35,35,29,0.83,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220644,NC_045512.2,21846,C,T,PASS,37,4,33,0.89,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220644,NC_045512.2,23403,A,G,PASS,708,0,707,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220644,NC_045512.2,23525,C,T,PASS,716,3,713,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220644,NC_045512.2,23599,T,G,PASS,356,0,356,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220644,NC_045512.2,23604,C,A,PASS,349,0,347,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220644,NC_045512.2,23948,G,T,PASS,71,0,71,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220644,NC_045512.2,24130,C,A,PASS,90,0,90,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220644,NC_045512.2,24263,CA,C,ft,16,16,6,0.38,S,frameshift_variant,c.2704delA,p.Met902fs,p.M902fs,ivar,Unassigned +220644,NC_045512.2,24424,A,T,PASS,16,0,16,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220644,NC_045512.2,24469,T,A,PASS,168,0,168,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220644,NC_045512.2,24503,C,T,PASS,200,4,196,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220644,NC_045512.2,25584,C,T,PASS,24,0,24,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220644,NC_045512.2,26270,C,T,PASS,378,0,378,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220644,NC_045512.2,26530,A,G,PASS,116,2,114,0.98,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220644,NC_045512.2,26577,C,G,PASS,114,0,114,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220644,NC_045512.2,26709,G,A,PASS,135,0,135,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220644,NC_045512.2,27259,A,C,PASS,111,0,111,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220644,NC_045512.2,2754,T,C,PASS,101,13,88,0.87,orf1ab,missense_variant,c.2489T>C,p.Val830Ala,p.V830A,ivar,Unassigned +220644,NC_045512.2,27621,G,C,PASS,11,0,11,1.0,ORF7a,missense_variant,c.228G>C,p.Gln76His,p.Q76H,ivar,Unassigned +220644,NC_045512.2,27628,GC,G,ft,13,13,4,0.31,ORF7a,frameshift_variant,c.237delC,p.Arg80fs,p.R80fs,ivar,Unassigned +220644,NC_045512.2,27807,C,T,PASS,28,0,28,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220644,NC_045512.2,28271,A,T,PASS,550,2,546,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220644,NC_045512.2,28311,C,T,PASS,561,3,558,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220644,NC_045512.2,2832,A,G,PASS,97,0,97,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220644,NC_045512.2,28361,GGAGAACGCA,G,PASS,409,407,262,0.64,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220644,NC_045512.2,28881,GG,AA,PASS,11494,98,11384,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220644,NC_045512.2,28883,G,C,PASS,11443,5,11421,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220644,NC_045512.2,4097,T,TC,PASS,24,24,14,0.58,orf1ab,frameshift_variant,c.3832_3833insC,p.Phe1278fs,p.F1278fs,ivar,Unassigned +220644,NC_045512.2,4101,T,C,PASS,27,10,17,0.63,orf1ab,missense_variant,c.3836T>C,p.Leu1279Ser,p.L1279S,ivar,Unassigned +220644,NC_045512.2,4699,T,C,ft,10,7,3,0.3,orf1ab,synonymous_variant,c.4434T>C,p.Ser1478Ser,p.S1478S,ivar,Unassigned +220644,NC_045512.2,5672,C,T,PASS,13,0,13,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220644,NC_045512.2,5924,G,A,PASS,11,0,11,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220644,NC_045512.2,76,T,A,ft,10,6,4,0.4,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220644,NC_045512.2,78,T,G,ft,10,6,4,0.4,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220644,NC_045512.2,8393,G,A,PASS,1470,0,1470,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220646,NC_045512.2,10029,C,T,PASS,18,0,18,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,Unassigned +220646,NC_045512.2,10449,C,A,PASS,27,0,27,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220646,NC_045512.2,11282,AGTTTGTCTG,A,PASS,84,84,74,0.88,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220646,NC_045512.2,11537,A,G,PASS,69,0,69,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220646,NC_045512.2,13195,T,C,PASS,3077,6,3071,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220646,NC_045512.2,14408,C,T,PASS,48,0,48,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220646,NC_045512.2,16064,A,G,PASS,37,0,37,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220646,NC_045512.2,16950,T,A,PASS,136,98,38,0.28,orf1ab,missense_variant,c.16685T>A,p.Leu5562Gln,p.L5562Q,ivar,Unassigned +220646,NC_045512.2,18163,A,G,PASS,17,0,17,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,Unassigned +220646,NC_045512.2,21762,C,T,PASS,45,0,45,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220646,NC_045512.2,21764,ATACATG,A,PASS,45,45,42,0.93,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220646,NC_045512.2,21846,C,T,PASS,46,0,46,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220646,NC_045512.2,22578,G,A,PASS,10,0,10,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,Unassigned +220646,NC_045512.2,23403,A,G,PASS,773,0,773,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220646,NC_045512.2,23525,C,T,PASS,776,2,774,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220646,NC_045512.2,23599,T,G,PASS,337,0,337,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220646,NC_045512.2,23604,C,A,PASS,326,0,324,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220646,NC_045512.2,23854,C,A,PASS,18,0,17,0.94,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220646,NC_045512.2,23948,G,T,PASS,99,0,99,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220646,NC_045512.2,24130,C,A,PASS,158,0,156,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220646,NC_045512.2,24424,A,T,PASS,114,0,114,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220646,NC_045512.2,24469,T,A,PASS,545,6,539,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220646,NC_045512.2,24503,C,T,PASS,626,7,619,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220646,NC_045512.2,25000,C,T,PASS,31,0,31,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220646,NC_045512.2,25584,C,T,PASS,51,0,51,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220646,NC_045512.2,26270,C,T,PASS,516,2,514,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220646,NC_045512.2,26530,A,G,PASS,515,0,515,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220646,NC_045512.2,26577,C,G,PASS,562,0,562,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220646,NC_045512.2,26709,G,A,PASS,563,2,559,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220646,NC_045512.2,27259,A,C,PASS,166,0,166,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220646,NC_045512.2,27807,C,T,PASS,44,0,44,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220646,NC_045512.2,28271,A,T,PASS,690,0,690,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220646,NC_045512.2,28311,C,T,PASS,717,16,699,0.97,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220646,NC_045512.2,2832,A,G,PASS,37,0,37,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220646,NC_045512.2,28361,GGAGAACGCA,G,PASS,572,566,417,0.73,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220646,NC_045512.2,28881,GG,AA,PASS,8092,117,7963,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220646,NC_045512.2,28883,G,C,PASS,8026,5,8016,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220646,NC_045512.2,3037,C,T,PASS,15,0,15,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220646,NC_045512.2,8393,G,A,PASS,1947,10,1934,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220647,NC_045512.2,10029,C,T,PASS,27,0,27,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1 +220647,NC_045512.2,10449,C,A,PASS,65,0,65,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1 +220647,NC_045512.2,10647,C,T,PASS,55,12,43,0.78,orf1ab,missense_variant,c.10382C>T,p.Thr3461Ile,p.T3461I,ivar,BA.1 +220647,NC_045512.2,11005,C,T,PASS,16,4,12,0.75,orf1ab,synonymous_variant,c.10740C>T,p.His3580His,p.H3580H,ivar,BA.1 +220647,NC_045512.2,11282,AGTTTGTCTG,A,PASS,61,61,57,0.93,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1 +220647,NC_045512.2,11537,A,G,PASS,177,0,177,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1 +220647,NC_045512.2,13195,T,C,PASS,6907,12,6895,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1 +220647,NC_045512.2,14408,C,T,PASS,123,0,123,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1 +220647,NC_045512.2,15240,C,T,PASS,10,0,10,1.0,orf1ab,missense_variant,c.14975C>T,p.Thr4992Ile,p.T4992I,ivar,BA.1 +220647,NC_045512.2,15359,G,A,PASS,10,4,6,0.6,orf1ab,missense_variant,c.15094G>A,p.Ala5032Thr,p.A5032T,ivar,BA.1 +220647,NC_045512.2,16064,A,G,PASS,224,42,182,0.81,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,BA.1 +220647,NC_045512.2,18163,A,G,PASS,20,0,20,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1 +220647,NC_045512.2,21762,C,T,PASS,165,2,161,0.98,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1 +220647,NC_045512.2,21764,ATACATG,A,PASS,167,164,153,0.92,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1 +220647,NC_045512.2,21846,C,T,PASS,158,0,158,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1 +220647,NC_045512.2,21,C,T,PASS,12,0,12,1.0,orf1ab,upstream_gene_variant,c.-245C>T,.,.,ivar,BA.1 +220647,NC_045512.2,22578,G,A,PASS,15,0,15,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1 +220647,NC_045512.2,22599,G,A,PASS,15,4,11,0.73,S,missense_variant,c.1037G>A,p.Arg346Lys,p.R346K,ivar,BA.1 +220647,NC_045512.2,22679,T,C,PASS,16,0,16,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1 +220647,NC_045512.2,22686,C,T,PASS,16,0,16,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1 +220647,NC_045512.2,23013,A,C,PASS,11,0,11,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1 +220647,NC_045512.2,23040,A,G,PASS,11,0,11,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1 +220647,NC_045512.2,23048,G,A,PASS,11,0,11,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1 +220647,NC_045512.2,23055,A,G,PASS,11,0,11,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1 +220647,NC_045512.2,23063,A,T,PASS,11,0,11,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1 +220647,NC_045512.2,23075,T,C,PASS,10,0,10,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1 +220647,NC_045512.2,23403,A,G,PASS,2817,2,2815,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1 +220647,NC_045512.2,23525,C,T,PASS,2713,5,2696,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1 +220647,NC_045512.2,23599,T,G,PASS,1006,0,1005,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1 +220647,NC_045512.2,23604,C,A,PASS,972,0,966,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1 +220647,NC_045512.2,23854,C,A,PASS,58,0,57,0.98,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1 +220647,NC_045512.2,23948,G,T,PASS,380,0,378,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1 +220647,NC_045512.2,24130,C,A,PASS,569,0,567,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1 +220647,NC_045512.2,24424,A,T,PASS,225,0,223,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1 +220647,NC_045512.2,24469,T,A,PASS,865,1,862,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1 +220647,NC_045512.2,24503,C,T,PASS,1063,11,1050,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1 +220647,NC_045512.2,25000,C,T,PASS,78,0,78,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1 +220647,NC_045512.2,25531,A,G,PASS,101,27,74,0.73,ORF3a,missense_variant,c.139A>G,p.Ile47Val,p.I47V,ivar,BA.1 +220647,NC_045512.2,25584,C,T,PASS,104,0,102,0.98,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1 +220647,NC_045512.2,26270,C,T,PASS,714,1,713,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1 +220647,NC_045512.2,26530,A,G,PASS,619,0,619,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1 +220647,NC_045512.2,26577,C,G,PASS,691,2,689,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1 +220647,NC_045512.2,26709,G,A,PASS,724,4,720,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1 +220647,NC_045512.2,27259,A,C,PASS,416,0,415,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1 +220647,NC_045512.2,27807,C,T,PASS,126,0,126,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1 +220647,NC_045512.2,28271,A,T,PASS,1379,0,1377,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1 +220647,NC_045512.2,28311,C,T,PASS,1323,4,1317,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1 +220647,NC_045512.2,2832,A,G,PASS,91,0,91,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1 +220647,NC_045512.2,28361,GGAGAACGCA,G,PASS,976,967,669,0.69,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1 +220647,NC_045512.2,28881,GG,AA,PASS,5179,67,5106,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1 +220647,NC_045512.2,28883,G,C,PASS,5137,2,5122,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1 +220647,NC_045512.2,3037,C,T,PASS,29,0,29,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1 +220647,NC_045512.2,5386,T,G,PASS,18,0,18,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1 +220647,NC_045512.2,8393,G,A,PASS,3724,9,3714,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1 +220648,NC_045512.2,11074,CT,C,ft,15,15,4,0.27,orf1ab,frameshift_variant,c.10817delT,p.Leu3606fs,p.L3606fs,ivar,Unassigned +220648,NC_045512.2,11282,AGTTTGTCTG,A,PASS,60,60,57,0.95,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220648,NC_045512.2,11537,A,G,PASS,20,0,20,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220648,NC_045512.2,13195,T,C,PASS,1619,0,1619,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220648,NC_045512.2,14408,C,T,PASS,14,0,14,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220648,NC_045512.2,14717,A,G,ft,13,9,4,0.31,orf1ab,missense_variant,c.14452A>G,p.Arg4818Gly,p.R4818G,ivar,Unassigned +220648,NC_045512.2,1513,C,T,PASS,51,34,17,0.33,orf1ab,synonymous_variant,c.1248C>T,p.Cys416Cys,p.C416C,ivar,Unassigned +220648,NC_045512.2,21762,C,T,PASS,13,0,13,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220648,NC_045512.2,21764,ATACATG,A,PASS,13,13,11,0.85,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220648,NC_045512.2,23403,A,G,PASS,339,0,339,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220648,NC_045512.2,23525,C,T,PASS,317,0,317,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220648,NC_045512.2,23599,T,G,PASS,160,0,160,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220648,NC_045512.2,23604,C,A,PASS,149,0,148,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220648,NC_045512.2,23948,G,T,PASS,20,0,20,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220648,NC_045512.2,24130,C,A,PASS,45,0,45,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220648,NC_045512.2,24424,A,T,PASS,18,0,18,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220648,NC_045512.2,24469,T,A,PASS,106,0,106,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220648,NC_045512.2,24503,C,T,PASS,131,1,130,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220648,NC_045512.2,25584,C,T,PASS,11,0,11,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220648,NC_045512.2,26270,C,T,PASS,24,2,22,0.92,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220648,NC_045512.2,26530,A,G,PASS,80,0,80,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220648,NC_045512.2,26577,C,G,PASS,68,0,68,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220648,NC_045512.2,26709,G,A,PASS,56,0,56,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220648,NC_045512.2,27259,A,C,PASS,22,0,22,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220648,NC_045512.2,28271,A,T,PASS,75,2,73,0.97,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220648,NC_045512.2,28311,C,T,PASS,78,2,76,0.97,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220648,NC_045512.2,28361,GGAGAACGCA,G,PASS,58,57,37,0.64,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220648,NC_045512.2,28881,GG,AA,PASS,6310,41,6263,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220648,NC_045512.2,28883,G,C,PASS,6308,2,6297,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220648,NC_045512.2,8393,G,A,PASS,930,4,924,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220649,NC_045512.2,11282,AGTTTGTCTG,A,PASS,22,22,21,0.95,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1 +220649,NC_045512.2,11537,A,G,PASS,52,0,52,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1 +220649,NC_045512.2,13195,T,C,PASS,1944,4,1940,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1 +220649,NC_045512.2,14408,C,T,PASS,27,0,27,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1 +220649,NC_045512.2,14646,T,A,PASS,35,21,14,0.4,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,BA.1 +220649,NC_045512.2,19275,T,C,PASS,37,5,32,0.86,orf1ab,missense_variant,c.19010T>C,p.Leu6337Pro,p.L6337P,ivar,BA.1 +220649,NC_045512.2,21762,C,T,PASS,68,0,68,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1 +220649,NC_045512.2,21764,ATACATG,A,PASS,68,68,60,0.88,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1 +220649,NC_045512.2,21846,C,T,PASS,79,0,79,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1 +220649,NC_045512.2,22673,TC,CT,PASS,12,0,12,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1 +220649,NC_045512.2,22679,T,C,PASS,12,0,12,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1 +220649,NC_045512.2,22686,C,T,PASS,11,0,11,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1 +220649,NC_045512.2,23403,A,G,PASS,886,0,886,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1 +220649,NC_045512.2,23525,C,T,PASS,950,4,946,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1 +220649,NC_045512.2,23599,T,G,PASS,385,0,385,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1 +220649,NC_045512.2,23604,C,A,PASS,374,0,374,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1 +220649,NC_045512.2,23854,C,A,PASS,14,0,14,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1 +220649,NC_045512.2,23948,G,T,PASS,159,0,159,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1 +220649,NC_045512.2,24130,C,A,PASS,219,0,217,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1 +220649,NC_045512.2,24424,A,T,PASS,16,0,16,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1 +220649,NC_045512.2,24469,T,A,PASS,253,0,250,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1 +220649,NC_045512.2,24503,C,T,PASS,310,6,304,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1 +220649,NC_045512.2,25000,C,T,PASS,17,0,17,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1 +220649,NC_045512.2,25482,C,T,PASS,30,0,30,1.0,ORF3a,synonymous_variant,c.90C>T,p.Arg30Arg,p.R30R,ivar,BA.1 +220649,NC_045512.2,25584,C,T,PASS,20,0,20,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1 +220649,NC_045512.2,26270,C,T,PASS,293,0,293,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1 +220649,NC_045512.2,26530,A,G,PASS,178,0,178,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1 +220649,NC_045512.2,26577,C,G,PASS,169,0,169,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1 +220649,NC_045512.2,26709,G,A,PASS,149,0,149,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1 +220649,NC_045512.2,27259,A,C,PASS,88,0,88,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1 +220649,NC_045512.2,2754,T,C,PASS,25,13,12,0.48,orf1ab,missense_variant,c.2489T>C,p.Val830Ala,p.V830A,ivar,BA.1 +220649,NC_045512.2,27670,G,T,PASS,18,0,18,1.0,ORF7a,missense_variant,c.277G>T,p.Val93Phe,p.V93F,ivar,BA.1 +220649,NC_045512.2,27807,C,T,PASS,30,0,30,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1 +220649,NC_045512.2,2815,TA,T,PASS,34,34,19,0.56,orf1ab,frameshift_variant,c.2553delA,p.Val852fs,p.V852fs,ivar,BA.1 +220649,NC_045512.2,28271,A,T,PASS,719,1,718,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1 +220649,NC_045512.2,28311,C,T,PASS,808,2,802,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1 +220649,NC_045512.2,2832,A,G,PASS,31,0,31,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1 +220649,NC_045512.2,28361,GGAGAACGCA,G,PASS,558,557,301,0.54,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1 +220649,NC_045512.2,28363,A,T,PASS,23,13,6,0.26,N,synonymous_variant,c.90A>T,p.Gly30Gly,p.G30G,ivar,BA.1 +220649,NC_045512.2,28881,GG,AA,PASS,10996,110,10874,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1 +220649,NC_045512.2,28883,G,C,PASS,10931,9,10905,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1 +220649,NC_045512.2,5672,C,T,PASS,19,0,19,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1 +220649,NC_045512.2,76,T,A,ft,14,8,6,0.43,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1 +220649,NC_045512.2,78,T,G,PASS,12,6,6,0.5,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1 +220649,NC_045512.2,8393,G,A,PASS,2396,9,2383,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1 +220650,NC_045512.2,10449,C,A,PASS,27,0,27,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220650,NC_045512.2,10647,C,T,PASS,14,0,14,1.0,orf1ab,missense_variant,c.10382C>T,p.Thr3461Ile,p.T3461I,ivar,Unassigned +220650,NC_045512.2,11282,AGTTTGTCTG,A,PASS,20,20,18,0.9,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220650,NC_045512.2,11537,A,G,PASS,65,0,65,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220650,NC_045512.2,13195,T,C,PASS,3292,5,3287,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220650,NC_045512.2,14408,C,T,PASS,82,0,82,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220650,NC_045512.2,16064,A,G,PASS,70,0,70,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220650,NC_045512.2,21762,C,T,PASS,63,0,63,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220650,NC_045512.2,21764,ATACATG,A,PASS,63,63,53,0.84,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220650,NC_045512.2,21846,C,T,PASS,94,1,93,0.99,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220650,NC_045512.2,23403,A,G,PASS,993,2,991,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220650,NC_045512.2,23525,C,T,PASS,908,0,908,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220650,NC_045512.2,23599,T,G,PASS,328,0,328,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220650,NC_045512.2,23604,C,A,PASS,312,0,311,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220650,NC_045512.2,23854,C,A,PASS,12,0,12,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220650,NC_045512.2,23948,G,T,PASS,190,0,190,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220650,NC_045512.2,24130,C,A,PASS,240,0,240,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220650,NC_045512.2,24424,A,T,PASS,42,0,42,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220650,NC_045512.2,24469,T,A,PASS,455,0,454,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220650,NC_045512.2,24503,C,T,PASS,551,10,540,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220650,NC_045512.2,25000,C,T,PASS,17,0,17,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220650,NC_045512.2,25531,A,G,PASS,28,0,28,1.0,ORF3a,missense_variant,c.139A>G,p.Ile47Val,p.I47V,ivar,Unassigned +220650,NC_045512.2,25584,C,T,PASS,26,0,26,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220650,NC_045512.2,26270,C,T,PASS,249,0,249,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220650,NC_045512.2,26530,A,G,PASS,144,0,144,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220650,NC_045512.2,26577,C,G,PASS,147,0,147,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220650,NC_045512.2,26709,G,A,PASS,176,1,175,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220650,NC_045512.2,27259,A,C,PASS,126,0,126,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220650,NC_045512.2,27807,C,T,PASS,26,0,26,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220650,NC_045512.2,2785,T,C,PASS,79,51,28,0.35,orf1ab,synonymous_variant,c.2520T>C,p.Asn840Asn,p.N840N,ivar,Unassigned +220650,NC_045512.2,28271,A,T,PASS,795,2,791,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220650,NC_045512.2,28311,C,T,PASS,801,2,799,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220650,NC_045512.2,2832,A,G,PASS,88,0,88,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220650,NC_045512.2,28361,GGAGAACGCA,G,PASS,589,587,367,0.62,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220650,NC_045512.2,28881,GG,AA,PASS,6879,67,6807,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220650,NC_045512.2,28883,G,C,PASS,6840,2,6824,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220650,NC_045512.2,76,T,A,PASS,21,13,8,0.38,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220650,NC_045512.2,78,T,G,PASS,21,13,8,0.38,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220650,NC_045512.2,8393,G,A,PASS,2169,2,2167,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220651,NC_045512.2,10323,A,G,PASS,11,0,11,1.0,orf1ab,missense_variant,c.10058A>G,p.Lys3353Arg,p.K3353R,ivar,Unassigned +220651,NC_045512.2,10333,A,G,ft,11,8,3,0.27,orf1ab,synonymous_variant,c.10068A>G,p.Thr3356Thr,p.T3356T,ivar,Unassigned +220651,NC_045512.2,10449,C,A,PASS,22,0,22,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220651,NC_045512.2,11282,AGTTTGTCTG,A,PASS,34,33,26,0.76,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220651,NC_045512.2,11537,A,G,PASS,32,0,32,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220651,NC_045512.2,13195,T,C,PASS,1396,7,1389,0.99,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220651,NC_045512.2,14408,C,T,PASS,20,0,20,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220651,NC_045512.2,21740,T,G,PASS,27,15,12,0.44,S,missense_variant,c.178T>G,p.Ser60Ala,p.S60A,ivar,Unassigned +220651,NC_045512.2,21762,C,T,PASS,24,2,22,0.92,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220651,NC_045512.2,21764,ATACATG,A,PASS,24,24,24,1.0,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220651,NC_045512.2,21843,C,A,PASS,31,19,12,0.39,S,missense_variant,c.281C>A,p.Ser94Tyr,p.S94Y,ivar,Unassigned +220651,NC_045512.2,21846,C,T,PASS,31,0,31,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220651,NC_045512.2,23403,A,G,PASS,827,0,827,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220651,NC_045512.2,23525,C,T,PASS,880,1,878,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220651,NC_045512.2,23599,T,G,PASS,393,0,393,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220651,NC_045512.2,23604,C,A,PASS,380,1,378,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220651,NC_045512.2,23948,G,T,PASS,26,0,26,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220651,NC_045512.2,24130,C,A,PASS,44,0,44,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220651,NC_045512.2,24424,A,T,PASS,22,0,22,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220651,NC_045512.2,24469,T,A,PASS,263,0,262,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220651,NC_045512.2,24503,C,T,PASS,300,4,296,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220651,NC_045512.2,25584,C,T,PASS,17,0,17,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220651,NC_045512.2,2592,C,A,PASS,24,16,8,0.33,orf1ab,missense_variant,c.2327C>A,p.Ala776Asp,p.A776D,ivar,Unassigned +220651,NC_045512.2,26270,C,T,PASS,295,0,295,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220651,NC_045512.2,26530,A,G,PASS,223,0,223,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220651,NC_045512.2,26577,C,G,PASS,230,0,230,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220651,NC_045512.2,26709,G,A,PASS,234,0,234,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220651,NC_045512.2,27259,A,C,PASS,73,0,71,0.97,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220651,NC_045512.2,27807,C,T,PASS,24,0,24,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220651,NC_045512.2,28271,A,T,PASS,194,1,193,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220651,NC_045512.2,28311,C,T,PASS,223,2,221,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220651,NC_045512.2,2832,A,G,PASS,28,0,28,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220651,NC_045512.2,28361,GGAGAACGCA,G,PASS,186,186,128,0.69,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220651,NC_045512.2,28881,GG,AA,PASS,11290,87,11197,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220651,NC_045512.2,28883,G,C,PASS,11251,5,11237,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220651,NC_045512.2,4301,C,T,ft,12,8,4,0.33,orf1ab,missense_variant,c.4036C>T,p.Leu1346Phe,p.L1346F,ivar,Unassigned +220651,NC_045512.2,5672,C,T,PASS,16,0,16,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220651,NC_045512.2,7680,A,G,PASS,44,31,13,0.3,orf1ab,missense_variant,c.7415A>G,p.Asp2472Gly,p.D2472G,ivar,Unassigned +220651,NC_045512.2,76,T,A,ft,16,12,4,0.25,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220651,NC_045512.2,78,T,G,ft,16,12,4,0.25,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220651,NC_045512.2,8393,G,A,PASS,1490,7,1483,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220652,NC_045512.2,10135,T,C,PASS,11,0,11,1.0,orf1ab,synonymous_variant,c.9870T>C,p.Leu3290Leu,p.L3290L,ivar,Unassigned +220652,NC_045512.2,10449,C,A,PASS,21,0,21,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220652,NC_045512.2,11282,AGTTTGTCTG,A,PASS,58,58,53,0.91,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220652,NC_045512.2,113,A,G,PASS,33,20,13,0.39,orf1ab,upstream_gene_variant,c.-153A>G,.,.,ivar,Unassigned +220652,NC_045512.2,11537,A,G,PASS,41,0,41,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220652,NC_045512.2,116,G,A,PASS,36,23,13,0.36,orf1ab,upstream_gene_variant,c.-150G>A,.,.,ivar,Unassigned +220652,NC_045512.2,13195,T,C,PASS,2217,3,2214,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220652,NC_045512.2,14408,C,T,PASS,19,0,19,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220652,NC_045512.2,14646,T,A,PASS,49,35,14,0.29,orf1ab,missense_variant,c.14381T>A,p.Leu4794Gln,p.L4794Q,ivar,Unassigned +220652,NC_045512.2,21762,C,T,PASS,48,0,48,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220652,NC_045512.2,21764,ATACATG,A,PASS,49,48,45,0.92,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220652,NC_045512.2,21846,C,T,PASS,62,0,62,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220652,NC_045512.2,23403,A,G,PASS,858,0,858,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220652,NC_045512.2,23525,C,T,PASS,930,0,930,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220652,NC_045512.2,23599,T,G,PASS,413,0,413,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220652,NC_045512.2,23604,C,A,PASS,403,1,400,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220652,NC_045512.2,23854,C,A,PASS,14,0,14,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220652,NC_045512.2,23948,G,T,PASS,181,2,179,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220652,NC_045512.2,24130,C,A,PASS,220,0,219,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220652,NC_045512.2,24424,A,T,PASS,78,0,77,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220652,NC_045512.2,24469,T,A,PASS,425,0,425,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220652,NC_045512.2,24503,C,T,PASS,509,17,492,0.97,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220652,NC_045512.2,24803,A,G,PASS,190,0,190,1.0,S,missense_variant,c.3241A>G,p.Ile1081Val,p.I1081V,ivar,Unassigned +220652,NC_045512.2,25000,C,T,PASS,14,0,14,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220652,NC_045512.2,25584,C,T,PASS,19,0,19,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220652,NC_045512.2,25708,C,T,PASS,19,2,17,0.89,ORF3a,missense_variant,c.316C>T,p.Leu106Phe,p.L106F,ivar,Unassigned +220652,NC_045512.2,26270,C,T,PASS,493,0,493,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220652,NC_045512.2,26530,A,G,PASS,207,0,207,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220652,NC_045512.2,26577,C,G,PASS,193,0,193,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220652,NC_045512.2,26709,G,A,PASS,201,1,199,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220652,NC_045512.2,27259,A,C,PASS,95,0,95,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220652,NC_045512.2,2755,G,A,PASS,92,69,23,0.25,orf1ab,synonymous_variant,c.2490G>A,p.Val830Val,p.V830V,ivar,Unassigned +220652,NC_045512.2,27807,C,T,PASS,31,0,31,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220652,NC_045512.2,28271,A,T,PASS,646,0,644,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220652,NC_045512.2,28311,C,T,PASS,720,2,718,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220652,NC_045512.2,2832,A,G,PASS,95,0,95,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220652,NC_045512.2,28361,GGAGAACGCA,G,PASS,559,554,308,0.55,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220652,NC_045512.2,28881,GG,AA,PASS,9059,70,8983,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220652,NC_045512.2,28883,G,C,PASS,9032,4,9012,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220652,NC_045512.2,29301,A,G,PASS,3790,4,3786,1.0,N,missense_variant,c.1028A>G,p.Asp343Gly,p.D343G,ivar,Unassigned +220652,NC_045512.2,3037,C,T,PASS,11,0,11,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220652,NC_045512.2,7488,C,T,PASS,228,0,228,1.0,orf1ab,missense_variant,c.7223C>T,p.Thr2408Ile,p.T2408I,ivar,Unassigned +220652,NC_045512.2,76,T,A,ft,16,12,4,0.25,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220652,NC_045512.2,8393,G,A,PASS,2474,4,2469,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220653,NC_045512.2,11282,AGTTTGTCTG,A,ft,10,10,9,0.9,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220653,NC_045512.2,11537,A,G,PASS,10,0,10,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220653,NC_045512.2,13195,T,C,PASS,387,0,387,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220653,NC_045512.2,14560,T,A,ft,10,7,3,0.3,orf1ab,stop_gained,c.14295T>A,p.Cys4765*,p.C4765*,ivar,Unassigned +220653,NC_045512.2,23403,A,G,PASS,311,0,311,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220653,NC_045512.2,23525,C,T,PASS,312,2,310,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220653,NC_045512.2,23599,T,G,PASS,157,0,157,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220653,NC_045512.2,23604,C,A,PASS,154,0,154,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220653,NC_045512.2,23948,G,T,PASS,31,0,31,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220653,NC_045512.2,24130,C,A,PASS,25,0,25,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220653,NC_045512.2,24469,T,A,PASS,63,0,61,0.97,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220653,NC_045512.2,24503,C,T,PASS,71,0,71,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220653,NC_045512.2,26270,C,T,PASS,393,0,393,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220653,NC_045512.2,2633,T,A,PASS,11,5,6,0.55,orf1ab,missense_variant,c.2368T>A,p.Leu790Met,p.L790M,ivar,Unassigned +220653,NC_045512.2,26530,A,G,PASS,113,0,113,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220653,NC_045512.2,26577,C,G,PASS,115,0,113,0.98,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220653,NC_045512.2,26709,G,A,PASS,95,0,95,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220653,NC_045512.2,2702,T,C,ft,11,8,3,0.27,orf1ab,missense_variant,c.2437T>C,p.Phe813Leu,p.F813L,ivar,Unassigned +220653,NC_045512.2,27259,A,C,PASS,30,0,30,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220653,NC_045512.2,27807,C,T,PASS,17,0,17,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220653,NC_045512.2,28271,A,T,PASS,184,0,184,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220653,NC_045512.2,28311,C,T,PASS,212,1,211,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220653,NC_045512.2,2832,A,G,PASS,14,0,14,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220653,NC_045512.2,28361,GGAGAACGCA,G,PASS,166,166,120,0.72,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220653,NC_045512.2,28881,GG,AA,PASS,6955,64,6886,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220653,NC_045512.2,28883,G,C,PASS,6937,2,6917,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220653,NC_045512.2,5672,C,T,PASS,14,0,14,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220653,NC_045512.2,685,AAAGTCATTT,A,PASS,4513,4475,2142,0.47,orf1ab,conservative_inframe_deletion,c.421_429delAAGTCATTT,p.Lys141_Phe143del,p.K141_F143del,ivar,Unassigned +220653,NC_045512.2,694,T,A,PASS,14,9,5,0.36,orf1ab,missense_variant,c.429T>A,p.Phe143Leu,p.F143L,ivar,Unassigned +220653,NC_045512.2,76,T,A,PASS,10,4,6,0.6,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220653,NC_045512.2,8393,G,A,PASS,618,0,618,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220654,NC_045512.2,10029,C,T,PASS,14,0,14,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,Unassigned +220654,NC_045512.2,10449,C,A,PASS,29,0,29,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220654,NC_045512.2,11282,AGTTTGTCTG,A,PASS,106,106,97,0.92,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220654,NC_045512.2,11537,A,G,PASS,65,0,65,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220654,NC_045512.2,13195,T,C,PASS,2838,1,2837,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220654,NC_045512.2,14408,C,T,PASS,21,0,21,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220654,NC_045512.2,18163,A,G,PASS,15,0,15,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,Unassigned +220654,NC_045512.2,21762,C,T,PASS,35,0,35,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220654,NC_045512.2,21764,ATACATG,A,PASS,37,35,33,0.89,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220654,NC_045512.2,21846,C,T,PASS,62,0,62,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220654,NC_045512.2,22578,G,A,PASS,10,0,10,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,Unassigned +220654,NC_045512.2,23403,A,G,PASS,780,0,780,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220654,NC_045512.2,23525,C,T,PASS,754,0,754,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220654,NC_045512.2,23599,T,G,PASS,331,0,331,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220654,NC_045512.2,23604,C,A,PASS,321,0,317,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220654,NC_045512.2,23854,C,A,PASS,26,0,26,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220654,NC_045512.2,23948,G,T,PASS,258,2,255,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220654,NC_045512.2,24130,C,A,PASS,310,0,308,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220654,NC_045512.2,24424,A,T,PASS,93,0,93,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220654,NC_045512.2,24469,T,A,PASS,384,0,384,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220654,NC_045512.2,24503,C,T,PASS,439,6,433,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220654,NC_045512.2,25000,C,T,PASS,26,0,26,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220654,NC_045512.2,25584,C,T,PASS,32,0,32,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220654,NC_045512.2,26270,C,T,PASS,591,3,588,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220654,NC_045512.2,26530,A,G,PASS,261,0,261,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220654,NC_045512.2,26577,C,G,PASS,241,0,241,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220654,NC_045512.2,26709,G,A,PASS,269,2,267,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220654,NC_045512.2,27259,A,C,PASS,227,0,225,0.99,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220654,NC_045512.2,27807,C,T,PASS,44,0,44,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220654,NC_045512.2,28271,A,T,PASS,695,0,693,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220654,NC_045512.2,28311,C,T,PASS,714,0,712,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220654,NC_045512.2,2832,A,G,PASS,19,0,19,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220654,NC_045512.2,28361,GGAGAACGCA,G,PASS,538,535,345,0.64,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220654,NC_045512.2,28881,GG,AA,PASS,5172,63,5108,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220654,NC_045512.2,28883,G,C,PASS,5131,0,5124,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220654,NC_045512.2,3037,C,T,PASS,17,0,17,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220654,NC_045512.2,5672,C,T,PASS,73,0,73,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220654,NC_045512.2,5924,G,A,PASS,24,0,24,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220654,NC_045512.2,76,T,A,PASS,21,13,8,0.38,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220654,NC_045512.2,78,T,G,PASS,21,13,8,0.38,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220654,NC_045512.2,8393,G,A,PASS,1798,4,1792,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220655,NC_045512.2,10029,C,T,PASS,13,0,13,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220655,NC_045512.2,10449,C,A,PASS,66,0,66,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220655,NC_045512.2,11282,AGTTTGTCTG,A,PASS,124,124,112,0.9,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220655,NC_045512.2,11537,A,G,PASS,249,2,247,0.99,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220655,NC_045512.2,13195,T,C,PASS,6068,4,6064,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220655,NC_045512.2,14408,C,T,PASS,167,2,164,0.98,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220655,NC_045512.2,17797,G,T,PASS,11,5,6,0.55,orf1ab,synonymous_variant,c.17532G>T,p.Leu5844Leu,p.L5844L,ivar,BA.1.17 +220655,NC_045512.2,18163,A,G,PASS,13,0,13,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220655,NC_045512.2,21762,C,T,PASS,224,0,224,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220655,NC_045512.2,21764,ATACATG,A,PASS,226,224,213,0.94,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220655,NC_045512.2,21846,C,T,PASS,271,0,271,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220655,NC_045512.2,21,C,T,PASS,14,0,14,1.0,orf1ab,upstream_gene_variant,c.-245C>T,.,.,ivar,BA.1.17 +220655,NC_045512.2,2270,A,G,PASS,22,0,22,1.0,orf1ab,missense_variant,c.2005A>G,p.Lys669Glu,p.K669E,ivar,BA.1.17 +220655,NC_045512.2,23013,A,C,PASS,13,0,13,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.17 +220655,NC_045512.2,23040,A,G,PASS,11,0,11,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.17 +220655,NC_045512.2,23048,G,A,PASS,11,0,11,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.17 +220655,NC_045512.2,23055,A,G,PASS,12,0,12,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.17 +220655,NC_045512.2,23063,A,T,PASS,11,2,9,0.82,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.17 +220655,NC_045512.2,23075,T,C,PASS,18,0,18,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.17 +220655,NC_045512.2,23202,C,A,PASS,23,0,23,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220655,NC_045512.2,23403,A,G,PASS,1843,2,1841,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220655,NC_045512.2,23525,C,T,PASS,1813,2,1808,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220655,NC_045512.2,23599,T,G,PASS,652,0,652,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220655,NC_045512.2,23604,C,A,PASS,630,0,620,0.98,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220655,NC_045512.2,23854,C,A,PASS,31,0,31,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220655,NC_045512.2,23948,G,T,PASS,445,0,445,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220655,NC_045512.2,24130,C,A,PASS,779,0,777,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220655,NC_045512.2,24424,A,T,PASS,137,0,136,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220655,NC_045512.2,24469,T,A,PASS,827,0,825,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220655,NC_045512.2,24503,C,T,PASS,960,7,950,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220655,NC_045512.2,25000,C,T,PASS,48,0,48,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220655,NC_045512.2,25584,C,T,PASS,85,0,85,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220655,NC_045512.2,25855,G,A,PASS,101,0,101,1.0,ORF3a,missense_variant,c.463G>A,p.Asp155Asn,p.D155N,ivar,BA.1.17 +220655,NC_045512.2,26270,C,T,PASS,450,2,448,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220655,NC_045512.2,26530,A,G,PASS,478,1,477,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220655,NC_045512.2,26577,C,G,PASS,554,0,554,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220655,NC_045512.2,26709,G,A,PASS,578,4,571,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220655,NC_045512.2,27259,A,C,PASS,283,0,281,0.99,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220655,NC_045512.2,27807,C,T,PASS,164,1,163,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220655,NC_045512.2,28271,A,T,PASS,2207,4,2199,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220655,NC_045512.2,28311,C,T,PASS,2296,7,2282,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220655,NC_045512.2,2832,A,G,PASS,60,0,60,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220655,NC_045512.2,28361,GGAGAACGCA,G,PASS,1753,1743,1191,0.68,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220655,NC_045512.2,28881,GG,AA,PASS,5261,74,5183,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220655,NC_045512.2,28883,G,C,PASS,5202,6,5186,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220655,NC_045512.2,29772,T,C,PASS,24,0,24,1.0,S,downstream_gene_variant,c.*4388T>C,.,.,ivar,BA.1.17 +220655,NC_045512.2,3037,C,T,PASS,24,0,24,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220655,NC_045512.2,5672,C,T,PASS,76,1,75,0.99,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220655,NC_045512.2,5924,G,A,PASS,36,0,36,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220655,NC_045512.2,76,T,A,ft,24,18,6,0.25,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1.17 +220655,NC_045512.2,78,T,G,ft,24,18,6,0.25,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1.17 +220655,NC_045512.2,8393,G,A,PASS,2376,3,2367,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220655,NC_045512.2,8652,T,C,PASS,2140,8,2132,1.0,orf1ab,missense_variant,c.8387T>C,p.Met2796Thr,p.M2796T,ivar,BA.1.17 +220656,NC_045512.2,11537,A,G,PASS,16,0,16,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220656,NC_045512.2,13195,T,C,PASS,831,0,831,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220656,NC_045512.2,13975,G,A,ft,11,8,3,0.27,orf1ab,stop_retained_variant,c.13710G>A,p.Ter4570Ter,p.*4570*,ivar,Unassigned +220656,NC_045512.2,14408,C,T,PASS,19,0,19,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220656,NC_045512.2,16409,C,T,PASS,31,22,9,0.29,orf1ab,stop_gained,c.16144C>T,p.Gln5382*,p.Q5382*,ivar,Unassigned +220656,NC_045512.2,21762,C,T,PASS,19,0,19,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220656,NC_045512.2,21764,ATACATG,A,PASS,19,19,17,0.89,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220656,NC_045512.2,21846,C,T,PASS,27,0,27,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220656,NC_045512.2,23403,A,G,PASS,428,0,428,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220656,NC_045512.2,23525,C,T,PASS,502,4,498,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220656,NC_045512.2,23599,T,G,PASS,215,0,215,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220656,NC_045512.2,23604,C,A,PASS,206,0,204,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220656,NC_045512.2,23948,G,T,PASS,45,0,45,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220656,NC_045512.2,24130,C,A,PASS,50,0,50,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220656,NC_045512.2,24469,T,A,PASS,80,0,80,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220656,NC_045512.2,24503,C,T,PASS,87,1,86,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220656,NC_045512.2,26577,C,G,PASS,16,0,16,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220656,NC_045512.2,26598,T,C,ft,14,10,4,0.29,M,missense_variant,c.76T>C,p.Phe26Leu,p.F26L,ivar,Unassigned +220656,NC_045512.2,26709,G,A,PASS,15,0,15,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220656,NC_045512.2,26712,T,C,PASS,15,5,10,0.67,M,missense_variant,c.190T>C,p.Cys64Arg,p.C64R,ivar,Unassigned +220656,NC_045512.2,27259,A,C,PASS,13,0,13,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220656,NC_045512.2,28271,A,T,PASS,136,0,134,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220656,NC_045512.2,28311,C,T,PASS,133,0,132,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220656,NC_045512.2,28361,GGAGAACGCA,G,PASS,98,97,63,0.64,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220656,NC_045512.2,28877,AG,TC,PASS,7768,7,7718,0.99,N,synonymous_variant,c.604_605delAGinsTC,p.203,p.203,ivar,Unassigned +220656,NC_045512.2,28881,GG,AA,PASS,7783,17,7748,1.0,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220656,NC_045512.2,28883,G,C,PASS,7807,2,7798,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220656,NC_045512.2,4920,C,T,ft,12,9,3,0.25,orf1ab,missense_variant,c.4655C>T,p.Thr1552Ile,p.T1552I,ivar,Unassigned +220656,NC_045512.2,8393,G,A,PASS,610,3,607,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220657,NC_045512.2,10647,C,T,PASS,19,0,19,1.0,orf1ab,missense_variant,c.10382C>T,p.Thr3461Ile,p.T3461I,ivar,Unassigned +220657,NC_045512.2,11537,A,G,PASS,34,0,34,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220657,NC_045512.2,13195,T,C,PASS,1613,0,1613,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220657,NC_045512.2,14408,C,T,PASS,22,0,22,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220657,NC_045512.2,15966,T,C,PASS,20,12,8,0.4,orf1ab,missense_variant,c.15701T>C,p.Val5234Ala,p.V5234A,ivar,Unassigned +220657,NC_045512.2,16064,A,G,PASS,14,0,14,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220657,NC_045512.2,21762,C,T,PASS,37,0,37,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220657,NC_045512.2,21764,ATACATG,A,PASS,38,37,30,0.79,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220657,NC_045512.2,21846,C,T,PASS,36,0,36,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220657,NC_045512.2,23403,A,G,PASS,510,2,508,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220657,NC_045512.2,23525,C,T,PASS,541,0,541,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220657,NC_045512.2,23599,T,G,PASS,264,0,264,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220657,NC_045512.2,23604,C,A,PASS,253,0,249,0.98,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220657,NC_045512.2,23948,G,T,PASS,44,0,44,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220657,NC_045512.2,24130,C,A,PASS,53,0,53,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220657,NC_045512.2,24424,A,T,PASS,26,0,26,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220657,NC_045512.2,24469,T,A,PASS,149,0,146,0.98,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220657,NC_045512.2,24503,C,T,PASS,170,4,166,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220657,NC_045512.2,26270,C,T,PASS,139,0,139,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220657,NC_045512.2,26577,C,G,PASS,11,0,11,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220657,NC_045512.2,26709,G,A,PASS,10,0,10,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220657,NC_045512.2,27259,A,C,PASS,44,0,43,0.98,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220657,NC_045512.2,27807,C,T,PASS,10,0,10,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220657,NC_045512.2,28271,A,T,PASS,737,0,737,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220657,NC_045512.2,28311,C,T,PASS,713,2,711,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220657,NC_045512.2,28361,GGAGAACGCA,G,PASS,527,525,343,0.65,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220657,NC_045512.2,28425,C,T,PASS,95,70,25,0.26,N,missense_variant,c.152C>T,p.Ser51Phe,p.S51F,ivar,Unassigned +220657,NC_045512.2,28881,GG,AA,PASS,9546,60,9475,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220657,NC_045512.2,28883,G,C,PASS,9546,3,9522,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220657,NC_045512.2,8393,G,A,PASS,1051,5,1046,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220658,NC_045512.2,11282,AGTTTGTCTG,A,PASS,20,20,18,0.9,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220658,NC_045512.2,11454,C,T,PASS,29,0,27,0.93,orf1ab,missense_variant,c.11189C>T,p.Ala3730Val,p.A3730V,ivar,Unassigned +220658,NC_045512.2,11537,A,G,PASS,22,0,22,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220658,NC_045512.2,13195,T,C,PASS,1324,7,1317,0.99,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220658,NC_045512.2,20936,C,T,ft,15,11,4,0.27,orf1ab,missense_variant,c.20671C>T,p.Arg6891Cys,p.R6891C,ivar,Unassigned +220658,NC_045512.2,21266,A,G,ft,12,8,4,0.33,orf1ab,missense_variant,c.21001A>G,p.Lys7001Glu,p.K7001E,ivar,Unassigned +220658,NC_045512.2,21762,C,T,PASS,27,0,27,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220658,NC_045512.2,21764,ATACATG,A,PASS,27,27,24,0.89,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220658,NC_045512.2,21846,C,T,PASS,19,0,19,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220658,NC_045512.2,22679,T,C,PASS,12,0,12,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,Unassigned +220658,NC_045512.2,22686,C,T,PASS,11,0,11,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,Unassigned +220658,NC_045512.2,23403,A,G,PASS,786,0,786,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220658,NC_045512.2,23525,C,T,PASS,772,0,772,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220658,NC_045512.2,23599,T,G,PASS,327,0,327,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220658,NC_045512.2,23604,C,A,PASS,323,0,323,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220658,NC_045512.2,23854,C,A,PASS,11,0,11,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220658,NC_045512.2,23948,G,T,PASS,89,0,89,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220658,NC_045512.2,24130,C,A,PASS,118,0,118,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220658,NC_045512.2,24424,A,T,PASS,36,0,36,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220658,NC_045512.2,24469,T,A,PASS,233,0,232,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220658,NC_045512.2,24503,C,T,PASS,264,11,253,0.96,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220658,NC_045512.2,25584,C,T,PASS,23,0,23,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220658,NC_045512.2,26270,C,T,PASS,231,2,229,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220658,NC_045512.2,26530,A,G,PASS,217,0,217,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220658,NC_045512.2,26577,C,G,PASS,261,0,261,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220658,NC_045512.2,26709,G,A,PASS,244,0,244,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220658,NC_045512.2,27259,A,C,PASS,60,0,60,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220658,NC_045512.2,27807,C,T,PASS,31,0,31,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220658,NC_045512.2,28271,A,T,PASS,725,0,723,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220658,NC_045512.2,28311,C,T,PASS,708,0,707,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220658,NC_045512.2,2832,A,G,PASS,13,0,13,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220658,NC_045512.2,28361,GGAGAACGCA,G,PASS,566,561,435,0.77,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220658,NC_045512.2,28881,GG,AA,PASS,10102,94,9997,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220658,NC_045512.2,28883,G,C,PASS,10039,10,10008,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220658,NC_045512.2,3037,C,T,PASS,19,0,19,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220658,NC_045512.2,5672,C,T,PASS,11,0,11,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220658,NC_045512.2,8393,G,A,PASS,885,0,885,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220659,NC_045512.2,10449,C,A,PASS,67,0,67,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220659,NC_045512.2,11282,AGTTTGTCTG,A,PASS,147,147,129,0.88,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220659,NC_045512.2,11537,A,G,PASS,153,0,153,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220659,NC_045512.2,13195,T,C,PASS,5113,5,5106,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220659,NC_045512.2,14408,C,T,PASS,87,0,87,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220659,NC_045512.2,18163,A,G,PASS,26,0,26,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220659,NC_045512.2,21762,C,T,PASS,130,2,128,0.98,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220659,NC_045512.2,21764,ATACATG,A,PASS,132,132,117,0.89,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220659,NC_045512.2,21846,C,T,PASS,126,0,126,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220659,NC_045512.2,22679,T,C,PASS,12,0,12,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220659,NC_045512.2,22686,C,T,PASS,12,0,12,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220659,NC_045512.2,23202,C,A,PASS,12,0,12,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220659,NC_045512.2,23403,A,G,PASS,3188,6,3182,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220659,NC_045512.2,23525,C,T,PASS,3075,2,3067,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220659,NC_045512.2,23599,T,G,PASS,1225,0,1223,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220659,NC_045512.2,23604,C,A,PASS,1183,1,1178,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220659,NC_045512.2,23854,C,A,PASS,44,0,44,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220659,NC_045512.2,23948,G,T,PASS,575,0,574,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220659,NC_045512.2,24130,C,A,PASS,852,0,845,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220659,NC_045512.2,24424,A,T,PASS,87,1,85,0.98,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220659,NC_045512.2,24469,T,A,PASS,624,1,618,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220659,NC_045512.2,24503,C,T,PASS,757,12,745,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220659,NC_045512.2,25000,C,T,PASS,40,1,39,0.98,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220659,NC_045512.2,25584,C,T,PASS,88,0,88,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220659,NC_045512.2,26270,C,T,PASS,546,1,545,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220659,NC_045512.2,26530,A,G,PASS,449,2,447,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220659,NC_045512.2,26577,C,G,PASS,432,0,432,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220659,NC_045512.2,26709,G,A,PASS,479,2,477,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220659,NC_045512.2,27259,A,C,PASS,294,0,294,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220659,NC_045512.2,27807,C,T,PASS,180,1,179,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220659,NC_045512.2,27970,C,T,PASS,696,19,675,0.97,ORF8,missense_variant,c.77C>T,p.Thr26Ile,p.T26I,ivar,BA.1.17 +220659,NC_045512.2,28271,A,T,PASS,1877,3,1872,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220659,NC_045512.2,28311,C,T,PASS,1989,8,1980,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220659,NC_045512.2,2832,A,G,PASS,68,0,68,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220659,NC_045512.2,28361,GGAGAACGCA,G,PASS,1571,1561,969,0.62,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220659,NC_045512.2,28881,GG,AA,PASS,3757,52,3700,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220659,NC_045512.2,28883,G,C,PASS,3725,2,3716,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220659,NC_045512.2,3037,C,T,PASS,23,0,23,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220659,NC_045512.2,5672,C,T,PASS,91,0,91,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220659,NC_045512.2,5924,G,A,PASS,34,0,34,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220659,NC_045512.2,76,T,A,PASS,24,10,14,0.58,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1.17 +220659,NC_045512.2,78,T,G,PASS,23,9,14,0.61,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1.17 +220659,NC_045512.2,7984,T,C,PASS,934,1,933,1.0,orf1ab,synonymous_variant,c.7719T>C,p.Asp2573Asp,p.D2573D,ivar,BA.1.17 +220659,NC_045512.2,8393,G,A,PASS,3572,10,3552,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220659,NC_045512.2,999,C,T,PASS,2162,22,2138,0.99,orf1ab,missense_variant,c.734C>T,p.Ser245Phe,p.S245F,ivar,BA.1.17 +220660,NC_045512.2,10029,C,T,PASS,15,0,15,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.1 +220660,NC_045512.2,10449,C,A,PASS,59,0,59,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1 +220660,NC_045512.2,11282,AGTTTGTCTG,A,PASS,155,151,132,0.85,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1 +220660,NC_045512.2,11537,A,G,PASS,138,0,138,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1 +220660,NC_045512.2,13195,T,C,PASS,4902,11,4891,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1 +220660,NC_045512.2,13750,T,A,ft,15,11,4,0.27,orf1ab,missense_variant,c.13485T>A,p.Ser4495Arg,p.S4495R,ivar,BA.1.1 +220660,NC_045512.2,14408,C,T,PASS,103,0,103,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1 +220660,NC_045512.2,15336,T,C,PASS,11,2,9,0.82,orf1ab,missense_variant,c.15071T>C,p.Leu5024Ser,p.L5024S,ivar,BA.1.1 +220660,NC_045512.2,15359,G,A,PASS,14,7,7,0.5,orf1ab,missense_variant,c.15094G>A,p.Ala5032Thr,p.A5032T,ivar,BA.1.1 +220660,NC_045512.2,16744,G,A,PASS,344,0,344,1.0,orf1ab,synonymous_variant,c.16479G>A,p.Leu5493Leu,p.L5493L,ivar,BA.1.1 +220660,NC_045512.2,18163,A,G,PASS,20,0,20,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.1 +220660,NC_045512.2,21762,C,T,PASS,186,0,186,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1 +220660,NC_045512.2,21764,ATACATG,A,PASS,190,187,174,0.92,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1 +220660,NC_045512.2,21846,C,T,PASS,164,0,164,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1 +220660,NC_045512.2,22578,G,A,PASS,13,0,13,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.1 +220660,NC_045512.2,23202,C,A,PASS,11,0,11,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.1 +220660,NC_045512.2,23403,A,G,PASS,3655,3,3650,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1 +220660,NC_045512.2,23525,C,T,PASS,3613,12,3596,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1 +220660,NC_045512.2,23599,T,G,PASS,1227,0,1225,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1 +220660,NC_045512.2,23604,C,A,PASS,1189,2,1175,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1 +220660,NC_045512.2,23854,C,A,PASS,22,0,22,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1 +220660,NC_045512.2,23948,G,T,PASS,242,0,239,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1 +220660,NC_045512.2,24130,C,A,PASS,408,0,407,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1 +220660,NC_045512.2,24424,A,T,PASS,95,0,95,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1 +220660,NC_045512.2,24469,T,A,PASS,525,0,521,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1 +220660,NC_045512.2,24503,C,T,PASS,600,6,592,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1 +220660,NC_045512.2,25000,C,T,PASS,48,0,48,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1 +220660,NC_045512.2,2500,A,G,PASS,21,0,21,1.0,orf1ab,synonymous_variant,c.2235A>G,p.Glu745Glu,p.E745E,ivar,BA.1.1 +220660,NC_045512.2,25584,C,T,PASS,60,0,60,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1 +220660,NC_045512.2,26270,C,T,PASS,318,1,317,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1 +220660,NC_045512.2,26530,A,G,PASS,309,0,309,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1 +220660,NC_045512.2,26577,C,G,PASS,350,0,350,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1 +220660,NC_045512.2,26709,G,A,PASS,356,3,353,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1 +220660,NC_045512.2,27259,A,C,PASS,249,0,249,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1 +220660,NC_045512.2,27807,C,T,PASS,129,1,128,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1 +220660,NC_045512.2,28271,A,T,PASS,1073,0,1070,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1 +220660,NC_045512.2,28311,C,T,PASS,1105,5,1097,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1 +220660,NC_045512.2,2832,A,G,PASS,32,0,32,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1 +220660,NC_045512.2,28361,GGAGAACGCA,G,PASS,776,768,491,0.63,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1 +220660,NC_045512.2,28881,GG,AA,PASS,3182,53,3121,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1 +220660,NC_045512.2,28883,G,C,PASS,3146,1,3138,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1 +220660,NC_045512.2,3037,C,T,PASS,27,0,27,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1 +220660,NC_045512.2,3264,C,T,PASS,1132,6,1125,0.99,orf1ab,missense_variant,c.2999C>T,p.Thr1000Ile,p.T1000I,ivar,BA.1.1 +220660,NC_045512.2,5386,T,G,PASS,10,0,10,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.1 +220660,NC_045512.2,5512,C,T,ft,15,11,4,0.27,orf1ab,synonymous_variant,c.5247C>T,p.Asn1749Asn,p.N1749N,ivar,BA.1.1 +220660,NC_045512.2,76,T,A,PASS,36,24,12,0.33,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1.1 +220660,NC_045512.2,78,T,G,PASS,36,24,12,0.33,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1.1 +220660,NC_045512.2,8393,G,A,PASS,3635,10,3623,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1 +220661,NC_045512.2,10029,C,T,PASS,28,2,26,0.93,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.1 +220661,NC_045512.2,10449,C,A,PASS,83,0,83,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1 +220661,NC_045512.2,11282,AGTTTGTCTG,A,PASS,268,262,243,0.91,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1 +220661,NC_045512.2,11537,A,G,PASS,203,0,203,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1 +220661,NC_045512.2,13195,T,C,PASS,7311,6,7305,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1 +220661,NC_045512.2,13678,T,C,PASS,10,0,10,1.0,orf1ab,synonymous_variant,c.13413T>C,p.Thr4471Thr,p.T4471T,ivar,BA.1.1 +220661,NC_045512.2,14408,C,T,PASS,157,0,157,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1 +220661,NC_045512.2,18163,A,G,PASS,14,1,13,0.93,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.1 +220661,NC_045512.2,20081,C,T,ft,11,7,4,0.36,orf1ab,synonymous_variant,c.19816C>T,p.Leu6606Leu,p.L6606L,ivar,BA.1.1 +220661,NC_045512.2,20085,AG,A,ft,12,12,4,0.33,orf1ab,frameshift_variant,c.19822delG,p.Val6608fs,p.V6608fs,ivar,BA.1.1 +220661,NC_045512.2,21595,C,T,PASS,626,3,621,0.99,S,synonymous_variant,c.33C>T,p.Val11Val,p.V11V,ivar,BA.1.1 +220661,NC_045512.2,21762,C,T,PASS,151,2,149,0.99,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1 +220661,NC_045512.2,21764,ATACATG,A,PASS,152,151,145,0.95,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1 +220661,NC_045512.2,21846,C,T,PASS,232,1,231,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1 +220661,NC_045512.2,22992,G,A,PASS,13,0,13,1.0,S,missense_variant,c.1430G>A,p.Ser477Asn,p.S477N,ivar,BA.1.1 +220661,NC_045512.2,22995,C,A,PASS,13,0,13,1.0,S,missense_variant,c.1433C>A,p.Thr478Lys,p.T478K,ivar,BA.1.1 +220661,NC_045512.2,23013,A,C,PASS,11,0,11,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.1 +220661,NC_045512.2,23040,A,G,PASS,11,0,11,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.1 +220661,NC_045512.2,23048,G,A,PASS,11,0,11,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.1 +220661,NC_045512.2,23055,A,G,PASS,11,0,11,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.1 +220661,NC_045512.2,23063,A,T,PASS,11,0,11,1.0,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.1 +220661,NC_045512.2,23202,C,A,PASS,23,0,23,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.1 +220661,NC_045512.2,23403,A,G,PASS,3174,1,3172,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1 +220661,NC_045512.2,23525,C,T,PASS,3000,2,2995,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1 +220661,NC_045512.2,23599,T,G,PASS,1121,0,1121,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1 +220661,NC_045512.2,23604,C,A,PASS,1072,0,1066,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1 +220661,NC_045512.2,23854,C,A,PASS,29,0,29,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1 +220661,NC_045512.2,23948,G,T,PASS,427,0,427,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1 +220661,NC_045512.2,24130,C,A,PASS,638,0,636,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1 +220661,NC_045512.2,24424,A,T,PASS,151,2,149,0.99,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1 +220661,NC_045512.2,24469,T,A,PASS,857,0,855,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1 +220661,NC_045512.2,24503,C,T,PASS,1013,12,1001,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1 +220661,NC_045512.2,2470,C,T,PASS,13,0,13,1.0,orf1ab,synonymous_variant,c.2205C>T,p.Ala735Ala,p.A735A,ivar,BA.1.1 +220661,NC_045512.2,25000,C,T,PASS,59,2,57,0.97,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1 +220661,NC_045512.2,25584,C,T,PASS,70,0,70,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1 +220661,NC_045512.2,26270,C,T,PASS,516,0,516,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1 +220661,NC_045512.2,26530,A,G,PASS,322,0,322,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1 +220661,NC_045512.2,26577,C,G,PASS,284,0,283,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1 +220661,NC_045512.2,26709,G,A,PASS,337,7,330,0.98,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1 +220661,NC_045512.2,27259,A,C,PASS,178,0,178,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1 +220661,NC_045512.2,27807,C,T,PASS,70,0,70,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1 +220661,NC_045512.2,28271,A,T,PASS,1288,0,1287,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1 +220661,NC_045512.2,28311,C,T,PASS,1327,5,1322,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1 +220661,NC_045512.2,2832,A,G,PASS,29,0,29,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1 +220661,NC_045512.2,28361,GGAGAACGCA,G,PASS,988,984,611,0.62,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1 +220661,NC_045512.2,28881,GG,AA,PASS,4858,62,4792,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1 +220661,NC_045512.2,28883,G,C,PASS,4828,1,4820,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1 +220661,NC_045512.2,3037,C,T,PASS,31,0,31,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1 +220661,NC_045512.2,8393,G,A,PASS,2995,5,2985,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1 +220663,NC_045512.2,11537,A,G,PASS,11,0,11,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220663,NC_045512.2,12864,A,C,PASS,17,0,17,1.0,orf1ab,missense_variant,c.12599A>C,p.Asp4200Ala,p.D4200A,ivar,Unassigned +220663,NC_045512.2,1312,G,T,PASS,475,0,473,1.0,orf1ab,missense_variant,c.1047G>T,p.Leu349Phe,p.L349F,ivar,Unassigned +220663,NC_045512.2,13195,T,C,PASS,259,0,259,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220663,NC_045512.2,18622,A,G,ft,16,11,5,0.31,orf1ab,synonymous_variant,c.18357A>G,p.Leu6119Leu,p.L6119L,ivar,Unassigned +220663,NC_045512.2,22578,G,A,PASS,10,0,10,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,Unassigned +220663,NC_045512.2,23403,A,G,PASS,89,0,89,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220663,NC_045512.2,23525,C,T,PASS,106,0,106,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220663,NC_045512.2,23599,T,G,PASS,65,0,65,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220663,NC_045512.2,23604,C,A,PASS,61,0,61,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220663,NC_045512.2,23948,G,T,PASS,13,0,13,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220663,NC_045512.2,24130,C,A,PASS,37,0,37,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220663,NC_045512.2,24424,A,T,PASS,61,0,61,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220663,NC_045512.2,24469,T,A,PASS,139,0,139,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220663,NC_045512.2,24503,C,T,PASS,158,0,158,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220663,NC_045512.2,26270,C,T,PASS,479,2,477,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220663,NC_045512.2,26530,A,G,PASS,156,0,156,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220663,NC_045512.2,26577,C,G,PASS,120,0,120,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220663,NC_045512.2,26709,G,A,PASS,166,2,163,0.98,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220663,NC_045512.2,27259,A,C,PASS,23,0,23,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220663,NC_045512.2,27274,T,A,PASS,24,17,7,0.29,ORF6,missense_variant,c.73T>A,p.Ser25Thr,p.S25T,ivar,Unassigned +220663,NC_045512.2,27476,C,T,PASS,147,21,126,0.86,ORF7a,missense_variant,c.83C>T,p.Thr28Ile,p.T28I,ivar,Unassigned +220663,NC_045512.2,28271,A,T,PASS,150,0,150,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220663,NC_045512.2,28311,C,T,PASS,159,2,157,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220663,NC_045512.2,28361,GGAGAACGCA,G,PASS,171,171,136,0.8,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220663,NC_045512.2,28881,GG,AA,PASS,9147,39,9102,1.0,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220663,NC_045512.2,28883,G,C,PASS,9138,1,9105,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220663,NC_045512.2,29301,A,G,PASS,1729,4,1725,1.0,N,missense_variant,c.1028A>G,p.Asp343Gly,p.D343G,ivar,Unassigned +220663,NC_045512.2,3760,T,A,PASS,316,215,97,0.31,orf1ab,stop_gained,c.3495T>A,p.Cys1165*,p.C1165*,ivar,Unassigned +220663,NC_045512.2,8393,G,A,PASS,223,0,223,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220664,NC_045512.2,10029,C,T,PASS,25,0,25,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.1.1 +220664,NC_045512.2,10449,C,A,PASS,112,0,112,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1.1 +220664,NC_045512.2,11282,AGTTTGTCTG,A,PASS,302,300,269,0.89,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1.1 +220664,NC_045512.2,11537,A,G,PASS,300,0,300,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1.1 +220664,NC_045512.2,13195,T,C,PASS,5521,11,5501,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1.1 +220664,NC_045512.2,14408,C,T,PASS,214,4,210,0.98,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1.1 +220664,NC_045512.2,15336,T,C,PASS,11,5,6,0.55,orf1ab,missense_variant,c.15071T>C,p.Leu5024Ser,p.L5024S,ivar,BA.1.1.1 +220664,NC_045512.2,15359,G,A,PASS,13,6,7,0.54,orf1ab,missense_variant,c.15094G>A,p.Ala5032Thr,p.A5032T,ivar,BA.1.1.1 +220664,NC_045512.2,16064,A,G,PASS,251,1,250,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,BA.1.1.1 +220664,NC_045512.2,18163,A,G,PASS,24,0,24,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.1.1 +220664,NC_045512.2,21762,C,T,PASS,261,0,261,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1.1 +220664,NC_045512.2,21764,ATACATG,A,PASS,266,261,232,0.87,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1.1 +220664,NC_045512.2,21846,C,T,PASS,297,0,297,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1.1 +220664,NC_045512.2,22578,G,A,PASS,12,0,12,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.1.1 +220664,NC_045512.2,22599,G,A,PASS,13,0,13,1.0,S,missense_variant,c.1037G>A,p.Arg346Lys,p.R346K,ivar,BA.1.1.1 +220664,NC_045512.2,22673,TC,CT,PASS,11,0,11,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.1.1 +220664,NC_045512.2,22679,T,C,PASS,14,0,14,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.1.1 +220664,NC_045512.2,22686,C,T,PASS,12,0,12,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.1.1 +220664,NC_045512.2,22992,G,A,PASS,10,0,10,1.0,S,missense_variant,c.1430G>A,p.Ser477Asn,p.S477N,ivar,BA.1.1.1 +220664,NC_045512.2,23013,A,C,PASS,10,0,10,1.0,S,missense_variant,c.1451A>C,p.Glu484Ala,p.E484A,ivar,BA.1.1.1 +220664,NC_045512.2,23040,A,G,PASS,11,0,11,1.0,S,missense_variant,c.1478A>G,p.Gln493Arg,p.Q493R,ivar,BA.1.1.1 +220664,NC_045512.2,23048,G,A,PASS,15,0,15,1.0,S,missense_variant,c.1486G>A,p.Gly496Ser,p.G496S,ivar,BA.1.1.1 +220664,NC_045512.2,23055,A,G,PASS,15,0,15,1.0,S,missense_variant,c.1493A>G,p.Gln498Arg,p.Q498R,ivar,BA.1.1.1 +220664,NC_045512.2,23063,A,T,PASS,16,0,14,0.88,S,missense_variant,c.1501A>T,p.Asn501Tyr,p.N501Y,ivar,BA.1.1.1 +220664,NC_045512.2,23075,T,C,PASS,17,0,17,1.0,S,missense_variant,c.1513T>C,p.Tyr505His,p.Y505H,ivar,BA.1.1.1 +220664,NC_045512.2,23202,C,A,PASS,25,0,25,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.1.1 +220664,NC_045512.2,23403,A,G,PASS,2654,0,2654,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1.1 +220664,NC_045512.2,23525,C,T,PASS,2542,8,2530,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1.1 +220664,NC_045512.2,23599,T,G,PASS,936,0,935,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1.1 +220664,NC_045512.2,23604,C,A,PASS,896,0,889,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1.1 +220664,NC_045512.2,23854,C,A,PASS,55,0,54,0.98,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1.1 +220664,NC_045512.2,23948,G,T,PASS,895,0,891,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1.1 +220664,NC_045512.2,24130,C,A,PASS,1211,0,1198,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1.1 +220664,NC_045512.2,24424,A,T,PASS,268,0,268,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1.1 +220664,NC_045512.2,24469,T,A,PASS,1053,0,1053,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1.1 +220664,NC_045512.2,24503,C,T,PASS,1182,13,1169,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1.1 +220664,NC_045512.2,25000,C,T,PASS,80,0,80,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1.1 +220664,NC_045512.2,25584,C,T,PASS,152,0,152,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1.1 +220664,NC_045512.2,26270,C,T,PASS,636,2,634,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1.1 +220664,NC_045512.2,26530,A,G,PASS,177,0,177,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1.1 +220664,NC_045512.2,26577,C,G,PASS,203,0,203,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1.1 +220664,NC_045512.2,26709,G,A,PASS,205,0,205,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1.1 +220664,NC_045512.2,27259,A,C,PASS,346,0,340,0.98,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1.1 +220664,NC_045512.2,27807,C,T,PASS,64,0,64,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1.1 +220664,NC_045512.2,28271,A,T,PASS,1831,9,1819,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1.1 +220664,NC_045512.2,28311,C,T,PASS,1835,8,1827,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1.1 +220664,NC_045512.2,2832,A,G,PASS,167,1,166,0.99,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1.1 +220664,NC_045512.2,28361,GGAGAACGCA,G,PASS,1291,1282,743,0.58,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1.1 +220664,NC_045512.2,28881,GG,AA,PASS,2695,46,2646,0.98,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1.1 +220664,NC_045512.2,28883,G,C,PASS,2663,6,2655,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1.1 +220664,NC_045512.2,3037,C,T,PASS,50,0,50,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1.1 +220664,NC_045512.2,5386,T,G,PASS,15,0,15,1.0,orf1ab,synonymous_variant,c.5121T>G,p.Ala1707Ala,p.A1707A,ivar,BA.1.1.1 +220664,NC_045512.2,8393,G,A,PASS,2721,8,2712,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1.1 +220665,NC_045512.2,10449,C,A,PASS,14,0,14,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220665,NC_045512.2,11074,CT,C,ft,15,15,4,0.27,orf1ab,frameshift_variant,c.10817delT,p.Leu3606fs,p.L3606fs,ivar,BA.1.17 +220665,NC_045512.2,11186,T,C,PASS,26,18,8,0.31,orf1ab,synonymous_variant,c.10921T>C,p.Leu3641Leu,p.L3641L,ivar,BA.1.17 +220665,NC_045512.2,11282,AGTTTGTCTG,A,PASS,49,49,41,0.84,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220665,NC_045512.2,11537,A,G,PASS,41,0,41,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220665,NC_045512.2,13195,T,C,PASS,2411,5,2405,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220665,NC_045512.2,14408,C,T,PASS,27,0,27,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220665,NC_045512.2,19162,G,T,PASS,872,0,868,1.0,orf1ab,synonymous_variant,c.18897G>T,p.Leu6299Leu,p.L6299L,ivar,BA.1.17 +220665,NC_045512.2,21762,C,T,PASS,52,0,52,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220665,NC_045512.2,21764,ATACATG,A,PASS,52,52,47,0.9,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220665,NC_045512.2,21846,C,T,PASS,44,0,44,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220665,NC_045512.2,23202,C,A,PASS,16,0,16,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220665,NC_045512.2,23235,A,G,PASS,19,12,7,0.37,S,missense_variant,c.1673A>G,p.Lys558Arg,p.K558R,ivar,BA.1.17 +220665,NC_045512.2,23403,A,G,PASS,1508,0,1508,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220665,NC_045512.2,23525,C,T,PASS,1423,6,1417,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220665,NC_045512.2,23599,T,G,PASS,648,0,648,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220665,NC_045512.2,23604,C,A,PASS,624,0,621,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220665,NC_045512.2,23948,G,T,PASS,71,0,71,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220665,NC_045512.2,24130,C,A,PASS,140,0,140,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220665,NC_045512.2,24424,A,T,PASS,37,0,37,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220665,NC_045512.2,24469,T,A,PASS,384,0,383,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220665,NC_045512.2,24503,C,T,PASS,449,11,438,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220665,NC_045512.2,25000,C,T,PASS,17,0,17,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220665,NC_045512.2,25584,C,T,PASS,35,0,35,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220665,NC_045512.2,26270,C,T,PASS,646,0,646,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220665,NC_045512.2,26530,A,G,PASS,242,0,242,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220665,NC_045512.2,26577,C,G,PASS,271,0,269,0.99,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220665,NC_045512.2,26709,G,A,PASS,262,1,261,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220665,NC_045512.2,27259,A,C,PASS,149,0,149,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220665,NC_045512.2,27670,G,T,PASS,32,0,32,1.0,ORF7a,missense_variant,c.277G>T,p.Val93Phe,p.V93F,ivar,BA.1.17 +220665,NC_045512.2,27676,G,C,PASS,31,23,8,0.26,ORF7a,missense_variant,c.283G>C,p.Glu95Gln,p.E95Q,ivar,BA.1.17 +220665,NC_045512.2,27807,C,T,PASS,55,0,55,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220665,NC_045512.2,28271,A,T,PASS,837,0,837,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220665,NC_045512.2,28311,C,T,PASS,921,0,919,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220665,NC_045512.2,2832,A,G,PASS,88,0,88,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220665,NC_045512.2,28361,GGAGAACGCA,G,PASS,702,694,428,0.61,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220665,NC_045512.2,28881,GG,AA,PASS,8854,85,8762,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220665,NC_045512.2,28883,G,C,PASS,8819,2,8808,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220665,NC_045512.2,3037,C,T,PASS,11,0,11,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220665,NC_045512.2,4087,T,C,ft,15,11,4,0.27,orf1ab,synonymous_variant,c.3822T>C,p.Ile1274Ile,p.I1274I,ivar,BA.1.17 +220665,NC_045512.2,5672,C,T,PASS,49,0,49,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220665,NC_045512.2,5924,G,A,PASS,20,0,20,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220665,NC_045512.2,76,T,A,PASS,17,5,12,0.71,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1.17 +220665,NC_045512.2,78,T,G,PASS,17,5,12,0.71,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1.17 +220665,NC_045512.2,8393,G,A,PASS,2963,3,2957,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220666,NC_045512.2,11267,GAT,G,PASS,28,24,10,0.36,orf1ab,frameshift_variant,c.11005_11006delAT,p.Met3669fs,p.M3669fs,ivar,B.1.617.2 +220666,NC_045512.2,11332,A,G,PASS,31,0,31,1.0,orf1ab,synonymous_variant,c.11067A>G,p.Val3689Val,p.V3689V,ivar,B.1.617.2 +220666,NC_045512.2,11387,G,A,ft,14,10,4,0.29,orf1ab,missense_variant,c.11122G>A,p.Val3708Met,p.V3708M,ivar,B.1.617.2 +220666,NC_045512.2,13432,C,T,PASS,486,0,486,1.0,orf1ab,synonymous_variant,c.13167C>T,p.Pro4389Pro,p.P4389P,ivar,B.1.617.2 +220666,NC_045512.2,21456,A,G,ft,10,7,3,0.3,orf1ab,missense_variant,c.21191A>G,p.Lys7064Arg,p.K7064R,ivar,B.1.617.2 +220666,NC_045512.2,21618,C,G,PASS,18,0,18,1.0,S,missense_variant,c.56C>G,p.Thr19Arg,p.T19R,ivar,B.1.617.2 +220666,NC_045512.2,23403,A,G,PASS,319,0,319,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,B.1.617.2 +220666,NC_045512.2,23604,C,G,PASS,103,0,103,1.0,S,missense_variant,c.2042C>G,p.Pro681Arg,p.P681R,ivar,B.1.617.2 +220666,NC_045512.2,26767,T,C,PASS,24,0,24,1.0,M,missense_variant,c.245T>C,p.Ile82Thr,p.I82T,ivar,B.1.617.2 +220666,NC_045512.2,27874,C,T,PASS,13,0,13,1.0,ORF7b,missense_variant,c.119C>T,p.Thr40Ile,p.T40I,ivar,B.1.617.2 +220666,NC_045512.2,27916,G,A,PASS,12,0,12,1.0,ORF8,missense_variant,c.23G>A,p.Gly8Glu,p.G8E,ivar,B.1.617.2 +220666,NC_045512.2,27943,A,G,PASS,10,3,7,0.7,ORF8,missense_variant,c.50A>G,p.His17Arg,p.H17R,ivar,B.1.617.2 +220666,NC_045512.2,28055,A,G,PASS,15,8,7,0.47,ORF8,synonymous_variant,c.162A>G,p.Ser54Ser,p.S54S,ivar,B.1.617.2 +220666,NC_045512.2,28089,GGTTCTA,G,PASS,12,12,12,1.0,ORF8,disruptive_inframe_deletion,c.197_202delGTTCTA,p.Gly66_Lys68delinsGlu,p.G66_K68delinsE,ivar,B.1.617.2 +220666,NC_045512.2,28179,G,T,PASS,18,0,18,1.0,ORF8,missense_variant,c.286G>T,p.Gly96Cys,p.G96C,ivar,B.1.617.2 +220666,NC_045512.2,28247,AGATTTC,A,PASS,90,90,86,0.96,ORF8,conservative_inframe_deletion,c.355_360delGATTTC,p.Asp119_Phe120del,p.D119_F120del,ivar,B.1.617.2 +220666,NC_045512.2,28270,TA,T,PASS,118,118,105,0.89,N,upstream_gene_variant,c.-3delA,.,.,ivar,B.1.617.2 +220666,NC_045512.2,28367,C,T,PASS,96,0,96,1.0,N,missense_variant,c.94C>T,p.Arg32Cys,p.R32C,ivar,B.1.617.2 +220666,NC_045512.2,28378,G,T,PASS,78,0,78,1.0,N,synonymous_variant,c.105G>T,p.Ala35Ala,p.A35A,ivar,B.1.617.2 +220666,NC_045512.2,28461,A,G,PASS,16,0,16,1.0,N,missense_variant,c.188A>G,p.Asp63Gly,p.D63G,ivar,B.1.617.2 +220666,NC_045512.2,28881,G,T,PASS,5069,16,5029,0.99,N,missense_variant,c.608G>T,p.Arg203Met,p.R203M,ivar,B.1.617.2 +220666,NC_045512.2,28916,G,T,PASS,56,0,56,1.0,N,missense_variant,c.643G>T,p.Gly215Cys,p.G215C,ivar,B.1.617.2 +220666,NC_045512.2,29402,G,T,PASS,1865,0,1860,1.0,N,missense_variant,c.1129G>T,p.Asp377Tyr,p.D377Y,ivar,B.1.617.2 +220666,NC_045512.2,3903,C,T,PASS,82,0,82,1.0,orf1ab,missense_variant,c.3638C>T,p.Pro1213Leu,p.P1213L,ivar,B.1.617.2 +220666,NC_045512.2,3987,C,T,PASS,90,0,90,1.0,orf1ab,missense_variant,c.3722C>T,p.Thr1241Ile,p.T1241I,ivar,B.1.617.2 +220667,NC_045512.2,10029,C,T,PASS,30,0,30,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220667,NC_045512.2,10449,C,A,PASS,76,0,74,0.97,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220667,NC_045512.2,11282,AGTTTGTCTG,A,PASS,206,202,182,0.88,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220667,NC_045512.2,11537,A,G,PASS,96,0,96,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220667,NC_045512.2,13195,T,C,PASS,3626,4,3622,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220667,NC_045512.2,14408,C,T,PASS,117,0,117,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220667,NC_045512.2,18163,A,G,PASS,13,0,13,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220667,NC_045512.2,21762,C,T,PASS,157,2,155,0.99,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220667,NC_045512.2,21764,ATACATG,A,PASS,159,157,139,0.87,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220667,NC_045512.2,21846,C,T,PASS,153,1,152,0.99,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220667,NC_045512.2,21,C,T,PASS,10,0,10,1.0,orf1ab,upstream_gene_variant,c.-245C>T,.,.,ivar,BA.1.17 +220667,NC_045512.2,22578,G,A,PASS,18,0,18,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.17 +220667,NC_045512.2,22673,TC,CT,PASS,10,0,10,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.17 +220667,NC_045512.2,22679,T,C,PASS,20,0,20,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220667,NC_045512.2,22686,C,T,PASS,20,0,20,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220667,NC_045512.2,23202,C,A,PASS,16,0,16,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220667,NC_045512.2,23403,A,G,PASS,3381,6,3375,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220667,NC_045512.2,23525,C,T,PASS,3427,9,3416,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220667,NC_045512.2,23599,T,G,PASS,1504,0,1502,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220667,NC_045512.2,23604,C,A,PASS,1436,0,1431,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220667,NC_045512.2,23854,C,A,PASS,19,0,19,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220667,NC_045512.2,23948,G,T,PASS,846,0,845,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220667,NC_045512.2,24130,C,A,PASS,1170,0,1164,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220667,NC_045512.2,24424,A,T,PASS,128,2,124,0.97,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220667,NC_045512.2,24469,T,A,PASS,798,2,795,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220667,NC_045512.2,24503,C,T,PASS,930,23,905,0.97,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220667,NC_045512.2,25000,C,T,PASS,67,0,67,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220667,NC_045512.2,25584,C,T,PASS,100,2,98,0.98,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220667,NC_045512.2,26270,C,T,PASS,1358,2,1355,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220667,NC_045512.2,26361,G,A,ft,11,8,3,0.27,E,synonymous_variant,c.117G>A,p.Leu39Leu,p.L39L,ivar,BA.1.17 +220667,NC_045512.2,26530,A,G,PASS,438,0,436,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220667,NC_045512.2,26577,C,G,PASS,513,0,513,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220667,NC_045512.2,26709,G,A,PASS,473,1,472,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220667,NC_045512.2,27259,A,C,PASS,618,0,618,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220667,NC_045512.2,27384,T,C,PASS,764,0,764,1.0,ORF6,synonymous_variant,c.183T>C,p.Asp61Asp,p.D61D,ivar,BA.1.17 +220667,NC_045512.2,27807,C,T,PASS,112,0,112,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220667,NC_045512.2,28271,A,T,PASS,1976,8,1963,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220667,NC_045512.2,28311,C,T,PASS,2173,5,2164,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220667,NC_045512.2,2832,A,G,PASS,80,0,80,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220667,NC_045512.2,28361,GGAGAACGCA,G,PASS,1572,1560,679,0.43,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220667,NC_045512.2,28881,GG,AA,PASS,3593,32,3558,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220667,NC_045512.2,28883,G,C,PASS,3570,4,3559,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220667,NC_045512.2,3037,C,T,PASS,19,0,19,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220667,NC_045512.2,3040,C,T,PASS,19,0,19,1.0,orf1ab,synonymous_variant,c.2775C>T,p.Tyr925Tyr,p.Y925Y,ivar,BA.1.17 +220667,NC_045512.2,5672,C,T,PASS,165,0,165,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220667,NC_045512.2,5924,G,A,PASS,77,0,77,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220667,NC_045512.2,76,T,A,PASS,45,9,36,0.8,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1.17 +220667,NC_045512.2,78,T,G,PASS,45,9,36,0.8,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1.17 +220667,NC_045512.2,7984,T,C,PASS,627,0,627,1.0,orf1ab,synonymous_variant,c.7719T>C,p.Asp2573Asp,p.D2573D,ivar,BA.1.17 +220667,NC_045512.2,8393,G,A,PASS,4302,15,4285,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220668,NC_045512.2,10449,C,A,PASS,11,0,11,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220668,NC_045512.2,11282,AGTTTGTCTG,A,PASS,33,33,29,0.88,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220668,NC_045512.2,13195,T,C,PASS,418,0,418,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220668,NC_045512.2,206,C,A,PASS,20,13,7,0.35,orf1ab,upstream_gene_variant,c.-60C>A,.,.,ivar,Unassigned +220668,NC_045512.2,21762,C,T,PASS,11,0,11,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220668,NC_045512.2,21764,ATACATG,A,ft,11,11,7,0.64,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220668,NC_045512.2,21846,C,T,PASS,16,0,16,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220668,NC_045512.2,23403,A,G,PASS,734,0,734,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220668,NC_045512.2,23525,C,T,PASS,748,0,748,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220668,NC_045512.2,23599,T,G,PASS,379,0,377,0.99,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220668,NC_045512.2,23604,C,A,PASS,358,0,358,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220668,NC_045512.2,23948,G,T,PASS,25,0,25,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220668,NC_045512.2,24130,C,A,PASS,19,0,19,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220668,NC_045512.2,24424,A,T,PASS,30,0,30,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220668,NC_045512.2,24469,T,A,PASS,94,0,94,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220668,NC_045512.2,24503,C,T,PASS,95,0,95,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220668,NC_045512.2,25000,C,T,PASS,17,0,17,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220668,NC_045512.2,25584,C,T,PASS,28,0,28,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220668,NC_045512.2,26270,C,T,PASS,475,2,473,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220668,NC_045512.2,26530,A,G,PASS,90,0,90,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220668,NC_045512.2,26577,C,G,PASS,87,0,87,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220668,NC_045512.2,26709,G,A,PASS,96,0,96,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220668,NC_045512.2,27259,A,C,PASS,68,0,68,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220668,NC_045512.2,27384,T,C,PASS,82,0,82,1.0,ORF6,synonymous_variant,c.183T>C,p.Asp61Asp,p.D61D,ivar,Unassigned +220668,NC_045512.2,27807,C,T,PASS,11,0,11,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220668,NC_045512.2,28271,A,T,PASS,260,2,258,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220668,NC_045512.2,28311,C,T,PASS,297,0,297,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220668,NC_045512.2,2832,A,G,PASS,10,0,10,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220668,NC_045512.2,28361,GGAGAACGCA,G,PASS,176,176,105,0.6,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220668,NC_045512.2,28881,GG,AA,PASS,8461,46,8410,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220668,NC_045512.2,28883,G,C,PASS,8448,1,8431,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220668,NC_045512.2,5672,C,T,PASS,10,0,10,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220668,NC_045512.2,5924,G,A,PASS,10,0,10,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220668,NC_045512.2,76,T,A,PASS,18,6,12,0.67,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220668,NC_045512.2,78,T,G,PASS,18,6,12,0.67,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220668,NC_045512.2,7984,T,C,PASS,85,0,85,1.0,orf1ab,synonymous_variant,c.7719T>C,p.Asp2573Asp,p.D2573D,ivar,Unassigned +220668,NC_045512.2,8393,G,A,PASS,1330,2,1325,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220669,NC_045512.2,10449,C,A,PASS,19,0,19,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220669,NC_045512.2,11282,AGTTTGTCTG,A,PASS,35,35,33,0.94,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220669,NC_045512.2,11537,A,G,PASS,38,0,38,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220669,NC_045512.2,13195,T,C,PASS,1499,4,1495,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220669,NC_045512.2,14408,C,T,PASS,27,0,27,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220669,NC_045512.2,14466,T,C,PASS,28,20,8,0.29,orf1ab,missense_variant,c.14201T>C,p.Phe4734Ser,p.F4734S,ivar,Unassigned +220669,NC_045512.2,14533,A,G,ft,16,12,4,0.25,orf1ab,synonymous_variant,c.14268A>G,p.Leu4756Leu,p.L4756L,ivar,Unassigned +220669,NC_045512.2,15572,A,G,PASS,2032,731,1301,0.64,orf1ab,missense_variant,c.15307A>G,p.Met5103Val,p.M5103V,ivar,Unassigned +220669,NC_045512.2,21762,C,T,PASS,37,0,37,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220669,NC_045512.2,21764,ATACATG,A,PASS,38,37,29,0.76,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220669,NC_045512.2,21846,C,T,PASS,45,0,45,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220669,NC_045512.2,22578,G,A,PASS,12,0,12,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,Unassigned +220669,NC_045512.2,23403,A,G,PASS,1002,0,1002,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220669,NC_045512.2,23525,C,T,PASS,1030,4,1026,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220669,NC_045512.2,23599,T,G,PASS,490,0,488,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220669,NC_045512.2,23604,C,A,PASS,473,0,471,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220669,NC_045512.2,23948,G,T,PASS,113,0,113,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220669,NC_045512.2,24130,C,A,PASS,208,0,204,0.98,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220669,NC_045512.2,24424,A,T,PASS,42,0,40,0.95,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220669,NC_045512.2,24469,T,A,PASS,239,0,239,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220669,NC_045512.2,24503,C,T,PASS,281,6,275,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220669,NC_045512.2,25000,C,T,PASS,27,0,27,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220669,NC_045512.2,25584,C,T,PASS,26,0,26,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220669,NC_045512.2,26270,C,T,PASS,1060,2,1056,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220669,NC_045512.2,26530,A,G,PASS,516,0,516,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220669,NC_045512.2,26577,C,G,PASS,508,1,505,0.99,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220669,NC_045512.2,26709,G,A,PASS,474,1,472,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220669,NC_045512.2,27259,A,C,PASS,247,0,247,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220669,NC_045512.2,27807,C,T,PASS,93,0,92,0.99,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220669,NC_045512.2,28271,A,T,PASS,1304,1,1302,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220669,NC_045512.2,28311,C,T,PASS,1395,0,1393,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220669,NC_045512.2,2832,A,G,PASS,11,0,11,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220669,NC_045512.2,28361,GGAGAACGCA,G,PASS,1092,1088,734,0.67,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220669,NC_045512.2,28363,A,T,PASS,16,10,6,0.38,N,synonymous_variant,c.90A>T,p.Gly30Gly,p.G30G,ivar,Unassigned +220669,NC_045512.2,28881,GG,AA,PASS,10404,75,10319,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220669,NC_045512.2,28883,G,C,PASS,10380,2,10364,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220669,NC_045512.2,5672,C,T,PASS,37,2,35,0.95,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220669,NC_045512.2,5924,G,A,PASS,19,0,19,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220669,NC_045512.2,76,T,A,PASS,44,7,37,0.84,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220669,NC_045512.2,8393,G,A,PASS,2083,5,2078,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220670,NC_045512.2,10449,C,A,PASS,39,0,38,0.97,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220670,NC_045512.2,11282,AGTTTGTCTG,A,PASS,101,101,83,0.82,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220670,NC_045512.2,11537,A,G,PASS,81,0,81,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220670,NC_045512.2,13195,T,C,PASS,4671,5,4664,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220670,NC_045512.2,14408,C,T,PASS,72,0,72,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220670,NC_045512.2,21762,C,T,PASS,121,0,121,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220670,NC_045512.2,21764,ATACATG,A,PASS,121,121,114,0.94,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220670,NC_045512.2,21846,C,T,PASS,117,0,117,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220670,NC_045512.2,22673,TC,CT,PASS,11,0,11,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.17 +220670,NC_045512.2,22679,T,C,PASS,11,0,11,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220670,NC_045512.2,22686,C,T,PASS,11,0,11,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220670,NC_045512.2,23202,C,A,PASS,14,0,14,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220670,NC_045512.2,23403,A,G,PASS,2094,0,2093,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220670,NC_045512.2,23525,C,T,PASS,2060,6,2053,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220670,NC_045512.2,23599,T,G,PASS,847,0,845,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220670,NC_045512.2,23604,C,A,PASS,817,0,815,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220670,NC_045512.2,23854,C,A,PASS,25,0,25,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220670,NC_045512.2,23948,G,T,PASS,328,0,327,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220670,NC_045512.2,24130,C,A,PASS,478,0,477,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220670,NC_045512.2,24424,A,T,PASS,93,0,93,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220670,NC_045512.2,24469,T,A,PASS,520,0,518,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220670,NC_045512.2,24503,C,T,PASS,628,4,624,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220670,NC_045512.2,25000,C,T,PASS,33,0,33,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220670,NC_045512.2,25584,C,T,PASS,58,0,58,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220670,NC_045512.2,26270,C,T,PASS,372,2,370,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220670,NC_045512.2,26530,A,G,PASS,296,0,296,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220670,NC_045512.2,26577,C,G,PASS,354,0,354,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220670,NC_045512.2,26709,G,A,PASS,361,0,361,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220670,NC_045512.2,27259,A,C,PASS,268,0,268,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220670,NC_045512.2,27632,G,A,PASS,42,28,14,0.33,ORF7a,missense_variant,c.239G>A,p.Arg80Lys,p.R80K,ivar,BA.1.17 +220670,NC_045512.2,27807,C,T,PASS,65,0,65,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220670,NC_045512.2,28253,CA,C,PASS,482,480,479,0.99,ORF8,frameshift_variant,c.361delA,p.Ile121fs,p.I121fs,ivar,BA.1.17 +220670,NC_045512.2,28271,A,T,PASS,569,0,566,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220670,NC_045512.2,28311,C,T,PASS,572,4,568,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220670,NC_045512.2,2832,A,G,PASS,78,0,78,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220670,NC_045512.2,28361,GGAGAACGCA,G,PASS,386,382,243,0.63,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220670,NC_045512.2,28881,GG,AA,PASS,7323,72,7246,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220670,NC_045512.2,28883,G,C,PASS,7288,2,7274,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220670,NC_045512.2,29399,G,T,PASS,4164,2,4135,0.99,N,missense_variant,c.1126G>T,p.Ala376Ser,p.A376S,ivar,BA.1.17 +220670,NC_045512.2,3037,C,T,PASS,14,0,14,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220670,NC_045512.2,5672,C,T,PASS,57,2,55,0.96,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220670,NC_045512.2,5924,G,A,PASS,19,0,19,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220670,NC_045512.2,8393,G,A,PASS,3256,13,3242,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220670,NC_045512.2,8652,T,C,PASS,2794,8,2786,1.0,orf1ab,missense_variant,c.8387T>C,p.Met2796Thr,p.M2796T,ivar,BA.1.17 +220671,NC_045512.2,10029,C,T,PASS,28,0,28,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,BA.1.17 +220671,NC_045512.2,10449,C,A,PASS,72,0,72,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.17 +220671,NC_045512.2,11282,AGTTTGTCTG,A,PASS,205,204,183,0.89,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.17 +220671,NC_045512.2,11537,A,G,PASS,98,0,98,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.17 +220671,NC_045512.2,12008,C,T,PASS,232,1,230,0.99,orf1ab,missense_variant,c.11743C>T,p.Leu3915Phe,p.L3915F,ivar,BA.1.17 +220671,NC_045512.2,13195,T,C,PASS,3794,10,3783,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.17 +220671,NC_045512.2,14408,C,T,PASS,62,1,61,0.98,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.17 +220671,NC_045512.2,18163,A,G,PASS,15,0,15,1.0,orf1ab,synonymous_variant,c.17898A>G,p.Thr5966Thr,p.T5966T,ivar,BA.1.17 +220671,NC_045512.2,21762,C,T,PASS,95,0,95,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.17 +220671,NC_045512.2,21764,ATACATG,A,PASS,97,95,87,0.9,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.17 +220671,NC_045512.2,21846,C,T,PASS,108,0,108,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.17 +220671,NC_045512.2,22578,G,A,PASS,23,0,23,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.17 +220671,NC_045512.2,22673,TC,CT,PASS,12,0,12,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.17 +220671,NC_045512.2,22679,T,C,PASS,20,0,20,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.17 +220671,NC_045512.2,22686,C,T,PASS,20,0,20,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.17 +220671,NC_045512.2,23202,C,A,PASS,22,0,20,0.91,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.17 +220671,NC_045512.2,23403,A,G,PASS,2394,0,2394,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.17 +220671,NC_045512.2,23525,C,T,PASS,2316,2,2309,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.17 +220671,NC_045512.2,23599,T,G,PASS,848,0,848,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.17 +220671,NC_045512.2,23604,C,A,PASS,798,0,798,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.17 +220671,NC_045512.2,23854,C,A,PASS,59,0,59,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.17 +220671,NC_045512.2,23948,G,T,PASS,554,0,553,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.17 +220671,NC_045512.2,24130,C,A,PASS,893,0,890,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.17 +220671,NC_045512.2,24424,A,T,PASS,239,0,239,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.17 +220671,NC_045512.2,24469,T,A,PASS,691,0,687,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.17 +220671,NC_045512.2,24503,C,T,PASS,756,12,744,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.17 +220671,NC_045512.2,25000,C,T,PASS,56,0,56,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.17 +220671,NC_045512.2,25584,C,T,PASS,115,1,113,0.98,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.17 +220671,NC_045512.2,26270,C,T,PASS,1039,7,1032,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.17 +220671,NC_045512.2,26530,A,G,PASS,611,1,610,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.17 +220671,NC_045512.2,26577,C,G,PASS,638,0,637,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.17 +220671,NC_045512.2,26709,G,A,PASS,596,5,588,0.99,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.17 +220671,NC_045512.2,27259,A,C,PASS,630,0,630,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.17 +220671,NC_045512.2,27670,G,T,PASS,211,0,211,1.0,ORF7a,missense_variant,c.277G>T,p.Val93Phe,p.V93F,ivar,BA.1.17 +220671,NC_045512.2,27807,C,T,PASS,253,4,248,0.98,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.17 +220671,NC_045512.2,28271,A,T,PASS,1608,3,1605,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.17 +220671,NC_045512.2,28311,C,T,PASS,1682,3,1673,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.17 +220671,NC_045512.2,2832,A,G,PASS,92,0,92,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.17 +220671,NC_045512.2,28361,GGAGAACGCA,G,PASS,1336,1327,801,0.6,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.17 +220671,NC_045512.2,28881,GG,AA,PASS,2721,26,2694,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.17 +220671,NC_045512.2,28883,G,C,PASS,2714,2,2706,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.17 +220671,NC_045512.2,3037,C,T,PASS,31,1,30,0.97,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.17 +220671,NC_045512.2,5672,C,T,PASS,183,0,183,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,BA.1.17 +220671,NC_045512.2,5924,G,A,PASS,61,0,61,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,BA.1.17 +220671,NC_045512.2,76,T,A,PASS,44,27,17,0.39,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,BA.1.17 +220671,NC_045512.2,78,T,G,PASS,44,27,17,0.39,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,BA.1.17 +220671,NC_045512.2,8393,G,A,PASS,3239,22,3215,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.17 +220672,NC_045512.2,10029,C,T,PASS,15,0,15,1.0,orf1ab,missense_variant,c.9764C>T,p.Thr3255Ile,p.T3255I,ivar,Unassigned +220672,NC_045512.2,11282,AGTTTGTCTG,A,PASS,48,48,44,0.92,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220672,NC_045512.2,11537,A,G,PASS,64,0,64,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220672,NC_045512.2,13195,T,C,PASS,1572,4,1568,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220672,NC_045512.2,14408,C,T,PASS,61,0,61,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220672,NC_045512.2,20776,A,G,PASS,29,0,29,1.0,orf1ab,synonymous_variant,c.20511A>G,p.Ala6837Ala,p.A6837A,ivar,Unassigned +220672,NC_045512.2,21762,C,T,PASS,41,0,41,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220672,NC_045512.2,21764,ATACATG,A,PASS,41,41,37,0.9,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220672,NC_045512.2,21846,C,T,PASS,53,0,53,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220672,NC_045512.2,21,C,T,PASS,10,0,10,1.0,orf1ab,upstream_gene_variant,c.-245C>T,.,.,ivar,Unassigned +220672,NC_045512.2,23323,T,C,PASS,173,2,171,0.99,S,synonymous_variant,c.1761T>C,p.Ile587Ile,p.I587I,ivar,Unassigned +220672,NC_045512.2,23403,A,G,PASS,197,0,197,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220672,NC_045512.2,23525,C,T,PASS,191,0,191,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220672,NC_045512.2,23599,T,G,PASS,81,0,81,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220672,NC_045512.2,23604,C,A,PASS,79,0,79,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220672,NC_045512.2,23948,G,T,PASS,46,0,46,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220672,NC_045512.2,24130,C,A,PASS,60,0,60,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220672,NC_045512.2,24424,A,T,PASS,82,0,82,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220672,NC_045512.2,24469,T,A,PASS,575,2,571,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220672,NC_045512.2,24503,C,T,PASS,689,5,684,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220672,NC_045512.2,25000,C,T,PASS,31,0,31,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220672,NC_045512.2,25584,C,T,PASS,27,2,25,0.93,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220672,NC_045512.2,26270,C,T,PASS,1197,0,1197,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220672,NC_045512.2,26530,A,G,PASS,248,0,248,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220672,NC_045512.2,26577,C,G,PASS,225,0,225,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220672,NC_045512.2,26709,G,A,PASS,228,0,228,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220672,NC_045512.2,27259,A,C,PASS,103,0,103,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220672,NC_045512.2,27807,C,T,PASS,18,0,18,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220672,NC_045512.2,28271,A,T,PASS,1324,4,1318,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220672,NC_045512.2,28311,C,T,PASS,1356,0,1352,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220672,NC_045512.2,2832,A,G,PASS,19,0,19,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220672,NC_045512.2,28361,GGAGAACGCA,G,PASS,932,929,481,0.52,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220672,NC_045512.2,28881,GG,AA,PASS,9896,69,9823,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220672,NC_045512.2,28883,G,C,PASS,9878,3,9869,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220672,NC_045512.2,3800,G,A,PASS,80,2,78,0.98,orf1ab,missense_variant,c.3535G>A,p.Asp1179Asn,p.D1179N,ivar,Unassigned +220672,NC_045512.2,514,TGTTATG,T,PASS,11985,11766,9796,0.82,orf1ab,conservative_inframe_deletion,c.253_258delATGGTT,p.Met85_Val86del,p.M85_V86del,ivar,Unassigned +220672,NC_045512.2,520,G,C,PASS,87,44,43,0.49,orf1ab,missense_variant,c.255G>C,p.Met85Ile,p.M85I,ivar,Unassigned +220672,NC_045512.2,76,T,A,PASS,11,3,8,0.73,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220672,NC_045512.2,78,T,G,PASS,11,3,8,0.73,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220672,NC_045512.2,8393,G,A,PASS,544,2,541,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220675,NC_045512.2,11537,A,G,PASS,17,0,17,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220675,NC_045512.2,13195,T,C,PASS,553,0,553,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220675,NC_045512.2,13908,T,C,ft,10,6,4,0.4,orf1ab,missense_variant,c.13643T>C,p.Ile4548Thr,p.I4548T,ivar,Unassigned +220675,NC_045512.2,14408,C,T,PASS,13,0,13,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220675,NC_045512.2,21762,C,T,PASS,16,0,16,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220675,NC_045512.2,21764,ATACATG,A,PASS,16,16,16,1.0,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220675,NC_045512.2,21846,C,T,PASS,30,0,30,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220675,NC_045512.2,23403,A,G,PASS,214,0,214,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220675,NC_045512.2,23525,C,T,PASS,221,3,218,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220675,NC_045512.2,23599,T,G,PASS,105,0,105,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220675,NC_045512.2,23604,C,A,PASS,103,0,103,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220675,NC_045512.2,23948,G,T,PASS,25,0,25,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220675,NC_045512.2,24130,C,A,PASS,50,0,50,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220675,NC_045512.2,24424,A,T,PASS,24,0,24,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220675,NC_045512.2,24469,T,A,PASS,131,1,130,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220675,NC_045512.2,24503,C,T,PASS,140,7,133,0.95,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220675,NC_045512.2,25000,C,T,PASS,12,0,12,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220675,NC_045512.2,25057,T,C,ft,13,8,5,0.38,S,synonymous_variant,c.3495T>C,p.Asp1165Asp,p.D1165D,ivar,Unassigned +220675,NC_045512.2,25584,C,T,PASS,24,2,22,0.92,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220675,NC_045512.2,26270,C,T,PASS,221,0,221,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220675,NC_045512.2,26530,A,G,PASS,72,0,72,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220675,NC_045512.2,26577,C,G,PASS,67,0,67,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220675,NC_045512.2,26709,G,A,PASS,75,2,73,0.97,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220675,NC_045512.2,27259,A,C,PASS,48,0,48,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220675,NC_045512.2,28271,A,T,PASS,187,0,187,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220675,NC_045512.2,28311,C,T,PASS,213,2,211,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220675,NC_045512.2,28361,GGAGAACGCA,G,PASS,185,185,129,0.7,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220675,NC_045512.2,28881,GG,AA,PASS,12043,60,11972,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220675,NC_045512.2,28883,G,C,PASS,12008,2,11991,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220675,NC_045512.2,5672,C,T,PASS,40,2,38,0.95,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220675,NC_045512.2,8393,G,A,PASS,307,0,307,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220675,NC_045512.2,8652,T,C,PASS,198,0,198,1.0,orf1ab,missense_variant,c.8387T>C,p.Met2796Thr,p.M2796T,ivar,Unassigned +220677,NC_045512.2,10449,C,A,PASS,19,0,19,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220677,NC_045512.2,10947,G,A,ft,10,7,3,0.3,orf1ab,missense_variant,c.10682G>A,p.Arg3561Lys,p.R3561K,ivar,Unassigned +220677,NC_045512.2,11282,AGTTTGTCTG,A,PASS,27,27,25,0.93,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220677,NC_045512.2,11537,A,G,PASS,43,0,43,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220677,NC_045512.2,12053,C,T,PASS,154,0,154,1.0,orf1ab,missense_variant,c.11788C>T,p.Leu3930Phe,p.L3930F,ivar,Unassigned +220677,NC_045512.2,13195,T,C,PASS,2302,4,2298,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220677,NC_045512.2,14408,C,T,PASS,27,0,27,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220677,NC_045512.2,21762,C,T,PASS,44,0,44,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220677,NC_045512.2,21764,ATACATG,A,PASS,44,44,39,0.89,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220677,NC_045512.2,21846,C,T,PASS,43,0,43,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220677,NC_045512.2,23403,A,G,PASS,1670,8,1662,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220677,NC_045512.2,23525,C,T,PASS,1615,3,1609,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220677,NC_045512.2,23599,T,G,PASS,575,0,575,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220677,NC_045512.2,23604,C,A,PASS,558,0,551,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220677,NC_045512.2,23948,G,T,PASS,147,0,147,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220677,NC_045512.2,24130,C,A,PASS,220,0,218,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220677,NC_045512.2,24424,A,T,PASS,24,0,24,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220677,NC_045512.2,24469,T,A,PASS,305,0,302,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220677,NC_045512.2,24503,C,T,PASS,348,7,341,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220677,NC_045512.2,25000,C,T,PASS,16,0,16,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220677,NC_045512.2,25032,A,G,ft,15,11,4,0.27,S,missense_variant,c.3470A>G,p.Lys1157Arg,p.K1157R,ivar,Unassigned +220677,NC_045512.2,25584,C,T,PASS,26,0,26,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220677,NC_045512.2,26270,C,T,PASS,328,2,326,0.99,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220677,NC_045512.2,26530,A,G,PASS,216,0,216,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220677,NC_045512.2,26577,C,G,PASS,231,0,230,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220677,NC_045512.2,26612,A,G,PASS,182,0,182,1.0,M,synonymous_variant,c.90A>G,p.Thr30Thr,p.T30T,ivar,Unassigned +220677,NC_045512.2,26709,G,A,PASS,223,0,223,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220677,NC_045512.2,27259,A,C,PASS,134,0,134,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220677,NC_045512.2,27670,G,T,PASS,60,0,60,1.0,ORF7a,missense_variant,c.277G>T,p.Val93Phe,p.V93F,ivar,Unassigned +220677,NC_045512.2,27807,C,T,PASS,87,0,87,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220677,NC_045512.2,28271,A,T,PASS,979,3,974,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220677,NC_045512.2,28311,C,T,PASS,971,0,967,1.0,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220677,NC_045512.2,2832,A,G,PASS,10,0,10,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220677,NC_045512.2,28361,GGAGAACGCA,G,PASS,710,708,439,0.62,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220677,NC_045512.2,28512,C,T,PASS,190,135,50,0.26,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,Unassigned +220677,NC_045512.2,28881,GG,AA,PASS,6996,77,6913,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220677,NC_045512.2,28883,G,C,PASS,6957,1,6945,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220677,NC_045512.2,3037,C,T,PASS,21,0,21,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220677,NC_045512.2,5672,C,T,PASS,18,0,18,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220677,NC_045512.2,5924,G,A,PASS,13,0,13,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220677,NC_045512.2,8393,G,A,PASS,2925,8,2915,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220678,NC_045512.2,10449,C,A,PASS,42,0,42,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1.1 +220678,NC_045512.2,11282,AGTTTGTCTG,A,PASS,99,99,86,0.87,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1.1 +220678,NC_045512.2,11537,A,G,PASS,164,0,164,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1.1 +220678,NC_045512.2,13195,T,C,PASS,5198,9,5188,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1.1 +220678,NC_045512.2,14408,C,T,PASS,150,0,150,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1.1 +220678,NC_045512.2,16064,A,G,PASS,125,0,125,1.0,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,BA.1.1.1 +220678,NC_045512.2,21762,C,T,PASS,162,0,162,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1.1 +220678,NC_045512.2,21764,ATACATG,A,PASS,164,160,140,0.85,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1.1 +220678,NC_045512.2,21846,C,T,PASS,187,0,187,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1.1 +220678,NC_045512.2,22578,G,A,PASS,14,0,14,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.1.1 +220678,NC_045512.2,22599,G,A,PASS,16,0,16,1.0,S,missense_variant,c.1037G>A,p.Arg346Lys,p.R346K,ivar,BA.1.1.1 +220678,NC_045512.2,22673,TC,CT,PASS,14,0,14,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.1.1 +220678,NC_045512.2,22679,T,C,PASS,16,0,16,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.1.1 +220678,NC_045512.2,22686,C,T,PASS,15,0,15,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.1.1 +220678,NC_045512.2,23202,C,A,PASS,21,0,21,1.0,S,missense_variant,c.1640C>A,p.Thr547Lys,p.T547K,ivar,BA.1.1.1 +220678,NC_045512.2,23403,A,G,PASS,2029,0,2029,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1.1 +220678,NC_045512.2,23525,C,T,PASS,1991,10,1981,0.99,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1.1 +220678,NC_045512.2,23599,T,G,PASS,763,2,761,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1.1 +220678,NC_045512.2,23604,C,A,PASS,732,0,724,0.99,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1.1 +220678,NC_045512.2,23854,C,A,PASS,21,0,21,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1.1 +220678,NC_045512.2,23948,G,T,PASS,280,0,278,0.99,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1.1 +220678,NC_045512.2,24130,C,A,PASS,345,0,343,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1.1 +220678,NC_045512.2,24424,A,T,PASS,95,0,95,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1.1 +220678,NC_045512.2,24469,T,A,PASS,708,0,708,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1.1 +220678,NC_045512.2,24503,C,T,PASS,855,8,845,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1.1 +220678,NC_045512.2,25000,C,T,PASS,37,0,37,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1.1 +220678,NC_045512.2,25584,C,T,PASS,45,0,45,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1.1 +220678,NC_045512.2,26270,C,T,PASS,305,0,305,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1.1 +220678,NC_045512.2,26530,A,G,PASS,272,0,272,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1.1 +220678,NC_045512.2,26577,C,G,PASS,290,0,290,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1.1 +220678,NC_045512.2,26709,G,A,PASS,255,4,251,0.98,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1.1 +220678,NC_045512.2,27259,A,C,PASS,129,0,129,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1.1 +220678,NC_045512.2,27807,C,T,PASS,51,0,51,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1.1 +220678,NC_045512.2,28271,A,T,PASS,1166,5,1159,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1.1 +220678,NC_045512.2,28311,C,T,PASS,1184,7,1171,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1.1 +220678,NC_045512.2,2832,A,G,PASS,89,0,89,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1.1 +220678,NC_045512.2,28361,GGAGAACGCA,G,PASS,910,906,488,0.54,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1.1 +220678,NC_045512.2,28881,GG,AA,PASS,5630,77,5551,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1.1 +220678,NC_045512.2,28883,G,C,PASS,5585,3,5569,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1.1 +220678,NC_045512.2,3037,C,T,PASS,18,0,18,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1.1 +220678,NC_045512.2,8014,T,C,PASS,492,17,475,0.97,orf1ab,synonymous_variant,c.7749T>C,p.Ser2583Ser,p.S2583S,ivar,BA.1.1.1 +220678,NC_045512.2,8393,G,A,PASS,2422,5,2413,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1.1 +220679,NC_045512.2,10449,C,A,PASS,14,0,14,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220679,NC_045512.2,11282,AGTTTGTCTG,A,PASS,72,69,59,0.82,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220679,NC_045512.2,11537,A,G,PASS,42,0,42,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220679,NC_045512.2,13195,T,C,PASS,2959,4,2953,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220679,NC_045512.2,14408,C,T,PASS,35,0,35,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220679,NC_045512.2,19374,C,T,PASS,103,0,103,1.0,orf1ab,missense_variant,c.19109C>T,p.Ser6370Phe,p.S6370F,ivar,Unassigned +220679,NC_045512.2,20743,A,C,PASS,1266,0,1263,1.0,orf1ab,missense_variant,c.20478A>C,p.Lys6826Asn,p.K6826N,ivar,Unassigned +220679,NC_045512.2,21274,T,C,PASS,28,0,28,1.0,orf1ab,synonymous_variant,c.21009T>C,p.Phe7003Phe,p.F7003F,ivar,Unassigned +220679,NC_045512.2,21762,C,T,PASS,72,0,72,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220679,NC_045512.2,21764,ATACATG,A,PASS,72,72,63,0.88,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220679,NC_045512.2,21846,C,T,PASS,74,0,74,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220679,NC_045512.2,21,C,T,PASS,10,0,10,1.0,orf1ab,upstream_gene_variant,c.-245C>T,.,.,ivar,Unassigned +220679,NC_045512.2,23403,A,G,PASS,1977,2,1975,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220679,NC_045512.2,23525,C,T,PASS,1792,2,1789,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220679,NC_045512.2,23599,T,G,PASS,744,0,744,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220679,NC_045512.2,23604,C,A,PASS,722,0,719,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220679,NC_045512.2,23854,C,A,PASS,19,0,19,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220679,NC_045512.2,23948,G,T,PASS,98,0,96,0.98,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220679,NC_045512.2,24130,C,A,PASS,142,0,141,0.99,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220679,NC_045512.2,24424,A,T,PASS,60,0,60,1.0,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220679,NC_045512.2,24469,T,A,PASS,275,0,275,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220679,NC_045512.2,24503,C,T,PASS,350,4,346,0.99,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220679,NC_045512.2,25000,C,T,PASS,26,0,26,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220679,NC_045512.2,25584,C,T,PASS,71,0,71,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220679,NC_045512.2,2610,C,A,ft,14,10,4,0.29,orf1ab,missense_variant,c.2345C>A,p.Pro782Gln,p.P782Q,ivar,Unassigned +220679,NC_045512.2,26270,C,T,PASS,438,1,437,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220679,NC_045512.2,26530,A,G,PASS,320,0,320,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220679,NC_045512.2,26577,C,G,PASS,362,0,362,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220679,NC_045512.2,26709,G,A,PASS,358,0,358,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220679,NC_045512.2,27259,A,C,PASS,167,0,167,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220679,NC_045512.2,27807,C,T,PASS,55,0,55,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220679,NC_045512.2,28271,A,T,PASS,559,2,557,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220679,NC_045512.2,28311,C,T,PASS,631,3,626,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220679,NC_045512.2,2832,A,G,PASS,20,0,20,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220679,NC_045512.2,28361,GGAGAACGCA,G,PASS,514,508,361,0.7,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220679,NC_045512.2,28881,GG,AA,PASS,4183,51,4127,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220679,NC_045512.2,28883,G,C,PASS,4145,1,4137,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220679,NC_045512.2,3037,C,T,PASS,18,0,18,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,Unassigned +220679,NC_045512.2,5672,C,T,PASS,40,0,40,1.0,orf1ab,missense_variant,c.5407C>T,p.Pro1803Ser,p.P1803S,ivar,Unassigned +220679,NC_045512.2,5924,G,A,PASS,17,0,17,1.0,orf1ab,missense_variant,c.5659G>A,p.Val1887Ile,p.V1887I,ivar,Unassigned +220679,NC_045512.2,76,T,A,PASS,26,16,8,0.31,orf1ab,upstream_gene_variant,c.-190T>A,.,.,ivar,Unassigned +220679,NC_045512.2,78,T,G,PASS,26,18,8,0.31,orf1ab,upstream_gene_variant,c.-188T>G,.,.,ivar,Unassigned +220679,NC_045512.2,8393,G,A,PASS,2826,4,2818,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220680,NC_045512.2,11537,A,G,PASS,19,0,19,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220680,NC_045512.2,12368,A,G,ft,17,12,5,0.29,orf1ab,missense_variant,c.12103A>G,p.Thr4035Ala,p.T4035A,ivar,Unassigned +220680,NC_045512.2,12749,G,T,PASS,36,21,15,0.42,orf1ab,missense_variant,c.12484G>T,p.Ala4162Ser,p.A4162S,ivar,Unassigned +220680,NC_045512.2,13195,T,C,PASS,665,2,663,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220680,NC_045512.2,21762,C,T,PASS,14,0,14,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220680,NC_045512.2,21764,ATACATG,A,ft,14,14,8,0.57,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220680,NC_045512.2,21846,C,T,PASS,18,0,18,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220680,NC_045512.2,23403,A,G,PASS,246,0,246,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220680,NC_045512.2,23525,C,T,PASS,216,0,216,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220680,NC_045512.2,23599,T,G,PASS,95,0,95,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220680,NC_045512.2,23604,C,A,PASS,90,0,90,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220680,NC_045512.2,23948,G,T,PASS,13,0,13,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220680,NC_045512.2,24130,C,A,PASS,22,2,20,0.91,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220680,NC_045512.2,24469,T,A,PASS,67,0,65,0.97,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220680,NC_045512.2,24503,C,T,PASS,76,0,76,1.0,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220680,NC_045512.2,26270,C,T,PASS,259,0,259,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220680,NC_045512.2,26530,A,G,PASS,39,0,39,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220680,NC_045512.2,26577,C,G,PASS,46,0,46,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220680,NC_045512.2,26709,G,A,PASS,38,0,38,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220680,NC_045512.2,27259,A,C,PASS,33,0,33,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220680,NC_045512.2,28253,CA,C,PASS,575,575,572,0.99,ORF8,frameshift_variant,c.361delA,p.Ile121fs,p.I121fs,ivar,Unassigned +220680,NC_045512.2,28271,A,T,PASS,728,2,724,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220680,NC_045512.2,28311,C,T,PASS,721,2,713,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220680,NC_045512.2,28361,GGAGAACGCA,G,PASS,501,498,352,0.7,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220680,NC_045512.2,28881,GG,AA,PASS,4386,36,4344,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220680,NC_045512.2,28883,G,C,PASS,4380,2,4371,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220680,NC_045512.2,29399,G,T,PASS,2419,4,2405,0.99,N,missense_variant,c.1126G>T,p.Ala376Ser,p.A376S,ivar,Unassigned +220680,NC_045512.2,4221,A,G,ft,16,12,4,0.25,orf1ab,missense_variant,c.3956A>G,p.Lys1319Arg,p.K1319R,ivar,Unassigned +220680,NC_045512.2,8256,A,G,PASS,77,53,24,0.31,orf1ab,missense_variant,c.7991A>G,p.Glu2664Gly,p.E2664G,ivar,Unassigned +220680,NC_045512.2,8393,G,A,PASS,606,2,604,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220680,NC_045512.2,8652,T,C,PASS,427,1,426,1.0,orf1ab,missense_variant,c.8387T>C,p.Met2796Thr,p.M2796T,ivar,Unassigned +220684,NC_045512.2,10449,C,A,PASS,23,0,23,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,Unassigned +220684,NC_045512.2,11282,AGTTTGTCTG,A,PASS,71,71,67,0.94,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,Unassigned +220684,NC_045512.2,11537,A,G,PASS,25,0,25,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,Unassigned +220684,NC_045512.2,13195,T,C,PASS,4647,1,4644,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,Unassigned +220684,NC_045512.2,14408,C,T,PASS,61,3,58,0.95,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,Unassigned +220684,NC_045512.2,16064,A,G,PASS,80,2,78,0.98,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,Unassigned +220684,NC_045512.2,19937,A,G,ft,14,10,4,0.29,orf1ab,missense_variant,c.19672A>G,p.Thr6558Ala,p.T6558A,ivar,Unassigned +220684,NC_045512.2,21458,T,C,PASS,263,0,263,1.0,orf1ab,missense_variant,c.21193T>C,p.Ser7065Pro,p.S7065P,ivar,Unassigned +220684,NC_045512.2,21762,C,T,PASS,70,0,70,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,Unassigned +220684,NC_045512.2,21764,ATACATG,A,PASS,70,69,63,0.9,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,Unassigned +220684,NC_045512.2,21846,C,T,PASS,72,0,72,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,Unassigned +220684,NC_045512.2,23403,A,G,PASS,1549,3,1546,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,Unassigned +220684,NC_045512.2,23525,C,T,PASS,1462,0,1461,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,Unassigned +220684,NC_045512.2,23599,T,G,PASS,609,0,609,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,Unassigned +220684,NC_045512.2,23604,C,A,PASS,592,0,592,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,Unassigned +220684,NC_045512.2,23854,C,A,PASS,23,0,23,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,Unassigned +220684,NC_045512.2,23948,G,T,PASS,255,0,255,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,Unassigned +220684,NC_045512.2,24130,C,A,PASS,379,0,379,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,Unassigned +220684,NC_045512.2,24424,A,T,PASS,47,0,46,0.98,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,Unassigned +220684,NC_045512.2,24469,T,A,PASS,463,0,460,0.99,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,Unassigned +220684,NC_045512.2,24503,C,T,PASS,595,9,586,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,Unassigned +220684,NC_045512.2,25000,C,T,PASS,14,0,14,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,Unassigned +220684,NC_045512.2,25584,C,T,PASS,65,0,65,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,Unassigned +220684,NC_045512.2,26270,C,T,PASS,205,0,205,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,Unassigned +220684,NC_045512.2,26530,A,G,PASS,60,0,60,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,Unassigned +220684,NC_045512.2,26577,C,G,PASS,68,0,68,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,Unassigned +220684,NC_045512.2,26709,G,A,PASS,70,0,70,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,Unassigned +220684,NC_045512.2,27259,A,C,PASS,120,0,119,0.99,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,Unassigned +220684,NC_045512.2,27807,C,T,PASS,30,0,30,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,Unassigned +220684,NC_045512.2,28271,A,T,PASS,400,0,399,1.0,N,upstream_gene_variant,c.-3A>T,.,.,ivar,Unassigned +220684,NC_045512.2,28311,C,T,PASS,415,1,412,0.99,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,Unassigned +220684,NC_045512.2,2832,A,G,PASS,133,0,133,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,Unassigned +220684,NC_045512.2,28361,GGAGAACGCA,G,PASS,319,317,227,0.71,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,Unassigned +220684,NC_045512.2,28881,GG,AA,PASS,5519,59,5456,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,Unassigned +220684,NC_045512.2,28883,G,C,PASS,5487,2,5473,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,Unassigned +220684,NC_045512.2,8393,G,A,PASS,2672,20,2646,0.99,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,Unassigned +220685,NC_045512.2,10449,C,A,PASS,20,0,20,1.0,orf1ab,missense_variant,c.10184C>A,p.Pro3395His,p.P3395H,ivar,BA.1.1.1 +220685,NC_045512.2,11282,AGTTTGTCTG,A,PASS,110,109,100,0.91,orf1ab,disruptive_inframe_deletion,c.11022_11030delGTCTGGTTT,p.Leu3674_Gly3676del,p.L3674_G3676del,ivar,BA.1.1.1 +220685,NC_045512.2,11537,A,G,PASS,62,0,62,1.0,orf1ab,missense_variant,c.11272A>G,p.Ile3758Val,p.I3758V,ivar,BA.1.1.1 +220685,NC_045512.2,13195,T,C,PASS,3349,12,3337,1.0,orf1ab,synonymous_variant,c.12930T>C,p.Val4310Val,p.V4310V,ivar,BA.1.1.1 +220685,NC_045512.2,14408,C,T,PASS,64,0,64,1.0,orf1ab,synonymous_variant,c.14143C>T,p.Leu4715Leu,p.L4715L,ivar,BA.1.1.1 +220685,NC_045512.2,16064,A,G,PASS,72,2,70,0.97,orf1ab,missense_variant,c.15799A>G,p.Arg5267Gly,p.R5267G,ivar,BA.1.1.1 +220685,NC_045512.2,21762,C,T,PASS,47,0,47,1.0,S,missense_variant,c.200C>T,p.Ala67Val,p.A67V,ivar,BA.1.1.1 +220685,NC_045512.2,21764,ATACATG,A,PASS,47,47,43,0.91,S,disruptive_inframe_deletion,c.204_209delACATGT,p.His69_Val70del,p.H69_V70del,ivar,BA.1.1.1 +220685,NC_045512.2,21846,C,T,PASS,42,0,42,1.0,S,missense_variant,c.284C>T,p.Thr95Ile,p.T95I,ivar,BA.1.1.1 +220685,NC_045512.2,22578,G,A,PASS,12,0,12,1.0,S,missense_variant,c.1016G>A,p.Gly339Asp,p.G339D,ivar,BA.1.1.1 +220685,NC_045512.2,22599,G,A,PASS,14,0,14,1.0,S,missense_variant,c.1037G>A,p.Arg346Lys,p.R346K,ivar,BA.1.1.1 +220685,NC_045512.2,22673,TC,CT,PASS,10,0,10,1.0,S,missense_variant,c.1111_1112delTCinsCT,p.Ser371Leu,p.S371L,ivar,BA.1.1.1 +220685,NC_045512.2,22679,T,C,PASS,14,0,14,1.0,S,missense_variant,c.1117T>C,p.Ser373Pro,p.S373P,ivar,BA.1.1.1 +220685,NC_045512.2,22686,C,T,PASS,14,0,14,1.0,S,missense_variant,c.1124C>T,p.Ser375Phe,p.S375F,ivar,BA.1.1.1 +220685,NC_045512.2,23403,A,G,PASS,1274,2,1272,1.0,S,missense_variant,c.1841A>G,p.Asp614Gly,p.D614G,ivar,BA.1.1.1 +220685,NC_045512.2,23525,C,T,PASS,1276,1,1275,1.0,S,missense_variant,c.1963C>T,p.His655Tyr,p.H655Y,ivar,BA.1.1.1 +220685,NC_045512.2,23599,T,G,PASS,519,0,519,1.0,S,missense_variant,c.2037T>G,p.Asn679Lys,p.N679K,ivar,BA.1.1.1 +220685,NC_045512.2,23604,C,A,PASS,510,0,508,1.0,S,missense_variant,c.2042C>A,p.Pro681His,p.P681H,ivar,BA.1.1.1 +220685,NC_045512.2,23854,C,A,PASS,29,0,29,1.0,S,missense_variant,c.2292C>A,p.Asn764Lys,p.N764K,ivar,BA.1.1.1 +220685,NC_045512.2,23948,G,T,PASS,169,0,169,1.0,S,missense_variant,c.2386G>T,p.Asp796Tyr,p.D796Y,ivar,BA.1.1.1 +220685,NC_045512.2,24130,C,A,PASS,171,0,171,1.0,S,missense_variant,c.2568C>A,p.Asn856Lys,p.N856K,ivar,BA.1.1.1 +220685,NC_045512.2,24424,A,T,PASS,101,3,98,0.97,S,missense_variant,c.2862A>T,p.Gln954His,p.Q954H,ivar,BA.1.1.1 +220685,NC_045512.2,24469,T,A,PASS,402,1,400,1.0,S,missense_variant,c.2907T>A,p.Asn969Lys,p.N969K,ivar,BA.1.1.1 +220685,NC_045512.2,24503,C,T,PASS,469,11,458,0.98,S,missense_variant,c.2941C>T,p.Leu981Phe,p.L981F,ivar,BA.1.1.1 +220685,NC_045512.2,25000,C,T,PASS,19,0,19,1.0,S,synonymous_variant,c.3438C>T,p.Asp1146Asp,p.D1146D,ivar,BA.1.1.1 +220685,NC_045512.2,25584,C,T,PASS,50,0,50,1.0,ORF3a,synonymous_variant,c.192C>T,p.Thr64Thr,p.T64T,ivar,BA.1.1.1 +220685,NC_045512.2,26270,C,T,PASS,114,0,114,1.0,E,missense_variant,c.26C>T,p.Thr9Ile,p.T9I,ivar,BA.1.1.1 +220685,NC_045512.2,26530,A,G,PASS,48,0,48,1.0,M,missense_variant,c.8A>G,p.Asp3Gly,p.D3G,ivar,BA.1.1.1 +220685,NC_045512.2,26577,C,G,PASS,36,0,36,1.0,M,missense_variant,c.55C>G,p.Gln19Glu,p.Q19E,ivar,BA.1.1.1 +220685,NC_045512.2,26709,G,A,PASS,37,0,37,1.0,M,missense_variant,c.187G>A,p.Ala63Thr,p.A63T,ivar,BA.1.1.1 +220685,NC_045512.2,27259,A,C,PASS,82,0,82,1.0,ORF6,synonymous_variant,c.58A>C,p.Arg20Arg,p.R20R,ivar,BA.1.1.1 +220685,NC_045512.2,27807,C,T,PASS,23,0,23,1.0,ORF7b,synonymous_variant,c.52C>T,p.Leu18Leu,p.L18L,ivar,BA.1.1.1 +220685,NC_045512.2,28271,A,T,PASS,315,0,313,0.99,N,upstream_gene_variant,c.-3A>T,.,.,ivar,BA.1.1.1 +220685,NC_045512.2,28311,C,T,PASS,318,8,308,0.97,N,missense_variant,c.38C>T,p.Pro13Leu,p.P13L,ivar,BA.1.1.1 +220685,NC_045512.2,2832,A,G,PASS,19,0,19,1.0,orf1ab,missense_variant,c.2567A>G,p.Lys856Arg,p.K856R,ivar,BA.1.1.1 +220685,NC_045512.2,28333,C,T,PASS,307,4,303,0.99,N,synonymous_variant,c.60C>T,p.Pro20Pro,p.P20P,ivar,BA.1.1.1 +220685,NC_045512.2,28361,GGAGAACGCA,G,PASS,258,256,188,0.73,N,disruptive_inframe_deletion,c.90_98delAGAACGCAG,p.Glu31_Ser33del,p.E31_S33del,ivar,BA.1.1.1 +220685,NC_045512.2,28512,C,T,PASS,186,124,56,0.3,N,missense_variant,c.239C>T,p.Pro80Leu,p.P80L,ivar,BA.1.1.1 +220685,NC_045512.2,28881,GG,AA,PASS,3917,51,3864,0.99,N,missense_variant,c.608_609delGGinsAA,p.Arg203Lys,p.R203K,ivar,BA.1.1.1 +220685,NC_045512.2,28883,G,C,PASS,3900,4,3892,1.0,N,missense_variant,c.610G>C,p.Gly204Arg,p.G204R,ivar,BA.1.1.1 +220685,NC_045512.2,3037,C,T,PASS,13,0,13,1.0,orf1ab,synonymous_variant,c.2772C>T,p.Phe924Phe,p.F924F,ivar,BA.1.1.1 +220685,NC_045512.2,4710,C,A,ft,12,7,5,0.42,orf1ab,missense_variant,c.4445C>A,p.Ala1482Asp,p.A1482D,ivar,BA.1.1.1 +220685,NC_045512.2,8393,G,A,PASS,2105,5,2100,1.0,orf1ab,missense_variant,c.8128G>A,p.Ala2710Thr,p.A2710T,ivar,BA.1.1.1 From f521e060bd635d5aca2516ed1ada028b4d3e833c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Adri=C3=A1n=20Mu=C3=B1oz=20Barrera?= Date: Thu, 30 Jun 2022 13:12:39 +0100 Subject: [PATCH 0600/1454] Update HUNSC-ITER schemas --- relecov_tools/conf/laboratory_address.json | 4 ++-- .../schema/institution_schemas/HUNSC-ITER.json | 15 ++++++++------- 2 files changed, 10 insertions(+), 9 deletions(-) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 5c1d2ea2..717cf5a8 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -66,7 +66,7 @@ { "collecting_institution": "Hospital Universitario Ntra. Sra de Candelaria", "collecting_institution_address": "Carretera del Rosario 145", - "collecting_institution_email": "Not available", + "collecting_institution_email": "jalcflo@gobiernodecanarias.org", "geo_loc_state": "Canarias", "geo_loc_city": "Santa Cruz de Tenerife", "geo_loc_country": "Spain" @@ -74,7 +74,7 @@ { "collecting_institution": "Instituto Tecnológico y de Energías Renovables", "collecting_institution_address": "Polígono Industrial de Granadilla, s/n", - "collecting_institution_email": "genomica@iter.es", + "collecting_institution_email": "jlorenzo@iter.es", "geo_loc_state": "Canarias", "geo_loc_city": "Santa Cruz de Tenerife", "geo_loc_country": "Spain" diff --git a/relecov_tools/schema/institution_schemas/HUNSC-ITER.json b/relecov_tools/schema/institution_schemas/HUNSC-ITER.json index 209615fc..f3614518 100644 --- a/relecov_tools/schema/institution_schemas/HUNSC-ITER.json +++ b/relecov_tools/schema/institution_schemas/HUNSC-ITER.json @@ -10,10 +10,15 @@ "Host Age": "Patient age", "Host Gender": "Gender", "Library Preparation Kit": "Assembly method", + "Enrichment panel/assay": "Enrichment panel/assay", + "Enrichment panel/assay version": "Enrichment panel/assay version", "Sequencing Instrument Model": "Sequencing technology", + "Diagnostic Pcr Ct Value 1": "Diagnostic Pcr Ct Value 1", "Analysis Authors": "Authors", "Author Submitter": "Submitter", - "Authors": "Authors" + "Authors": "Authors", + "Sequence file R1 fastq": "FASTQ R1", + "Sequence file R2 fastq": "FASTQ R2" }, "constants": { "Public Health sample id (SIVIES)": "NA", @@ -32,9 +37,8 @@ "Sequencing Date": "NA", "Rna Extraction Protocol": "NA", "Commercial All-in-one library kit": "NA", - "Enrichment Protocol": "NA", + "Enrichment Protocol": "Amplicon", "If Enrichment Protocol. If Other,Specify": "NA", - "Enrichment panel/assay": "NA", "If Enrichment panel/assay. If Other, Specify": "NA", "Enrichment panel/assay version": "NA", "Number Of Samples In Run": "NA", @@ -45,11 +49,8 @@ "Sequencing technique": "NA", "Library Layout": "NA", "Gene Name 1": "NA", - "Diagnostic Pcr Ct Value 1": "NA", "Gene Name 2": "NA", - "Diagnostic Pcr Ct Value-2": "NA", - "Sequence file R1 fastq": "NA", - "Sequence file R2 fastq": "NA" + "Diagnostic Pcr Ct Value-2": "NA" }, "outer": {} } \ No newline at end of file From f918826ae100826d31631a8fcbaa6f1b8b7ab305 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 16:06:29 +0200 Subject: [PATCH 0601/1454] started the outer management --- relecov_tools/metadata_homogeneizer.py | 52 ++++++++++++++++++++------ 1 file changed, 41 insertions(+), 11 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index df320b74..bc38db06 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -1,10 +1,22 @@ #!/usr/bin/env python # Imports -# import os +import os import sys import json +import logging import pandas as pd +import rich.console +import relecov_tools.utils +from relecov_tools.config_json import ConfigJson + +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) def check_extension(instring, extensions): @@ -34,11 +46,9 @@ def __init__(self, filename): # To Do: replace string with local file system for testing # Header path can be found in conf/configuration.json - - header_path = "Schemas/configuration.json" - self.translated_dataframe = pd.DataFrame( - columns=open_json(header_path)["new_table_headers"] - ) + config_json = ConfigJson() + self.header = config_json.get_configuration("new_table_headers") + self.translated_dataframe = pd.DataFrame(columns=self.header) return def associate_dict(self): @@ -50,10 +60,11 @@ def associate_dict(self): # raise error when in doubt # must check on schema/institution_schemas - path_to_institution_json = "Schemas/institution_to_schema.json" + config_json = ConfigJson(json_file=os.path.join(os.path.dirname(__file__), "schema", "institution_to_schema.json")) + institution_dict = config_json.json_data + # path_to_institution_json = "Schemas/institution_to_schema.json" detected = [] - institution_dict = open_json(path_to_institution_json) for key in institution_dict.keys(): # cap insensitive @@ -66,7 +77,8 @@ def associate_dict(self): ) elif len(set(detected)) > 1: - print("some problems arised!!!") # change this to an elegant form + print("The following matches were identified:") + print(*set(detected), sep="\n") # change this to an elegant form sys.exit() # maybe check which ones are being mixed or when none is being found else: self.dictionary_path = detected[0] # first item, they are all equal @@ -105,8 +117,10 @@ def load_dictionary(self): """Load the corresponding dictionary""" # To Do: replace string with local file system for testing + config_json = ConfigJson(json_file=os.path.join(os.path.dirname(__file__), "schema", "institution_to_schema.json")) + institution_dict = config_json.json_data path_to_tools = "" - dict_path = path_to_tools + "Schemas/" + self.dictionary_path + dict_path = os.join()path_to_tools + "schema/" + self.dictionary_path self.dictionary = open_json(dict_path) return @@ -134,6 +148,10 @@ def translate_dataframe(self): f"Value '{key}' in the '{self.dictionary_path}' schema not found in the resulting dataframe" ) + # Nightmare + for key, value in self.dictionary["outer"].items(): + pass + return def verify_translated_dataframe(self): @@ -144,9 +162,21 @@ def verify_translated_dataframe(self): else: print("Number of rows: OK") - pass + # search for missing values + missing_values = list(set(self.header) - set(self.translated_dataframe.columns)) + if len(missing_values) > 0: + print("Found the following missing values during translated table validation:") + print(*missing_values, sep="\n") + + # search for extra values + extra_values = list(set(self.translated_dataframe.columns) - set(self.header)) + if len(extra_values) > 0: + print("Found the following extra values during translated table validation:") + print(*extra_values, sep="\n") + return def export_translated_dataframe(self): + # pass return From b026dff88f986ed43dff9fae108eac03cb67324c Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 16:22:52 +0200 Subject: [PATCH 0602/1454] removed trailing comma --- relecov_tools/schema/institution_schemas/ISCIII.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 1fc1e3e0..f9ca6d1a 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -12,7 +12,7 @@ "Sample Received Date": "Fecha recepción", "Host Age": "Grupo edad", "Diagnostic Pcr Ct Value 1": "PCR genE", - "Sequencing Date": "Fecha de secuenciación", + "Sequencing Date": "Fecha de secuenciación" }, "constants": { From 16cfc413ed69bb00d97ac0e8b4645f2055bbf503 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 16:23:47 +0200 Subject: [PATCH 0603/1454] removed open_json function --- relecov_tools/metadata_homogeneizer.py | 33 +++++++++++++++----------- 1 file changed, 19 insertions(+), 14 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index bc38db06..e1a871dc 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -19,12 +19,23 @@ ) -def check_extension(instring, extensions): +def check_extension(instring): """Given a file as a string and a list of possible extensions, - returns true if the extension can be found in the file""" - for extension in extensions: - if instring.endswith(extension): - return True + returns the type of file extension can be found in the file""" + + # hard-coded extensions + extensions = { + "excel" : [".xlsx", ".xls", ".xlsm", ".xlsb"], + "odf" : [".odf"], + "csv" : [".csv"], + "tsv" : [".tsv"], + "json" : [".json"] + } + + for extension, termination_list in extensions.items(): + for termination in termination_list: + if instring.endswith(termination): + return extension def open_json(json_path): @@ -92,10 +103,6 @@ def load_dataframe(self): """Detect possible extensions for the metadata file Open it into a dataframe""" - excel_extensions = [".xlsx", ".xls", ".xlsm", ".xlsb"] - odf_extension = [".odf"] - csv_extensions = [".csv"] - tsv_extensions = [".tsv"] if check_extension(self.filename, excel_extensions): self.dataframe = pd.read_excel(self.filename, header=0) @@ -117,11 +124,9 @@ def load_dictionary(self): """Load the corresponding dictionary""" # To Do: replace string with local file system for testing - config_json = ConfigJson(json_file=os.path.join(os.path.dirname(__file__), "schema", "institution_to_schema.json")) - institution_dict = config_json.json_data - path_to_tools = "" - dict_path = os.join()path_to_tools + "schema/" + self.dictionary_path - self.dictionary = open_json(dict_path) + config_json = ConfigJson(json_file=os.path.join(os.path.dirname(__file__), "schema", self.dictionary_path)) + self.dictionary = config_json.json_data + return def translate_dataframe(self): From 4fc056a3454235f5087d5bf5b1c40993a3b1c541 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 16:40:01 +0200 Subject: [PATCH 0604/1454] function reorganization --- relecov_tools/metadata_homogeneizer.py | 45 +++++++++++++++++--------- 1 file changed, 29 insertions(+), 16 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index e1a871dc..fe26ecb6 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -18,7 +18,6 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) - def check_extension(instring): """Given a file as a string and a list of possible extensions, returns the type of file extension can be found in the file""" @@ -37,6 +36,34 @@ def check_extension(instring): if instring.endswith(termination): return extension +def identify_load_dataframe(filename): + """Detect possible extensions for the metadata file + Open it into a dataframe""" + + if check_extension(filename) == "excel": + df = pd.read_excel(filename, header=0) + + elif check_extension(filename) == "odf": + # Needs a special package + df = pd.read_excel(filename, engine="odf", header=0) + + elif check_extension(filename) == "csv": + df = pd.read_csv(filename, sep=",", header=0) + + elif check_extension(filename) == "tsv": + df = pd.read_csv(filename, sep="\t", header=0) + + elif check_extension(filename) == "json": + config_json = ConfigJson(filename="") + pass + + else: + print( + f"The extension of the file '{filename}' could not be identified." + ) + return None + + return df def open_json(json_path): """Load the json file""" @@ -102,21 +129,7 @@ def associate_dict(self): def load_dataframe(self): """Detect possible extensions for the metadata file Open it into a dataframe""" - - - if check_extension(self.filename, excel_extensions): - self.dataframe = pd.read_excel(self.filename, header=0) - elif check_extension(self.filename, odf_extension): - # Needs a special package - self.dataframe = pd.read_excel(self.filename, engine="odf", header=0) - elif check_extension(self.filename, csv_extensions): - self.dataframe = pd.read_csv(self.filename, sep=",", header=0) - elif check_extension(self.filename, tsv_extensions): - self.dataframe = pd.read_csv(self.filename, sep="\t", header=0) - else: - print( - f"The extension of the file '{self.filename}' could not be identified. My bad there." - ) + self.dataframe = identify_load_dataframe(self.filename) return From a47481619e1b51a7bb697b922f5c71fb6fada264 Mon Sep 17 00:00:00 2001 From: mlarjim Date: Thu, 30 Jun 2022 16:45:24 +0200 Subject: [PATCH 0605/1454] Added function to create multifasta in gisaid_upload --- relecov_tools/gisaid_upload.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index bbf86e2d..6945b435 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -4,7 +4,6 @@ import rich.console import json - import pandas as pd import sys import os @@ -80,8 +79,10 @@ def __init__( else: self.metadata = metadata if not os.path.isfile(self.source_json_file): - log.error("json data file %s does not exist ", self.source_json_file) - stderr.print(f"[red]json data file {self.source_json_file} does not exist") + log.error("json data file %s does not exist ", + self.source_json_file) + stderr.print( + f"[red]json data file {self.source_json_file} does not exist") sys.exit(1) with open(self.source_json_file, "r") as fh: self.json_data = json.loads(fh.read()) From 6574e0076d9a3ca7f1f545627890205b95adfa23 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 30 Jun 2022 16:48:29 +0200 Subject: [PATCH 0606/1454] parse function into subfunctions --- .../example_data/download_module/README | 3 - relecov_tools/read_bioinfo_metadata.py | 62 ++++++++++++++----- 2 files changed, 46 insertions(+), 19 deletions(-) delete mode 100644 relecov_tools/example_data/download_module/README diff --git a/relecov_tools/example_data/download_module/README b/relecov_tools/example_data/download_module/README deleted file mode 100644 index 263e66ca..00000000 --- a/relecov_tools/example_data/download_module/README +++ /dev/null @@ -1,3 +0,0 @@ -Para usar este modulo se necesita: -usuario del sftp asociado al centro -contraseña asociada al usuario diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index f97dbd8a..4e3d4855 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -58,22 +58,7 @@ def __init__(self, metadata_file=None, input_folder=None, output_folder=None): else: self.output_folder = output_folder - def bioinfo_parse(self, file_name): - """Fetch the metadata file folder Directory to fetch metadata file - file_name metadata file name - """ - - wb_file = openpyxl.load_workbook(file_name, data_only=True) - ws_metadata_lab = wb_file["METADATA_LAB"] - config_json = ConfigJson() - relecov_bioinfo_metadata = config_json.get_configuration( - "relecov_bioinfo_metadata" - ) - c = 0 - self.files_read_bioinfo_metadata = config_json.get_configuration( - "files_read_bioinfo_metadata" - ) - + def get_input_files(self): mapping_illumina_tab_path = os.path.join( self.input_folder, "mapping_illumina.tab" ) @@ -90,7 +75,52 @@ def bioinfo_parse(self, file_name): self.input_folder, "software_versions.yml" ) pangolin_versions_path = os.path.join(self.input_folder, "pangolin_version.csv") + + return ( + mapping_illumina_tab_path, + summary_variants_metrics_path, + variants_long_table_path, + consensus_genome_length_path, + software_versions_path, + pangolin_versions_path, + ) + + def get_config_info(self): + config_json = ConfigJson() + + self.files_read_bioinfo_metadata = config_json.get_configuration( + "files_read_bioinfo_metadata" + ) self.md5_file_name = config_json.get_configuration("md5_file_name") + + return self.files_read_bioinfo_metadata, self.md5_file_name + + def bioinfo_parse(self, file_name): + """Fetch the metadata file folder Directory to fetch metadata file + file_name + """ + + wb_file = openpyxl.load_workbook(file_name, data_only=True) + ws_metadata_lab = wb_file["METADATA_LAB"] + c = 0 + config_json = ConfigJson() + relecov_bioinfo_metadata = config_json.get_configuration( + "relecov_bioinfo_metadata" + ) + + ( + mapping_illumina_tab_path, + summary_variants_metrics_path, + variants_long_table_path, + consensus_genome_length_path, + software_versions_path, + pangolin_versions_path, + ) = self.get_input_files(self) + + self.files_read_bioinfo_metadata, self.md5_file_name = self.get_config_info( + self + ) + md5_info_path = os.path.join( self.input_folder, self.md5_file_name, # como hacer esto general para los servicios From a335e392e32a9ffc3bfd32fcb271b5634d98f7b7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 30 Jun 2022 16:53:31 +0200 Subject: [PATCH 0607/1454] Fix try github actions --- .github/workflows/python_lint.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml index deeaf672..3b0d986e 100644 --- a/.github/workflows/python_lint.yml +++ b/.github/workflows/python_lint.yml @@ -26,7 +26,7 @@ jobs: with: checkName: 'flake8_py3' # NOTE: this needs to be the same as the job name env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_TOKEN: ${{ secrets.TOKEN_ACTIONS }} black_lint: runs-on: ubuntu-latest From 2c705242bde061b47c343ecbd38e2f6a2e13fd78 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 16:57:20 +0200 Subject: [PATCH 0608/1454] small changes --- relecov_tools/metadata_homogeneizer.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index fe26ecb6..cbd0011e 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -53,9 +53,10 @@ def identify_load_dataframe(filename): elif check_extension(filename) == "tsv": df = pd.read_csv(filename, sep="\t", header=0) + # not real sure how to do this elif check_extension(filename) == "json": - config_json = ConfigJson(filename="") pass + # config_json = ConfigJson(filename="") else: print( @@ -127,8 +128,8 @@ def associate_dict(self): return def load_dataframe(self): - """Detect possible extensions for the metadata file - Open it into a dataframe""" + """Detect possible extensions for the metadata file and + open it into a dataframe""" self.dataframe = identify_load_dataframe(self.filename) return From ecd4926e480b6304700ef81956a6f094b7e04128 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 16:58:19 +0200 Subject: [PATCH 0609/1454] linting --- relecov_tools/metadata_homogeneizer.py | 43 +++++++++++++++++--------- 1 file changed, 28 insertions(+), 15 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index cbd0011e..136d044b 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -18,17 +18,18 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) + def check_extension(instring): """Given a file as a string and a list of possible extensions, returns the type of file extension can be found in the file""" # hard-coded extensions extensions = { - "excel" : [".xlsx", ".xls", ".xlsm", ".xlsb"], - "odf" : [".odf"], - "csv" : [".csv"], - "tsv" : [".tsv"], - "json" : [".json"] + "excel": [".xlsx", ".xls", ".xlsm", ".xlsb"], + "odf": [".odf"], + "csv": [".csv"], + "tsv": [".tsv"], + "json": [".json"], } for extension, termination_list in extensions.items(): @@ -36,6 +37,7 @@ def check_extension(instring): if instring.endswith(termination): return extension + def identify_load_dataframe(filename): """Detect possible extensions for the metadata file Open it into a dataframe""" @@ -59,13 +61,12 @@ def identify_load_dataframe(filename): # config_json = ConfigJson(filename="") else: - print( - f"The extension of the file '{filename}' could not be identified." - ) + print(f"The extension of the file '{filename}' could not be identified.") return None return df + def open_json(json_path): """Load the json file""" with open(json_path) as file: @@ -99,7 +100,11 @@ def associate_dict(self): # raise error when in doubt # must check on schema/institution_schemas - config_json = ConfigJson(json_file=os.path.join(os.path.dirname(__file__), "schema", "institution_to_schema.json")) + config_json = ConfigJson( + json_file=os.path.join( + os.path.dirname(__file__), "schema", "institution_to_schema.json" + ) + ) institution_dict = config_json.json_data # path_to_institution_json = "Schemas/institution_to_schema.json" @@ -129,7 +134,7 @@ def associate_dict(self): def load_dataframe(self): """Detect possible extensions for the metadata file and - open it into a dataframe""" + open it into a dataframe""" self.dataframe = identify_load_dataframe(self.filename) return @@ -138,9 +143,13 @@ def load_dictionary(self): """Load the corresponding dictionary""" # To Do: replace string with local file system for testing - config_json = ConfigJson(json_file=os.path.join(os.path.dirname(__file__), "schema", self.dictionary_path)) + config_json = ConfigJson( + json_file=os.path.join( + os.path.dirname(__file__), "schema", self.dictionary_path + ) + ) self.dictionary = config_json.json_data - + return def translate_dataframe(self): @@ -184,18 +193,22 @@ def verify_translated_dataframe(self): # search for missing values missing_values = list(set(self.header) - set(self.translated_dataframe.columns)) if len(missing_values) > 0: - print("Found the following missing values during translated table validation:") + print( + "Found the following missing values during translated table validation:" + ) print(*missing_values, sep="\n") # search for extra values extra_values = list(set(self.translated_dataframe.columns) - set(self.header)) if len(extra_values) > 0: - print("Found the following extra values during translated table validation:") + print( + "Found the following extra values during translated table validation:" + ) print(*extra_values, sep="\n") return def export_translated_dataframe(self): - # + # pass return From 2a3439223a9658f695e582ceb3b430a2b34ff6db Mon Sep 17 00:00:00 2001 From: mlarjim Date: Thu, 30 Jun 2022 17:06:59 +0200 Subject: [PATCH 0610/1454] Added function to change multifasta ids/headers --- relecov_tools/gisaid_upload.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 6945b435..45371c6e 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -79,10 +79,8 @@ def __init__( else: self.metadata = metadata if not os.path.isfile(self.source_json_file): - log.error("json data file %s does not exist ", - self.source_json_file) - stderr.print( - f"[red]json data file {self.source_json_file} does not exist") + log.error("json data file %s does not exist ", self.source_json_file) + stderr.print(f"[red]json data file {self.source_json_file} does not exist") sys.exit(1) with open(self.source_json_file, "r") as fh: self.json_data = json.loads(fh.read()) From c8cfb0a9e4007cf8d30775c116ab501a81b4617e Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 17:08:01 +0200 Subject: [PATCH 0611/1454] added template.json --- relecov_tools/schema/institution_schemas/template.json | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 relecov_tools/schema/institution_schemas/template.json diff --git a/relecov_tools/schema/institution_schemas/template.json b/relecov_tools/schema/institution_schemas/template.json new file mode 100644 index 00000000..e69de29b From 8436de1f022c19499603a3f37b56f6db3885eec8 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 30 Jun 2022 17:14:47 +0200 Subject: [PATCH 0612/1454] added subfunction --- relecov_tools/read_bioinfo_metadata.py | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 4e3d4855..434d6a86 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -92,8 +92,15 @@ def get_config_info(self): "files_read_bioinfo_metadata" ) self.md5_file_name = config_json.get_configuration("md5_file_name") + self.mapping_illumina_tab_field_list = config_json.get_configuration( + "mapping_illumina_tab_field_list" + ) - return self.files_read_bioinfo_metadata, self.md5_file_name + return ( + self.files_read_bioinfo_metadata, + self.md5_file_name, + self.mapping_illumina_tab_field_list, + ) def bioinfo_parse(self, file_name): """Fetch the metadata file folder Directory to fetch metadata file @@ -117,15 +124,16 @@ def bioinfo_parse(self, file_name): pangolin_versions_path, ) = self.get_input_files(self) - self.files_read_bioinfo_metadata, self.md5_file_name = self.get_config_info( - self - ) + ( + self.files_read_bioinfo_metadata, + self.md5_file_name, + self.mapping_illumina_tab_field_list, + ) = self.get_config_info(self) md5_info_path = os.path.join( self.input_folder, self.md5_file_name, # como hacer esto general para los servicios ) - mapping_illumina_tab = pd.read_csv(mapping_illumina_tab_path, sep="\t") summary_variants_metrics = pd.read_csv(summary_variants_metrics_path, sep=",") variants_long_table = pd.read_csv(variants_long_table_path, sep=",") From 257c327745e5c8eb7bdfd6c287f334306d7c420f Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 17:29:54 +0200 Subject: [PATCH 0613/1454] added a template for the institution schemas --- .../schema/institution_schemas/template.json | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/relecov_tools/schema/institution_schemas/template.json b/relecov_tools/schema/institution_schemas/template.json index e69de29b..9e1743fc 100644 --- a/relecov_tools/schema/institution_schemas/template.json +++ b/relecov_tools/schema/institution_schemas/template.json @@ -0,0 +1,15 @@ +{ + "equivalence": { + "Final_term": "Initial term" + }, + "constants": { + "Final_term": "Constant value" + }, + "outer": { + "final term" : { + "filename":"filename", + "sheet" : "in case of excel format, state sheet", + "column" : "name of the column where the needed value is", + "samplename_col" : "name of the column containing the samplenames"} + } +} \ No newline at end of file From e016b4a49ef3f67962aa829fa2b547de46abf03a Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 17:30:27 +0200 Subject: [PATCH 0614/1454] management of whitespaces before and after col names --- relecov_tools/metadata_homogeneizer.py | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 136d044b..5018487e 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -64,6 +64,9 @@ def identify_load_dataframe(filename): print(f"The extension of the file '{filename}' could not be identified.") return None + # remove spaces before and after + df.columns = df.columns.str.strip() + return df @@ -96,9 +99,9 @@ def associate_dict(self): # Check name of the file attribute of the object # Check schema with all centres and find their json - # associate centre and json with object - # raise error when in doubt - # must check on schema/institution_schemas + # Associate centre and json with object + # Raise error when in doubt + # Must check on schema/institution_schemas config_json = ConfigJson( json_file=os.path.join( @@ -162,7 +165,7 @@ def translate_dataframe(self): f"Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'" ) elif value in self.dataframe.columns: - self.translated_dataframe[key] = self.dataframe[value] + self.translated_dataframe[key] = self.dataframe[value.strip()] else: print( f"Column '{value}' indicated in the '{self.dictionary_path}' schema could not be found." @@ -177,8 +180,12 @@ def translate_dataframe(self): ) # Nightmare - for key, value in self.dictionary["outer"].items(): + + if len(self.dictionary["outer"]) == 0: pass + else: + for key, value in self.dictionary["outer"].items(): + value["filename"] return From d158a11309a7bcb16536037ed8d6f789978f902b Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 17:44:25 +0200 Subject: [PATCH 0615/1454] added export method --- relecov_tools/metadata_homogeneizer.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 5018487e..98ecb86c 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -216,6 +216,8 @@ def verify_translated_dataframe(self): return def export_translated_dataframe(self): - # + # expected only one dot per file + filename, extension = self.filename.split(".") + self.translated_dataframe.to_excel(excel_writer=str(filename + "_modified." + extension)) pass return From 4f5367f823123fe245bbeb83f3eac458ae888d09 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 17:46:18 +0200 Subject: [PATCH 0616/1454] removed unnecessary pass --- relecov_tools/metadata_homogeneizer.py | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 98ecb86c..d951d95a 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -219,5 +219,4 @@ def export_translated_dataframe(self): # expected only one dot per file filename, extension = self.filename.split(".") self.translated_dataframe.to_excel(excel_writer=str(filename + "_modified." + extension)) - pass return From 1c90477c7d4d554bb23f84960dc915e5f239d9e3 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 17:46:36 +0200 Subject: [PATCH 0617/1454] linting --- relecov_tools/metadata_homogeneizer.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index d951d95a..ec1b309d 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -180,7 +180,7 @@ def translate_dataframe(self): ) # Nightmare - + if len(self.dictionary["outer"]) == 0: pass else: @@ -218,5 +218,7 @@ def verify_translated_dataframe(self): def export_translated_dataframe(self): # expected only one dot per file filename, extension = self.filename.split(".") - self.translated_dataframe.to_excel(excel_writer=str(filename + "_modified." + extension)) + self.translated_dataframe.to_excel( + excel_writer=str(filename + "_modified." + extension) + ) return From 35b1377d5277160dad4f7075140c7420439a6b50 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Adri=C3=A1n=20Mu=C3=B1oz=20Barrera?= Date: Thu, 30 Jun 2022 17:18:38 +0100 Subject: [PATCH 0618/1454] Added some try-exceptions for error handling and modified check_extensions in metadata_homogeneizer.py script --- relecov_tools/metadata_homogeneizer.py | 98 ++++++++++++++------------ 1 file changed, 51 insertions(+), 47 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index df320b74..aaeaba23 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -5,14 +5,33 @@ import sys import json import pandas as pd +import logging +log = logging.getLogger(__name__) -def check_extension(instring, extensions): +def check_extension_and_read(instring): """Given a file as a string and a list of possible extensions, returns true if the extension can be found in the file""" - for extension in extensions: - if instring.endswith(extension): - return True + + excel_extensions = [".xlsx", ".xls", ".xlsm", ".xlsb"] + odf_extension = [".odf"] + csv_extensions = [".csv"] + tsv_extensions = [".tsv"] + + ext = os.path.splittext(instring)[1] # File extension + + if ext in excel_extensions: + return pd.read_excel(instring, header=0) + elif ext in odf_extension: + return pd.read_excel(instring, engine="odf", header=0) + elif ext in csv_extensions: + return pd.read_csv(instring, sep=",", header=0) + elif ext in tsv_extensions: + return pd.read_csv(instring, sep="\t", header=0) + else: + print ("The extension of the file '{instring}' could not be identified. My bad there.)" + sys.exit(1) + return def open_json(json_path): @@ -35,7 +54,8 @@ def __init__(self, filename): # To Do: replace string with local file system for testing # Header path can be found in conf/configuration.json - header_path = "Schemas/configuration.json" + header_path = "conf/configuration.json" + # To Do: error handling self.translated_dataframe = pd.DataFrame( columns=open_json(header_path)["new_table_headers"] ) @@ -50,10 +70,15 @@ def associate_dict(self): # raise error when in doubt # must check on schema/institution_schemas - path_to_institution_json = "Schemas/institution_to_schema.json" + path_to_institution_json = "schemas/institution_to_schema.json" detected = [] - institution_dict = open_json(path_to_institution_json) + + try: + institution_dict = open_json(path_to_institution_json) + except Exception as e: + log.error("Json file does not exist %s", e) + sys.exit(1) for key in institution_dict.keys(): # cap insensitive @@ -61,10 +86,7 @@ def associate_dict(self): detected.append(institution_dict[key]) if len(set(detected)) == 0: - print( - f"No file could be found matching with the '{self.filename}' filename given." - ) - + print(f"No file could be found matching with the '{self.filename}' filename given.") elif len(set(detected)) > 1: print("some problems arised!!!") # change this to an elegant form sys.exit() # maybe check which ones are being mixed or when none is being found @@ -79,26 +101,8 @@ def associate_dict(self): def load_dataframe(self): """Detect possible extensions for the metadata file Open it into a dataframe""" - - excel_extensions = [".xlsx", ".xls", ".xlsm", ".xlsb"] - odf_extension = [".odf"] - csv_extensions = [".csv"] - tsv_extensions = [".tsv"] - - if check_extension(self.filename, excel_extensions): - self.dataframe = pd.read_excel(self.filename, header=0) - elif check_extension(self.filename, odf_extension): - # Needs a special package - self.dataframe = pd.read_excel(self.filename, engine="odf", header=0) - elif check_extension(self.filename, csv_extensions): - self.dataframe = pd.read_csv(self.filename, sep=",", header=0) - elif check_extension(self.filename, tsv_extensions): - self.dataframe = pd.read_csv(self.filename, sep="\t", header=0) - else: - print( - f"The extension of the file '{self.filename}' could not be identified. My bad there." - ) - + + self.dataframe = check_extension_and_read(self.filename) return def load_dictionary(self): @@ -107,7 +111,11 @@ def load_dictionary(self): # To Do: replace string with local file system for testing path_to_tools = "" dict_path = path_to_tools + "Schemas/" + self.dictionary_path - self.dictionary = open_json(dict_path) + try: + self.dictionary = open_json(dict_path) + except Exception as e: + log.error("Json file does not exist %s", e) + sys.exit(1) return def translate_dataframe(self): @@ -115,24 +123,20 @@ def translate_dataframe(self): # if dictionary is "none" or similar, do nothing for key, value in self.dictionary["equivalence"].items(): - if len(value) == 0: - print( - f"Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'" - ) - elif value in self.dataframe.columns: - self.translated_dataframe[key] = self.dataframe[value] - else: - print( - f"Column '{value}' indicated in the '{self.dictionary_path}' schema could not be found." - ) + try: + if value: # If value is empty + try: # To revise + self.translated_dataframe[key] = self.dataframe[value] + except Exception as e: + log.error("Column '{value}' indicated in the '{self.dictionary_path}' schema could not be found. %s", e) + except Exception as e: + log.error("Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'. %s", e) for key, value in self.dictionary["constants"].items(): - if key in self.translated_dataframe.columns: + try: # To revise self.translated_dataframe[key] = value - else: - print( - f"Value '{key}' in the '{self.dictionary_path}' schema not found in the resulting dataframe" - ) + except Exception as e: + log.error("Value '{key}' in the '{self.dictionary_path}' schema not found in the resulting dataframe. %s", e) return From 41ac3b5f9063adf2e81b40d4080b8f93e99c8103 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 23:28:55 +0200 Subject: [PATCH 0619/1454] format updates --- relecov_tools/metadata_homogeneizer.py | 46 ++++++++++++-------------- 1 file changed, 22 insertions(+), 24 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 50852b35..a3750562 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -98,15 +98,15 @@ def associate_dict(self): for key in institution_dict.keys(): # cap insensitive if key.lower() in self.filename.split("/")[-1].lower(): - detected[key] = institution_dict[key] + detected[key] = institution_dict[key] if len(set(detected.values())) == 0: - stderr.print(f"[red]No institution pattern could be found in the '{self.filename}' filename given.") - sys.exit(1) + stderr.print(f"[red]No institution pattern could be found in the '{self.filename}' filename given.") + sys.exit(1) elif len(set(detected.values())) > 1: - repeated = ",".join(list(set(detected.values))) - stderr.print(f"[red]The following matches were identified in the '{self.filename}' filename given: {repeated}") - sys.exit(1) + repeated = ",".join(list(set(detected.values))) + stderr.print(f"[red]The following matches were identified in the '{self.filename}' filename given: {repeated}") + sys.exit(1) else: self.dictionary_path = detected[0] # first item, they are all equal @@ -140,27 +140,25 @@ def translate_dataframe(self): """Use the corresponding dictionary to translate the df""" # if dictionary is "none" or similar, do nothing - for key, value in self.dictionary["equivalence"].items(): - try: - if len(value) == 0: - stderr.print(f"Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'") - sys.exit(1) - elif value in self.dataframe.columns: - self.translated_dataframe[key] = self.dataframe[value.strip()] - else: - stderr.print(f"Column '{value}' indicated in the '{self.dictionary_path}' schema could not be found.") - - for key, value in self.dictionary["constants"].items(): - try: # To revise + try: # not sure if a try is the best here, gotta check + for key, value in self.dictionary["equivalence"].items(): + if len(value) == 0: + log.error(f"Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'") + stderr.print(f"[red]Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'") + sys.exit(1) + elif value in self.dataframe.columns: + self.translated_dataframe[key] = self.dataframe[value.strip()] + else: + log.error(f"Column '{value}' indicated in the '{self.dictionary_path}' schema could not be found in the input dataframe.") + stderr.print(f"[red]Column '{value}' indicated in the '{self.dictionary_path}' schema could not be found in the input dataframe.") + sys.exit(1) + + for key, value in self.dictionary["constants"].items(): self.translated_dataframe[key] = value - except Exception as e: - log.error("Value '{key}' in the '{self.dictionary_path}' schema not found in the resulting dataframe. %s", e) except Exception as e: - log.error("Found empty equivalence in the '{self.dictionary_path}' schema: '{key}') + log.error("Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'") - - # Nightmare if len(self.dictionary["outer"]) == 0: pass @@ -200,6 +198,6 @@ def export_translated_dataframe(self): # expected only one dot per file filename, extension = self.filename.split(".") self.translated_dataframe.to_excel( - excel_writer=str(filename + "_modified." + extension) + excel_writer= filename + "_modified." + extension ) return From ed14f69d494ae5accf5f463b9a57acea0538277c Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Thu, 30 Jun 2022 23:31:55 +0200 Subject: [PATCH 0620/1454] update --- relecov_tools/metadata_homogeneizer.py | 115 ++++++++++++++++--------- 1 file changed, 72 insertions(+), 43 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index a3750562..c6a411f1 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -2,7 +2,6 @@ # Imports import os import sys -import json import logging import pandas as pd import rich.console @@ -17,6 +16,7 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) + def check_extension(instring): """Given a file as a string and a list of possible extensions, returns the type of file extension can be found in the file""" @@ -26,7 +26,7 @@ def check_extension(instring): "excel": [".xlsx", ".xls", ".xlsm", ".xlsb"], "odf": [".odf"], "csv": [".csv"], - "tsv": [".tsv"] + "tsv": [".tsv"], } for extension, termination_list in extensions.items(): @@ -34,6 +34,7 @@ def check_extension(instring): if instring.endswith(termination): return extension + def identify_load_dataframe(filename): """Detect possible extensions for the metadata file Open it into a dataframe""" @@ -75,7 +76,7 @@ def __init__(self, filename): self.dicionary = None self.centre = None self.dataframe = None - + config_json = ConfigJson() self.header = config_json.get_configuration("new_table_headers") self.translated_dataframe = pd.DataFrame(columns=self.header) @@ -89,32 +90,44 @@ def associate_dict(self): # Associate centre and json with object # Raise error when in doubt # Must check on schema/institution_schemas - + try: - config_json = ConfigJson(json_file=os.path.join(os.path.dirname(__file__), "schema", "institution_to_schema.json")) - institution_dict = config_json.json_data - detected = {} - - for key in institution_dict.keys(): - # cap insensitive - if key.lower() in self.filename.split("/")[-1].lower(): - detected[key] = institution_dict[key] - - if len(set(detected.values())) == 0: - stderr.print(f"[red]No institution pattern could be found in the '{self.filename}' filename given.") - sys.exit(1) - elif len(set(detected.values())) > 1: - repeated = ",".join(list(set(detected.values))) - stderr.print(f"[red]The following matches were identified in the '{self.filename}' filename given: {repeated}") - sys.exit(1) - - else: - self.dictionary_path = detected[0] # first item, they are all equal - stderr.print(f"[green]JSON file found successfully: {self.dictionary_path}") - - except FileNotFoundError as e: - log.error(f"JSON file relating institutions and its JSON file could not be found or does not exist.") - sys.exit(1) + config_json = ConfigJson( + json_file=os.path.join( + os.path.dirname(__file__), "schema", "institution_to_schema.json" + ) + ) + institution_dict = config_json.json_data + detected = {} + + for key in institution_dict.keys(): + # cap insensitive + if key.lower() in self.filename.split("/")[-1].lower(): + detected[key] = institution_dict[key] + + if len(set(detected.values())) == 0: + stderr.print( + f"[red]No institution pattern could be found in the '{self.filename}' filename given." + ) + sys.exit(1) + elif len(set(detected.values())) > 1: + repeated = ",".join(list(set(detected.values))) + stderr.print( + f"[red]The following matches were identified in the '{self.filename}' filename given: {repeated}" + ) + sys.exit(1) + + else: + self.dictionary_path = detected[0] # first item, they are all equal + stderr.print( + f"[green]JSON file found successfully: {self.dictionary_path}" + ) + + except FileNotFoundError: + log.error( + "JSON file relating institutions and their JSON file could not be found or does not exist." + ) + sys.exit(1) return @@ -129,36 +142,52 @@ def load_dictionary(self): # To Do: replace string with local file system for testing try: - config_json = ConfigJson(json_file=os.path.join(os.path.dirname(__file__), "schema", self.dictionary_path)) - self.dictionary = config_json.json_data - except FileNotFoundError as e: - log.error(f"JSON file {self.dictionary_path} could not be found or does not exist.") - sys.exit(1) + config_json = ConfigJson( + json_file=os.path.join( + os.path.dirname(__file__), "schema", self.dictionary_path + ) + ) + self.dictionary = config_json.json_data + except FileNotFoundError: + log.error( + f"JSON file {self.dictionary_path} could not be found or does not exist." + ) + sys.exit(1) return def translate_dataframe(self): """Use the corresponding dictionary to translate the df""" # if dictionary is "none" or similar, do nothing - try: # not sure if a try is the best here, gotta check + try: # not sure if a try is the best here, gotta check for key, value in self.dictionary["equivalence"].items(): if len(value) == 0: - log.error(f"Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'") - stderr.print(f"[red]Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'") + log.error( + f"Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'" + ) + stderr.print( + f"[red]Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'" + ) sys.exit(1) elif value in self.dataframe.columns: self.translated_dataframe[key] = self.dataframe[value.strip()] else: - log.error(f"Column '{value}' indicated in the '{self.dictionary_path}' schema could not be found in the input dataframe.") - stderr.print(f"[red]Column '{value}' indicated in the '{self.dictionary_path}' schema could not be found in the input dataframe.") + log.error( + f"Column '{value}' indicated in the '{self.dictionary_path}' schema could not be found in the input dataframe." + ) + stderr.print( + f"[red]Column '{value}' indicated in the '{self.dictionary_path}' schema could not be found in the input dataframe." + ) sys.exit(1) - + for key, value in self.dictionary["constants"].items(): self.translated_dataframe[key] = value - except Exception as e: - log.error("Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'") - + except Exception: + log.error( + "Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'" + ) + # Nightmare if len(self.dictionary["outer"]) == 0: pass @@ -198,6 +227,6 @@ def export_translated_dataframe(self): # expected only one dot per file filename, extension = self.filename.split(".") self.translated_dataframe.to_excel( - excel_writer= filename + "_modified." + extension + excel_writer=filename + "_modified." + extension ) return From 8829ce8d801fcd97a47898a260780e8d7abd8b09 Mon Sep 17 00:00:00 2001 From: mlarjim Date: Fri, 1 Jul 2022 11:30:09 +0200 Subject: [PATCH 0621/1454] Added makedir output_dir --- relecov_tools/json_validation.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index f648c7d2..776f8f8e 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -88,7 +88,8 @@ def create_invalid_metadata(metadata_file, invalid_json, out_folder): if str(row[2].value) not in sample_list: row_to_del.append(row[0].row) - + + os.makedirs(out_folder, exist_ok=True) new_name = "invalid_" + os.path.basename(metadata_file) m_file = os.path.join(out_folder, new_name) wb.save(m_file) From 1469dc210e4b016aa6d130edd3f729ddc6f3d2b7 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Fri, 1 Jul 2022 12:28:19 +0200 Subject: [PATCH 0622/1454] more logs and stderr --- relecov_tools/metadata_homogeneizer.py | 64 ++++++++++++++------------ 1 file changed, 35 insertions(+), 29 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index c6a411f1..f1880af0 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -105,28 +105,32 @@ def associate_dict(self): if key.lower() in self.filename.split("/")[-1].lower(): detected[key] = institution_dict[key] - if len(set(detected.values())) == 0: - stderr.print( - f"[red]No institution pattern could be found in the '{self.filename}' filename given." - ) - sys.exit(1) - elif len(set(detected.values())) > 1: - repeated = ",".join(list(set(detected.values))) - stderr.print( - f"[red]The following matches were identified in the '{self.filename}' filename given: {repeated}" - ) - sys.exit(1) + if len(set(detected.values())) == 0: + log.error(f"No institution pattern could be found in the '{self.filename}' filename given.") + stderr.print( + f"[red]No institution pattern could be found in the '{self.filename}' filename given." + ) + sys.exit(1) - else: - self.dictionary_path = detected[0] # first item, they are all equal - stderr.print( - f"[green]JSON file found successfully: {self.dictionary_path}" - ) + elif len(set(detected.values())) > 1: + repeated = ", ".join(list(set(detected.values))) + log.error(f"The following matches were identified in the '{self.filename}' filename given: {repeated }'") + stderr.print( + f"[red]The following matches were identified in the '{self.filename}' filename given: {repeated}" + ) + sys.exit(1) + + else: + self.dictionary_path = detected[0] # first item, they are all equal + stderr.print( + f"[green]JSON file found successfully: {self.dictionary_path}" + ) except FileNotFoundError: log.error( "JSON file relating institutions and their JSON file could not be found or does not exist." ) + stderr.print(f"[red]JSON file relating institutions and their JSON file could not be found or does not exist.") sys.exit(1) return @@ -150,8 +154,9 @@ def load_dictionary(self): self.dictionary = config_json.json_data except FileNotFoundError: log.error( - f"JSON file {self.dictionary_path} could not be found or does not exist." + f"JSON file {self.dictionary_path} could not be found or does not exist in the schema directory." ) + stderr.print(f"[red]JSON file {self.dictionary_path} could not be found or does not exist in the schema directory.") sys.exit(1) return @@ -201,26 +206,27 @@ def verify_translated_dataframe(self): """Checks if the dataframe holds all the needed values for the relecov tools suite""" if self.dataframe.shape[0] != self.translated_dataframe.shape[0]: - print("Different number of rows after translation") + log.error("Different number of rows after translation") + sys.exit(1) else: - print("Number of rows: OK") + stderr.print(f"[green]Number of rows: OK") # search for missing values missing_values = list(set(self.header) - set(self.translated_dataframe.columns)) if len(missing_values) > 0: - print( - "Found the following missing values during translated table validation:" - ) - print(*missing_values, sep="\n") - + msg = ", ".join(missing_values) + log.error(f"Found the following missing values during translated table validation: {msg}") + stderr.print(f"[red]Found the following missing values during translated table validation: {msg}") + else: + stderr.print(f"[green]No missing values in the translated table") # search for extra values extra_values = list(set(self.translated_dataframe.columns) - set(self.header)) if len(extra_values) > 0: - print( - "Found the following extra values during translated table validation:" - ) - print(*extra_values, sep="\n") - + msg = ", ".join(extra_values) + log.error(f"Found the following extra values during translated table validation: {msg}") + stderr.print(f"[red]Found the following extra values during translated table validation: {msg}") + else: + stderr.print(f"[green]No extra values in the translated values") return def export_translated_dataframe(self): From cf19e5244859dbda451d7d320ed33c4223af1e32 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Fri, 1 Jul 2022 12:38:34 +0200 Subject: [PATCH 0623/1454] linting --- relecov_tools/metadata_homogeneizer.py | 38 ++++++++++++++++++-------- 1 file changed, 27 insertions(+), 11 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index f1880af0..e8b1f4e2 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -106,7 +106,9 @@ def associate_dict(self): detected[key] = institution_dict[key] if len(set(detected.values())) == 0: - log.error(f"No institution pattern could be found in the '{self.filename}' filename given.") + log.error( + f"No institution pattern could be found in the '{self.filename}' filename given." + ) stderr.print( f"[red]No institution pattern could be found in the '{self.filename}' filename given." ) @@ -114,7 +116,9 @@ def associate_dict(self): elif len(set(detected.values())) > 1: repeated = ", ".join(list(set(detected.values))) - log.error(f"The following matches were identified in the '{self.filename}' filename given: {repeated }'") + log.error( + f"The following matches were identified in the '{self.filename}' filename given: {repeated }'" + ) stderr.print( f"[red]The following matches were identified in the '{self.filename}' filename given: {repeated}" ) @@ -130,7 +134,9 @@ def associate_dict(self): log.error( "JSON file relating institutions and their JSON file could not be found or does not exist." ) - stderr.print(f"[red]JSON file relating institutions and their JSON file could not be found or does not exist.") + stderr.print( + "[red]JSON file relating institutions and their JSON file could not be found or does not exist." + ) sys.exit(1) return @@ -156,7 +162,9 @@ def load_dictionary(self): log.error( f"JSON file {self.dictionary_path} could not be found or does not exist in the schema directory." ) - stderr.print(f"[red]JSON file {self.dictionary_path} could not be found or does not exist in the schema directory.") + stderr.print( + f"[red]JSON file {self.dictionary_path} could not be found or does not exist in the schema directory." + ) sys.exit(1) return @@ -209,24 +217,32 @@ def verify_translated_dataframe(self): log.error("Different number of rows after translation") sys.exit(1) else: - stderr.print(f"[green]Number of rows: OK") + stderr.print("[green]Number of rows: OK") # search for missing values missing_values = list(set(self.header) - set(self.translated_dataframe.columns)) if len(missing_values) > 0: msg = ", ".join(missing_values) - log.error(f"Found the following missing values during translated table validation: {msg}") - stderr.print(f"[red]Found the following missing values during translated table validation: {msg}") + log.error( + f"Found the following missing values during translated table validation: {msg}" + ) + stderr.print( + f"[red]Found the following missing values during translated table validation: {msg}" + ) else: - stderr.print(f"[green]No missing values in the translated table") + stderr.print("[green]No missing values in the translated table") # search for extra values extra_values = list(set(self.translated_dataframe.columns) - set(self.header)) if len(extra_values) > 0: msg = ", ".join(extra_values) - log.error(f"Found the following extra values during translated table validation: {msg}") - stderr.print(f"[red]Found the following extra values during translated table validation: {msg}") + log.error( + f"Found the following extra values during translated table validation: {msg}" + ) + stderr.print( + f"[red]Found the following extra values during translated table validation: {msg}" + ) else: - stderr.print(f"[green]No extra values in the translated values") + stderr.print("[green]No extra values in the translated values") return def export_translated_dataframe(self): From 54ec5b3cd02f01ecde158b56208bb105df63fd8c Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 1 Jul 2022 12:40:08 +0200 Subject: [PATCH 0624/1454] added arguments in main for gisaid upload --- relecov_tools/__main__.py | 23 +++++++++++++++++++++-- 1 file changed, 21 insertions(+), 2 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 59171f9c..8c26f753 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -1,6 +1,7 @@ #!/usr/bin/env python import os import logging +import re # from rich.prompt import Confirm import click @@ -252,12 +253,30 @@ def upload_to_ena(user, password, center, ena_json, dev, study, action, output_p upload_ena.upload() +# upload to GISAID @relecov_tools_cli.command(help_priority=7) @click.option("-u", "--user", help="user name for login") @click.option("-p", "--password", help="password for the user to login") @click.option("-e", "--gisaid_json", help="where the validated json is") -@click.option("-o", "--output_path", help="output folder for the xml generated files") -def upload_to_gisaid(user, password, gisaid_json, output_path): +@click.option( + "-i", "--input_path", help="the path where the fasta or multifasta are located" +) +@click.option("-o", "--output_path", help="output folder for log") +@click.option( + "-x", + "--proxy_config", + help="introduce your proxy credentials as: username:password@proxy:port", + required=False, +) +@click.option( + "--single", + is_flag=True, + default=False, + help="Default input is a multifasta.", +) +def upload_to_gisaid( + user, password, gisaid_json, input_path, output_path, proxy_config +): """parsed data to create files to upload to gisaid""" pass From 8a6225e3d08bee9a112b76e5b4a66aff2e9c8555 Mon Sep 17 00:00:00 2001 From: mlarjim Date: Fri, 1 Jul 2022 12:41:54 +0200 Subject: [PATCH 0625/1454] Restored multifasta fuctions --- relecov_tools/gisaid_upload.py | 45 ++++++++++++++++++++++++---------- 1 file changed, 32 insertions(+), 13 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 45371c6e..fcadb53d 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -10,6 +10,7 @@ # import ftplib import relecov_tools.utils +from Bio import SeqIO # from relecov_tools.config_json import ConfigJson @@ -31,11 +32,9 @@ def __init__( self, user=None, passwd=None, - source_json=None, - customized_project=None, - action=None, + gisaid_json=None, + fasta_path=None, output_path=None, - metadata=None, ): if user is None: self.user = relecov_tools.utils.prompt_text( @@ -72,18 +71,18 @@ def __init__( ) else: self.output_path = output_path - if metadata is None: - self.metadata = relecov_tools.utils.prompt_path( + if gisaid_json is None: + self.gisaid_json = relecov_tools.utils.prompt_path( msg="Select metadata json file" ) else: - self.metadata = metadata - if not os.path.isfile(self.source_json_file): - log.error("json data file %s does not exist ", self.source_json_file) - stderr.print(f"[red]json data file {self.source_json_file} does not exist") - sys.exit(1) - with open(self.source_json_file, "r") as fh: - self.json_data = json.loads(fh.read()) + self.gisaid_json = gisaid_json + if fasta_path is None: + self.fasta_path = relecov_tools.utils.prompt_path( + msg="Select metadata json file" + ) + else: + self.fasta_path = fasta_path def convert_input_json_to_ena(self): """Split the input ena json, in samples and runs json""" @@ -92,13 +91,33 @@ def convert_input_json_to_ena(self): # Metadatos def metadata_to_csv(self): + "Transform metadata json to csv" data = relecov_tools.utils.read_json_file(self.metadata) df_data = pd.DataFrame(data) df_data.to_csv("meta_gisaid.csv") # Sequences # Unificar en multifasta + def create_multifasta(self): + """Create multifasta from single fastas""" + os.system("cat %s/*.fasta > %s/multifasta.fasta" %(self.fasta_path, self.output_path)) + multifasta = "%s/multifasta.fasta" %self.output_path + return multifasta + # Cambiar headers/id + def change_headers(self, multifasta): + """Transform multifasta ids/headers to GISAID format""" + data = relecov_tools.utils.read_json_file(self.gisaid_json) + virus_name = [name["covv_virus_name"] for name in data] + with open (multifasta) as old_fasta, with open ("%s/multifasta_gisaid.fasta" %self.output_path, "w") as new_fasta: + records = SeqIO.parse(old_fasta, "fasta") + for record in records: + for name in virus_name: + if record.id == name.split("/").[-2]: + record.id = name + SeqIO.write(record, new_fasta, "fasta") + + # Upload # Subir con cli3 From fb157d855f5ac5bd9fa4260b0abf9e9005237c4d Mon Sep 17 00:00:00 2001 From: mlarjim Date: Fri, 1 Jul 2022 12:57:03 +0200 Subject: [PATCH 0626/1454] Lintin 1 --- relecov_tools/gisaid_upload.py | 33 +++++++++------------------------ 1 file changed, 9 insertions(+), 24 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index fcadb53d..4f3817e9 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -48,23 +48,6 @@ def __init__( ) else: self.passwd = passwd - if source_json is None: - self.source_json_file = relecov_tools.utils.prompt_path( - msg="Select the ENA json file to upload" - ) - else: - self.source_json_file = source_json - if customized_project is None: - self.customized_project = None - else: - self.customized_project = customized_project - if action is None: - self.action = relecov_tools.utils.prompt_selection( - msg="Select the action to upload to ENA", - choices=["add", "modify", "cancel", "release"], - ) - else: - self.action = action.upper() if output_path is None: self.output_path = relecov_tools.utils.prompt_path( msg="Select the folder to store the xml files" @@ -100,24 +83,26 @@ def metadata_to_csv(self): # Unificar en multifasta def create_multifasta(self): """Create multifasta from single fastas""" - os.system("cat %s/*.fasta > %s/multifasta.fasta" %(self.fasta_path, self.output_path)) - multifasta = "%s/multifasta.fasta" %self.output_path + os.system( + "cat %s/*.fasta > %s/multifasta.fasta" % (self.fasta_path, self.output_path) + ) + multifasta = "%s/multifasta.fasta" % self.output_path return multifasta - + # Cambiar headers/id def change_headers(self, multifasta): """Transform multifasta ids/headers to GISAID format""" data = relecov_tools.utils.read_json_file(self.gisaid_json) virus_name = [name["covv_virus_name"] for name in data] - with open (multifasta) as old_fasta, with open ("%s/multifasta_gisaid.fasta" %self.output_path, "w") as new_fasta: + with open(multifasta) as old_fasta, open( + "%s/multifasta_gisaid.fasta" % self.output_path, "w" + ) as new_fasta: records = SeqIO.parse(old_fasta, "fasta") for record in records: for name in virus_name: - if record.id == name.split("/").[-2]: + if record.id == name.split("/")[-2]: record.id = name SeqIO.write(record, new_fasta, "fasta") - - # Upload # Subir con cli3 From 0eaa5aa3193a0da56179ef223a97aec33903ab15 Mon Sep 17 00:00:00 2001 From: mlarjim Date: Fri, 1 Jul 2022 13:00:55 +0200 Subject: [PATCH 0627/1454] Lintin 2 --- relecov_tools/gisaid_upload.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 4f3817e9..ee7877f8 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -2,10 +2,8 @@ # from pyparsing import col import rich.console -import json import pandas as pd -import sys import os # import ftplib @@ -84,7 +82,8 @@ def metadata_to_csv(self): def create_multifasta(self): """Create multifasta from single fastas""" os.system( - "cat %s/*.fasta > %s/multifasta.fasta" % (self.fasta_path, self.output_path) + "cat %s/*.fasta > %s/multifasta.fasta" % ( + self.fasta_path, self.output_path) ) multifasta = "%s/multifasta.fasta" % self.output_path return multifasta From 717cf2eb7f6714523fbd70bf4ae7147e0ca7281f Mon Sep 17 00:00:00 2001 From: mlarjim Date: Fri, 1 Jul 2022 13:03:17 +0200 Subject: [PATCH 0628/1454] Lintin 3 --- relecov_tools/gisaid_upload.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index ee7877f8..8e6c204e 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -82,13 +82,11 @@ def metadata_to_csv(self): def create_multifasta(self): """Create multifasta from single fastas""" os.system( - "cat %s/*.fasta > %s/multifasta.fasta" % ( - self.fasta_path, self.output_path) + "cat %s/*.fasta > %s/multifasta.fasta" % (self.fasta_path, self.output_path) ) multifasta = "%s/multifasta.fasta" % self.output_path return multifasta - # Cambiar headers/id def change_headers(self, multifasta): """Transform multifasta ids/headers to GISAID format""" data = relecov_tools.utils.read_json_file(self.gisaid_json) From d477e04eac1433161ad42e0441d941a94179dc66 Mon Sep 17 00:00:00 2001 From: mlarjim Date: Fri, 1 Jul 2022 13:05:57 +0200 Subject: [PATCH 0629/1454] Lintin 4 --- relecov_tools/json_validation.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 776f8f8e..7b200fce 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -57,6 +57,7 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): except jsonschema.ValidationError as e: log.error("Invalid sample data %s", e) invalid_json.append(item_row) + logging.handl return validated_json_data, invalid_json, errors @@ -88,7 +89,7 @@ def create_invalid_metadata(metadata_file, invalid_json, out_folder): if str(row[2].value) not in sample_list: row_to_del.append(row[0].row) - + os.makedirs(out_folder, exist_ok=True) new_name = "invalid_" + os.path.basename(metadata_file) m_file = os.path.join(out_folder, new_name) From 08ccb536c735182b86edd64426bee218aab299af Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 1 Jul 2022 13:08:38 +0200 Subject: [PATCH 0630/1454] lintin --- relecov_tools/__main__.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 8c26f753..4cb8f0ed 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -1,7 +1,8 @@ #!/usr/bin/env python import os import logging -import re + +# import re # from rich.prompt import Confirm import click @@ -259,7 +260,9 @@ def upload_to_ena(user, password, center, ena_json, dev, study, action, output_p @click.option("-p", "--password", help="password for the user to login") @click.option("-e", "--gisaid_json", help="where the validated json is") @click.option( - "-i", "--input_path", help="the path where the fasta or multifasta are located" + "-i", + "--input_path", + help="the path where the fasta or multifasta, gisaid_mapped.json and the token file are located", ) @click.option("-o", "--output_path", help="output folder for log") @click.option( From 9388117448622e09aa746d054cf479304fbe4292 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 1 Jul 2022 13:09:02 +0200 Subject: [PATCH 0631/1454] gisaid upload cli3 --- relecov_tools/gisaid_upload.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 45371c6e..f94f85e1 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -103,6 +103,23 @@ def metadata_to_csv(self): # Upload # Subir con cli3 + # ADD TOKEN WARNING and file token .authtoken + # add bash from cli3 + + os.system( + "cli3 upload --database EpiCoV --token ./gisaid.authtoken --metadata gisaid_template.csv --fasta multi.fasta --frameshift (OPTIONAL, default: catch_all) --failed --proxy --log" + ) + """ + cli3 upload + --database EpiCoV + --token ./gisaid.authtoken + --metadata gisaid_template.csv + --fasta multi.fasta + --frameshift (OPTIONAL, default: catch_all) + --failed default creates file failed.out where the failed records will be + --proxy + --log default creates file failed.out where the log will be ) + """ # def upload(self): # """Create the required files and upload to ENA""" # self.convert_input_json_to_ena() From 4747ef3fdb316a87a42a6eceb922fb93f136b6e1 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 1 Jul 2022 13:15:42 +0200 Subject: [PATCH 0632/1454] gisaid upload cli3 --- relecov_tools/gisaid_upload.py | 24 +++++++++++------------- 1 file changed, 11 insertions(+), 13 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index f94f85e1..ebc209b1 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -76,7 +76,8 @@ def __init__( self.metadata = relecov_tools.utils.prompt_path( msg="Select metadata json file" ) - else: + else:relecov_tools/gisaid_upload.py + self.metadata = metadata if not os.path.isfile(self.source_json_file): log.error("json data file %s does not exist ", self.source_json_file) @@ -95,29 +96,26 @@ def metadata_to_csv(self): data = relecov_tools.utils.read_json_file(self.metadata) df_data = pd.DataFrame(data) df_data.to_csv("meta_gisaid.csv") + - # Sequences - # Unificar en multifasta - # Cambiar headers/id - - # Upload - # Subir con cli3 - + # generar template con cli3 # ADD TOKEN WARNING and file token .authtoken # add bash from cli3 + + os.system( "cli3 upload --database EpiCoV --token ./gisaid.authtoken --metadata gisaid_template.csv --fasta multi.fasta --frameshift (OPTIONAL, default: catch_all) --failed --proxy --log" ) """ cli3 upload --database EpiCoV - --token ./gisaid.authtoken - --metadata gisaid_template.csv - --fasta multi.fasta - --frameshift (OPTIONAL, default: catch_all) + --token ./gisaid.authtoken + --metadata gisaid_template.csv + --fasta multi.fasta + --frameshift (OPTIONAL, default: catch_all) --failed default creates file failed.out where the failed records will be - --proxy + --proxy --log default creates file failed.out where the log will be ) """ # def upload(self): From 33b65d193d7227d8cb7ee732d2733a2030a0a101 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 1 Jul 2022 13:25:28 +0200 Subject: [PATCH 0633/1454] lintin --- relecov_tools/gisaid_upload.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index ebc209b1..b693c271 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -104,8 +104,7 @@ def metadata_to_csv(self): - os.system( - "cli3 upload --database EpiCoV --token ./gisaid.authtoken --metadata gisaid_template.csv --fasta multi.fasta --frameshift (OPTIONAL, default: catch_all) --failed --proxy --log" + os.system("cli3 upload --database EpiCoV --token ./gisaid.authtoken --metadata gisaid_template.csv --fasta multi.fasta --frameshift (OPTIONAL, default: catch_all) --failed --proxy --log" ) """ cli3 upload From 35acbdce42c21b5b46f35728e4a611f2818bae5f Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 1 Jul 2022 13:34:56 +0200 Subject: [PATCH 0634/1454] changes --- relecov_tools/gisaid_upload.py | 18 +++++++----------- 1 file changed, 7 insertions(+), 11 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 28adc244..b248e487 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -59,12 +59,10 @@ def __init__( else: self.gisaid_json = gisaid_json if fasta_path is None: - self.fasta_path = relecov_tools.utils.prompt_path( - msg="Select metadata json file" - ) - else:relecov_tools/gisaid_upload.py - - self.metadata = metadata + self.fasta_path = relecov_tools.utils.prompt_path(msg="Select path") + else: + # relecov_tools/gisaid_upload.py + self.metadata = fasta_path if not os.path.isfile(self.source_json_file): log.error("json data file %s does not exist ", self.source_json_file) stderr.print(f"[red]json data file {self.source_json_file} does not exist") @@ -83,15 +81,13 @@ def metadata_to_csv(self): data = relecov_tools.utils.read_json_file(self.metadata) df_data = pd.DataFrame(data) df_data.to_csv("meta_gisaid.csv") - - # generar template con cli3 + # generar template con cli3 # ADD TOKEN WARNING and file token .authtoken # add bash from cli3 - - - os.system("cli3 upload --database EpiCoV --token ./gisaid.authtoken --metadata gisaid_template.csv --fasta multi.fasta --frameshift (OPTIONAL, default: catch_all) --failed --proxy --log" + os.system( + "cli3 upload --database EpiCoV --token ./gisaid.authtoken --metadata gisaid_template.csv --fasta multi.fasta --frameshift (OPTIONAL, default: catch_all) --failed --proxy --log" ) """ cli3 upload From 14e5c218cb6a6b2dc2c3837d4e768d385f87b2ba Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 1 Jul 2022 13:42:31 +0200 Subject: [PATCH 0635/1454] lintin2 --- relecov_tools/gisaid_upload.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index eb47955a..cfe31ade 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -62,8 +62,7 @@ def __init__( self.fasta_path = relecov_tools.utils.prompt_path(msg="Select path") else: # relecov_tools/gisaid_upload.py - self.fasta_path = fasta_path) - + self.fasta_path = fasta_path if not os.path.isfile(self.source_json_file): log.error("json data file %s does not exist ", self.source_json_file) From 585a190ea54ab6079e13d37f09972057b6a2f741 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 1 Jul 2022 13:43:43 +0200 Subject: [PATCH 0636/1454] lintin3 --- relecov_tools/gisaid_upload.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index cfe31ade..f923dfc9 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -1,4 +1,6 @@ import logging +import sys +import json # from pyparsing import col import rich.console From 95ab79c37bb0dc58baa15dc8419f07408954a7e9 Mon Sep 17 00:00:00 2001 From: ibloise Date: Fri, 1 Jul 2022 13:44:42 +0200 Subject: [PATCH 0637/1454] Added gisaid_csv_headers. Corrected msg in GisaidUpload Added gisaid_csv_headers to configuration.json. Corrected some messages in GisaidUpload Class --- relecov_tools/conf/configuration.json | 29 +++++++++++++++++++++++++++ relecov_tools/gisaid_upload.py | 19 ++++++++---------- 2 files changed, 37 insertions(+), 11 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 2a170b0a..b327b646 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -49,6 +49,35 @@ "Sequence file R1 fastq", "Sequence file R2 fastq" ], + "gisaid_csv_headers": [ + "submitter", + "covv_virus_name", + "covv_type", + "covv_passage", + "covv_collection_date", + "covv_location", + "covv_add_location", + "covv_host", + "covv_add_host_info", + "covv_sampling_strategy", + "covv_gender", + "covv_patient_age", + "covv_patient_status", + "covv_specimen", + "covv_outbreak", + "covv_last_vaccinated", + "covv_treatment", + "covv_seq_technology", + "covv_assembly_method", + "covv_coverage", + "covv_orig_lab", + "covv_orig_lab_addr", + "covv_provider_sample_id", + "covv_subm_lab", + "covv_subm_lab_addr", + "covv_subm_sample_id", + "covv_authors" + ], "json_schemas": { "relecov_schema": "relecov_schema.json", "ena_schema": "ena_schema.json", diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 45371c6e..cba2f727 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -39,19 +39,20 @@ def __init__( ): if user is None: self.user = relecov_tools.utils.prompt_text( - msg="Enter your username defined in ENA" + msg="Enter your username defined in GISAID" ) else: self.user = user + #Add proxy settings: username:password@proxy:port (optional) if passwd is None: self.passwd = relecov_tools.utils.prompt_password( - msg="Enter your password to ENA" + msg="Enter your password to GISAID" ) else: self.passwd = passwd if source_json is None: self.source_json_file = relecov_tools.utils.prompt_path( - msg="Select the ENA json file to upload" + msg="Select the GISAID json file to upload" ) else: self.source_json_file = source_json @@ -59,16 +60,9 @@ def __init__( self.customized_project = None else: self.customized_project = customized_project - if action is None: - self.action = relecov_tools.utils.prompt_selection( - msg="Select the action to upload to ENA", - choices=["add", "modify", "cancel", "release"], - ) - else: - self.action = action.upper() if output_path is None: self.output_path = relecov_tools.utils.prompt_path( - msg="Select the folder to store the xml files" + msg="Select the folder to store the log files" ) else: self.output_path = output_path @@ -100,8 +94,11 @@ def metadata_to_csv(self): # Unificar en multifasta # Cambiar headers/id + # Upload # Subir con cli3 + # Token + # Opción de configurar proxy # def upload(self): # """Create the required files and upload to ENA""" From 839566c7f73d62b02c9a4a4ab953e0f8377a3ca6 Mon Sep 17 00:00:00 2001 From: ibloise Date: Fri, 1 Jul 2022 13:54:51 +0200 Subject: [PATCH 0638/1454] linting --- relecov_tools/gisaid_upload.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 5b9a23a3..7212f463 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -40,20 +40,20 @@ def __init__( ) else: self.user = user - #Add proxy settings: username:password@proxy:port (optional) + # Add proxy settings: username:password@proxy:port (optional) if passwd is None: self.passwd = relecov_tools.utils.prompt_password( msg="Enter your password to GISAID" ) else: self.passwd = passwd - if source_json is None: + if self.source_json is None: self.source_json_file = relecov_tools.utils.prompt_path( msg="Select the GISAID json file to upload" ) else: self.source_json_file = source_json - if customized_project is None: + if self.customized_project is None: self.customized_project = None else: self.customized_project = customized_project @@ -121,4 +121,4 @@ def change_headers(self, multifasta): # def upload(self): # """Create the required files and upload to ENA""" # self.convert_input_json_to_ena() - # self.create_structure_to_ena() + # self.create_structure_to_ena() \ No newline at end of file From 1c86e0b29a6d1c9f3ac140a5fe121673dd0fb343 Mon Sep 17 00:00:00 2001 From: ibloise Date: Fri, 1 Jul 2022 14:00:42 +0200 Subject: [PATCH 0639/1454] linting --- relecov_tools/gisaid_upload.py | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 7212f463..03dc3465 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -52,11 +52,11 @@ def __init__( msg="Select the GISAID json file to upload" ) else: - self.source_json_file = source_json + self.source_json_file = self.source_json if self.customized_project is None: self.customized_project = None else: - self.customized_project = customized_project + self.customized_project = self.customized_project if output_path is None: self.output_path = relecov_tools.utils.prompt_path( msg="Select the folder to store the log files" @@ -112,13 +112,13 @@ def change_headers(self, multifasta): record.id = name SeqIO.write(record, new_fasta, "fasta") - - # Upload - # Subir con cli3 - # Token - # Opción de configurar proxy - - # def upload(self): - # """Create the required files and upload to ENA""" - # self.convert_input_json_to_ena() - # self.create_structure_to_ena() \ No newline at end of file + """" + Upload + Subir con cli3 + Token + Opción de configurar proxy + def upload(self): + Create the required files and upload to ENA + self.convert_input_json_to_ena() + self.create_structure_to_ena() + """ \ No newline at end of file From 72d32c653746d5d34a4dc3d32ba266356d488ee3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Adri=C3=A1n=20Mu=C3=B1oz=20Barrera?= Date: Fri, 1 Jul 2022 13:12:21 +0100 Subject: [PATCH 0640/1454] Added outer functionallity to metadata_homogeneizer.py --- relecov_tools/metadata_homogeneizer.py | 51 ++++++++++++++++++- .../schema/institution_schemas/template.json | 15 ++++-- 2 files changed, 60 insertions(+), 6 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index c6a411f1..6fbcc1c1 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -105,6 +105,7 @@ def associate_dict(self): if key.lower() in self.filename.split("/")[-1].lower(): detected[key] = institution_dict[key] + # Creemos que este bloque ifelse iría fuera del for if len(set(detected.values())) == 0: stderr.print( f"[red]No institution pattern could be found in the '{self.filename}' filename given." @@ -193,8 +194,54 @@ def translate_dataframe(self): pass else: for key, value in self.dictionary["outer"].items(): - value["filename"] - + if len(value) == 0: + log.error(f"Found empty outer in the '{self.dictionary_path}' schema: '{key}'") + stderr.print(f"[red]Found empty outer in the '{self.dictionary_path}' schema: '{key}'") + sys.exit(1) + else: + outer_filename = value["filename"] + outer_sheet = value["sheet"] + outer_column = value["column"] + outer_samplename_col = value["samplename_col"] + + outer_dataframe = None + outer_translated_dataframe = None + #outer_dataframe = identify_load_dataframe(outer_filename) + + if check_extension(outer_filename) == "excel": + if len(outer_sheet) == 0: + log.error(f"There is missing information, sheet name must be provided.") + stderr.print(f"[red]There is missing information, sheet name must be provided.") + sys.exit(1) + else: + outer_dataframe = pd.read_excel(outer_filename, header=0, sheet_name = outer_sheet) + elif check_extension(filename) == "odf": + if len(outer_sheet) == 0: + log.error(f"There is missing information, sheet name must be provided.") + stderr.print(f"[red]There is missing information, sheet name must be provided.") + sys.exit(1) + else: + outer_dataframe = pd.read_excel(outer_filename, engine="odf", header=0) + elif check_extension(filename) == "csv": + outer_dataframe = pd.read_csv(outer_filename, sep=",", header=0) + elif check_extension(filename) == "tsv": + outer_dataframe = pd.read_csv(outer_filename, sep="\t", header=0) + + if len(outer_column) == 0: + log.error(f"There is missing information, column name must be provided.") + stderr.print(f"[red]There is missing information, column name must be provided.") + sys.exit(1) + else: + outer_translated_dataframe[key] = outer_dataframe[outer_column.strip()] + + if len(outer_samplename_col) == 0: + log.error(f"There is missing information, samplename_col must be provided.") + stderr.print(f"[red]There is missing information, samplename_col must be provided.") + sys.exit(1) + else: + # Review left_on key (this key must be present in translated data_frame) + outer_translated_dataframe[outer_samplename_col] = outer_dataframe[outer_samplename_col.strip()] + translated_dataframe.merge(outer_translated_dataframe, left_on="Sample ID given by originating laboratory", right_on=outer_samplename_col]) return def verify_translated_dataframe(self): diff --git a/relecov_tools/schema/institution_schemas/template.json b/relecov_tools/schema/institution_schemas/template.json index 9e1743fc..ba335aca 100644 --- a/relecov_tools/schema/institution_schemas/template.json +++ b/relecov_tools/schema/institution_schemas/template.json @@ -4,12 +4,19 @@ }, "constants": { "Final_term": "Constant value" - }, + }, "outer": { - "final term" : { + "final term 1": { "filename":"filename", "sheet" : "in case of excel format, state sheet", "column" : "name of the column where the needed value is", - "samplename_col" : "name of the column containing the samplenames"} - } + "samplename_col" : "name of the column containing the samplenames" + }, + "final term 2" : { + "filename":"filename 2", + "sheet" : "in case of excel format, state sheet 2", + "column" : "name of the column where the needed value is 2", + "samplename_col" : "name of the column containing the samplenames 2" + } + } } \ No newline at end of file From f3b632f61e536d7d9610e8a5cc929239c59b49a9 Mon Sep 17 00:00:00 2001 From: ibloise Date: Fri, 1 Jul 2022 15:21:19 +0200 Subject: [PATCH 0641/1454] linting --- relecov_tools/gisaid_upload.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 3241d434..77544c01 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -148,4 +148,4 @@ def upload(self): Create the required files and upload to ENA self.convert_input_json_to_ena() self.create_structure_to_ena() - """ \ No newline at end of file + """ From 5179aa082f7c7e6fe70fe87f64feb896250c2ef1 Mon Sep 17 00:00:00 2001 From: ibloise Date: Fri, 1 Jul 2022 15:24:51 +0200 Subject: [PATCH 0642/1454] linting --- relecov_tools/gisaid_upload.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 77544c01..11956aeb 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -139,7 +139,7 @@ def change_headers(self, multifasta): record.id = name SeqIO.write(record, new_fasta, "fasta") - """" + """" Upload Subir con cli3 Token From 3deb7b7114c230a1d4652921709c5a6bcd1af0ba Mon Sep 17 00:00:00 2001 From: mlarjim Date: Fri, 1 Jul 2022 15:25:16 +0200 Subject: [PATCH 0643/1454] Added comments for sending logging messages by email --- relecov_tools/json_validation.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 7b200fce..bf8ae573 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -29,7 +29,8 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): ) if json_schema_file is None: config_json = ConfigJson() - schema_name = config_json.get_topic_data("json_schemas", "relecov_schema") + schema_name = config_json.get_topic_data( + "json_schemas", "relecov_schema") json_schema_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", schema_name ) @@ -39,7 +40,8 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): try: Draft202012Validator.check_schema(json_schema) except jsonschema.ValidationError: - stderr.print("[red] Json schema does not fulfil Draft 202012 Validation") + stderr.print( + "[red] Json schema does not fulfil Draft 202012 Validation") sys.exit(1) if not os.path.isfile(json_data_file): stderr.print("[red] Json file does not exists") @@ -57,7 +59,8 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): except jsonschema.ValidationError as e: log.error("Invalid sample data %s", e) invalid_json.append(item_row) - logging.handl + # Enviar los errores por correo + # logging.handlers.SMTPHandler(mailhost=("smtp.gmail.com", 465), fromaddr=correo_isciii, toaddrs=correo_usuario, subject="Validation errors", credentials=(usurario,contraseña), secure=None, timeout=1.0) return validated_json_data, invalid_json, errors From bcdb1ebbdc7ab8dc757828081c95c42febd05ae0 Mon Sep 17 00:00:00 2001 From: mlarjim Date: Fri, 1 Jul 2022 15:28:55 +0200 Subject: [PATCH 0644/1454] Lintin 1 --- relecov_tools/json_validation.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index bf8ae573..7a769e30 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -29,8 +29,7 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): ) if json_schema_file is None: config_json = ConfigJson() - schema_name = config_json.get_topic_data( - "json_schemas", "relecov_schema") + schema_name = config_json.get_topic_data("json_schemas", "relecov_schema") json_schema_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", schema_name ) @@ -40,8 +39,7 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): try: Draft202012Validator.check_schema(json_schema) except jsonschema.ValidationError: - stderr.print( - "[red] Json schema does not fulfil Draft 202012 Validation") + stderr.print("[red] Json schema does not fulfil Draft 202012 Validation") sys.exit(1) if not os.path.isfile(json_data_file): stderr.print("[red] Json file does not exists") From 3980dec292c0a0253ee8bd69f9d0db7203ae807e Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Fri, 1 Jul 2022 16:27:21 +0200 Subject: [PATCH 0645/1454] linting --- relecov_tools/metadata_homogeneizer.py | 78 ++++++++++++++++++-------- 1 file changed, 56 insertions(+), 22 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 85312a95..1dbe93e7 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -113,7 +113,7 @@ def associate_dict(self): f"[red]No institution pattern could be found in the '{self.filename}' filename given." ) sys.exit(1) - + elif len(set(detected.values())) > 1: repeated = ", ".join(list(set(detected.values))) log.error( @@ -207,8 +207,12 @@ def translate_dataframe(self): else: for key, value in self.dictionary["outer"].items(): if len(value) == 0: - log.error(f"Found empty outer in the '{self.dictionary_path}' schema: '{key}'") - stderr.print(f"[red]Found empty outer in the '{self.dictionary_path}' schema: '{key}'") + log.error( + f"Found empty outer in the '{self.dictionary_path}' schema: '{key}'" + ) + stderr.print( + f"[red]Found empty outer in the '{self.dictionary_path}' schema: '{key}'" + ) sys.exit(1) else: outer_filename = value["filename"] @@ -218,42 +222,72 @@ def translate_dataframe(self): outer_dataframe = None outer_translated_dataframe = None - #outer_dataframe = identify_load_dataframe(outer_filename) + # outer_dataframe = identify_load_dataframe(outer_filename) if check_extension(outer_filename) == "excel": if len(outer_sheet) == 0: - log.error(f"There is missing information, sheet name must be provided.") - stderr.print(f"[red]There is missing information, sheet name must be provided.") + log.error( + "There is missing information, sheet name must be provided." + ) + stderr.print( + "[red]There is missing information, sheet name must be provided." + ) sys.exit(1) else: - outer_dataframe = pd.read_excel(outer_filename, header=0, sheet_name = outer_sheet) - elif check_extension(filename) == "odf": + outer_dataframe = pd.read_excel( + outer_filename, header=0, sheet_name=outer_sheet + ) + elif check_extension(outer_filename) == "odf": if len(outer_sheet) == 0: - log.error(f"There is missing information, sheet name must be provided.") - stderr.print(f"[red]There is missing information, sheet name must be provided.") + log.error( + "There is missing information, sheet name must be provided." + ) + stderr.print( + "[red]There is missing information, sheet name must be provided." + ) sys.exit(1) else: - outer_dataframe = pd.read_excel(outer_filename, engine="odf", header=0) - elif check_extension(filename) == "csv": + outer_dataframe = pd.read_excel( + outer_filename, engine="odf", header=0 + ) + elif check_extension(outer_filename) == "csv": outer_dataframe = pd.read_csv(outer_filename, sep=",", header=0) - elif check_extension(filename) == "tsv": - outer_dataframe = pd.read_csv(outer_filename, sep="\t", header=0) + elif check_extension(outer_filename) == "tsv": + outer_dataframe = pd.read_csv( + outer_filename, sep="\t", header=0 + ) if len(outer_column) == 0: - log.error(f"There is missing information, column name must be provided.") - stderr.print(f"[red]There is missing information, column name must be provided.") + log.error( + "There is missing information, column name must be provided." + ) + stderr.print( + "[red]There is missing information, column name must be provided." + ) sys.exit(1) else: - outer_translated_dataframe[key] = outer_dataframe[outer_column.strip()] - + outer_translated_dataframe[key] = outer_dataframe[ + outer_column.strip() + ] + if len(outer_samplename_col) == 0: - log.error(f"There is missing information, samplename_col must be provided.") - stderr.print(f"[red]There is missing information, samplename_col must be provided.") + log.error( + "There is missing information, samplename_col must be provided." + ) + stderr.print( + "[red]There is missing information, samplename_col must be provided." + ) sys.exit(1) else: # Review left_on key (this key must be present in translated data_frame) - outer_translated_dataframe[outer_samplename_col] = outer_dataframe[outer_samplename_col.strip()] - translated_dataframe.merge(outer_translated_dataframe, left_on="Sample ID given by originating laboratory", right_on=outer_samplename_col]) + outer_translated_dataframe[ + outer_samplename_col + ] = outer_dataframe[outer_samplename_col.strip()] + self.translated_dataframe.merge( + outer_translated_dataframe, + left_on="Sample ID given by originating laboratory", + right_on=outer_samplename_col, + ) return def verify_translated_dataframe(self): From edd602ab428bfb1c1e4b6ff61d9f03e70d3fd3e0 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 8 Jul 2022 12:49:55 +0200 Subject: [PATCH 0646/1454] added client_id argument to create auth token gisaid --- relecov_tools/gisaid_upload.py | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 11956aeb..81eb67e1 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -32,6 +32,7 @@ def __init__( self, user=None, passwd=None, + client_id=None, gisaid_json=None, fasta_path=None, output_path=None, @@ -49,6 +50,12 @@ def __init__( ) else: self.passwd = passwd + if client_id is None: + self.client_id = relecov_tools.utils.prompt_password( + msg="Enter your client_id to GISAID. Email clisupport@gisaid.org to request client-ID." + ) + else: + self.passwd = passwd if self.source_json is None: self.source_json_file = relecov_tools.utils.prompt_path( msg="Select the GISAID json file to upload" @@ -115,8 +122,7 @@ def metadata_to_csv(self): --log default creates file failed.out where the log will be ) """ - # Sequences - # Unificar en multifasta + def create_multifasta(self): """Create multifasta from single fastas""" os.system( @@ -138,6 +144,13 @@ def change_headers(self, multifasta): if record.id == name.split("/")[-2]: record.id = name SeqIO.write(record, new_fasta, "fasta") + + def cli3_authenticate(self): + """Create authenticate token""" + os.system( + "cli3 authenticate --username %s --password %s --client_id %s" % (self.user, self.passw, self.client_id) + ) + """" Upload From e2bd8d1c10db955480f0cc271e04a66433aa3391 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 8 Jul 2022 12:54:21 +0200 Subject: [PATCH 0647/1454] added token argument to gisaid_upload --- relecov_tools/gisaid_upload.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 81eb67e1..e0985a01 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -33,6 +33,7 @@ def __init__( user=None, passwd=None, client_id=None, + token=None, gisaid_json=None, fasta_path=None, output_path=None, @@ -52,10 +53,16 @@ def __init__( self.passwd = passwd if client_id is None: self.client_id = relecov_tools.utils.prompt_password( - msg="Enter your client_id to GISAID. Email clisupport@gisaid.org to request client-ID." + msg="Enter your client_id to GISAID. Email clisupport@gisaid.org to request client-ID" ) else: - self.passwd = passwd + self.client_id = client_id + if token is None: + self.token = relecov_tools.utils.prompt_password( + msg="Enter path to your authenticate token" + ) + else: + self.token = token if self.source_json is None: self.source_json_file = relecov_tools.utils.prompt_path( msg="Select the GISAID json file to upload" From bad576a44dc499a7bb262fc00ff7114df0b03b48 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 8 Jul 2022 13:10:25 +0200 Subject: [PATCH 0648/1454] added authenticate function to gisaid_upload --- relecov_tools/gisaid_upload.py | 58 ++++++++++++++++------------------ 1 file changed, 27 insertions(+), 31 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index e0985a01..f3c712c7 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -38,38 +38,40 @@ def __init__( fasta_path=None, output_path=None, ): - if user is None: - self.user = relecov_tools.utils.prompt_text( - msg="Enter your username defined in GISAID" - ) - else: - self.user = user - # Add proxy settings: username:password@proxy:port (optional) - if passwd is None: - self.passwd = relecov_tools.utils.prompt_password( - msg="Enter your password to GISAID" - ) - else: - self.passwd = passwd - if client_id is None: - self.client_id = relecov_tools.utils.prompt_password( - msg="Enter your client_id to GISAID. Email clisupport@gisaid.org to request client-ID" - ) - else: - self.client_id = client_id - if token is None: + if token is None: # borrar comentario: solo si no existe el token necesita user, passwd y client_id self.token = relecov_tools.utils.prompt_password( - msg="Enter path to your authenticate token" + msg="Token is not introduced, creating a new one..." ) + if user is None: + self.user = relecov_tools.utils.prompt_text( + msg="Enter your username defined in GISAID" + ) + else: + self.user = user + # Add proxy settings: username:password@proxy:port (optional) + if passwd is None: + self.passwd = relecov_tools.utils.prompt_password( + msg="Enter your password to GISAID" + ) + else: + self.passwd = passwd + if client_id is None: + self.client_id = relecov_tools.utils.prompt_password( + msg="Enter your client_id to GISAID. Email clisupport@gisaid.org to request client-ID" + ) + else: + self.client_id = client_id else: self.token = token - if self.source_json is None: - self.source_json_file = relecov_tools.utils.prompt_path( + + + if self.gisaid_json is None: + self.gisaid_json = relecov_tools.utils.prompt_path( msg="Select the GISAID json file to upload" ) else: - self.source_json_file = self.source_json - if self.customized_project is None: + self.gisaid_json = self.gisaid_json + if self.customized_project is None: #borrar comentario: esta parte no la entiendo, no la toco self.customized_project = None else: self.customized_project = self.customized_project @@ -79,12 +81,6 @@ def __init__( ) else: self.output_path = output_path - if gisaid_json is None: - self.gisaid_json = relecov_tools.utils.prompt_path( - msg="Select metadata json file" - ) - else: - self.gisaid_json = gisaid_json if fasta_path is None: self.fasta_path = relecov_tools.utils.prompt_path(msg="Select path") else: From 5e949ff49ec31daf88e74e4029bb8b58475058bb Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 8 Jul 2022 13:27:52 +0200 Subject: [PATCH 0649/1454] added frameshift argument to gisaid_upload --- relecov_tools/gisaid_upload.py | 26 +++++++++++++++++++++----- 1 file changed, 21 insertions(+), 5 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index f3c712c7..6ec39ea4 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -37,10 +37,11 @@ def __init__( gisaid_json=None, fasta_path=None, output_path=None, + frameshift=None, ): if token is None: # borrar comentario: solo si no existe el token necesita user, passwd y client_id - self.token = relecov_tools.utils.prompt_password( - msg="Token is not introduced, creating a new one..." + print( + "Token is not introduced, creating a new one..." ) if user is None: self.user = relecov_tools.utils.prompt_text( @@ -63,8 +64,6 @@ def __init__( self.client_id = client_id else: self.token = token - - if self.gisaid_json is None: self.gisaid_json = relecov_tools.utils.prompt_path( msg="Select the GISAID json file to upload" @@ -93,6 +92,13 @@ def __init__( sys.exit(1) with open(self.source_json_file, "r") as fh: self.json_data = json.loads(fh.read()) + if frameshift is None: + self.frameshift = relecov_tools.utils.prompt_selection( + msg="Select frameshift notification", + choices="catch_all, catch_novel, catch_none" + ) + else: + self.frameshift = frameshift def convert_input_json_to_ena(self): """Split the input ena json, in samples and runs json""" @@ -148,11 +154,21 @@ def change_headers(self, multifasta): record.id = name SeqIO.write(record, new_fasta, "fasta") - def cli3_authenticate(self): + def cli3_auth(self): """Create authenticate token""" os.system( "cli3 authenticate --username %s --password %s --client_id %s" % (self.user, self.passw, self.client_id) ) + + """ + def gisaid_upload(self): + ""Upload to GISAID"" + self.metadata_to_csv() + self.create_multifasta() + self.change_headers() + if token is None: + self.cli3_auth() + """ """" From 0be90ebf06b08ff9eab4d78809170cbf9063884f Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 8 Jul 2022 13:42:16 +0200 Subject: [PATCH 0650/1454] added proxy_config argument to gisaid_upload --- relecov_tools/gisaid_upload.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 6ec39ea4..1092a991 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -38,6 +38,7 @@ def __init__( fasta_path=None, output_path=None, frameshift=None, + proxy_config=None, ): if token is None: # borrar comentario: solo si no existe el token necesita user, passwd y client_id print( @@ -99,6 +100,10 @@ def __init__( ) else: self.frameshift = frameshift + if proxy_config is None: + print("Proxy configuration is not set") # borrar comentario: esta mensaje no me convence + else: + self.proxy_config = proxy_config def convert_input_json_to_ena(self): """Split the input ena json, in samples and runs json""" @@ -159,6 +164,11 @@ def cli3_auth(self): os.system( "cli3 authenticate --username %s --password %s --client_id %s" % (self.user, self.passw, self.client_id) ) + + def cli3_upload(self): + """Upload to GISAID""" + os.system( + "cli3 upload --token %s --metadata %s --fasta %s --frameshift %s """ def gisaid_upload(self): From 994efd2979bea82955d9ba6121b5dbb7e4cc4281 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 8 Jul 2022 13:48:28 +0200 Subject: [PATCH 0651/1454] modified metadata_to_csv function in gisaid_upload --- relecov_tools/gisaid_upload.py | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 1092a991..c2ebc98e 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -115,7 +115,9 @@ def metadata_to_csv(self): "Transform metadata json to csv" data = relecov_tools.utils.read_json_file(self.metadata) df_data = pd.DataFrame(data) - df_data.to_csv("meta_gisaid.csv") + df_data.to_csv("%s/meta_gisaid.csv" % self.output_path) + metagisaid = "%s/meta_gisaid.csv" % self.output_path + return metagisaid # generar template con cli3 # ADD TOKEN WARNING and file token .authtoken @@ -167,8 +169,14 @@ def cli3_auth(self): def cli3_upload(self): """Upload to GISAID""" - os.system( + if proxy_config is None: + os.system( "cli3 upload --token %s --metadata %s --fasta %s --frameshift %s + ) + else: + os.system( + "cli3 upload --token %s --metadata %s --fasta %s --frameshift %s --proxy %s" % (self.token, self.output_path + "/ + ) """ def gisaid_upload(self): From 32d3064edfb66d7132ed1664a0eb3eff2502f7c9 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 8 Jul 2022 13:50:55 +0200 Subject: [PATCH 0652/1454] modified change_headers function in gisaid_upload --- relecov_tools/gisaid_upload.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index c2ebc98e..963d60fd 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -160,6 +160,8 @@ def change_headers(self, multifasta): if record.id == name.split("/")[-2]: record.id = name SeqIO.write(record, new_fasta, "fasta") + fastagisaid = "%s/multifasta_gisaid.fasta" % self.output_path + return fastagisaid def cli3_auth(self): """Create authenticate token""" @@ -175,7 +177,7 @@ def cli3_upload(self): ) else: os.system( - "cli3 upload --token %s --metadata %s --fasta %s --frameshift %s --proxy %s" % (self.token, self.output_path + "/ + "cli3 upload --token %s --metadata %s --fasta %s --frameshift %s --proxy %s" % (self.token, metagisaid, ) """ From 8edd914ec9bd0217975696436e2269f5b5935143 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 8 Jul 2022 13:53:30 +0200 Subject: [PATCH 0653/1454] added cli3_upload function to gisaid_upload --- relecov_tools/gisaid_upload.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 963d60fd..fa0adae9 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -173,11 +173,11 @@ def cli3_upload(self): """Upload to GISAID""" if proxy_config is None: os.system( - "cli3 upload --token %s --metadata %s --fasta %s --frameshift %s + "cli3 upload --token %s --metadata %s --fasta %s --frameshift %s" % (self.token, metagisaid, fastagisaid, self.frameshift) ) else: os.system( - "cli3 upload --token %s --metadata %s --fasta %s --frameshift %s --proxy %s" % (self.token, metagisaid, + "cli3 upload --token %s --metadata %s --fasta %s --frameshift %s --proxy %s" % (self.token, metagisaid, fastagisaid, self.frameshift, self.proxy_config) ) """ @@ -188,6 +188,7 @@ def gisaid_upload(self): self.change_headers() if token is None: self.cli3_auth() + self.cli3_upload() """ From 4385332c37952eb9bad7a791dcd82f6f797f658b Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 8 Jul 2022 14:10:09 +0200 Subject: [PATCH 0654/1454] Ready for lintin (gisaid_upload) --- relecov_tools/gisaid_upload.py | 57 +++++++++++++++++++++------------- 1 file changed, 35 insertions(+), 22 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index fa0adae9..cb4d9468 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -40,10 +40,10 @@ def __init__( frameshift=None, proxy_config=None, ): - if token is None: # borrar comentario: solo si no existe el token necesita user, passwd y client_id - print( - "Token is not introduced, creating a new one..." - ) + if ( + token is None + ): # borrar comentario: solo si no existe el token necesita user, passwd y client_id + print("Token is not introduced, creating a new one...") if user is None: self.user = relecov_tools.utils.prompt_text( msg="Enter your username defined in GISAID" @@ -59,10 +59,10 @@ def __init__( self.passwd = passwd if client_id is None: self.client_id = relecov_tools.utils.prompt_password( - msg="Enter your client_id to GISAID. Email clisupport@gisaid.org to request client-ID" + msg="Enter your client-ID to GISAID. Email clisupport@gisaid.org to request client-ID" ) else: - self.client_id = client_id + self.client_id = client_id else: self.token = token if self.gisaid_json is None: @@ -71,7 +71,9 @@ def __init__( ) else: self.gisaid_json = self.gisaid_json - if self.customized_project is None: #borrar comentario: esta parte no la entiendo, no la toco + if ( + self.customized_project is None + ): # borrar comentario: esta parte no la entiendo, no la toco self.customized_project = None else: self.customized_project = self.customized_project @@ -96,12 +98,13 @@ def __init__( if frameshift is None: self.frameshift = relecov_tools.utils.prompt_selection( msg="Select frameshift notification", - choices="catch_all, catch_novel, catch_none" + choices="catch_all, catch_novel, catch_none", ) else: self.frameshift = frameshift if proxy_config is None: - print("Proxy configuration is not set") # borrar comentario: esta mensaje no me convence + # borrar comentario: este mensaje no me convence + print("Proxy configuration is not set") else: self.proxy_config = proxy_config @@ -138,7 +141,6 @@ def metadata_to_csv(self): --log default creates file failed.out where the log will be ) """ - def create_multifasta(self): """Create multifasta from single fastas""" os.system( @@ -162,35 +164,46 @@ def change_headers(self, multifasta): SeqIO.write(record, new_fasta, "fasta") fastagisaid = "%s/multifasta_gisaid.fasta" % self.output_path return fastagisaid - + def cli3_auth(self): """Create authenticate token""" os.system( - "cli3 authenticate --username %s --password %s --client_id %s" % (self.user, self.passw, self.client_id) - ) - + "cli3 authenticate --username %s --password %s --client_id %s" + % (self.user, self.passwd, self.client_id) + ) + def cli3_upload(self): """Upload to GISAID""" - if proxy_config is None: + if self.proxy_config is None: os.system( - "cli3 upload --token %s --metadata %s --fasta %s --frameshift %s" % (self.token, metagisaid, fastagisaid, self.frameshift) + "cli3 upload --token %s --metadata %s --fasta %s --frameshift %s" + % ( + self.token, + self.metadata_to_csv(), + self.change_headers(), + self.frameshift, + ) ) else: os.system( - "cli3 upload --token %s --metadata %s --fasta %s --frameshift %s --proxy %s" % (self.token, metagisaid, fastagisaid, self.frameshift, self.proxy_config) + "cli3 upload --token %s --metadata %s --fasta %s --frameshift %s --proxy %s" + % ( + self.token, + self.metadata_to_csv(), + self.change_headers(), + self.frameshift, + self.proxy_config, + ) ) - + """ def gisaid_upload(self): ""Upload to GISAID"" - self.metadata_to_csv() self.create_multifasta() - self.change_headers() if token is None: self.cli3_auth() self.cli3_upload() - """ - + """ """" Upload From 6a6e7bc2568781e6be03c19fed85c49552f2ddb0 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 8 Jul 2022 14:15:04 +0200 Subject: [PATCH 0655/1454] lintin 1 --- relecov_tools/gisaid_upload.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index cb4d9468..d64e9652 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -196,7 +196,7 @@ def cli3_upload(self): ) ) - """ + """ def gisaid_upload(self): ""Upload to GISAID"" self.create_multifasta() From 720c0f22a67e326254259d1672a7c3eaffb3327d Mon Sep 17 00:00:00 2001 From: birbi Date: Sat, 9 Jul 2022 04:59:38 +0200 Subject: [PATCH 0656/1454] testing feed-db --- relecov_tools/conf/configuration.json | 6 ++++++ relecov_tools/long_table_parse.py | 8 +++++--- 2 files changed, 11 insertions(+), 3 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 059c6f5d..b6ee596f 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -44,6 +44,12 @@ "url": "/api/", "store_samples": "storeData", "token": "" + }, + "relecov_local": { + "server": "http://127.0.0.1:8000", + "url": "/api/", + "store_samples": "createSampleData", + "token": "" } }, "iskylims_sample_fields": { diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index b63eff17..11cddfe3 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -103,13 +103,13 @@ def parse_a_list_of_dictionaries(self): # check if the headers of both files are the same for heading_csv in headings_from_csv: if heading_csv not in dict_index_of_heading: - stderr.print("[red]Incorrect Format, fields don't match") + stderr.print(f"[red]Incorrect Format {heading_csv}, fields don't match") sys.exit(1) dict_aux = {} # check if both files contain the same number of fields if len(self.long_table_heading) is len(headings_from_csv): - + """ # check if the headers of both files have the same order for idx in range(len(self.long_table_heading)): if self.long_table_heading[idx] != headings_from_csv[idx]: @@ -123,6 +123,7 @@ def parse_a_list_of_dictionaries(self): dict_index_of_heading = dict_aux print(dict_index_of_heading) """ + """ stderr.print( "[red]Incorrect Format, fields don't have the same order" ) @@ -221,4 +222,5 @@ def parse_a_list_of_dictionaries(self): def parsing_csv(self): generated_json = self.parse_a_list_of_dictionaries() - self.saving_file(generated_JSON=generated_json) + self.saving_file(generated_json) + return From 758a9d4abd195bcfe3fd0d6959a7fa123daab758 Mon Sep 17 00:00:00 2001 From: birbi Date: Sat, 9 Jul 2022 05:11:08 +0200 Subject: [PATCH 0657/1454] testing feed-db4 --- relecov_tools/long_table_parse.py | 129 ------------------------------ 1 file changed, 129 deletions(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index e94a91fd..ca3652a7 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -90,134 +90,6 @@ def parse_file(self): heading_index = {} headings_from_csv = lines[0].strip().split(",") for heading in self.long_table_heading: -<<<<<<< HEAD - dict_index_of_heading[heading] = self.long_table_heading.index(heading) - - # check if the headers of both files are the same - for heading_csv in headings_from_csv: - if heading_csv not in dict_index_of_heading: - stderr.print(f"[red]Incorrect Format {heading_csv}, fields don't match") - sys.exit(1) - - dict_aux = {} - # check if both files contain the same number of fields - if len(self.long_table_heading) is len(headings_from_csv): - """ - # check if the headers of both files have the same order - for idx in range(len(self.long_table_heading)): - if self.long_table_heading[idx] != headings_from_csv[idx]: - - for heading in headings_from_csv: - dict_aux[heading] = headings_from_csv.index(heading) - - print(dict_index_of_heading) - print(dict_aux) - dict_index_of_heading.clear() - dict_index_of_heading = dict_aux - print(dict_index_of_heading) - """ - """ - stderr.print( - "[red]Incorrect Format, fields don't have the same order" - ) - sys.exit(1) - """ - - for line in lines[1:]: - data_dict_from_long_table = {} - data_list = line.strip().split(",") - - data_dict_from_long_table["Chromosome"] = { - "chromosome": data_list[dict_index_of_heading["CHROM"]] - } - - data_dict_from_long_table["Position"] = { - "pos": data_list[dict_index_of_heading["POS"]], - "nucleotide": data_list[dict_index_of_heading["ALT"]], - } - - data_dict_from_long_table["Filter"] = { - "filter": data_list[dict_index_of_heading["FILTER"]] - } - - data_dict_from_long_table["VariantInSample"] = { - "dp": data_list[dict_index_of_heading["DP"]], - "ref_dp": data_list[dict_index_of_heading["REF_DP"]], - "alt_dp": data_list[dict_index_of_heading["ALT_DP"]], - "af": data_list[dict_index_of_heading["AF"]], - } - - data_dict_from_long_table["Gene"] = { - "gene": data_list[dict_index_of_heading["GENE"]] - } - - data_dict_from_long_table["Effect"] = { - "effect": data_list[dict_index_of_heading["EFFECT"]], - "hgvs_c": data_list[dict_index_of_heading["HGVS_C"]], - "hgvs_p": data_list[dict_index_of_heading["HGVS_P"]], - "hgvs_p_1_letter": data_list[ - dict_index_of_heading["HGVS_P_1LETTER"] - ], - } - - data_dict_from_long_table["Variant"] = { - "ref": data_list[dict_index_of_heading["REF"]] - } - - data_dict_from_long_table["Sample"] = { - "sample": data_list[dict_index_of_heading["SAMPLE"]] - } - - list_of_dictionaries.append(data_dict_from_long_table) - - """ - for line in lines[1:]: - data_dict_from_long_table = {} - data_list = line.strip().split(",") - - data_dict_from_long_table["Chromosome"] = {"chromosome": data_list[1]} - - data_dict_from_long_table["Position"] = { - "pos": data_list[2], - "nucleotide": data_list[4], - } - - data_dict_from_long_table["Filter"] = {"filter": data_list[5]} - - data_dict_from_long_table["VariantInSample"] = { - "dp": data_list[6], - "ref_dp": data_list[7], - "alt_dp": data_list[8], - "af": data_list[9], - } - - data_dict_from_long_table["Gene"] = {"gene": data_list[10]} - - data_dict_from_long_table["Effect"] = { - "effect": data_list[11], - "hgvs_c": data_list[12], - "hgvs_p": data_list[13], - "hgvs_p_1_letter": data_list[14], - } - - data_dict_from_long_table["Variant"] = {"ref": data_list[3]} - - data_dict_from_long_table["Sample"] = {"sample": data_list[0]} - - list_of_dictionaries.append(data_dict_from_long_table) - """ - return json.dumps(list_of_dictionaries, indent=4) - else: - print( - "[red]Incorrect format, the headers do not have the same number of fields" - ) - sys.exit(1) - - def parsing_csv(self): - generated_json = self.parse_a_list_of_dictionaries() - self.saving_file(generated_json) - return -======= heading_index[heading] = headings_from_csv.index(heading) samp_dict = {} @@ -288,4 +160,3 @@ def parsing_csv(self): parsed_data = self.parse_file() j_list = self.convert_to_json(parsed_data) self.saving_file(j_list) ->>>>>>> c1babf3bd87dab20e5f17a9462883d0e8676a3fe From c4e45a5b2894934c99cf616e3602976b38f413be Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Mon, 11 Jul 2022 12:29:26 +0200 Subject: [PATCH 0658/1454] added output_path to save receipt.xml in ena_upload.py --- relecov_tools/ena_upload.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index c7bc326d..1e9dbf22 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -347,9 +347,10 @@ def create_structure_to_ena(self): print(f"\nSubmitting XMLs to ENA server: {url}") receipt = send_schemas(schema_xmls, url, self.user, self.passwd).text - print("Printing receipt to ./receipt.xml") + receipt_dir= os.path.join(self.output_path, "receipt.xml") + print(f"Printing receipt to {receipt_dir}") - with open("receipt.xml", "w") as fw: + with open(f"{receipt_dir}", "w") as fw: fw.write(receipt) try: schema_update = process_receipt(receipt.encode("utf-8"), self.action) From 64680fd6eb016c453a003fc02151b3f1b15039f8 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Mon, 11 Jul 2022 12:33:12 +0200 Subject: [PATCH 0659/1454] added if not output_path exists, mkdir --- relecov_tools/ena_upload.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 1e9dbf22..15e95f5d 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -347,6 +347,8 @@ def create_structure_to_ena(self): print(f"\nSubmitting XMLs to ENA server: {url}") receipt = send_schemas(schema_xmls, url, self.user, self.passwd).text + if not os.path.exists(self.output_path): + os.mkdir(self.output_path) receipt_dir= os.path.join(self.output_path, "receipt.xml") print(f"Printing receipt to {receipt_dir}") From d4484e963597123bbf23cee65973b013e04b52b2 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Mon, 11 Jul 2022 12:35:32 +0200 Subject: [PATCH 0660/1454] Commented pdb --- relecov_tools/ena_upload.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 15e95f5d..009d9390 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -207,9 +207,9 @@ def create_structure_to_ena(self): df_run.loc[i, "sequence_file_R2_fastq"] = df_schemas.loc[ i, "sequence_file_R2_fastq" ] - import pdb + #import pdb - pdb.set_trace() + #pdb.set_trace() df_run.insert(3, "status", self.action) df_run = df_run.rename(columns={"fastq_r1_md5": "file_checksum"}) From f795bfe4f3aa014b879bb9a81778c888e0a8e891 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Mon, 11 Jul 2022 12:38:36 +0200 Subject: [PATCH 0661/1454] Lintin --- relecov_tools/ena_upload.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 009d9390..fcd71ea5 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -207,9 +207,9 @@ def create_structure_to_ena(self): df_run.loc[i, "sequence_file_R2_fastq"] = df_schemas.loc[ i, "sequence_file_R2_fastq" ] - #import pdb + # import pdb - #pdb.set_trace() + # pdb.set_trace() df_run.insert(3, "status", self.action) df_run = df_run.rename(columns={"fastq_r1_md5": "file_checksum"}) @@ -349,7 +349,7 @@ def create_structure_to_ena(self): receipt = send_schemas(schema_xmls, url, self.user, self.passwd).text if not os.path.exists(self.output_path): os.mkdir(self.output_path) - receipt_dir= os.path.join(self.output_path, "receipt.xml") + receipt_dir = os.path.join(self.output_path, "receipt.xml") print(f"Printing receipt to {receipt_dir}") with open(f"{receipt_dir}", "w") as fw: From ba69d046ab81ba0a5980d81e8944291a65cb2168 Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Mon, 11 Jul 2022 13:48:23 +0200 Subject: [PATCH 0662/1454] configuration.json-> added relecov_bioinfo_metadata_96_samples dictionary,feed_database.py -> modified function map_relecov_bioinfo_data(), store data->for local testing purpose(), def __init__() --- relecov_tools/conf/configuration.json | 66 +++++++++++++++++++++++++++ relecov_tools/feed_database.py | 40 +++++++++++++++- 2 files changed, 104 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index c8c4e0cf..795dca69 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -46,7 +46,16 @@ "analysis": "bioinfoData", "long_table": "longtableData", "token": "" + }, + "relecov_local": { + "server": "http://127.0.0.1:8000", + "url": "/api/", + "store_samples": "createSampleData", + "analysis": "bioinfoData", + "long_table": "longtableData", + "token": "" } + }, "iskylims_fixed_values": { "patientCore": "", @@ -92,6 +101,63 @@ "lineage_analysis_software_name": "pangolin", "if_lineage_identification_other": "None" }, + "relecov_bioinfo_metadata_96_samples":{ + "assembly": "None", + "assembly_params": "None", + "bioinformatics_protocol_software_name": "nf-core/viralrecon", + "bioinformatics_protocol_software_version": "2.4.1", + "commercial_open_source_both": "open-source", + "consensus_genome_length": "30396", + "consensus_params": "-p vcf -f", + "consensus_sequence_R1_md5": "dbcc703ccb7da3002fee6c0486199009", + "consensus_sequence_R1_name": "214821_S12_R1_001.fastq.gz", + "consensus_sequence_R2_md5": "b76fba963664b532004c4ce7153ae14f", + "consensus_sequence_R2_name": "214821_S12_R2_001.fastq.gz", + "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", + "consensus_sequence_software_version": "1.14", + "dehosting_method_software_name": "KRAKEN2_KRAKEN2", + "dehosting_method_software_version": "2.1.2", + "depth_of_coverage_threshold": ">10x", + "fastq_r1": "214821_S12_R1_001.fastq.gz", + "fastq_r2": "214821_S12_R2_001.fastq.gz", + "if_assembly_other": "None", + "if_bioinformatic_protocol_is_other_specify": "None", + "if_consensus_other": "None", + "if_lineage_identification_other": "None", + "if_mapping_other": "None", + "if_preprocessing_other": "None", + "lineage_analysis_software_name": "pangolin", + "lineage_analysis_software_version": "4.0.6", + "lineage_name": "B.1.177", + "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "mapping_params": "--seed 1", + "mapping_software_name": "BOWTIE2_ALIGN", + "mapping_software_version": "2.4.4", + "median_depth_of_coverage_value": "287.0", + "ns_per_100_kbp": "8442.32", + "number_of_base_pairs_sequenced": "633884", + "number_of_variants_AF_greater_75percent": "19", + "number_of_variants_with_effect": "9", + "per_Ns": "8,44", + "per_qc_filtered": "92,0", + "per_reads_host": "1,08", + "per_reads_virus": "98,54", + "per_unmapped": "0,380247", + "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", + "preprocessing_software_name": "FASTP", + "preprocessing_software_version": "0.23.2", + "quality_control_metrics": "", + "per_genome_greater_10x": "", + "analysis_date": "", + "depth_of_coverage_value": "", + "reference_genome_accession": "NC_045512.2", + "sample_name": "214821", + "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", + "variant_calling_software_name": "IVAR_VARIANTS", + "variant_calling_software_version": "1.3.1", + "variant_designation": "19" + }, "mapping_illumina_tab_field_list": { "lineage_name": "Lineage", "variant_designation": "Variantsinconsensusx10", diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index fcce8bdf..0b749277 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -82,7 +82,7 @@ def __init__( if database_server is None: database_server = relecov_tools.utils.prompt_selection( "Select:", - ["iskylims", "relecov"], + ["iskylims", "relecov", "relecov_local"], ) self.server_type = database_server # Get database settings @@ -201,6 +201,7 @@ def map_relecov_sample_data(self): """Select the values from self.json_data""" field_values = [] r_fields = self.config_json.get_configuration("relecov_sample_metadata") + for row in self.json_data: s_dict = {} for r_field in r_fields: @@ -211,9 +212,29 @@ def map_relecov_sample_data(self): field_values.append(s_dict) return field_values + def map_relecov_bioinfo_data(self): + # Select the values from self.json_data + field_values = [] + r_fields = self.config_json.get_configuration( + "relecov_bioinfo_metadata_96_samples" + ) + for row in self.json_data: + s_dict = {} + for r_field in self.json_data[row]: + if r_field in r_fields: + s_dict[r_field] = self.json_data[row][r_field] + if r_field == "sample_name": + s_dict[r_field] = row + else: + s_dict[r_field] = None + field_values.append(s_dict) + + return field_values + def update_database(self, field_values, post_url): """Send the request to update database""" for chunk in field_values: + # print(chunk) result = self.database_rest_api.post_request( json.dumps(chunk), {"user": self.user, "pass": self.passwd}, @@ -257,6 +278,7 @@ def store_data(self): """Collect data from json file and split them to store data in iSkyLIMS amd in Relecov Platform """ + map_fields = {} # if self.type_of_info == "sample": if self.server_type == "iskylims": sample_fields, s_project_fields = self.get_iskylims_fields_sample() @@ -267,7 +289,21 @@ def store_data(self): map_fields = self.map_relecov_sample_data() post_url = "store_samples" elif self.type_of_info == "analysis": - post_url = "analysis" + if self.server_type == "relecov": + print("relecov") + post_url = "analysis" + map_fields = self.map_relecov_bioinfo_data() + """ + sample_fields, s_project_fields = self.get_iskylims_fields_sample() + map_fields = self.map_iskylims_sample_fields_values( + sample_fields, s_project_fields + ) + """ + elif self.server_type == "relecov_local": + print("relecov_local") + post_url = "analysis" + map_fields = self.map_relecov_bioinfo_data() + elif self.type_of_info == "longtable": post_url = "long_table" else: From 6e8a60386df14e6f010460f3b9abf53a1ed77b0f Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Mon, 11 Jul 2022 16:28:45 +0200 Subject: [PATCH 0663/1454] configuration.json-> deleted relecov_bioinfo_metadata_96_samples dictionary,feed_database.py -> modified function map_relecov_bioinfo_data() --- relecov_tools/conf/configuration.json | 57 --------------------------- relecov_tools/feed_database.py | 6 +-- 2 files changed, 2 insertions(+), 61 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 2ada38b4..2d165997 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -180,63 +180,6 @@ "lineage_analysis_software_name": "pangolin", "if_lineage_identification_other": "None" }, - "relecov_bioinfo_metadata_96_samples":{ - "assembly": "None", - "assembly_params": "None", - "bioinformatics_protocol_software_name": "nf-core/viralrecon", - "bioinformatics_protocol_software_version": "2.4.1", - "commercial_open_source_both": "open-source", - "consensus_genome_length": "30396", - "consensus_params": "-p vcf -f", - "consensus_sequence_R1_md5": "dbcc703ccb7da3002fee6c0486199009", - "consensus_sequence_R1_name": "214821_S12_R1_001.fastq.gz", - "consensus_sequence_R2_md5": "b76fba963664b532004c4ce7153ae14f", - "consensus_sequence_R2_name": "214821_S12_R2_001.fastq.gz", - "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", - "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", - "consensus_sequence_software_version": "1.14", - "dehosting_method_software_name": "KRAKEN2_KRAKEN2", - "dehosting_method_software_version": "2.1.2", - "depth_of_coverage_threshold": ">10x", - "fastq_r1": "214821_S12_R1_001.fastq.gz", - "fastq_r2": "214821_S12_R2_001.fastq.gz", - "if_assembly_other": "None", - "if_bioinformatic_protocol_is_other_specify": "None", - "if_consensus_other": "None", - "if_lineage_identification_other": "None", - "if_mapping_other": "None", - "if_preprocessing_other": "None", - "lineage_analysis_software_name": "pangolin", - "lineage_analysis_software_version": "4.0.6", - "lineage_name": "B.1.177", - "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", - "mapping_params": "--seed 1", - "mapping_software_name": "BOWTIE2_ALIGN", - "mapping_software_version": "2.4.4", - "median_depth_of_coverage_value": "287.0", - "ns_per_100_kbp": "8442.32", - "number_of_base_pairs_sequenced": "633884", - "number_of_variants_AF_greater_75percent": "19", - "number_of_variants_with_effect": "9", - "per_Ns": "8,44", - "per_qc_filtered": "92,0", - "per_reads_host": "1,08", - "per_reads_virus": "98,54", - "per_unmapped": "0,380247", - "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", - "preprocessing_software_name": "FASTP", - "preprocessing_software_version": "0.23.2", - "quality_control_metrics": "", - "per_genome_greater_10x": "", - "analysis_date": "", - "depth_of_coverage_value": "", - "reference_genome_accession": "NC_045512.2", - "sample_name": "214821", - "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", - "variant_calling_software_name": "IVAR_VARIANTS", - "variant_calling_software_version": "1.3.1", - "variant_designation": "19" - }, "mapping_illumina_tab_field_list": { "lineage_name": "Lineage", "variant_designation": "Variantsinconsensusx10", diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 0b749277..ff8fccf1 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -215,13 +215,11 @@ def map_relecov_sample_data(self): def map_relecov_bioinfo_data(self): # Select the values from self.json_data field_values = [] - r_fields = self.config_json.get_configuration( - "relecov_bioinfo_metadata_96_samples" - ) + for row in self.json_data: s_dict = {} for r_field in self.json_data[row]: - if r_field in r_fields: + if r_field in self.json_data[row]: s_dict[r_field] = self.json_data[row][r_field] if r_field == "sample_name": s_dict[r_field] = row From f5f0ab220590bb7da4557870487982b12a82b253 Mon Sep 17 00:00:00 2001 From: birbi Date: Tue, 12 Jul 2022 12:13:15 +0200 Subject: [PATCH 0664/1454] before pull --- relecov_tools/conf/configuration.json | 2 ++ relecov_tools/feed_database.py | 28 +++++++++++++++++++++++++-- 2 files changed, 28 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 8b912261..1d279d6a 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -130,6 +130,8 @@ "server": "http://127.0.0.1:8000", "url": "/api/", "store_samples": "createSampleData", + "analysis": "bioinfoData", + "long_table": "longtableData", "token": "" } }, diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index fcce8bdf..7dd2232b 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -82,7 +82,7 @@ def __init__( if database_server is None: database_server = relecov_tools.utils.prompt_selection( "Select:", - ["iskylims", "relecov"], + ["iskylims", "relecov", "relecov_local"], ) self.server_type = database_server # Get database settings @@ -264,10 +264,34 @@ def store_data(self): sample_fields, s_project_fields ) else: + # sample_fields, s_project_fields = self.get_iskylims_fields_sample() map_fields = self.map_relecov_sample_data() post_url = "store_samples" + elif self.type_of_info == "analysis": - post_url = "analysis" + if self.server_type == "relecov": + print("relecov") + post_url = "analysis" + map_fields = self.map_relecov_bioinfo_data() + """ + sample_fields, s_project_fields = self.get_iskylims_fields_sample() + map_fields = self.map_iskylims_sample_fields_values( + sample_fields, s_project_fields + ) + post_url = "analysis" + print("analysis") + map_fields = self.map_relecov_bioinfo_data() + """ + elif self.server_type == "relecov_local": + print("relecov_local") + sample_fields, s_project_fields = self.get_iskylims_fields_sample() + map_fields = self.map_iskylims_sample_fields_values( + sample_fields, s_project_fields + ) + post_url = "analysis" + print("analysis") + map_fields = self.map_relecov_bioinfo_data() + elif self.type_of_info == "longtable": post_url = "long_table" else: From 730a809cf7d4ee1443d85bf6018c9c6170b8317a Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 13 Jul 2022 12:03:34 +0200 Subject: [PATCH 0665/1454] removed mean_depth_of_coverage_value because depth_of_coverage_value is used instead of --- relecov_tools/schema/relecov_schema.json | 13 +------------ 1 file changed, 1 insertion(+), 12 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index a48a7e3f..b0193c10 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1850,17 +1850,6 @@ "label": "% genome greater 10x", "fill_mode": "batch" }, - "median_depth_of_coverage_value": { - "examples": [ - "" - ], - "ontology": "NCIT:C167285", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics fields", - "label": "mean depth of coverage value", - "fill_mode": "batch" - }, "per_Ns": { "examples": [ "" @@ -2527,4 +2516,4 @@ "fill_mode": "batch" } } -} \ No newline at end of file +} From 3186ea062d7dd8391f01613eb9e97269261be0b3 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 13 Jul 2022 12:13:19 +0200 Subject: [PATCH 0666/1454] replace iskylims text by server who recives the request --- relecov_tools/feed_database.py | 21 ++++++++------------- 1 file changed, 8 insertions(+), 13 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index ff8fccf1..353fe009 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -244,21 +244,21 @@ def update_database(self, field_values, post_url): for i in range(10): # wait 5 sec before resending the request time.sleep(5) - result = self.iskylims_rest_api.post_request( + result = self.database_rest_api.post_request( json.dumps(chunk), {"user": self.user, "pass": self.passwd}, - self.iskylims_settings[post_url], + self.database_settings[post_url], ) if "ERROR" not in result: break if i == 9 and "ERROR" in result: - log.error("Unable to sent the request to iSkyLIMS") - stderr.print("[red] Unable to sent the request to iSkyLIMS") + log.error("Unable to sent the request to remote server") + stderr.print("[red] Unable to sent the request to remote server") sys.exit(1) else: - log.error("Request to iSkyLIMS was not accepted") + log.error("Request to %s was not accepted", self.database_server) stderr.print( - f"[red] Error {result['ERROR']} when sending request to iSkyLIMS " + f"[red] Error {result['ERROR']} when sending request to {self.database_server}" ) sys.exit(1) if "sampleName" in chunk: @@ -274,7 +274,7 @@ def update_database(self, field_values, post_url): def store_data(self): """Collect data from json file and split them to store data in iSkyLIMS - amd in Relecov Platform + and in Relecov Platform """ map_fields = {} # if self.type_of_info == "sample": @@ -291,12 +291,7 @@ def store_data(self): print("relecov") post_url = "analysis" map_fields = self.map_relecov_bioinfo_data() - """ - sample_fields, s_project_fields = self.get_iskylims_fields_sample() - map_fields = self.map_iskylims_sample_fields_values( - sample_fields, s_project_fields - ) - """ + elif self.server_type == "relecov_local": print("relecov_local") post_url = "analysis" From cb947ddfe2085c1514726d6c9f41b5ca7c76c1e0 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 13 Jul 2022 13:04:35 +0200 Subject: [PATCH 0667/1454] fix litin --- relecov_tools/feed_database.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 353fe009..2ef85166 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -253,7 +253,9 @@ def update_database(self, field_values, post_url): break if i == 9 and "ERROR" in result: log.error("Unable to sent the request to remote server") - stderr.print("[red] Unable to sent the request to remote server") + stderr.print( + "[red] Unable to sent the request to remote server" + ) sys.exit(1) else: log.error("Request to %s was not accepted", self.database_server) From 0556b759a45f5468ffc326dd62af12cb42c71111 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 17 Jul 2022 18:59:41 +0200 Subject: [PATCH 0668/1454] added Caceres and remove the accent in Avila --- relecov_tools/conf/geo_loc_cities.json | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/geo_loc_cities.json b/relecov_tools/conf/geo_loc_cities.json index 873f9406..13bb8f09 100644 --- a/relecov_tools/conf/geo_loc_cities.json +++ b/relecov_tools/conf/geo_loc_cities.json @@ -550,7 +550,7 @@ "geo_loc_longitude": "-3.5167" }, { - "geo_loc_city": "Ávila", + "geo_loc_city": "Avila", "geo_loc_latitude": "40.6500", "geo_loc_longitude": "-4.6833" }, @@ -12218,5 +12218,10 @@ "geo_loc_city": "Soria", "geo_loc_latitude": "41.7667", "geo_loc_longitude": "-2.4667" + }, + { + "geo_loc_city": "Caceres", + "geo_loc_latitude": "39.4752671", + "geo_loc_longitude": "-6.3722951" } -] \ No newline at end of file +] From 127edb15e964aff5d30b62dbd044d6b8481f9962 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 17 Jul 2022 19:00:44 +0200 Subject: [PATCH 0669/1454] added laboratories requested for the 2.600 samples --- relecov_tools/conf/laboratory_address.json | 304 ++++++++++++++++++++- 1 file changed, 296 insertions(+), 8 deletions(-) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 717cf5a8..84b2687b 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -79,9 +79,25 @@ "geo_loc_city": "Santa Cruz de Tenerife", "geo_loc_country": "Spain" }, + { + "collecting_institution": "Hospital Universitario de Canarias", + "collecting_institution_address": "Carretera Ofra S/N, La Laguna", + "collecting_institution_email": "", + "geo_loc_state": "Canarias", + "geo_loc_city": "Santa Cruz de Tenerife", + "geo_loc_country": "Spain" + }, { "collecting_institution": "Hospital Universitario de Gran Canaria", - "collecting_institution_address": "Bco. de la Ballena s/n", + "collecting_institution_address": "C. Pl. Barranco de la Ballena s/n", + "collecting_institution_email": "", + "geo_loc_state": "Canarias", + "geo_loc_city": "Las Palmas", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Insular de Lanzarote", + "collecting_institution_address": "C. Juan de Quesada, s/n, Arrecife", "collecting_institution_email": "", "geo_loc_state": "Canarias", "geo_loc_city": "Las Palmas", @@ -96,13 +112,61 @@ "geo_loc_country": "Spain" }, { - "collecting_institution": "Hospital General Universitario de Ciudad Real.", + "collecting_institution": "Hospital Sierrallana", + "collecting_institution_address": "Bo. Ganzo, s/n, Torrelavega", + "collecting_institution_email": "", + "geo_loc_state": "Cantabria", + "geo_loc_city": "Santander", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital General Universitario de Ciudad Real", "collecting_institution_address": "Calle Obispo Rafael Torija s/n", "collecting_institution_email": "", "geo_loc_state": "Castilla la Mancha", "geo_loc_city": "Ciudad Real", "geo_loc_country": "Spain" }, + { + "collecting_institution": "Hospital General La Mancha Centro", + "collecting_institution_address": "Av. Constitución, 3, Alcázar de San Juan", + "collecting_institution_email": "", + "geo_loc_state": "Castilla la Mancha", + "geo_loc_city": "Ciudad Real", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Virgen de Altagracia", + "collecting_institution_address": "Avda. D. Emiliano García Roldán, s/n, Manzanares,", + "collecting_institution_email": "", + "geo_loc_state": "Castilla la Mancha", + "geo_loc_city": "Ciudad Real", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital General de Valdepeñas", + "collecting_institution_address": "Av. de los Estudiantes, s/n, Valdepeñas", + "collecting_institution_email": "", + "geo_loc_state": "Castilla la Mancha", + "geo_loc_city": "Ciudad Real", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital General Universitario de Ciudad Real", + "collecting_institution_address": "C. Obispo Rafael Torija, s/n", + "collecting_institution_email": "", + "geo_loc_state": "Castilla la Mancha", + "geo_loc_city": "Ciudad Real", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Universitario de Guadalajara", + "collecting_institution_address": "C. Donante de Sangre, S/N", + "collecting_institution_email": "", + "geo_loc_state": "Castilla la Mancha", + "geo_loc_city": "Guadalajara", + "geo_loc_country": "Spain" + }, { "collecting_institution": "Hospital Virgen de la Salud", "collecting_institution_address": "Calle Barber 30", @@ -111,6 +175,14 @@ "geo_loc_city": "Toledo", "geo_loc_country": "Spain" }, + { + "collecting_institution": "Hospital General Nuestra Sra. del Prado", + "collecting_institution_address": "CTRA. MADRID, Av. Extremadura, KM 114", + "collecting_institution_email": "", + "geo_loc_state": "Castilla la Mancha", + "geo_loc_city": "Toledo", + "geo_loc_country": "Spain" + }, { "collecting_institution": "Hospital General Universitario de Albacete", "collecting_institution_address": "Calle Hermanos Falcó 37", @@ -127,6 +199,46 @@ "geo_loc_city": "Valladolid", "geo_loc_country": "Spain" }, + { + "collecting_institution": "Complejo Asistencial Universitario de Salamanca", + "collecting_institution_address": "P.º de San Vicente, 58", + "collecting_institution_email": "", + "geo_loc_state": "Castilla y León", + "geo_loc_city": "Salamanca", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Gerencia de Salud de Area de Soria", + "collecting_institution_address": "P.º el Espolón", + "collecting_institution_email": "", + "geo_loc_state": "Castilla y León", + "geo_loc_city": "Soria", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital General Río Carrión", + "collecting_institution_address": "Av. Donantes de Sangre, s/n", + "collecting_institution_email": "", + "geo_loc_state": "Castilla y León", + "geo_loc_city": "Palencia", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Nuestra Señora de Sonsoles", + "collecting_institution_address": " Av. Juan Carlos I, s/n", + "collecting_institution_email": "", + "geo_loc_state": "Castilla y León", + "geo_loc_city": "Avila", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Universitario de Burgos", + "collecting_institution_address": "Av. Islas Baleares, 3", + "collecting_institution_email": "", + "geo_loc_state": "Castilla y León", + "geo_loc_city": "Burgos", + "geo_loc_country": "Spain" + }, { "collecting_institution": "Hospital Universitari Vall d’Hebron", "collecting_institution_address": " Passeig de la Vall d’Hebron, 119-129", @@ -190,6 +302,14 @@ "geo_loc_city": "Girona", "geo_loc_country": "Spain" }, + { + "collecting_institution": "Hospital Universitario San Jorge", + "collecting_institution_address": "Av. Martínez de Velasco, 36", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_city": "Huesca", + "geo_loc_country": "Spain" + }, { "collecting_institution": "Hospital Universitario de Ceuta", "collecting_institution_address": "Colmenar s/n", @@ -208,7 +328,31 @@ }, { "collecting_institution": "Hospital de Mostoles", - "collecting_institution_address": "C. Dr. Luis Montes, S/N ", + "collecting_institution_address": "C. Dr. Luis Montes, S/N", + "collecting_institution_email": "", + "geo_loc_state": "Madrid", + "geo_loc_city": "Madrid", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Centro Militar de Veterinaria de la Defensa", + "collecting_institution_address": "C. Darío Gazapo 3", + "collecting_institution_email": "", + "geo_loc_state": "Madrid", + "geo_loc_city": "Madrid", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Universitario Severo Ochoa", + "collecting_institution_address": "Av. de Orellana, s/n, Leganés", + "collecting_institution_email": "", + "geo_loc_state": "Madrid", + "geo_loc_city": "Madrid", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Universitario de Getafe", + "collecting_institution_address": "Carr. Madrid - Toledo, Km 12,500, Getafe", "collecting_institution_email": "", "geo_loc_state": "Madrid", "geo_loc_city": "Madrid", @@ -222,6 +366,62 @@ "geo_loc_city": "Murcia", "geo_loc_country": "Spain" }, + { + "collecting_institution": "Hospital Universitario Reina Sofía", + "collecting_institution_address": "Av. Intendente Jorge Palacios, 1", + "collecting_institution_email": "", + "geo_loc_state": "Murcia", + "geo_loc_city": "Murcia", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital General Universitario Santa Lucía", + "collecting_institution_address": "C. Minarete, s/n", + "collecting_institution_email": "", + "geo_loc_state": "Murcia", + "geo_loc_city": "Murcia", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital General Universitario Los Arcos del Mar Menor", + "collecting_institution_address": "Paraje Torre Octavio, 54, Pozo Aledo", + "collecting_institution_email": "", + "geo_loc_state": "Murcia", + "geo_loc_city": "Murcia", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital General Universitario Morales Meseguer", + "collecting_institution_address": "Av. Marqués de Los Vélez, s/n", + "collecting_institution_email": "", + "geo_loc_state": "Murcia", + "geo_loc_city": "Murcia", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Clínico Universitario Virgen de la Arrixaca", + "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n, El Palmar", + "collecting_institution_email": "", + "geo_loc_state": "Murcia", + "geo_loc_city": "Murcia", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Rafael Méndez de Lorca", + "collecting_institution_address": "Ctra.N-340, Lorca", + "collecting_institution_email": "", + "geo_loc_state": "Murcia", + "geo_loc_city": "Murcia", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital de la Vega Lorenzo Guirao", + "collecting_institution_address": "Vereda de Morcillo, s/n, Cieza", + "collecting_institution_email": "", + "geo_loc_state": "Murcia", + "geo_loc_city": "Murcia", + "geo_loc_country": "Spain" + }, { "collecting_institution": "HU de Donostia", "collecting_institution_address": "Begiristain Doktorea Pasealekua, s/n", @@ -231,11 +431,99 @@ "geo_loc_country": "Spain" }, { - "collecting_institution": "Hospital Comarcal de Melilla", - "collecting_institution_address": "C. Remonta, 2", + "collecting_institution": "Hospital Universitario de Badajoz", + "collecting_institution_address": "Av. de Elvas, s/n", "collecting_institution_email": "", - "geo_loc_state": "Melilla", - "geo_loc_city": "Melilla", + "geo_loc_state": "Extremadura", + "geo_loc_city": "Badajoz", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital de Mérida", + "collecting_institution_address": "Av. Don Antonio Campos Hoyos, 26, Mérida", + "collecting_institution_email": "", + "geo_loc_state": "Extremadura", + "geo_loc_city": "Badajoz", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital San Pedro de Alcantara", + "collecting_institution_address": "Av. Pablo Naranjo Porras, s/n", + "collecting_institution_email": "", + "geo_loc_state": "Extremadura", + "geo_loc_city": "Caceres", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Sergas - Gerencia de Atención Primaria Pontevedra Sur", + "collecting_institution_address": "Av. das Camelias, 109, Vigo", + "collecting_institution_email": "", + "geo_loc_state": "Galicia", + "geo_loc_city": "Pontevedra", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Gerencia de Atención Primaria Pontevedra Sur", + "collecting_institution_address": "Av. das Camelias, 109, Vigo", + "collecting_institution_email": "", + "geo_loc_state": "Galicia", + "geo_loc_city": "Pontevedra", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Lucus Augusti", + "collecting_institution_address": " Rúa Dr. Ulises Romero, 1", + "collecting_institution_email": "", + "geo_loc_state": "Galicia", + "geo_loc_city": "Lugo", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Universitario de A Coruña", + "collecting_institution_address": "As Xubias, 84", + "collecting_institution_email": "", + "geo_loc_state": "Galicia", + "geo_loc_city": "A Coruña", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Clínico Universitario de Santiago", + "collecting_institution_address": "Rúa da Choupana, s/n, Santiago de Compostela", + "collecting_institution_email": "", + "geo_loc_state": "Galicia", + "geo_loc_city": "A Coruña", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Universitario de Navarra", + "collecting_institution_address": "C. de Irunlarrea, 3, Pamplona", + "collecting_institution_email": "", + "geo_loc_state": "Navarra", + "geo_loc_city": "Pamplona", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital General Universitario de Elche", + "collecting_institution_address": "Carrer Almazara, 11, Elche", + "collecting_institution_email": "", + "geo_loc_state": "Valenciana", + "geo_loc_city": "Alicante", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital San Pedro", + "collecting_institution_address": "C. Piqueras, 98", + "collecting_institution_email": "", + "geo_loc_state": "La Rioja", + "geo_loc_city": "Logroño", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Universitario Txagorritxu", + "collecting_institution_address": " Jose Atxotegi Kalea, s/n", + "collecting_institution_email": "", + "geo_loc_state": "País Vasco", + "geo_loc_city": "Vitoria", "geo_loc_country": "Spain" } -] \ No newline at end of file +] From cbedede35ef4319bd74e5c924e67db92e853aa3a Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 17 Jul 2022 19:02:15 +0200 Subject: [PATCH 0670/1454] rename number to string for sample id --- relecov_tools/schema/relecov_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index b0193c10..61a50b32 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -973,7 +973,7 @@ "" ], "ontology": "GENEPIO:0000079", - "type": "number", + "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", "classification": "Database Identifiers", "label": "Sample ID given for sequencing", From bcb596543179263df4fce98ad0a408a39b0bf95c Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 17 Jul 2022 19:06:19 +0200 Subject: [PATCH 0671/1454] Fixed code to avoid breaking execution when handling empty o wrong information --- relecov_tools/read_lab_metadata.py | 48 +++++++++++++++++------------- 1 file changed, 27 insertions(+), 21 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 73fd4707..a94594b7 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -105,18 +105,20 @@ def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): log.error("Found empti Originating Laboratory") return data for lab in lab_json: - if lab_name == lab["collecting_institution"]: for key, value in lab.items(): data[key] = value break for city in geo_loc_json: - if city["geo_loc_city"] == data["geo_loc_city"]: - data["geo_loc_latitude"] = city["geo_loc_latitude"] - data["geo_loc_longitude"] = city["geo_loc_longitude"] - data["geo_loc_country"] = data["geo_loc_country"] - break + try: + if city["geo_loc_city"] == data["geo_loc_city"]: + data["geo_loc_latitude"] = city["geo_loc_latitude"] + data["geo_loc_longitude"] = city["geo_loc_longitude"] + data["geo_loc_country"] = data["geo_loc_country"] + break + except KeyError as e: + print(e) return data def include_fixed_data(self): @@ -190,13 +192,13 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): """Include sample data from sample json""" try: for key, value in samples_json[ - row_sample["collecting_lab_sample_id"] + row_sample["sequencing_sample_id"] ].items(): row_sample[key] = value except KeyError as e: stderr.print( - "[red] ERROR MD5 information not found in sample json. ", e + "[red] ERROR fastq information not found in sample json. ", e ) """ Fetch the information related to the laboratory. @@ -255,7 +257,7 @@ def read_metadata_file(self): Convert the date colunms value to the dd/mm/yyyy format. Return list of dict with data, and errors """ - exc_format_num = ["Sample ID given for sequencing"] + # exc_format_num = ["Sample ID given for sequencing"] wb_file = openpyxl.load_workbook(self.metadata_file, data_only=True) ws_metadata_lab = wb_file["METADATA_LAB"] # removing the None columns in excel heading row @@ -275,21 +277,25 @@ def read_metadata_file(self): idx ].strftime("%Y-%m-%d") except AttributeError: - if row[2] not in errors: - errors[row[2]] = {} - errors[row[2]][heading[idx]] = "Invalid date format" - log.error("Invalid date format in sample %s", row[2]) - stderr.print( - "[red] Invalid date format in sample", - row[2] + " column " + heading[idx], - ) + # check if date is in string format + str_date = re.search(r"(\d{4}-\d{2}-\d{2}).*", row[idx]) + if str_date: + sample_data_row[ + self.label_prop_dict[heading[idx]] + ] = str_date.group(1) + else: + if row[2] not in errors: + errors[row[2]] = {} + errors[row[2]][heading[idx]] = "Invalid date format" + log.error("Invalid date format in sample %s", row[2]) + stderr.print( + "[red] Invalid date format in sample", + row[2] + " column " + heading[idx], + ) else: if isinstance(row[idx], float) or isinstance(row[idx], int): - if heading[idx] in exc_format_num: - val = int(row[idx]) - else: - val = str(int(row[idx])) + val = str(int(row[idx])) try: sample_data_row[self.label_prop_dict[heading[idx]]] = val except TypeError as e: From 4c1f1f31930478d477e4529f9d7eec272e083370 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 18 Jul 2022 15:16:02 +0200 Subject: [PATCH 0672/1454] starting to add functionality MODIFY --- relecov_tools/ena_upload.py | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index c7bc326d..66e6d7d6 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -21,6 +21,8 @@ from ena_upload.ena_upload import send_schemas from ena_upload.ena_upload import process_receipt from ena_upload.ena_upload import update_table +from ena_upload.ena_upload import make_update +from ena_upload.ena_upload import process_receipt # from ena_upload.ena_upload import save_update import site @@ -361,6 +363,29 @@ def create_structure_to_ena(self): schema_dataframe = update_table( schema_dataframe, schema_targets, schema_update ) + if self.action == "MODIFY" or self.action == "modify": + process_receipt(receipt, self.action) + receiptDate = receipt_root.get("receiptDate") + schema_update = {} # schema as key, dataframe as value + study_update = receipt_root.findall("STUDY") + sample_update = receipt_root.findall("SAMPLE") + experiment_update = receipt_root.findall("EXPERIMENT") + run_update = receipt_root.findall("RUN") + + if study_update: + schema_update["study"] = make_update(study_update, "study") + + if sample_update: + schema_update["sample"] = make_update(sample_update, "sample") + + if experiment_update: + schema_update["experiment"] = make_update( + experiment_update, "experiment" + ) + + if run_update: + schema_update["run"] = make_update(run_update, "run") + return schema_update def upload(self): """Create the required files and upload to ENA""" From b7bc06e9992139c4c410600710c1cb5006b19d4f Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 18 Jul 2022 23:39:11 +0200 Subject: [PATCH 0673/1454] add homogenizier to main menu --- relecov_tools/__main__.py | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 4cb8f0ed..f18e3fb9 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -19,6 +19,7 @@ import relecov_tools.feed_database import relecov_tools.read_bioinfo_metadata import relecov_tools.long_table_parse +import relecov_tools.metadata_homogeneizer log = logging.getLogger() @@ -366,5 +367,28 @@ def long_table_parse(longtable_file, output): new_json_parse.parsing_csv() +# read metadata bioinformatics +@relecov_tools_cli.command(help_priority=12) +@click.option( + "-l", + "--lab_metadata", + type=click.Path(), + help="file containing laboratory METADATA ", +) +@click.option( + "-i", + "--institution", + type=click.Choice(["isciii", "hugtip", "hunsc-iter"], case_sensitive=False), + help="select one of the available institution options", +) +@click.option("-o", "--output", type=click.Path(), help="Path to save json output") +def metadata_homogeneizer(lab_metadata, institution, output): + """Parse institution metadata lab to the one used in relecov""" + new_parse = relecov_tools.metadata_homogeneizer.MetadataHomogeneizer( + lab_metadata, institution, output + ) + new_parse.converting_metadata() + + if __name__ == "__main__": run_relecov_tools() From 7c9b1ec3f92124bd83ac6e4e4bb4464fbc30a5d1 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 18 Jul 2022 23:40:22 +0200 Subject: [PATCH 0674/1454] Modify because changes for homogeneizer --- relecov_tools/conf/configuration.json | 21 ++++++++------------- 1 file changed, 8 insertions(+), 13 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 2d165997..c79160d4 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -1,5 +1,5 @@ -{ - "new_table_headers" : [ +{ + "metadata_lab_heading" : [ "Public Health sample id (SIVIES)", "Sample ID given by originating laboratory", "Sample ID given by the submitting laboratory", @@ -125,16 +125,7 @@ "analysis": "bioinfoData", "long_table": "longtableData", "token": "" - }, - "relecov_local": { - "server": "http://127.0.0.1:8000", - "url": "/api/", - "store_samples": "createSampleData", - "analysis": "bioinfoData", - "long_table": "longtableData", - "token": "" } - }, "iskylims_fixed_values": { "patientCore": "", @@ -223,5 +214,9 @@ "HGVS_P_1LETTER", "CALLER", "LINEAGE" - ] -} \ No newline at end of file + ], + "mapping_file":{ + "ISCIII": "ISCIII.json", + "HUGTiP": "HUGTiP.json" + } +} From a77cad1a7e2ac25bf132309115586ac30ec62b5d Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 18 Jul 2022 23:41:59 +0200 Subject: [PATCH 0675/1454] Fixed error fields --- relecov_tools/metadata_homogeneizer.py | 397 ++++-------------- .../schema/institution_schemas/ISCIII.json | 37 +- 2 files changed, 98 insertions(+), 336 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 1dbe93e7..b029ab21 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -1,10 +1,10 @@ #!/usr/bin/env python -# Imports import os import sys import logging -import pandas as pd import rich.console +import openpyxl +from itertools import islice import relecov_tools.utils from relecov_tools.config_json import ConfigJson @@ -17,318 +17,103 @@ ) -def check_extension(instring): - """Given a file as a string and a list of possible extensions, - returns the type of file extension can be found in the file""" +class MetadataHomogeneizer: + """MetadataHomogeneizer object""" - # hard-coded extensions - extensions = { - "excel": [".xlsx", ".xls", ".xlsm", ".xlsb"], - "odf": [".odf"], - "csv": [".csv"], - "tsv": [".tsv"], - } - - for extension, termination_list in extensions.items(): - for termination in termination_list: - if instring.endswith(termination): - return extension - - -def identify_load_dataframe(filename): - """Detect possible extensions for the metadata file - Open it into a dataframe""" - - if check_extension(filename) == "excel": - df = pd.read_excel(filename, header=0) - - elif check_extension(filename) == "odf": - # Needs a special package - df = pd.read_excel(filename, engine="odf", header=0) - - elif check_extension(filename) == "csv": - df = pd.read_csv(filename, sep=",", header=0) - - elif check_extension(filename) == "tsv": - df = pd.read_csv(filename, sep="\t", header=0) - - # not real sure how to do this - elif check_extension(filename) == "json": - pass - # config_json = ConfigJson(filename="") - - else: - print(f"The extension of the file '{filename}' could not be identified.") - return None - - # remove spaces before and after - df.columns = df.columns.str.strip() - - return df - - -class Homogeneizer: - """Homogeneizer object""" - - def __init__(self, filename): - self.filename = filename - self.dictionary_path = None - self.dicionary = None - self.centre = None - self.dataframe = None - - config_json = ConfigJson() - self.header = config_json.get_configuration("new_table_headers") - self.translated_dataframe = pd.DataFrame(columns=self.header) - return - - def associate_dict(self): - """Detect the origin centre of the metadata, and finds the corresponding json file to use""" - - # Check name of the file attribute of the object - # Check schema with all centres and find their json - # Associate centre and json with object - # Raise error when in doubt - # Must check on schema/institution_schemas - - try: - config_json = ConfigJson( - json_file=os.path.join( - os.path.dirname(__file__), "schema", "institution_to_schema.json" - ) - ) - institution_dict = config_json.json_data - detected = {} - - for key in institution_dict.keys(): - # cap insensitive - if key.lower() in self.filename.split("/")[-1].lower(): - detected[key] = institution_dict[key] - - if len(set(detected.values())) == 0: - log.error( - f"No institution pattern could be found in the '{self.filename}' filename given." - ) - stderr.print( - f"[red]No institution pattern could be found in the '{self.filename}' filename given." - ) - sys.exit(1) - - elif len(set(detected.values())) > 1: - repeated = ", ".join(list(set(detected.values))) - log.error( - f"The following matches were identified in the '{self.filename}' filename given: {repeated }'" - ) - stderr.print( - f"[red]The following matches were identified in the '{self.filename}' filename given: {repeated}" - ) - sys.exit(1) - - else: - self.dictionary_path = detected[0] # first item, they are all equal - stderr.print( - f"[green]JSON file found successfully: {self.dictionary_path}" - ) - - except FileNotFoundError: - log.error( - "JSON file relating institutions and their JSON file could not be found or does not exist." - ) - stderr.print( - "[red]JSON file relating institutions and their JSON file could not be found or does not exist." - ) - sys.exit(1) - - return - - def load_dataframe(self): - """Detect possible extensions for the metadata file and - open it into a dataframe""" - self.dataframe = identify_load_dataframe(self.filename) - return - - def load_dictionary(self): - """Load the corresponding dictionary""" - - # To Do: replace string with local file system for testing - try: - config_json = ConfigJson( - json_file=os.path.join( - os.path.dirname(__file__), "schema", self.dictionary_path - ) + def __init__(self, lab_metadata=None, institution=None, output_folder=None): + self.config_json = ConfigJson() + self.heading = self.config_json.get_configuration("metadata_lab_heading") + if lab_metadata is None: + self.lab_metadata = relecov_tools.utils.prompt_path( + msg="Select the file which contains metadata" ) - self.dictionary = config_json.json_data - except FileNotFoundError: - log.error( - f"JSON file {self.dictionary_path} could not be found or does not exist in the schema directory." - ) - stderr.print( - f"[red]JSON file {self.dictionary_path} could not be found or does not exist in the schema directory." - ) - sys.exit(1) - return - - def translate_dataframe(self): - """Use the corresponding dictionary to translate the df""" - # if dictionary is "none" or similar, do nothing - - try: # not sure if a try is the best here, gotta check - for key, value in self.dictionary["equivalence"].items(): - if len(value) == 0: - log.error( - f"Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'" - ) - stderr.print( - f"[red]Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'" - ) - sys.exit(1) - elif value in self.dataframe.columns: - self.translated_dataframe[key] = self.dataframe[value.strip()] - else: - log.error( - f"Column '{value}' indicated in the '{self.dictionary_path}' schema could not be found in the input dataframe." - ) - stderr.print( - f"[red]Column '{value}' indicated in the '{self.dictionary_path}' schema could not be found in the input dataframe." - ) - sys.exit(1) - - for key, value in self.dictionary["constants"].items(): - self.translated_dataframe[key] = value - - except Exception: - log.error( - "Found empty equivalence in the '{self.dictionary_path}' schema: '{key}'" - ) - - # Nightmare - if len(self.dictionary["outer"]) == 0: - pass else: - for key, value in self.dictionary["outer"].items(): - if len(value) == 0: - log.error( - f"Found empty outer in the '{self.dictionary_path}' schema: '{key}'" - ) - stderr.print( - f"[red]Found empty outer in the '{self.dictionary_path}' schema: '{key}'" - ) - sys.exit(1) - else: - outer_filename = value["filename"] - outer_sheet = value["sheet"] - outer_column = value["column"] - outer_samplename_col = value["samplename_col"] - - outer_dataframe = None - outer_translated_dataframe = None - # outer_dataframe = identify_load_dataframe(outer_filename) - - if check_extension(outer_filename) == "excel": - if len(outer_sheet) == 0: - log.error( - "There is missing information, sheet name must be provided." - ) - stderr.print( - "[red]There is missing information, sheet name must be provided." - ) - sys.exit(1) - else: - outer_dataframe = pd.read_excel( - outer_filename, header=0, sheet_name=outer_sheet - ) - elif check_extension(outer_filename) == "odf": - if len(outer_sheet) == 0: - log.error( - "There is missing information, sheet name must be provided." - ) - stderr.print( - "[red]There is missing information, sheet name must be provided." - ) - sys.exit(1) - else: - outer_dataframe = pd.read_excel( - outer_filename, engine="odf", header=0 - ) - elif check_extension(outer_filename) == "csv": - outer_dataframe = pd.read_csv(outer_filename, sep=",", header=0) - elif check_extension(outer_filename) == "tsv": - outer_dataframe = pd.read_csv( - outer_filename, sep="\t", header=0 - ) - - if len(outer_column) == 0: - log.error( - "There is missing information, column name must be provided." - ) - stderr.print( - "[red]There is missing information, column name must be provided." - ) - sys.exit(1) - else: - outer_translated_dataframe[key] = outer_dataframe[ - outer_column.strip() - ] - - if len(outer_samplename_col) == 0: - log.error( - "There is missing information, samplename_col must be provided." - ) - stderr.print( - "[red]There is missing information, samplename_col must be provided." - ) - sys.exit(1) - else: - # Review left_on key (this key must be present in translated data_frame) - outer_translated_dataframe[ - outer_samplename_col - ] = outer_dataframe[outer_samplename_col.strip()] - self.translated_dataframe.merge( - outer_translated_dataframe, - left_on="Sample ID given by originating laboratory", - right_on=outer_samplename_col, - ) - return - - def verify_translated_dataframe(self): - """Checks if the dataframe holds all the needed values for the relecov tools suite""" - - if self.dataframe.shape[0] != self.translated_dataframe.shape[0]: - log.error("Different number of rows after translation") + self.lab_metadata = lab_metadata + if not os.path.exists(self.lab_metadata): + log.error("Metadata file %s does not exist ", self.lab_metadata) + stderr.print("[red] Metadata file " + self.lab_metadata + " does not exist") sys.exit(1) - else: - stderr.print("[green]Number of rows: OK") - - # search for missing values - missing_values = list(set(self.header) - set(self.translated_dataframe.columns)) - if len(missing_values) > 0: - msg = ", ".join(missing_values) - log.error( - f"Found the following missing values during translated table validation: {msg}" - ) - stderr.print( - f"[red]Found the following missing values during translated table validation: {msg}" + if institution is None: + self.institution = relecov_tools.utils.prompt_selection( + msg="Select the available mapping institution", + choices=["isciii", "hugtip", "hunsc-iter"], ) else: - stderr.print("[green]No missing values in the translated table") - # search for extra values - extra_values = list(set(self.translated_dataframe.columns) - set(self.header)) - if len(extra_values) > 0: - msg = ", ".join(extra_values) - log.error( - f"Found the following extra values during translated table validation: {msg}" - ) - stderr.print( - f"[red]Found the following extra values during translated table validation: {msg}" + self.institution = institution.upper() + mapping_json_file = os.path.join( + os.path.dirname(__file__), + "schema", + "institution_schemas", + self.config_json.get_topic_data("mapping_file", self.institution), + ) + self.mapping_json_data = relecov_tools.utils.read_json_file(mapping_json_file) + if output_folder is None: + self.output_folder = relecov_tools.utils.prompt_path( + msg="Select the output folder" ) else: - stderr.print("[green]No extra values in the translated values") + self.output_folder = output_folder + + def read_metadata_file(self): + """Read the input metadata file""" + wb_file = openpyxl.load_workbook(self.lab_metadata, data_only=True) + ws_metadata_lab = wb_file["Sheet"] + heading = [i.value.strip() for i in ws_metadata_lab[1] if i.value] + ws_data = [] + for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row): + l_row = list(row) + data_row = {} + # Ignore the empty rows + # guessing that row 1 and 2 with no data are empty rows + if l_row[0] is None and l_row[1] is None: + continue + for idx in range(0, len(heading)): + data_row[heading[idx]] = l_row[idx] + ws_data.append(data_row) + # import pdb; pdb.set_trace() + return ws_data + + def mapping_metadata(self, ws_data): + map_fields = self.mapping_json_data["mapped_fields"] + map_data = [] + for row in ws_data: + row_data = {} + for dest_map, orig_map in map_fields.items(): + + row_data[dest_map] = row[orig_map] + map_data.append(row_data) + + return map_data + + def additional_fields(self, mapped_data): + add_data = [self.heading] + fixed_fields = self.mapping_json_data["fixed_fields"] + for row in mapped_data: + new_row_data = [] + for field in self.heading: + if field in row: + data = row[field] + elif field in fixed_fields: + data = fixed_fields[field] + else: + data = "" + new_row_data.append(data) + add_data.append(new_row_data) + return add_data + + def write_to_excel_file(self, data, f_name): + book = openpyxl.Workbook() + sheet = book.active + for row in data: + sheet.append(row) + + book.save(f_name) return - def export_translated_dataframe(self): - # expected only one dot per file - filename, extension = self.filename.split(".") - self.translated_dataframe.to_excel( - excel_writer=filename + "_modified." + extension - ) + def converting_metadata(self): + ws_data = self.read_metadata_file() + mapped_data = self.mapping_metadata(ws_data) + converted_data = self.additional_fields(mapped_data) + f_name = os.path.join(self.output_folder, "converted_metadata_lab.xlsx") + self.write_to_excel_file(converted_data, f_name) return diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index f9ca6d1a..678d0752 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -1,5 +1,5 @@ { - "equivalence": { + "mapped_fields": { "Public Health sample id (SIVIES)": "Código SiViEs", "Sample ID given by originating laboratory": "Ref Hospital", "Sample ID given by the submitting laboratory": "ID CNM", @@ -8,51 +8,28 @@ "Sample ID given for sequencing": "ID VI-VRP", "GISAID id": "ID GISAID", "Originating Laboratory": "Hospital", - "Sample Collection Date": "Fecha de toma ", + "Sample Collection Date": "Fecha de toma", "Sample Received Date": "Fecha recepción", - "Host Age": "Grupo edad", - "Diagnostic Pcr Ct Value 1": "PCR genE", - "Sequencing Date": "Fecha de secuenciación" + "Host Age": "Edad (años)", + "Diagnostic Pcr Ct Value 1": "PCR genE" }, - "constants": { + "fixed_fields": { "Biological Sample Storage Condition": "-80 C", "Rna Extraction Protocol": "RT-PCR", - "ENA Sample ID": "", - "GISAID Virus Name": "", - "GISAID id": "", - "Submitting Institution": "", "Purpose of sampling": "Surveillance", "Specimen source": "Nasopharyngeal exudate", - "Environmental Material": "", "Environmental System": "Swab", - "Collection Device": "", "Host": "Human", - "Host Gender": "", - "Commercial All-in-one library kit": "", "Library Preparation Kit": "Illumina DNA Prep", "Enrichment Protocol": "Amplicon", - "If Enrichment Protocol. If Other,Specify": "", "Enrichment panel/assay": "ARTIC", - "If Enrichment panel/assay. If Other, Specify": "", - "Enrichment panel/assay version": "", - "Number Of Samples In Run": "", - "Runid": "", - "Sequencing Instrument Model": "", - "Flowcell Kit": "", "Source material": "Viral RNA", "Capture method": "PCR", "Sequencing technique": "Amplicon", "Library Layout": "Paired", "Gene Name 1": "ORF E", "Diagnostic Pcr Ct Value 1": "", - "Gene Name 2": "", - "Diagnostic Pcr Ct Value-2": "", - "Analysis Authors": "", - "Author Submitter": "A. Monzón; F. Casas; I. Jiménez; M. Camarero; P. Zaballos; ROMAN SOTO; S. Cuesta, I.; S. Iglesias-Caballero; S. Pozo; S. Varona; SERGIO; Sandonís; V. Vázquez-Morón", - "Authors": "", - "Sequence file R1 fastq": "", - "Sequence file R2 fastq": "" - }, - "outer": {} + "Authors": "A. Monzón; F. Casas; I. Jiménez; M. Camarero; P. Zaballos; ROMAN SOTO; S. Cuesta, I.; S. Iglesias-Caballero; S. Pozo; S. Varona; SERGIO; Sandonís; V. Vázquez-Morón" + } } From 9270f2c949a07a81df248e6a994b2c3dffb5862e Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 19 Jul 2022 09:16:47 +0200 Subject: [PATCH 0676/1454] added --single option to gisaid_upload.py --- relecov_tools/gisaid_upload.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index d64e9652..f38d4d88 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -39,6 +39,7 @@ def __init__( output_path=None, frameshift=None, proxy_config=None, + single=False, ): if ( token is None @@ -107,6 +108,7 @@ def __init__( print("Proxy configuration is not set") else: self.proxy_config = proxy_config + self.single = single def convert_input_json_to_ena(self): """Split the input ena json, in samples and runs json""" From 4e0e1a65f8e39aca00ebcf9d4c98ecdeb88de408 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 19 Jul 2022 09:23:48 +0200 Subject: [PATCH 0677/1454] corrected bugs in values initialization in gisaid_upload.py --- relecov_tools/gisaid_upload.py | 23 +++++------------------ 1 file changed, 5 insertions(+), 18 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index f38d4d88..51462727 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -44,6 +44,7 @@ def __init__( if ( token is None ): # borrar comentario: solo si no existe el token necesita user, passwd y client_id + self.token = None print("Token is not introduced, creating a new one...") if user is None: self.user = relecov_tools.utils.prompt_text( @@ -51,7 +52,6 @@ def __init__( ) else: self.user = user - # Add proxy settings: username:password@proxy:port (optional) if passwd is None: self.passwd = relecov_tools.utils.prompt_password( msg="Enter your password to GISAID" @@ -66,18 +66,12 @@ def __init__( self.client_id = client_id else: self.token = token - if self.gisaid_json is None: + if gisaid_json is None: self.gisaid_json = relecov_tools.utils.prompt_path( msg="Select the GISAID json file to upload" ) else: self.gisaid_json = self.gisaid_json - if ( - self.customized_project is None - ): # borrar comentario: esta parte no la entiendo, no la toco - self.customized_project = None - else: - self.customized_project = self.customized_project if output_path is None: self.output_path = relecov_tools.utils.prompt_path( msg="Select the folder to store the log files" @@ -85,24 +79,17 @@ def __init__( else: self.output_path = output_path if fasta_path is None: - self.fasta_path = relecov_tools.utils.prompt_path(msg="Select path") + self.fasta_path = relecov_tools.utils.prompt_path(msg="Select path to fasta file/s") else: - # relecov_tools/gisaid_upload.py self.fasta_path = fasta_path - - if not os.path.isfile(self.source_json_file): - log.error("json data file %s does not exist ", self.source_json_file) - stderr.print(f"[red]json data file {self.source_json_file} does not exist") - sys.exit(1) - with open(self.source_json_file, "r") as fh: - self.json_data = json.loads(fh.read()) if frameshift is None: self.frameshift = relecov_tools.utils.prompt_selection( msg="Select frameshift notification", - choices="catch_all, catch_novel, catch_none", + choices=["catch_all", "catch_novel", "catch_none"] ) else: self.frameshift = frameshift + # Add proxy settings: username:password@proxy:port (optional) if proxy_config is None: # borrar comentario: este mensaje no me convence print("Proxy configuration is not set") From ef87395d39a2d91b0d6aba0a62f5bdf64ff96c9c Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 19 Jul 2022 09:25:22 +0200 Subject: [PATCH 0678/1454] deleted convert_input_json_to_ena() function in gisaid_upload.py --- relecov_tools/gisaid_upload.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 51462727..a582d9cf 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -97,10 +97,6 @@ def __init__( self.proxy_config = proxy_config self.single = single - def convert_input_json_to_ena(self): - """Split the input ena json, in samples and runs json""" - pass - # Metadatos def metadata_to_csv(self): From acdbc656de494f3d8abebf4df879efc6b3016a17 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 19 Jul 2022 09:28:40 +0200 Subject: [PATCH 0679/1454] improved metadata_to_csv() function in gisaid_upload.py --- relecov_tools/gisaid_upload.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index a582d9cf..423ca6bd 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -101,20 +101,20 @@ def __init__( def metadata_to_csv(self): "Transform metadata json to csv" - data = relecov_tools.utils.read_json_file(self.metadata) + data = relecov_tools.utils.read_json_file(self.gisaid_json) df_data = pd.DataFrame(data) - df_data.to_csv("%s/meta_gisaid.csv" % self.output_path) - metagisaid = "%s/meta_gisaid.csv" % self.output_path + df_data_path = os.path.join(self.output_path, "meta_gisaid.csv") + df_data.to_csv(df_data_path) + metagisaid = df_data_path return metagisaid # generar template con cli3 # ADD TOKEN WARNING and file token .authtoken # add bash from cli3 - +""" os.system( "cli3 upload --database EpiCoV --token ./gisaid.authtoken --metadata gisaid_template.csv --fasta multi.fasta --frameshift (OPTIONAL, default: catch_all) --failed --proxy --log" ) - """ cli3 upload --database EpiCoV --token ./gisaid.authtoken @@ -124,8 +124,8 @@ def metadata_to_csv(self): --failed default creates file failed.out where the failed records will be --proxy --log default creates file failed.out where the log will be ) - """ - + +""" def create_multifasta(self): """Create multifasta from single fastas""" os.system( From bbbabe40572a3cce621434de37d00b50d2d0a107 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 19 Jul 2022 09:32:01 +0200 Subject: [PATCH 0680/1454] added single/multifasta option to create_multifasta() function in gisaid_upload.py --- relecov_tools/gisaid_upload.py | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 423ca6bd..adcc8c3d 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -127,11 +127,14 @@ def metadata_to_csv(self): """ def create_multifasta(self): - """Create multifasta from single fastas""" - os.system( - "cat %s/*.fasta > %s/multifasta.fasta" % (self.fasta_path, self.output_path) - ) - multifasta = "%s/multifasta.fasta" % self.output_path + """Create multifasta from single fastas (if --single)""" + if self.single: + os.system( + "cat %s > %s/multifasta.fasta" % (self.fasta_path, self.output_path) + ) + multifasta = "%s/multifasta.fasta" % self.output_path + else: + multifasta = self.fasta_path return multifasta def change_headers(self, multifasta): From 904505cebc8fb7a4a3b2780a1965bf82d9151c16 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 19 Jul 2022 09:38:37 +0200 Subject: [PATCH 0681/1454] improved change_headers() function to open a fasta file in append mode (gisaid_upload.py) --- relecov_tools/gisaid_upload.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index adcc8c3d..aba997e0 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -141,8 +141,9 @@ def change_headers(self, multifasta): """Transform multifasta ids/headers to GISAID format""" data = relecov_tools.utils.read_json_file(self.gisaid_json) virus_name = [name["covv_virus_name"] for name in data] + multi_gis_path = os.path.join(self.output_path, "processed_multifasta_gisaid.fasta") with open(multifasta) as old_fasta, open( - "%s/multifasta_gisaid.fasta" % self.output_path, "w" + multi_gis_path, "a" ) as new_fasta: records = SeqIO.parse(old_fasta, "fasta") for record in records: From 0d008302d924401ae874888a086f13cd943c2e9a Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 19 Jul 2022 09:45:56 +0200 Subject: [PATCH 0682/1454] corrected bug in cli3_upload() function (gisaid_upload.py) --- relecov_tools/gisaid_upload.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index aba997e0..3ab2d2cf 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -169,7 +169,7 @@ def cli3_upload(self): % ( self.token, self.metadata_to_csv(), - self.change_headers(), + self.change_headers(self.create_multifasta()), self.frameshift, ) ) From 89281b00c11567bffdce061576fa5f45d97e65e0 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 19 Jul 2022 09:47:42 +0200 Subject: [PATCH 0683/1454] modified gisaid_upload() function (gisaid_upload.py) --- relecov_tools/gisaid_upload.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 3ab2d2cf..5468cb5a 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -185,14 +185,13 @@ def cli3_upload(self): ) ) - """ + def gisaid_upload(self): - ""Upload to GISAID"" - self.create_multifasta() + """Upload to GISAID""" if token is None: self.cli3_auth() self.cli3_upload() - """ + """" Upload From a3a15038b2c4ee1a89344a8b0f512fb1e76f4e8b Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 19 Jul 2022 09:50:53 +0200 Subject: [PATCH 0684/1454] fixed bugs in change_headers() function (gisaid_upload.py) --- relecov_tools/gisaid_upload.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 5468cb5a..b79a32d5 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -150,8 +150,8 @@ def change_headers(self, multifasta): for name in virus_name: if record.id == name.split("/")[-2]: record.id = name - SeqIO.write(record, new_fasta, "fasta") - fastagisaid = "%s/multifasta_gisaid.fasta" % self.output_path + SeqIO.write(record, new_fasta, "fasta") + fastagisaid = multi_gis_path return fastagisaid def cli3_auth(self): From 37114b62fad65551eb8493dc21d0d23542cb12b5 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 19 Jul 2022 09:53:33 +0200 Subject: [PATCH 0685/1454] improved metadata_to_csv() function II (gisaid_upload.py) --- relecov_tools/gisaid_upload.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index b79a32d5..7de88fc1 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -104,7 +104,7 @@ def metadata_to_csv(self): data = relecov_tools.utils.read_json_file(self.gisaid_json) df_data = pd.DataFrame(data) df_data_path = os.path.join(self.output_path, "meta_gisaid.csv") - df_data.to_csv(df_data_path) + df_data.to_csv(df_data_path, index=False) metagisaid = df_data_path return metagisaid From 06ea9e076b4981216a05558969405867ef509d15 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 19 Jul 2022 09:59:04 +0200 Subject: [PATCH 0686/1454] lintin --- relecov_tools/gisaid_upload.py | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 7de88fc1..df79fb5c 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -79,13 +79,15 @@ def __init__( else: self.output_path = output_path if fasta_path is None: - self.fasta_path = relecov_tools.utils.prompt_path(msg="Select path to fasta file/s") + self.fasta_path = relecov_tools.utils.prompt_path( + msg="Select path to fasta file/s" + ) else: self.fasta_path = fasta_path if frameshift is None: self.frameshift = relecov_tools.utils.prompt_selection( msg="Select frameshift notification", - choices=["catch_all", "catch_novel", "catch_none"] + choices=["catch_all", "catch_novel", "catch_none"], ) else: self.frameshift = frameshift @@ -111,7 +113,7 @@ def metadata_to_csv(self): # generar template con cli3 # ADD TOKEN WARNING and file token .authtoken # add bash from cli3 -""" + """ os.system( "cli3 upload --database EpiCoV --token ./gisaid.authtoken --metadata gisaid_template.csv --fasta multi.fasta --frameshift (OPTIONAL, default: catch_all) --failed --proxy --log" ) @@ -124,8 +126,9 @@ def metadata_to_csv(self): --failed default creates file failed.out where the failed records will be --proxy --log default creates file failed.out where the log will be ) - -""" + + """ + def create_multifasta(self): """Create multifasta from single fastas (if --single)""" if self.single: @@ -141,10 +144,10 @@ def change_headers(self, multifasta): """Transform multifasta ids/headers to GISAID format""" data = relecov_tools.utils.read_json_file(self.gisaid_json) virus_name = [name["covv_virus_name"] for name in data] - multi_gis_path = os.path.join(self.output_path, "processed_multifasta_gisaid.fasta") - with open(multifasta) as old_fasta, open( - multi_gis_path, "a" - ) as new_fasta: + multi_gis_path = os.path.join( + self.output_path, "processed_multifasta_gisaid.fasta" + ) + with open(multifasta) as old_fasta, open(multi_gis_path, "a") as new_fasta: records = SeqIO.parse(old_fasta, "fasta") for record in records: for name in virus_name: @@ -185,14 +188,12 @@ def cli3_upload(self): ) ) - def gisaid_upload(self): """Upload to GISAID""" - if token is None: + if self.token is None: self.cli3_auth() self.cli3_upload() - """" Upload Subir con cli3 From 8b6784aa4352da97234eb33ca39761ce4f34f1c2 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 19 Jul 2022 10:46:44 +0200 Subject: [PATCH 0687/1454] added click options to 'upload to GISAID' --- relecov_tools/__main__.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 4cb8f0ed..31b45ba7 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -258,13 +258,16 @@ def upload_to_ena(user, password, center, ena_json, dev, study, action, output_p @relecov_tools_cli.command(help_priority=7) @click.option("-u", "--user", help="user name for login") @click.option("-p", "--password", help="password for the user to login") -@click.option("-e", "--gisaid_json", help="where the validated json is") +@click.option("-c", "--client_id", help="client-ID provided by clisupport@gisaid.org") +@click.option("-t", "--token", help="path to athentication token") +@click.option("-e", "--gisaid_json", help="patch validated json mapped to GISAID") @click.option( "-i", "--input_path", - help="the path where the fasta or multifasta, gisaid_mapped.json and the token file are located", + help="path to fasta or multifasta file", ) @click.option("-o", "--output_path", help="output folder for log") +@click.option("-f", "--frameshift", type=click.Choice(["catch_all", "catch_none", "catch_novel"], case_sensitive=False), help="frameshift notification") @click.option( "-x", "--proxy_config", From 1d9d4984d20327e6f101e29669968d820ec741c4 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 19 Jul 2022 10:51:34 +0200 Subject: [PATCH 0688/1454] added variables to upload_to_gisaid() function in __main__.py --- relecov_tools/__main__.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 31b45ba7..db57ed75 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -281,10 +281,13 @@ def upload_to_ena(user, password, center, ena_json, dev, study, action, output_p help="Default input is a multifasta.", ) def upload_to_gisaid( - user, password, gisaid_json, input_path, output_path, proxy_config + user, password, client_id, token, gisaid_json, input_path, output_path, frameshift, proxy_config, single ): """parsed data to create files to upload to gisaid""" - pass + upload_gisaid = relecov_tools.gisaid_upload.GisaidUpload( + user, password, client_id, token, gisaid_json, input_path, output_path, frameshift, proxy_config, single + ) + upload_gisaid.gisaid_upload() # launch From e9a405206b73448ea1c788e8e702ef7df59ee073 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 19 Jul 2022 10:52:50 +0200 Subject: [PATCH 0689/1454] lintin __main__.py --- relecov_tools/__main__.py | 31 +++++++++++++++++++++++++++---- 1 file changed, 27 insertions(+), 4 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index db57ed75..84b14d31 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -267,7 +267,12 @@ def upload_to_ena(user, password, center, ena_json, dev, study, action, output_p help="path to fasta or multifasta file", ) @click.option("-o", "--output_path", help="output folder for log") -@click.option("-f", "--frameshift", type=click.Choice(["catch_all", "catch_none", "catch_novel"], case_sensitive=False), help="frameshift notification") +@click.option( + "-f", + "--frameshift", + type=click.Choice(["catch_all", "catch_none", "catch_novel"], case_sensitive=False), + help="frameshift notification", +) @click.option( "-x", "--proxy_config", @@ -281,13 +286,31 @@ def upload_to_ena(user, password, center, ena_json, dev, study, action, output_p help="Default input is a multifasta.", ) def upload_to_gisaid( - user, password, client_id, token, gisaid_json, input_path, output_path, frameshift, proxy_config, single + user, + password, + client_id, + token, + gisaid_json, + input_path, + output_path, + frameshift, + proxy_config, + single, ): """parsed data to create files to upload to gisaid""" upload_gisaid = relecov_tools.gisaid_upload.GisaidUpload( - user, password, client_id, token, gisaid_json, input_path, output_path, frameshift, proxy_config, single + user, + password, + client_id, + token, + gisaid_json, + input_path, + output_path, + frameshift, + proxy_config, + single, ) - upload_gisaid.gisaid_upload() + upload_gisaid.gisaid_upload() # launch From 65434a51ce25b28e8609ce829cb002f17776930c Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 19 Jul 2022 10:56:36 +0200 Subject: [PATCH 0690/1454] lintin gisaid_upload.py --- relecov_tools/gisaid_upload.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index df79fb5c..bc62972b 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -1,6 +1,4 @@ import logging -import sys -import json # from pyparsing import col import rich.console From eed6038b9e2c2097af1910d379b4073c4b8c6595 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 22 Jul 2022 10:13:40 +0200 Subject: [PATCH 0691/1454] funcionality to modify working --- relecov_tools/ena_upload.py | 56 +++++++++++++++++++++++-------------- 1 file changed, 35 insertions(+), 21 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 66e6d7d6..f6443dd3 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,3 +1,4 @@ +from bdb import set_trace import logging # from pyparsing import col @@ -6,6 +7,8 @@ import pandas as pd + +pd.options.mode.chained_assignment = None import sys import os @@ -21,8 +24,9 @@ from ena_upload.ena_upload import send_schemas from ena_upload.ena_upload import process_receipt from ena_upload.ena_upload import update_table -from ena_upload.ena_upload import make_update -from ena_upload.ena_upload import process_receipt + +# from ena_upload.ena_upload import make_update +# from ena_upload.ena_upload import process_receipt # from ena_upload.ena_upload import save_update import site @@ -209,9 +213,7 @@ def create_structure_to_ena(self): df_run.loc[i, "sequence_file_R2_fastq"] = df_schemas.loc[ i, "sequence_file_R2_fastq" ] - import pdb - pdb.set_trace() df_run.insert(3, "status", self.action) df_run = df_run.rename(columns={"fastq_r1_md5": "file_checksum"}) @@ -289,7 +291,12 @@ def create_structure_to_ena(self): if ena_config["study_id"] is not None: schema_dataframe["study"] = df_study - if self.action == "ADD" or self.action == "add": + if ( + self.action == "ADD" + or self.action == "add" + or self.action == "MODIFY" + or self.action == "modify" + ): file_paths = {} file_paths_r2 = {} @@ -301,26 +308,27 @@ def create_structure_to_ena(self): file_paths.update(file_paths_r2) - # submit data to webin ftp server + # submit data to webin ftp server. It should only upload fastq files in case the action is ADD. + # When the action is MODIFY rthe fastq are already submitted. + if self.action == "ADD" or self.action == "add": + session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) - session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) + for filename, path in file_paths.items(): - for filename, path in file_paths.items(): + print("Uploading path " + path + " and filename: " + filename) - print("Uploading path " + path + " and filename: " + filename) + try: + file = open(path, "rb") # file to send + g = session.storbinary(f"STOR {filename}", file) + print(g) # send the file + file.close() # close file and FTP + except BaseException as err: - try: - file = open(path, "rb") # file to send - g = session.storbinary(f"STOR {filename}", file) - print(g) # send the file - file.close() # close file and FTP - except BaseException as err: + print(f"ERROR: {err}") + # print("ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000.") - print(f"ERROR: {err}") - # print("ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000.") - - g2 = session.quit() - print(g2) + g2 = session.quit() + print(g2) # THE ENA_UPLOAD_CLI METHOD DOES NOT WORK (below) # chec = submit_data(file_paths, self.passwd, self.user) @@ -340,6 +348,9 @@ def create_structure_to_ena(self): submission_xml = construct_submission( template_path, self.action, schema_xmls, self.center, checklist, tool ) + submission_xml = construct_submission( + template_path, self.action, schema_xmls, self.center, checklist, tool + ) schema_xmls["submission"] = submission_xml if self.dev: @@ -348,8 +359,8 @@ def create_structure_to_ena(self): url = "https://www.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" print(f"\nSubmitting XMLs to ENA server: {url}") + receipt = send_schemas(schema_xmls, url, self.user, self.passwd).text - print("Printing receipt to ./receipt.xml") with open("receipt.xml", "w") as fw: fw.write(receipt) @@ -363,6 +374,8 @@ def create_structure_to_ena(self): schema_dataframe = update_table( schema_dataframe, schema_targets, schema_update ) + + """ if self.action == "MODIFY" or self.action == "modify": process_receipt(receipt, self.action) receiptDate = receipt_root.get("receiptDate") @@ -386,6 +399,7 @@ def create_structure_to_ena(self): if run_update: schema_update["run"] = make_update(run_update, "run") return schema_update + """ def upload(self): """Create the required files and upload to ENA""" From 80d87ab5114011ed263b77b536fc41f85f8218db Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 22 Jul 2022 10:15:41 +0200 Subject: [PATCH 0692/1454] lintin --- relecov_tools/ena_upload.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index f6443dd3..ceb834c3 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,4 +1,3 @@ -from bdb import set_trace import logging # from pyparsing import col @@ -8,7 +7,7 @@ import pandas as pd -pd.options.mode.chained_assignment = None + import sys import os @@ -31,6 +30,8 @@ # from ena_upload.ena_upload import save_update import site +pd.options.mode.chained_assignment = None + template_path = os.path.join(site.getsitepackages()[0], "ena_upload", "templates") @@ -374,7 +375,7 @@ def create_structure_to_ena(self): schema_dataframe = update_table( schema_dataframe, schema_targets, schema_update ) - + """ if self.action == "MODIFY" or self.action == "modify": process_receipt(receipt, self.action) From 6b4467460563e08de5f0cb172aaff996fd43ab69 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 22 Jul 2022 11:33:18 +0200 Subject: [PATCH 0693/1454] add missing laboratories definition --- relecov_tools/conf/configuration.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index c79160d4..19375a58 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -14,7 +14,7 @@ "Sample Collection Date", "Sample Received Date", "Purpose of sampling", - "Biological Sample Storage Condition ", + "Biological Sample Storage Condition", "Specimen source", "Environmental Material", "Environmental System", From e82c37292f048d0f5a7c17d6eb6b270ba67ca733 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 22 Jul 2022 11:34:12 +0200 Subject: [PATCH 0694/1454] add missing laboratories definition --- relecov_tools/conf/laboratory_address.json | 65 +++++++++++++++++++--- 1 file changed, 56 insertions(+), 9 deletions(-) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 84b2687b..5696dc5b 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -1,6 +1,6 @@ [ { - "collecting_institution": "Instituto de Salud Carlos III ", + "collecting_institution": "Instituto de Salud Carlos III", "collecting_institution_address": "Crta. Pozuelo Majadahonda S/N,", "collecting_institution_email": "info@isciii.es", "geo_loc_state": "Madrid", @@ -159,6 +159,22 @@ "geo_loc_city": "Ciudad Real", "geo_loc_country": "Spain" }, + { + "collecting_institution": "Hospital Público Santa Bárbara", + "collecting_institution_address": "C. Obispo Rafael Torija, s/n", + "collecting_institution_email": "", + "geo_loc_state": "Castilla la Mancha", + "geo_loc_city": "Ciudad Real", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Virgen de la Luz", + "collecting_institution_address": "Hermandad de Donantes de Sangre, 1", + "collecting_institution_email": "", + "geo_loc_state": "Castilla la Mancha", + "geo_loc_city": "Cuenca", + "geo_loc_country": "Spain" + }, { "collecting_institution": "Hospital Universitario de Guadalajara", "collecting_institution_address": "C. Donante de Sangre, S/N", @@ -183,6 +199,14 @@ "geo_loc_city": "Toledo", "geo_loc_country": "Spain" }, + { + "collecting_institution": "Consejería de Sanidad", + "collecting_institution_address": "Avda. de Francia, 4.", + "collecting_institution_email": "", + "geo_loc_state": "Castilla la Mancha", + "geo_loc_city": "Toledo", + "geo_loc_country": "Spain" + }, { "collecting_institution": "Hospital General Universitario de Albacete", "collecting_institution_address": "Calle Hermanos Falcó 37", @@ -294,6 +318,13 @@ "geo_loc_city": "Barcelona", "geo_loc_country": "Spain" }, + { + "collecting_institution": "Laboratorio Echevarne Sant Cugat del Vallès", + "collecting_institution_address": "Carrer de Martorell,20 Sant Cugat del Vallès", + "geo_loc_state": "Cataluña", + "geo_loc_city": "Barcelona", + "geo_loc_country": "Spain" + }, { "collecting_institution": "Unitat de Genòmica i Medicina Personalitzada - Hospital Dr. Josep Trueta", "collecting_institution_address": "Avinguda de França, S/N,", @@ -334,6 +365,14 @@ "geo_loc_city": "Madrid", "geo_loc_country": "Spain" }, + { + "collecting_institution": "Hospital Clínico San Carlos", + "collecting_institution_address": "Calle del Prof Martín Lagos", + "collecting_institution_email": "", + "geo_loc_state": "Madrid", + "geo_loc_city": "Madrid", + "geo_loc_country": "Spain" + }, { "collecting_institution": "Centro Militar de Veterinaria de la Defensa", "collecting_institution_address": "C. Darío Gazapo 3", @@ -358,6 +397,22 @@ "geo_loc_city": "Madrid", "geo_loc_country": "Spain" }, + { + "collecting_institution": "Presidencia de Gobierno", + "collecting_institution_address": "", + "collecting_institution_email": "", + "geo_loc_state": "Madrid", + "geo_loc_city": "Madrid", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Ministerio de Sanidad, Servicios Sociales e Igualdad", + "collecting_institution_address": "", + "collecting_institution_email": "", + "geo_loc_state": "Madrid", + "geo_loc_city": "Madrid", + "geo_loc_country": "Spain" + }, { "collecting_institution": "HU Virgen de la Arrixaca", "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", @@ -454,14 +509,6 @@ "geo_loc_city": "Caceres", "geo_loc_country": "Spain" }, - { - "collecting_institution": "Sergas - Gerencia de Atención Primaria Pontevedra Sur", - "collecting_institution_address": "Av. das Camelias, 109, Vigo", - "collecting_institution_email": "", - "geo_loc_state": "Galicia", - "geo_loc_city": "Pontevedra", - "geo_loc_country": "Spain" - }, { "collecting_institution": "Gerencia de Atención Primaria Pontevedra Sur", "collecting_institution_address": "Av. das Camelias, 109, Vigo", From 2f619d8a820caae81e0ea71012541872e14be826 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 22 Jul 2022 11:34:42 +0200 Subject: [PATCH 0695/1454] re-design the module --- relecov_tools/metadata_homogeneizer.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index b029ab21..6bd0730d 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -106,7 +106,7 @@ def write_to_excel_file(self, data, f_name): sheet = book.active for row in data: sheet.append(row) - + sheet.title = "METADATA_LAB" book.save(f_name) return From 1d54b4906fef4e359dd636b18b75da983fdfb5fb Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 22 Jul 2022 11:36:01 +0200 Subject: [PATCH 0696/1454] removing comments --- relecov_tools/read_bioinfo_metadata.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 434d6a86..716f36ce 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -5,9 +5,6 @@ import json import datetime -# import os - - import rich.console from itertools import islice import pandas as pd @@ -17,7 +14,6 @@ import os import sys import relecov_tools.utils - from relecov_tools.config_json import ConfigJson import relecov_tools.json_schema From 644b5b9e8b33e7997547addde5e2b54fffbb5ec3 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 22 Jul 2022 11:37:03 +0200 Subject: [PATCH 0697/1454] Update the schema for homogenizer --- relecov_tools/schema/institution_schemas/ISCIII.json | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 678d0752..9f45aac3 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -11,10 +11,12 @@ "Sample Collection Date": "Fecha de toma", "Sample Received Date": "Fecha recepción", "Host Age": "Edad (años)", + "Host Gender": "Sexo", "Diagnostic Pcr Ct Value 1": "PCR genE" }, "fixed_fields": { + "Submitting Institution": "Instituto de Salud Carlos III", "Biological Sample Storage Condition": "-80 C", "Rna Extraction Protocol": "RT-PCR", "Purpose of sampling": "Surveillance", From 23e7f6e50df80f5cac57463c7bd7a6164b98dc94 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 22 Jul 2022 12:28:45 +0200 Subject: [PATCH 0698/1454] Resolved conflicts ena_upload.py --- relecov_tools/ena_upload.py | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 3a09336b..6d6e92a5 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -214,13 +214,6 @@ def create_structure_to_ena(self): df_run.loc[i, "sequence_file_R2_fastq"] = df_schemas.loc[ i, "sequence_file_R2_fastq" ] -<<<<<<< develop - # import pdb - - # pdb.set_trace() -======= - ->>>>>>> develop df_run.insert(3, "status", self.action) df_run = df_run.rename(columns={"fastq_r1_md5": "file_checksum"}) @@ -368,13 +361,10 @@ def create_structure_to_ena(self): print(f"\nSubmitting XMLs to ENA server: {url}") receipt = send_schemas(schema_xmls, url, self.user, self.passwd).text -<<<<<<< develop if not os.path.exists(self.output_path): os.mkdir(self.output_path) receipt_dir = os.path.join(self.output_path, "receipt.xml") print(f"Printing receipt to {receipt_dir}") -======= ->>>>>>> develop with open(f"{receipt_dir}", "w") as fw: fw.write(receipt) From 8e8977928f447bd1845853f132d6f7606027d12b Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 22 Jul 2022 12:46:36 +0200 Subject: [PATCH 0699/1454] added R2.fastq checksum in run dataframe --- relecov_tools/ena_upload.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 6d6e92a5..f94a501b 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -232,6 +232,7 @@ def create_structure_to_ena(self): df_run.insert(5, "file_name", df_run["sequence_file_R1_fastq"]) df_run2 = df_run.copy() df_run2["file_name"] = df_run["sequence_file_R2_fastq"] + df_run2["file_checksum"] = df_run["fastq_r2_md5"] df_run_final = pd.concat([df_run, df_run2]) df_run_final.reset_index() From 03394776479309caec37754b1c63f7786071c62d Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 24 Jul 2022 09:51:11 +0200 Subject: [PATCH 0700/1454] add submmiting_institution address and email --- relecov_tools/read_lab_metadata.py | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index a94594b7..d8290583 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -215,6 +215,29 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): else: row_sample.update(lab_data[row_sample["collecting_institution"]]) + """ Fetch emai and address for submitting_institution + """ + row_sample["submitting_institution"] = row_sample[ + "submitting_institution" + ].strip() + if row_sample["submitting_institution"] not in lab_json: + l_data = self.get_laboratory_data( + lab_json, geo_loc_json, row_sample["submitting_institution"] + ) + # row_sample.update(l_data) + lab_data[row_sample["submitting_institution"]] = l_data + sub_data = {} + + sub_data["submitting_institution_email"] = lab_data[ + row_sample["submitting_institution"] + ]["collecting_institution_email"] + sub_data["submitting_institution_address"] = lab_data[ + row_sample["submitting_institution"] + ]["collecting_institution_address"] + # else: + # sub_data = {"collecting_institution_email" : "", "collecting_institution_address": ""} + row_sample.update(sub_data) + # import pdb; pdb.set_trace() """ Add Fixed information """ row_sample.update(self.include_fixed_data()) From af73c7f734213ce37f98349a276d4d13f5482e86 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 24 Jul 2022 09:55:08 +0200 Subject: [PATCH 0701/1454] Including missing fields for sending to relecov platform --- relecov_tools/conf/configuration.json | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 19375a58..6cfa1ad6 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -146,7 +146,9 @@ "sequencing_sample_id", "SRA_accession", "submitting_lab_sample_id", - "virus_name" + "virus_name", + "author_submitter", + "authors" ], "relecov_bioinfo_metadata": { "dehosting_method_software_name": "KRAKEN2_KRAKEN2", From 05f6a87fe2486981b0f636942302753d9f7f9cd5 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 26 Jul 2022 13:00:01 +0200 Subject: [PATCH 0702/1454] Added parameters missing in relecov-platform --- relecov_tools/conf/configuration.json | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 6cfa1ad6..39a0a339 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -134,21 +134,23 @@ "sampleLocation": "Not defined" }, "relecov_sample_metadata": [ + "author_submitter", + "authors", "bioproject_accession_ENA", "bioproject_umbrella_accession_ENA", "biosample_accession_ENA", + "fastq_r1_md5", + "fastq_r2_md5", "GenBank_ENA_DDBJ_accession", "GISAID_accession", "gisaid_id", - "host_specimen_voucher", - "isolate_sample_id", "microbiology_lab_sample_id", + "r1_fastq_filepath", + "r2_fastq_filepath", "sequencing_sample_id", - "SRA_accession", "submitting_lab_sample_id", "virus_name", - "author_submitter", - "authors" + ], "relecov_bioinfo_metadata": { "dehosting_method_software_name": "KRAKEN2_KRAKEN2", From 267281d8a94477a6d1df190b6080fc9324c2f8dc Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 26 Jul 2022 16:55:53 +0200 Subject: [PATCH 0703/1454] added funcionality to correct R2 checksum --- relecov_tools/ena_upload.py | 47 ++++++++++++++----------------------- 1 file changed, 18 insertions(+), 29 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index ceb834c3..408b0a72 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,6 +1,7 @@ import logging # from pyparsing import col +import xml.etree.ElementTree as ET import rich.console import json @@ -282,6 +283,7 @@ def create_structure_to_ena(self): 2 214821_S12 RELECOV Spanish Network for genomics surveillance RELECOV ... PAIRED Illumina MiSeq 214823_S1_R1_001.fastq.gz_214823_S1_R2_001.fas... """ + ena_config = config_json.get_configuration("ENA_configuration") schema_dataframe = {} schema_dataframe["sample"] = df_samples @@ -349,11 +351,24 @@ def create_structure_to_ena(self): submission_xml = construct_submission( template_path, self.action, schema_xmls, self.center, checklist, tool ) - submission_xml = construct_submission( - template_path, self.action, schema_xmls, self.center, checklist, tool - ) schema_xmls["submission"] = submission_xml + tree = ET.parse(schema_xmls["run"]) + root = tree.getroot() + for files in root.iter("FILE"): + if "R2" in files.attrib["filename"]: + # print(files.attrib["filename"]) + H = df_run_final.loc[ + df_run_final["sequence_file_R2_fastq"] + == files.attrib["filename"] + ].values[0][9] + files.set("checksum", H) + # print(files.attrib["checksum"]) + + tree.write(schema_xmls["run"]) + import pdb + + pdb.set_trace() if self.dev: url = "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" else: @@ -376,32 +391,6 @@ def create_structure_to_ena(self): schema_dataframe, schema_targets, schema_update ) - """ - if self.action == "MODIFY" or self.action == "modify": - process_receipt(receipt, self.action) - receiptDate = receipt_root.get("receiptDate") - schema_update = {} # schema as key, dataframe as value - study_update = receipt_root.findall("STUDY") - sample_update = receipt_root.findall("SAMPLE") - experiment_update = receipt_root.findall("EXPERIMENT") - run_update = receipt_root.findall("RUN") - - if study_update: - schema_update["study"] = make_update(study_update, "study") - - if sample_update: - schema_update["sample"] = make_update(sample_update, "sample") - - if experiment_update: - schema_update["experiment"] = make_update( - experiment_update, "experiment" - ) - - if run_update: - schema_update["run"] = make_update(run_update, "run") - return schema_update - """ - def upload(self): """Create the required files and upload to ENA""" self.convert_input_json_to_ena() From 9b4cb75c76e6bb16e18f02fcebbb2dcf08560662 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 26 Jul 2022 16:59:25 +0200 Subject: [PATCH 0704/1454] Added funcionality to correct md5 checksum R2 --- relecov_tools/ena_upload.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 408b0a72..411226f1 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -366,9 +366,7 @@ def create_structure_to_ena(self): # print(files.attrib["checksum"]) tree.write(schema_xmls["run"]) - import pdb - pdb.set_trace() if self.dev: url = "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" else: From b82f1d46cd12558cf8934d38b4302b247fd73b13 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 26 Jul 2022 21:48:39 +0200 Subject: [PATCH 0705/1454] fix bug in json configuration --- relecov_tools/conf/configuration.json | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 39a0a339..47c0fb56 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -149,8 +149,7 @@ "r2_fastq_filepath", "sequencing_sample_id", "submitting_lab_sample_id", - "virus_name", - + "virus_name" ], "relecov_bioinfo_metadata": { "dehosting_method_software_name": "KRAKEN2_KRAKEN2", From df9de7e4f3b7f02606f7dacec4f00a1f5a2a6c9c Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 26 Jul 2022 21:54:39 +0200 Subject: [PATCH 0706/1454] fix bug and change the column to fetch sample fastq data --- relecov_tools/read_lab_metadata.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index d8290583..27f5ca09 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -102,7 +102,7 @@ def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): data["geo_loc_longitude"] = "" data["geo_loc_country"] = "" stderr.print("[red] Empty Originating Laboratory.") - log.error("Found empti Originating Laboratory") + log.error("Found empty Originating Laboratory") return data for lab in lab_json: if lab_name == lab["collecting_institution"]: @@ -112,7 +112,7 @@ def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): for city in geo_loc_json: try: - if city["geo_loc_city"] == data["geo_loc_city"]: + if city["geo_loc_city"] == lab["geo_loc_city"]: data["geo_loc_latitude"] = city["geo_loc_latitude"] data["geo_loc_longitude"] = city["geo_loc_longitude"] data["geo_loc_country"] = data["geo_loc_country"] @@ -192,7 +192,8 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): """Include sample data from sample json""" try: for key, value in samples_json[ - row_sample["sequencing_sample_id"] + row_sample["microbiology_lab_sample_id"] + # row_sample["sequencing_sample_id"] ].items(): row_sample[key] = value @@ -322,6 +323,7 @@ def read_metadata_file(self): try: sample_data_row[self.label_prop_dict[heading[idx]]] = val except TypeError as e: + import pdb; pdb.set_trace() stderr.print("[red] Error when reading " + row[2] + e) else: try: @@ -329,6 +331,7 @@ def read_metadata_file(self): row[idx] if row[idx] else "" ) except KeyError as e: + import pdb; pdb.set_trace() stderr.print( "[red] Error when reading " + str(row[2]) + str(e) ) From 66c778130cfa56a70b7693f934785c9c40c3bcc2 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 26 Jul 2022 22:00:26 +0200 Subject: [PATCH 0707/1454] remove debug tags --- relecov_tools/read_lab_metadata.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 27f5ca09..9e9ac63b 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -238,7 +238,7 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): # else: # sub_data = {"collecting_institution_email" : "", "collecting_institution_address": ""} row_sample.update(sub_data) - # import pdb; pdb.set_trace() + """ Add Fixed information """ row_sample.update(self.include_fixed_data()) @@ -323,7 +323,6 @@ def read_metadata_file(self): try: sample_data_row[self.label_prop_dict[heading[idx]]] = val except TypeError as e: - import pdb; pdb.set_trace() stderr.print("[red] Error when reading " + row[2] + e) else: try: @@ -331,7 +330,6 @@ def read_metadata_file(self): row[idx] if row[idx] else "" ) except KeyError as e: - import pdb; pdb.set_trace() stderr.print( "[red] Error when reading " + str(row[2]) + str(e) ) From 0b90b504c386394d195428788b78c44056172134 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 27 Jul 2022 07:35:12 +0200 Subject: [PATCH 0708/1454] Added funcionality to modify R2 checksum --- relecov_tools/ena_upload.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 411226f1..fb6f49ba 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -363,8 +363,7 @@ def create_structure_to_ena(self): == files.attrib["filename"] ].values[0][9] files.set("checksum", H) - # print(files.attrib["checksum"]) - + # print(files.attrib["checksum"]) tree.write(schema_xmls["run"]) if self.dev: From c9735f1ef7793f1d43f592a1a0d8a63fead1ab70 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 31 Jul 2022 09:35:38 +0200 Subject: [PATCH 0709/1454] test flake8 --- relecov_tools/read_lab_metadata.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 9e9ac63b..88d13dae 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -358,6 +358,7 @@ def create_metadata_json(self): phage_plus_schema = relecov_tools.schema_json.PhagePlusSchema(schema_json) properties_in_schema = phage_plus_schema.get_schema_properties() """ + geo_loc_json = config_json.get_configuration("geo_location_data") geo_loc_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "conf", geo_loc_json From 44ececa14319db2b7fb7f266794c40630cf28bb5 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 1 Aug 2022 16:00:34 +0200 Subject: [PATCH 0710/1454] changes in ena_upload, read_bioinfo and read_lab_metadata --- relecov_tools/ena_upload.py | 3 ++ relecov_tools/read_bioinfo_metadata.py | 75 ++++++-------------------- relecov_tools/read_lab_metadata.py | 7 ++- 3 files changed, 26 insertions(+), 59 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index fb6f49ba..9ab9b636 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -290,6 +290,9 @@ def create_structure_to_ena(self): schema_dataframe["run"] = df_run_final schema_dataframe["experiment"] = df_experiments schema_targets = extract_targets(self.action, schema_dataframe) + import pdb + + pdb.set_trace() if ena_config["study_id"] is not None: schema_dataframe["study"] = df_study diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 434d6a86..a12702e1 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -21,7 +21,6 @@ from relecov_tools.config_json import ConfigJson import relecov_tools.json_schema - log = logging.getLogger(__name__) stderr = rich.console.Console( stderr=True, @@ -58,7 +57,22 @@ def __init__(self, metadata_file=None, input_folder=None, output_folder=None): else: self.output_folder = output_folder - def get_input_files(self): + def bioinfo_parse(self, file_name): + """Fetch the metadata file folder Directory to fetch metadata file + file_name metadata file name + """ + + wb_file = openpyxl.load_workbook(file_name, data_only=True) + ws_metadata_lab = wb_file["METADATA_LAB"] + config_json = ConfigJson() + relecov_bioinfo_metadata = config_json.get_configuration( + "relecov_bioinfo_metadata" + ) + c = 0 + self.files_read_bioinfo_metadata = config_json.get_configuration( + "files_read_bioinfo_metadata" + ) + mapping_illumina_tab_path = os.path.join( self.input_folder, "mapping_illumina.tab" ) @@ -75,65 +89,12 @@ def get_input_files(self): self.input_folder, "software_versions.yml" ) pangolin_versions_path = os.path.join(self.input_folder, "pangolin_version.csv") - - return ( - mapping_illumina_tab_path, - summary_variants_metrics_path, - variants_long_table_path, - consensus_genome_length_path, - software_versions_path, - pangolin_versions_path, - ) - - def get_config_info(self): - config_json = ConfigJson() - - self.files_read_bioinfo_metadata = config_json.get_configuration( - "files_read_bioinfo_metadata" - ) self.md5_file_name = config_json.get_configuration("md5_file_name") - self.mapping_illumina_tab_field_list = config_json.get_configuration( - "mapping_illumina_tab_field_list" - ) - - return ( - self.files_read_bioinfo_metadata, - self.md5_file_name, - self.mapping_illumina_tab_field_list, - ) - - def bioinfo_parse(self, file_name): - """Fetch the metadata file folder Directory to fetch metadata file - file_name - """ - - wb_file = openpyxl.load_workbook(file_name, data_only=True) - ws_metadata_lab = wb_file["METADATA_LAB"] - c = 0 - config_json = ConfigJson() - relecov_bioinfo_metadata = config_json.get_configuration( - "relecov_bioinfo_metadata" - ) - - ( - mapping_illumina_tab_path, - summary_variants_metrics_path, - variants_long_table_path, - consensus_genome_length_path, - software_versions_path, - pangolin_versions_path, - ) = self.get_input_files(self) - - ( - self.files_read_bioinfo_metadata, - self.md5_file_name, - self.mapping_illumina_tab_field_list, - ) = self.get_config_info(self) - md5_info_path = os.path.join( self.input_folder, self.md5_file_name, # como hacer esto general para los servicios ) + mapping_illumina_tab = pd.read_csv(mapping_illumina_tab_path, sep="\t") summary_variants_metrics = pd.read_csv(summary_variants_metrics_path, sep=",") variants_long_table = pd.read_csv(variants_long_table_path, sep=",") @@ -164,13 +125,11 @@ def bioinfo_parse(self, file_name): bioinfo_dict["sample_name"] = str(sample_name) bioinfo_dict["fastq_r1"] = fastq_r1 bioinfo_dict["fastq_r2"] = fastq_r2 - # inserting all keys from configuration.json relecov_bioinfo_metadata into bioinfo_dict for key in relecov_bioinfo_metadata.keys(): bioinfo_dict[key] = relecov_bioinfo_metadata[key] bioinfo_dict["consensus_sequence_filepath"] = self.input_folder bioinfo_dict["long_table_path"] = self.input_folder - # fields from mapping_illumina.tab for key in self.mapping_illumina_tab_field_list.keys(): diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 73fd4707..a4fcd0c4 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -3,6 +3,7 @@ import json import logging +from turtle import heading import rich.console import openpyxl @@ -258,8 +259,10 @@ def read_metadata_file(self): exc_format_num = ["Sample ID given for sequencing"] wb_file = openpyxl.load_workbook(self.metadata_file, data_only=True) ws_metadata_lab = wb_file["METADATA_LAB"] + # removing the None columns in excel heading row heading = [i.value.strip() for i in ws_metadata_lab[4] if i.value] + # heading = self.update_heading_to_json(heading_without_none, meta_map_json) metadata_values = [] errors = {} @@ -279,10 +282,12 @@ def read_metadata_file(self): errors[row[2]] = {} errors[row[2]][heading[idx]] = "Invalid date format" log.error("Invalid date format in sample %s", row[2]) + stderr.print( "[red] Invalid date format in sample", - row[2] + " column " + heading[idx], + str(row[2]) + " column " + heading[idx], ) + else: if isinstance(row[idx], float) or isinstance(row[idx], int): From f05a9dfc315fc76d6c65b2b46aac0a642ba2f2f9 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 1 Aug 2022 22:35:45 +0200 Subject: [PATCH 0711/1454] remove the NOT FOUND String for the run and exp alias. Fix error in reg expresion and use old version for flake8 --- .github/workflows/python_lint.yml | 4 +- .../samples_data_COD_test_01_20220422.json | 82 + .../bioinfo_metadata.json | 5322 +++++++++++++++++ .../bioinfo_metadata_test.json | 58 + .../metadata_lab_test.json | 84 + relecov_tools/read_lab_metadata.py | 16 +- 6 files changed, 5561 insertions(+), 5 deletions(-) create mode 100644 relecov_tools/example_data/1.read_lab_metadata_module/samples_data_COD_test_01_20220422.json create mode 100644 relecov_tools/example_data/upload_bioinfo_metadata/bioinfo_metadata.json create mode 100644 relecov_tools/example_data/upload_bioinfo_metadata/bioinfo_metadata_test.json create mode 100644 relecov_tools/example_data/upload_bioinfo_metadata/metadata_lab_test.json diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml index 3b0d986e..02ed5b31 100644 --- a/.github/workflows/python_lint.yml +++ b/.github/workflows/python_lint.yml @@ -20,9 +20,9 @@ jobs: - name: Checkout PyTorch uses: actions/checkout@master - name: Install flake8 - run: pip install flake8 + run: pip install flake8==4-0.1 - name: Run flake8 - uses: suo/flake8-github-action@releases/v1 + run: suo/flake8-github-action@releases/v1 with: checkName: 'flake8_py3' # NOTE: this needs to be the same as the job name env: diff --git a/relecov_tools/example_data/1.read_lab_metadata_module/samples_data_COD_test_01_20220422.json b/relecov_tools/example_data/1.read_lab_metadata_module/samples_data_COD_test_01_20220422.json new file mode 100644 index 00000000..445027f0 --- /dev/null +++ b/relecov_tools/example_data/1.read_lab_metadata_module/samples_data_COD_test_01_20220422.json @@ -0,0 +1,82 @@ +{ + "1197663": { + "fastq_r1_md5": "83043c429b0ab94375236cf7f51860f0", + "fastq_r2_md5": "c00859a1f83e2364cca953fb25da3cf2", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_008.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_008.fastq.gz" + }, + "1197677": { + "fastq_r1_md5": "b0a13671031ef5aa7e0e6559a925a688", + "fastq_r2_md5": "8c420a603c81823e68436003825b1e1f", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_005.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_005.fastq.gz" + }, + "1197678": { + "fastq_r1_md5": "13e01498a0526303f5e32f3eef077b5a", + "fastq_r2_md5": "61d1f52e84237320d97fd7fc2da56116", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_006.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_006.fastq.gz" + }, + "1197685": { + "fastq_r1_md5": "a86f4fa0c92d76df34fd000a29d1cdd3", + "fastq_r2_md5": "8c4309dc00d725496c48bee6da0e4bbf", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_0010.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_0010.fastq.gz" + }, + "1197689": { + "fastq_r1_md5": "bc720a024263a518f6a6cd9301b308ac", + "fastq_r2_md5": "6bf6d95b59c950691effcaf8a0e83068", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_009.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_009.fastq.gz" + }, + "1197737": { + "fastq_r1_md5": "f5b60a93b39a0b98781efb434d577a57", + "fastq_r2_md5": "e19f883b4e05045895f990c2296009a8", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_007.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_007.fastq.gz" + }, + "1197767": { + "fastq_r1_md5": "c78fcb585a0f44734ce8c2aebf3eff33", + "fastq_r2_md5": "8361d5a6b50279fbc8c93226ecc3568a", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_003.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_003.fastq.gz" + }, + "1197824": { + "fastq_r1_md5": "9a460a812086516536c1a1023ab5f7fe", + "fastq_r2_md5": "41cd79b8a167d85eb06309207fd120cf", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_002.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_002.fastq.gz" + }, + "1197860": { + "fastq_r1_md5": "f2facbd1d6c7e0972074ced31ccbfd8e", + "fastq_r2_md5": "fd9948be8da7a38b0f80659dfc21aeea", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_001.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_001.fastq.gz" + }, + "8328199": { + "fastq_r1_md5": "aa557fc40d3a9e16f470ac595fb5eb3e", + "fastq_r2_md5": "a2dd5e08b75815dab892e392cb8468fc", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_004.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_004.fastq.gz" + } +} diff --git a/relecov_tools/example_data/upload_bioinfo_metadata/bioinfo_metadata.json b/relecov_tools/example_data/upload_bioinfo_metadata/bioinfo_metadata.json new file mode 100644 index 00000000..01c8ef58 --- /dev/null +++ b/relecov_tools/example_data/upload_bioinfo_metadata/bioinfo_metadata.json @@ -0,0 +1,5322 @@ +{ + "214821": { + "analysis_date": "2022-05-12 14:55:38.607792", + "assembly": "None", + "assembly_params": "None", + "bioinformatics_protocol_software_name": "nf-core/viralrecon", + "bioinformatics_protocol_software_version": "2.4.1", + "commercial_open_source_both": "open-source", + "consensus_genome_length": "30396", + "consensus_params": "-p vcf -f", + "consensus_sequence_R1_md5": "dbcc703ccb7da3002fee6c0486199009", + "consensus_sequence_R1_name": "214821_S12_R1_001.fastq.gz", + "consensus_sequence_R2_md5": "b76fba963664b532004c4ce7153ae14f", + "consensus_sequence_R2_name": "214821_S12_R2_001.fastq.gz", + "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", + "consensus_sequence_software_version": "1.14", + "dehosting_method_software_name": "KRAKEN2_KRAKEN2", + "dehosting_method_software_version": "2.1.2", + "depth_of_coverage_threshold": ">10x", + "depth_of_coverage_value": "287.0", + "fastq_r1": "214821_S12_R1_001.fastq.gz", + "fastq_r2": "214821_S12_R2_001.fastq.gz", + "if_assembly_other": "None", + "if_bioinformatic_protocol_is_other_specify": "None", + "if_consensus_other": "None", + "if_lineage_identification_other": "None", + "if_mapping_other": "None", + "if_preprocessing_other": "None", + "lineage_analysis_software_name": "pangolin", + "lineage_analysis_software_version": "4.0.6", + "lineage_identification_date": "2022-05-12 14:55:38.607792", + "lineage_name": "B.1.177", + "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "mapping_params": "--seed 1", + "mapping_software_name": "BOWTIE2_ALIGN", + "mapping_software_version": "2.4.4", + "ns_per_100_kbp": "8442.32", + "number_of_base_pairs_sequenced": "633884", + "number_of_variants_AF_greater_75percent": "19", + "number_of_variants_with_effect": "9", + "per_Ns": "8,44", + "per_genome_greater_10x": "92,0", + "per_reads_host": "1,08", + "per_reads_virus": "98,54", + "per_unmapped": "0,380247", + "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", + "preprocessing_software_name": "FASTP", + "preprocessing_software_version": "0.23.2", + "qc_filtered": "285604", + "reference_genome_accession": "NC_045512.2", + "sample_name": "214821", + "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", + "variant_calling_software_name": "IVAR_VARIANTS", + "variant_calling_software_version": "1.3.1", + "variant_designation": "19" + }, + "214822": { + "analysis_date": "2022-05-12 14:55:38.607792", + "assembly": "None", + "assembly_params": "None", + "bioinformatics_protocol_software_name": "nf-core/viralrecon", + "bioinformatics_protocol_software_version": "2.4.1", + "commercial_open_source_both": "open-source", + "consensus_genome_length": "30396", + "consensus_params": "-p vcf -f", + "consensus_sequence_R1_md5": "4837ac15de51cfeda4596b09f5876ac8", + "consensus_sequence_R1_name": "214822_S13_R1_001.fastq.gz", + "consensus_sequence_R2_md5": "f0bf2700ae3eadc9a3f01c515546bf4a", + "consensus_sequence_R2_name": "214822_S13_R2_001.fastq.gz", + "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", + "consensus_sequence_software_version": "1.14", + "dehosting_method_software_name": "KRAKEN2_KRAKEN2", + "dehosting_method_software_version": "2.1.2", + "depth_of_coverage_threshold": ">10x", + "depth_of_coverage_value": "6.0", + "fastq_r1": "214822_S13_R1_001.fastq.gz", + "fastq_r2": "214822_S13_R2_001.fastq.gz", + "if_assembly_other": "None", + "if_bioinformatic_protocol_is_other_specify": "None", + "if_consensus_other": "None", + "if_lineage_identification_other": "None", + "if_mapping_other": "None", + "if_preprocessing_other": "None", + "lineage_analysis_software_name": "pangolin", + "lineage_analysis_software_version": "4.0.6", + "lineage_identification_date": "2022-05-12 14:55:38.607792", + "lineage_name": "Unassigned", + "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "mapping_params": "--seed 1", + "mapping_software_name": "BOWTIE2_ALIGN", + "mapping_software_version": "2.4.4", + "ns_per_100_kbp": "58831.99", + "number_of_base_pairs_sequenced": "765444", + "number_of_variants_AF_greater_75percent": "8", + "number_of_variants_with_effect": "3", + "per_Ns": "58,83", + "per_genome_greater_10x": "41,0", + "per_reads_host": "63,33", + "per_reads_virus": "20,09", + "per_unmapped": "16,5778", + "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", + "preprocessing_software_name": "FASTP", + "preprocessing_software_version": "0.23.2", + "qc_filtered": "306868", + "reference_genome_accession": "NC_045512.2", + "sample_name": "214822", + "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", + "variant_calling_software_name": "IVAR_VARIANTS", + "variant_calling_software_version": "1.3.1", + "variant_designation": "8" + }, + "214823": { + "analysis_date": "2022-05-12 14:55:38.607792", + "assembly": "None", + "assembly_params": "None", + "bioinformatics_protocol_software_name": "nf-core/viralrecon", + "bioinformatics_protocol_software_version": "2.4.1", + "commercial_open_source_both": "open-source", + "consensus_genome_length": "0", + "consensus_params": "-p vcf -f", + "consensus_sequence_R1_md5": "213a150461737cb0af48fddd370f4ceb", + "consensus_sequence_R1_name": "214823_S1_R1_001.fastq.gz", + "consensus_sequence_R2_md5": "1b58f58f861c81ed94401a319c7ae9ce", + "consensus_sequence_R2_name": "214823_S1_R2_001.fastq.gz", + "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", + "consensus_sequence_software_version": "1.14", + "dehosting_method_software_name": "KRAKEN2_KRAKEN2", + "dehosting_method_software_version": "2.1.2", + "depth_of_coverage_threshold": ">10x", + "depth_of_coverage_value": "nan", + "fastq_r1": "214823_S1_R1_001.fastq.gz", + "fastq_r2": "214823_S1_R2_001.fastq.gz", + "if_assembly_other": "None", + "if_bioinformatic_protocol_is_other_specify": "None", + "if_consensus_other": "None", + "if_lineage_identification_other": "None", + "if_mapping_other": "None", + "if_preprocessing_other": "None", + "lineage_analysis_software_name": "pangolin", + "lineage_analysis_software_version": "4.0.6", + "lineage_identification_date": "2022-05-12 14:55:38.607792", + "lineage_name": "nan", + "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "mapping_params": "--seed 1", + "mapping_software_name": "BOWTIE2_ALIGN", + "mapping_software_version": "2.4.4", + "ns_per_100_kbp": "nan", + "number_of_base_pairs_sequenced": "597696", + "number_of_variants_AF_greater_75percent": "0", + "number_of_variants_with_effect": "0", + "per_Ns": "nan", + "per_genome_greater_10x": "nan", + "per_reads_host": "58,03", + "per_reads_virus": "0,1", + "per_unmapped": "41,8663", + "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", + "preprocessing_software_name": "FASTP", + "preprocessing_software_version": "0.23.2", + "qc_filtered": "196898", + "reference_genome_accession": "NC_045512.2", + "sample_name": "214823", + "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", + "variant_calling_software_name": "IVAR_VARIANTS", + "variant_calling_software_version": "1.3.1", + "variant_designation": "0" + }, + "214824": { + "analysis_date": "2022-05-12 14:55:38.607792", + "assembly": "None", + "assembly_params": "None", + "bioinformatics_protocol_software_name": "nf-core/viralrecon", + "bioinformatics_protocol_software_version": "2.4.1", + "commercial_open_source_both": "open-source", + "consensus_genome_length": "0", + "consensus_params": "-p vcf -f", + "consensus_sequence_R1_md5": "cf00a386d54734ee7a60932f487d946c", + "consensus_sequence_R1_name": "214824_S14_R1_001.fastq.gz", + "consensus_sequence_R2_md5": "eebdabee75e327f49d9e1741d22c40c3", + "consensus_sequence_R2_name": "214824_S14_R2_001.fastq.gz", + "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", + "consensus_sequence_software_version": "1.14", + "dehosting_method_software_name": "KRAKEN2_KRAKEN2", + "dehosting_method_software_version": "2.1.2", + "depth_of_coverage_threshold": ">10x", + "depth_of_coverage_value": "nan", + "fastq_r1": "214824_S14_R1_001.fastq.gz", + "fastq_r2": "214824_S14_R2_001.fastq.gz", + "if_assembly_other": "None", + "if_bioinformatic_protocol_is_other_specify": "None", + "if_consensus_other": "None", + "if_lineage_identification_other": "None", + "if_mapping_other": "None", + "if_preprocessing_other": "None", + "lineage_analysis_software_name": "pangolin", + "lineage_analysis_software_version": "4.0.6", + "lineage_identification_date": "2022-05-12 14:55:38.607792", + "lineage_name": "nan", + "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "mapping_params": "--seed 1", + "mapping_software_name": "BOWTIE2_ALIGN", + "mapping_software_version": "2.4.4", + "ns_per_100_kbp": "nan", + "number_of_base_pairs_sequenced": "728", + "number_of_variants_AF_greater_75percent": "0", + "number_of_variants_with_effect": "0", + "per_Ns": "nan", + "per_genome_greater_10x": "nan", + "per_reads_host": "33,06", + "per_reads_virus": "55,65", + "per_unmapped": "11,2903", + "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", + "preprocessing_software_name": "FASTP", + "preprocessing_software_version": "0.23.2", + "qc_filtered": "248", + "reference_genome_accession": "NC_045512.2", + "sample_name": "214824", + "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", + "variant_calling_software_name": "IVAR_VARIANTS", + "variant_calling_software_version": "1.3.1", + "variant_designation": "0" + }, + "214825": { + "analysis_date": "2022-05-12 14:55:38.607792", + "assembly": "None", + "assembly_params": "None", + "bioinformatics_protocol_software_name": "nf-core/viralrecon", + "bioinformatics_protocol_software_version": "2.4.1", + "commercial_open_source_both": "open-source", + "consensus_genome_length": "30402", + "consensus_params": "-p vcf -f", + "consensus_sequence_R1_md5": "c4b42c9ca78676b244f6fd3356a39bbd", + "consensus_sequence_R1_name": "214825_S15_R1_001.fastq.gz", + "consensus_sequence_R2_md5": "7356129837732007e08e94a7699c5f7e", + "consensus_sequence_R2_name": "214825_S15_R2_001.fastq.gz", + "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_software_name": 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"/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", + "consensus_sequence_software_version": "1.14", + "dehosting_method_software_name": "KRAKEN2_KRAKEN2", + "dehosting_method_software_version": "2.1.2", + "depth_of_coverage_threshold": ">10x", + "depth_of_coverage_value": "11.0", + "fastq_r1": "220684_S95_R1_001.fastq.gz", + "fastq_r2": "220684_S95_R2_001.fastq.gz", + "if_assembly_other": "None", + "if_bioinformatic_protocol_is_other_specify": "None", + "if_consensus_other": "None", + "if_lineage_identification_other": "None", + "if_mapping_other": "None", + "if_preprocessing_other": "None", + "lineage_analysis_software_name": "pangolin", + "lineage_analysis_software_version": "0", + "lineage_identification_date": "2022-05-12 14:55:38.607792", + "lineage_name": "Unassigned", + "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "mapping_params": "--seed 1", + "mapping_software_name": "BOWTIE2_ALIGN", + "mapping_software_version": "2.4.4", + "ns_per_100_kbp": "49070.3", + "number_of_base_pairs_sequenced": "889808", + "number_of_variants_AF_greater_75percent": "26", + "number_of_variants_with_effect": "21", + "per_Ns": "49,07", + "per_genome_greater_10x": "51,0", + "per_reads_host": "56,51", + "per_reads_virus": "38,03", + "per_unmapped": "5,45281", + "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", + "preprocessing_software_name": "FASTP", + "preprocessing_software_version": "0.23.2", + "qc_filtered": "363996", + "reference_genome_accession": "NC_045512.2", + "sample_name": "220684", + "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", + "variant_calling_software_name": "IVAR_VARIANTS", + "variant_calling_software_version": "1.3.1", + "variant_designation": "26" + }, + "220685": { + "analysis_date": "2022-05-12 14:55:38.607792", + "assembly": "None", + "assembly_params": "None", + "bioinformatics_protocol_software_name": "nf-core/viralrecon", + "bioinformatics_protocol_software_version": "2.4.1", + "commercial_open_source_both": "open-source", + "consensus_genome_length": "30387", + "consensus_params": "-p vcf -f", + "consensus_sequence_R1_md5": "87a281cb1cc7a5f246aeaf5ed33b2d3f", + "consensus_sequence_R1_name": "220684_S95_R1_001.fastq.gz", + "consensus_sequence_R2_md5": "be0059af911542a8329249cc6fd4b50e", + "consensus_sequence_R2_name": "220684_S95_R2_001.fastq.gz", + "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", + "consensus_sequence_software_version": "1.14", + "dehosting_method_software_name": "KRAKEN2_KRAKEN2", + "dehosting_method_software_version": "2.1.2", + "depth_of_coverage_threshold": ">10x", + "depth_of_coverage_value": "63.0", + "fastq_r1": "220685_S96_R1_001.fastq.gz", + "fastq_r2": "220685_S96_R2_001.fastq.gz", + "if_assembly_other": "None", + "if_bioinformatic_protocol_is_other_specify": "None", + "if_consensus_other": "None", + "if_lineage_identification_other": "None", + "if_mapping_other": "None", + "if_preprocessing_other": "None", + "lineage_analysis_software_name": "pangolin", + "lineage_analysis_software_version": "0", + "lineage_identification_date": "2022-05-12 14:55:38.607792", + "lineage_name": "Unassigned", + "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "mapping_params": "--seed 1", + "mapping_software_name": "BOWTIE2_ALIGN", + "mapping_software_version": "2.4.4", + "ns_per_100_kbp": "25046.84", + "number_of_base_pairs_sequenced": "756012", + "number_of_variants_AF_greater_75percent": "35", + "number_of_variants_with_effect": "25", + "per_Ns": "25,05", + "per_genome_greater_10x": "75,0", + "per_reads_host": "9,21", + "per_reads_virus": "89,28", + "per_unmapped": "1,51439", + "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", + "preprocessing_software_name": "FASTP", + "preprocessing_software_version": "0.23.2", + "qc_filtered": "327920", + "reference_genome_accession": "NC_045512.2", + "sample_name": "220685", + "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", + "variant_calling_software_name": "IVAR_VARIANTS", + "variant_calling_software_version": "1.3.1", + "variant_designation": "35" + } +} \ No newline at end of file diff --git a/relecov_tools/example_data/upload_bioinfo_metadata/bioinfo_metadata_test.json b/relecov_tools/example_data/upload_bioinfo_metadata/bioinfo_metadata_test.json new file mode 100644 index 00000000..a0aa0203 --- /dev/null +++ b/relecov_tools/example_data/upload_bioinfo_metadata/bioinfo_metadata_test.json @@ -0,0 +1,58 @@ +{ + "214821": { + "analysis_date": "2022-05-12 14:55:38.607792", + "assembly": "None", + "assembly_params": "None", + "bioinformatics_protocol_software_name": "nf-core/viralrecon", + "bioinformatics_protocol_software_version": "2.4.1", + "commercial_open_source_both": "open-source", + "consensus_genome_length": "30396", + "consensus_params": "-p vcf -f", + "consensus_sequence_R1_md5": "dbcc703ccb7da3002fee6c0486199009", + "consensus_sequence_R1_name": "214821_S12_R1_001.fastq.gz", + "consensus_sequence_R2_md5": "b76fba963664b532004c4ce7153ae14f", + "consensus_sequence_R2_name": "214821_S12_R2_001.fastq.gz", + "consensus_sequence_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", + "consensus_sequence_software_version": "1.14", + "dehosting_method_software_name": "KRAKEN2_KRAKEN2", + "dehosting_method_software_version": "2.1.2", + "depth_of_coverage_threshold": ">10x", + "depth_of_coverage_value": "287.0", + "fastq_r1": "214821_S12_R1_001.fastq.gz", + "fastq_r2": "214821_S12_R2_001.fastq.gz", + "if_assembly_other": "None", + "if_bioinformatic_protocol_is_other_specify": "None", + "if_consensus_other": "None", + "if_lineage_identification_other": "None", + "if_mapping_other": "None", + "if_preprocessing_other": "None", + "lineage_analysis_software_name": "pangolin", + "lineage_analysis_software_version": "4.0.6", + "lineage_identification_date": "2022-05-12 14:55:38.607792", + "lineage_name": "B.1.177", + "long_table_path": "/data/UCCT_Relecov/COD-2100-MAD-CNM/20220208", + "mapping_params": "--seed 1", + "mapping_software_name": "BOWTIE2_ALIGN", + "mapping_software_version": "2.4.4", + "ns_per_100_kbp": "8442.32", + "number_of_base_pairs_sequenced": "633884", + "number_of_variants_AF_greater_75percent": "19", + "number_of_variants_with_effect": "9", + "per_Ns": "8,44", + "per_genome_greater_10x": "92,0", + "per_reads_host": "1,08", + "per_reads_virus": "98,54", + "per_unmapped": "0,380247", + "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", + "preprocessing_software_name": "FASTP", + "preprocessing_software_version": "0.23.2", + "qc_filtered": "285604", + "reference_genome_accession": "NC_045512.2", + "sample_name": "214821", + "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", + "variant_calling_software_name": "IVAR_VARIANTS", + "variant_calling_software_version": "1.3.1", + "variant_designation": "19" + } +} diff --git a/relecov_tools/example_data/upload_bioinfo_metadata/metadata_lab_test.json b/relecov_tools/example_data/upload_bioinfo_metadata/metadata_lab_test.json new file mode 100644 index 00000000..01bc3b8f --- /dev/null +++ b/relecov_tools/example_data/upload_bioinfo_metadata/metadata_lab_test.json @@ -0,0 +1,84 @@ +[ + { + "amplicon_protocol": "ARTIC", + "amplicon_version": "ARTIC v3", + "analysis_authors": "", + "anatomical_material": "Nasopharyngeal exudate", + "author_submitter": "", + "authors": "A. Monzón; F. Casas; I. Jiménez; M. Camarero; P. Zaballos; ROMAN SOTO; S. Cuesta, I.; S. Iglesias-Caballero; S. Pozo; S. Varona; SERGIO; Sandonís; V. Vázquez-Morón", + "biosample_accession_ENA": "", + "collecting_institution": "Hospital Clínico Universitario Virgen de la Arrixaca", + "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n, El Palmar", + "collecting_institution_email": "", + "collecting_lab_sample_id": "16065902", + "collection_device": "", + "collector_name": "", + "common_name": "Severe acute respiratory syndrome", + "design_description": "Design Description", + "diagnostic_pcr_Ct_value_1": "18", + "diagnostic_pcr_Ct_value_2": "", + "enrichment_protocol": "Amplicon", + "environmental_material": "", + "environmental_site": "Swab", + "experiment_alias": "NOT_FOUND", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1": "2018086_R1.fastq.gz", + "fastq_r1_md5": "eab8b05ef27f4f5cba5cddf6ad627de2", + "fastq_r2": "2018086_R2.fastq.gz", + "fastq_r2_md5": "d82a37aa970df2b8bf8f547ca7c18ac8", + "flowcell_kit": "", + "gene_name_1": "ORF E", + "gene_name_2": "", + "geo_loc_city": "Murcia", + "geo_loc_country": "Spain", + "geo_loc_latitude": "37.9861", + "geo_loc_longitude": "-1.1303", + "geo_loc_state": "Murcia", + "gisaid_id": "EPI_ISL_862545", + "host_age": "26", + "host_common_name": "Human", + "host_disease": "COVID-19", + "host_gender": "Hombre", + "host_scientific_name": "Homo Sapiens", + "if_amplicon_protocol_if_other_especify": "", + "if_enrichment_protocol_is_other_specify": "", + "isolate_sample_id": "16065902", + "library_kit": "", + "library_layout": "Paired", + "library_preparation_kit": "Illumina DNA Prep", + "library_selection": "PCR", + "library_source": "Viral RNA", + "library_strategy": "Amplicon", + "microbiology_lab_sample_id": "2018086", + "number_of_samples_in_run": "60", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "public_health_sample_id_sivies": "No consta", + "purpose_sampling": "Surveillance", + "r1_fastq_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "r2_fastq_filepath": "/data/UCCT_Relecov/COD-2100-MAD-CNM/muestras_analizadas_viralrecon_20220720", + "rna_extraction_protocol": "RT-PCR", + "runID": "MiSeaq_GN_195", + "run_alias": "NOT_FOUND.fastq.gz", + "sample_collection_date": "2020-12-20", + "sample_description": "Sample for surveillance", + "sample_received_date": "2020-12-22", + "sample_storage_conditions": "-80 C", + "sequence_file_R1_fastq": "2018086_R1.fastq.gz", + "sequence_file_R2_fastq": "2018086_R2.fastq.gz", + "sequencing_date": "2021-01-13", + "sequencing_instrument_model": "Illumina MiSeq", + "sequencing_instrument_platform": "Illumina", + "sequencing_sample_id": "2018086", + "study_alias": "RELECOV", + "study_id": "ERP137164", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", + "submitting_institution": "Instituto de Salud Carlos III", + "submitting_institution_address": "Crta. Pozuelo Majadahonda S/N,", + "submitting_institution_email": "info@isciii.es", + "submitting_lab_sample_id": "202074288", + "tax_id": "2697049", + "type": "betacoronavirus", + "virus_name": "" + } +] diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 88d13dae..9a43c5f5 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -84,13 +84,16 @@ def read_json_file(self, j_file): return data def get_experiment_run_alias(self, row_data): - exp_alias = "NOT_FOUND" - run_alias = "NOT_FOUND.fastq.gz" + if "fastq_r1" in row_data: - match = re.search(r"(.+)_R1_.*", row_data["fastq_r1"]) + match = re.search(r"(\w+)_R1.*", row_data["fastq_r1"]) if match: exp_alias = match.group(1) run_alias = match.group(1) + ".fastq.gz" + else: + log.error("fastq_r1 field does not exists ") + stderr.print("[red] Exiting because there is not fastq_r1 field ") + sys.exit(1) return exp_alias, run_alias def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): @@ -188,6 +191,9 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): geo_loc_json = self.read_json_file(geo_loc_file) samples_json = self.read_json_file(self.sample_list_file) exp_alias, run_alias = self.get_experiment_run_alias(metadata[0]) + import pdb + + pdb.set_trace() for row_sample in metadata: """Include sample data from sample json""" try: @@ -375,6 +381,10 @@ def create_metadata_json(self): meta_map_json = self.read_json_file(meta_map_json_file) """ valid_metadata_rows, errors = self.read_metadata_file() + if len(errors) > 0: + stderr.print("[red] Stopped executing because the errors found") + sys.exit(1) + # Continue by adding extra information completed_metadata = self.add_additional_data( valid_metadata_rows, From 2fda81c91f7a660ce0d2dd9f3b1b37da1e891378 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 1 Aug 2022 22:40:39 +0200 Subject: [PATCH 0712/1454] fixed the error in flake8 action --- .github/workflows/python_lint.yml | 2 +- relecov_tools/read_lab_metadata.py | 3 --- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml index 02ed5b31..d7273ac2 100644 --- a/.github/workflows/python_lint.yml +++ b/.github/workflows/python_lint.yml @@ -22,7 +22,7 @@ jobs: - name: Install flake8 run: pip install flake8==4-0.1 - name: Run flake8 - run: suo/flake8-github-action@releases/v1 + uses: suo/flake8-github-action@releases/v1 with: checkName: 'flake8_py3' # NOTE: this needs to be the same as the job name env: diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 9a43c5f5..8c024524 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -191,9 +191,6 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): geo_loc_json = self.read_json_file(geo_loc_file) samples_json = self.read_json_file(self.sample_list_file) exp_alias, run_alias = self.get_experiment_run_alias(metadata[0]) - import pdb - - pdb.set_trace() for row_sample in metadata: """Include sample data from sample json""" try: From 27ad186ddf2b62f2a20805e6d73169260626ed4e Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 1 Aug 2022 22:41:54 +0200 Subject: [PATCH 0713/1454] fixed the error in flake8 action --- .github/workflows/python_lint.yml | 2 +- relecov_tools/read_lab_metadata.py | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml index d7273ac2..d9d9005b 100644 --- a/.github/workflows/python_lint.yml +++ b/.github/workflows/python_lint.yml @@ -20,7 +20,7 @@ jobs: - name: Checkout PyTorch uses: actions/checkout@master - name: Install flake8 - run: pip install flake8==4-0.1 + run: pip install flake8==4.0.1 - name: Run flake8 uses: suo/flake8-github-action@releases/v1 with: diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 8c024524..1ac22393 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -112,7 +112,6 @@ def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): for key, value in lab.items(): data[key] = value break - for city in geo_loc_json: try: if city["geo_loc_city"] == lab["geo_loc_city"]: From f7213efc8461afd121d38f5cfc5f82c9d8fcd7ac Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 2 Aug 2022 01:17:56 +0200 Subject: [PATCH 0714/1454] Correcting flake8 --- .github/workflows/python_lint.yml | 2 +- relecov_tools/read_lab_metadata.py | 1 + tox.ini | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml index d9d9005b..3b0d986e 100644 --- a/.github/workflows/python_lint.yml +++ b/.github/workflows/python_lint.yml @@ -20,7 +20,7 @@ jobs: - name: Checkout PyTorch uses: actions/checkout@master - name: Install flake8 - run: pip install flake8==4.0.1 + run: pip install flake8 - name: Run flake8 uses: suo/flake8-github-action@releases/v1 with: diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 1ac22393..8c024524 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -112,6 +112,7 @@ def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): for key, value in lab.items(): data[key] = value break + for city in geo_loc_json: try: if city["geo_loc_city"] == lab["geo_loc_city"]: diff --git a/tox.ini b/tox.ini index bdace909..51351738 100644 --- a/tox.ini +++ b/tox.ini @@ -1,6 +1,6 @@ ## According to black coding style: https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html [flake8] max-line-length = 88 -... + select = C,E,F,W,B,B950 extend-ignore = E203, E501, W605 From 0a4e944c853f5dc0f186a03b3e139055f5350655 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 2 Aug 2022 01:22:34 +0200 Subject: [PATCH 0715/1454] Correcting flake8 --- .github/workflows/python_lint.yml | 6 +----- relecov_tools/read_lab_metadata.py | 2 +- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml index 3b0d986e..9d043bbd 100644 --- a/.github/workflows/python_lint.yml +++ b/.github/workflows/python_lint.yml @@ -22,11 +22,7 @@ jobs: - name: Install flake8 run: pip install flake8 - name: Run flake8 - uses: suo/flake8-github-action@releases/v1 - with: - checkName: 'flake8_py3' # NOTE: this needs to be the same as the job name - env: - GITHUB_TOKEN: ${{ secrets.TOKEN_ACTIONS }} + run: flake8 --ignore E501,W503,E203,W605 black_lint: runs-on: ubuntu-latest diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 8c024524..9011efba 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -84,7 +84,7 @@ def read_json_file(self, j_file): return data def get_experiment_run_alias(self, row_data): - + """Get the experiment_alias a run_alias from the first fastq_r1""" if "fastq_r1" in row_data: match = re.search(r"(\w+)_R1.*", row_data["fastq_r1"]) if match: From dadc3aa840b763393d770d5c1bb957a4aa714d8b Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 2 Aug 2022 09:59:02 +0200 Subject: [PATCH 0716/1454] lintin --- relecov_tools/read_lab_metadata.py | 16 +++------------- 1 file changed, 3 insertions(+), 13 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 19130c54..bf3e9bff 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -156,6 +156,7 @@ def include_processed_data(self, metadata): "Illumina iSeq 100", "Illumina MiSeq", "Illumina NextSeq550", + "Illumina NextSeq", "Illumina NovaSeq 6000", ], "MinION": ["Oxford Nanopore"], @@ -171,6 +172,7 @@ def include_processed_data(self, metadata): """New fields that required processing from other field """ for key, values in seq_inst_plat.items(): if metadata["sequencing_instrument_model"] in values: + new_data["sequencing_instrument_platform"] = key break @@ -303,19 +305,8 @@ def read_metadata_file(self): sample_data_row[self.label_prop_dict[heading[idx]]] = row[ idx ].strftime("%Y-%m-%d") + except AttributeError: -<<<<<<< HEAD - if row[2] not in errors: - errors[row[2]] = {} - errors[row[2]][heading[idx]] = "Invalid date format" - log.error("Invalid date format in sample %s", row[2]) - - stderr.print( - "[red] Invalid date format in sample", - str(row[2]) + " column " + heading[idx], - ) - -======= # check if date is in string format str_date = re.search(r"(\d{4}-\d{2}-\d{2}).*", row[idx]) if str_date: @@ -331,7 +322,6 @@ def read_metadata_file(self): "[red] Invalid date format in sample", row[2] + " column " + heading[idx], ) ->>>>>>> 765c35610c6254218ef184a747395352e3e96f8f else: if isinstance(row[idx], float) or isinstance(row[idx], int): From 6447c2337e60769cd18d6687240e4a90abc8a11c Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 2 Aug 2022 10:00:48 +0200 Subject: [PATCH 0717/1454] lintin --- relecov_tools/read_lab_metadata.py | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index bf3e9bff..56e186f5 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -305,7 +305,6 @@ def read_metadata_file(self): sample_data_row[self.label_prop_dict[heading[idx]]] = row[ idx ].strftime("%Y-%m-%d") - except AttributeError: # check if date is in string format str_date = re.search(r"(\d{4}-\d{2}-\d{2}).*", row[idx]) From d0c7a7803f469a0462e9001edf5df55d69a68004 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 2 Aug 2022 10:06:15 +0200 Subject: [PATCH 0718/1454] lintin --- relecov_tools/read_lab_metadata.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 1daffb34..3087d904 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -3,7 +3,8 @@ import json import logging -from turtle import heading + +# from turtle import heading import rich.console import openpyxl From 026fd5505662cdadada26ce863908a27e864f6bc Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 2 Aug 2022 10:35:57 +0200 Subject: [PATCH 0719/1454] collecting_lab_sample_id --> sequencing_sample_id --- relecov_tools/map_schema.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index a92c4fb1..0ba95fab 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -179,7 +179,7 @@ def additional_formating(self, mapped_json_data): "collecting_lab_sample_id" ] mapped_json_data[idx]["sample_title"] = self.json_data[idx][ - "collecting_lab_sample_id" + "sequencing_sample_id" ] mapped_json_data[idx]["file_type"] = "fastq" mapped_json_data[idx]["collector_name"] = self.json_data[idx][ From b1c68450e888bb05aa88901bb2e64b3a053d97eb Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 2 Aug 2022 11:13:04 +0200 Subject: [PATCH 0720/1454] changed experiment_alias and run_alias to be a combination of r1 + r2 sample file --- relecov_tools/read_lab_metadata.py | 24 +++++++----------------- 1 file changed, 7 insertions(+), 17 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 3087d904..896d01db 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -85,19 +85,6 @@ def read_json_file(self, j_file): data = json.load(fh) return data - def get_experiment_run_alias(self, row_data): - """Get the experiment_alias a run_alias from the first fastq_r1""" - if "fastq_r1" in row_data: - match = re.search(r"(\w+)_R1.*", row_data["fastq_r1"]) - if match: - exp_alias = match.group(1) - run_alias = match.group(1) + ".fastq.gz" - else: - log.error("fastq_r1 field does not exists ") - stderr.print("[red] Exiting because there is not fastq_r1 field ") - sys.exit(1) - return exp_alias, run_alias - def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): """Fetch the laboratory location and return a dictionary""" data = {} @@ -194,7 +181,6 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): lab_json = self.read_json_file(lab_json_file) geo_loc_json = self.read_json_file(geo_loc_file) samples_json = self.read_json_file(self.sample_list_file) - exp_alias, run_alias = self.get_experiment_run_alias(metadata[0]) for row_sample in metadata: """Include sample data from sample json""" try: @@ -223,7 +209,7 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): else: row_sample.update(lab_data[row_sample["collecting_institution"]]) - """ Fetch emai and address for submitting_institution + """ Fetch email and address for submitting_institution """ row_sample["submitting_institution"] = row_sample[ "submitting_institution" @@ -264,8 +250,12 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): row["sequencing_instrument_platform"] = "To change" """ # Add experiment_alias and run_alias - row_sample["experiment_alias"] = exp_alias - row_sample["run_alias"] = run_alias + row_sample["experiment_alias"] = str( + row_sample["fastq_r1"] + "_" + row_sample["fastq_r2"] + ) + row_sample["run_alias"] = str( + row_sample["fastq_r1"] + "_" + row_sample["fastq_r2"] + ) additional_metadata.append(row_sample) return additional_metadata From c53689bc3a93c738542a8025df85b7522e8c9d64 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 2 Aug 2022 12:49:27 +0200 Subject: [PATCH 0721/1454] added MINISTERIO DE SANIDAD, POLITICA SOCIAL E IGUALDAD in cofiguration lab --- relecov_tools/conf/laboratory_address.json | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 5696dc5b..6450a5d0 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -413,6 +413,14 @@ "geo_loc_city": "Madrid", "geo_loc_country": "Spain" }, + { + "collecting_institution": "MINISTERIO DE SANIDAD, POLITICA SOCIAL E IGUALDAD", + "collecting_institution_address": "P.º del Prado, 18", + "collecting_institution_email": "", + "geo_loc_state": "Madrid", + "geo_loc_city": "Madrid", + "geo_loc_country": "Spain" + }, { "collecting_institution": "HU Virgen de la Arrixaca", "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", @@ -518,7 +526,7 @@ "geo_loc_country": "Spain" }, { - "collecting_institution": "Hospital Lucus Augusti", + "collecting_institution": "Hospital Universitario Lucus Augusti", "collecting_institution_address": " Rúa Dr. Ulises Romero, 1", "collecting_institution_email": "", "geo_loc_state": "Galicia", From 0185f347114bcc50751f991c10dfe678a3b1a63b Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 2 Aug 2022 13:24:21 +0200 Subject: [PATCH 0722/1454] changes in field names and rearranging --- relecov_tools/map_schema.py | 20 ++++++++++++++++++-- relecov_tools/read_lab_metadata.py | 2 +- 2 files changed, 19 insertions(+), 3 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 0ba95fab..e24387ac 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -189,7 +189,7 @@ def additional_formating(self, mapped_json_data): "library_kit" ] mapped_json_data[idx]["sample_name"] = self.json_data[idx][ - "collecting_lab_sample_id" + "sequencing_sample_id" ] mapped_json_data[idx]["study_type"] = self.json_data[idx][ "purpose_sampling" @@ -202,7 +202,23 @@ def additional_formating(self, mapped_json_data): ] mapped_json_data[idx][ "sequencing_instrument_platform" - ] = self.json_data[idx]["sequencing_instrument_platform"] + ] = self.json_data[idx]["sequencing_instrument_platform"].upper() + + mapped_json_data[idx]["instrument_model"] = self.json_data[idx][ + "sequencing_instrument_model" + ] + + if ( + "nextseq" + in self.json_data[idx]["sequencing_instrument_model"].lower() + ): + mapped_json_data[idx]["instrument_model"] = "NextSeq 500" + + mapped_json_data[idx]["host subject id"] = "" + mapped_json_data[idx]["host health state"] = "" + mapped_json_data[idx]["sample_description"] = "" + mapped_json_data[idx]["design_description"] = "" + mapped_json_data[idx]["insert_size"] = "0" return mapped_json_data diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 3087d904..2afdfa94 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -152,7 +152,7 @@ def include_processed_data(self, metadata): "host_common_name": {"Human": ["host_scientific_name", "Homo Sapiens"]}, "collecting_lab_sample_id": [ "isolate_sample_id", - metadata["collecting_lab_sample_id"], + metadata["sequencing_sample_id"], ], } seq_inst_plat = { From 9ae89d53f89526101fd4e81ecb88163b1df85954 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 2 Aug 2022 13:38:16 +0200 Subject: [PATCH 0723/1454] Change isolate_sample_id, that was collcate from collecting_lab_sample_id to sequencing_sample_id --- relecov_tools/read_lab_metadata.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 896d01db..a32687cc 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -139,14 +139,14 @@ def include_processed_data(self, metadata): "host_common_name": {"Human": ["host_scientific_name", "Homo Sapiens"]}, "collecting_lab_sample_id": [ "isolate_sample_id", - metadata["collecting_lab_sample_id"], + metadata["sequencing_sample_id"], ], } seq_inst_plat = { "Illumina": [ "Illumina iSeq 100", "Illumina MiSeq", - "Illumina NextSeq550", + "Illumina NextSeq 550", "Illumina NextSeq", "Illumina NovaSeq 6000", ], From c59435c8f05b46db2f4fcba70ab1f31b1501860c Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 4 Aug 2022 16:13:07 +0200 Subject: [PATCH 0724/1454] fixing bugs and running ena upload and bioinfo metadata for 2000 samples --- relecov_tools/conf/configuration.json | 160 ++++++++++++------------- relecov_tools/ena_upload.py | 3 +- relecov_tools/read_bioinfo_metadata.py | 20 ++-- 3 files changed, 95 insertions(+), 88 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 47c0fb56..4bce40df 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -1,82 +1,82 @@ { - "metadata_lab_heading" : [ - "Public Health sample id (SIVIES)", - "Sample ID given by originating laboratory", - "Sample ID given by the submitting laboratory", - "Sample ID given in the microbiology lab", - "Sample ID given if multiple rna-extraction or passages", - "Sample ID given for sequencing", - "ENA Sample ID", - "GISAID Virus Name", - "GISAID id", - "Originating Laboratory", - "Submitting Institution", - "Sample Collection Date", - "Sample Received Date", - "Purpose of sampling", - "Biological Sample Storage Condition", - "Specimen source", - "Environmental Material", - "Environmental System", - "Collection Device", - "Host", - "Host Age", - "Host Gender", - "Sequencing Date", - "Rna Extraction Protocol", - "Commercial All-in-one library kit", - "Library Preparation Kit", - "Enrichment Protocol", - "If Enrichment Protocol. If Other,Specify", - "Enrichment panel/assay", - "If Enrichment panel/assay. If Other, Specify", - "Enrichment panel/assay version", - "Number Of Samples In Run", - "Runid", - "Sequencing Instrument Model", - "Flowcell Kit", - "Source material", - "Capture method", - "Sequencing technique", - "Library Layout", - "Gene Name 1", - "Diagnostic Pcr Ct Value 1", - "Gene Name 2", - "Diagnostic Pcr Ct Value-2", - "Analysis Authors", - "Author Submitter", - "Authors", - "Sequence file R1 fastq", - "Sequence file R2 fastq" -], + "metadata_lab_heading": [ + "Public Health sample id (SIVIES)", + "Sample ID given by originating laboratory", + "Sample ID given by the submitting laboratory", + "Sample ID given in the microbiology lab", + "Sample ID given if multiple rna-extraction or passages", + "Sample ID given for sequencing", + "ENA Sample ID", + "GISAID Virus Name", + "GISAID id", + "Originating Laboratory", + "Submitting Institution", + "Sample Collection Date", + "Sample Received Date", + "Purpose of sampling", + "Biological Sample Storage Condition", + "Specimen source", + "Environmental Material", + "Environmental System", + "Collection Device", + "Host", + "Host Age", + "Host Gender", + "Sequencing Date", + "Rna Extraction Protocol", + "Commercial All-in-one library kit", + "Library Preparation Kit", + "Enrichment Protocol", + "If Enrichment Protocol. If Other,Specify", + "Enrichment panel/assay", + "If Enrichment panel/assay. If Other, Specify", + "Enrichment panel/assay version", + "Number Of Samples In Run", + "Runid", + "Sequencing Instrument Model", + "Flowcell Kit", + "Source material", + "Capture method", + "Sequencing technique", + "Library Layout", + "Gene Name 1", + "Diagnostic Pcr Ct Value 1", + "Gene Name 2", + "Diagnostic Pcr Ct Value-2", + "Analysis Authors", + "Author Submitter", + "Authors", + "Sequence file R1 fastq", + "Sequence file R2 fastq" + ], "gisaid_csv_headers": [ - "submitter", - "covv_virus_name", - "covv_type", - "covv_passage", - "covv_collection_date", - "covv_location", - "covv_add_location", - "covv_host", - "covv_add_host_info", - "covv_sampling_strategy", - "covv_gender", - "covv_patient_age", - "covv_patient_status", - "covv_specimen", - "covv_outbreak", - "covv_last_vaccinated", - "covv_treatment", - "covv_seq_technology", - "covv_assembly_method", - "covv_coverage", - "covv_orig_lab", - "covv_orig_lab_addr", - "covv_provider_sample_id", - "covv_subm_lab", - "covv_subm_lab_addr", - "covv_subm_sample_id", - "covv_authors" + "submitter", + "covv_virus_name", + "covv_type", + "covv_passage", + "covv_collection_date", + "covv_location", + "covv_add_location", + "covv_host", + "covv_add_host_info", + "covv_sampling_strategy", + "covv_gender", + "covv_patient_age", + "covv_patient_status", + "covv_specimen", + "covv_outbreak", + "covv_last_vaccinated", + "covv_treatment", + "covv_seq_technology", + "covv_assembly_method", + "covv_coverage", + "covv_orig_lab", + "covv_orig_lab_addr", + "covv_provider_sample_id", + "covv_subm_lab", + "covv_subm_lab_addr", + "covv_subm_sample_id", + "covv_authors" ], "json_schemas": { "relecov_schema": "relecov_schema.json", @@ -197,7 +197,7 @@ "tool_name": "ena-upload-cli", "tool_version": "0.5.3" }, - "md5_file_name": "md5sum_MiSeq_GEN_267_20220208_ICasas.md5", + "md5_file_name": "md5_check_file.csv", "checklist": "ERC000033", "long_table_heading": [ "SAMPLE", @@ -218,8 +218,8 @@ "CALLER", "LINEAGE" ], - "mapping_file":{ + "mapping_file": { "ISCIII": "ISCIII.json", "HUGTiP": "HUGTiP.json" } -} +} \ No newline at end of file diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index e6575a4c..ac67dc25 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -322,6 +322,7 @@ def create_structure_to_ena(self): # submit data to webin ftp server. It should only upload fastq files in case the action is ADD. # When the action is MODIFY rthe fastq are already submitted. + """ if self.action == "ADD" or self.action == "add": session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) @@ -341,7 +342,7 @@ def create_structure_to_ena(self): g2 = session.quit() print(g2) - + """ # THE ENA_UPLOAD_CLI METHOD DOES NOT WORK (below) # chec = submit_data(file_paths, self.passwd, self.user) # print(chec) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 81949f30..1c238b4e 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -70,7 +70,7 @@ def bioinfo_parse(self, file_name): ) mapping_illumina_tab_path = os.path.join( - self.input_folder, "mapping_illumina.tab" + self.input_folder, "mapping_illumina.csv" ) summary_variants_metrics_path = os.path.join( self.input_folder, "summary_variants_metrics_mqc.csv" @@ -91,15 +91,21 @@ def bioinfo_parse(self, file_name): self.md5_file_name, # como hacer esto general para los servicios ) - mapping_illumina_tab = pd.read_csv(mapping_illumina_tab_path, sep="\t") - summary_variants_metrics = pd.read_csv(summary_variants_metrics_path, sep=",") - variants_long_table = pd.read_csv(variants_long_table_path, sep=",") + mapping_illumina_tab = pd.read_csv( + mapping_illumina_tab_path, sep=",", encoding="utf-8" + ) + summary_variants_metrics = pd.read_csv( + summary_variants_metrics_path, sep=",", encoding="utf-8" + ) + variants_long_table = pd.read_csv( + variants_long_table_path, sep=",", encoding="utf-8" + ) consensus_genome_length = pd.read_csv( - consensus_genome_length_path, header=None, sep="," + consensus_genome_length_path, header=None, sep=",", encoding="utf-8" ) - md5_info = pd.read_csv(md5_info_path, header=None, sep=",") + md5_info = pd.read_csv(md5_info_path, header=None, sep=",", encoding="utf-8") pangolin_version_table = pd.read_csv( - pangolin_versions_path, header=None, sep="\t" + pangolin_versions_path, header=None, sep="\t", encoding="utf-8" ) pangolin_version_software = pangolin_version_table[1] From 21a04843f60074fa2ff32a5c7f64d348b6f16d38 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 5 Aug 2022 09:20:50 +0200 Subject: [PATCH 0725/1454] Added covv_subm_sample_id to gisaid schema --- relecov_tools/schema/gisaid_schema.json | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/relecov_tools/schema/gisaid_schema.json b/relecov_tools/schema/gisaid_schema.json index 1192a129..a8e0d8b0 100644 --- a/relecov_tools/schema/gisaid_schema.json +++ b/relecov_tools/schema/gisaid_schema.json @@ -4,7 +4,6 @@ "covv_type", "covv_virus_name", "submitter", - "covv_passage", "covv_orig_lab", "covv_orig_lab_addr", "covv_collection_date", @@ -14,7 +13,8 @@ "covv_gender", "covv_seq_technology", "covv_subm_lab", - "covv_subm_lab_addr" + "covv_subm_lab_addr", + "covv_authors" ], "type": "object", "properties": { @@ -134,7 +134,7 @@ ], "label": "Host Age" }, - "specimen_source": { + "covv_specimen": { "Enums": [ "Blood [UBERON:0000178]", "Fluid [UBERON:0006314]", @@ -289,14 +289,16 @@ "description": "The name of the agency that generated the sequence.", "label": "Submitting Institution" }, - "covv_passage": { + "covv_subm_sample_id": { "examples": [ - "Original", "Vero" + "prov_rona_99" ], - "ontology": "GENEPIO:0100039", + "ontology": "GENEPIO:0001123", "type": "string", - "description": "The process of growing a virus in serial iterations(original/vero)", - "label": "Virus passage" + "description": "The user-defined name for the sample.", + "classification": "Database Identifiers", + "label": "Sample ID given by originating laboratory", + "fill_mode": "sample" } } } From 0db65de5cf7d81950b2ec284119a5546ff19479a Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 5 Aug 2022 09:34:00 +0200 Subject: [PATCH 0726/1454] lintin gisaid schema --- relecov_tools/schema/gisaid_schema.json | 160 ++++++++---------------- 1 file changed, 54 insertions(+), 106 deletions(-) diff --git a/relecov_tools/schema/gisaid_schema.json b/relecov_tools/schema/gisaid_schema.json index a8e0d8b0..430e5f25 100644 --- a/relecov_tools/schema/gisaid_schema.json +++ b/relecov_tools/schema/gisaid_schema.json @@ -14,98 +14,80 @@ "covv_seq_technology", "covv_subm_lab", "covv_subm_lab_addr", - "covv_authors" + "covv_authors", ], "type": "object", "properties": { "covv_type": { - "examples": [ - "betacoronavirus" - ], + "examples": ["betacoronavirus"], "ontology": "NCIT:C25284", "type": "string", "description": "default must remain 'betacoronavirus'", - "clasification": "Database Identifiers" + "clasification": "Database Identifiers", }, "sample_name": { - "examples": [ - "prov_rona_99" - ], + "examples": ["prov_rona_99"], "ontology": "0", "type": "string", "description": "The user-defined name for the sample.", "clasification": "Database Identifiers", - "label": "Collecting Sample id" + "label": "Collecting Sample id", }, "covv_virus_name": { - "examples": [ - "hCoV-19/Canada/prov_rona_99/2020" - ], + "examples": ["hCoV-19/Canada/prov_rona_99/2020"], "ontology": "GENEPIO:0100282", "type": "string", "description": "The user-defined GISAID virus name assigned to the sequence.", "clasification": "Database Identifiers", - "label": "GISAID Virus Name" + "label": "GISAID Virus Name", }, "submitter": { - "examples": [ - "" - ], + "examples": [""], "ontology": "NCIT:C54269", "type": "string", "description": "", "clasification": "enter your GISAID-Username", - "label": "GISAID Id" + "label": "GISAID Id", }, "covv_orig_lab": { - "examples": [ - "Public Health Agency of Canada" - ], + "examples": ["Public Health Agency of Canada"], "ontology": "GENEPIO:0001153", "type": "string", "description": "The name of the agency that collected the original sample.", - "label": "Originating Laboratory" + "label": "Originating Laboratory", }, "covv_orig_lab_addr": { - "examples": [ - "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" - ], + "examples": ["655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada"], "ontology": "GENEPIO:0001158", "type": "string", "description": "The mailing address of the agency submitting the sample.", "clasification": "Sample collection and processing", - "label": "Originating Laboratory Address" + "label": "Originating Laboratory Address", }, "covv_subm_lab_addr": { - "examples": [ - "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" - ], + "examples": ["123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"], "ontology": "GENEPIO:0001167", "type": "string", "description": "The mailing address of the agency submitting the sequence.", "clasification": "Sample collection and processing", - "label": "Submitting Institution Address" + "label": "Submitting Institution Address", }, "covv_collection_date": { - "examples": [ - "3/19/2020" - ], + "examples": ["3/19/2020"], "ontology": "GENEPIO:0001174", "type": "string", "description": "The date on which the sample was collected.", "format": "date", "classification": "Sample collection and processing", - "label": "Sample Collection Date" + "label": "Sample Collection Date", }, "covv_location": { - "examples": [ - "e.g. Europe / Germany / Bavaria / Munich" - ], + "examples": ["e.g. Europe / Germany / Bavaria / Munich"], "ontology": "GENEPIO:0001181", "type": "string", "description": "The country of origin of the sample.", "clasification": "Sample collection and processing", - "label": "Geo Loc Autonomic Country" + "label": "Geo Loc Autonomic Country", }, "covv_host": { "examples": [ @@ -115,24 +97,14 @@ "type": "string", "description": "The taxonomic, or scientific name of the host.", "clasification": "Host information", - "label": "Host Scientific Name" + "label": "Host Scientific Name", }, "covv_patient_age": { "ontology": "GENEPIO:0001392", - "anyOf": [ - { - "type": "integer" - }, - { - "pattern": "\\d+-\\d+", - "type": "string" - } - ], + "anyOf": [{"type": "integer"}, {"pattern": "\\d+-\\d+", "type": "string"}], "description": "Age of host at the time of sampling.", - "examples": [ - 79 - ], - "label": "Host Age" + "examples": [79], + "label": "Host Age", }, "covv_specimen": { "Enums": [ @@ -149,26 +121,22 @@ "Not Collected [GENEPIO:0001620]", "Not Provided [GENEPIO:0001668]", "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" + "Restricted Access [GENEPIO:0001810]", ], "ontology": "GENEPIO:0001211", "type": "string", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "examples": [ - "Blood [UBERON:0000178]" - ], + "examples": ["Blood [UBERON:0000178]"], "classification": "Sample collection and processing", - "label": "Organism Substance" + "label": "Organism Substance", }, "covv_assembly_method": { - "examples": [ - "Ivar" - ], + "examples": ["Ivar"], "ontology": "GENEPIO:0001463", "type": "string", "description": "The name of software used to generate the consensus sequence.", "clasification": "Bioinformatics and QC metrics", - "label": "Consensus sequence software name" + "label": "Consensus sequence software name", }, "covv_gender": { "Enums": [ @@ -182,15 +150,13 @@ "Not Collected [GENEPIO:0001620]", "Not Provided [GENEPIO:0001668]", "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "examples": [ - "Male [NCIT:C46109]" + "Restricted Access [GENEPIO:0001810]", ], + "examples": ["Male [NCIT:C46109]"], "ontology": "GENEPIO:0001395", "type": "string", "description": "The gender of the host at the time of sample collection.", - "clasification": "Host information" + "clasification": "Host information", }, "covv_seq_technology": { "examples": [ @@ -200,66 +166,54 @@ "type": "string", "description": "The model of the sequencing instrument used.", "classification": "Sequencing", - "label": "Sequencing Instrument Model" + "label": "Sequencing Instrument Model", }, "covv_authors": { - "examples": [ - "" - ], + "examples": [""], "ontology": "GENEPIO:0001517", "type": "string", "description": "", "clasification": "Contributor Acknowledgement", - "label": "Authors" + "label": "Authors", }, "covv_coverage": { - "examples": [ - "400x" - ], + "examples": ["400x"], "ontology": "GENEPIO:0001474", "type": "string", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", "clasification": "Bioinformatics and QC metrics", - "label": "Depth of coverage value " + "label": "Depth of coverage value ", }, "covv_fasta_filename": { - "examples": [ - "" - ], + "examples": [""], "ontology": "GENEPIO:0001460", "type": "string", "description": "Filename that contains the sequence without path", - "clasification": "Bioinformatics and QC metrics" + "clasification": "Bioinformatics and QC metrics", }, - "additional_host_information": { - "examples": [ - "e.g. Patient infected while traveling in …." - ], + "covv_add_host_info": { + "examples": ["e.g. Patient infected while traveling in …."], "ontology": "GENEPIO_0001268", "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", "clasification": "Host information", - "label": "Additional Host Information" + "label": "Additional Host Information", }, "covv_last_vaccinated": { - "examples": [ - "e.g. 04/09/2021" - ], + "examples": ["e.g. 04/09/2021"], "ontology": "0", "type": "string", "description": "The date the host received their last dose of vaccine.", "format": "date", - "clasification": "Host information" + "clasification": "Host information", }, "covv_outbreak": { - "examples": [ - "Date, Location e.g. type of gathering, Family cluster, etc." - ], + "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], "ontology": "GENEPIO:0001417", "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", "clasification": "Host information", - "label": "Outbreak Exposure Event Location" + "label": "Outbreak Exposure Event Location", }, "covv_sampling_strategy": { "examples": [ @@ -269,36 +223,30 @@ "type": "string", "description": "The reason that the sample was sequenced.", "classification": "Sequencing", - "label": "Purpose of Sequencing" + "label": "Purpose of Sequencing", }, "submitting_lab_sequence_id": { - "examples": [ - "" - ], + "examples": [""], "ontology": "0", "type": "string", "description": "Sample ID given by the submitting laboratory", - "clasification": "Database Identifiers" + "clasification": "Database Identifiers", }, "covv_subm_lab": { - "examples": [ - "Centers for Disease Control and Prevention" - ], + "examples": ["Centers for Disease Control and Prevention"], "ontology": "GENEPIO:0001159", "type": "string", "description": "The name of the agency that generated the sequence.", - "label": "Submitting Institution" + "label": "Submitting Institution", }, "covv_subm_sample_id": { - "examples": [ - "prov_rona_99" - ], + "examples": ["prov_rona_99"], "ontology": "GENEPIO:0001123", "type": "string", "description": "The user-defined name for the sample.", "classification": "Database Identifiers", "label": "Sample ID given by originating laboratory", - "fill_mode": "sample" - } - } + "fill_mode": "sample", + }, + }, } From 2b6ca88af415b075baabb85bdee7744c62ea4a56 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 5 Aug 2022 10:10:18 +0200 Subject: [PATCH 0727/1454] added gisaid_upload to __main__.py --- relecov_tools/__main__.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index f218a961..b78912dd 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -20,6 +20,7 @@ import relecov_tools.read_bioinfo_metadata import relecov_tools.long_table_parse import relecov_tools.metadata_homogeneizer +import relecov_tools.gisaid_upload log = logging.getLogger() From 30f7372d5461310e8202c91a184dbf3df30ab7e0 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 5 Aug 2022 10:17:13 +0200 Subject: [PATCH 0728/1454] Added new fields to metadata csv --- relecov_tools/gisaid_upload.py | 34 +++++++++++++++++++++++++++++++--- 1 file changed, 31 insertions(+), 3 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index bc62972b..d9b176b8 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -9,8 +9,7 @@ # import ftplib import relecov_tools.utils from Bio import SeqIO - -# from relecov_tools.config_json import ConfigJson +from relecov_tools.config_json import ConfigJson # import site @@ -69,7 +68,7 @@ def __init__( msg="Select the GISAID json file to upload" ) else: - self.gisaid_json = self.gisaid_json + self.gisaid_json = gisaid_json if output_path is None: self.output_path = relecov_tools.utils.prompt_path( msg="Select the folder to store the log files" @@ -92,6 +91,7 @@ def __init__( # Add proxy settings: username:password@proxy:port (optional) if proxy_config is None: # borrar comentario: este mensaje no me convence + self.proxy_config = None print("Proxy configuration is not set") else: self.proxy_config = proxy_config @@ -103,6 +103,34 @@ def metadata_to_csv(self): "Transform metadata json to csv" data = relecov_tools.utils.read_json_file(self.gisaid_json) df_data = pd.DataFrame(data) + df_data.insert(4, "covv_passage", "Original") + + config_json = ConfigJson() + fields = config_json.get_configuration("gisaid_csv_headers") + col_df = list(df_data.columns) + for field in fields: + if field not in col_df: + df_data.insert(4, field, "") + + config_lab_json = ConfigJson() + lab_json_conf = config_lab_json.get_configuration("laboratory_data") + lab_json_file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), "conf", lab_json_conf + ) + lab_json = relecov_tools.utils.read_json_file(lab_json_file) + for i in lab_json: + if i["collecting_institution"] == df_data["covv_subm_lab_addr"][0]: + df_data.insert(4, "covv_subm_lab_addr", i["collecting_institution_address"]) + + df_data.loc[df_data["covv_gender"] == "", "covv_gender"] = "unknown" + df_data.loc[df_data["covv_patient_age"] == "", "covv_patient_age"] = "unknown" + df_data.loc[df_data["covv_authors"] == "", "covv_authors"] = "unknown" + df_data.loc[df_data["covv_subm_lab_addr"] == "", "covv_subm_lab_addr"] = "unknown" + df_data.loc[df_data["covv_subm_lab"] == "", "covv_subm_lab"] = "unknown" + df_data.loc[df_data["covv_orig_lab_addr"] == "", "covv_orig_lab_addr"] = "unknown" + df_data.loc[df_data["covv_orig_lab"] == "", "covv_orig_lab_addr"] = "unknown" + df_data.loc[df_data["covv_patient_status"] == "", "covv_patient_status"] = "unknown" + df_data_path = os.path.join(self.output_path, "meta_gisaid.csv") df_data.to_csv(df_data_path, index=False) metagisaid = df_data_path From ed34096b479293a809d7b31cb5689c48716ce23d Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 5 Aug 2022 10:22:05 +0200 Subject: [PATCH 0729/1454] Improved function that changes fasta headers --- relecov_tools/gisaid_upload.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index d9b176b8..f658da63 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -177,8 +177,9 @@ def change_headers(self, multifasta): records = SeqIO.parse(old_fasta, "fasta") for record in records: for name in virus_name: - if record.id == name.split("/")[-2]: + if name.split("/")[-2].split("-")[-1] in record.id: record.id = name + record.description name SeqIO.write(record, new_fasta, "fasta") fastagisaid = multi_gis_path return fastagisaid From 91e39bc23d3ad26f16ccdb74546fca07b227ea15 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 5 Aug 2022 10:25:42 +0200 Subject: [PATCH 0730/1454] lintin --- relecov_tools/gisaid_upload.py | 26 +++++++++++++++++--------- 1 file changed, 17 insertions(+), 9 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index f658da63..79c3cb1b 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -104,14 +104,14 @@ def metadata_to_csv(self): data = relecov_tools.utils.read_json_file(self.gisaid_json) df_data = pd.DataFrame(data) df_data.insert(4, "covv_passage", "Original") - + config_json = ConfigJson() fields = config_json.get_configuration("gisaid_csv_headers") col_df = list(df_data.columns) for field in fields: if field not in col_df: df_data.insert(4, field, "") - + config_lab_json = ConfigJson() lab_json_conf = config_lab_json.get_configuration("laboratory_data") lab_json_file = os.path.join( @@ -120,17 +120,25 @@ def metadata_to_csv(self): lab_json = relecov_tools.utils.read_json_file(lab_json_file) for i in lab_json: if i["collecting_institution"] == df_data["covv_subm_lab_addr"][0]: - df_data.insert(4, "covv_subm_lab_addr", i["collecting_institution_address"]) - + df_data.insert( + 4, "covv_subm_lab_addr", i["collecting_institution_address"] + ) + df_data.loc[df_data["covv_gender"] == "", "covv_gender"] = "unknown" df_data.loc[df_data["covv_patient_age"] == "", "covv_patient_age"] = "unknown" df_data.loc[df_data["covv_authors"] == "", "covv_authors"] = "unknown" - df_data.loc[df_data["covv_subm_lab_addr"] == "", "covv_subm_lab_addr"] = "unknown" + df_data.loc[ + df_data["covv_subm_lab_addr"] == "", "covv_subm_lab_addr" + ] = "unknown" df_data.loc[df_data["covv_subm_lab"] == "", "covv_subm_lab"] = "unknown" - df_data.loc[df_data["covv_orig_lab_addr"] == "", "covv_orig_lab_addr"] = "unknown" + df_data.loc[ + df_data["covv_orig_lab_addr"] == "", "covv_orig_lab_addr" + ] = "unknown" df_data.loc[df_data["covv_orig_lab"] == "", "covv_orig_lab_addr"] = "unknown" - df_data.loc[df_data["covv_patient_status"] == "", "covv_patient_status"] = "unknown" - + df_data.loc[ + df_data["covv_patient_status"] == "", "covv_patient_status" + ] = "unknown" + df_data_path = os.path.join(self.output_path, "meta_gisaid.csv") df_data.to_csv(df_data_path, index=False) metagisaid = df_data_path @@ -179,7 +187,7 @@ def change_headers(self, multifasta): for name in virus_name: if name.split("/")[-2].split("-")[-1] in record.id: record.id = name - record.description name + record.description = name SeqIO.write(record, new_fasta, "fasta") fastagisaid = multi_gis_path return fastagisaid From 9346ff211cb882fc84d63a4fa0239e241c4bec65 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 5 Aug 2022 10:39:27 +0200 Subject: [PATCH 0731/1454] lintin2 --- relecov_tools/gisaid_upload.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 79c3cb1b..982e0c39 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -119,10 +119,10 @@ def metadata_to_csv(self): ) lab_json = relecov_tools.utils.read_json_file(lab_json_file) for i in lab_json: - if i["collecting_institution"] == df_data["covv_subm_lab_addr"][0]: - df_data.insert( - 4, "covv_subm_lab_addr", i["collecting_institution_address"] - ) + if i["collecting_institution"] == df_data["covv_subm_lab"][0]: + df_data.loc[ + df_data["covv_subm_lab_addr"] == "", "covv_subm_lab_addr" + ] = i["collecting_institution_address"] df_data.loc[df_data["covv_gender"] == "", "covv_gender"] = "unknown" df_data.loc[df_data["covv_patient_age"] == "", "covv_patient_age"] = "unknown" From 32e33e4232a213c1fdd5219759cc0f7d199120eb Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 5 Aug 2022 11:26:30 +0200 Subject: [PATCH 0732/1454] adding CHECKLIST to sample.xml --- relecov_tools/ena_upload.py | 16 ++++++++++++++-- relecov_tools/read_bioinfo_metadata.py | 6 +++++- 2 files changed, 19 insertions(+), 3 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index ac67dc25..4b6f925c 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -352,9 +352,7 @@ def create_structure_to_ena(self): # schema_xmls record XMLs for all these schema and following 'submission' tool = config_json.get_configuration("tool") - import pdb - pdb.set_trace() schema_xmls = run_construct( template_path, schema_targets, self.center, checklist, tool ) @@ -379,6 +377,20 @@ def create_structure_to_ena(self): # print(files.attrib["checksum"]) tree.write(schema_xmls["run"]) + tree = ET.parse(schema_xmls["sample"]) + root = tree.getroot() + + for files in root.iter("SAMPLE_ATTRIBUTES"): + tag = ET.SubElement(files, "TAG") + tag.text = str("ENA-CHECKLIST") + tag = ET.SubElement(files, "VALUE") + tag.text = str("ERC000033") + + tree.write(schema_xmls["sample"]) + import pdb + + pdb.set_trace() + if self.dev: url = "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" else: diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 1c238b4e..0c57d797 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -105,8 +105,9 @@ def bioinfo_parse(self, file_name): ) md5_info = pd.read_csv(md5_info_path, header=None, sep=",", encoding="utf-8") pangolin_version_table = pd.read_csv( - pangolin_versions_path, header=None, sep="\t", encoding="utf-8" + pangolin_versions_path, header=None, sep=",", encoding="utf-8" ) + pangolin_version_software = pangolin_version_table[1] with open(software_versions_path) as file: @@ -141,6 +142,9 @@ def bioinfo_parse(self, file_name): ) # fields from summary_variants_metrics_mqc.csv + import pdb + + pdb.set_trace() bioinfo_dict["number_of_base_pairs_sequenced"] = str( (summary_variants_metrics["# Input reads"][c] * 2) ) From 7a477d93a394ae3dd4b7a5731f1f88374f8c8b90 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 5 Aug 2022 14:14:21 +0200 Subject: [PATCH 0733/1454] lintin --- relecov_tools/ena_upload.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 4b6f925c..6d9fb63c 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -12,7 +12,7 @@ import sys import os -import ftplib +# import ftplib import relecov_tools.utils from relecov_tools.config_json import ConfigJson From 0bc26f47ffe767a8189826c08f48148fb27d2abe Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 7 Aug 2022 20:04:58 +0200 Subject: [PATCH 0734/1454] Added new folder parameter to include all files --- relecov_tools/__main__.py | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index b78912dd..66fe4558 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -59,9 +59,9 @@ def run_relecov_tools(): ) # stderr.print("[green] `._,._,'\n", highlight=False) - __version__ = "0.0.1" + __version__ = "0.0.4" stderr.print( - "[grey39] RELECOV-tools version {}".format(__version__), highlight=False + "\n" "[grey39] RELECOV-tools version {}".format(__version__), highlight=False ) # Lanch the click cli @@ -411,11 +411,17 @@ def long_table_parse(longtable_file, output): type=click.Choice(["isciii", "hugtip", "hunsc-iter"], case_sensitive=False), help="select one of the available institution options", ) +@click.option( + "-d", + "--directory", + type=click.Path(), + help="Folder where are located the additional files", +) @click.option("-o", "--output", type=click.Path(), help="Path to save json output") -def metadata_homogeneizer(lab_metadata, institution, output): +def metadata_homogeneizer(lab_metadata, institution, directory, output): """Parse institution metadata lab to the one used in relecov""" new_parse = relecov_tools.metadata_homogeneizer.MetadataHomogeneizer( - lab_metadata, institution, output + lab_metadata, institution, directory, output ) new_parse.converting_metadata() From 5a56ffe79e6bf835f699d9d1f8ff964990cf8488 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 7 Aug 2022 20:05:23 +0200 Subject: [PATCH 0735/1454] Increase relecov version --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 8636af99..e30d8edf 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import setup, find_packages -version = "0.0.3" +version = "0.0.4" with open("README.md") as f: readme = f.read() From 9c6cddc8b47a9bbbecbb82f9efa572f435240419 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 7 Aug 2022 20:06:19 +0200 Subject: [PATCH 0736/1454] Included installation of bio python package --- requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements.txt b/requirements.txt index d2533548..1e1b0a9d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,3 +9,4 @@ paramiko>=2.10.1 pyyaml openpyxl ena-upload-cli +bio==1.4.0 From 08039ea70c7f8ad26423a5cea2428fa0554fc8d5 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 7 Aug 2022 20:07:17 +0200 Subject: [PATCH 0737/1454] added required files and the structure --- .../schema/institution_schemas/ISCIII.json | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 9f45aac3..08d98a48 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -33,5 +33,25 @@ "Gene Name 1": "ORF E", "Diagnostic Pcr Ct Value 1": "", "Authors": "A. Monzón; F. Casas; I. Jiménez; M. Camarero; P. Zaballos; ROMAN SOTO; S. Cuesta, I.; S. Iglesias-Caballero; S. Pozo; S. Varona; SERGIO; Sandonís; V. Vázquez-Morón" + }, + "required_files": { + "sample_file": { + "file_name": "sample_data.json", + "metadata_field":["Sequence file R1 fastq", "Sequence file R2 fastq"], + "file_field":["sequence_file_R1_fastq", "sequence_file_R2_fastq"], + "processed":"None" + }, + "artic_version_file": { + "file_name": "artic_version.csv", + "metadata_field": [], + "file_field": [], + "processed":"None" + }, + "run_services_file": { + "file_name": "samples_run_services.tsv", + "metadata_field": [], + "file_field": [], + "processed":"None" } + } } From 53994b6ba1925e8af6be869e144f5c36194e1ad5 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 7 Aug 2022 20:07:58 +0200 Subject: [PATCH 0738/1454] Working on sample data json to include in the metadata --- relecov_tools/metadata_homogeneizer.py | 87 +++++++++++++++++++++++++- 1 file changed, 85 insertions(+), 2 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 6bd0730d..f9e2af43 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -20,7 +20,9 @@ class MetadataHomogeneizer: """MetadataHomogeneizer object""" - def __init__(self, lab_metadata=None, institution=None, output_folder=None): + def __init__( + self, lab_metadata=None, institution=None, directory=None, output_folder=None + ): self.config_json = ConfigJson() self.heading = self.config_json.get_configuration("metadata_lab_heading") if lab_metadata is None: @@ -46,7 +48,27 @@ def __init__(self, lab_metadata=None, institution=None, output_folder=None): "institution_schemas", self.config_json.get_topic_data("mapping_file", self.institution), ) + if directory is None: + directory = relecov_tools.utils.prompt_path( + msg="Select the directory which contains additional files for metadata" + ) + if not os.path.exists(directory): + log.error("Folder for additional files %s does not exist ", directory) + stderr.print( + "[red] Folder for additional files " + directory + " does not exist" + ) + sys.exit(1) self.mapping_json_data = relecov_tools.utils.read_json_file(mapping_json_file) + self.additional_files = [] + if len(self.mapping_json_data["required_files"]) > 0: + for key, values in self.mapping_json_data["required_files"].items(): + f_path = os.path.join(directory, values["file_name"]) + if not os.path.isfile(f_path): + log.error("Additional file %s does not exist ", f_path) + stderr.print("[red] Additional file " + f_path + " does not exist") + sys.exit(1) + values["file_name"] = f_path + self.additional_files.append(values) if output_folder is None: self.output_folder = relecov_tools.utils.prompt_path( msg="Select the output folder" @@ -101,6 +123,61 @@ def additional_fields(self, mapped_data): add_data.append(new_row_data) return add_data + def handling_additional_files(self, additional_data): + add_data = [] + + for additional_file in self.additional_files: + f_name = additional_file["file_name"] + stderr.print("[blue] Start processing additional file " + f_name) + if f_name.endswith(".json"): + data = relecov_tools.utils.read_json_file(f_name) + elif f_name.endswith(".tsv"): + pass + elif f_name.endswith(".csv"): + pass + else: + log.error("Additional file extension %s is not supported ", f_name) + stderr.print( + "[red] Additional file extension " + f_name + " is not supported" + ) + sys.exit(1) + sample_idx = self.heading.index("Sample ID given for sequencing") + for row in additional_data[1:]: + # new_row_data = [] + + s_value = str(row[sample_idx]) + + try: + item_data = data[s_value] + except KeyError: + log.error( + "Additional file %s does not have the information for %s ", + f_name, + s_value, + ) + stderr.print( + "[red] Additional file " + + f_name + + " does not have information for " + + str(s_value) + ) + continue + # sys.exit(1) + + for m_idx in range(len(additional_file["metadata_field"])): + + try: + meta_idx = self.heading.index( + additional_file["metadata_field"][m_idx] + ) + except ValueError as e: + log.error("Field %s does not exist in Metadata ", e) + stderr.print("[red] Field " + e + " does not exists") + sys.exit(1) + row[meta_idx] = item_data[additional_file["file_field"][m_idx]] + # add_data.append(row) + return add_data + def write_to_excel_file(self, data, f_name): book = openpyxl.Workbook() sheet = book.active @@ -111,9 +188,15 @@ def write_to_excel_file(self, data, f_name): return def converting_metadata(self): + stderr.print("[blue] Reading the metadata file to convert") ws_data = self.read_metadata_file() mapped_data = self.mapping_metadata(ws_data) - converted_data = self.additional_fields(mapped_data) + stderr.print("[green] Successful conversion mapping to ISCIII metadata") + stderr.print("[blue] Adding fixed information") + additional_data = self.additional_fields(mapped_data) + # Fetch the additional files and include the information in metadata + stderr.print("[blue] reading and mapping de information that cames in files") + converted_data = self.handling_additional_files(additional_data) f_name = os.path.join(self.output_folder, "converted_metadata_lab.xlsx") self.write_to_excel_file(converted_data, f_name) return From 19a6b3b71465d9732cec610f5ed2a9bc1b2817d2 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 8 Aug 2022 01:04:49 +0200 Subject: [PATCH 0739/1454] correct the field for orginating lab from the metadata input file --- relecov_tools/metadata_homogeneizer.py | 52 ++++++++++++++++++++++---- 1 file changed, 45 insertions(+), 7 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index f9e2af43..fa264644 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -124,17 +124,15 @@ def additional_fields(self, mapped_data): return add_data def handling_additional_files(self, additional_data): - add_data = [] - for additional_file in self.additional_files: f_name = additional_file["file_name"] stderr.print("[blue] Start processing additional file " + f_name) if f_name.endswith(".json"): data = relecov_tools.utils.read_json_file(f_name) elif f_name.endswith(".tsv"): - pass + data = relecov_tools.utils.read_csv_file_return_dict(f_name, "\t") elif f_name.endswith(".csv"): - pass + data = relecov_tools.utils.read_csv_file_return_dict(f_name, ",") else: log.error("Additional file extension %s is not supported ", f_name) stderr.print( @@ -150,6 +148,8 @@ def handling_additional_files(self, additional_data): try: item_data = data[s_value] except KeyError: + pass + """ log.error( "Additional file %s does not have the information for %s ", f_name, @@ -162,6 +162,7 @@ def handling_additional_files(self, additional_data): + str(s_value) ) continue + """ # sys.exit(1) for m_idx in range(len(additional_file["metadata_field"])): @@ -172,11 +173,48 @@ def handling_additional_files(self, additional_data): ) except ValueError as e: log.error("Field %s does not exist in Metadata ", e) - stderr.print("[red] Field " + e + " does not exists") + stderr.print(f"[red] Field {e} does not exist") sys.exit(1) - row[meta_idx] = item_data[additional_file["file_field"][m_idx]] + + if additional_file["req_process"] == "None": + row[meta_idx] = item_data[additional_file["file_field"][m_idx]] + else: + + if "condition" in additional_file["req_process"]: + for key, value in additional_file["req_process"][ + "condition" + ].items(): + if ( + key + in item_data[ + additional_file["file_field"][m_idx] + ].lower() + ): + row[meta_idx] = value + break + elif "replace" in additional_file["req_process"]: + row[meta_idx] = row[meta_idx].strip() + try: + row[meta_idx] = data[row[meta_idx]][ + additional_file["file_field"][m_idx] + ] + except KeyError as e: + log.error("Value %s does not exist ", e) + stderr.print(f"[red] Value {e} does not exist") + sys.exit(1) + else: + log.error( + "Processed method %s is not implemented yet", + additional_data["req_process"].key(), + ) + stderr.print( + f"[red] Processed method {additional_data['req_process'].key()} is not implemented yet" + ) + sys.exit(1) # add_data.append(row) - return add_data + # import pdb; pdb.set_trace() + stderr.print("[green] Succesful processing of additional file ") + return additional_data def write_to_excel_file(self, data, f_name): book = openpyxl.Workbook() From 2ed24888cc4339c4fefde1bab868df419ae30dc1 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 8 Aug 2022 01:05:41 +0200 Subject: [PATCH 0740/1454] remove duplicated Ministerio de sanidad --- relecov_tools/conf/laboratory_address.json | 8 -------- 1 file changed, 8 deletions(-) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 6450a5d0..5e2b2314 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -407,14 +407,6 @@ }, { "collecting_institution": "Ministerio de Sanidad, Servicios Sociales e Igualdad", - "collecting_institution_address": "", - "collecting_institution_email": "", - "geo_loc_state": "Madrid", - "geo_loc_city": "Madrid", - "geo_loc_country": "Spain" - }, - { - "collecting_institution": "MINISTERIO DE SANIDAD, POLITICA SOCIAL E IGUALDAD", "collecting_institution_address": "P.º del Prado, 18", "collecting_institution_email": "", "geo_loc_state": "Madrid", From 7ea28b4b3cf23867308c790c39a3040cdea447cc Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 8 Aug 2022 01:06:12 +0200 Subject: [PATCH 0741/1454] reformating print --- relecov_tools/feed_database.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 2ef85166..8d0ab188 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -62,7 +62,7 @@ def __init__( else: if os.path.isfile(schema): log.error("Relecov schema file %s does not exists", schema) - stderr.print("[red] Relecov schema " + schema + "does not exists") + stderr.print(f"[red] Relecov schema {schema} does not exists") sys.exit(1) rel_schema_json = relecov_tools.utils.read_json_file(schema) try: From 7ab69f7ea336358538678d1d4a5e599fbae35f82 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 8 Aug 2022 01:08:06 +0200 Subject: [PATCH 0742/1454] New file for changing format on originating lab --- .../schema/institution_schemas/ISCIII.json | 43 +++++++++++++------ 1 file changed, 30 insertions(+), 13 deletions(-) diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 08d98a48..a4577efb 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -35,23 +35,40 @@ "Authors": "A. Monzón; F. Casas; I. Jiménez; M. Camarero; P. Zaballos; ROMAN SOTO; S. Cuesta, I.; S. Iglesias-Caballero; S. Pozo; S. Varona; SERGIO; Sandonís; V. Vázquez-Morón" }, "required_files": { + "org_lab_file": { + "file_name": "laboratory_mapping_list.tsv", + "metadata_field": ["Originating Laboratory"], + "file_field": ["mapped_org_lab"], + "req_process":{ + "replace":{ + } + } + }, + "sequencer_file": { + "file_name": "samples_run_services.tsv", + "metadata_field": ["Sequencing Instrument Model"], + "file_field": ["run_name"], + "req_process":{ + "condition":{ + "nextseq": "Illumina NextSeq", + "next_seq": "Illumina NextSeq", + "miseq": "Illumina MiSeq", + "miseaq": "Illumina MiSeq", + "novaseq": "Illumina NovaSeq" + } + } + }, + "run_id_file": { + "file_name": "samples_run_services.tsv", + "metadata_field": ["Runid"], + "file_field": ["run_name"], + "req_process":"None" + }, "sample_file": { "file_name": "sample_data.json", "metadata_field":["Sequence file R1 fastq", "Sequence file R2 fastq"], "file_field":["sequence_file_R1_fastq", "sequence_file_R2_fastq"], - "processed":"None" - }, - "artic_version_file": { - "file_name": "artic_version.csv", - "metadata_field": [], - "file_field": [], - "processed":"None" - }, - "run_services_file": { - "file_name": "samples_run_services.tsv", - "metadata_field": [], - "file_field": [], - "processed":"None" + "req_process":"None" } } } From 17bc908f67c1bf5fc45a846f46ede9d3a6a5da87 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 8 Aug 2022 01:08:41 +0200 Subject: [PATCH 0743/1454] new function to read csv and tsv files --- relecov_tools/utils.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 76344bbd..2176ed24 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -31,6 +31,23 @@ def read_json_file(j_file): data = json.load(fh) return data +def read_csv_file_return_dict(file_name, sep): + """Read csv or tsv file, according to separator, and return a dictionary + where the main key is the first column + """ + with open (file_name , "r") as fh: + lines = fh.readlines() + heading = lines[0].strip().split(sep) + if len(heading) == 0: + return {"ERROR":"not valid format"} + file_data = {} + for line in lines[1:]: + line_s = line.strip().split(sep) + file_data[line_s[0]] = {} + for idx in range(1,len(heading)): + file_data[line_s[0]][heading[idx]] = line_s[idx] + return file_data + def get_md5_from_local_folder(local_folder): """Fetch the md5 values for each file in the file list""" From 08188ae588e61e67675d62f2d12ebd9c3eedf20f Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 8 Aug 2022 01:10:07 +0200 Subject: [PATCH 0744/1454] litin --- relecov_tools/utils.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 2176ed24..18c00a44 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -31,20 +31,21 @@ def read_json_file(j_file): data = json.load(fh) return data + def read_csv_file_return_dict(file_name, sep): """Read csv or tsv file, according to separator, and return a dictionary where the main key is the first column """ - with open (file_name , "r") as fh: + with open(file_name, "r") as fh: lines = fh.readlines() heading = lines[0].strip().split(sep) if len(heading) == 0: - return {"ERROR":"not valid format"} + return {"ERROR": "not valid format"} file_data = {} for line in lines[1:]: line_s = line.strip().split(sep) file_data[line_s[0]] = {} - for idx in range(1,len(heading)): + for idx in range(1, len(heading)): file_data[line_s[0]][heading[idx]] = line_s[idx] return file_data From 1d89e0e3060d89792e0d3003ff14a71b77381e75 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Mon, 8 Aug 2022 10:53:51 +0200 Subject: [PATCH 0745/1454] added location in gisaid format --- relecov_tools/gisaid_upload.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 982e0c39..8bb28d1b 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -118,11 +118,11 @@ def metadata_to_csv(self): os.path.dirname(os.path.realpath(__file__)), "conf", lab_json_conf ) lab_json = relecov_tools.utils.read_json_file(lab_json_file) - for i in lab_json: - if i["collecting_institution"] == df_data["covv_subm_lab"][0]: - df_data.loc[ - df_data["covv_subm_lab_addr"] == "", "covv_subm_lab_addr" - ] = i["collecting_institution_address"] + for lab in lab_json: + for i in range(len(df_data)): + if lab["collecting_institution"] == df_data["covv_subm_lab"][i]: + df_data["covv_location"][i] = " / ".join (["Europe", lab["geo_loc_country"], lab["geo_loc_state"], lab["geo_loc_city"]]) + df_data.loc[df_data["covv_gender"] == "", "covv_gender"] = "unknown" df_data.loc[df_data["covv_patient_age"] == "", "covv_patient_age"] = "unknown" @@ -134,7 +134,7 @@ def metadata_to_csv(self): df_data.loc[ df_data["covv_orig_lab_addr"] == "", "covv_orig_lab_addr" ] = "unknown" - df_data.loc[df_data["covv_orig_lab"] == "", "covv_orig_lab_addr"] = "unknown" + df_data.loc[df_data["covv_orig_lab"] == "", "covv_orig_lab"] = "unknown" df_data.loc[ df_data["covv_patient_status"] == "", "covv_patient_status" ] = "unknown" @@ -202,7 +202,7 @@ def cli3_auth(self): def cli3_upload(self): """Upload to GISAID""" if self.proxy_config is None: - os.system( + print( "cli3 upload --token %s --metadata %s --fasta %s --frameshift %s" % ( self.token, @@ -212,7 +212,7 @@ def cli3_upload(self): ) ) else: - os.system( + print( "cli3 upload --token %s --metadata %s --fasta %s --frameshift %s --proxy %s" % ( self.token, From d7c586d045859662cad3e3d6c4ac36ccc22d05d5 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Mon, 8 Aug 2022 11:53:44 +0200 Subject: [PATCH 0746/1454] debug --- relecov_tools/gisaid_upload.py | 41 ++++++++++++++++++---------------- 1 file changed, 22 insertions(+), 19 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 8bb28d1b..c1786534 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -98,9 +98,27 @@ def __init__( self.single = single # Metadatos + + def complete_mand_fields(self, dataframe): + """Complete mandatory empty fields with 'unknown'""" + dataframe.loc[dataframe["covv_gender"] == "", "covv_gender"] = "unknown" + dataframe.loc[dataframe["covv_patient_age"] == "", "covv_patient_age"] = "unknown" + dataframe.loc[dataframe["covv_authors"] == "", "covv_authors"] = "unknown" + dataframe.loc[ + dataframe["covv_subm_lab_addr"] == "", "covv_subm_lab_addr" + ] = "unknown" + dataframe.loc[dataframe["covv_subm_lab"] == "", "covv_subm_lab"] = "unknown" + dataframe.loc[ + dataframe["covv_orig_lab_addr"] == "", "covv_orig_lab_addr" + ] = "unknown" + dataframe.loc[dataframe["covv_orig_lab"] == "", "covv_orig_lab"] = "unknown" + dataframe.loc[ + dataframe["covv_patient_status"] == "", "covv_patient_status" + ] = "unknown" + return dataframe def metadata_to_csv(self): - "Transform metadata json to csv" + """Transform metadata json to csv""" data = relecov_tools.utils.read_json_file(self.gisaid_json) df_data = pd.DataFrame(data) df_data.insert(4, "covv_passage", "Original") @@ -120,27 +138,12 @@ def metadata_to_csv(self): lab_json = relecov_tools.utils.read_json_file(lab_json_file) for lab in lab_json: for i in range(len(df_data)): - if lab["collecting_institution"] == df_data["covv_subm_lab"][i]: + if lab["collecting_institution"] == df_data["covv_orig_lab"][i]: df_data["covv_location"][i] = " / ".join (["Europe", lab["geo_loc_country"], lab["geo_loc_state"], lab["geo_loc_city"]]) - - df_data.loc[df_data["covv_gender"] == "", "covv_gender"] = "unknown" - df_data.loc[df_data["covv_patient_age"] == "", "covv_patient_age"] = "unknown" - df_data.loc[df_data["covv_authors"] == "", "covv_authors"] = "unknown" - df_data.loc[ - df_data["covv_subm_lab_addr"] == "", "covv_subm_lab_addr" - ] = "unknown" - df_data.loc[df_data["covv_subm_lab"] == "", "covv_subm_lab"] = "unknown" - df_data.loc[ - df_data["covv_orig_lab_addr"] == "", "covv_orig_lab_addr" - ] = "unknown" - df_data.loc[df_data["covv_orig_lab"] == "", "covv_orig_lab"] = "unknown" - df_data.loc[ - df_data["covv_patient_status"] == "", "covv_patient_status" - ] = "unknown" - + df_data_comp= self.complete_mand_fields(df_data) df_data_path = os.path.join(self.output_path, "meta_gisaid.csv") - df_data.to_csv(df_data_path, index=False) + df_data_comp.to_csv(df_data_path, index=False) metagisaid = df_data_path return metagisaid From f7be6411265b3a1689c1530a70aaef1ce8f6f295 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Mon, 8 Aug 2022 12:11:58 +0200 Subject: [PATCH 0747/1454] made it functional --- relecov_tools/gisaid_upload.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index c1786534..0b2b4a7c 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -205,7 +205,7 @@ def cli3_auth(self): def cli3_upload(self): """Upload to GISAID""" if self.proxy_config is None: - print( + os.system( "cli3 upload --token %s --metadata %s --fasta %s --frameshift %s" % ( self.token, @@ -215,7 +215,7 @@ def cli3_upload(self): ) ) else: - print( + os.system( "cli3 upload --token %s --metadata %s --fasta %s --frameshift %s --proxy %s" % ( self.token, From 075f5b907997ab553398bc903c1d389ad17e3eb4 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Mon, 8 Aug 2022 12:13:55 +0200 Subject: [PATCH 0748/1454] lintin --- relecov_tools/gisaid_upload.py | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 0b2b4a7c..0c0cb075 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -98,11 +98,13 @@ def __init__( self.single = single # Metadatos - + def complete_mand_fields(self, dataframe): """Complete mandatory empty fields with 'unknown'""" dataframe.loc[dataframe["covv_gender"] == "", "covv_gender"] = "unknown" - dataframe.loc[dataframe["covv_patient_age"] == "", "covv_patient_age"] = "unknown" + dataframe.loc[ + dataframe["covv_patient_age"] == "", "covv_patient_age" + ] = "unknown" dataframe.loc[dataframe["covv_authors"] == "", "covv_authors"] = "unknown" dataframe.loc[ dataframe["covv_subm_lab_addr"] == "", "covv_subm_lab_addr" @@ -139,9 +141,16 @@ def metadata_to_csv(self): for lab in lab_json: for i in range(len(df_data)): if lab["collecting_institution"] == df_data["covv_orig_lab"][i]: - df_data["covv_location"][i] = " / ".join (["Europe", lab["geo_loc_country"], lab["geo_loc_state"], lab["geo_loc_city"]]) - - df_data_comp= self.complete_mand_fields(df_data) + df_data["covv_location"][i] = " / ".join( + [ + "Europe", + lab["geo_loc_country"], + lab["geo_loc_state"], + lab["geo_loc_city"], + ] + ) + + df_data_comp = self.complete_mand_fields(df_data) df_data_path = os.path.join(self.output_path, "meta_gisaid.csv") df_data_comp.to_csv(df_data_path, index=False) metagisaid = df_data_path From 73881e2b50005a9222a7feaa3be1dacd7e877acb Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 8 Aug 2022 13:04:42 +0200 Subject: [PATCH 0749/1454] fixing iinstrument platform bug --- relecov_tools/ena_upload.py | 18 ++++++++---------- relecov_tools/map_schema.py | 21 ++++++++++++++++++++- 2 files changed, 28 insertions(+), 11 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 6d9fb63c..e69eb5a0 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -12,7 +12,7 @@ import sys import os -# import ftplib +import ftplib import relecov_tools.utils from relecov_tools.config_json import ConfigJson @@ -322,7 +322,7 @@ def create_structure_to_ena(self): # submit data to webin ftp server. It should only upload fastq files in case the action is ADD. # When the action is MODIFY rthe fastq are already submitted. - """ + if self.action == "ADD" or self.action == "add": session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) @@ -342,7 +342,7 @@ def create_structure_to_ena(self): g2 = session.quit() print(g2) - """ + # THE ENA_UPLOAD_CLI METHOD DOES NOT WORK (below) # chec = submit_data(file_paths, self.passwd, self.user) # print(chec) @@ -381,15 +381,13 @@ def create_structure_to_ena(self): root = tree.getroot() for files in root.iter("SAMPLE_ATTRIBUTES"): - tag = ET.SubElement(files, "TAG") - tag.text = str("ENA-CHECKLIST") - tag = ET.SubElement(files, "VALUE") - tag.text = str("ERC000033") + tag = ET.SubElement(files, "SAMPLE_ATTRIBUTE") + tag_2 = ET.SubElement(tag, "TAG") + tag_2.text = str("ENA-CHECKLIST") + tag_2 = ET.SubElement(tag, "VALUE") + tag_2.text = str("ERC000033") tree.write(schema_xmls["sample"]) - import pdb - - pdb.set_trace() if self.dev: url = "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index a143221a..95092788 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -215,7 +215,26 @@ def additional_formating(self, mapped_json_data): "nextseq" in self.json_data[idx]["sequencing_instrument_model"].lower() ): - mapped_json_data[idx]["instrument_model"] = "NextSeq 500" + if ( + "500" + in self.json_data[idx]["sequencing_instrument_model"].lower() + ): + mapped_json_data[idx]["instrument_model"] = "NextSeq 500" + if ( + "1000" + in self.json_data[idx]["sequencing_instrument_model"].lower() + ): + mapped_json_data[idx]["instrument_model"] = "NextSeq 1000" + if ( + "2000" + in self.json_data[idx]["sequencing_instrument_model"].lower() + ): + mapped_json_data[idx]["instrument_model"] = "NextSeq 2000" + if ( + "550" + in self.json_data[idx]["sequencing_instrument_model"].lower() + ): + mapped_json_data[idx]["instrument_model"] = "NextSeq 550" mapped_json_data[idx]["host subject id"] = "" mapped_json_data[idx]["host health state"] = "" From ada2c1edb2905e2d1d637036f48b97d224bcbdf3 Mon Sep 17 00:00:00 2001 From: Alema91 Date: Mon, 8 Aug 2022 15:26:43 +0200 Subject: [PATCH 0750/1454] Add data type string to SAMPLE column from long_variants_table --- relecov_tools/read_bioinfo_metadata.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 0c57d797..0a9245f0 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -98,7 +98,7 @@ def bioinfo_parse(self, file_name): summary_variants_metrics_path, sep=",", encoding="utf-8" ) variants_long_table = pd.read_csv( - variants_long_table_path, sep=",", encoding="utf-8" + variants_long_table_path, sep=",", encoding="utf-8", dtype={"SAMPLE": "string"} ) consensus_genome_length = pd.read_csv( consensus_genome_length_path, header=None, sep=",", encoding="utf-8" @@ -142,12 +142,10 @@ def bioinfo_parse(self, file_name): ) # fields from summary_variants_metrics_mqc.csv - import pdb - - pdb.set_trace() bioinfo_dict["number_of_base_pairs_sequenced"] = str( (summary_variants_metrics["# Input reads"][c] * 2) ) + bioinfo_dict["ns_per_100_kbp"] = str( summary_variants_metrics["# Ns per 100kb consensus"][c] ) @@ -156,6 +154,7 @@ def bioinfo_parse(self, file_name): ) # fields from variants_long_table.csv + bioinfo_dict["reference_genome_accession"] = str( variants_long_table["CHROM"][c] ) @@ -174,7 +173,6 @@ def bioinfo_parse(self, file_name): bioinfo_dict["consensus_sequence_R2_md5"] = str( md5_info.iloc[c * 2 + 1, 0][0:32] ) - bioinfo_dict["dehosting_method_software_version"] = str( list(software_versions["KRAKEN2_KRAKEN2"].values())[0] ) From 1aa2d9b8d6eca1782ea2bedfb2e8e2b724fcbdb8 Mon Sep 17 00:00:00 2001 From: Alema91 Date: Mon, 8 Aug 2022 15:41:41 +0200 Subject: [PATCH 0751/1454] linting --- relecov_tools/read_bioinfo_metadata.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 0a9245f0..d93bc056 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -98,7 +98,10 @@ def bioinfo_parse(self, file_name): summary_variants_metrics_path, sep=",", encoding="utf-8" ) variants_long_table = pd.read_csv( - variants_long_table_path, sep=",", encoding="utf-8", dtype={"SAMPLE": "string"} + variants_long_table_path, + sep=",", + encoding="utf-8", + dtype={"SAMPLE": "string"}, ) consensus_genome_length = pd.read_csv( consensus_genome_length_path, header=None, sep=",", encoding="utf-8" @@ -152,9 +155,7 @@ def bioinfo_parse(self, file_name): bioinfo_dict["qc_filtered"] = str( summary_variants_metrics["# Trimmed reads (fastp)"][c] ) - # fields from variants_long_table.csv - bioinfo_dict["reference_genome_accession"] = str( variants_long_table["CHROM"][c] ) From 7d07f5d869b68a000d446964ed52efc663f16420 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 9 Aug 2022 17:19:06 +0200 Subject: [PATCH 0752/1454] modifying to select sample by name not in order --- relecov_tools/read_bioinfo_metadata.py | 49 +++++++++++++++++--------- 1 file changed, 33 insertions(+), 16 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 0c57d797..8d061720 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -135,44 +135,61 @@ def bioinfo_parse(self, file_name): bioinfo_dict["long_table_path"] = self.input_folder # fields from mapping_illumina.tab + mapping_illumina_tab_sample = mapping_illumina_tab.loc[ + mapping_illumina_tab["sample"] == bioinfo_dict["sample_name"] + ] + for key in self.mapping_illumina_tab_field_list.keys(): bioinfo_dict[key] = str( - mapping_illumina_tab[self.mapping_illumina_tab_field_list[key]][c] + mapping_illumina_tab_sample.loc[ + mapping_illumina_tab["sample"] == bioinfo_dict["sample_name"] + ][self.mapping_illumina_tab_field_list[key]].values[0] ) # fields from summary_variants_metrics_mqc.csv - import pdb - pdb.set_trace() bioinfo_dict["number_of_base_pairs_sequenced"] = str( - (summary_variants_metrics["# Input reads"][c] * 2) + summary_variants_metrics.loc[ + summary_variants_metrics["Sample"] == bioinfo_dict["sample_name"] + ]["# Input reads"].values[0] + * 2 ) + bioinfo_dict["ns_per_100_kbp"] = str( - summary_variants_metrics["# Ns per 100kb consensus"][c] + summary_variants_metrics.loc[ + summary_variants_metrics["Sample"] == bioinfo_dict["sample_name"] + ]["# Ns per 100kb consensus"].values[0] ) + bioinfo_dict["qc_filtered"] = str( - summary_variants_metrics["# Trimmed reads (fastp)"][c] + summary_variants_metrics.loc[ + summary_variants_metrics["Sample"] == bioinfo_dict["sample_name"] + ]["# Trimmed reads (fastp)"].values[0] ) # fields from variants_long_table.csv - bioinfo_dict["reference_genome_accession"] = str( - variants_long_table["CHROM"][c] - ) - bioinfo_dict["consensus_genome_length"] = str( - consensus_genome_length.iloc[c, 0] - ) + + chrom = variants_long_table.loc[ + variants_long_table["SAMPLE"] == bioinfo_dict["sample_name"] + ]["CHROM"] + import pdb + + pdb.set_trace() + bioinfo_dict["reference_genome_accession"] = str(chrom) + # bioinfo_dict["consensus_genome_length"] = str(consensus_genome_length.iloc[c, 0]) + bioinfo_dict["consensus_genome_length"] = "TEMPORARY VALUE" bioinfo_dict["consensus_sequence_R1_name"] = str( - md5_info.iloc[c * 2, 0][34:60] + md5_info.loc[md5_info[0] == bioinfo_dict["sample_name"]].values[0, 2] ) bioinfo_dict["consensus_sequence_R2_name"] = str( - md5_info.iloc[c * 2 + 1, 0][34:60] + md5_info.loc[md5_info[0] == bioinfo_dict["sample_name"]].values[1, 2] ) bioinfo_dict["consensus_sequence_R1_md5"] = str( - md5_info.iloc[c * 2, 0][0:32] + md5_info.loc[md5_info[0] == bioinfo_dict["sample_name"]].values[0, 2] ) bioinfo_dict["consensus_sequence_R2_md5"] = str( - md5_info.iloc[c * 2 + 1, 0][0:32] + md5_info.loc[md5_info[0] == bioinfo_dict["sample_name"]].values[1, 1] ) bioinfo_dict["dehosting_method_software_version"] = str( From 300c073bc9946f136f6135270eff9c02a3f3ec82 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 9 Aug 2022 22:49:04 +0200 Subject: [PATCH 0753/1454] remove -l parameter to indicate the metadata lab. now it must be inside folder --- relecov_tools/__main__.py | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 66fe4558..1e659ad4 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -399,12 +399,6 @@ def long_table_parse(longtable_file, output): # read metadata bioinformatics @relecov_tools_cli.command(help_priority=12) -@click.option( - "-l", - "--lab_metadata", - type=click.Path(), - help="file containing laboratory METADATA ", -) @click.option( "-i", "--institution", @@ -418,10 +412,10 @@ def long_table_parse(longtable_file, output): help="Folder where are located the additional files", ) @click.option("-o", "--output", type=click.Path(), help="Path to save json output") -def metadata_homogeneizer(lab_metadata, institution, directory, output): +def metadata_homogeneizer(institution, directory, output): """Parse institution metadata lab to the one used in relecov""" new_parse = relecov_tools.metadata_homogeneizer.MetadataHomogeneizer( - lab_metadata, institution, directory, output + institution, directory, output ) new_parse.converting_metadata() From 3e0d661824f6a653350bccbce60d8185f4f0e97b Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 9 Aug 2022 22:54:00 +0200 Subject: [PATCH 0754/1454] Change the format that additional files are handle based on functions --- .../schema/institution_schemas/ISCIII.json | 131 +++++++++--------- 1 file changed, 68 insertions(+), 63 deletions(-) diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index a4577efb..748dc8fe 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -1,74 +1,79 @@ { - "mapped_fields": { - "Public Health sample id (SIVIES)": "Código SiViEs", - "Sample ID given by originating laboratory": "Ref Hospital", - "Sample ID given by the submitting laboratory": "ID CNM", - "Sample ID given in the microbiology lab": "ID VI-VRP", - "Sample ID given if multiple rna-extraction or passages": "ID VI-VRP", - "Sample ID given for sequencing": "ID VI-VRP", - "GISAID id": "ID GISAID", - "Originating Laboratory": "Hospital", - "Sample Collection Date": "Fecha de toma", - "Sample Received Date": "Fecha recepción", - "Host Age": "Edad (años)", - "Host Gender": "Sexo", - "Diagnostic Pcr Ct Value 1": "PCR genE" - - }, - "fixed_fields": { - "Submitting Institution": "Instituto de Salud Carlos III", - "Biological Sample Storage Condition": "-80 C", - "Rna Extraction Protocol": "RT-PCR", - "Purpose of sampling": "Surveillance", - "Specimen source": "Nasopharyngeal exudate", - "Environmental System": "Swab", - "Host": "Human", - "Library Preparation Kit": "Illumina DNA Prep", - "Enrichment Protocol": "Amplicon", - "Enrichment panel/assay": "ARTIC", - "Source material": "Viral RNA", - "Capture method": "PCR", - "Sequencing technique": "Amplicon", - "Library Layout": "Paired", - "Gene Name 1": "ORF E", - "Diagnostic Pcr Ct Value 1": "", - "Authors": "A. Monzón; F. Casas; I. Jiménez; M. Camarero; P. Zaballos; ROMAN SOTO; S. Cuesta, I.; S. Iglesias-Caballero; S. Pozo; S. Varona; SERGIO; Sandonís; V. Vázquez-Morón" - }, + "pyhon_file": "ISCIII.py", "required_files": { + "meta_file": { + "file_name": "new_lab_metadata2022_07_20_13_35_38.xlsx", + "mapped_fields": { + "Public Health sample id (SIVIES)": "Código SiViEs", + "Sample ID given by originating laboratory": "Ref Hospital", + "Sample ID given by the submitting laboratory": "ID CNM", + "Sample ID given in the microbiology lab": "ID VI-VRP", + "Sample ID given if multiple rna-extraction or passages": "ID VI-VRP", + "Sample ID given for sequencing": "ID VI-VRP", + "GISAID id": "ID GISAID", + "Originating Laboratory": "Hospital", + "Sample Collection Date": "Fecha de toma", + "Sample Received Date": "Fecha recepción", + "Host Age": "Edad (años)", + "Host Gender": "Sexo", + "Diagnostic Pcr Ct Value 1": "PCR genE" + }, + "fixed_fields": { + "Submitting Institution": "Instituto de Salud Carlos III", + "Biological Sample Storage Condition": "-80 C", + "Rna Extraction Protocol": "RT-PCR", + "Purpose of sampling": "Surveillance", + "Specimen source": "Nasopharyngeal exudate", + "Environmental System": "Swab", + "Host": "Human", + "Library Preparation Kit": "Illumina DNA Prep", + "Enrichment Protocol": "Amplicon", + "Enrichment panel/assay": "ARTIC", + "Source material": "Viral RNA", + "Capture method": "PCR", + "Sequencing technique": "Amplicon", + "Library Layout": "Paired", + "Gene Name 1": "ORF E", + "Diagnostic Pcr Ct Value 1": "", + "Authors": "" + }, + "function" : "None" + }, + "sample_file": { + "file_name": "sample_data.json", + "mapped_fields": { + "Sequence file R1 fastq": "sequence_file_R1_fastq", + "Sequence file R2 fastq": "sequence_file_R2_fastq" + }, + "function":"None" + }, + "run_id_file": { + "file_name": "samples_run_services.tsv", + "mapped_fields":{ + "Runid": "run_name" + }, + "function":"None" + }, "org_lab_file": { "file_name": "laboratory_mapping_list.tsv", - "metadata_field": ["Originating Laboratory"], - "file_field": ["mapped_org_lab"], - "req_process":{ - "replace":{ - } - } + "mapped_fields":{ + "Originating Laboratory": "mapped_org_lab" + }, + "function": "replace_originating_lab" }, "sequencer_file": { "file_name": "samples_run_services.tsv", - "metadata_field": ["Sequencing Instrument Model"], - "file_field": ["run_name"], - "req_process":{ - "condition":{ - "nextseq": "Illumina NextSeq", - "next_seq": "Illumina NextSeq", - "miseq": "Illumina MiSeq", - "miseaq": "Illumina MiSeq", - "novaseq": "Illumina NovaSeq" - } - } - }, - "run_id_file": { - "file_name": "samples_run_services.tsv", - "metadata_field": ["Runid"], - "file_field": ["run_name"], - "req_process":"None" + "mapped_fields":{ + "Sequencing Instrument Model": "run_name" + }, + "function": "added_seq_inst_model" }, - "sample_file": { - "file_name": "sample_data.json", - "metadata_field":["Sequence file R1 fastq", "Sequence file R2 fastq"], - "file_field":["sequence_file_R1_fastq", "sequence_file_R2_fastq"], - "req_process":"None" + "host_gender_file": { + "file_name": "", + "mapped_fields":{ + "Host Gender": "" + }, + "function": "translate_gender_to_english" } } } From 9e814d5a16c11bd360ac63cb49715b55bf4755a3 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 9 Aug 2022 23:13:49 +0200 Subject: [PATCH 0755/1454] modified to support to handled institution functions to set additional fields --- relecov_tools/metadata_homogeneizer.py | 204 +++++++++++++------------ 1 file changed, 107 insertions(+), 97 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index fa264644..ae178ce8 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -20,21 +20,10 @@ class MetadataHomogeneizer: """MetadataHomogeneizer object""" - def __init__( - self, lab_metadata=None, institution=None, directory=None, output_folder=None - ): + def __init__(self, institution=None, directory=None, output_folder=None): self.config_json = ConfigJson() self.heading = self.config_json.get_configuration("metadata_lab_heading") - if lab_metadata is None: - self.lab_metadata = relecov_tools.utils.prompt_path( - msg="Select the file which contains metadata" - ) - else: - self.lab_metadata = lab_metadata - if not os.path.exists(self.lab_metadata): - log.error("Metadata file %s does not exist ", self.lab_metadata) - stderr.print("[red] Metadata file " + self.lab_metadata + " does not exist") - sys.exit(1) + if institution is None: self.institution = relecov_tools.utils.prompt_selection( msg="Select the available mapping institution", @@ -59,9 +48,45 @@ def __init__( ) sys.exit(1) self.mapping_json_data = relecov_tools.utils.read_json_file(mapping_json_file) + + try: + lab_metadata = self.mapping_json_data["required_files"]["meta_file"][ + "file_name" + ] + except KeyError: + log.error("Metadata File is not defined in schema") + stderr.print("[red] Metadata File is not defined in schema") + sys.exit(1) + metadata_path = os.path.join(directory, lab_metadata) + if not os.path.isfile(metadata_path): + log.error("Metadata File %s does not exists", metadata_path) + stderr.print("[red] Metadata File " + metadata_path + "does not exists") + sys.exit(1) + self.lab_metadata = metadata_path + # Check if python file is defined + function_file = self.mapping_json_data["pyhon_file"] + if function_file == "": + self.function_file = None + else: + self.function_file = os.path.join( + os.path.dirname(__file__), "institution_scripts", function_file + ) + if not os.path.isfile(self.function_file): + log.error("File with functions %s does not exist ", self.function_file) + stderr.print( + "[red] File with functions " + + self.function_file + + " does not exist" + ) + sys.exit(1) self.additional_files = [] - if len(self.mapping_json_data["required_files"]) > 0: + if len(self.mapping_json_data["required_files"]) > 1: for key, values in self.mapping_json_data["required_files"].items(): + if key == "meta_file": + continue + if values["file_name"] == "": + self.additional_files.append(values) + continue f_path = os.path.join(directory, values["file_name"]) if not os.path.isfile(f_path): log.error("Additional file %s does not exist ", f_path) @@ -96,7 +121,9 @@ def read_metadata_file(self): return ws_data def mapping_metadata(self, ws_data): - map_fields = self.mapping_json_data["mapped_fields"] + map_fields = self.mapping_json_data["required_files"]["meta_file"][ + "mapped_fields" + ] map_data = [] for row in ws_data: row_data = {} @@ -109,7 +136,9 @@ def mapping_metadata(self, ws_data): def additional_fields(self, mapped_data): add_data = [self.heading] - fixed_fields = self.mapping_json_data["fixed_fields"] + fixed_fields = self.mapping_json_data["required_files"]["meta_file"][ + "fixed_fields" + ] for row in mapped_data: new_row_data = [] for field in self.heading: @@ -124,95 +153,76 @@ def additional_fields(self, mapped_data): return add_data def handling_additional_files(self, additional_data): + for additional_file in self.additional_files: - f_name = additional_file["file_name"] - stderr.print("[blue] Start processing additional file " + f_name) - if f_name.endswith(".json"): - data = relecov_tools.utils.read_json_file(f_name) - elif f_name.endswith(".tsv"): - data = relecov_tools.utils.read_csv_file_return_dict(f_name, "\t") - elif f_name.endswith(".csv"): - data = relecov_tools.utils.read_csv_file_return_dict(f_name, ",") - else: - log.error("Additional file extension %s is not supported ", f_name) - stderr.print( - "[red] Additional file extension " + f_name + " is not supported" - ) - sys.exit(1) - sample_idx = self.heading.index("Sample ID given for sequencing") - for row in additional_data[1:]: - # new_row_data = [] - - s_value = str(row[sample_idx]) - - try: - item_data = data[s_value] - except KeyError: - pass - """ - log.error( - "Additional file %s does not have the information for %s ", - f_name, - s_value, - ) + if additional_file["file_name"] != "": + f_name = additional_file["file_name"] + stderr.print("[blue] Start processing additional file " + f_name) + if f_name.endswith(".json"): + data = relecov_tools.utils.read_json_file(f_name) + elif f_name.endswith(".tsv"): + data = relecov_tools.utils.read_csv_file_return_dict(f_name, "\t") + elif f_name.endswith(".csv"): + data = relecov_tools.utils.read_csv_file_return_dict(f_name, ",") + else: + log.error("Additional file extension %s is not supported ", f_name) stderr.print( - "[red] Additional file " + "[red] Additional file extension " + f_name - + " does not have information for " - + str(s_value) + + " is not supported" ) - continue - """ - # sys.exit(1) - - for m_idx in range(len(additional_file["metadata_field"])): + sys.exit(1) + sample_idx = self.heading.index("Sample ID given for sequencing") + else: + data = "" + if additional_file["function"] == "None": + for row in additional_data[1:]: + # new_row_data = [] + s_value = str(row[sample_idx]) try: - meta_idx = self.heading.index( - additional_file["metadata_field"][m_idx] + item_data = data[s_value] + except KeyError: + pass + """ + log.error( + "Additional file %s does not have the information for %s ", + f_name, + s_value, + ) + stderr.print( + "[red] Additional file " + + f_name + + " does not have information for " + + str(s_value) ) - except ValueError as e: - log.error("Field %s does not exist in Metadata ", e) - stderr.print(f"[red] Field {e} does not exist") - sys.exit(1) - - if additional_file["req_process"] == "None": - row[meta_idx] = item_data[additional_file["file_field"][m_idx]] - else: - - if "condition" in additional_file["req_process"]: - for key, value in additional_file["req_process"][ - "condition" - ].items(): - if ( - key - in item_data[ - additional_file["file_field"][m_idx] - ].lower() - ): - row[meta_idx] = value - break - elif "replace" in additional_file["req_process"]: - row[meta_idx] = row[meta_idx].strip() - try: - row[meta_idx] = data[row[meta_idx]][ - additional_file["file_field"][m_idx] - ] - except KeyError as e: - log.error("Value %s does not exist ", e) - stderr.print(f"[red] Value {e} does not exist") - sys.exit(1) - else: - log.error( - "Processed method %s is not implemented yet", - additional_data["req_process"].key(), - ) - stderr.print( - f"[red] Processed method {additional_data['req_process'].key()} is not implemented yet" - ) + continue + """ + # sys.exit(1) + for m_field, f_field in additional_file["mapped_fields"].items(): + try: + meta_idx = self.heading.index(m_field) + except ValueError as e: + log.error("Field %s does not exist in Metadata ", e) + stderr.print(f"[red] Field {e} does not exist") sys.exit(1) - # add_data.append(row) - # import pdb; pdb.set_trace() + row[meta_idx] = item_data[f_field] + + # import pdb; pdb.set_trace() + else: + func_name = additional_file["function"] + stderr.print("[yellow] Start processing function " + func_name) + exec( + "from relecov_tools.institution_scripts." + + self.institution + + " import " + + func_name + ) + eval( + func_name + + "(additional_data, data, additional_file['mapped_fields'], self.heading)" + ) + stderr.print("[green] Succesful processing of additional file ") return additional_data From fa13c25ef1b522c62302d54aa0ba1cc2beae6ff2 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 9 Aug 2022 23:14:15 +0200 Subject: [PATCH 0756/1454] defined functions for ISCIII --- relecov_tools/institution_scripts/ISCIII.py | 76 +++++++++++++++++++ relecov_tools/institution_scripts/__init__.py | 0 2 files changed, 76 insertions(+) create mode 100644 relecov_tools/institution_scripts/ISCIII.py create mode 100644 relecov_tools/institution_scripts/__init__.py diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py new file mode 100644 index 00000000..9bb8610d --- /dev/null +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -0,0 +1,76 @@ +#!/usr/bin/env python +import sys + +import logging +import rich.console +import relecov_tools.utils + +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + + +def replace_originating_lab(metadata, f_data, mapped_fields, heading): + """Replace the format text in the originating lab and replace by the ones + defined in the System + """ + for row in metadata[1:]: + for key, val in mapped_fields.items(): + meta_idx = heading.index(key) + try: + row[meta_idx] = f_data[row[meta_idx].strip()][val].strip() + except KeyError as e: + log.error("Value %s does not exist ", e) + stderr.print(f"[red] Value {e} does not exist") + sys.exit(1) + return metadata + + +def added_seq_inst_model(metadata, f_data, mapped_fields, heading): + """Set the type of sequencer instrument based on the run name""" + s_idx = heading.index("Sample ID given for sequencing") + for row in metadata[1:]: + for key, val in mapped_fields.items(): + m_idx = heading.index(key) + + try: + run_name = f_data[str(row[s_idx])][val].lower() + except KeyError as e: + log.error("Value %s does not exist ", e) + stderr.print(f"[red] Value {e} does not exist") + sys.exit(1) + if "nextseq" in run_name: + row[m_idx] = "Illumina NextSeq" + elif "next_seq" in run_name: + row[m_idx] = "Illumina NextSeq" + elif "miseq" in run_name: + row[m_idx] = "Illumina MiSeq" + elif "miseaq" in run_name: + row[m_idx] = "Illumina MiSeq" + elif "novaseq" in run_name: + row[m_idx] = "Illumina NovaSeq" + else: + log.error("Value %s is not defined in the mapping ", run_name) + stderr.print(f"[red] Value {run_name} is not defined in the mapping") + sys.exit(1) + return metadata + + +def translate_gender_to_english(metadata, f_data, mapped_fields, heading): + """Translate into english the host gender that is written in spanish""" + for row in metadata: + for key, val in mapped_fields.items(): + m_idx = heading.index(key) + if row[m_idx] is None: + row[m_idx] = "Unknown" + elif "hombre" in row[m_idx].lower(): + row[m_idx] = "Male" + elif "mujer" in row[m_idx].lower(): + row[m_idx] = "Female" + elif "desconocido" in row[m_idx].lower(): + row[m_idx] = "Unknown" + return metadata diff --git a/relecov_tools/institution_scripts/__init__.py b/relecov_tools/institution_scripts/__init__.py new file mode 100644 index 00000000..e69de29b From 35c1ee2d24513c080c378f15380d7195fc5d3652 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 10 Aug 2022 11:43:40 +0200 Subject: [PATCH 0757/1454] checking for samples contained not equal --- relecov_tools/read_bioinfo_metadata.py | 69 +++++++++++++++++--------- 1 file changed, 46 insertions(+), 23 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 66db6cc3..75efe308 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -104,7 +104,7 @@ def bioinfo_parse(self, file_name): dtype={"SAMPLE": "string"}, ) consensus_genome_length = pd.read_csv( - consensus_genome_length_path, header=None, sep=",", encoding="utf-8" + consensus_genome_length_path, header=None, sep="\t", encoding="utf-8" ) md5_info = pd.read_csv(md5_info_path, header=None, sep=",", encoding="utf-8") pangolin_version_table = pd.read_csv( @@ -124,6 +124,7 @@ def bioinfo_parse(self, file_name): for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): # row = ws_metadata_lab[5] sample_name = row[5] + print(sample_name) fastq_r1 = row[47] fastq_r2 = row[48] @@ -138,61 +139,83 @@ def bioinfo_parse(self, file_name): bioinfo_dict["long_table_path"] = self.input_folder # fields from mapping_illumina.tab - mapping_illumina_tab_sample = mapping_illumina_tab.loc[ - mapping_illumina_tab["sample"] == bioinfo_dict["sample_name"] + mapping_illumina_tab_sample = mapping_illumina_tab[ + mapping_illumina_tab["sample"].str.contains(bioinfo_dict["sample_name"]) ] - for key in self.mapping_illumina_tab_field_list.keys(): + # for key in self.mapping_illumina_tab_field_list.keys(): + config_keys = list(self.mapping_illumina_tab_field_list.keys()) - bioinfo_dict[key] = str( - mapping_illumina_tab_sample.loc[ - mapping_illumina_tab["sample"] == bioinfo_dict["sample_name"] - ][self.mapping_illumina_tab_field_list[key]].values[0] - ) + for i in config_keys: + bioinfo_dict[i] = mapping_illumina_tab_sample[ + self.mapping_illumina_tab_field_list[i] + ].values[0] # fields from summary_variants_metrics_mqc.csv bioinfo_dict["number_of_base_pairs_sequenced"] = str( summary_variants_metrics.loc[ - summary_variants_metrics["Sample"] == bioinfo_dict["sample_name"] + summary_variants_metrics["Sample"].str.contains( + bioinfo_dict["sample_name"] + ) ]["# Input reads"].values[0] * 2 ) bioinfo_dict["ns_per_100_kbp"] = str( summary_variants_metrics.loc[ - summary_variants_metrics["Sample"] == bioinfo_dict["sample_name"] + summary_variants_metrics["Sample"].str.contains( + bioinfo_dict["sample_name"] + ) ]["# Ns per 100kb consensus"].values[0] ) bioinfo_dict["qc_filtered"] = str( summary_variants_metrics.loc[ - summary_variants_metrics["Sample"] == bioinfo_dict["sample_name"] + summary_variants_metrics["Sample"].str.contains( + bioinfo_dict["sample_name"] + ) ]["# Trimmed reads (fastp)"].values[0] ) # fields from variants_long_table.csv chrom = variants_long_table.loc[ - variants_long_table["SAMPLE"] == bioinfo_dict["sample_name"] + variants_long_table["SAMPLE"].str.contains(bioinfo_dict["sample_name"]) ]["CHROM"] - import pdb - pdb.set_trace() - bioinfo_dict["reference_genome_accession"] = str(chrom) - # bioinfo_dict["consensus_genome_length"] = str(consensus_genome_length.iloc[c, 0]) - bioinfo_dict["consensus_genome_length"] = "TEMPORARY VALUE" + bioinfo_dict["reference_genome_accession"] = chrom.values[0] + # fields from consensus_genome_length + cons_array = consensus_genome_length.loc[ + consensus_genome_length[0].str.contains(bioinfo_dict["sample_name"]) + ] + if len(cons_array) > 1: + for i in cons_array: + if cons_array.values[i, 1] != 0: + bioinfo_dict["consensus_genome_length"] = str( + cons_array.values[i, 1] + ) + # fields from md5 file bioinfo_dict["consensus_sequence_R1_name"] = str( - md5_info.loc[md5_info[0] == bioinfo_dict["sample_name"]].values[0, 2] + md5_info.loc[ + md5_info[0].str.contains(bioinfo_dict["sample_name"]) + ].values[0, 2] ) bioinfo_dict["consensus_sequence_R2_name"] = str( - md5_info.loc[md5_info[0] == bioinfo_dict["sample_name"]].values[1, 2] + md5_info.loc[ + md5_info[0].str.contains(bioinfo_dict["sample_name"]) + ].values[1, 2] ) bioinfo_dict["consensus_sequence_R1_md5"] = str( - md5_info.loc[md5_info[0] == bioinfo_dict["sample_name"]].values[0, 2] + md5_info.loc[ + md5_info[0].str.contains(bioinfo_dict["sample_name"]) + ].values[0, 2] ) bioinfo_dict["consensus_sequence_R2_md5"] = str( - md5_info.loc[md5_info[0] == bioinfo_dict["sample_name"]].values[1, 1] + md5_info.loc[ + md5_info[0].str.contains(bioinfo_dict["sample_name"]) + ].values[1, 1] ) + # fields from software version file bioinfo_dict["dehosting_method_software_version"] = str( list(software_versions["KRAKEN2_KRAKEN2"].values())[0] ) @@ -213,7 +236,7 @@ def bioinfo_parse(self, file_name): bioinfo_dict["mapping_software_version"] = str( list(software_versions["BOWTIE2_ALIGN"].values())[0] ) - + # files from pangolin.csv file bioinfo_dict["lineage_analysis_software_version"] = str( pangolin_version_software.iloc[c] ) From 0ff56b9c104a68e00c6435a8b6b8fdb2bff282d2 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 10 Aug 2022 14:10:47 +0200 Subject: [PATCH 0758/1454] change number_of_variants_in_consensus and adjustment in date fields --- relecov_tools/read_bioinfo_metadata.py | 88 +++++++++++++++++++------- 1 file changed, 64 insertions(+), 24 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 75efe308..c2ce86e8 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -4,6 +4,7 @@ import logging import json import datetime +import re import rich.console from itertools import islice @@ -27,7 +28,13 @@ class BioinfoMetadata: - def __init__(self, metadata_file=None, input_folder=None, output_folder=None): + def __init__( + self, + metadata_file=None, + input_folder=None, + output_folder=None, + mapping_illumina=None, + ): if metadata_file is None: self.metadata_file = relecov_tools.utils.prompt_path( msg="Select the excel file which contains metadata" @@ -52,6 +59,12 @@ def __init__(self, metadata_file=None, input_folder=None, output_folder=None): ) else: self.output_folder = output_folder + if mapping_illumina is None: + self.mapping_illumina = relecov_tools.utils.prompt_path( + msg="Select the mapping illumina file" + ) + else: + self.mapping_illumina = mapping_illumina def bioinfo_parse(self, file_name): """Fetch the metadata file folder Directory to fetch metadata file @@ -70,8 +83,9 @@ def bioinfo_parse(self, file_name): ) mapping_illumina_tab_path = os.path.join( - self.input_folder, "mapping_illumina.csv" + self.input_folder, self.mapping_illumina ) + summary_variants_metrics_path = os.path.join( self.input_folder, "summary_variants_metrics_mqc.csv" ) @@ -108,11 +122,9 @@ def bioinfo_parse(self, file_name): ) md5_info = pd.read_csv(md5_info_path, header=None, sep=",", encoding="utf-8") pangolin_version_table = pd.read_csv( - pangolin_versions_path, header=None, sep=",", encoding="utf-8" + pangolin_versions_path, header=None, sep="\t", encoding="utf-8" ) - pangolin_version_software = pangolin_version_table[1] - with open(software_versions_path) as file: software_versions = yaml.load(file, Loader=yaml.FullLoader) @@ -147,9 +159,11 @@ def bioinfo_parse(self, file_name): config_keys = list(self.mapping_illumina_tab_field_list.keys()) for i in config_keys: - bioinfo_dict[i] = mapping_illumina_tab_sample[ - self.mapping_illumina_tab_field_list[i] - ].values[0] + bioinfo_dict[i] = str( + mapping_illumina_tab_sample[ + self.mapping_illumina_tab_field_list[i] + ].values[0] + ) # fields from summary_variants_metrics_mqc.csv @@ -179,11 +193,18 @@ def bioinfo_parse(self, file_name): ) # fields from variants_long_table.csv - chrom = variants_long_table.loc[ - variants_long_table["SAMPLE"].str.contains(bioinfo_dict["sample_name"]) - ]["CHROM"] + if os.path.isfile( + self.input_folder + bioinfo_dict["sample_name"] + ".consensus.fa" + ): + chrom = variants_long_table.loc[ + variants_long_table["SAMPLE"].str.contains( + bioinfo_dict["sample_name"] + ) + ]["CHROM"] + bioinfo_dict["reference_genome_accession"] = str(chrom.values[0]) + else: + bioinfo_dict["reference_genome_accession"] = "NC_045512.2" - bioinfo_dict["reference_genome_accession"] = chrom.values[0] # fields from consensus_genome_length cons_array = consensus_genome_length.loc[ consensus_genome_length[0].str.contains(bioinfo_dict["sample_name"]) @@ -198,7 +219,7 @@ def bioinfo_parse(self, file_name): bioinfo_dict["consensus_sequence_R1_name"] = str( md5_info.loc[ md5_info[0].str.contains(bioinfo_dict["sample_name"]) - ].values[0, 2] + ].values[0, 1] ) bioinfo_dict["consensus_sequence_R2_name"] = str( md5_info.loc[ @@ -237,22 +258,41 @@ def bioinfo_parse(self, file_name): list(software_versions["BOWTIE2_ALIGN"].values())[0] ) # files from pangolin.csv file + bioinfo_dict["lineage_analysis_software_version"] = str( - pangolin_version_software.iloc[c] + pangolin_version_table.loc[ + pangolin_version_table[0].str.contains(bioinfo_dict["sample_name"]) + ].values[0][1] ) - - c_time = os.path.getctime(variants_long_table_path) - dt_c = datetime.datetime.fromtimestamp(c_time) - bioinfo_dict["analysis_date"] = str(dt_c) - bioinfo_dict["lineage_identification_date"] = str(dt_c) + bioinfo_dict["variant_designation"] = str( + pangolin_version_table.loc[ + pangolin_version_table[0].str.contains(bioinfo_dict["sample_name"]) + ].values[0][2] + ) + """ + last_modified = os.path.getctime(variants_long_table_path) + last_modified_date = datetime.datetime.fromtimestamp(last_modified) + bioinfo_dict["analysis_date"] = str(last_modified_date) """ - IDEA - pango_time = os.path.getctime( - self.input_folder + "/" + str(sample_name) + ".pangolin.csv" + + string = re.split("(\d+)", self.mapping_illumina)[1] + year, month, day = int(string[:4]), int(string[4:6]), int(string[6:-1]) + x = datetime.datetime(year, month, day) + bioinfo_dict["analysis_date"] = x.strftime("%b %d %Y %H:%M:%S") + + pango_file_path = ( + self.input_folder + bioinfo_dict["sample_name"] + ".pangolin.csv" ) - dt_pango = datetime.datetime.fromtimestamp(pango_time) - """ + if os.path.isfile(pango_file_path): + pango_last_modified = os.path.getctime(pango_file_path) + pango_last_modified_date = datetime.datetime.fromtimestamp( + pango_last_modified + ) + bioinfo_dict["lineage_identification_date"] = str( + pango_last_modified_date + ) + bioinfo_list[str(sample_name)] = bioinfo_dict c = c + 1 From 53d4c12415461492ff70953a06c1638baea463f4 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 10 Aug 2022 14:11:17 +0200 Subject: [PATCH 0759/1454] added new arg mapping_illumina --- relecov_tools/__main__.py | 10 ++++++++-- relecov_tools/conf/configuration.json | 3 +-- 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 66fe4558..4f5402b0 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -368,13 +368,19 @@ def update_db(user, password, json, schema, type, databaseServer): @click.option( "-o", "--metadata-out", type=click.Path(), help="Path to save output metadata file" ) -def read_bioinfo_metadata(metadata_file, input_folder, metadata_out): +@click.option( + "-p", + "--mapping-illumina", + type=click.Path(), + help="Name of the mapping_illumina file", +) +def read_bioinfo_metadata(metadata_file, input_folder, metadata_out, mapping_illumina): """ Create the json compliant from the Bioinfo Metadata. """ new_bioinfo_metadata = relecov_tools.read_bioinfo_metadata.BioinfoMetadata( - metadata_file, input_folder, metadata_out + metadata_file, input_folder, metadata_out, mapping_illumina ) new_bioinfo_metadata.bioinfo_parse(metadata_file) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 4bce40df..f981f055 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -176,14 +176,13 @@ }, "mapping_illumina_tab_field_list": { "lineage_name": "Lineage", - "variant_designation": "Variantsinconsensusx10", "per_genome_greater_10x": "Coverage>10x(%)", "per_reads_host": "%readshost", "per_reads_virus": "%readsvirus", "per_unmapped": "%unmapedreads", "per_Ns": "%Ns10x", "depth_of_coverage_value": "medianDPcoveragevirus", - "number_of_variants_AF_greater_75percent": "Variantsinconsensusx10", + "number_of_variants_in_consensus": "Variantsinconsensusx10", "number_of_variants_with_effect": "MissenseVariants" }, "files_read_bioinfo_metadata": { From 2ac9f1daddbf70c0eed24075d1e1ce9046ad0ef4 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 10 Aug 2022 14:18:46 +0200 Subject: [PATCH 0760/1454] changed field name --- relecov_tools/schema/relecov_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 61a50b32..4845535c 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1861,7 +1861,7 @@ "label": "%Ns", "fill_mode": "batch" }, - "number_of_variants_AF_greater_75percent": { + "number_of_variants_in_consensus": { "examples": [ "" ], @@ -2516,4 +2516,4 @@ "fill_mode": "batch" } } -} +} \ No newline at end of file From 9a11f41f2ab645f3bc1e67d28e04befa2a568ba6 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 10 Aug 2022 15:44:19 +0200 Subject: [PATCH 0761/1454] lintin --- relecov_tools/read_bioinfo_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index c2ce86e8..8389aa08 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -275,7 +275,7 @@ def bioinfo_parse(self, file_name): bioinfo_dict["analysis_date"] = str(last_modified_date) """ - + # get the date from pangolin files string = re.split("(\d+)", self.mapping_illumina)[1] year, month, day = int(string[:4]), int(string[4:6]), int(string[6:-1]) x = datetime.datetime(year, month, day) From 7b37deba087167a431b5870cdff490a840886919 Mon Sep 17 00:00:00 2001 From: Alema91 Date: Thu, 11 Aug 2022 11:26:22 +0200 Subject: [PATCH 0762/1454] Changes in coordenates of array for md5 and fastq name --- relecov_tools/read_bioinfo_metadata.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 8389aa08..99bdcac2 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -219,7 +219,7 @@ def bioinfo_parse(self, file_name): bioinfo_dict["consensus_sequence_R1_name"] = str( md5_info.loc[ md5_info[0].str.contains(bioinfo_dict["sample_name"]) - ].values[0, 1] + ].values[0, 2] ) bioinfo_dict["consensus_sequence_R2_name"] = str( md5_info.loc[ @@ -229,13 +229,14 @@ def bioinfo_parse(self, file_name): bioinfo_dict["consensus_sequence_R1_md5"] = str( md5_info.loc[ md5_info[0].str.contains(bioinfo_dict["sample_name"]) - ].values[0, 2] + ].values[0, 1] ) bioinfo_dict["consensus_sequence_R2_md5"] = str( md5_info.loc[ md5_info[0].str.contains(bioinfo_dict["sample_name"]) ].values[1, 1] ) + # fields from software version file bioinfo_dict["dehosting_method_software_version"] = str( list(software_versions["KRAKEN2_KRAKEN2"].values())[0] From d3cd2f70e0e9da9a3a1d25758cf1f374cd3ca0af Mon Sep 17 00:00:00 2001 From: Alema91 Date: Thu, 11 Aug 2022 12:03:05 +0200 Subject: [PATCH 0763/1454] linting --- relecov_tools/read_bioinfo_metadata.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 99bdcac2..9b8c9037 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -172,8 +172,7 @@ def bioinfo_parse(self, file_name): summary_variants_metrics["Sample"].str.contains( bioinfo_dict["sample_name"] ) - ]["# Input reads"].values[0] - * 2 + ]["# Input reads"].values[0] * 2 ) bioinfo_dict["ns_per_100_kbp"] = str( From 773ea7ccff1c09be1568b3daf2784cc85990d504 Mon Sep 17 00:00:00 2001 From: Alema91 Date: Thu, 11 Aug 2022 12:03:26 +0200 Subject: [PATCH 0764/1454] black --- relecov_tools/read_bioinfo_metadata.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 9b8c9037..99bdcac2 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -172,7 +172,8 @@ def bioinfo_parse(self, file_name): summary_variants_metrics["Sample"].str.contains( bioinfo_dict["sample_name"] ) - ]["# Input reads"].values[0] * 2 + ]["# Input reads"].values[0] + * 2 ) bioinfo_dict["ns_per_100_kbp"] = str( From a88659ee848196341874b0a4e0f2f3b984e16d38 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 11 Aug 2022 12:31:09 +0200 Subject: [PATCH 0765/1454] adding host_subject_id and host_Health_state --- relecov_tools/map_schema.py | 2 +- relecov_tools/schema/ena_schema.json | 13 ++++++++++++ relecov_tools/schema/relecov_schema.json | 26 ++++++++++++++++++++++++ 3 files changed, 40 insertions(+), 1 deletion(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 95092788..1fcb81ab 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -237,7 +237,7 @@ def additional_formating(self, mapped_json_data): mapped_json_data[idx]["instrument_model"] = "NextSeq 550" mapped_json_data[idx]["host subject id"] = "" - mapped_json_data[idx]["host health state"] = "" + mapped_json_data[idx]["host health state"] = "unknown" mapped_json_data[idx]["sample_description"] = "" mapped_json_data[idx]["design_description"] = "" mapped_json_data[idx]["insert_size"] = "0" diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 24407f52..b8b0dfd3 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -621,6 +621,19 @@ "sample" ] }, + "host_health_state": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001388", + "type": "string", + "description": " Status of the host", + "clasification": "Host information", + "label": "Host health state", + "table": [ + "sample" + ] + }, "host_sex": { "Enums": [ "Female [NCIT:C46110]", diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 4845535c..ddb1aae4 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -380,6 +380,32 @@ "label": "Organism", "fill_mode": "batch" }, + "host_subject_id": { + "examples": [ + "e.g. #131" + ], + "ontology": "GENEPIO:0001398", + "type": "string", + "description": "a unique identifier by which each subject can be referred to, de-identified.", + "clasification": "Host information", + "label": "Host Subject Id", + "table": [ + "sample" + ] + }, + "host_health_state": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001388", + "type": "string", + "description": " Status of the host", + "clasification": "Host information", + "label": "Host health state", + "table": [ + "sample" + ] + }, "host_scientific_name": { "Enums": [ "Bos taurus [NCBITaxon:9913]", From 57680ae5dbb6c6a70f768057180c0f9e1345f3a9 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 11 Aug 2022 12:55:37 +0200 Subject: [PATCH 0766/1454] added parameters to send the request to relecov --- relecov_tools/__main__.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 1e659ad4..cef892c9 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -137,14 +137,18 @@ def relecov_tools_cli(verbose, log_file): @relecov_tools_cli.command(help_priority=2) @click.option("-u", "--user", help="User name for login to sftp server") @click.option("-p", "--password", help="password for the user to login") +@click.option("-r_u", "--user_relecov", help="User name for updating data to relecov") +@click.option("-p_r", "--password_relecov", help="password for relecov user") @click.option( "-f", "--conf_file", help="Configuration file (no params file)", ) -def download(user, password, conf_file): +def download(user, password, conf_file, user_relecov, password_relecov): """Download files located in sftp server.""" - sftp_connection = relecov_tools.sftp_handle.SftpHandle(user, password, conf_file) + sftp_connection = relecov_tools.sftp_handle.SftpHandle( + user, password, conf_file, user_relecov, password_relecov + ) sftp_connection.download() From 7c253bddb996ae97ac91dad8a9ee6a9219965e0c Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 11 Aug 2022 12:59:36 +0200 Subject: [PATCH 0767/1454] added sequence_file_R1_fastq and sequence_file_R2_fastq that were missing in the parameters to upload to iSkyLIMS --- relecov_tools/conf/configuration.json | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 4bce40df..669c1f2b 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -124,6 +124,7 @@ "store_samples": "createSampleData", "analysis": "bioinfoData", "long_table": "longtableData", + "sftp_info": "sftpInfo", "token": "" } }, @@ -147,6 +148,8 @@ "microbiology_lab_sample_id", "r1_fastq_filepath", "r2_fastq_filepath", + "sequence_file_R1_fastq", + "sequence_file_R2_fastq", "sequencing_sample_id", "submitting_lab_sample_id", "virus_name" @@ -222,4 +225,4 @@ "ISCIII": "ISCIII.json", "HUGTiP": "HUGTiP.json" } -} \ No newline at end of file +} From 0f2aa1e4413f1ecf793573dca4d3af9002fea1ea Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 11 Aug 2022 13:01:02 +0200 Subject: [PATCH 0768/1454] added new file for gisaid authors and include key for mapping --- .../schema/institution_schemas/ISCIII.json | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 748dc8fe..13a47a05 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -45,6 +45,7 @@ "Sequence file R1 fastq": "sequence_file_R1_fastq", "Sequence file R2 fastq": "sequence_file_R2_fastq" }, + "mapped_key": "Sample ID given for sequencing", "function":"None" }, "run_id_file": { @@ -52,6 +53,7 @@ "mapped_fields":{ "Runid": "run_name" }, + "mapped_key": "Sample ID given for sequencing", "function":"None" }, "org_lab_file": { @@ -59,6 +61,7 @@ "mapped_fields":{ "Originating Laboratory": "mapped_org_lab" }, + "mapped_key": "", "function": "replace_originating_lab" }, "sequencer_file": { @@ -66,6 +69,7 @@ "mapped_fields":{ "Sequencing Instrument Model": "run_name" }, + "mapped_key": "", "function": "added_seq_inst_model" }, "host_gender_file": { @@ -73,7 +77,16 @@ "mapped_fields":{ "Host Gender": "" }, + "mapped_key": "", "function": "translate_gender_to_english" + }, + "authors_file": { + "file_name": "gisaid_authors.tsv", + "mapped_fields":{ + "Authors": "authors" + }, + "mapped_key": "GISAID id", + "function": "None" } } } From a13315413b03ed371c376368924ec274d729a537 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 11 Aug 2022 13:02:05 +0200 Subject: [PATCH 0769/1454] include key for mapping --- relecov_tools/metadata_homogeneizer.py | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index ae178ce8..c12ceabf 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -172,32 +172,30 @@ def handling_additional_files(self, additional_data): + " is not supported" ) sys.exit(1) - sample_idx = self.heading.index("Sample ID given for sequencing") + else: data = "" if additional_file["function"] == "None": + mapping_idx = self.heading.index(additional_file["mapped_key"]) for row in additional_data[1:]: # new_row_data = [] - s_value = str(row[sample_idx]) + s_value = str(row[mapping_idx]) try: item_data = data[s_value] except KeyError: - pass - """ log.error( "Additional file %s does not have the information for %s ", f_name, s_value, ) stderr.print( - "[red] Additional file " + "[yellow] Additional file " + f_name + " does not have information for " + str(s_value) ) continue - """ # sys.exit(1) for m_field, f_field in additional_file["mapped_fields"].items(): try: @@ -243,7 +241,7 @@ def converting_metadata(self): stderr.print("[blue] Adding fixed information") additional_data = self.additional_fields(mapped_data) # Fetch the additional files and include the information in metadata - stderr.print("[blue] reading and mapping de information that cames in files") + stderr.print("[blue] reading and mapping de information that are in files") converted_data = self.handling_additional_files(additional_data) f_name = os.path.join(self.output_folder, "converted_metadata_lab.xlsx") self.write_to_excel_file(converted_data, f_name) From 0532e08f9affdc25d5972eda2acc13087cc49bca Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 11 Aug 2022 13:03:38 +0200 Subject: [PATCH 0770/1454] include in class definition the user/passwd of relecov --- relecov_tools/sftp_handle.py | 45 +++++++++++++++++++++++++++++++++--- 1 file changed, 42 insertions(+), 3 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 7fc902d6..d623fdc4 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -14,6 +14,7 @@ import openpyxl import relecov_tools.utils from relecov_tools.config_json import ConfigJson +from relecov_tools.rest_api import RestApi log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -25,7 +26,14 @@ class SftpHandle: - def __init__(self, user=None, passwd=None, conf_file=None): + def __init__( + self, + user=None, + passwd=None, + conf_file=None, + user_relecov=None, + password_relecov=None, + ): """Initializes the sftp object""" config_json = ConfigJson() self.allowed_sample_ext = config_json.get_configuration( @@ -98,6 +106,10 @@ def __init__(self, user=None, passwd=None, conf_file=None): msg="Enter your password" ) self.client = None + external_servers = config_json.get_topic_data("external_url", "relecov") + self.relecov_server = external_servers["server"] + self.relecov_url = external_servers["url"] + self.relecov_post_url = external_servers["sftp_info"] def open_connection(self): """Establish sftp connection""" @@ -343,6 +355,29 @@ def delete_remote_files(self, folder, files): continue return + def create_json_with_downloaded_samples(self, sample_file_list, folder): + """From the download information prepare a json file""" + sample_dict = {} + for sample in sample_file_list: + sample_dict[sample] = {"folder": folder} + return json.dumps(sample_dict, indent=4, sort_keys=True, ensure_ascii=False) + + def send_info_to_server(self, json_data): + rest_api = RestApi(self.database_server, self.database_url) + error_counts = 0 + for item in json_data: + result = rest_api.post_request(item, "", self.relecov_post_url) + if "ERROR" in result: + error_counts += 1 + log.error("Request was not accepted %s", result["ERROR"]) + stderr.print( + "[red] Error " + result["ERROR"] + " when sending request}" + ) + if error_counts == 0: + log.info("Request was not accepted %s", result["ERROR"]) + stderr.print("[green] Successful upload information to server") + return + def delete_local_folder(self, local_folder): """Delete download folder because files does not complain requisites""" shutil.rmtree(local_folder, ignore_errors=True) @@ -405,11 +440,15 @@ def download(self): if self.validate_download_files( sample_file_list, result_data["local_folder"] ): - self.create_tmp_files_with_metadata_info( result_data["local_folder"], sample_file_list, md5_files, meta_file ) - # self.delete_remote_files(folder, files) + # Collect data to send the request to relecov_platform + json_sample_data = self.create_json_with_downloaded_samples( + sample_file_list, folder + ) + for record in json_sample_data: + pass else: log.info("Deleting local folder %s", result_data["local_folder"]) self.delete_local_folder(result_data["local_folder"]) From 3139c851cbf74dd56266866ed90c7ce86b292051 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 11 Aug 2022 15:40:58 +0200 Subject: [PATCH 0771/1454] working on host_subject_id --- relecov_tools/map_schema.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 1fcb81ab..9a7de01d 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -236,7 +236,7 @@ def additional_formating(self, mapped_json_data): ): mapped_json_data[idx]["instrument_model"] = "NextSeq 550" - mapped_json_data[idx]["host subject id"] = "" + # mapped_json_data[idx]["host subject id"] = "" mapped_json_data[idx]["host health state"] = "unknown" mapped_json_data[idx]["sample_description"] = "" mapped_json_data[idx]["design_description"] = "" From 0eeeb056835bd231f7a30df433284d1c16715eba Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Thu, 11 Aug 2022 15:59:05 +0200 Subject: [PATCH 0772/1454] modified configuration.json --- relecov_tools/conf/configuration.json | 2 +- relecov_tools/feed_database.py | 16 +++++++++------- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 2d165997..a0bd3a86 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -119,7 +119,7 @@ "token": "" }, "relecov": { - "server": "http://relecov-platform.isciiides.es", + "server": "http://relecov-platform.isciiides.es:8000", "url": "/api/", "store_samples": "createSampleData", "analysis": "bioinfoData", diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index ff8fccf1..e695f544 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -238,6 +238,7 @@ def update_database(self, field_values, post_url): {"user": self.user, "pass": self.passwd}, self.database_settings[post_url], ) + if "ERROR" in result: if result["ERROR"] == "Server not available": # retry to connect to server @@ -291,17 +292,18 @@ def store_data(self): print("relecov") post_url = "analysis" map_fields = self.map_relecov_bioinfo_data() - """ - sample_fields, s_project_fields = self.get_iskylims_fields_sample() - map_fields = self.map_iskylims_sample_fields_values( - sample_fields, s_project_fields - ) - """ + + + # sample_fields, s_project_fields = self.get_iskylims_fields_sample() + # map_fields = self.map_iskylims_sample_fields_values( + # sample_fields, s_project_fields + # ) + elif self.server_type == "relecov_local": print("relecov_local") post_url = "analysis" map_fields = self.map_relecov_bioinfo_data() - + post_url = "analysis" elif self.type_of_info == "longtable": post_url = "long_table" else: From 4fb4f4a65fcd5f7f5f897b42cee3417cf9957e06 Mon Sep 17 00:00:00 2001 From: birbi Date: Thu, 11 Aug 2022 18:58:52 +0200 Subject: [PATCH 0773/1454] modified: relecov_tools/conf/configuration.json --- relecov_tools/conf/configuration.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 2d165997..a0bd3a86 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -119,7 +119,7 @@ "token": "" }, "relecov": { - "server": "http://relecov-platform.isciiides.es", + "server": "http://relecov-platform.isciiides.es:8000", "url": "/api/", "store_samples": "createSampleData", "analysis": "bioinfoData", From 5ff41e302197cb28a915e20129ef22a57ead5e7c Mon Sep 17 00:00:00 2001 From: birbi Date: Thu, 11 Aug 2022 19:20:27 +0200 Subject: [PATCH 0774/1454] sampes to relecov_local --- relecov_tools/conf/configuration.json | 9 +++++++++ relecov_tools/feed_database.py | 4 ++++ 2 files changed, 13 insertions(+) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index ca48fa84..d06fcbe0 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -126,6 +126,15 @@ "long_table": "longtableData", "sftp_info": "sftpInfo", "token": "" + }, + "relecov_local": { + "server": "http://127.0.0.1:8000", + "url": "/api/", + "store_samples": "createSampleData", + "analysis": "bioinfoData", + "long_table": "longtableData", + "sftp_info": "sftpInfo", + "token": "" } }, "iskylims_fixed_values": { diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 9652e568..06e02727 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -285,6 +285,10 @@ def store_data(self): map_fields = self.map_iskylims_sample_fields_values( sample_fields, s_project_fields ) + elif self.server_type == "relecov_local": + print("relecov_local") + # post_url = "sample" + map_fields = self.map_relecov_sample_data() else: # sample_fields, s_project_fields = self.get_iskylims_fields_sample() map_fields = self.map_relecov_sample_data() From 45dd522b72dd5d6191d792d360088e59a5d825fb Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 12 Aug 2022 12:06:49 +0200 Subject: [PATCH 0775/1454] changes for instrument model --- relecov_tools/ena_upload.py | 12 ++++++++++-- relecov_tools/map_schema.py | 20 +++++++++++--------- relecov_tools/read_lab_metadata.py | 9 ++++++++- 3 files changed, 29 insertions(+), 12 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index e69eb5a0..67e08248 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -159,7 +159,7 @@ def create_structure_to_ena(self): "collector_name", "collecting_institution", "isolate", - "host subject id", + "host_subject_id", "host health state", "sample_description", ] @@ -172,6 +172,7 @@ def create_structure_to_ena(self): "geographic_location_(country_and/or_sea)": "geographic location (country and/or sea)" } ) + df_samples = df_samples.rename(columns={"host_subject_id": "host subject id"}) df_samples = df_samples.rename(columns={"collection_date": "collection date"}) df_samples = df_samples.rename(columns={"host_common_name": "host common name"}) df_samples = df_samples.rename(columns={"host_common_name": "host common name"}) @@ -191,6 +192,7 @@ def create_structure_to_ena(self): df_samples.insert(4, "ENA_CHECKLIST", checklist) # df_samples.insert(5, "sample_description", df_schemas["sample_description"]) # df_samples + """ alias title taxon_id host health state ... scientific_name collector name collecting institution isolate 0 212164375 212164375 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212164375 @@ -267,6 +269,10 @@ def create_structure_to_ena(self): ] ] + df_experiments["instrument_model"] = df_experiments[ + "instrument_model" + ].str.lower() + df_experiments.insert(3, "status", self.action) for i in range(len(df_experiments)): @@ -293,6 +299,7 @@ def create_structure_to_ena(self): 2 214821_S12 RELECOV Spanish Network for genomics surveillance RELECOV ... PAIRED Illumina MiSeq 214823_S1_R1_001.fastq.gz_214823_S1_R2_001.fas... """ + ena_config = config_json.get_configuration("ENA_configuration") schema_dataframe = {} schema_dataframe["sample"] = df_samples @@ -322,7 +329,7 @@ def create_structure_to_ena(self): # submit data to webin ftp server. It should only upload fastq files in case the action is ADD. # When the action is MODIFY rthe fastq are already submitted. - + """ if self.action == "ADD" or self.action == "add": session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) @@ -342,6 +349,7 @@ def create_structure_to_ena(self): g2 = session.quit() print(g2) + """ # THE ENA_UPLOAD_CLI METHOD DOES NOT WORK (below) # chec = submit_data(file_paths, self.passwd, self.user) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 9a7de01d..76b371db 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -182,9 +182,7 @@ def additional_formating(self, mapped_json_data): "sequencing_sample_id" ] mapped_json_data[idx]["file_type"] = "fastq" - mapped_json_data[idx]["collector_name"] = self.json_data[idx][ - "author_submitter" - ] + # mapped_json_data[idx]["collector_name"] = self.json_data[idx][ "author_submitter"] mapped_json_data[idx]["library_name"] = self.json_data[idx][ "library_kit" ] @@ -207,10 +205,6 @@ def additional_formating(self, mapped_json_data): "sequencing_instrument_platform" ] = self.json_data[idx]["sequencing_instrument_platform"].upper() - mapped_json_data[idx]["instrument_model"] = self.json_data[idx][ - "sequencing_instrument_model" - ] - if ( "nextseq" in self.json_data[idx]["sequencing_instrument_model"].lower() @@ -235,9 +229,17 @@ def additional_formating(self, mapped_json_data): in self.json_data[idx]["sequencing_instrument_model"].lower() ): mapped_json_data[idx]["instrument_model"] = "NextSeq 550" + if ( + "illumina nextseq" + in self.json_data[idx]["sequencing_instrument_model"].lower() + ): + mapped_json_data[idx]["instrument_model"] = "NextSeq 550" + else: + mapped_json_data[idx]["instrument_model"] = self.json_data[idx][ + "sequencing_instrument_model" + ] - # mapped_json_data[idx]["host subject id"] = "" - mapped_json_data[idx]["host health state"] = "unknown" + mapped_json_data[idx]["host health state"] = "not provided" mapped_json_data[idx]["sample_description"] = "" mapped_json_data[idx]["design_description"] = "" mapped_json_data[idx]["insert_size"] = "0" diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index a32687cc..af31d82c 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -3,6 +3,7 @@ import json import logging +from queue import Empty # from turtle import heading import rich.console @@ -128,7 +129,12 @@ def include_fixed_data(self): def include_fields_already_set(self, row_sample): processed_data = {} - processed_data["collector_name"] = row_sample["author_submitter"] + + if row_sample["author_submitter"] == "": + processed_data["collector_name"] = "unknown" + else: + processed_data["collector_name"] = row_sample["author_submitter"] + processed_data["host_subject_id"] = row_sample["microbiology_lab_sample_id"] return processed_data @@ -256,6 +262,7 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): row_sample["run_alias"] = str( row_sample["fastq_r1"] + "_" + row_sample["fastq_r2"] ) + additional_metadata.append(row_sample) return additional_metadata From 701a50064d396c873bff2a8565068ef38d744feb Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 12 Aug 2022 15:03:20 +0200 Subject: [PATCH 0776/1454] change Unkown to Not Provided, to be accepted by ENA --- relecov_tools/institution_scripts/ISCIII.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index 9bb8610d..d2788aa4 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -62,15 +62,17 @@ def added_seq_inst_model(metadata, f_data, mapped_fields, heading): def translate_gender_to_english(metadata, f_data, mapped_fields, heading): """Translate into english the host gender that is written in spanish""" - for row in metadata: + for row in metadata[1:]: for key, val in mapped_fields.items(): m_idx = heading.index(key) if row[m_idx] is None: - row[m_idx] = "Unknown" + row[m_idx] = "not applicable" elif "hombre" in row[m_idx].lower(): row[m_idx] = "Male" elif "mujer" in row[m_idx].lower(): row[m_idx] = "Female" elif "desconocido" in row[m_idx].lower(): - row[m_idx] = "Unknown" + row[m_idx] = "Not Provided" + else: + row[m_idx] = "not applicable" return metadata From 7f0b08f145105fc8a5ce3bfb23ed500af9d28e7b Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 12 Aug 2022 15:04:11 +0200 Subject: [PATCH 0777/1454] including files for artic version, run date and number of samples in run --- .../schema/institution_schemas/ISCIII.json | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 13a47a05..c77d94f5 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -87,6 +87,30 @@ }, "mapped_key": "GISAID id", "function": "None" + }, + "run_date": { + "file_name": "runName_runDate.tsv", + "mapped_fields":{ + "Sequencing Date": "run_date" + }, + "mapped_key": "Runid", + "function": "None" + }, + "samples_in_run": { + "file_name": "run_and_num_of_samples.csv", + "mapped_fields":{ + "Number Of Samples In Run": "num_samples" + }, + "mapped_key": "Runid", + "function": "None" + }, + "artic_version": { + "file_name": "samples_artic_version.tsv", + "mapped_fields":{ + "Enrichment panel/assay version": "artic_version" + }, + "mapped_key": "Sample ID given for sequencing", + "function":"None" } } } From e29fe8a65b2d229cd29be36a7c9899370086bfa4 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 12 Aug 2022 16:00:55 +0200 Subject: [PATCH 0778/1454] rename If Enrichment panel/assay If other specify by: If Enrichment panel/assay Is other specify --- relecov_tools/schema/relecov_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index ddb1aae4..d3e69ddd 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1080,7 +1080,7 @@ "type": "string", "description": "", "classification": "Sequencing", - "label": "If Enrichment panel/assay If Other, Especify", + "label": "If Enrichment panel/assay Is Other, Especify", "fill_mode": "batch" }, "amplicon_version": { @@ -2542,4 +2542,4 @@ "fill_mode": "batch" } } -} \ No newline at end of file +} From d0f79729c7468b2effba16889fd45c238bc8b066 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 12 Aug 2022 16:03:10 +0200 Subject: [PATCH 0779/1454] rename If Enrichment panel/assay. If other specify by: If Enrichment panel/assay Is other specify --- relecov_tools/conf/configuration.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 915455a7..f9ec798b 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -27,9 +27,9 @@ "Commercial All-in-one library kit", "Library Preparation Kit", "Enrichment Protocol", - "If Enrichment Protocol. If Other,Specify", + "If Enrichment Protocol Is Other,Specify", "Enrichment panel/assay", - "If Enrichment panel/assay. If Other, Specify", + "If Enrichment panel/assay Is Other, Specify", "Enrichment panel/assay version", "Number Of Samples In Run", "Runid", From db690d791e24b32906928e1216113e40992838b0 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 12 Aug 2022 16:14:22 +0200 Subject: [PATCH 0780/1454] Rename If Enrichment panel/assay Is Other, Especify by: If Enrichment panel/assay Is Other, Specify --- relecov_tools/read_lab_metadata.py | 2 ++ relecov_tools/schema/relecov_schema.json | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index a32687cc..3669d18b 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -322,6 +322,7 @@ def read_metadata_file(self): try: sample_data_row[self.label_prop_dict[heading[idx]]] = val except TypeError as e: + import pdb; pdb.set_trace() stderr.print("[red] Error when reading " + row[2] + e) else: try: @@ -329,6 +330,7 @@ def read_metadata_file(self): row[idx] if row[idx] else "" ) except KeyError as e: + import pdb; pdb.set_trace() stderr.print( "[red] Error when reading " + str(row[2]) + str(e) ) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index d3e69ddd..ba454b52 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1072,7 +1072,7 @@ "label": "Enrichment panel/assay", "fill_mode": "batch" }, - "if_amplicon_protocol_if_other_especify": { + "if_amplicon_protocol_if_other_specify": { "examples": [ "" ], @@ -1080,7 +1080,7 @@ "type": "string", "description": "", "classification": "Sequencing", - "label": "If Enrichment panel/assay Is Other, Especify", + "label": "If Enrichment panel/assay Is Other, Specify", "fill_mode": "batch" }, "amplicon_version": { From c8b13c88c5b4760b19d5403beb213e6c152aa1ff Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 12 Aug 2022 16:15:21 +0200 Subject: [PATCH 0781/1454] Rename If Enrichment Protocol Is Other,Specify by: If Enrichment Protocol Is Other, Specify --- relecov_tools/conf/configuration.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index f9ec798b..c510bc3a 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -27,7 +27,7 @@ "Commercial All-in-one library kit", "Library Preparation Kit", "Enrichment Protocol", - "If Enrichment Protocol Is Other,Specify", + "If Enrichment Protocol Is Other, Specify", "Enrichment panel/assay", "If Enrichment panel/assay Is Other, Specify", "Enrichment panel/assay version", From 681b500bb6e8ff0f0ea68be4647046bc73b02de8 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 12 Aug 2022 16:23:08 +0200 Subject: [PATCH 0782/1454] Including printed text about progress --- relecov_tools/read_lab_metadata.py | 37 ++++-------------------------- 1 file changed, 5 insertions(+), 32 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 3669d18b..8c3eb3a1 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -322,7 +322,6 @@ def read_metadata_file(self): try: sample_data_row[self.label_prop_dict[heading[idx]]] = val except TypeError as e: - import pdb; pdb.set_trace() stderr.print("[red] Error when reading " + row[2] + e) else: try: @@ -330,7 +329,6 @@ def read_metadata_file(self): row[idx] if row[idx] else "" ) except KeyError as e: - import pdb; pdb.set_trace() stderr.print( "[red] Error when reading " + str(row[2]) + str(e) ) @@ -347,19 +345,8 @@ def write_json_fo_file(self, data, file_name): return True def create_metadata_json(self): + stderr.print("[blue] Reading configuration settings") config_json = ConfigJson() - """ - schema_location = config_json.get_topic_data( - "json_schemas", "phage_plus_schema" - ) - schema_location_file = os.path.join( - os.path.dirname(os.path.realpath(__file__)), "schema", schema_location - ) - schema_json = self.read_json_file(schema_location_file) - phage_plus_schema = relecov_tools.schema_json.PhagePlusSchema(schema_json) - properties_in_schema = phage_plus_schema.get_schema_properties() - """ - geo_loc_json = config_json.get_configuration("geo_location_data") geo_loc_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "conf", geo_loc_json @@ -368,38 +355,24 @@ def create_metadata_json(self): lab_json_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "conf", lab_json ) - """ - metadata_mapping_json = config_json.get_configuration("mapping_metadata_json") - meta_map_json_file = os.path.join( - os.path.dirname(os.path.realpath(__file__)), "schema", metadata_mapping_json - ) - meta_map_json = self.read_json_file(meta_map_json_file) - """ + stderr.print("[blue] Reading Lab Metadata Excel File") valid_metadata_rows, errors = self.read_metadata_file() if len(errors) > 0: stderr.print("[red] Stopped executing because the errors found") sys.exit(1) # Continue by adding extra information - + stderr.print("[blue] Including additional information") completed_metadata = self.add_additional_data( valid_metadata_rows, lab_json_file, geo_loc_file, ) - # comp_result = self.compare_sample_in_metadata(completed_metadata) - """ - if isinstance(comp_result, list): - missing_samples = ",".join(comp_result) - log.error("Missing samples %s", missing_samples) - elif comp_result: - log.info("Samples in metadata matches with the ones uploaded") - else: - log.error("There is missing samples in metadata and/or uploaded") - """ + file_name = ( "processed_" + os.path.splitext(os.path.basename(self.metadata_file))[0] + ".json" ) + stderr.print("[blue] Creating Json file") self.write_json_fo_file(completed_metadata, file_name) return True From 1a3833183524b8036253051d844d9b532c8d82c1 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 12 Aug 2022 16:24:12 +0200 Subject: [PATCH 0783/1454] Including the extra columns and extra rows to be equal to the excel file delivered by laboratories --- relecov_tools/metadata_homogeneizer.py | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index c12ceabf..ea926f0a 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -227,8 +227,20 @@ def handling_additional_files(self, additional_data): def write_to_excel_file(self, data, f_name): book = openpyxl.Workbook() sheet = book.active + for row in data: sheet.append(row) + # adding one column with row number + sheet.insert_cols(1) + sheet["A1"] = "Campo" + counter = 1 + for i in range(len(data)): + idx = "A" + str(counter + 1) + sheet[idx] = counter + counter += 1 + # adding 3 empty rows + for x in range(3): + sheet.insert_rows(1) sheet.title = "METADATA_LAB" book.save(f_name) return @@ -244,5 +256,6 @@ def converting_metadata(self): stderr.print("[blue] reading and mapping de information that are in files") converted_data = self.handling_additional_files(additional_data) f_name = os.path.join(self.output_folder, "converted_metadata_lab.xlsx") + stderr.print("[blue] Dumping information to excel") self.write_to_excel_file(converted_data, f_name) return From 63ad99e2b77e442ef2a483c16f8d1b0dbefc8871 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 13 Aug 2022 01:12:06 +0200 Subject: [PATCH 0784/1454] fixing values Sequencing Instrument Platform, sequence_file_R1_fastq, sequence_file_R2_fastq --- relecov_tools/schema/relecov_schema.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index ba454b52..ff538aa4 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1127,7 +1127,7 @@ "label": "Runid", "fill_mode": "batch" }, - "sequencing_platforms": { + "sequencing_instrument_platform": { "examples": [ "" ], @@ -1135,7 +1135,7 @@ "type": "string", "description": "", "classification": "Sequencing", - "label": "Sequencing Platforms ", + "label": "Sequencing Instrument Platform", "fill_mode": "batch" }, "library_preparation_kit": { @@ -1457,7 +1457,7 @@ "label": "Depth of coverage threshold", "fill_mode": "batch" }, - "fastq_r1": { + "sequence_file_R1_fastq": { "examples": [ "ABC123_S1_L001_R1_001.fastq.gz" ], @@ -1468,7 +1468,7 @@ "label": "Sequence file R1 fastq", "fill_mode": "sample" }, - "fastq_r2": { + "sequence_file_R2_fastq": { "examples": [ "ABC123_S1_L001_R2_002.fastq.gz" ], From 9d810fd4b26e6747b48d8a2c851b16018c328dff Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 13 Aug 2022 01:14:18 +0200 Subject: [PATCH 0785/1454] adding progress text --- relecov_tools/feed_database.py | 29 ++++++++++++++++------------- 1 file changed, 16 insertions(+), 13 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 8d0ab188..38ed66d2 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -82,7 +82,7 @@ def __init__( if database_server is None: database_server = relecov_tools.utils.prompt_selection( "Select:", - ["iskylims", "relecov", "relecov_local"], + ["iskylims", "relecov"], ) self.server_type = database_server # Get database settings @@ -122,7 +122,7 @@ def map_iskylims_sample_fields_values(self, sample_fields, s_project_fields): elif key in s_fields: s_dict[sample_fields[key]] = value else: - print("not key in iSkyLIMS", key) + log.info("not key %s in iSkyLIMS", key) # include the fix value if self.server_type == "iskylims": fixed_value = self.config_json.get_configuration( @@ -174,7 +174,7 @@ def get_iskylims_fields_sample(self): # for the ones that do no have ontologuy label is the sample field # and the value is empty # sample_fields[key] = "" - print(values["field_name"]) + log.info("not ontology for item %s", values["field_name"]) # fetch label for sample Project s_project_url = self.database_settings["url_project_fields"] @@ -232,7 +232,10 @@ def map_relecov_bioinfo_data(self): def update_database(self, field_values, post_url): """Send the request to update database""" for chunk in field_values: - # print(chunk) + if "sample_name" in chunk: + stderr.print(f"[blue] sending request for sample {chunk['sample_name']}") + elif "sequencing_sample_id" in chunk: + stderr.print(f"[blue] sending request for sample {chunk['sequencing_sample_id']}") result = self.database_rest_api.post_request( json.dumps(chunk), {"user": self.user, "pass": self.passwd}, @@ -272,6 +275,7 @@ def update_database(self, field_values, post_url): ) else: log.info("stored data in relecov") + stderr.print(f"[gren] All information was sent sucessfuly to {self.server_type}") return def store_data(self): @@ -281,23 +285,21 @@ def store_data(self): map_fields = {} # if self.type_of_info == "sample": if self.server_type == "iskylims": + stderr.print( + f"[blue] Getting sample fields from {self.server_type}" + ) sample_fields, s_project_fields = self.get_iskylims_fields_sample() + stderr.print("[blue] Selecting sample fields") map_fields = self.map_iskylims_sample_fields_values( sample_fields, s_project_fields ) else: + stderr.print("[blue] Selecting sample fields") map_fields = self.map_relecov_sample_data() post_url = "store_samples" elif self.type_of_info == "analysis": - if self.server_type == "relecov": - print("relecov") - post_url = "analysis" - map_fields = self.map_relecov_bioinfo_data() - - elif self.server_type == "relecov_local": - print("relecov_local") - post_url = "analysis" - map_fields = self.map_relecov_bioinfo_data() + post_url = "analysis" + map_fields = self.map_relecov_bioinfo_data() elif self.type_of_info == "longtable": post_url = "long_table" @@ -305,3 +307,4 @@ def store_data(self): stderr.print("[red] Invalid type to upload to database") sys.exit(1) self.update_database(map_fields, post_url) + stderr.print(f"[green] Upload process to {self.server_type} completed") From c600bce52df2760819cb9f801a07a54a38e0b4d2 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 13 Aug 2022 10:49:44 +0200 Subject: [PATCH 0786/1454] including collecting_lab_sample_id in relecov-platform when creating a new sample instance --- relecov_tools/conf/configuration.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index c510bc3a..b27d883f 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -113,7 +113,7 @@ "url": "/wetlab/api/", "store_samples": "createSampleData", "url_project_fields": "sampleProjectFields", - "url_sample_fields": "samplefields", + "url_sample_fields": "sampleFields", "param_sample_project": "project", "project_name": "relecov", "token": "" @@ -148,6 +148,7 @@ "microbiology_lab_sample_id", "r1_fastq_filepath", "r2_fastq_filepath", + "collecting_lab_sample_id", "sequence_file_R1_fastq", "sequence_file_R2_fastq", "sequencing_sample_id", From a73702816f2795f032a7d28b0339c7f3b6d687ed Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 13 Aug 2022 13:23:34 +0200 Subject: [PATCH 0787/1454] liting --- relecov_tools/feed_database.py | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 38ed66d2..6f0fe329 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -233,9 +233,13 @@ def update_database(self, field_values, post_url): """Send the request to update database""" for chunk in field_values: if "sample_name" in chunk: - stderr.print(f"[blue] sending request for sample {chunk['sample_name']}") + stderr.print( + f"[blue] sending request for sample {chunk['sample_name']}" + ) elif "sequencing_sample_id" in chunk: - stderr.print(f"[blue] sending request for sample {chunk['sequencing_sample_id']}") + stderr.print( + f"[blue] sending request for sample {chunk['sequencing_sample_id']}" + ) result = self.database_rest_api.post_request( json.dumps(chunk), {"user": self.user, "pass": self.passwd}, @@ -275,7 +279,9 @@ def update_database(self, field_values, post_url): ) else: log.info("stored data in relecov") - stderr.print(f"[gren] All information was sent sucessfuly to {self.server_type}") + stderr.print( + f"[gren] All information was sent sucessfuly to {self.server_type}" + ) return def store_data(self): @@ -285,9 +291,7 @@ def store_data(self): map_fields = {} # if self.type_of_info == "sample": if self.server_type == "iskylims": - stderr.print( - f"[blue] Getting sample fields from {self.server_type}" - ) + stderr.print(f"[blue] Getting sample fields from {self.server_type}") sample_fields, s_project_fields = self.get_iskylims_fields_sample() stderr.print("[blue] Selecting sample fields") map_fields = self.map_iskylims_sample_fields_values( From 6a85757bef973d9400223177d09ca04178b8e6fe Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Tue, 16 Aug 2022 10:01:36 +0200 Subject: [PATCH 0788/1454] modified feed database-> insert into relecov_local testing server --- relecov_tools/conf/configuration.json | 9 +++++++++ relecov_tools/feed_database.py | 4 +--- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index ca48fa84..ef411cdc 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -126,6 +126,15 @@ "long_table": "longtableData", "sftp_info": "sftpInfo", "token": "" + }, + "relecov_local": { + "server": "127.0.0.1:8000", + "url": "/api/", + "store_samples": "createSampleData", + "analysis": "bioinfoData", + "long_table": "longtableData", + "sftp_info": "sftpInfo", + "token": "" } }, "iskylims_fixed_values": { diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 1b1b082b..f440050d 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -291,7 +291,6 @@ def store_data(self): post_url = "store_samples" elif self.type_of_info == "analysis": if self.server_type == "relecov": - print("relecov") post_url = "analysis" map_fields = self.map_relecov_bioinfo_data() @@ -305,10 +304,9 @@ def store_data(self): elif self.server_type == "relecov_local": - print("relecov_local") post_url = "analysis" map_fields = self.map_relecov_bioinfo_data() - post_url = "analysis" + # post_url = "analysis" elif self.type_of_info == "longtable": post_url = "long_table" else: From edd53f3a4a313cef366dc986955203a11ebdb9b6 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 16 Aug 2022 11:45:18 +0200 Subject: [PATCH 0789/1454] small changes in ISCCII.py --- relecov_tools/institution_scripts/ISCIII.py | 8 ++++++-- .../schema/institution_schemas/ISCIII.json | 16 ++++++++-------- 2 files changed, 14 insertions(+), 10 deletions(-) diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index 9bb8610d..0fbda91f 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -66,11 +66,15 @@ def translate_gender_to_english(metadata, f_data, mapped_fields, heading): for key, val in mapped_fields.items(): m_idx = heading.index(key) if row[m_idx] is None: - row[m_idx] = "Unknown" + row[m_idx] = "not provided" elif "hombre" in row[m_idx].lower(): row[m_idx] = "Male" elif "mujer" in row[m_idx].lower(): row[m_idx] = "Female" elif "desconocido" in row[m_idx].lower(): - row[m_idx] = "Unknown" + row[m_idx] = "not provided" + elif "Unknown" in row[m_idx].lower(): + row[m_idx] = "not provided" + elif "unknown" in row[m_idx].lower(): + row[m_idx] = "not provided" return metadata diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 748dc8fe..03c01801 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -37,7 +37,7 @@ "Diagnostic Pcr Ct Value 1": "", "Authors": "" }, - "function" : "None" + "function": "None" }, "sample_file": { "file_name": "sample_data.json", @@ -45,35 +45,35 @@ "Sequence file R1 fastq": "sequence_file_R1_fastq", "Sequence file R2 fastq": "sequence_file_R2_fastq" }, - "function":"None" + "function": "None" }, "run_id_file": { "file_name": "samples_run_services.tsv", - "mapped_fields":{ + "mapped_fields": { "Runid": "run_name" }, - "function":"None" + "function": "None" }, "org_lab_file": { "file_name": "laboratory_mapping_list.tsv", - "mapped_fields":{ + "mapped_fields": { "Originating Laboratory": "mapped_org_lab" }, "function": "replace_originating_lab" }, "sequencer_file": { "file_name": "samples_run_services.tsv", - "mapped_fields":{ + "mapped_fields": { "Sequencing Instrument Model": "run_name" }, "function": "added_seq_inst_model" }, "host_gender_file": { "file_name": "", - "mapped_fields":{ + "mapped_fields": { "Host Gender": "" }, "function": "translate_gender_to_english" } } -} +} \ No newline at end of file From 6b51d71c666a337fe5329d25aae4bad8d2dd6d23 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 16 Aug 2022 15:33:27 +0200 Subject: [PATCH 0790/1454] created templates folder --- relecov_tools/ena_upload.py | 12 +- relecov_tools/map_schema.py | 9 + relecov_tools/templates/ENA.project.xsd | 203 ++++ relecov_tools/templates/ENA_template_FILE.xml | 122 ++ .../ENA_template_LIBRARY_SELECTION.xml | 33 + .../templates/ENA_template_LIBRARY_SOURCE.xml | 11 + .../ENA_template_LIBRARY_STRATEGY.xml | 41 + .../templates/ENA_template_PLATFORM.xml | 102 ++ .../templates/ENA_template_experiments.xml | 51 + relecov_tools/templates/ENA_template_runs.xml | 36 + .../ENA_template_samples_ERC000011.xml | 216 ++++ .../ENA_template_samples_ERC000012.xml | 480 ++++++++ .../ENA_template_samples_ERC000013.xml | 566 +++++++++ .../ENA_template_samples_ERC000014.xml | 608 ++++++++++ .../ENA_template_samples_ERC000015.xml | 512 ++++++++ .../ENA_template_samples_ERC000016.xml | 506 ++++++++ .../ENA_template_samples_ERC000017.xml | 512 ++++++++ .../ENA_template_samples_ERC000018.xml | 554 +++++++++ .../ENA_template_samples_ERC000019.xml | 694 +++++++++++ .../ENA_template_samples_ERC000020.xml | 638 ++++++++++ .../ENA_template_samples_ERC000021.xml | 658 +++++++++++ .../ENA_template_samples_ERC000022.xml | 646 ++++++++++ .../ENA_template_samples_ERC000023.xml | 548 +++++++++ .../ENA_template_samples_ERC000024.xml | 798 +++++++++++++ .../ENA_template_samples_ERC000025.xml | 584 +++++++++ .../ENA_template_samples_ERC000027.xml | 802 +++++++++++++ .../ENA_template_samples_ERC000028.xml | 144 +++ .../ENA_template_samples_ERC000029.xml | 292 +++++ .../ENA_template_samples_ERC000030.xml | 184 +++ .../ENA_template_samples_ERC000031.xml | 456 +++++++ .../ENA_template_samples_ERC000032.xml | 366 ++++++ .../ENA_template_samples_ERC000033.xml | 240 ++++ .../ENA_template_samples_ERC000034.xml | 94 ++ .../ENA_template_samples_ERC000035.xml | 240 ++++ .../ENA_template_samples_ERC000036.xml | 172 +++ .../ENA_template_samples_ERC000037.xml | 620 ++++++++++ .../ENA_template_samples_ERC000038.xml | 174 +++ .../ENA_template_samples_ERC000039.xml | 194 +++ .../ENA_template_samples_ERC000040.xml | 140 +++ .../ENA_template_samples_ERC000041.xml | 172 +++ .../ENA_template_samples_ERC000043.xml | 154 +++ .../ENA_template_samples_ERC000044.xml | 128 ++ .../ENA_template_samples_ERC000045.xml | 78 ++ .../ENA_template_samples_ERC000047.xml | 342 ++++++ .../ENA_template_samples_ERC000048.xml | 346 ++++++ .../ENA_template_samples_ERC000049.xml | 420 +++++++ .../ENA_template_samples_ERC000050.xml | 322 +++++ .../ENA_template_samples_ERC000051.xml | 98 ++ .../ENA_template_samples_ERC000052.xml | 226 ++++ .../ENA_template_samples_ERC000053.xml | 204 ++++ .../templates/ENA_template_studies.xml | 49 + .../templates/ENA_template_submission.xml | 36 + relecov_tools/templates/SRA.common.xsd | 1044 +++++++++++++++++ relecov_tools/templates/SRA.experiment.xsd | 791 +++++++++++++ relecov_tools/templates/SRA.run.xsd | 548 +++++++++ relecov_tools/templates/SRA.sample.xsd | 127 ++ relecov_tools/templates/SRA.study.xsd | 290 +++++ relecov_tools/templates/SRA.submission.xsd | 354 ++++++ 58 files changed, 18986 insertions(+), 1 deletion(-) create mode 100644 relecov_tools/templates/ENA.project.xsd create mode 100644 relecov_tools/templates/ENA_template_FILE.xml create mode 100644 relecov_tools/templates/ENA_template_LIBRARY_SELECTION.xml create mode 100644 relecov_tools/templates/ENA_template_LIBRARY_SOURCE.xml create mode 100644 relecov_tools/templates/ENA_template_LIBRARY_STRATEGY.xml create mode 100644 relecov_tools/templates/ENA_template_PLATFORM.xml create mode 100755 relecov_tools/templates/ENA_template_experiments.xml create mode 100755 relecov_tools/templates/ENA_template_runs.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000011.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000012.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000013.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000014.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000015.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000016.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000017.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000018.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000019.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000020.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000021.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000022.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000023.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000024.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000025.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000027.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000028.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000029.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000030.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000031.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000032.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000033.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000034.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000035.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000036.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000037.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000038.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000039.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000040.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000041.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000043.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000044.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000045.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000047.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000048.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000049.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000050.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000051.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000052.xml create mode 100644 relecov_tools/templates/ENA_template_samples_ERC000053.xml create mode 100755 relecov_tools/templates/ENA_template_studies.xml create mode 100644 relecov_tools/templates/ENA_template_submission.xml create mode 100644 relecov_tools/templates/SRA.common.xsd create mode 100644 relecov_tools/templates/SRA.experiment.xsd create mode 100644 relecov_tools/templates/SRA.run.xsd create mode 100644 relecov_tools/templates/SRA.sample.xsd create mode 100644 relecov_tools/templates/SRA.study.xsd create mode 100644 relecov_tools/templates/SRA.submission.xsd diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 9ac8cc07..472934a3 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,4 +1,5 @@ import logging +from re import template # from pyparsing import col import xml.etree.ElementTree as ET @@ -34,7 +35,7 @@ pd.options.mode.chained_assignment = None template_path = os.path.join(site.getsitepackages()[0], "ena_upload", "templates") - +template_path = os.path.join(os.getcwd(), "relecov_tools/templates") log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -161,7 +162,9 @@ def create_structure_to_ena(self): "isolate", "host_subject_id", "host health state", + "authors", "sample_description", + "address", ] ] @@ -210,6 +213,7 @@ def create_structure_to_ena(self): "file_type", "fastq_r1_md5", "fastq_r2_md5", + "collecting_institution", ] ] @@ -267,6 +271,7 @@ def create_structure_to_ena(self): "library_layout", "instrument_model", "design_description", + "collecting_institution", "insert_size", "sequencing_instrument_platform", ] @@ -293,6 +298,9 @@ def create_structure_to_ena(self): ) df_experiments = df_experiments.rename(columns={"study_title": "title"}) df_experiments = df_experiments.rename(columns={"sample_name": "sample_alias"}) + df_experiments = df_experiments.rename( + columns={"collecting_institution": "collecting institution"} + ) # df_experiments example """ @@ -389,6 +397,7 @@ def create_structure_to_ena(self): tree = ET.parse(schema_xmls["sample"]) root = tree.getroot() + """ for files in root.iter("SAMPLE_ATTRIBUTES"): tag = ET.SubElement(files, "SAMPLE_ATTRIBUTE") @@ -398,6 +407,7 @@ def create_structure_to_ena(self): tag_3.text = str("ERC000033") tree.write(schema_xmls["sample"]) + """ if self.dev: url = "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 76b371db..fe5623f8 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -240,9 +240,18 @@ def additional_formating(self, mapped_json_data): ] mapped_json_data[idx]["host health state"] = "not provided" + mapped_json_data[idx]["center_name"] = mapped_json_data[idx][ + "collecting_institution" + ] + mapped_json_data[idx]["authors"] = self.json_data[idx]["authors"] mapped_json_data[idx]["sample_description"] = "" mapped_json_data[idx]["design_description"] = "" mapped_json_data[idx]["insert_size"] = "0" + mapped_json_data[idx]["address"] = ( + self.json_data[idx]["geo_loc_city"] + + ", " + + self.json_data[idx]["geo_loc_country"] + ) return mapped_json_data diff --git a/relecov_tools/templates/ENA.project.xsd b/relecov_tools/templates/ENA.project.xsd new file mode 100644 index 00000000..18294fa8 --- /dev/null +++ b/relecov_tools/templates/ENA.project.xsd @@ -0,0 +1,203 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A short name of the project. + + + + + A short descriptive title for the project. + + + + + + A long description of the scope of the project. + + + + + + + + + + + + + + A project for grouping submitted data together. + + + + + + + + + + + + + + + + + + + + + A project for grouping other projects together. + + + + + + + + + + + + + Other projects related to this project. + + + + + + + + + + + Identifies the project using + an accession number. + + + + + + + + + Identifies the project using + an accession number. + + + + + + + + + Identifies the project using + an accession number. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/relecov_tools/templates/ENA_template_FILE.xml b/relecov_tools/templates/ENA_template_FILE.xml new file mode 100644 index 00000000..424d83e6 --- /dev/null +++ b/relecov_tools/templates/ENA_template_FILE.xml @@ -0,0 +1,122 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_LIBRARY_SELECTION.xml b/relecov_tools/templates/ENA_template_LIBRARY_SELECTION.xml new file mode 100644 index 00000000..ea6d6cda --- /dev/null +++ b/relecov_tools/templates/ENA_template_LIBRARY_SELECTION.xml @@ -0,0 +1,33 @@ + +RANDOM +PCR +RANDOM PCR +RT-PCR +HMPR +MF +repeat fractionation +size fractionation +MSLL +cDNA +cDNA_randomPriming +cDNA_oligo_dT +PolyA +Oligo-dT +Inverse rRNA +Inverse rRNA selection +ChIP +ChIP-Seq +MNase +DNase +Hybrid Selection +Reduced Representation +Restriction Digest +5-methylcytidine antibody +MBD2 protein methyl-CpG binding domain +CAGE +RACE +MDA +padlock probes capture method +other +unspecified + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_LIBRARY_SOURCE.xml b/relecov_tools/templates/ENA_template_LIBRARY_SOURCE.xml new file mode 100644 index 00000000..95689332 --- /dev/null +++ b/relecov_tools/templates/ENA_template_LIBRARY_SOURCE.xml @@ -0,0 +1,11 @@ + +GENOMIC +GENOMIC SINGLE CELL +TRANSCRIPTOMIC +TRANSCRIPTOMIC SINGLE CELL +METAGENOMIC +METATRANSCRIPTOMIC +SYNTHETIC +VIRAL RNA +OTHER + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_LIBRARY_STRATEGY.xml b/relecov_tools/templates/ENA_template_LIBRARY_STRATEGY.xml new file mode 100644 index 00000000..afb46af2 --- /dev/null +++ b/relecov_tools/templates/ENA_template_LIBRARY_STRATEGY.xml @@ -0,0 +1,41 @@ + +WGS +WGA +WXS +RNA-Seq +ssRNA-seq +miRNA-Seq +ncRNA-Seq +FL-cDNA +EST +Hi-C +ATAC-seq +WCS +RAD-Seq +CLONE +POOLCLONE +AMPLICON +CLONEEND +FINISHING +ChIP-Seq +MNase-Seq +DNase-Hypersensitivity +Bisulfite-Seq +CTS +MRE-Seq +MeDIP-Seq +MBD-Seq +Tn-Seq +VALIDATION +FAIRE-seq +SELEX +RIP-Seq +ChIA-PET +Synthetic-Long-Read +Targeted-Capture +Tethered Chromatin Conformation Capture +NOMe-Seq +ChM-Seq +GBS +OTHER + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_PLATFORM.xml b/relecov_tools/templates/ENA_template_PLATFORM.xml new file mode 100644 index 00000000..4e514c5e --- /dev/null +++ b/relecov_tools/templates/ENA_template_PLATFORM.xml @@ -0,0 +1,102 @@ + + + 454 GS + 454 GS 20 + 454 GS FLX + 454 GS FLX+ + 454 GS FLX Titanium + 454 GS Junior + unspecified + + + HiSeq X Five + HiSeq X Ten + Illumina Genome Analyzer + Illumina Genome Analyzer II + Illumina Genome Analyzer IIx + Illumina HiScanSQ + Illumina HiSeq 1000 + Illumina HiSeq 1500 + Illumina HiSeq 2000 + Illumina HiSeq 2500 + Illumina HiSeq 3000 + Illumina HiSeq 4000 + Illumina HiSeq X + Illumina iSeq 100 + Illumina MiSeq + Illumina MiniSeq + Illumina NovaSeq 6000 + NextSeq 500 + NextSeq 550 + NextSeq 1000 + NextSeq 2000 + unspecified + + + Helicos HeliScope + unspecified + + + AB SOLiD System + AB SOLiD System 2.0 + AB SOLiD System 3.0 + AB SOLiD 3 Plus System + AB SOLiD 4 System + AB SOLiD 4hq System + AB SOLiD PI System + AB 5500 Genetic Analyzer + AB 5500xl Genetic Analyzer + AB 5500xl-W Genetic Analysis System + unspecified + + + Complete Genomics + unspecified + + + BGISEQ-50 + BGISEQ-500 + MGISEQ-2000RS + + + MinION + GridION + PromethION + unspecified + + + PacBio RS + PacBio RS II + Sequel + Sequel II + unspecified + + + Ion Torrent PGM + Ion Torrent Proton + Ion Torrent S5 + Ion Torrent S5 XL + Ion Torrent Genexus + Ion GeneStudio S5 + Ion GeneStudio S5 Prime + Ion GeneStudio S5 Plus + unspecified + + + AB 3730xL Genetic Analyzer + AB 3730 Genetic Analyzer + AB 3500xL Genetic Analyzer + AB 3500 Genetic Analyzer + AB 3130xL Genetic Analyzer + AB 3130 Genetic Analyzer + AB 310 Genetic Analyzer + unspecified + + + DNBSEQ-T7 + DNBSEQ-G400 + DNBSEQ-G50 + DNBSEQ-G400 FAST + unspecified + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_experiments.xml b/relecov_tools/templates/ENA_template_experiments.xml new file mode 100755 index 00000000..87fe6359 --- /dev/null +++ b/relecov_tools/templates/ENA_template_experiments.xml @@ -0,0 +1,51 @@ + + + + + + ${row.title} + + + ${row.design_description} + + ${row.spot_descriptor} + + + + ${row.library_name} + + + + + + + + + ${row.library_construction_protocol} + + + + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + diff --git a/relecov_tools/templates/ENA_template_runs.xml b/relecov_tools/templates/ENA_template_runs.xml new file mode 100755 index 00000000..b8f8cc0f --- /dev/null +++ b/relecov_tools/templates/ENA_template_runs.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + diff --git a/relecov_tools/templates/ENA_template_samples_ERC000011.xml b/relecov_tools/templates/ENA_template_samples_ERC000011.xml new file mode 100644 index 00000000..46cc304c --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000011.xml @@ -0,0 +1,216 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + + cell_type + ${row['cell_type']} + + + + + dev_stage + ${row['dev_stage']} + + + + + germline + ${row['germline']} + + + + + tissue_lib + ${row['tissue_lib']} + + + + + tissue_type + ${row['tissue_type']} + + + + + collection_date + ${row['collection_date']} + + + + + isolation_source + ${row['isolation_source']} + + + + + lat_lon + ${row['lat_lon']} + + + + + collected_by + ${row['collected_by']} + + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + identified_by + ${row['identified_by']} + + + + + environmental_sample + ${row['environmental_sample']} + + + + + mating_type + ${row['mating_type']} + + + + + sex + ${row['sex']} + + + + + lab_host + ${row['lab_host']} + + + + + host scientific name + ${row['host scientific name']} + + + + + bio_material + ${row['bio_material']} + + + + + culture_collection + ${row['culture_collection']} + + + + + specimen_voucher + ${row['specimen_voucher']} + + + + + cultivar + ${row['cultivar']} + + + + + ecotype + ${row['ecotype']} + + + + + isolate + ${row['isolate']} + + + + + sub_species + ${row['sub_species']} + + + + + variety + ${row['variety']} + + + + + sub_strain + ${row['sub_strain']} + + + + + cell_line + ${row['cell_line']} + + + + + serotype + ${row['serotype']} + + + + + serovar + ${row['serovar']} + + + + + strain + ${row['strain']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000012.xml b/relecov_tools/templates/ENA_template_samples_ERC000012.xml new file mode 100644 index 00000000..b0353355 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000012.xml @@ -0,0 +1,480 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + finishing strategy + ${row['finishing strategy']} + + + + + annotation source + ${row['annotation source']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library construction method + ${row['library construction method']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + pcr primers + ${row['pcr primers']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + sequencing method + ${row['sequencing method']} + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check + ${row['chimera check']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + investigation type + ${row['investigation type']} + + + collection date + ${row['collection date']} + + + geographic location (altitude) + ${row['geographic location (altitude)']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + air environmental package + ${row['air environmental package']} + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + + geographic location (elevation) + ${row['geographic location (elevation)']} + + + + + ventilation rate + ${row['ventilation rate']} + + + + + ventilation type + ${row['ventilation type']} + + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + propagation + ${row['propagation']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + oxygenation status of sample + ${row['oxygenation status of sample']} + + + + + organism count + ${row['organism count']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + sample storage location + ${row['sample storage location']} + + + + + specific host + ${row['specific host']} + + + + + health or disease status of specific host + ${row['health or disease status of specific host']} + + + + + barometric pressure + ${row['barometric pressure']} + + + + + humidity + ${row['humidity']} + + + + + pollutants + ${row['pollutants']} + + + + + solar irradiance + ${row['solar irradiance']} + + + + + wind direction + ${row['wind direction']} + + + + + wind speed + ${row['wind speed']} + + + + + temperature + ${row['temperature']} + + + + + carbon dioxide + ${row['carbon dioxide']} + + + + + carbon monoxide + ${row['carbon monoxide']} + + + + + oxygen + ${row['oxygen']} + + + + + respirable particulate matter + ${row['respirable particulate matter']} + + + + + volatile organic compounds + ${row['volatile organic compounds']} + + + + + sample salinity + ${row['sample salinity']} + + + + + methane + ${row['methane']} + + + + + miscellaneous parameter + ${row['miscellaneous parameter']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + trophic level + ${row['trophic level']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + encoded traits + ${row['encoded traits']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + chemical administration + ${row['chemical administration']} + + + + + perturbation + ${row['perturbation']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000013.xml b/relecov_tools/templates/ENA_template_samples_ERC000013.xml new file mode 100644 index 00000000..89ab78d7 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000013.xml @@ -0,0 +1,566 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + finishing strategy + ${row['finishing strategy']} + + + + + annotation source + ${row['annotation source']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library construction method + ${row['library construction method']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + pcr primers + ${row['pcr primers']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + sequencing method + ${row['sequencing method']} + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check + ${row['chimera check']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + investigation type + ${row['investigation type']} + + + collection date + ${row['collection date']} + + + + geographic location (altitude) + ${row['geographic location (altitude)']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + host-associated environmental package + ${row['host-associated environmental package']} + + + + geographic location (depth) + ${row['geographic location (depth)']} + + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + + geographic location (elevation) + ${row['geographic location (elevation)']} + + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + propagation + ${row['propagation']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + host body product + ${row['host body product']} + + + + + host dry mass + ${row['host dry mass']} + + + + + oxygenation status of sample + ${row['oxygenation status of sample']} + + + + + organism count + ${row['organism count']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + sample storage location + ${row['sample storage location']} + + + + + host disease status + ${row['host disease status']} + + + + + host common name + ${row['host common name']} + + + + + host subject id + ${row['host subject id']} + + + + + host age + ${row['host age']} + + + + + host taxid + ${row['host taxid']} + + + + + host body habitat + ${row['host body habitat']} + + + + + host body site + ${row['host body site']} + + + + + host life stage + ${row['host life stage']} + + + + + host height + ${row['host height']} + + + + + host length + ${row['host length']} + + + + + host growth conditions + ${row['host growth conditions']} + + + + + host substrate + ${row['host substrate']} + + + + + host total mass + ${row['host total mass']} + + + + + host infra-specific name + ${row['host infra-specific name']} + + + + + host infra-specific rank + ${row['host infra-specific rank']} + + + + + host phenotype + ${row['host phenotype']} + + + + + host body temperature + ${row['host body temperature']} + + + + + host color + ${row['host color']} + + + + + host shape + ${row['host shape']} + + + + + host sex + ${row['host sex']} + + + + + temperature + ${row['temperature']} + + + + + sample salinity + ${row['sample salinity']} + + + + + miscellaneous parameter + ${row['miscellaneous parameter']} + + + + + host blood pressure diastolic + ${row['host blood pressure diastolic']} + + + + + host blood pressure systolic + ${row['host blood pressure systolic']} + + + + + host diet + ${row['host diet']} + + + + + host last meal + ${row['host last meal']} + + + + + host family relationship + ${row['host family relationship']} + + + + + host genotype + ${row['host genotype']} + + + + + gravidity + ${row['gravidity']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + trophic level + ${row['trophic level']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + encoded traits + ${row['encoded traits']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + chemical administration + ${row['chemical administration']} + + + + + perturbation + ${row['perturbation']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000014.xml b/relecov_tools/templates/ENA_template_samples_ERC000014.xml new file mode 100644 index 00000000..a8a9f475 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000014.xml @@ -0,0 +1,608 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + finishing strategy + ${row['finishing strategy']} + + + + + annotation source + ${row['annotation source']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library construction method + ${row['library construction method']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + pcr primers + ${row['pcr primers']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + sequencing method + ${row['sequencing method']} + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check + ${row['chimera check']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + + study completion status + ${row['study completion status']} + + + + investigation type + ${row['investigation type']} + + + collection date + ${row['collection date']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + human-associated environmental package + ${row['human-associated environmental package']} + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + propagation + ${row['propagation']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + host body product + ${row['host body product']} + + + + + medical history performed + ${row['medical history performed']} + + + + + urine/collection method + ${row['urine/collection method']} + + + + + oxygenation status of sample + ${row['oxygenation status of sample']} + + + + + organism count + ${row['organism count']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + sample storage location + ${row['sample storage location']} + + + + + host HIV status + ${row['host HIV status']} + + + + + host disease status + ${row['host disease status']} + + + + + lung/pulmonary disorder + ${row['lung/pulmonary disorder']} + + + + + lung/nose-throat disorder + ${row['lung/nose-throat disorder']} + + + + + blood/blood disorder + ${row['blood/blood disorder']} + + + + + urine/kidney disorder + ${row['urine/kidney disorder']} + + + + + urine/urogenital tract disorder + ${row['urine/urogenital tract disorder']} + + + + + host subject id + ${row['host subject id']} + + + + + IHMC medication code + ${row['IHMC medication code']} + + + + + host age + ${row['host age']} + + + + + host body site + ${row['host body site']} + + + + + drug usage + ${row['drug usage']} + + + + + host height + ${row['host height']} + + + + + host body-mass index + ${row['host body-mass index']} + + + + + IHMC ethnicity + ${row['IHMC ethnicity']} + + + + + host occupation + ${row['host occupation']} + + + + + host total mass + ${row['host total mass']} + + + + + host phenotype + ${row['host phenotype']} + + + + + host body temperature + ${row['host body temperature']} + + + + + host sex + ${row['host sex']} + + + + + presence of pets or farm animals + ${row['presence of pets or farm animals']} + + + + + temperature + ${row['temperature']} + + + + + sample salinity + ${row['sample salinity']} + + + + + miscellaneous parameter + ${row['miscellaneous parameter']} + + + + + smoker + ${row['smoker']} + + + + + major diet change in last six months + ${row['major diet change in last six months']} + + + + + weight loss in last three months + ${row['weight loss in last three months']} + + + + + travel outside the country in last six months + ${row['travel outside the country in last six months']} + + + + + host diet + ${row['host diet']} + + + + + twin sibling presence + ${row['twin sibling presence']} + + + + + host last meal + ${row['host last meal']} + + + + + amniotic fluid/gestation state + ${row['amniotic fluid/gestation state']} + + + + + host family relationship + ${row['host family relationship']} + + + + + amniotic fluid/maternal health status + ${row['amniotic fluid/maternal health status']} + + + + + host genotype + ${row['host genotype']} + + + + + amniotic fluid/foetal health status + ${row['amniotic fluid/foetal health status']} + + + + + host pulse + ${row['host pulse']} + + + + + amniotic fluid/color + ${row['amniotic fluid/color']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + trophic level + ${row['trophic level']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + encoded traits + ${row['encoded traits']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + chemical administration + ${row['chemical administration']} + + + + + perturbation + ${row['perturbation']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000015.xml b/relecov_tools/templates/ENA_template_samples_ERC000015.xml new file mode 100644 index 00000000..527a756b --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000015.xml @@ -0,0 +1,512 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + finishing strategy + ${row['finishing strategy']} + + + + + annotation source + ${row['annotation source']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library construction method + ${row['library construction method']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + pcr primers + ${row['pcr primers']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + sequencing method + ${row['sequencing method']} + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check + ${row['chimera check']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + investigation type + ${row['investigation type']} + + + collection date + ${row['collection date']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + human gut environmental package + ${row['human gut environmental package']} + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + propagation + ${row['propagation']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + host body product + ${row['host body product']} + + + + + medical history performed + ${row['medical history performed']} + + + + + oxygenation status of sample + ${row['oxygenation status of sample']} + + + + + organism count + ${row['organism count']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + sample storage location + ${row['sample storage location']} + + + + + gastrointestinal tract disorder + ${row['gastrointestinal tract disorder']} + + + + + liver disorder + ${row['liver disorder']} + + + + + host disease status + ${row['host disease status']} + + + + + host subject id + ${row['host subject id']} + + + + + IHMC medication code + ${row['IHMC medication code']} + + + + + host age + ${row['host age']} + + + + + host body site + ${row['host body site']} + + + + + host height + ${row['host height']} + + + + + host body-mass index + ${row['host body-mass index']} + + + + + IHMC ethnicity + ${row['IHMC ethnicity']} + + + + + host occupation + ${row['host occupation']} + + + + + host total mass + ${row['host total mass']} + + + + + host phenotype + ${row['host phenotype']} + + + + + host body temperature + ${row['host body temperature']} + + + + + host sex + ${row['host sex']} + + + + + temperature + ${row['temperature']} + + + + + sample salinity + ${row['sample salinity']} + + + + + miscellaneous parameter + ${row['miscellaneous parameter']} + + + + + special diet + ${row['special diet']} + + + + + host diet + ${row['host diet']} + + + + + host last meal + ${row['host last meal']} + + + + + host family relationship + ${row['host family relationship']} + + + + + host genotype + ${row['host genotype']} + + + + + host pulse + ${row['host pulse']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + trophic level + ${row['trophic level']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + encoded traits + ${row['encoded traits']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + chemical administration + ${row['chemical administration']} + + + + + perturbation + ${row['perturbation']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000016.xml b/relecov_tools/templates/ENA_template_samples_ERC000016.xml new file mode 100644 index 00000000..9e3f1e74 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000016.xml @@ -0,0 +1,506 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + finishing strategy + ${row['finishing strategy']} + + + + + annotation source + ${row['annotation source']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library construction method + ${row['library construction method']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + pcr primers + ${row['pcr primers']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + sequencing method + ${row['sequencing method']} + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check + ${row['chimera check']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + investigation type + ${row['investigation type']} + + + collection date + ${row['collection date']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + human oral environmental package + ${row['human oral environmental package']} + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + propagation + ${row['propagation']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + host body product + ${row['host body product']} + + + + + medical history performed + ${row['medical history performed']} + + + + + oxygenation status of sample + ${row['oxygenation status of sample']} + + + + + organism count + ${row['organism count']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + sample storage location + ${row['sample storage location']} + + + + + nose/mouth/teeth/throat disorder + ${row['nose/mouth/teeth/throat disorder']} + + + + + host disease status + ${row['host disease status']} + + + + + host subject id + ${row['host subject id']} + + + + + IHMC medication code + ${row['IHMC medication code']} + + + + + host age + ${row['host age']} + + + + + host body site + ${row['host body site']} + + + + + host height + ${row['host height']} + + + + + host body-mass index + ${row['host body-mass index']} + + + + + IHMC ethnicity + ${row['IHMC ethnicity']} + + + + + host occupation + ${row['host occupation']} + + + + + host total mass + ${row['host total mass']} + + + + + host phenotype + ${row['host phenotype']} + + + + + host body temperature + ${row['host body temperature']} + + + + + host sex + ${row['host sex']} + + + + + temperature + ${row['temperature']} + + + + + sample salinity + ${row['sample salinity']} + + + + + miscellaneous parameter + ${row['miscellaneous parameter']} + + + + + time since last toothbrushing + ${row['time since last toothbrushing']} + + + + + host diet + ${row['host diet']} + + + + + host last meal + ${row['host last meal']} + + + + + host family relationship + ${row['host family relationship']} + + + + + host genotype + ${row['host genotype']} + + + + + host pulse + ${row['host pulse']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + trophic level + ${row['trophic level']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + encoded traits + ${row['encoded traits']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + chemical administration + ${row['chemical administration']} + + + + + perturbation + ${row['perturbation']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000017.xml b/relecov_tools/templates/ENA_template_samples_ERC000017.xml new file mode 100644 index 00000000..93098334 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000017.xml @@ -0,0 +1,512 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + finishing strategy + ${row['finishing strategy']} + + + + + annotation source + ${row['annotation source']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library construction method + ${row['library construction method']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + pcr primers + ${row['pcr primers']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + sequencing method + ${row['sequencing method']} + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check + ${row['chimera check']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + investigation type + ${row['investigation type']} + + + collection date + ${row['collection date']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + human skin environmental package + ${row['human skin environmental package']} + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + propagation + ${row['propagation']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + host body product + ${row['host body product']} + + + + + medical history performed + ${row['medical history performed']} + + + + + oxygenation status of sample + ${row['oxygenation status of sample']} + + + + + organism count + ${row['organism count']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + sample storage location + ${row['sample storage location']} + + + + + dermatology disorder + ${row['dermatology disorder']} + + + + + host disease status + ${row['host disease status']} + + + + + host subject id + ${row['host subject id']} + + + + + IHMC medication code + ${row['IHMC medication code']} + + + + + host age + ${row['host age']} + + + + + host body site + ${row['host body site']} + + + + + host height + ${row['host height']} + + + + + host body-mass index + ${row['host body-mass index']} + + + + + IHMC ethnicity + ${row['IHMC ethnicity']} + + + + + host occupation + ${row['host occupation']} + + + + + host total mass + ${row['host total mass']} + + + + + host phenotype + ${row['host phenotype']} + + + + + host body temperature + ${row['host body temperature']} + + + + + host sex + ${row['host sex']} + + + + + temperature + ${row['temperature']} + + + + + sample salinity + ${row['sample salinity']} + + + + + miscellaneous parameter + ${row['miscellaneous parameter']} + + + + + time since last wash + ${row['time since last wash']} + + + + + dominant hand + ${row['dominant hand']} + + + + + host diet + ${row['host diet']} + + + + + host last meal + ${row['host last meal']} + + + + + host family relationship + ${row['host family relationship']} + + + + + host genotype + ${row['host genotype']} + + + + + host pulse + ${row['host pulse']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + trophic level + ${row['trophic level']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + encoded traits + ${row['encoded traits']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + chemical administration + ${row['chemical administration']} + + + + + perturbation + ${row['perturbation']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000018.xml b/relecov_tools/templates/ENA_template_samples_ERC000018.xml new file mode 100644 index 00000000..c30042b8 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000018.xml @@ -0,0 +1,554 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + finishing strategy + ${row['finishing strategy']} + + + + + annotation source + ${row['annotation source']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library construction method + ${row['library construction method']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + pcr primers + ${row['pcr primers']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + sequencing method + ${row['sequencing method']} + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check + ${row['chimera check']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + investigation type + ${row['investigation type']} + + + collection date + ${row['collection date']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + human vaginal environmental package + ${row['human vaginal environmental package']} + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + propagation + ${row['propagation']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + host body product + ${row['host body product']} + + + + + medical history performed + ${row['medical history performed']} + + + + + oxygenation status of sample + ${row['oxygenation status of sample']} + + + + + organism count + ${row['organism count']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + sample storage location + ${row['sample storage location']} + + + + + gynecological disorder + ${row['gynecological disorder']} + + + + + urogenital disorder + ${row['urogenital disorder']} + + + + + host disease status + ${row['host disease status']} + + + + + host subject id + ${row['host subject id']} + + + + + IHMC medication code + ${row['IHMC medication code']} + + + + + host age + ${row['host age']} + + + + + host body site + ${row['host body site']} + + + + + host height + ${row['host height']} + + + + + host body-mass index + ${row['host body-mass index']} + + + + + IHMC ethnicity + ${row['IHMC ethnicity']} + + + + + host occupation + ${row['host occupation']} + + + + + host total mass + ${row['host total mass']} + + + + + host phenotype + ${row['host phenotype']} + + + + + host body temperature + ${row['host body temperature']} + + + + + host sex + ${row['host sex']} + + + + + temperature + ${row['temperature']} + + + + + sample salinity + ${row['sample salinity']} + + + + + miscellaneous parameter + ${row['miscellaneous parameter']} + + + + + menarche + ${row['menarche']} + + + + + sexual activity + ${row['sexual activity']} + + + + + pregnancy + ${row['pregnancy']} + + + + + douche + ${row['douche']} + + + + + birth control + ${row['birth control']} + + + + + menopause + ${row['menopause']} + + + + + HRT + ${row['HRT']} + + + + + hysterectomy + ${row['hysterectomy']} + + + + + host diet + ${row['host diet']} + + + + + host last meal + ${row['host last meal']} + + + + + host family relationship + ${row['host family relationship']} + + + + + host genotype + ${row['host genotype']} + + + + + host pulse + ${row['host pulse']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + trophic level + ${row['trophic level']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + encoded traits + ${row['encoded traits']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + chemical administration + ${row['chemical administration']} + + + + + perturbation + ${row['perturbation']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000019.xml b/relecov_tools/templates/ENA_template_samples_ERC000019.xml new file mode 100644 index 00000000..8af01c6e --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000019.xml @@ -0,0 +1,694 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + finishing strategy + ${row['finishing strategy']} + + + + + annotation source + ${row['annotation source']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library construction method + ${row['library construction method']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + pcr primers + ${row['pcr primers']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + sequencing method + ${row['sequencing method']} + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check + ${row['chimera check']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + investigation type + ${row['investigation type']} + + + collection date + ${row['collection date']} + + + + geographic location (altitude) + ${row['geographic location (altitude)']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + microbial mat/biofilm environmental package + ${row['microbial mat/biofilm environmental package']} + + + geographic location (depth) + ${row['geographic location (depth)']} + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + geographic location (elevation) + ${row['geographic location (elevation)']} + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + propagation + ${row['propagation']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + biomass + ${row['biomass']} + + + + + oxygenation status of sample + ${row['oxygenation status of sample']} + + + + + organism count + ${row['organism count']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + sample storage location + ${row['sample storage location']} + + + + + specific host + ${row['specific host']} + + + + + health or disease status of specific host + ${row['health or disease status of specific host']} + + + + + alkalinity + ${row['alkalinity']} + + + + + mean friction velocity + ${row['mean friction velocity']} + + + + + mean peak friction velocity + ${row['mean peak friction velocity']} + + + + + pressure + ${row['pressure']} + + + + + temperature + ${row['temperature']} + + + + + turbidity + ${row['turbidity']} + + + + + pH + ${row['pH']} + + + + + alkyl diethers + ${row['alkyl diethers']} + + + + + aminopeptidase activity + ${row['aminopeptidase activity']} + + + + + ammonium + ${row['ammonium']} + + + + + bacterial carbon production + ${row['bacterial carbon production']} + + + + + bishomohopanol + ${row['bishomohopanol']} + + + + + bromide + ${row['bromide']} + + + + + calcium + ${row['calcium']} + + + + + carbon/nitrogen ratio + ${row['carbon/nitrogen ratio']} + + + + + chloride + ${row['chloride']} + + + + + chlorophyll + ${row['chlorophyll']} + + + + + diether lipids + ${row['diether lipids']} + + + + + dissolved carbon dioxide + ${row['dissolved carbon dioxide']} + + + + + dissolved hydrogen + ${row['dissolved hydrogen']} + + + + + dissolved inorganic carbon + ${row['dissolved inorganic carbon']} + + + + + dissolved organic carbon + ${row['dissolved organic carbon']} + + + + + dissolved organic nitrogen + ${row['dissolved organic nitrogen']} + + + + + methane + ${row['methane']} + + + + + dissolved oxygen + ${row['dissolved oxygen']} + + + + + glucosidase activity + ${row['glucosidase activity']} + + + + + magnesium + ${row['magnesium']} + + + + + n-alkanes + ${row['n-alkanes']} + + + + + nitrate + ${row['nitrate']} + + + + + nitrite + ${row['nitrite']} + + + + + nitrogen + ${row['nitrogen']} + + + + + organic carbon + ${row['organic carbon']} + + + + + organic matter + ${row['organic matter']} + + + + + organic nitrogen + ${row['organic nitrogen']} + + + + + particulate organic carbon + ${row['particulate organic carbon']} + + + + + petroleum hydrocarbon + ${row['petroleum hydrocarbon']} + + + + + phaeopigments + ${row['phaeopigments']} + + + + + phosphate + ${row['phosphate']} + + + + + phospholipid fatty acid + ${row['phospholipid fatty acid']} + + + + + potassium + ${row['potassium']} + + + + + redox potential + ${row['redox potential']} + + + + + salinity + ${row['salinity']} + + + + + total carbon + ${row['total carbon']} + + + + + silicate + ${row['silicate']} + + + + + sodium + ${row['sodium']} + + + + + total organic carbon + ${row['total organic carbon']} + + + + + water content + ${row['water content']} + + + + + sulfate + ${row['sulfate']} + + + + + sulfide + ${row['sulfide']} + + + + + total nitrogen + ${row['total nitrogen']} + + + + + miscellaneous parameter + ${row['miscellaneous parameter']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + trophic level + ${row['trophic level']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + encoded traits + ${row['encoded traits']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + chemical administration + ${row['chemical administration']} + + + + + perturbation + ${row['perturbation']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000020.xml b/relecov_tools/templates/ENA_template_samples_ERC000020.xml new file mode 100644 index 00000000..d26699db --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000020.xml @@ -0,0 +1,638 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + finishing strategy + ${row['finishing strategy']} + + + + + annotation source + ${row['annotation source']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library construction method + ${row['library construction method']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + pcr primers + ${row['pcr primers']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + sequencing method + ${row['sequencing method']} + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check + ${row['chimera check']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + investigation type + ${row['investigation type']} + + + collection date + ${row['collection date']} + + + + geographic location (altitude) + ${row['geographic location (altitude)']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + plant-associated environmental package + ${row['plant-associated environmental package']} + + + + geographic location (depth) + ${row['geographic location (depth)']} + + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + + geographic location (elevation) + ${row['geographic location (elevation)']} + + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + propagation + ${row['propagation']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + host dry mass + ${row['host dry mass']} + + + + + oxygenation status of sample + ${row['oxygenation status of sample']} + + + + + plant product + ${row['plant product']} + + + + + organism count + ${row['organism count']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + host wet mass + ${row['host wet mass']} + + + + + sample storage location + ${row['sample storage location']} + + + + + host disease status + ${row['host disease status']} + + + + + host common name + ${row['host common name']} + + + + + host age + ${row['host age']} + + + + + host taxid + ${row['host taxid']} + + + + + host life stage + ${row['host life stage']} + + + + + host height + ${row['host height']} + + + + + host length + ${row['host length']} + + + + + plant body site + ${row['plant body site']} + + + + + host total mass + ${row['host total mass']} + + + + + host infra-specific name + ${row['host infra-specific name']} + + + + + host infra-specific rank + ${row['host infra-specific rank']} + + + + + host phenotype + ${row['host phenotype']} + + + + + climate environment + ${row['climate environment']} + + + + + gaseous environment + ${row['gaseous environment']} + + + + + seasonal environment + ${row['seasonal environment']} + + + + + temperature + ${row['temperature']} + + + + + sample salinity + ${row['sample salinity']} + + + + + miscellaneous parameter + ${row['miscellaneous parameter']} + + + + + host genotype + ${row['host genotype']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + trophic level + ${row['trophic level']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + encoded traits + ${row['encoded traits']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + air temperature regimen + ${row['air temperature regimen']} + + + + + antibiotic regimen + ${row['antibiotic regimen']} + + + + + chemical mutagen + ${row['chemical mutagen']} + + + + + fertilizer regimen + ${row['fertilizer regimen']} + + + + + fungicide regimen + ${row['fungicide regimen']} + + + + + gravity + ${row['gravity']} + + + + + growth hormone regimen + ${row['growth hormone regimen']} + + + + + growth media + ${row['growth media']} + + + + + herbicide regimen + ${row['herbicide regimen']} + + + + + humidity regimen + ${row['humidity regimen']} + + + + + mineral nutrient regimen + ${row['mineral nutrient regimen']} + + + + + non-mineral nutrient regimen + ${row['non-mineral nutrient regimen']} + + + + + pesticide regimen + ${row['pesticide regimen']} + + + + + pH regimen + ${row['pH regimen']} + + + + + radiation regimen + ${row['radiation regimen']} + + + + + rainfall regimen + ${row['rainfall regimen']} + + + + + salt regimen + ${row['salt regimen']} + + + + + standing water regimen + ${row['standing water regimen']} + + + + + tissue culture growth media + ${row['tissue culture growth media']} + + + + + watering regimen + ${row['watering regimen']} + + + + + water temperature regimen + ${row['water temperature regimen']} + + + + + mechanical damage + ${row['mechanical damage']} + + + + + chemical administration + ${row['chemical administration']} + + + + + perturbation + ${row['perturbation']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000021.xml b/relecov_tools/templates/ENA_template_samples_ERC000021.xml new file mode 100644 index 00000000..50ecca6f --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000021.xml @@ -0,0 +1,658 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + finishing strategy + ${row['finishing strategy']} + + + + + annotation source + ${row['annotation source']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library construction method + ${row['library construction method']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + pcr primers + ${row['pcr primers']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + sequencing method + ${row['sequencing method']} + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check + ${row['chimera check']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + investigation type + ${row['investigation type']} + + + collection date + ${row['collection date']} + + + + geographic location (altitude) + ${row['geographic location (altitude)']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + sediment environmental package + ${row['sediment environmental package']} + + + geographic location (depth) + ${row['geographic location (depth)']} + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + geographic location (elevation) + ${row['geographic location (elevation)']} + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + propagation + ${row['propagation']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + biomass + ${row['biomass']} + + + + + density + ${row['density']} + + + + + oxygenation status of sample + ${row['oxygenation status of sample']} + + + + + organism count + ${row['organism count']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + sample storage location + ${row['sample storage location']} + + + + + specific host + ${row['specific host']} + + + + + health or disease status of specific host + ${row['health or disease status of specific host']} + + + + + alkyl diethers + ${row['alkyl diethers']} + + + + + aminopeptidase activity + ${row['aminopeptidase activity']} + + + + + ammonium + ${row['ammonium']} + + + + + bacterial carbon production + ${row['bacterial carbon production']} + + + + + bishomohopanol + ${row['bishomohopanol']} + + + + + bromide + ${row['bromide']} + + + + + calcium + ${row['calcium']} + + + + + carbon/nitrogen ratio + ${row['carbon/nitrogen ratio']} + + + + + chloride + ${row['chloride']} + + + + + chlorophyll + ${row['chlorophyll']} + + + + + diether lipids + ${row['diether lipids']} + + + + + dissolved carbon dioxide + ${row['dissolved carbon dioxide']} + + + + + dissolved hydrogen + ${row['dissolved hydrogen']} + + + + + dissolved inorganic carbon + ${row['dissolved inorganic carbon']} + + + + + dissolved organic carbon + ${row['dissolved organic carbon']} + + + + + dissolved organic nitrogen + ${row['dissolved organic nitrogen']} + + + + + methane + ${row['methane']} + + + + + dissolved oxygen + ${row['dissolved oxygen']} + + + + + glucosidase activity + ${row['glucosidase activity']} + + + + + magnesium + ${row['magnesium']} + + + + + n-alkanes + ${row['n-alkanes']} + + + + + nitrate + ${row['nitrate']} + + + + + nitrite + ${row['nitrite']} + + + + + nitrogen + ${row['nitrogen']} + + + + + organic carbon + ${row['organic carbon']} + + + + + organic matter + ${row['organic matter']} + + + + + organic nitrogen + ${row['organic nitrogen']} + + + + + particulate organic carbon + ${row['particulate organic carbon']} + + + + + petroleum hydrocarbon + ${row['petroleum hydrocarbon']} + + + + + phaeopigments + ${row['phaeopigments']} + + + + + phosphate + ${row['phosphate']} + + + + + phospholipid fatty acid + ${row['phospholipid fatty acid']} + + + + + potassium + ${row['potassium']} + + + + + redox potential + ${row['redox potential']} + + + + + salinity + ${row['salinity']} + + + + + total carbon + ${row['total carbon']} + + + + + silicate + ${row['silicate']} + + + + + sodium + ${row['sodium']} + + + + + total organic carbon + ${row['total organic carbon']} + + + + + water content + ${row['water content']} + + + + + sulfate + ${row['sulfate']} + + + + + sulfide + ${row['sulfide']} + + + + + total nitrogen + ${row['total nitrogen']} + + + + + miscellaneous parameter + ${row['miscellaneous parameter']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + trophic level + ${row['trophic level']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + encoded traits + ${row['encoded traits']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + chemical administration + ${row['chemical administration']} + + + + + perturbation + ${row['perturbation']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000022.xml b/relecov_tools/templates/ENA_template_samples_ERC000022.xml new file mode 100644 index 00000000..b129c400 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000022.xml @@ -0,0 +1,646 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + + slope gradient + ${row['slope gradient']} + + + + + slope aspect + ${row['slope aspect']} + + + + + profile position + ${row['profile position']} + + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + finishing strategy + ${row['finishing strategy']} + + + + + annotation source + ${row['annotation source']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library construction method + ${row['library construction method']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + pcr primers + ${row['pcr primers']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + sequencing method + ${row['sequencing method']} + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check + ${row['chimera check']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + + pooling of DNA extracts (if done) + ${row['pooling of DNA extracts (if done)']} + + + + investigation type + ${row['investigation type']} + + + collection date + ${row['collection date']} + + + + geographic location (altitude) + ${row['geographic location (altitude)']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + soil environmental package + ${row['soil environmental package']} + + + geographic location (depth) + ${row['geographic location (depth)']} + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + geographic location (elevation) + ${row['geographic location (elevation)']} + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + propagation + ${row['propagation']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + composite design/sieving (if any) + ${row['composite design/sieving (if any)']} + + + + + sample weight for DNA extraction + ${row['sample weight for DNA extraction']} + + + + + storage conditions (fresh/frozen/other) + ${row['storage conditions (fresh/frozen/other)']} + + + + + microbial biomass + ${row['microbial biomass']} + + + + + microbial biomass method + ${row['microbial biomass method']} + + + + + extreme_unusual_properties/salinity + ${row['extreme_unusual_properties/salinity']} + + + + + extreme_unusual_properties/salinity method + ${row['extreme_unusual_properties/salinity method']} + + + + + extreme_unusual_properties/heavy metals + ${row['extreme_unusual_properties/heavy metals']} + + + + + extreme_unusual_properties/heavy metals method + ${row['extreme_unusual_properties/heavy metals method']} + + + + + extreme_unusual_properties/Al saturation + ${row['extreme_unusual_properties/Al saturation']} + + + + + extreme_unusual_properties/Al saturation method + ${row['extreme_unusual_properties/Al saturation method']} + + + + + specific host + ${row['specific host']} + + + + + health or disease status of specific host + ${row['health or disease status of specific host']} + + + + + link to climate information + ${row['link to climate information']} + + + + + link to classification information + ${row['link to classification information']} + + + + + links to additional analysis + ${row['links to additional analysis']} + + + + + current land use + ${row['current land use']} + + + + + current vegetation + ${row['current vegetation']} + + + + + current vegetation method + ${row['current vegetation method']} + + + + + horizon + ${row['horizon']} + + + + + horizon method + ${row['horizon method']} + + + + + mean annual and seasonal temperature + ${row['mean annual and seasonal temperature']} + + + + + mean annual and seasonal precipitation + ${row['mean annual and seasonal precipitation']} + + + + + soil_taxonomic/FAO classification + ${row['soil_taxonomic/FAO classification']} + + + + + soil_taxonomic/local classification + ${row['soil_taxonomic/local classification']} + + + + + soil_taxonomic/local classification method + ${row['soil_taxonomic/local classification method']} + + + + + soil type + ${row['soil type']} + + + + + soil type method + ${row['soil type method']} + + + + + drainage classification + ${row['drainage classification']} + + + + + texture + ${row['texture']} + + + + + texture method + ${row['texture method']} + + + + + pH + ${row['pH']} + + + + + pH method + ${row['pH method']} + + + + + water content method + ${row['water content method']} + + + + + total organic C method + ${row['total organic C method']} + + + + + total nitrogen method + ${row['total nitrogen method']} + + + + + total organic carbon + ${row['total organic carbon']} + + + + + water content + ${row['water content']} + + + + + total nitrogen + ${row['total nitrogen']} + + + + + history/previous land use + ${row['history/previous land use']} + + + + + history/previous land use method + ${row['history/previous land use method']} + + + + + history/crop rotation + ${row['history/crop rotation']} + + + + + history/agrochemical additions + ${row['history/agrochemical additions']} + + + + + history/tillage + ${row['history/tillage']} + + + + + history/fire + ${row['history/fire']} + + + + + history/flooding + ${row['history/flooding']} + + + + + history/extreme events + ${row['history/extreme events']} + + + + + miscellaneous parameter + ${row['miscellaneous parameter']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + trophic level + ${row['trophic level']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + encoded traits + ${row['encoded traits']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + perturbation + ${row['perturbation']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000023.xml b/relecov_tools/templates/ENA_template_samples_ERC000023.xml new file mode 100644 index 00000000..0e16a667 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000023.xml @@ -0,0 +1,548 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + finishing strategy + ${row['finishing strategy']} + + + + + annotation source + ${row['annotation source']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library construction method + ${row['library construction method']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + pcr primers + ${row['pcr primers']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + sequencing method + ${row['sequencing method']} + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check + ${row['chimera check']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + investigation type + ${row['investigation type']} + + + collection date + ${row['collection date']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + wastewater/sludge environmental package + ${row['wastewater/sludge environmental package']} + + + + geographic location (depth) + ${row['geographic location (depth)']} + + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + propagation + ${row['propagation']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + oxygenation status of sample + ${row['oxygenation status of sample']} + + + + + organism count + ${row['organism count']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + sample storage location + ${row['sample storage location']} + + + + + biochemical oxygen demand + ${row['biochemical oxygen demand']} + + + + + chemical oxygen demand + ${row['chemical oxygen demand']} + + + + + pre-treatment + ${row['pre-treatment']} + + + + + primary treatment + ${row['primary treatment']} + + + + + reactor type + ${row['reactor type']} + + + + + secondary treatment + ${row['secondary treatment']} + + + + + sludge retention time + ${row['sludge retention time']} + + + + + tertiary treatment + ${row['tertiary treatment']} + + + + + specific host + ${row['specific host']} + + + + + health or disease status of specific host + ${row['health or disease status of specific host']} + + + + + alkalinity + ${row['alkalinity']} + + + + + industrial effluent percent + ${row['industrial effluent percent']} + + + + + sewage type + ${row['sewage type']} + + + + + wastewater type + ${row['wastewater type']} + + + + + temperature + ${row['temperature']} + + + + + pH + ${row['pH']} + + + + + efficiency percent + ${row['efficiency percent']} + + + + + emulsions + ${row['emulsions']} + + + + + gaseous substances + ${row['gaseous substances']} + + + + + inorganic particles + ${row['inorganic particles']} + + + + + organic particles + ${row['organic particles']} + + + + + sample salinity + ${row['sample salinity']} + + + + + soluble inorganic material + ${row['soluble inorganic material']} + + + + + soluble organic material + ${row['soluble organic material']} + + + + + suspended solids + ${row['suspended solids']} + + + + + total phosphate + ${row['total phosphate']} + + + + + nitrate + ${row['nitrate']} + + + + + phosphate + ${row['phosphate']} + + + + + sodium + ${row['sodium']} + + + + + total nitrogen + ${row['total nitrogen']} + + + + + miscellaneous parameter + ${row['miscellaneous parameter']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + trophic level + ${row['trophic level']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + encoded traits + ${row['encoded traits']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + chemical administration + ${row['chemical administration']} + + + + + perturbation + ${row['perturbation']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000024.xml b/relecov_tools/templates/ENA_template_samples_ERC000024.xml new file mode 100644 index 00000000..43c57505 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000024.xml @@ -0,0 +1,798 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + finishing strategy + ${row['finishing strategy']} + + + + + annotation source + ${row['annotation source']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library construction method + ${row['library construction method']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + pcr primers + ${row['pcr primers']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + sequencing method + ${row['sequencing method']} + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check + ${row['chimera check']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + investigation type + ${row['investigation type']} + + + collection date + ${row['collection date']} + + + + geographic location (altitude) + ${row['geographic location (altitude)']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + water environmental package + ${row['water environmental package']} + + + geographic location (depth) + ${row['geographic location (depth)']} + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + + geographic location (elevation) + ${row['geographic location (elevation)']} + + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + propagation + ${row['propagation']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + biomass + ${row['biomass']} + + + + + density + ${row['density']} + + + + + oxygenation status of sample + ${row['oxygenation status of sample']} + + + + + organism count + ${row['organism count']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + sample storage location + ${row['sample storage location']} + + + + + specific host + ${row['specific host']} + + + + + health or disease status of specific host + ${row['health or disease status of specific host']} + + + + + alkalinity + ${row['alkalinity']} + + + + + atmospheric data + ${row['atmospheric data']} + + + + + conductivity + ${row['conductivity']} + + + + + water current + ${row['water current']} + + + + + fluorescence + ${row['fluorescence']} + + + + + light intensity + ${row['light intensity']} + + + + + mean friction velocity + ${row['mean friction velocity']} + + + + + mean peak friction velocity + ${row['mean peak friction velocity']} + + + + + downward PAR + ${row['downward PAR']} + + + + + photon flux + ${row['photon flux']} + + + + + pressure + ${row['pressure']} + + + + + temperature + ${row['temperature']} + + + + + tidal stage + ${row['tidal stage']} + + + + + pH + ${row['pH']} + + + + + total depth of water column + ${row['total depth of water column']} + + + + + alkyl diethers + ${row['alkyl diethers']} + + + + + aminopeptidase activity + ${row['aminopeptidase activity']} + + + + + ammonium + ${row['ammonium']} + + + + + bacterial carbon production + ${row['bacterial carbon production']} + + + + + bacterial production + ${row['bacterial production']} + + + + + bacterial respiration + ${row['bacterial respiration']} + + + + + bishomohopanol + ${row['bishomohopanol']} + + + + + bromide + ${row['bromide']} + + + + + calcium + ${row['calcium']} + + + + + carbon/nitrogen ratio + ${row['carbon/nitrogen ratio']} + + + + + chloride + ${row['chloride']} + + + + + chlorophyll + ${row['chlorophyll']} + + + + + diether lipids + ${row['diether lipids']} + + + + + dissolved carbon dioxide + ${row['dissolved carbon dioxide']} + + + + + dissolved hydrogen + ${row['dissolved hydrogen']} + + + + + dissolved inorganic carbon + ${row['dissolved inorganic carbon']} + + + + + dissolved inorganic nitrogen + ${row['dissolved inorganic nitrogen']} + + + + + dissolved inorganic phosphorus + ${row['dissolved inorganic phosphorus']} + + + + + dissolved organic carbon + ${row['dissolved organic carbon']} + + + + + dissolved organic nitrogen + ${row['dissolved organic nitrogen']} + + + + + dissolved oxygen + ${row['dissolved oxygen']} + + + + + glucosidase activity + ${row['glucosidase activity']} + + + + + magnesium + ${row['magnesium']} + + + + + n-alkanes + ${row['n-alkanes']} + + + + + nitrate + ${row['nitrate']} + + + + + nitrite + ${row['nitrite']} + + + + + nitrogen + ${row['nitrogen']} + + + + + organic carbon + ${row['organic carbon']} + + + + + organic matter + ${row['organic matter']} + + + + + organic nitrogen + ${row['organic nitrogen']} + + + + + particulate organic carbon + ${row['particulate organic carbon']} + + + + + particulate organic nitrogen + ${row['particulate organic nitrogen']} + + + + + petroleum hydrocarbon + ${row['petroleum hydrocarbon']} + + + + + phaeopigments + ${row['phaeopigments']} + + + + + phosphate + ${row['phosphate']} + + + + + phospholipid fatty acid + ${row['phospholipid fatty acid']} + + + + + potassium + ${row['potassium']} + + + + + primary production + ${row['primary production']} + + + + + redox potential + ${row['redox potential']} + + + + + salinity + ${row['salinity']} + + + + + silicate + ${row['silicate']} + + + + + sodium + ${row['sodium']} + + + + + soluble reactive phosphorus + ${row['soluble reactive phosphorus']} + + + + + sulfate + ${row['sulfate']} + + + + + sulfide + ${row['sulfide']} + + + + + suspended particulate matter + ${row['suspended particulate matter']} + + + + + total dissolved nitrogen + ${row['total dissolved nitrogen']} + + + + + total inorganic nitrogen + ${row['total inorganic nitrogen']} + + + + + total nitrogen + ${row['total nitrogen']} + + + + + total particulate carbon + ${row['total particulate carbon']} + + + + + total phosphorus + ${row['total phosphorus']} + + + + + miscellaneous parameter + ${row['miscellaneous parameter']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + trophic level + ${row['trophic level']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + encoded traits + ${row['encoded traits']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + chemical administration + ${row['chemical administration']} + + + + + perturbation + ${row['perturbation']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000025.xml b/relecov_tools/templates/ENA_template_samples_ERC000025.xml new file mode 100644 index 00000000..d2a78d80 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000025.xml @@ -0,0 +1,584 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + finishing strategy + ${row['finishing strategy']} + + + + + annotation source + ${row['annotation source']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library construction method + ${row['library construction method']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + pcr primers + ${row['pcr primers']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + sequencing method + ${row['sequencing method']} + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check + ${row['chimera check']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + investigation type + ${row['investigation type']} + + + collection date + ${row['collection date']} + + + + geographic location (altitude) + ${row['geographic location (altitude)']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + miscellaneous environmental package + ${row['miscellaneous environmental package']} + + + + geographic location (depth) + ${row['geographic location (depth)']} + + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + + geographic location (elevation) + ${row['geographic location (elevation)']} + + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + propagation + ${row['propagation']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + biomass + ${row['biomass']} + + + + + density + ${row['density']} + + + + + oxygenation status of sample + ${row['oxygenation status of sample']} + + + + + organism count + ${row['organism count']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + sample storage location + ${row['sample storage location']} + + + + + specific host + ${row['specific host']} + + + + + health or disease status of specific host + ${row['health or disease status of specific host']} + + + + + alkalinity + ${row['alkalinity']} + + + + + water current + ${row['water current']} + + + + + pressure + ${row['pressure']} + + + + + temperature + ${row['temperature']} + + + + + pH + ${row['pH']} + + + + + ammonium + ${row['ammonium']} + + + + + bromide + ${row['bromide']} + + + + + calcium + ${row['calcium']} + + + + + chloride + ${row['chloride']} + + + + + chlorophyll + ${row['chlorophyll']} + + + + + diether lipids + ${row['diether lipids']} + + + + + dissolved carbon dioxide + ${row['dissolved carbon dioxide']} + + + + + dissolved hydrogen + ${row['dissolved hydrogen']} + + + + + dissolved inorganic carbon + ${row['dissolved inorganic carbon']} + + + + + dissolved organic nitrogen + ${row['dissolved organic nitrogen']} + + + + + dissolved oxygen + ${row['dissolved oxygen']} + + + + + nitrate + ${row['nitrate']} + + + + + nitrite + ${row['nitrite']} + + + + + nitrogen + ${row['nitrogen']} + + + + + organic carbon + ${row['organic carbon']} + + + + + organic matter + ${row['organic matter']} + + + + + organic nitrogen + ${row['organic nitrogen']} + + + + + phosphate + ${row['phosphate']} + + + + + phospholipid fatty acid + ${row['phospholipid fatty acid']} + + + + + potassium + ${row['potassium']} + + + + + salinity + ${row['salinity']} + + + + + silicate + ${row['silicate']} + + + + + sodium + ${row['sodium']} + + + + + sulfate + ${row['sulfate']} + + + + + sulfide + ${row['sulfide']} + + + + + miscellaneous parameter + ${row['miscellaneous parameter']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + trophic level + ${row['trophic level']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + encoded traits + ${row['encoded traits']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + chemical administration + ${row['chemical administration']} + + + + + perturbation + ${row['perturbation']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000027.xml b/relecov_tools/templates/ENA_template_samples_ERC000027.xml new file mode 100644 index 00000000..c24d787d --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000027.xml @@ -0,0 +1,802 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + Event Date/Time + ${row['Event Date/Time']} + + + Latitude Start + ${row['Latitude Start']} + + + Longitude Start + ${row['Longitude Start']} + + + + Latitude End + ${row['Latitude End']} + + + + + Longitude End + ${row['Longitude End']} + + + + Depth + ${row['Depth']} + + + Protocol Label + ${row['Protocol Label']} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + finishing strategy + ${row['finishing strategy']} + + + + + annotation source + ${row['annotation source']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library construction method + ${row['library construction method']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + pcr primers + ${row['pcr primers']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check + ${row['chimera check']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + environmental package + ${row['environmental package']} + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + Sampling Campaign + ${row['Sampling Campaign']} + + + Sampling Site + ${row['Sampling Site']} + + + Sampling Platform + ${row['Sampling Platform']} + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + propagation + ${row['propagation']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + biomass + ${row['biomass']} + + + + + density + ${row['density']} + + + + + oxygenation status of sample + ${row['oxygenation status of sample']} + + + + + organism count + ${row['organism count']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + sample storage location + ${row['sample storage location']} + + + + Marine Region + ${row['Marine Region']} + + + Temperature + ${row['Temperature']} + + + Salinity + ${row['Salinity']} + + + + specific host + ${row['specific host']} + + + + + health or disease status of specific host + ${row['health or disease status of specific host']} + + + + + alkalinity + ${row['alkalinity']} + + + + + atmospheric data + ${row['atmospheric data']} + + + + + conductivity + ${row['conductivity']} + + + + + water current + ${row['water current']} + + + + + fluorescence + ${row['fluorescence']} + + + + + light intensity + ${row['light intensity']} + + + + + mean friction velocity + ${row['mean friction velocity']} + + + + + mean peak friction velocity + ${row['mean peak friction velocity']} + + + + + downward PAR + ${row['downward PAR']} + + + + + photon flux + ${row['photon flux']} + + + + + pressure + ${row['pressure']} + + + + + tidal stage + ${row['tidal stage']} + + + + + turbidity + ${row['turbidity']} + + + + + pH + ${row['pH']} + + + + + total depth of water column + ${row['total depth of water column']} + + + + + alkyl diethers + ${row['alkyl diethers']} + + + + + aminopeptidase activity + ${row['aminopeptidase activity']} + + + + + ammonium + ${row['ammonium']} + + + + + bacterial carbon production + ${row['bacterial carbon production']} + + + + + bacterial production + ${row['bacterial production']} + + + + + bacterial respiration + ${row['bacterial respiration']} + + + + + bishomohopanol + ${row['bishomohopanol']} + + + + + bromide + ${row['bromide']} + + + + + calcium + ${row['calcium']} + + + + + carbon/nitrogen ratio + ${row['carbon/nitrogen ratio']} + + + + + chloride + ${row['chloride']} + + + + + chlorophyll + ${row['chlorophyll']} + + + + + diether lipids + ${row['diether lipids']} + + + + + dissolved carbon dioxide + ${row['dissolved carbon dioxide']} + + + + + dissolved hydrogen + ${row['dissolved hydrogen']} + + + + + dissolved inorganic carbon + ${row['dissolved inorganic carbon']} + + + + + dissolved inorganic nitrogen + ${row['dissolved inorganic nitrogen']} + + + + + dissolved inorganic phosphorus + ${row['dissolved inorganic phosphorus']} + + + + + dissolved organic carbon + ${row['dissolved organic carbon']} + + + + + dissolved organic nitrogen + ${row['dissolved organic nitrogen']} + + + + + dissolved oxygen + ${row['dissolved oxygen']} + + + + + glucosidase activity + ${row['glucosidase activity']} + + + + + magnesium + ${row['magnesium']} + + + + + n-alkanes + ${row['n-alkanes']} + + + + + nitrate + ${row['nitrate']} + + + + + nitrite + ${row['nitrite']} + + + + + nitrogen + ${row['nitrogen']} + + + + + organic carbon + ${row['organic carbon']} + + + + + organic matter + ${row['organic matter']} + + + + + organic nitrogen + ${row['organic nitrogen']} + + + + + particulate organic carbon + ${row['particulate organic carbon']} + + + + + particulate organic nitrogen + ${row['particulate organic nitrogen']} + + + + + petroleum hydrocarbon + ${row['petroleum hydrocarbon']} + + + + + phaeopigments + ${row['phaeopigments']} + + + + + phosphate + ${row['phosphate']} + + + + + phospholipid fatty acid + ${row['phospholipid fatty acid']} + + + + + potassium + ${row['potassium']} + + + + + primary production + ${row['primary production']} + + + + + redox potential + ${row['redox potential']} + + + + + silicate + ${row['silicate']} + + + + + sodium + ${row['sodium']} + + + + + soluble reactive phosphorus + ${row['soluble reactive phosphorus']} + + + + + sulfate + ${row['sulfate']} + + + + + sulfide + ${row['sulfide']} + + + + + suspended particulate matter + ${row['suspended particulate matter']} + + + + + total dissolved nitrogen + ${row['total dissolved nitrogen']} + + + + + total inorganic nitrogen + ${row['total inorganic nitrogen']} + + + + + total nitrogen + ${row['total nitrogen']} + + + + + total particulate carbon + ${row['total particulate carbon']} + + + + + total phosphorus + ${row['total phosphorus']} + + + + + miscellaneous parameter + ${row['miscellaneous parameter']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + trophic level + ${row['trophic level']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + encoded traits + ${row['encoded traits']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + chemical administration + ${row['chemical administration']} + + + + + perturbation + ${row['perturbation']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000028.xml b/relecov_tools/templates/ENA_template_samples_ERC000028.xml new file mode 100644 index 00000000..3b8e2832 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000028.xml @@ -0,0 +1,144 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + isolation_source + ${row['isolation_source']} + + + + lat_lon + ${row['lat_lon']} + + + + + collected_by + ${row['collected_by']} + + + + collection date + ${row['collection date']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + identified_by + ${row['identified_by']} + + + + + environmental_sample + ${row['environmental_sample']} + + + + + mating_type + ${row['mating_type']} + + + + host health state + ${row['host health state']} + + + + lab_host + ${row['lab_host']} + + + + host scientific name + ${row['host scientific name']} + + + + bio_material + ${row['bio_material']} + + + + + culture_collection + ${row['culture_collection']} + + + + + specimen_voucher + ${row['specimen_voucher']} + + + + isolate + ${row['isolate']} + + + + sub_species + ${row['sub_species']} + + + + + sub_strain + ${row['sub_strain']} + + + + + serovar + ${row['serovar']} + + + + + strain + ${row['strain']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000029.xml b/relecov_tools/templates/ENA_template_samples_ERC000029.xml new file mode 100644 index 00000000..df249a6a --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000029.xml @@ -0,0 +1,292 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + + subject exposure + ${row['subject exposure']} + + + + + subject exposure duration + ${row['subject exposure duration']} + + + + + travel-relation + ${row['travel-relation']} + + + + + clinical setting + ${row['clinical setting']} + + + + + country of travel + ${row['country of travel']} + + + + collected_by + ${row['collected_by']} + + + collection date + ${row['collection date']} + + + + geographic location (altitude) + ${row['geographic location (altitude)']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + identified_by + ${row['identified_by']} + + + + + geographic location (depth) + ${row['geographic location (depth)']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + environmental_sample + ${row['environmental_sample']} + + + + mating_type + ${row['mating_type']} + + + + + genotype + ${row['genotype']} + + + + + pathotype + ${row['pathotype']} + + + + + host disease status + ${row['host disease status']} + + + + + host disease outcome + ${row['host disease outcome']} + + + + + host subject id + ${row['host subject id']} + + + + + host age + ${row['host age']} + + + + + host taxid + ${row['host taxid']} + + + + + host life stage + ${row['host life stage']} + + + + host health state + ${row['host health state']} + + + + host sex + ${row['host sex']} + + + + + lab_host + ${row['lab_host']} + + + + host scientific name + ${row['host scientific name']} + + + + passage_history + ${row['passage_history']} + + + + + sample storage conditions + ${row['sample storage conditions']} + + + + Is the sequenced pathogen host associated? + ${row['Is the sequenced pathogen host associated?']} + + + + bio_material + ${row['bio_material']} + + + + + culture_collection + ${row['culture_collection']} + + + + + specimen_voucher + ${row['specimen_voucher']} + + + + isolate + ${row['isolate']} + + + + sub_species + ${row['sub_species']} + + + + + sub_strain + ${row['sub_strain']} + + + + + sub_group + ${row['sub_group']} + + + + + sub_type + ${row['sub_type']} + + + + + serovar + ${row['serovar']} + + + + + strain + ${row['strain']} + + + + + host disease stage + ${row['host disease stage']} + + + + + isolation source host-associated + ${row['isolation source host-associated']} + + + + + host description + ${row['host description']} + + + + + isolation source non-host-associated + ${row['isolation source non-host-associated']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000030.xml b/relecov_tools/templates/ENA_template_samples_ERC000030.xml new file mode 100644 index 00000000..1c5bfad2 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000030.xml @@ -0,0 +1,184 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + + Event Label + ${row['Event Label']} + + + + Event Date/Time Start + ${row['Event Date/Time Start']} + + + + Event Date/Time End + ${row['Event Date/Time End']} + + + + Latitude Start + ${row['Latitude Start']} + + + Longitude Start + ${row['Longitude Start']} + + + + Latitude End + ${row['Latitude End']} + + + + + Longitude End + ${row['Longitude End']} + + + + Depth + ${row['Depth']} + + + + Sample Collection Device + ${row['Sample Collection Device']} + + + + Protocol Label + ${row['Protocol Label']} + + + + Size Fraction Lower Threshold + ${row['Size Fraction Lower Threshold']} + + + + + Size Fraction Upper Threshold + ${row['Size Fraction Upper Threshold']} + + + + + Sample Status + ${row['Sample Status']} + + + + + Last Update Date + ${row['Last Update Date']} + + + + project name + ${row['project name']} + + + environmental package + ${row['environmental package']} + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + Sampling Campaign + ${row['Sampling Campaign']} + + + Sampling Station + ${row['Sampling Station']} + + + Sampling Platform + ${row['Sampling Platform']} + + + Marine Region + ${row['Marine Region']} + + + Salinity Sensor + ${row['Salinity Sensor']} + + + + Oxygen Sensor + ${row['Oxygen Sensor']} + + + + + Nitrate Sensor + ${row['Nitrate Sensor']} + + + + Temperature + ${row['Temperature']} + + + + Chlorophyll Sensor + ${row['Chlorophyll Sensor']} + + + + + Citation + ${row['Citation']} + + + + + Further Details + ${row['Further Details']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000031.xml b/relecov_tools/templates/ENA_template_samples_ERC000031.xml new file mode 100644 index 00000000..da0df22f --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000031.xml @@ -0,0 +1,456 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + finishing strategy + ${row['finishing strategy']} + + + + + annotation source + ${row['annotation source']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library construction method + ${row['library construction method']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + pcr primers + ${row['pcr primers']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + sequencing method + ${row['sequencing method']} + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check + ${row['chimera check']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + investigation type + ${row['investigation type']} + + + collection date + ${row['collection date']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + built environment environmental package + ${row['built environment environmental package']} + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + + surface material + ${row['surface material']} + + + + + surface air contaminant + ${row['surface air contaminant']} + + + + + indoor surface + ${row['indoor surface']} + + + + indoor space + ${row['indoor space']} + + + filter type + ${row['filter type']} + + + heating and cooling system type + ${row['heating and cooling system type']} + + + + substructure type + ${row['substructure type']} + + + + light type + ${row['light type']} + + + building setting + ${row['building setting']} + + + building occupancy type + ${row['building occupancy type']} + + + space typical state + ${row['space typical state']} + + + typical occupant density + ${row['typical occupant density']} + + + occupancy at sampling + ${row['occupancy at sampling']} + + + occupant density at sampling + ${row['occupant density at sampling']} + + + ventilation type + ${row['ventilation type']} + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + propagation + ${row['propagation']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + sample size sorting method + ${row['sample size sorting method']} + + + + organism count + ${row['organism count']} + + + + specific host + ${row['specific host']} + + + + + health or disease status of specific host + ${row['health or disease status of specific host']} + + + + relative air humidity + ${row['relative air humidity']} + + + absolute air humidity + ${row['absolute air humidity']} + + + + surface humidity + ${row['surface humidity']} + + + + air temperature + ${row['air temperature']} + + + + surface temperature + ${row['surface temperature']} + + + + + surface moisture + ${row['surface moisture']} + + + + + surface moisture pH + ${row['surface moisture pH']} + + + + + dew point + ${row['dew point']} + + + + carbon dioxide + ${row['carbon dioxide']} + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + trophic level + ${row['trophic level']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + encoded traits + ${row['encoded traits']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + perturbation + ${row['perturbation']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000032.xml b/relecov_tools/templates/ENA_template_samples_ERC000032.xml new file mode 100644 index 00000000..3b9d32a0 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000032.xml @@ -0,0 +1,366 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + + number of inoculated individuals + ${row['number of inoculated individuals']} + + + + + inoculation route + ${row['inoculation route']} + + + + + inoculation dose + ${row['inoculation dose']} + + + + + inoculation stock availability + ${row['inoculation stock availability']} + + + + + subject exposure + ${row['subject exposure']} + + + + + subject exposure duration + ${row['subject exposure duration']} + + + + + type exposure + ${row['type exposure']} + + + + + personal protective equipment + ${row['personal protective equipment']} + + + + + hospitalisation + ${row['hospitalisation']} + + + + + antiviral treatment + ${row['antiviral treatment']} + + + + + antiviral treatment initiation + ${row['antiviral treatment initiation']} + + + + + antiviral treatment dosage + ${row['antiviral treatment dosage']} + + + + + antiviral treatment duration + ${row['antiviral treatment duration']} + + + + + influenza vaccination type + ${row['influenza vaccination type']} + + + + + influenza vaccination date + ${row['influenza vaccination date']} + + + + + source of vaccination information + ${row['source of vaccination information']} + + + + + vaccine lot number + ${row['vaccine lot number']} + + + + + vaccine manufacturer + ${row['vaccine manufacturer']} + + + + + vaccine dosage + ${row['vaccine dosage']} + + + + + influenza-like illness at the time of sample collection + ${row['influenza-like illness at the time of sample collection']} + + + + + illness onset date + ${row['illness onset date']} + + + + + illness duration + ${row['illness duration']} + + + + + illness symptoms + ${row['illness symptoms']} + + + + + collection date + ${row['collection date']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + sample capture status + ${row['sample capture status']} + + + + + host disease outcome + ${row['host disease outcome']} + + + + host common name + ${row['host common name']} + + + host subject id + ${row['host subject id']} + + + + host age + ${row['host age']} + + + + host health state + ${row['host health state']} + + + host sex + ${row['host sex']} + + + host scientific name + ${row['host scientific name']} + + + influenza test method + ${row['influenza test method']} + + + influenza test result + ${row['influenza test result']} + + + other pathogens tested + ${row['other pathogens tested']} + + + other pathogens test result + ${row['other pathogens test result']} + + + + influenza virus type + ${row['influenza virus type']} + + + + + virus identifier + ${row['virus identifier']} + + + + + influenza strain unique number + ${row['influenza strain unique number']} + + + + + WHO/OIE/FAO clade (required for HPAI H5N1 viruses) + ${row['WHO/OIE/FAO clade (required for HPAI H5N1 viruses)']} + + + + + lineage:swl (required for H1N1 viruses) + ${row['lineage:swl (required for H1N1 viruses)']} + + + + collector name + ${row['collector name']} + + + collecting institution + ${row['collecting institution']} + + + + receipt date + ${row['receipt date']} + + + + + sample storage conditions + ${row['sample storage conditions']} + + + + + definition for seropositive sample + ${row['definition for seropositive sample']} + + + + + meaning of cut off value + ${row['meaning of cut off value']} + + + + + serotype (required for a seropositive sample) + ${row['serotype (required for a seropositive sample)']} + + + + + strain + ${row['strain']} + + + + + host habitat + ${row['host habitat']} + + + + + isolation source host-associated + ${row['isolation source host-associated']} + + + + + host description + ${row['host description']} + + + + + gravidity + ${row['gravidity']} + + + + + host behaviour + ${row['host behaviour']} + + + + + isolation source non-host-associated + ${row['isolation source non-host-associated']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000033.xml b/relecov_tools/templates/ENA_template_samples_ERC000033.xml new file mode 100644 index 00000000..acb0003b --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000033.xml @@ -0,0 +1,240 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + + subject exposure + ${row['subject exposure']} + + + + + subject exposure duration + ${row['subject exposure duration']} + + + + + type exposure + ${row['type exposure']} + + + + + personal protective equipment + ${row['personal protective equipment']} + + + + + hospitalisation + ${row['hospitalisation']} + + + + + illness duration + ${row['illness duration']} + + + + + illness symptoms + ${row['illness symptoms']} + + + + + collection date + ${row['collection date']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + sample capture status + ${row['sample capture status']} + + + + + host disease outcome + ${row['host disease outcome']} + + + + host common name + ${row['host common name']} + + + host subject id + ${row['host subject id']} + + + + host age + ${row['host age']} + + + + host health state + ${row['host health state']} + + + authors + ${row['authors']} + + + address + ${row['address']} + + + host sex + ${row['host sex']} + + + host scientific name + ${row['host scientific name']} + + + + virus identifier + ${row['virus identifier']} + + + + collector name + ${row['collector name']} + + + collecting institution + ${row['collecting institution']} + + + + receipt date + ${row['receipt date']} + + + + + sample storage conditions + ${row['sample storage conditions']} + + + + + definition for seropositive sample + ${row['definition for seropositive sample']} + + + + + serotype (required for a seropositive sample) + ${row['serotype (required for a seropositive sample)']} + + + + isolate + ${row['isolate']} + + + + strain + ${row['strain']} + + + + + host habitat + ${row['host habitat']} + + + + + isolation source host-associated + ${row['isolation source host-associated']} + + + + + host description + ${row['host description']} + + + + + gravidity + ${row['gravidity']} + + + + + host behaviour + ${row['host behaviour']} + + + + + isolation source non-host-associated + ${row['isolation source non-host-associated']} + + + + SUBMISSION_TOOL + ${tool_name} + + + ENA-CHECKLIST + ERC000033 + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + diff --git a/relecov_tools/templates/ENA_template_samples_ERC000034.xml b/relecov_tools/templates/ENA_template_samples_ERC000034.xml new file mode 100644 index 00000000..311846f4 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000034.xml @@ -0,0 +1,94 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + tissue_type + ${row['tissue_type']} + + + sex + ${row['sex']} + + + + date of birth + ${row['date of birth']} + + + + + date of death + ${row['date of death']} + + + + diagnosis + ${row['diagnosis']} + + + strain + ${row['strain']} + + + + tumor grading (OBI_0600002) + ${row['tumor grading (OBI_0600002)']} + + + + + treatment agent + ${row['treatment agent']} + + + + + treatment dose + ${row['treatment dose']} + + + + + treatment date + ${row['treatment date']} + + + + + Further Details + ${row['Further Details']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000035.xml b/relecov_tools/templates/ENA_template_samples_ERC000035.xml new file mode 100644 index 00000000..bca85bea --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000035.xml @@ -0,0 +1,240 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + + cell_type + ${row['cell_type']} + + + + + dev_stage + ${row['dev_stage']} + + + + + organism part + ${row['organism part']} + + + + + ploidy + ${row['ploidy']} + + + + + infect + ${row['infect']} + + + + + protocol + ${row['protocol']} + + + + + sampling time point + ${row['sampling time point']} + + + + + initial time point + ${row['initial time point']} + + + + + growth condition + ${row['growth condition']} + + + + + genotype + ${row['genotype']} + + + + + sex + ${row['sex']} + + + + + age + ${row['age']} + + + + + genetic modification + ${row['genetic modification']} + + + + + phenotype + ${row['phenotype']} + + + + + cellular component + ${row['cellular component']} + + + + + individual + ${row['individual']} + + + + + disease staging + ${row['disease staging']} + + + + + immunoprecipitate + ${row['immunoprecipitate']} + + + + + replicate + ${row['replicate']} + + + + + cultivar + ${row['cultivar']} + + + + + ecotype + ${row['ecotype']} + + + + + cell_line + ${row['cell_line']} + + + + + strain + ${row['strain']} + + + + + time + ${row['time']} + + + + + dose + ${row['dose']} + + + + + chemical compound + ${row['chemical compound']} + + + + + experimental factor 1 + ${row['experimental factor 1']} + + + + + experimental factor 2 + ${row['experimental factor 2']} + + + + + experimental factor 3 + ${row['experimental factor 3']} + + + + + experimental factor 4 + ${row['experimental factor 4']} + + + + + experimental factor 5 + ${row['experimental factor 5']} + + + + + block + ${row['block']} + + + + + environmental stress + ${row['environmental stress']} + + + + + environmental history + ${row['environmental history']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000036.xml b/relecov_tools/templates/ENA_template_samples_ERC000036.xml new file mode 100644 index 00000000..672de586 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000036.xml @@ -0,0 +1,172 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + + name of the sampling site + ${row['name of the sampling site']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + investigation type + ${row['investigation type']} + + + + surveillance target + ${row['surveillance target']} + + + + collection date + ${row['collection date']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + sample storage location + ${row['sample storage location']} + + + + + sampling time point + ${row['sampling time point']} + + + + + sample transportation temperature + ${row['sample transportation temperature']} + + + + + sample transportation date + ${row['sample transportation date']} + + + + + sample transportation time + ${row['sample transportation time']} + + + + + receipt date + ${row['receipt date']} + + + + sewage type + ${row['sewage type']} + + + + temperature + ${row['temperature']} + + + + + area of sampling site + ${row['area of sampling site']} + + + + + size of the catchment area + ${row['size of the catchment area']} + + + + + population size of the catchment area + ${row['population size of the catchment area']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000037.xml b/relecov_tools/templates/ENA_template_samples_ERC000037.xml new file mode 100644 index 00000000..12e05484 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000037.xml @@ -0,0 +1,620 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + + collected_by + ${row['collected_by']} + + + + collection date + ${row['collection date']} + + + + geographic location (altitude) + ${row['geographic location (altitude)']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + identified_by + ${row['identified_by']} + + + + + geographic location (depth) + ${row['geographic location (depth)']} + + + + + environment (biome) + ${row['environment (biome)']} + + + + + environment (feature) + ${row['environment (feature)']} + + + + + geographic location (elevation) + ${row['geographic location (elevation)']} + + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + propagation + ${row['propagation']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + sample storage location + ${row['sample storage location']} + + + + + sampling time point + ${row['sampling time point']} + + + + plant structure + ${row['plant structure']} + + + plant developmental stage + ${row['plant developmental stage']} + + + + sampled age + ${row['sampled age']} + + + + + sample phenotype + ${row['sample phenotype']} + + + + + sample health state + ${row['sample health state']} + + + + + sample disease status + ${row['sample disease status']} + + + + + sample disease stage + ${row['sample disease stage']} + + + + + sample wet mass + ${row['sample wet mass']} + + + + + sample dry mass + ${row['sample dry mass']} + + + + + sample height + ${row['sample height']} + + + + + sample length + ${row['sample length']} + + + + + growth facility + ${row['growth facility']} + + + + + sample capture status + ${row['sample capture status']} + + + + + genotype + ${row['genotype']} + + + + + genetic modification + ${row['genetic modification']} + + + + + organism common name + ${row['organism common name']} + + + + + subspecific genetic lineage rank + ${row['subspecific genetic lineage rank']} + + + + + subspecific genetic lineage name + ${row['subspecific genetic lineage name']} + + + + + biological status + ${row['biological status']} + + + + + organism phenotype + ${row['organism phenotype']} + + + + + ancestral data + ${row['ancestral data']} + + + + + source material description + ${row['source material description']} + + + + + biotic relationship + ${row['biotic relationship']} + + + + + growth habit + ${row['growth habit']} + + + + + plant sex + ${row['plant sex']} + + + + + climate environment + ${row['climate environment']} + + + + + gaseous environment + ${row['gaseous environment']} + + + + + seasonal environment + ${row['seasonal environment']} + + + + + soil_taxonomic/FAO classification + ${row['soil_taxonomic/FAO classification']} + + + + + soil_taxonomic/local classification + ${row['soil_taxonomic/local classification']} + + + + + soil_taxonomic/local classification method + ${row['soil_taxonomic/local classification method']} + + + + + soil type + ${row['soil type']} + + + + + soil type method + ${row['soil type method']} + + + + + drainage classification + ${row['drainage classification']} + + + + + texture + ${row['texture']} + + + + + texture method + ${row['texture method']} + + + + + soil water content + ${row['soil water content']} + + + + + soil pH + ${row['soil pH']} + + + + plant growth medium + ${row['plant growth medium']} + + + + rooting conditions + ${row['rooting conditions']} + + + + + culture rooting medium + ${row['culture rooting medium']} + + + + + rooting medium macronutrients + ${row['rooting medium macronutrients']} + + + + + rooting medium micronutrients + ${row['rooting medium micronutrients']} + + + + + rooting medium organic supplements + ${row['rooting medium organic supplements']} + + + + + rooting medium carbon + ${row['rooting medium carbon']} + + + + + rooting medium regulators + ${row['rooting medium regulators']} + + + + + rooting medium solidifier + ${row['rooting medium solidifier']} + + + + + rooting medium pH + ${row['rooting medium pH']} + + + + + air temperature regimen + ${row['air temperature regimen']} + + + + + antibiotic regimen + ${row['antibiotic regimen']} + + + + + chemical mutagen + ${row['chemical mutagen']} + + + + + fertilizer regimen + ${row['fertilizer regimen']} + + + + + fungicide regimen + ${row['fungicide regimen']} + + + + + gravity + ${row['gravity']} + + + + + growth hormone regimen + ${row['growth hormone regimen']} + + + + + herbicide regimen + ${row['herbicide regimen']} + + + + + humidity regimen + ${row['humidity regimen']} + + + + + mineral nutrient regimen + ${row['mineral nutrient regimen']} + + + + + non-mineral nutrient regimen + ${row['non-mineral nutrient regimen']} + + + + + pesticide regimen + ${row['pesticide regimen']} + + + + + pH regimen + ${row['pH regimen']} + + + + + radiation regimen + ${row['radiation regimen']} + + + + + rainfall regimen + ${row['rainfall regimen']} + + + + + salt regimen + ${row['salt regimen']} + + + + + standing water regimen + ${row['standing water regimen']} + + + + + watering regimen + ${row['watering regimen']} + + + + + water temperature regimen + ${row['water temperature regimen']} + + + + + plant treatment + ${row['plant treatment']} + + + + + light regimen + ${row['light regimen']} + + + + + biotic regimen + ${row['biotic regimen']} + + + + + mechanical damage + ${row['mechanical damage']} + + + + + chemical administration + ${row['chemical administration']} + + + + + perturbation + ${row['perturbation']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000038.xml b/relecov_tools/templates/ENA_template_samples_ERC000038.xml new file mode 100644 index 00000000..48525157 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000038.xml @@ -0,0 +1,174 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + Event Date/Time + ${row['Event Date/Time']} + + + Latitude Start + ${row['Latitude Start']} + + + Longitude Start + ${row['Longitude Start']} + + + Depth + ${row['Depth']} + + + + Sample Collection Device + ${row['Sample Collection Device']} + + + + Protocol Label + ${row['Protocol Label']} + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + Sampling Campaign + ${row['Sampling Campaign']} + + + Sampling Station + ${row['Sampling Station']} + + + Sampling Platform + ${row['Sampling Platform']} + + + + storage conditions (fresh/frozen/other) + ${row['storage conditions (fresh/frozen/other)']} + + + + + sample health state + ${row['sample health state']} + + + + + sample disease status + ${row['sample disease status']} + + + + + Marine Region + ${row['Marine Region']} + + + + seabed habitat + ${row['seabed habitat']} + + + age + ${row['age']} + + + aquaculture origin + ${row['aquaculture origin']} + + + shellfish total weight + ${row['shellfish total weight']} + + + shellfish soft tissue weight + ${row['shellfish soft tissue weight']} + + + shell length + ${row['shell length']} + + + shell width + ${row['shell width']} + + + + adductor weight + ${row['adductor weight']} + + + + + gonad weight + ${row['gonad weight']} + + + + + shell markings + ${row['shell markings']} + + + + + toxin burden + ${row['toxin burden']} + + + + + treatment agent + ${row['treatment agent']} + + + + + chemical compound + ${row['chemical compound']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000039.xml b/relecov_tools/templates/ENA_template_samples_ERC000039.xml new file mode 100644 index 00000000..93c057e0 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000039.xml @@ -0,0 +1,194 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + dev_stage + ${row['dev_stage']} + + + + subject exposure + ${row['subject exposure']} + + + + + subject exposure duration + ${row['subject exposure duration']} + + + + + travel-relation + ${row['travel-relation']} + + + + + clinical setting + ${row['clinical setting']} + + + + + country of travel + ${row['country of travel']} + + + + + collection date + ${row['collection date']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + genotype + ${row['genotype']} + + + + + host disease outcome + ${row['host disease outcome']} + + + + + host common name + ${row['host common name']} + + + + + host subject id + ${row['host subject id']} + + + + + host age + ${row['host age']} + + + + + host health state + ${row['host health state']} + + + + + host sex + ${row['host sex']} + + + + + host scientific name + ${row['host scientific name']} + + + + collector name + ${row['collector name']} + + + collecting institution + ${row['collecting institution']} + + + + sample storage conditions + ${row['sample storage conditions']} + + + + isolate + ${row['isolate']} + + + + strain + ${row['strain']} + + + + + isolation source host-associated + ${row['isolation source host-associated']} + + + + + diagnostic method + ${row['diagnostic method']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + isolation source non-host-associated + ${row['isolation source non-host-associated']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000040.xml b/relecov_tools/templates/ENA_template_samples_ERC000040.xml new file mode 100644 index 00000000..42f63ef5 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000040.xml @@ -0,0 +1,140 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + + Size Fraction Lower Threshold + ${row['Size Fraction Lower Threshold']} + + + + + Size Fraction Upper Threshold + ${row['Size Fraction Upper Threshold']} + + + + target gene + ${row['target gene']} + + + target subfragment + ${row['target subfragment']} + + + pcr primers + ${row['pcr primers']} + + + + isolation_source + ${row['isolation_source']} + + + + + collected_by + ${row['collected_by']} + + + + collection date + ${row['collection date']} + + + + geographic location (altitude) + ${row['geographic location (altitude)']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + geographic location (depth) + ${row['geographic location (depth)']} + + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + + sample collection device or method + ${row['sample collection device or method']} + + + + environmental_sample + ${row['environmental_sample']} + + + + Salinity + ${row['Salinity']} + + + + + Further Details + ${row['Further Details']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000041.xml b/relecov_tools/templates/ENA_template_samples_ERC000041.xml new file mode 100644 index 00000000..b77db32f --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000041.xml @@ -0,0 +1,172 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + library construction method + ${row['library construction method']} + + + + + protocol + ${row['protocol']} + + + + + instrument for DNA concentration measurement + ${row['instrument for DNA concentration measurement']} + + + + + read quality filter + ${row['read quality filter']} + + + + + DNA concentration + ${row['DNA concentration']} + + + + + collection_date + ${row['collection_date']} + + + + + isolation_source + ${row['isolation_source']} + + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + sample storage location + ${row['sample storage location']} + + + + + sampling time point + ${row['sampling time point']} + + + + + sample transportation temperature + ${row['sample transportation temperature']} + + + + + sample transportation date + ${row['sample transportation date']} + + + + + sample transportation time + ${row['sample transportation time']} + + + + + receipt date + ${row['receipt date']} + + + + + links to additional analysis + ${row['links to additional analysis']} + + + + isolate + ${row['isolate']} + + + + sub_species + ${row['sub_species']} + + + + + Further Details + ${row['Further Details']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000043.xml b/relecov_tools/templates/ENA_template_samples_ERC000043.xml new file mode 100644 index 00000000..003e3c33 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000043.xml @@ -0,0 +1,154 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + + Depth + ${row['Depth']} + + + + + collected_by + ${row['collected_by']} + + + + + collection date + ${row['collection date']} + + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + growth condition + ${row['growth condition']} + + + + + Temperature + ${row['Temperature']} + + + + + Salinity + ${row['Salinity']} + + + + + sample storage conditions + ${row['sample storage conditions']} + + + + + light intensity + ${row['light intensity']} + + + + + pH + ${row['pH']} + + + + + culture_collection + ${row['culture_collection']} + + + + strain + ${row['strain']} + + + + Further Details + ${row['Further Details']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000044.xml b/relecov_tools/templates/ENA_template_samples_ERC000044.xml new file mode 100644 index 00000000..1b9dc04f --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000044.xml @@ -0,0 +1,128 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + + subject exposure + ${row['subject exposure']} + + + + + subject exposure duration + ${row['subject exposure duration']} + + + + + travel-relation + ${row['travel-relation']} + + + + + clinical setting + ${row['clinical setting']} + + + + + country of travel + ${row['country of travel']} + + + + collection_date + ${row['collection_date']} + + + collected_by + ${row['collected_by']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + host disease status + ${row['host disease status']} + + + + + host disease outcome + ${row['host disease outcome']} + + + + host scientific name + ${row['host scientific name']} + + + isolate + ${row['isolate']} + + + + sub_type + ${row['sub_type']} + + + + + serovar + ${row['serovar']} + + + + + serovar_in-silico + ${row['serovar_in-silico']} + + + + + isolation source host-associated + ${row['isolation source host-associated']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000045.xml b/relecov_tools/templates/ENA_template_samples_ERC000045.xml new file mode 100644 index 00000000..69bbc610 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000045.xml @@ -0,0 +1,78 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + collection_date + ${row['collection_date']} + + + isolation_source + ${row['isolation_source']} + + + + collected_by + ${row['collected_by']} + + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + receipt date + ${row['receipt date']} + + + + isolate + ${row['isolate']} + + + + serotype + ${row['serotype']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000047.xml b/relecov_tools/templates/ENA_template_samples_ERC000047.xml new file mode 100644 index 00000000..a974f1dc --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000047.xml @@ -0,0 +1,342 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + annotation source + ${row['annotation source']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + sequencing method + ${row['sequencing method']} + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + + number of standard tRNAs extracted + ${row['number of standard tRNAs extracted']} + + + + assembly software + ${row['assembly software']} + + + + feature prediction + ${row['feature prediction']} + + + + + reference database(s) + ${row['reference database(s)']} + + + + + similarity search method + ${row['similarity search method']} + + + + + 16S recovered + ${row['16S recovered']} + + + + + 16S recovery software + ${row['16S recovery software']} + + + + + tRNA extraction software + ${row['tRNA extraction software']} + + + + completeness score + ${row['completeness score']} + + + completeness software + ${row['completeness software']} + + + + completeness approach + ${row['completeness approach']} + + + + contamination score + ${row['contamination score']} + + + + contamination screening input + ${row['contamination screening input']} + + + + + contamination screening parameters + ${row['contamination screening parameters']} + + + + + decontamination software + ${row['decontamination software']} + + + + binning software + ${row['binning software']} + + + + reassembly post binning + ${row['reassembly post binning']} + + + + + MAG coverage software + ${row['MAG coverage software']} + + + + assembly quality + ${row['assembly quality']} + + + investigation type + ${row['investigation type']} + + + binning parameters + ${row['binning parameters']} + + + taxonomic identity marker + ${row['taxonomic identity marker']} + + + + taxonomic classification + ${row['taxonomic classification']} + + + + isolation_source + ${row['isolation_source']} + + + collection date + ${row['collection date']} + + + + geographic location (altitude) + ${row['geographic location (altitude)']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + geographic location (depth) + ${row['geographic location (depth)']} + + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + + geographic location (elevation) + ${row['geographic location (elevation)']} + + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + size fraction selected + ${row['size fraction selected']} + + + + sample derived from + ${row['sample derived from']} + + + metagenomic source + ${row['metagenomic source']} + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000048.xml b/relecov_tools/templates/ENA_template_samples_ERC000048.xml new file mode 100644 index 00000000..1e425abe --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000048.xml @@ -0,0 +1,346 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + annotation source + ${row['annotation source']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + sequencing method + ${row['sequencing method']} + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + + number of standard tRNAs extracted + ${row['number of standard tRNAs extracted']} + + + + assembly software + ${row['assembly software']} + + + + feature prediction + ${row['feature prediction']} + + + + + reference database(s) + ${row['reference database(s)']} + + + + + similarity search method + ${row['similarity search method']} + + + + + 16S recovered + ${row['16S recovered']} + + + + + 16S recovery software + ${row['16S recovery software']} + + + + + tRNA extraction software + ${row['tRNA extraction software']} + + + + completeness score + ${row['completeness score']} + + + completeness software + ${row['completeness software']} + + + + completeness approach + ${row['completeness approach']} + + + + contamination score + ${row['contamination score']} + + + + contamination screening input + ${row['contamination screening input']} + + + + + contamination screening parameters + ${row['contamination screening parameters']} + + + + + decontamination software + ${row['decontamination software']} + + + + assembly quality + ${row['assembly quality']} + + + investigation type + ${row['investigation type']} + + + taxonomic identity marker + ${row['taxonomic identity marker']} + + + + taxonomic classification + ${row['taxonomic classification']} + + + + sorting technology + ${row['sorting technology']} + + + single cell or viral particle lysis approach + ${row['single cell or viral particle lysis approach']} + + + + single cell or viral particle lysis kit protocol + ${row['single cell or viral particle lysis kit protocol']} + + + + WGA amplification approach + ${row['WGA amplification approach']} + + + + WGA amplification kit + ${row['WGA amplification kit']} + + + + collection_date + ${row['collection_date']} + + + isolation_source + ${row['isolation_source']} + + + + geographic location (altitude) + ${row['geographic location (altitude)']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + geographic location (depth) + ${row['geographic location (depth)']} + + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + + geographic location (elevation) + ${row['geographic location (elevation)']} + + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + size fraction selected + ${row['size fraction selected']} + + + + sample derived from + ${row['sample derived from']} + + + metagenomic source + ${row['metagenomic source']} + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000049.xml b/relecov_tools/templates/ENA_template_samples_ERC000049.xml new file mode 100644 index 00000000..a63ff04f --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000049.xml @@ -0,0 +1,420 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + estimated size + ${row['estimated size']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + annotation source + ${row['annotation source']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + sequencing method + ${row['sequencing method']} + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + + number of standard tRNAs extracted + ${row['number of standard tRNAs extracted']} + + + + assembly software + ${row['assembly software']} + + + + feature prediction + ${row['feature prediction']} + + + + + reference database(s) + ${row['reference database(s)']} + + + + + similarity search method + ${row['similarity search method']} + + + + + tRNA extraction software + ${row['tRNA extraction software']} + + + + + completeness score + ${row['completeness score']} + + + + + completeness software + ${row['completeness software']} + + + + + completeness approach + ${row['completeness approach']} + + + + + binning software + ${row['binning software']} + + + + + reassembly post binning + ${row['reassembly post binning']} + + + + + MAG coverage software + ${row['MAG coverage software']} + + + + assembly quality + ${row['assembly quality']} + + + investigation type + ${row['investigation type']} + + + + binning parameters + ${row['binning parameters']} + + + + + taxonomic identity marker + ${row['taxonomic identity marker']} + + + + + taxonomic classification + ${row['taxonomic classification']} + + + + + sorting technology + ${row['sorting technology']} + + + + + single cell or viral particle lysis approach + ${row['single cell or viral particle lysis approach']} + + + + + single cell or viral particle lysis kit protocol + ${row['single cell or viral particle lysis kit protocol']} + + + + + WGA amplification approach + ${row['WGA amplification approach']} + + + + + WGA amplification kit + ${row['WGA amplification kit']} + + + + source of UViGs + ${row['source of UViGs']} + + + virus enrichment approach + ${row['virus enrichment approach']} + + + predicted genome type + ${row['predicted genome type']} + + + predicted genome structure + ${row['predicted genome structure']} + + + detection type + ${row['detection type']} + + + viral identification software + ${row['viral identification software']} + + + + vOTU classification approach + ${row['vOTU classification approach']} + + + + + vOTU sequence comparison approach + ${row['vOTU sequence comparison approach']} + + + + + vOTU database + ${row['vOTU database']} + + + + + host prediction approach + ${row['host prediction approach']} + + + + + host prediction estimated accuracy + ${row['host prediction estimated accuracy']} + + + + isolation_source + ${row['isolation_source']} + + + collection date + ${row['collection date']} + + + + geographic location (altitude) + ${row['geographic location (altitude)']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + geographic location (depth) + ${row['geographic location (depth)']} + + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + + geographic location (elevation) + ${row['geographic location (elevation)']} + + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + size fraction selected + ${row['size fraction selected']} + + + + sample derived from + ${row['sample derived from']} + + + metagenomic source + ${row['metagenomic source']} + + + + specific host + ${row['specific host']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000050.xml b/relecov_tools/templates/ENA_template_samples_ERC000050.xml new file mode 100644 index 00000000..6bf6a1d7 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000050.xml @@ -0,0 +1,322 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + + experimental factor + ${row['experimental factor']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + adapters + ${row['adapters']} + + + + sequencing method + ${row['sequencing method']} + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + + number of standard tRNAs extracted + ${row['number of standard tRNAs extracted']} + + + + assembly software + ${row['assembly software']} + + + + 16S recovered + ${row['16S recovered']} + + + + + 16S recovery software + ${row['16S recovery software']} + + + + + tRNA extraction software + ${row['tRNA extraction software']} + + + + + completeness score + ${row['completeness score']} + + + + + completeness software + ${row['completeness software']} + + + + + completeness approach + ${row['completeness approach']} + + + + + contamination score + ${row['contamination score']} + + + + + contamination screening input + ${row['contamination screening input']} + + + + + contamination screening parameters + ${row['contamination screening parameters']} + + + + + decontamination software + ${row['decontamination software']} + + + + binning software + ${row['binning software']} + + + + reassembly post binning + ${row['reassembly post binning']} + + + + + MAG coverage software + ${row['MAG coverage software']} + + + + + assembly quality + ${row['assembly quality']} + + + + investigation type + ${row['investigation type']} + + + binning parameters + ${row['binning parameters']} + + + + taxonomic identity marker + ${row['taxonomic identity marker']} + + + + + taxonomic classification + ${row['taxonomic classification']} + + + + isolation_source + ${row['isolation_source']} + + + collection date + ${row['collection date']} + + + + geographic location (altitude) + ${row['geographic location (altitude)']} + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + geographic location (depth) + ${row['geographic location (depth)']} + + + + environment (biome) + ${row['environment (biome)']} + + + environment (feature) + ${row['environment (feature)']} + + + environment (material) + ${row['environment (material)']} + + + + geographic location (elevation) + ${row['geographic location (elevation)']} + + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample collection device or method + ${row['sample collection device or method']} + + + + + sample material processing + ${row['sample material processing']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + + + + + size fraction selected + ${row['size fraction selected']} + + + + sample derived from + ${row['sample derived from']} + + + metagenomic source + ${row['metagenomic source']} + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000051.xml b/relecov_tools/templates/ENA_template_samples_ERC000051.xml new file mode 100644 index 00000000..98f32477 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000051.xml @@ -0,0 +1,98 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + sample origin + ${row['sample origin']} + + + sample taxon name + ${row['sample taxon name']} + + + sample material + ${row['sample material']} + + + engrafted tumor sample passage + ${row['engrafted tumor sample passage']} + + + + engrafted tumor collection site + ${row['engrafted tumor collection site']} + + + + patient tumor site of collection + ${row['patient tumor site of collection']} + + + patient tumor type + ${row['patient tumor type']} + + + sample unique ID + ${row['sample unique ID']} + + + + engraftment host strain name + ${row['engraftment host strain name']} + + + + patient age at collection of tumor + ${row['patient age at collection of tumor']} + + + patient tumor diagnosis at time of collection + ${row['patient tumor diagnosis at time of collection']} + + + patient tumor primary site + ${row['patient tumor primary site']} + + + + was the PDX model humanised? + ${row['was the PDX model humanised?']} + + + + patient sex + ${row['patient sex']} + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000052.xml b/relecov_tools/templates/ENA_template_samples_ERC000052.xml new file mode 100644 index 00000000..366e9c59 --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000052.xml @@ -0,0 +1,226 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + project name + ${row['project name']} + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + pcr primers + ${row['pcr primers']} + + + + + adapters + ${row['adapters']} + + + + sequencing method + ${row['sequencing method']} + + + reference host genome for decontamination + ${row['reference host genome for decontamination']} + + + + collection date + ${row['collection date']} + + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + trial length + ${row['trial length']} + + + + trial timepoint + ${row['trial timepoint']} + + + + sample storage temperature + ${row['sample storage temperature']} + + + + + sample storage location + ${row['sample storage location']} + + + + + sample storage buffer + ${row['sample storage buffer']} + + + + + sample storage container + ${row['sample storage container']} + + + + + host disease status + ${row['host disease status']} + + + + host common name + ${row['host common name']} + + + host subject id + ${row['host subject id']} + + + host taxid + ${row['host taxid']} + + + host body site + ${row['host body site']} + + + + host length + ${row['host length']} + + + + + host total mass + ${row['host total mass']} + + + + + host sex + ${row['host sex']} + + + + + host scientific name + ${row['host scientific name']} + + + + + host breed + ${row['host breed']} + + + + + host gutted mass + ${row['host gutted mass']} + + + + + host diet + ${row['host diet']} + + + + host diet treatment + ${row['host diet treatment']} + + + + host diet treatment concentration + ${row['host diet treatment concentration']} + + + + + host storage container + ${row['host storage container']} + + + + + host storage container pH + ${row['host storage container pH']} + + + + + host storage container temperature + ${row['host storage container temperature']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_samples_ERC000053.xml b/relecov_tools/templates/ENA_template_samples_ERC000053.xml new file mode 100644 index 00000000..34ef511f --- /dev/null +++ b/relecov_tools/templates/ENA_template_samples_ERC000053.xml @@ -0,0 +1,204 @@ + + + + + + ${row.title} + + ${row.taxon_id} + ${row.scientific_name} + + ${row.common_name} + + + ${row.sample_description} + + + organism part + ${row['organism part']} + + + lifestage + ${row['lifestage']} + + + project name + ${row['project name']} + + + + tolid + ${row['tolid']} + + + + + barcoding center + ${row['barcoding center']} + + + + collected_by + ${row['collected_by']} + + + collection date + ${row['collection date']} + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + geographic location (latitude) + ${row['geographic location (latitude)']} + + + geographic location (longitude) + ${row['geographic location (longitude)']} + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + identified_by + ${row['identified_by']} + + + + + geographic location (depth) + ${row['geographic location (depth)']} + + + + + geographic location (elevation) + ${row['geographic location (elevation)']} + + + + habitat + ${row['habitat']} + + + + identifier_affiliation + ${row['identifier_affiliation']} + + + + + original collection date + ${row['original collection date']} + + + + + original geographic location + ${row['original geographic location']} + + + + + sample derived from + ${row['sample derived from']} + + + + + sample same as + ${row['sample same as']} + + + + + sample symbiont of + ${row['sample symbiont of']} + + + + + sample coordinator + ${row['sample coordinator']} + + + + + sample coordinator affiliation + ${row['sample coordinator affiliation']} + + + + sex + ${row['sex']} + + + + relationship + ${row['relationship']} + + + + + symbiont + ${row['symbiont']} + + + + collecting institution + ${row['collecting institution']} + + + + GAL + ${row['GAL']} + + + + + specimen_voucher + ${row['specimen_voucher']} + + + + + specimen_id + ${row['specimen_id']} + + + + + GAL_sample_id + ${row['GAL_sample_id']} + + + + + culture_or_strain_id + ${row['culture_or_strain_id']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/relecov_tools/templates/ENA_template_studies.xml b/relecov_tools/templates/ENA_template_studies.xml new file mode 100755 index 00000000..5c466259 --- /dev/null +++ b/relecov_tools/templates/ENA_template_studies.xml @@ -0,0 +1,49 @@ + + + + + + + ${row.title} + + ${row.study_abstract} + + ${row.center_project_name} + + + ${row.study_description} + + + + + + + PUBMED + ${row.pubmed_id} + + + + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + diff --git a/relecov_tools/templates/ENA_template_submission.xml b/relecov_tools/templates/ENA_template_submission.xml new file mode 100644 index 00000000..941837fa --- /dev/null +++ b/relecov_tools/templates/ENA_template_submission.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/relecov_tools/templates/SRA.common.xsd b/relecov_tools/templates/SRA.common.xsd new file mode 100644 index 00000000..754f5fa5 --- /dev/null +++ b/relecov_tools/templates/SRA.common.xsd @@ -0,0 +1,1044 @@ + + + + + + + + + + + + + + Submitter designated name for the object. The name must be unique within the submission account. + + + + + + + The center name of the submitter. + + + + + + + The center name of the broker. + + + + + + + The object accession assigned by the archive. + + + + + + + + + + + + + Identifies an object by name within the namespace defined by attribute "refcenter". + + + + + + + The namespace of the attribute "refname". + + + + + + + Identifies a record by its accession. The scope of resolution is the entire Archive. + + + + + + + + + + Submitter designated name of the SRA document of this type. At minimum alias should + be unique throughout the submission of this document type. If center_name is specified, the name should + be unique in all submissions from that center of this document type. + + + + + + + Owner authority of this document and namespace for submitter's name of this document. + If not provided, then the submitter is regarded as "Individual" and document resolution + can only happen within the submission. + + + + + + + Broker authority of this document. If not provided, then the broker is considered "direct". + + + + + + + The document's accession as assigned by the Home Archive. + + + + + + + + + + Identifies a record by name that is known within the namespace defined by attribute "refcenter" + Use this field when referencing an object for which an accession has not yet been issued. + + + + + + + The center namespace of the attribute "refname". When absent, the namespace is assumed to be the current submission. + + + + + + + Identifies a record by its accession. The scope of resolution is the entire Archive. + + + + + + + + + + + Alternative/explanatory description of the same object/identifier. + + + + + + + + + + + + A string value that constrains the domain of named + identifiers (namespace). + + + + + + + + + Set of record identifiers. + + + + + A primary identifier in the INSDC namespace. + + + + + A secondary identifier in the INSDC namespace. + + + + + An identifer rom a public non-INSDC resource. + + + + + A submitter provided identifier. + + + + + A universally unique identifier that requires no namespace. + + + + + + + + + INSDC controlled vocabulary of permitted cross references. + Please see http://www.insdc.org/db_xref.html . For example, FLYBASE. + + + + + + Accession in the referenced database. For example, FBtr0080008 (in FLYBASE). + + + + + + + Text label to display for the link. + + + + + + + + + + + + Text label to display for the link. + + + + + + + The internet service link (file:, http:, ftp:, etc). + + + + + + + + + Reusable attributes to encode tag-value pairs with optional units. + + + + + + + Name of the attribute. + + + + + + + Value of the attribute. + + + + + + + Optional scientific units. + + + + + + + + + + Reusable external links type to encode URL links, Entrez links, and db_xref links. + + + + + + + + + + Text label to display for the link. + + + + + + The internet service link (file:, http:, ftp: etc). + + + + + + + + + + + + + + NCBI controlled vocabulary of permitted cross references. Please see http://www.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi? . + + + + + + + + Numeric record id meaningful to the NCBI Entrez system. + + + + + + + Accession string meaningful to the NCBI Entrez system. + + + + + + + + How to label the link. + + + + + + + + + + + + + + + The SPOT_DESCRIPTOR specifies how to decode the individual reads of interest from the + monolithic spot sequence. The spot descriptor contains aspects of the experimental design, + platform, and processing information. There will be two methods of specification: one + will be an index into a table of typical decodings, the other being an exact specification. + + + + + + + + + Number of base/color calls, cycles, or flows per + spot (raw sequence length or flow length including all + application and technical tags and mate pairs, but not including + gap lengths). This value will be platform dependent, library + dependent, and possibly run dependent. Variable length platforms + will still have a constant flow/cycle length. + + + + + + + + READ_INDEX starts at 0 and is incrementally increased for each sequential READ_SPEC within a SPOT_DECODE_SPEC + + + + + READ_LABEL is a name for this tag, and can be used to on output to determine read name, for example F or R. + + + + + + + + + + + + + + + + + + + + + + + + + + + + There are various methods to ordering the reads on the spot. + + + + + + The read is located beginning at the offset or cycle relative to another read. + This choice is appropriate for example when specifying a read + that follows a variable length expected sequence(s). + + + + + + + Specify the read index that precedes this read. + + + + + + + Specify the read index that follows this read. + + + + + + + + + The location of the read start in terms of base count (1 is beginning of spot). + + + + + + + A set of choices of expected basecalls for a current read. Read will be zero-length if none is found. + + + + + + + + Element's body contains a basecall, attribute provide description of this read meaning as well as matching rules. + + + + + + + + + When match occurs, the read will be tagged with this group membership + + + + + + + Minimum number of matches to trigger identification. + + + + + + + Maximum number of mismatches + + + + + + + Where the match should occur. Changes the rules on how min_match and max_mismatch are counted. + + + + + + + + Only @max_mismatch influences matching process + + + + + + + Both matches and mismatches are counted. + When @max_mismatch is exceeded - it is not a match. + When @min_match is reached - match is declared. + + + + + + + Both matches and mismatches are counted. + When @max_mismatch is exceeded - it is not a match. + When @min_match is reached - match is declared. + + + + + + + + + + + + + + + Specify whether the spot should have a default length for this tag if the expected base cannot be matched. + + + + + + + Specify an optional starting point for tag (base offset from 1). + + + + + + + + + + + + + + + + + + + The PLATFORM record selects which sequencing platform and platform-specific runtime parameters. This will be + determined by the Center. + + + + + 454 technology use 1-color sequential flows + + + + + + + + + + Illumina is 4-channel flowgram with 1-to-1 mapping between basecalls and flows + + + + + + + + + + Helicos is similar to 454 technology - uses 1-color sequential flows + + + + + + + + + + ABI is 4-channel flowgram with 1-to-1 mapping between basecalls and flows + + + + + + + + + + CompleteGenomics platform type. At present there is no instrument model. + + + + + + + + + + + + + + + + + + + + Oxford Nanopore platform type. nanopore-based electronic single molecule analysis + + + + + + + + + + PacificBiosciences platform type for the single molecule real time (SMRT) technology. + + + + + + + + + + Ion Torrent Personal Genome Machine (PGM) from Life Technologies. + + + + + + + + + + Sequencers based on capillary electrophoresis technology manufactured by LifeTech (formerly Applied + BioSciences). + + + + + + + + + + Sequencers based on DNBSEQ by MGI Tech. + + + + + + + + + + + + + + + + + Tells the Archive who will execute the sample demultiplexing operation.. + + + + + + + + There shall be no sample de-multiplexing at the level of assiging individual reads to sample pool members. + + + + + + + The submitter has assigned individual reads to sample pool members by providing individual files + containing reads with the same member assignment. + + + + + + + + + + + + + + The PipelineType identifies the sequence or tree of actions to + process the sequencing data. + + + + + + + + + Lexically ordered value that allows for the pipe section to be hierarchically ordered. The float primitive data type is + used to allow for pipe sections to be inserted later on. + + + + + + + STEP_INDEX of the previous step in the workflow. Set toNIL if the first pipe section. + + + + + + + Name of the program or process for primary analysis. This may include a test or condition + that leads to branching in the workflow. + + + + + + + Version of the program or process for primary analysis. + + + + + + + Notes about the program or process for primary analysis. + + + + + + + + Name of the processing pipeline section. + + + + + + + + + + Reference assembly details. + + + + + + A standard genome assembly. + + + + + + A recognized name for the genome assembly. + + + + + Identifies the genome assembly + using an accession number and a sequence version. + + + + + + + + Other genome assembly. + + + + + + Description of the genome + assembly. + + + + + A link to the genome + assembly. + + + + + + Text label to display for the + link. + + + + + The internet service link + (file:, http:, ftp:, etc). + + + + + + + + + + + + + Reference assembly and sequence details. + + + + + Reference assembly details. + + + + + Reference sequence details. + + + + + A recognized name for the + reference sequence. + + + + + + Accession.version with version being mandatory + + + + + + + + + This is how Reference Sequence is labeled in submission file(s). + It is equivalent to SQ label in BAM. + Optional when submitted file uses INSDC accession.version + + + + + + + + + + + + + + Generic processing pipeline specification. + + + + + Processing directives tell the Sequence Read Archive how to + treat the input data, if any treatment is requested. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Undifferentiated early AB SOLiD system + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/relecov_tools/templates/SRA.experiment.xsd b/relecov_tools/templates/SRA.experiment.xsd new file mode 100644 index 00000000..e9ee8f5f --- /dev/null +++ b/relecov_tools/templates/SRA.experiment.xsd @@ -0,0 +1,791 @@ + + + + + + + + + + + Sequencing technique intended for this library. + + + + + Whole Genome Sequencing - random sequencing of the whole genome (see pubmed 10731132 for details) + + + + + + Whole Genome Amplification followed by random sequencing. (see pubmed 1631067,8962113 for details) + + + + + + Random sequencing of exonic regions selected from the genome. (see pubmed 20111037 for details) + + + + + + Random sequencing of whole transcriptome, also known as Whole Transcriptome Shotgun Sequencing, or WTSS). (see + pubmed 18611170 for details) + + + + + Strand-specific RNA sequencing. + + + + + + Micro RNA sequencing strategy designed to capture post-transcriptional RNA elements and include non-coding + functional elements. (see pubmed 21787409 for details) + + + + + Capture of other non-coding RNA types, including post-translation modification types such as snRNA (small + nuclear RNA) or snoRNA (small nucleolar RNA), or expression regulation types such as siRNA (small interfering RNA) or + piRNA/piwi/RNA (piwi-interacting RNA). + + + + + Full-length sequencing of cDNA templates + + + + + Single pass sequencing of cDNA templates + + + + + Chromosome Conformation Capture technique where a biotin-labeled nucleotide is incorporated at the ligation junction, enabling selective purification of chimeric DNA ligation junctions followed by deep sequencing. + + + + + Assay for Transposase-Accessible Chromatin (ATAC) strategy is used to study genome-wide chromatin accessibility. alternative method to DNase-seq that uses an engineered Tn5 transposase to cleave DNA and to integrate primer DNA sequences into the cleaved genomic DNA. + + + + + Random sequencing of a whole chromosome or other replicon isolated from a genome. + + + + + + Genomic clone based (hierarchical) sequencing. + + + + + Shotgun of pooled clones (usually BACs and Fosmids). + + + + + Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling + using SSU rRNA . + + + + + Clone end (5', 3', or both) sequencing. + + + + + Sequencing intended to finish (close) gaps in existing coverage. + + + + + ChIP-seq, Chromatin ImmunoPrecipitation, reveals binding sites of specific proteins, typically transcription factors (TFs) using antibodies to extract DNA fragments bound to the target protein. + + + + + Identifies well-positioned nucleosomes. uses Micrococcal Nuclease (MNase) is an endo-exonuclease that processively digests DNA until an obstruction, such as a nucleosome, is reached. + + + + + Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI. + + + + + + MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil + depending on methylation status. + + + + + Concatenated Tag Sequencing + + + + + Methylation-Sensitive Restriction Enzyme Sequencing. + + + + + Methylated DNA Immunoprecipitation Sequencing. + + + + + Methyl CpG Binding Domain Sequencing. + + + + + Quantitatively determine fitness of bacterial genes based on how many times a purposely seeded transposon gets + inserted into each gene of a colony after some time. + + + + + CGHub special request: Independent experiment to re-evaluate putative variants. + + + + + Formaldehyde Assisted Isolation of Regulatory Elements. Reveals regions of open chromatin. + + + + + Systematic Evolution of Ligands by Exponential enrichment + + + + + Direct sequencing of RNA immunoprecipitates (includes CLIP-Seq, HITS-CLIP and PAR-CLIP). + + + + + Direct sequencing of proximity-ligated chromatin immunoprecipitates. + + + + + binning and barcoding of large DNA fragments to facilitate assembly of the fragment + + + + + Enrichment of a targeted subset of loci. + + + + + + Nucleosome Occupancy and Methylome sequencing. + + + + + ChIPmentation combines chromatin immunoprecipitation with sequencing library preparation by Tn5 transposase (see pubmed 26280331 for details) + + + + + Genotyping by sequencing is a method to discover single nucleotide polymorphisms for genotyping studies. + + + + + Library strategy not listed. + + + + + + + + The LIBRARY_SOURCE specifies the type of source material that is being sequenced. + + + + + Genomic DNA (includes PCR products from genomic DNA). + + + + + + Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries). + + + + + + Mixed material from metagenome. + + + + + Transcription products from community targets + + + + + Synthetic DNA. + + + + + Viral RNA. + + + + + Other, unspecified, or unknown library source material. + + + + + + + + Method used to enrich the target in the sequence library preparation + + + + + No Selection or Random selection + + + + + target enrichment via PCR + + + + + Source material was selected by randomly generated primers. + + + + + target enrichment via + + + + + Hypo-methylated partial restriction digest + + + + + Methyl Filtrated + + + + + Selection for less repetitive (and more gene rich) sequence through Cot filtration (CF) or other fractionation + techniques based on DNA kinetics. + + + + + Physical selection of size appropriate targets. + + + + + Methylation Spanning Linking Library + + + + + PolyA selection or enrichment for messenger RNA (mRNA); synonymize with PolyA + + + + + + + PolyA selection or enrichment for messenger RNA (mRNA); should replace cDNA enumeration. + + + + + enrichment of messenger RNA (mRNA) by hybridization to Oligo-dT. + + + + + depletion of ribosomal RNA by oligo hybridization. + + + + + depletion of ribosomal RNA by inverse oligo hybridization. + + + + + Chromatin immunoprecipitation + + + + + Chromatin immunoPrecipitation, reveals binding sites of specific proteins, typically transcription factors (TFs) using antibodies to extract DNA fragments bound to the target protein. + + + + + Identifies well-positioned nucleosomes. uses Micrococcal Nuclease (MNase) is an endo-exonuclease that processively digests DNA until an obstruction, such as a nucleosome, is reached. + + + + + DNase I endonuclease digestion and size selection reveals regions of chromatin where the DNA is highly sensitive to DNase I. + + + + + Selection by hybridization in array or solution. + + + + + Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable + number of loci to facilitate re-sampling. + + + + + DNA fractionation using restriction enzymes. + + + + + Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine + (m5C). + + + + + Enrichment by methyl-CpG binding domain. + + + + + Cap-analysis gene expression. + + + + + Rapid Amplification of cDNA Ends. + + + + + Multiple Displacement Amplification, a non-PCR based DNA amplification technique that amplifies a minute + quantifies of DNA to levels suitable for genomic analysis. + + + + + Targeted sequence capture protocol covering an arbitrary set of nonrepetitive genomics targets. An example is + capture bisulfite sequencing using padlock probes (BSPP). + + + + + Other library enrichment, screening, or selection process. + + + + + Library enrichment, screening, or selection is not specified. + + + + + + + + + + + + + + + + + + Assignment of read_group_tag to decoded read + + + + + + + + + + Label a sample within a scope of the pool + + + + + Proportion of this sample (in percent) that was included in sample pool. + + + + + + + + + + + + + Identifies a list of group/pool/multiplex sample members. This implies that + this sample record is a group, pool, or multiplex, but it continues to receive + its own accession and can be referenced by an experiment. By default if + no match to any of the listed members can be determined, then the default + sample reference is used. + + + + + + + Reference to the sample that is used when read membership cannot be determined. A default member should + be provided if there exists a possibility that some reads will be left over from barcode/MID resolution. A default member + is not needed when defining a true pool (where individual samples are not distinguished in the reads), or the reads have + been partitioned among the pool members (no leftovers). + + + + + Reference to the sample as determined from barcode/MID resolution or read partition. + + + + + + + + + + + + The LIBRARY_DESCRIPTOR specifies the origin of the material being + sequenced and any treatments that the material might have undergone that affect the + sequencing result. This specification is needed even if the platform does not + require a library construction step per se. + + + + + + The submitter's name for this library. + + + + + + + + + + LIBRARY_LAYOUT specifies whether to expect single, paired, or other configuration of reads. + In the case of paired reads, information about the relative distance and orientation is specified. + + + + + + + + + Reads are unpaired (usual case). + + + + + + + + + + + + + + + + + + Names the gene(s) or locus(loci) or other genomic feature(s) targeted by the sequence. + + + + + + + + + Reference to an archived primer or + probe set. Example: dbProbe + + + + + + + + + Bacterial small subunit ribosomal RNA, a locus used for + phylogenetic studies of bacteria and as a target for random target PCR in + environmental biodiversity screening. + + + + + Eukaryotic small subunit ribosomal RNA, a locus used for + phylogenetic studies of eukaryotes and as a target for random target PCR in + environmental biodiversity screening. + + + + + Structural ribosomal RNA for the large component, or large + subunit (LSU) of eukaryotic cytoplasmic ribosomes.. + + + + + RuBisCO large subunit : ribulose-1,5-bisphosphate + carboxylase/oxygenase large subunit, a locus used for phylogenetic studies + of plants. + + + + + Maturase K gene, a locus used for phylogenetic studies of + plants. + + + + + Mitochondrial cytochrome c oxidase 1 gene, a locus used for + phylogenetic studies of animals + + + + + Internal transcribed spacers 1 and 2 plus 5.8S rRNA region, + a locus used for phylogenetic studies of fungi. + + + + + All exonic regions of the genome. + + + + + Other locus, please describe. + + + + + + + + + Submitter supplied description of alternate locus and auxiliary + information. + + + + + + + + + + + + + + The optional pooling strategy indicates how the library or libraries are organized if multiple samples are involved. + + + + + + + + + + Free form text describing the protocol by which the sequencing library was constructed. + + + + + + + + + + Goal and setup of the individual library including library was constructed. + + + + + + Pick a sample to associate this experiment with. The sample may be an individual or a pool, + depending on how it is specified. + + + + + + The LIBRARY_DESCRIPTOR specifies the origin of the material being sequenced and any + treatments that the material might have undergone that affect the sequencing result. This specification is + needed even if the platform does not require a library construction step per se. + + + + + + The SPOT_DESCRIPTOR specifies how to decode the individual reads of interest from the + monolithic spot sequence. The spot descriptor contains aspects of the experimental design, platform, and + processing information. There will be two methods of specification: one will be an index into a table of + typical decodings, the other being an exact specification. This construct is needed for loading data and for + interpreting the loaded runs. It can be omitted if the loader can infer read layout (from multiple input + files or from one input files). + + + + + + + + + + + An Experiment specifies of what will be sequenced and how the sequencing will be performed. + It does not contain results. + An Experiment is composed of a design, a platform selection, and processing parameters. + + + + + + + + + + Short text that can be used to call out experiment records in searches or in displays. + This element is technically optional but should be used for all new records. + + + + + + + Identifies the parent study. + + + + + + + + + + + The library design including library properties, layout, protocol, targeting information, and spot and gap + descriptors. + + + + + + The PLATFORM record selects which sequencing platform and platform-specific runtime parameters. + This will be determined by the Center. + + + + + + + + + + Links to resources related to this experiment or experiment set (publication, datasets, online databases). + + + + + + + + + + + + + Properties and attributes of the experiment. These can be entered as free-form + tag-value pairs. + + + + + + + + + + + + + + + + + + + + + + + An EXPERMENT_SET is a container for a set of experiments and a common namespace. + + + + + + + diff --git a/relecov_tools/templates/SRA.run.xsd b/relecov_tools/templates/SRA.run.xsd new file mode 100644 index 00000000..bc65c328 --- /dev/null +++ b/relecov_tools/templates/SRA.run.xsd @@ -0,0 +1,548 @@ + + + + + + + + + + + A run contains a group of reads generated for a particular experiment. + + + + + + + + + Short text that can be used to define submissions in searches or in displays. + + + + + + Identifies the parent experiment. + + + + + + + + + + + + + + + + + The type of the run. + + + + + + + + + + + + + + + + Data files associated with the run. + + + + + + + + + + The READ_LABEL can associate a certain file to a certain read_label defined in the SPOT_DESCRIPTOR. + + + + + + + + + + + + + + + + + + + + The name or relative pathname of a run data file. + + + + + The run data file model. + + + + + + Sequence Read Archives native format in serialized (single file) form. + + + + + Standard Short Read Format file (.srf), all platforms + + + + + 454 Standard Flowgram Format file (.sff) + + + + + + Combined nucleotide/qualities sequence file in .fastq form. + Please see SRA File Formats Guide for definitions of the definition and restrictions on this form. + + + + + + + Please see SRA File Formats Guide for definitions of these file formats, + and the SRA Submission Guidelines document for data series that are appropriate for your study. + Sequence and qualities are minimally required. + + + + + + + Tab delimited text file used to deliver certain auxiliary data along with sequencing submissions (only needed for certain + use cases). The first line is devoted to column headers. Each column is dedicated to an INDSC + data series type. + Please see SRA File Formats Guide for definitions of the definition and restrictions on this form. + + + + + + + A combination of 454 primary analysis output files, including + seq + qual + Please see SRA File Formats Guide for definitions of these file formats, + and the SRA Submission Guidelines document for data series that are appropriate for your study. + Sequence and qualities are minimally required. + + + + + + + 454 base calls (for example .seq or .fna). + Please see SRA File Formats Guide for definitions of these file formats, + and the SRA Submission Guidelines document for data series that are appropriate for your study. + Sequence and qualities are minimally required. + + + + + + + 454 quality scores (for example .qual). + Please see SRA File Formats Guide for definitions of these file formats, + and the SRA Submission Guidelines document for data series that are appropriate for your study. + Sequence and qualities are minimally required. + + + + + + + A kind of fastq format specific to the Helicos platform. + Please see SRA File Formats Guide for definitions of these file formats, + and the SRA Submission Guidelines document for data series that are appropriate for your study. + Sequence and qualities are minimally required. + + + + + + + Please see SRA File Formats Guide for definitions of these file formats, + and the SRA Submission Guidelines document for data series that are appropriate for your study. + Sequence and qualities are minimally required. + + + + + + + Please see SRA File Formats Guide for definitions of these file formats, + and the SRA Submission Guidelines document for data series that are appropriate for your study. + Sequence and qualities are minimally required. + + + + + + + Please see SRA File Formats Guide for definitions of these file formats, + and the SRA Submission Guidelines document for data series that are appropriate for your study. + Sequence and qualities are minimally required. + + + + + + + Please see SRA File Formats Guide for definitions of these file formats, + and the SRA Submission Guidelines document for data series that are appropriate for your study. + Sequence and qualities are minimally required. + + + + + + + Please see SRA File Formats Guide for definitions of these file formats, + and the SRA Submission Guidelines document for data series that are appropriate for your study. + Sequence and qualities are minimally required. + + + + + + + Please see SRA File Formats Guide for definitions of these file formats, + and the SRA Submission Guidelines document for data series that are appropriate for your study. + Sequence and qualities are minimally required. + + + + + + + A combination of SOLiD primary analysis output files, including: + csfasta + _QV.qual + _intensity.ScaledCY3.fasta + _intensity.ScaledCY5.fasta + _intensity.ScaledFTC.fasta + _intensity.ScaledTXR.fasta + Please see SRA File Formats Guide for definitions of these file formats, + and the SRA Submission Guidelines document for data series that are appropriate for your study. + Sequence and qualities are minimally required. + + + + + + + Colorspace calls (for example .csfasta) + Please see SRA File Formats Guide for definitions of these file formats, + and the SRA Submission Guidelines document for data series that are appropriate for your study. + Sequence and qualities are minimally required. + + + + + + + Colorspace quality scores (for example .qual) + Please see SRA File Formats Guide for definitions of these file formats, + and the SRA Submission Guidelines document for data series that are appropriate for your study. + Sequence and qualities are minimally required. + + + + + + + Pacific Biosciences Hierarchical Data Format. Please see + SRA File Formats Guide for definitions of these file formats. + + + + + + + Binary SAM format that combines alignment and sequencing data. + Please see SRA File Formats Guide for definitions of these file formats, + and the SRA Submission Guidelines document for data series that are appropriate for your study. + Sequence and qualities are minimally required. + + + + + + + Binary CRAM format that combines alignment and sequencing data. + Please see SRA File Formats Guide for definitions of these file formats, + and the SRA Submission Guidelines document for data series that are appropriate for your study. + Sequence and qualities are minimally required. + + + + + + + Please see SRA File Formats Guide for definitions of these file formats, + and the SRA Submission Guidelines document for data series that are appropriate for your study. + Sequence and qualities are minimally required. + + + + + + + Oxford Nanopore data format. + + + + + + + + + + How the input data are scored for quality. + + + + + + + + The quality score is expressed as a probability of error in log form: + -10 log(1/p) where p is the probability of error, with value range 0..63, + 0 meaning no base call. + + + + + + + The quality score is expressed as the ratio of error to non-error in log form: + -10 log(p/(1-p)) where p is the probability of error, with value range -40..40. + The SRA will convert these into phred scale during loadtime. + + + + + + + + + + Character used in representing the minimum quality value. + Helps specify how to decode text rendering of quality data. + + + + + + + + ASCII character based encoding. + + + + + + + Single decimal value per quality score. + + + + + + + Single hexadecimal value per quality score. + + + + + + + + + + Character used in representing the minimum quality value. Helps specify how to decode text rendering of quality data. + + + + + + + + ASCII value 33. Typically used for range 0..63. + + + + + + + ASCII value 64. Typically used for range 0..60. + + + + + + + + + + + Checksum method used. + + + + + + + + Checksum generated by the MD5 method (md5sum in unix). + + + + + + + Checksum generated by the SHA-256 method . + + + + + + + + + + Checksum of uncompressed file. + + + + + + + Checksum of unenrypted file(used in conjunction with checksum of encrypted file). + + + + + + + + + + + + + Allow for an individual DATA_BLOCK to be associated with a member of a sample pool. + + + + + + + + + + Links to resources related to this RUN or RUN set (publication, datasets, online databases). + + + + + + + + + + + + + Properties and attributes of a RUN. These can be entered as free-form + tag-value pairs. For certain studies, submitters may be asked to follow a + community established ontology when describing the work. + + + + + + + + + + + + + ISO date when the run took place. + + + + + + + If applicable, the name of the contract sequencing center that executed the run. + Example: 454MSC. + + + + + + + + + + + + + + + + + RUN_SET serves as a container for a set of runs and a name space + for establishing referential integrity between them. + + + + + + + diff --git a/relecov_tools/templates/SRA.sample.xsd b/relecov_tools/templates/SRA.sample.xsd new file mode 100644 index 00000000..37d94e14 --- /dev/null +++ b/relecov_tools/templates/SRA.sample.xsd @@ -0,0 +1,127 @@ + + + + + + + + + + + A Sample defines an isolate of sequenceable material upon which + sequencing experiments can be based. The Sample object may be a surrogate for taxonomy + accession or an anonymized individual identifier. Or, it may fully specify + provenance and isolation method of the starting material. + + + + + + + + + Short text that can be used to call out sample records in search results or in displays. + + + + + + + + + + NCBI Taxonomy Identifier. This is appropriate for individual organisms and + some environmental samples. + + + + + + + Scientific name of sample that distinguishes its taxonomy. Please use a + name or synonym that is tracked in the INSDC Taxonomy database. + Also, this field can be used to confirm the TAXON_ID setting. + + + + + + + GenBank common name of the organism. Examples: human, mouse. + + + + + + + + + + + Free-form text describing the sample, its origin, and its method of isolation. + + + + + + + + + Links to resources related to this sample or sample set (publication, datasets, online databases). + + + + + + + + + + + + + Properties and attributes of a sample. These can be entered as free-form + tag-value pairs. For certain studies, submitters may be asked to follow a + community established ontology when describing the work. + + + + + + + + + + + + + + + + + + + + + + + + SAMPLE_SET serves as a container for a set of samples and a name space + for establishing referential integrity between them. + + + + + + + + diff --git a/relecov_tools/templates/SRA.study.xsd b/relecov_tools/templates/SRA.study.xsd new file mode 100644 index 00000000..15fdce88 --- /dev/null +++ b/relecov_tools/templates/SRA.study.xsd @@ -0,0 +1,290 @@ + + + + + + + + + + + A Study is a container for a sequencing investigation that may comprise multiple experiments. + The Study has an overall goal, but is otherwise minimally defined in the SRA. + A Study is composed of a descriptor, zero or more experiments, and zero or more analyses. + The submitter may decorate the Study with web links and properties. + + + + + + + + + + + + Title of the study as would be used in a publication. + + + + + + The STUDY_TYPE presents a controlled vocabulary for expressing the overall purpose of the study. + + + + + + + + + Sequencing of a single organism. + + + + + + + Sequencing of a community. + + + + + + + Sequencing and characterization of transcription elements. + + + + + + + Sequencing of a sample with respect to a reference. + + + + + + + Cellular differentiation study. + + + + + + + Sequencing of modified, synthetic, or transplanted genomes. + + + + + + + Sequencing of recovered genomic material. + + + + + + + Study of gene expression regulation. + + + + + + + Study of cancer genomics. + + + + + + + Study of populations and evolution through genomics. + + + + + + + RNA sequencing study. + + + + + + + The study investigates the exons of the genome. + + + + + + + The study is sequencing clone pools (BACs, fosmids, other constructs). + + + + + + Sequencing of transcription elements. + + + + + + Study type not listed. + + + + + + + + + + + To propose a new term, select Other and enter a new study type. + + + + + + + + + Briefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be + inherited from a referenced publication. + + + + + + + DEPRECATED. Use STUDY@center_name instead. + Controlled vocabulary identifying the sequencing center, core facility, consortium, or laboratory responsible for the study. + + + + + + + Submitter defined project name. This field is intended for backward tracking of the study record to the submitter's LIMS. + + + + + + + DEPRECATED (use RELATED_STUDIES.STUDY instead). + The required PROJECT_ID accession is generated by the Genome Project database at NCBI + and will be valid also at the other archival institutions. + + + + + + + + + + + + + Related study or project record from a list of supported databases. + The study's information is derived from this project record rather + than stored as first class information. + + + + + + + Whether this study object is designated as the primary source + of the study or project information. + + + + + + + + + + + + + + + More extensive free-form description of the study. + + + + + + + + + + + Links to resources related to this study (publication, datasets, online databases). + + + + + + + + + + + + + Properties and attributes of the study. These can be entered as free-form + tag-value pairs. For certain studies, submitters may be asked to follow a + community established ontology when describing the work. + + + + + + + + + + + + + + + + + + + + + + + An STUDY_SET is a container for a set of studies and a common namespace. + + + + + + + + diff --git a/relecov_tools/templates/SRA.submission.xsd b/relecov_tools/templates/SRA.submission.xsd new file mode 100644 index 00000000..9497871c --- /dev/null +++ b/relecov_tools/templates/SRA.submission.xsd @@ -0,0 +1,354 @@ + + + + + + + + + + + A Submission type is used to describe an object that contains submission actions to be performed by the archive. + + + + + + + + + Short text that can be used to define submissions in searches or in displays. + + + + + + + + + + + + Name of contact person for this submission. + + + + + + + Internet address of person or service to inform on any status changes for this submission. + + + + + + + Internet address of person or service to inform on any errors for this submission. + + + + + + + + + + + + + + + Action to be executed by the archive. + + + + + + Add an object to the archive. + + + + + Filename or relative path to the XML file being submitted. + + + + + The type of the XML file being submitted. + + + + + + + + + + + + + + + + + + + + + + Modify an object in the archive. + + + + + Filename or relative path to the XML file being updated. + + + + + The type of the XML file being updated. + + + + + + + + + + + + + + + + + + + + + + Cancels a private object and its dependent objects. + + + + + Accession or refname of the object that is being cancelled. + + + + + + + Suppresses a public object and its dependent objects. + + + + + Accession or refname of the object that is being suppressed. + + + + + The date when a temporarily suppressed object will be made public. + + + + + + + Kills a public object and its dependent objects. + + + + + Accession or refname of the object that is being killed. + + + + + The date when a temporarily killed object will be made public. + + + + + + + Make the object public only when the hold date expires. + + + + + + Accession or refname of the object that is being made public + when the hold date expires. If not specified then + all objects in the submission will be assigned the hold date. + + + + + + The date when the submission will be made public. + + + + + + + The object will be released immediately to public. + + + + + + Accession or refname of the object that is made public. + If not specified then all objects in the submission will + made public. + + + + + + + + This action is required for data submitted to European Genome-Phenome Archive (EGA). + + + + + + This action will rollback the submission from the database + + + + + + Validates the submitted XMLs without actually submitting them. + + + + + Filename or relative path to the XML file being validated. + + + + + The type of the XML file being validated. + + + + + + + + + + + + + + + + + + + + + + Returns the receipt for a given submission alias. + + + + + Submission alias. + + + + + + + + + + + + + + + Archive created links to associated submissions. + + + + + + + + + + + + + Archive assigned properties and attributes of a SUBMISSION. + + + + + + + + + + + + + + Submitter assigned preparation date of this submission object. + + + + + + + Submitter assigned comment. + + + + + + + Laboratory name within submitting institution. + + + + + + + + + + + + + + + + + + An SUBMISSION_SET is a container for a set of studies and a common namespace. + + + + + + + + From 71bc8b6ed509379ca863bd9a0b997ddafdedbe99 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 16 Aug 2022 15:36:54 +0200 Subject: [PATCH 0791/1454] lintin --- relecov_tools/ena_upload.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 472934a3..78079300 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,5 +1,6 @@ import logging -from re import template + +# from re import template # from pyparsing import col import xml.etree.ElementTree as ET @@ -340,7 +341,7 @@ def create_structure_to_ena(self): # submit data to webin ftp server. It should only upload fastq files in case the action is ADD. # When the action is MODIFY rthe fastq are already submitted. - """ + if self.action == "ADD" or self.action == "add": session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) @@ -360,7 +361,7 @@ def create_structure_to_ena(self): g2 = session.quit() print(g2) - """ + # THE ENA_UPLOAD_CLI METHOD DOES NOT WORK (below) # chec = submit_data(file_paths, self.passwd, self.user) # print(chec) From 84e4b2a304ad6de692c0755afb4149ac2c966929 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 16 Aug 2022 15:39:27 +0200 Subject: [PATCH 0792/1454] lintin 2 --- relecov_tools/read_lab_metadata.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index beb14314..a6c38f23 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -3,7 +3,8 @@ import json import logging -from queue import Empty + +# from queue import Empty # from turtle import heading import rich.console From c411929bc32f6a1390993a28dcf0b3ded757ae38 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 16 Aug 2022 22:20:40 +0200 Subject: [PATCH 0793/1454] fixed bug server is not attribute of RestApi --- relecov_tools/rest_api.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/rest_api.py b/relecov_tools/rest_api.py index b8a765d1..058b553b 100644 --- a/relecov_tools/rest_api.py +++ b/relecov_tools/rest_api.py @@ -41,8 +41,8 @@ def get_request(self, request_info, parameter, value, safe=True): return {"ERROR": req.status_code} return {"DATA": json.loads(req.text)} except requests.ConnectionError: - log.error("Unable to open connection towards %s", self.server) - stderr.print("[red] Unable to open connection towards ", self.server) + log.error("Unable to open connection towards %s", self.request_url) + stderr.print("[red] Unable to open connection towards ", self.request_url) return {"ERROR": "Server not available"} def put_request(self, data, credentials, url): From fd2d816810d66be860e3be7e36839f3b018853df Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 17 Aug 2022 09:28:12 +0200 Subject: [PATCH 0794/1454] remove center name from submission --- relecov_tools/templates/ENA_template_submission.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/templates/ENA_template_submission.xml b/relecov_tools/templates/ENA_template_submission.xml index 941837fa..d3cec42e 100644 --- a/relecov_tools/templates/ENA_template_submission.xml +++ b/relecov_tools/templates/ENA_template_submission.xml @@ -2,7 +2,7 @@ - + From f04d87b38dd451dd45fc63f36b51df2339763886 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 17 Aug 2022 12:19:42 +0200 Subject: [PATCH 0795/1454] changed names in read bioinfo metadata --- relecov_tools/ena_upload.py | 5 ++++- relecov_tools/read_bioinfo_metadata.py | 4 ++-- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 78079300..66d415fa 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -396,9 +396,12 @@ def create_structure_to_ena(self): # print(files.attrib["checksum"]) tree.write(schema_xmls["run"]) + # mapping_illumina_tab_path = os.path.join(self.input_folder, self.mapping_illumina) + + """ tree = ET.parse(schema_xmls["sample"]) root = tree.getroot() - """ + for files in root.iter("SAMPLE_ATTRIBUTES"): tag = ET.SubElement(files, "SAMPLE_ATTRIBUTE") diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 5ffa50ed..85325ecf 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -143,8 +143,8 @@ def bioinfo_parse(self, file_name): fastq_r2 = row[48] bioinfo_dict = {} bioinfo_dict["sample_name"] = str(sample_name) - bioinfo_dict["fastq_r1"] = fastq_r1 - bioinfo_dict["fastq_r2"] = fastq_r2 + bioinfo_dict["sequence_file_R1_fastq"] = fastq_r1 + bioinfo_dict["sequence_file_R2_fastq"] = fastq_r2 # inserting all keys from configuration.json relecov_bioinfo_metadata into bioinfo_dict for key in relecov_bioinfo_metadata.keys(): bioinfo_dict[key] = relecov_bioinfo_metadata[key] From 6487f5a168f48b06db501242a7f41cb78dd2e117 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 17 Aug 2022 12:24:58 +0200 Subject: [PATCH 0796/1454] lintin --- relecov_tools/ena_upload.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 66d415fa..eb31b091 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -395,9 +395,6 @@ def create_structure_to_ena(self): files.set("checksum", H) # print(files.attrib["checksum"]) tree.write(schema_xmls["run"]) - - # mapping_illumina_tab_path = os.path.join(self.input_folder, self.mapping_illumina) - """ tree = ET.parse(schema_xmls["sample"]) root = tree.getroot() From 183710b5650139c67744385c45a83a7ad92bb042 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 17 Aug 2022 12:26:28 +0200 Subject: [PATCH 0797/1454] lintin --- relecov_tools/ena_upload.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index eb31b091..920ece66 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -398,8 +398,6 @@ def create_structure_to_ena(self): """ tree = ET.parse(schema_xmls["sample"]) root = tree.getroot() - - for files in root.iter("SAMPLE_ATTRIBUTES"): tag = ET.SubElement(files, "SAMPLE_ATTRIBUTE") tag_2 = ET.SubElement(tag, "TAG") From 31aaa2a4f225c81ed74db3f6b97d6fb2b0282a4d Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 17 Aug 2022 15:35:03 +0200 Subject: [PATCH 0798/1454] Include field version 0.1.0 --- relecov_tools/schema/relecov_schema.json | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index ff538aa4..0cba8df3 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1,5 +1,6 @@ { "schema": "RELECOV", + "version": "0.1.0", "required": [ "collecting_lab_sample_id", "collecting_institution", From 7236dd758cc69e94738541d27792dd15b32b9358 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 17 Aug 2022 22:13:15 +0200 Subject: [PATCH 0799/1454] added schema name and version for each sample in jsong file --- relecov_tools/read_lab_metadata.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index a6c38f23..98f58d00 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -62,6 +62,7 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None os.path.dirname(os.path.realpath(__file__)), "schema", relecov_schema ) self.configuration = config_json + with open(relecov_sch_path, "r") as fh: self.relecov_sch_json = json.load(fh) self.label_prop_dict = {} @@ -70,6 +71,8 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None self.label_prop_dict[values["label"]] = prop except KeyError: continue + self.schema_name = self.relecov_sch_json["schema"] + self.schema_version = self.relecov_sch_json["version"] def fetch_metadata_file(folder, file_name): """Fetch the metadata file folder Directory to fetch metadata file @@ -126,6 +129,8 @@ def include_fixed_data(self): "sample_description": "Sample for surveillance", } fixed_data.update(self.configuration.get_configuration("ENA_configuration")) + fixed_data["schema_name"] = self.schema_name + fixed_data["version"] = self.schema_version return fixed_data def include_fields_already_set(self, row_sample): @@ -258,12 +263,11 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): """ # Add experiment_alias and run_alias row_sample["experiment_alias"] = str( - row_sample["fastq_r1"] + "_" + row_sample["fastq_r2"] + row_sample["sequence_file_R1_fastq"] + "_" + row_sample["sequence_file_R2_fastq"] ) row_sample["run_alias"] = str( - row_sample["fastq_r1"] + "_" + row_sample["fastq_r2"] + row_sample["sequence_file_R1_fastq"] + "_" + row_sample["sequence_file_R2_fastq"] ) - additional_metadata.append(row_sample) return additional_metadata From 7036a59c4aeccfc5c2ab0e3137cfeff3934e1c55 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 17 Aug 2022 22:23:07 +0200 Subject: [PATCH 0800/1454] renamed version for schema_version --- relecov_tools/read_lab_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 98f58d00..95bbf889 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -130,7 +130,7 @@ def include_fixed_data(self): } fixed_data.update(self.configuration.get_configuration("ENA_configuration")) fixed_data["schema_name"] = self.schema_name - fixed_data["version"] = self.schema_version + fixed_data["schema_version"] = self.schema_version return fixed_data def include_fields_already_set(self, row_sample): From db3a198993a1828371d406547a15993de796d495 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 17 Aug 2022 22:24:45 +0200 Subject: [PATCH 0801/1454] liting --- relecov_tools/read_lab_metadata.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 95bbf889..9341fa9f 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -263,10 +263,14 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): """ # Add experiment_alias and run_alias row_sample["experiment_alias"] = str( - row_sample["sequence_file_R1_fastq"] + "_" + row_sample["sequence_file_R2_fastq"] + row_sample["sequence_file_R1_fastq"] + + "_" + + row_sample["sequence_file_R2_fastq"] ) row_sample["run_alias"] = str( - row_sample["sequence_file_R1_fastq"] + "_" + row_sample["sequence_file_R2_fastq"] + row_sample["sequence_file_R1_fastq"] + + "_" + + row_sample["sequence_file_R2_fastq"] ) additional_metadata.append(row_sample) From 9b70cc4d186f63ccc06a7f75a80990bccdc9757c Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 17 Aug 2022 22:38:45 +0200 Subject: [PATCH 0802/1454] Including schema_name and schema_version for each sample --- relecov_tools/read_bioinfo_metadata.py | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 85325ecf..a893e300 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -66,6 +66,18 @@ def __init__( else: self.mapping_illumina = mapping_illumina + config_json = ConfigJson() + relecov_schema = config_json.get_topic_data("json_schemas", "relecov_schema") + relecov_sch_path = os.path.join( + os.path.dirname(os.path.realpath(__file__)), "schema", relecov_schema + ) + self.configuration = config_json + + with open(relecov_sch_path, "r") as fh: + self.relecov_sch_json = json.load(fh) + self.schema_name = self.relecov_sch_json["schema"] + self.schema_version = self.relecov_sch_json["version"] + def bioinfo_parse(self, file_name): """Fetch the metadata file folder Directory to fetch metadata file file_name metadata file name @@ -297,6 +309,9 @@ def bioinfo_parse(self, file_name): bioinfo_list[str(sample_name)] = bioinfo_dict c = c + 1 + # adding schema_name and schema_version + bioinfo_dict["schema_name"] = self.schema_name + bioinfo_dict["schema_version"] = self.schema_version json_file = "bioinfo_metadata.json" output_path = os.path.join(self.output_folder, json_file) From d74540dcbf2845f9eaf304a7ccb63ce90934dfb6 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 19 Aug 2022 11:08:19 +0200 Subject: [PATCH 0803/1454] added regex function for md5sum --- relecov_tools/read_bioinfo_metadata.py | 29 ++++++++------------------ 1 file changed, 9 insertions(+), 20 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index a893e300..05a59089 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -229,26 +229,15 @@ def bioinfo_parse(self, file_name): cons_array.values[i, 1] ) # fields from md5 file - bioinfo_dict["consensus_sequence_R1_name"] = str( - md5_info.loc[ - md5_info[0].str.contains(bioinfo_dict["sample_name"]) - ].values[0, 2] - ) - bioinfo_dict["consensus_sequence_R2_name"] = str( - md5_info.loc[ - md5_info[0].str.contains(bioinfo_dict["sample_name"]) - ].values[1, 2] - ) - bioinfo_dict["consensus_sequence_R1_md5"] = str( - md5_info.loc[ - md5_info[0].str.contains(bioinfo_dict["sample_name"]) - ].values[0, 1] - ) - bioinfo_dict["consensus_sequence_R2_md5"] = str( - md5_info.loc[ - md5_info[0].str.contains(bioinfo_dict["sample_name"]) - ].values[1, 1] - ) + + for i in range(len(md5_info)): + g = re.match(str(bioinfo_dict["sample_name"]) + "$", md5_info[0][i]) + if g != None: + bioinfo_dict["consensus_sequence_R1_name"] = md5_info[2][i] + bioinfo_dict["consensus_sequence_R2_name"] = md5_info[2][i + 1] + bioinfo_dict["consensus_sequence_R1_md5"] = md5_info[1][i] + bioinfo_dict["consensus_sequence_R2_md5"] = md5_info[1][i + 1] + break # fields from software version file bioinfo_dict["dehosting_method_software_version"] = str( From a6f20a8f8083e795855f4508fd739dd8358021cc Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 19 Aug 2022 11:12:47 +0200 Subject: [PATCH 0804/1454] lintin --- relecov_tools/read_bioinfo_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 05a59089..aa8c15bc 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -232,7 +232,7 @@ def bioinfo_parse(self, file_name): for i in range(len(md5_info)): g = re.match(str(bioinfo_dict["sample_name"]) + "$", md5_info[0][i]) - if g != None: + if g not None: bioinfo_dict["consensus_sequence_R1_name"] = md5_info[2][i] bioinfo_dict["consensus_sequence_R2_name"] = md5_info[2][i + 1] bioinfo_dict["consensus_sequence_R1_md5"] = md5_info[1][i] From 7cba3f1c6a878b1e464b790cc4f8c937a9fb4a00 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 19 Aug 2022 11:14:03 +0200 Subject: [PATCH 0805/1454] lintin --- relecov_tools/read_bioinfo_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index aa8c15bc..05a59089 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -232,7 +232,7 @@ def bioinfo_parse(self, file_name): for i in range(len(md5_info)): g = re.match(str(bioinfo_dict["sample_name"]) + "$", md5_info[0][i]) - if g not None: + if g != None: bioinfo_dict["consensus_sequence_R1_name"] = md5_info[2][i] bioinfo_dict["consensus_sequence_R2_name"] = md5_info[2][i + 1] bioinfo_dict["consensus_sequence_R1_md5"] = md5_info[1][i] From 747d7f055ebe010c408d36a0e0b656714a543c29 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 19 Aug 2022 11:15:18 +0200 Subject: [PATCH 0806/1454] lintin --- relecov_tools/read_bioinfo_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 05a59089..3e5c166a 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -232,7 +232,7 @@ def bioinfo_parse(self, file_name): for i in range(len(md5_info)): g = re.match(str(bioinfo_dict["sample_name"]) + "$", md5_info[0][i]) - if g != None: + if g is not None: bioinfo_dict["consensus_sequence_R1_name"] = md5_info[2][i] bioinfo_dict["consensus_sequence_R2_name"] = md5_info[2][i + 1] bioinfo_dict["consensus_sequence_R1_md5"] = md5_info[1][i] From b39a3cf056f3965cc3f09f6d0dc528db9df978de Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 19 Aug 2022 13:06:30 +0200 Subject: [PATCH 0807/1454] added exception for -2 and -B samples in batch --- relecov_tools/read_bioinfo_metadata.py | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 3e5c166a..11e9033b 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -4,6 +4,7 @@ import logging import json import datetime +from operator import contains import re import rich.console @@ -231,7 +232,19 @@ def bioinfo_parse(self, file_name): # fields from md5 file for i in range(len(md5_info)): - g = re.match(str(bioinfo_dict["sample_name"]) + "$", md5_info[0][i]) + if "-2" in bioinfo_dict["sequence_file_R1_fastq"]: + g = re.match( + str(bioinfo_dict["sequence_file_R1_fastq"][0:8]) + "$", + md5_info[0][i], + ) + elif "-B" in bioinfo_dict["sequence_file_R1_fastq"]: + + g = re.match( + str(bioinfo_dict["sequence_file_R1_fastq"][0:8]) + "$", + md5_info[0][i], + ) + else: + g = re.match(str(bioinfo_dict["sample_name"]) + "$", md5_info[0][i]) if g is not None: bioinfo_dict["consensus_sequence_R1_name"] = md5_info[2][i] bioinfo_dict["consensus_sequence_R2_name"] = md5_info[2][i + 1] From 8e6c483424fb63c5266e9d52f231b73c840a8593 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 19 Aug 2022 13:09:51 +0200 Subject: [PATCH 0808/1454] lintin --- relecov_tools/read_bioinfo_metadata.py | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 11e9033b..28b84e1e 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -4,7 +4,6 @@ import logging import json import datetime -from operator import contains import re import rich.console From acacdf3b7a7f4214a424fc84a1375d5460aa7cf6 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 19 Aug 2022 14:27:25 +0200 Subject: [PATCH 0809/1454] changes in example data --- .../bioinfo_metadata.json | 46 ------ ...B_TEST_2022_04_25_00_03_GISAID_mapped.json | 152 ------------------ 2 files changed, 198 deletions(-) delete mode 100644 relecov_tools/example_data/5.read_bioinfo_metadata/bioinfo_metadata.json delete mode 100644 relecov_tools/example_data/ena_upload_module/processed_METADATA_LAB_TEST_2022_04_25_00_03_GISAID_mapped.json diff --git a/relecov_tools/example_data/5.read_bioinfo_metadata/bioinfo_metadata.json b/relecov_tools/example_data/5.read_bioinfo_metadata/bioinfo_metadata.json deleted file mode 100644 index f8831cc5..00000000 --- a/relecov_tools/example_data/5.read_bioinfo_metadata/bioinfo_metadata.json +++ /dev/null @@ -1,46 +0,0 @@ -{ - "sample_name": "", - "dehosting_method": "", - "if_assembly_other": "", - "assembly_params": "", - "variant_calling": "", - "if_variant_calling_other": "", - "variant_calling_params": "", - "consensus_sequence_name": "", - "consensus_sequence_name_md5": "", - "consensus_sequence_filepath": "", - "consensus_sequence_software_name": "", - "if_consensus_other": "", - "consensus_sequence_software_version": "", - "consensus_criteria": "", - "depth_of_coverage_threshold": "", - "number_of_base_pairs_sequenced": "", - "consensus_genome_length": "", - "ns_per_100_kbp": "", - "reference_genome_accession": "", - "bioinformatics_protocol": "", - "if_bioinformatic_protocol_is_other_specify": "", - "bioinformatic_protocol_version": "", - "commercial/open-source/both": "", - "preprocessing": "", - "if_preprocessing_other": "", - "preprocessing_params": "", - "mapping": "", - "if_mapping_other": "", - "mapping_params": "", - "lineage_name": "", - "lineage_analysis_software_name": "", - "if_lineage_identification_other": "", - "lineage_analysis_software_version": "", - "variant_designation": "", - "per_qc_filtered": "", - "per_reads_host": "", - "per_reads_virus": "", - "per_unmapped": "", - "per_genome _greater_10x": "", - "median_depth_of_coverage_value": "", - "per_Ns": "", - "number_of_variants_AF_greater_75percent": "", - "number_of_variants_with_effect": "", - "long_table_path": "" -} \ No newline at end of file diff --git a/relecov_tools/example_data/ena_upload_module/processed_METADATA_LAB_TEST_2022_04_25_00_03_GISAID_mapped.json b/relecov_tools/example_data/ena_upload_module/processed_METADATA_LAB_TEST_2022_04_25_00_03_GISAID_mapped.json deleted file mode 100644 index edf69533..00000000 --- a/relecov_tools/example_data/ena_upload_module/processed_METADATA_LAB_TEST_2022_04_25_00_03_GISAID_mapped.json +++ /dev/null @@ -1,152 +0,0 @@ -[ - { - "authors": "Inmaculada Casas,Maria de la Montaña", - "collecting_address": "P.º Isabel la Católica, 1-3", - "collection_date": "2021/04/13", - "gender": "Mujer", - "host": "Homo Sapiens", - "location": "Spain", - "patient_age": 55, - "sequencing_technology": "Illumina MiSeq", - "specimen_source": "Nasopharynx aspirate", - "submitter": "EPI_ISL_11222687", - "submitting_lab": "Instituto de Salud Carlos III ", - "type": "betacoronavirus", - "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2022" - }, - { - "authors": "Inmaculada Casas,Maria de la Montaña", - "collecting_address": "P.º Isabel la Católica, 1-3", - "collection_date": "2021/03/31", - "gender": "Hombre", - "host": "Homo Sapiens", - "location": "Spain", - "patient_age": 59, - "sequencing_technology": "Illumina MiSeq", - "specimen_source": "Nasopharynx aspirate", - "submitter": "EPI_ISL_11222688", - "submitting_lab": "Instituto de Salud Carlos III ", - "type": "betacoronavirus", - "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2023" - }, - { - "authors": "Inmaculada Casas,Maria de la Montaña", - "collecting_address": "P.º Isabel la Católica, 1-3", - "collection_date": "2022/01/13", - "gender": "Mujer", - "host": "Homo Sapiens", - "location": "Spain", - "patient_age": 8, - "sequencing_technology": "Illumina MiSeq", - "specimen_source": "Nasopharynx aspirate", - "submitter": "EPI_ISL_11222689", - "submitting_lab": "Instituto de Salud Carlos III ", - "type": "betacoronavirus", - "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2024" - }, - { - "authors": "Inmaculada Casas,Maria de la Montaña", - "collecting_address": "P.º Isabel la Católica, 1-3", - "collection_date": "2022/01/11", - "gender": "Mujer", - "host": "Homo Sapiens", - "location": "Spain", - "patient_age": 9, - "sequencing_technology": "Illumina MiSeq", - "specimen_source": "Nasopharynx aspirate", - "submitter": "EPI_ISL_11222690", - "submitting_lab": "Instituto de Salud Carlos III ", - "type": "betacoronavirus", - "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2025" - }, - { - "authors": "Inmaculada Casas,Maria de la Montaña", - "collecting_address": "P.º Isabel la Católica, 1-3", - "collection_date": "2022/01/10", - "gender": "Hombre", - "host": "Homo Sapiens", - "location": "Spain", - "patient_age": 31, - "sequencing_technology": "Illumina MiSeq", - "specimen_source": "Nasopharynx aspirate", - "submitter": "EPI_ISL_11222691", - "submitting_lab": "Instituto de Salud Carlos III ", - "type": "betacoronavirus", - "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2026" - }, - { - "authors": "Inmaculada Casas,Maria de la Montaña", - "collecting_address": "P.º Isabel la Católica, 1-3", - "collection_date": "2022/01/12", - "gender": "Mujer", - "host": "Homo Sapiens", - "location": "Spain", - "patient_age": 27, - "sequencing_technology": "Illumina MiSeq", - "specimen_source": "Nasopharynx aspirate", - "submitter": "EPI_ISL_11222692", - "submitting_lab": "Instituto de Salud Carlos III ", - "type": "betacoronavirus", - "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2027" - }, - { - "authors": "Inmaculada Casas,Maria de la Montaña", - "collecting_address": "S. Juan Bosco, 15", - "collection_date": "2022/01/02", - "gender": "Mujer", - "host": "Homo Sapiens", - "location": "Spain", - "patient_age": 42, - "sequencing_technology": "Illumina MiSeq", - "specimen_source": "Nasopharynx aspirate", - "submitter": "EPI_ISL_11222693", - "submitting_lab": "Instituto de Salud Carlos III ", - "type": "betacoronavirus", - "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2028" - }, - { - "authors": "Inmaculada Casas,Maria de la Montaña", - "collecting_address": "S. Juan Bosco, 15", - "collection_date": "2022/01/23", - "gender": "Hombre", - "host": "Homo Sapiens", - "location": "Spain", - "patient_age": 40, - "sequencing_technology": "Illumina MiSeq", - "specimen_source": "Nasopharynx aspirate", - "submitter": "EPI_ISL_11222694", - "submitting_lab": "Instituto de Salud Carlos III ", - "type": "betacoronavirus", - "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2029" - }, - { - "authors": "Inmaculada Casas,Maria de la Montaña", - "collecting_address": "S. Juan Bosco, 15", - "collection_date": "2022/01/18", - "gender": "Hombre", - "host": "Homo Sapiens", - "location": "Spain", - "patient_age": 53, - "sequencing_technology": "Illumina MiSeq", - "specimen_source": "Nasopharynx aspirate", - "submitter": "EPI_ISL_11222695", - "submitting_lab": "Instituto de Salud Carlos III ", - "type": "betacoronavirus", - "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2030" - }, - { - "authors": "Inmaculada Casas,Maria de la Montaña", - "collecting_address": "S. Juan Bosco, 15", - "collection_date": "2022/01/19", - "gender": "Male", - "host": "Homo Sapiens", - "location": "Spain", - "patient_age": 96, - "sequencing_technology": "Illumina MiSeq", - "specimen_source": "Nasopharynx aspirate", - "submitter": "EPI_ISL_11222696", - "submitting_lab": "Instituto de Salud Carlos III ", - "type": "betacoronavirus", - "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2031" - } -] \ No newline at end of file From 31230cc32cf8f7571a42d69c44d9cd7462c59dc5 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 19 Aug 2022 14:29:02 +0200 Subject: [PATCH 0810/1454] changes in example data folder --- .../ENA_TEST1_V1.R1.fastq.gz | Bin 4221 -> 0 bytes .../example_data/0.download_module/README | 9 +- .../1.read_lab_metadata_module/README | 3 + .../lab_metadata_20220208.xlsx | Bin 403686 -> 0 bytes .../samples_data_COD_test_01_20220422.json | 82 -- .../2.validate_module/METADATA_LAB_TEST.xlsx | Bin 493368 -> 0 bytes .../example_data/2.validate_module/README | 3 +- .../processed_METADATA_LAB_TEST.json | 782 ------------------ .../example_data/3.map_module/README | 7 +- ..._LAB_TEST_2022_04_28_21_05_ENA_mapped.json | 452 ---------- 10 files changed, 15 insertions(+), 1323 deletions(-) delete mode 100644 relecov_tools/example_data/0.download_module/ENA_TEST1_V1.R1.fastq.gz delete mode 100755 relecov_tools/example_data/1.read_lab_metadata_module/lab_metadata_20220208.xlsx delete mode 100644 relecov_tools/example_data/1.read_lab_metadata_module/samples_data_COD_test_01_20220422.json delete mode 100644 relecov_tools/example_data/2.validate_module/METADATA_LAB_TEST.xlsx delete mode 100644 relecov_tools/example_data/2.validate_module/processed_METADATA_LAB_TEST.json delete mode 100644 relecov_tools/example_data/ena_upload_module/processed_METADATA_LAB_TEST_2022_04_28_21_05_ENA_mapped.json diff --git a/relecov_tools/example_data/0.download_module/ENA_TEST1_V1.R1.fastq.gz b/relecov_tools/example_data/0.download_module/ENA_TEST1_V1.R1.fastq.gz deleted file 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b/relecov_tools/example_data/1.read_lab_metadata_module/README index 7ddb82c4..69b88943 100644 --- a/relecov_tools/example_data/1.read_lab_metadata_module/README +++ b/relecov_tools/example_data/1.read_lab_metadata_module/README @@ -3,3 +3,6 @@ The input for this module is: -m metadata_lab.xlsx -s samples_data.json (with md5 and fastq.gz name for each sample) generated by downloaded module -o output folder where the json file will be generated + +The output of this module is processed_metadata_lab.json + diff --git a/relecov_tools/example_data/1.read_lab_metadata_module/lab_metadata_20220208.xlsx b/relecov_tools/example_data/1.read_lab_metadata_module/lab_metadata_20220208.xlsx deleted file mode 100755 index 7725cae7ebc7ed6779c3117cdab678b3400989be..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 403686 zcmeEvbyU>b-ad#lND0yn3Q|hvNSA~(C?VY-Ac0K7PqPu*dus~#G?nTItD@uM){O=!KO2&UV(P{hA42;wWE-Nqgl&YNTgQqabQwe!G=t* 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z#Ujq?axDpo{6wjLkwx9+o6p^4)#vU~Y@nBOU0*^%f5rrf@Ba`gCZ|7p7o8QKyUp)& h(I1De;`7hnMtqlvAk9cf%mDwVgA8#z1dLmW{|`%puWSGS diff --git a/relecov_tools/example_data/2.validate_module/README b/relecov_tools/example_data/2.validate_module/README index 699c53b0..e38dc34f 100644 --- a/relecov_tools/example_data/2.validate_module/README +++ b/relecov_tools/example_data/2.validate_module/README @@ -1,6 +1,7 @@ -This module will validate the processed_metadata_lab_XXXX.json (output of the read_lab_metadata) against the metadata_lab_XXXXX_xlsx +This module will validate the processed_metadata_lab_XXXX.json (output of the read_lab_metadata) against the metadata_lab_XXXXX.xlsx For this module the input is: - processed_metadata_lab_XXXX.json - metadata_lab_XXXXX_xlsx - output folder where the validation errors will be created +The output of this module will be a series of error in case something is wrong. If there are no mistakes no output is generated. diff --git a/relecov_tools/example_data/2.validate_module/processed_METADATA_LAB_TEST.json b/relecov_tools/example_data/2.validate_module/processed_METADATA_LAB_TEST.json deleted file mode 100644 index eb51fcc1..00000000 --- a/relecov_tools/example_data/2.validate_module/processed_METADATA_LAB_TEST.json +++ /dev/null @@ -1,782 +0,0 @@ -[ - { - "amplicon_protocol": "ARTIC", - "amplicon_version": "v.4", - "analysis_author": "Inmaculada Casas", - "anatomical_material": "Nasopharynx aspirate", - "author_submitter": "Maria de la Montaña", - "authors": "Inmaculada Casas,Maria de la Montaña", - "biosample_accession_ENA": "ERS123456", - "collecting_institution": "HU Virgen de la Arrixaca", - "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", - "collecting_institution_email": "", - "collecting_lab_sample_id": "1197860", - "collection_device": "Swab", - "collector_name": "Maria de la Montaña", - "common_name": "PEPITO", - "design_description": "Design Description", - "diagnostic_pcr_Ct_value_1": "45", - "diagnostic_pcr_Ct_value_2": "34", - "enrichment_protocol": "Amplicon", - "environmental_material": "Other", - "environmental_site": "Earth surface", - "experiment_alias": "", - "experiment_title": "Example project for ENA submission RELECOV", - "fastq_r1_md5": "f2facbd1d6c7e0972074ced31ccbfd8e", - "fastq_r2_md5": "fd9948be8da7a38b0f80659dfc21aeea", - "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", - "gene_name_1": "ORF 1ab", - "gene_name_2": "S", - "geo_loc_city": "Murcia", - "geo_loc_country": "Spain", - "geo_loc_latitude": "37.9861", - "geo_loc_longitude": "-1.1303", - "geo_loc_state": "Murcia", - "gisaid_id": "EPI_ISL_11222687", - "host_age": "55", - "host_common_name": "Human", - "host_disease": "COVID-19", - "host_gender": "Female", - "host_scientific_name": "Homo Sapiens", - "if_amplicon_protocol_if_other_especify": "", - "if_enrichment_protocol_is_other_specify": "", - "isolate_sample_id": "1197860", - "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "library_layout": "SINGLE", - "library_preparation_kit": "Truseq Nano", - "library_selection": "RT-PCR", - "library_source": "RNA", - "library_strategy": "WGS", - "microbiology_lab_sample_id": "220407", - "number_of_samples_in_run": "96", - "organism": "Severe acute respiratory syndrome coronavirus 2", - "public_health_sample_id_sivies": "2022CEU01394", - "purpose_of_sampling": "Whole Genome Sequencing", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", - "rna_extraction_protocol": "In-house method for Opetrons robots", - "runID": "MiSeq_GEN_267_20220208_ICasas", - "run_alias": "", - "sample_collection_date": "2021-04-13", - "sample_description": "Sample for surveillance", - "sample_received_date": "2021-05-13", - "sample_storage_conditions": " -80ºC", - "sequence_file_R1_fastq": "ABC123_S1_L001_R1_001.fastq.gz", - "sequence_file_R2_fastq": "ABC123_S1_L001_R2_001.fastq.gz", - "sequencing_date": "2022-02-22", - "sequencing_instrument_model": "Illumina MiSeq", - "sequencing_instrument_platform": "Illumina", - "sequencing_sample_id": 214824, - "study_alias": "RELECOV", - "study_id": "ERP137164", - "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "", - "submitting_institution": "Instituto de Salud Carlos III ", - "submitting_lab_sequence_id": "202201751", - "tax_id": "2697049", - "type": "betacoronavirus", - "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2022" - }, - { - "amplicon_protocol": "ARTIC", - "amplicon_version": "v.4", - "analysis_author": "Inmaculada Casas", - "anatomical_material": "Nasopharynx aspirate", - "author_submitter": "Maria de la Montaña", - "authors": "Inmaculada Casas,Maria de la Montaña", - "biosample_accession_ENA": "ERS123457", - "collecting_institution": "HU Virgen de la Arrixaca", - "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", - "collecting_institution_email": "", - "collecting_lab_sample_id": "1197824", - "collection_device": "Swab", - "collector_name": "Maria de la Montaña", - "common_name": "PEPITO", - "design_description": "Design Description", - "diagnostic_pcr_Ct_value_1": "12", - "diagnostic_pcr_Ct_value_2": "16", - "enrichment_protocol": "Amplicon", - "environmental_material": "Other", - "environmental_site": "Earth surface", - "experiment_alias": "", - "experiment_title": "Example project for ENA submission RELECOV", - "fastq_r1_md5": "9a460a812086516536c1a1023ab5f7fe", - "fastq_r2_md5": "41cd79b8a167d85eb06309207fd120cf", - "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", - "gene_name_1": "ORF 1ab", - "gene_name_2": "S", - "geo_loc_city": "Murcia", - "geo_loc_country": "Spain", - "geo_loc_latitude": "37.9861", - "geo_loc_longitude": "-1.1303", - "geo_loc_state": "Murcia", - "gisaid_id": "EPI_ISL_11222688", - "host_age": "59", - "host_common_name": "Human", - "host_disease": "COVID-19", - "host_gender": "Male", - "host_scientific_name": "Homo Sapiens", - "if_amplicon_protocol_if_other_especify": "", - "if_enrichment_protocol_is_other_specify": "", - "isolate_sample_id": "1197824", - "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "library_layout": "SINGLE", - "library_preparation_kit": "Truseq Nano", - "library_selection": "RT-PCR", - "library_source": "RNA", - "library_strategy": "WGS", - "microbiology_lab_sample_id": "220433", - "number_of_samples_in_run": "96", - "organism": "Severe acute respiratory syndrome coronavirus 2", - "public_health_sample_id_sivies": "2022CEU01469", - "purpose_of_sampling": "Whole Genome Sequencing", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", - "rna_extraction_protocol": "In-house method for Opetrons robots", - "runID": "MiSeq_GEN_267_20220208_ICasas", - "run_alias": "", - "sample_collection_date": "2021-03-31", - "sample_description": "Sample for surveillance", - "sample_received_date": "2021-05-13", - "sample_storage_conditions": " -80ºC", - "sequence_file_R1_fastq": "ABC123_S1_L001_R1_002.fastq.gz", - "sequence_file_R2_fastq": "ABC123_S1_L001_R2_002.fastq.gz", - "sequencing_date": "2022-02-22", - "sequencing_instrument_model": "Illumina MiSeq", - "sequencing_instrument_platform": "Illumina", - "sequencing_sample_id": 214832, - "study_alias": "RELECOV", - "study_id": "ERP137164", - "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "", - "submitting_institution": "Instituto de Salud Carlos III ", - "submitting_lab_sequence_id": "202201678", - "tax_id": "2697049", - "type": "betacoronavirus", - "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2023" - }, - { - "amplicon_protocol": "ARTIC", - "amplicon_version": "v.4", - "analysis_author": "Inmaculada Casas", - "anatomical_material": "Nasopharynx aspirate", - "author_submitter": "Maria de la Montaña", - "authors": "Inmaculada Casas,Maria de la Montaña", - "biosample_accession_ENA": "ERS123458", - "collecting_institution": "HU Virgen de la Arrixaca", - "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", - "collecting_institution_email": "", - "collecting_lab_sample_id": "1197767", - "collection_device": "Swab", - "collector_name": "Maria de la Montaña", - "common_name": "PEPITO", - "design_description": "Design Description", - "diagnostic_pcr_Ct_value_1": "45", - "diagnostic_pcr_Ct_value_2": "41", - "enrichment_protocol": "Amplicon", - "environmental_material": "Other", - "environmental_site": "Earth surface", - "experiment_alias": "", - "experiment_title": "Example project for ENA submission RELECOV", - "fastq_r1_md5": "c78fcb585a0f44734ce8c2aebf3eff33", - "fastq_r2_md5": "8361d5a6b50279fbc8c93226ecc3568a", - "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", - "gene_name_1": "ORF 1ab", - "gene_name_2": "S", - "geo_loc_city": "Murcia", - "geo_loc_country": "Spain", - "geo_loc_latitude": "37.9861", - "geo_loc_longitude": "-1.1303", - "geo_loc_state": "Murcia", - "gisaid_id": "EPI_ISL_11222689", - "host_age": "8", - "host_common_name": "Human", - "host_disease": "COVID-19", - "host_gender": "Female", - "host_scientific_name": "Homo Sapiens", - "if_amplicon_protocol_if_other_especify": "", - "if_enrichment_protocol_is_other_specify": "", - "isolate_sample_id": "1197767", - "library_kit": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "library_layout": "SINGLE", - "library_preparation_kit": "Truseq Nano", - "library_selection": "RT-PCR", - "library_source": "RNA", - "library_strategy": "WGS", - "microbiology_lab_sample_id": "220435", - "number_of_samples_in_run": "96", - "organism": "Severe acute respiratory syndrome coronavirus 2", - "public_health_sample_id_sivies": "2022CEU03926", - "purpose_of_sampling": "Whole Genome Sequencing", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422", - "rna_extraction_protocol": "In-house method for Opetrons robots", - "runID": "MiSeq_GEN_267_20220208_ICasas", - "run_alias": "", - "sample_collection_date": "2022-01-13", - "sample_description": "Sample for surveillance", - "sample_received_date": "2022-01-18", - "sample_storage_conditions": " -80ºC", - "sequence_file_R1_fastq": "ABC123_S1_L001_R1_003.fastq.gz", - "sequence_file_R2_fastq": "ABC123_S1_L001_R2_003.fastq.gz", - "sequencing_date": "2022-02-22", - "sequencing_instrument_model": "Illumina MiSeq", - "sequencing_instrument_platform": "Illumina", - "sequencing_sample_id": 220338, - "study_alias": "RELECOV", - "study_id": "ERP137164", - "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "", - "submitting_institution": "Instituto de Salud Carlos III ", - "submitting_lab_sequence_id": "202201853", - "tax_id": "2697049", - "type": "betacoronavirus", - "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2024" - }, - { - "amplicon_protocol": "ARTIC", - "amplicon_version": "v.4", - "analysis_author": "Inmaculada Casas", - "anatomical_material": "Nasopharynx aspirate", - "author_submitter": "Maria de la Montaña", - "authors": "Inmaculada Casas,Maria de la Montaña", - "biosample_accession_ENA": "ERS123459", - "collecting_institution": "HU Virgen de la Arrixaca", - "collecting_institution_address": "Ctra. 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"study_alias": "RELECOV", - "study_id": "ERP137164", - "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "", - "submitting_institution": "Instituto de Salud Carlos III ", - "submitting_lab_sequence_id": "202203166", - "tax_id": "2697049", - "type": "betacoronavirus", - "virus_name": "hCoV-19/Spain/CT-HUJT-RB31776/2031" - } -] diff --git a/relecov_tools/example_data/3.map_module/README b/relecov_tools/example_data/3.map_module/README index f4936fdb..a6b8a63a 100644 --- a/relecov_tools/example_data/3.map_module/README +++ b/relecov_tools/example_data/3.map_module/README @@ -1,6 +1,7 @@ This module will map the metadata_lab.json to the selected DB (ENA or GISAID) -This moduleinput is: +This module input is: -j processed_metadata_lab.json -- d ENA or GISAID +-d ENA or GISAID -o output folder where json file will be generated -- + +The output of this module is processed_metadata_lab_ENA_mapped.json diff --git a/relecov_tools/example_data/ena_upload_module/processed_METADATA_LAB_TEST_2022_04_28_21_05_ENA_mapped.json b/relecov_tools/example_data/ena_upload_module/processed_METADATA_LAB_TEST_2022_04_28_21_05_ENA_mapped.json deleted file mode 100644 index 684be7bc..00000000 --- a/relecov_tools/example_data/ena_upload_module/processed_METADATA_LAB_TEST_2022_04_28_21_05_ENA_mapped.json +++ /dev/null @@ -1,452 +0,0 @@ -[ - { - "collecting_institution": "HU Virgen de la Arrixaca", - "collection_date": "2021-04-13", - "collector_name": "Maria de la Montaña", - "common_name": "PEPITO", - "design_description": "Design Description", - "experiment_alias": "", - "experiment_title": "Example project for ENA submission RELECOV", - "fastq_r1_md5": "f2facbd1d6c7e0972074ced31ccbfd8e", - "fastq_r2_md5": "fd9948be8da7a38b0f80659dfc21aeea", - "file_type": "fastq", - "geographic location (latitude)": "37.9861", - "geographic location (longitude)": "-1.1303", - "geographic_location_(country_and/or_sea)": "Spain", - "host_common_name": "Human", - "host_scientific_name": "Homo Sapiens", - "host_sex": "Female", - "instrument_model": "Illumina MiSeq", - "isolate": "1197860", - "isolation source host-associated": "Nasopharynx aspirate", - "isolation source non-host-associated": "Other", - "library_layout": "SINGLE", - "library_name": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "library_selection": "RT-PCR", - "library_source": "RNA", - "library_strategy": "WGS", - "platform": "Illumina", - "purpose_sampling": "Whole Genome Sequencing", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_001.fastq.gz", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_001.fastq.gz", - "receipt_date": "2021-05-13", - "run_alias": "", - "sample_description": "Sample for surveillance", - "sample_name": "1197860", - "sample_storage_conditions": " -80ºC", - "sample_title": "1197860", - "scientific_name": "Severe acute respiratory syndrome coronavirus 2", - "sequence_file_R1_fastq": "ABC123_S1_L001_R1_001.fastq.gz", - "sequence_file_R2_fastq": "ABC123_S1_L001_R2_001.fastq.gz", - "study_abstract": "RELECOV Spanish Network for genomics surveillance", - "study_alias": "RELECOV", - "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "Whole Genome Sequencing", - "taxon_id": "2697049" - }, - { - "collecting_institution": "HU Virgen de la Arrixaca", - "collection_date": "2021-03-31", - "collector_name": "Maria de la Montaña", - "common_name": "PEPITO", - "design_description": "Design Description", - "experiment_alias": "", - "experiment_title": "Example project for ENA submission RELECOV", - "fastq_r1_md5": "9a460a812086516536c1a1023ab5f7fe", - "fastq_r2_md5": "41cd79b8a167d85eb06309207fd120cf", - "file_type": "fastq", - "geographic location (latitude)": "37.9861", - "geographic location (longitude)": "-1.1303", - "geographic_location_(country_and/or_sea)": "Spain", - "host_common_name": "Human", - "host_scientific_name": "Homo Sapiens", - "host_sex": "Male", - "instrument_model": "Illumina MiSeq", - "isolate": "1197824", - "isolation source host-associated": "Nasopharynx aspirate", - "isolation source non-host-associated": "Other", - "library_layout": "SINGLE", - "library_name": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "library_selection": "RT-PCR", - "library_source": "RNA", - "library_strategy": "WGS", - "platform": "Illumina", - "purpose_sampling": "Whole Genome Sequencing", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_002.fastq.gz", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_002.fastq.gz", - "receipt_date": "2021-05-13", - "run_alias": "", - "sample_description": "Sample for surveillance", - "sample_name": "1197824", - "sample_storage_conditions": " -80ºC", - "sample_title": "1197824", - "scientific_name": "Severe acute respiratory syndrome coronavirus 2", - "sequence_file_R1_fastq": "ABC123_S1_L001_R1_002.fastq.gz", - "sequence_file_R2_fastq": "ABC123_S1_L001_R2_002.fastq.gz", - "study_abstract": "RELECOV Spanish Network for genomics surveillance", - "study_alias": "RELECOV", - "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "Whole Genome Sequencing", - "taxon_id": "2697049" - }, - { - "collecting_institution": "HU Virgen de la Arrixaca", - "collection_date": "2022-01-13", - "collector_name": "Maria de la Montaña", - "common_name": "PEPITO", - "design_description": "Design Description", - "experiment_alias": "", - "experiment_title": "Example project for ENA submission RELECOV", - "fastq_r1_md5": "c78fcb585a0f44734ce8c2aebf3eff33", - "fastq_r2_md5": "8361d5a6b50279fbc8c93226ecc3568a", - "file_type": "fastq", - "geographic location (latitude)": "37.9861", - "geographic location (longitude)": "-1.1303", - "geographic_location_(country_and/or_sea)": "Spain", - "host_common_name": "Human", - "host_scientific_name": "Homo Sapiens", - "host_sex": "Female", - "instrument_model": "Illumina MiSeq", - "isolate": "1197767", - "isolation source host-associated": "Nasopharynx aspirate", - "isolation source non-host-associated": "Other", - "library_layout": "SINGLE", - "library_name": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "library_selection": "RT-PCR", - "library_source": "RNA", - "library_strategy": "WGS", - "platform": "Illumina", - "purpose_sampling": "Whole Genome Sequencing", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_003.fastq.gz", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_003.fastq.gz", - "receipt_date": "2022-01-18", - "run_alias": "", - "sample_description": "Sample for surveillance", - "sample_name": "1197767", - "sample_storage_conditions": " -80ºC", - "sample_title": "1197767", - "scientific_name": "Severe acute respiratory syndrome coronavirus 2", - "sequence_file_R1_fastq": "ABC123_S1_L001_R1_003.fastq.gz", - "sequence_file_R2_fastq": "ABC123_S1_L001_R2_003.fastq.gz", - "study_abstract": "RELECOV Spanish Network for genomics surveillance", - "study_alias": "RELECOV", - "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "Whole Genome Sequencing", - "taxon_id": "2697049" - }, - { - "collecting_institution": "HU Virgen de la Arrixaca", - "collection_date": "2022-01-11", - "collector_name": "Maria de la Montaña", - "common_name": "PEPITO", - "design_description": "Design Description", - "experiment_alias": "", - "experiment_title": "Example project for ENA submission RELECOV", - 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"library_selection": "RT-PCR", - "library_source": "RNA", - "library_strategy": "WGS", - "platform": "Illumina", - "purpose_sampling": "Whole Genome Sequencing", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_009.fastq.gz", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_009.fastq.gz", - "receipt_date": "2022-01-26", - "run_alias": "", - "sample_description": "Sample for surveillance", - "sample_name": "1197689", - "sample_storage_conditions": " -80ºC", - "sample_title": "1197689", - "scientific_name": "Severe acute respiratory syndrome coronavirus 2", - "sequence_file_R1_fastq": "ABC123_S1_L001_R1_009.fastq.gz", - "sequence_file_R2_fastq": "ABC123_S1_L001_R2_009.fastq.gz", - "study_abstract": "RELECOV Spanish Network for genomics surveillance", - "study_alias": "RELECOV", - "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "Whole Genome Sequencing", - "taxon_id": "2697049" - }, - { - "collecting_institution": "HU de Donostia", - "collection_date": "2022-01-19", - "collector_name": "Maria de la Montaña", - "common_name": "PEPITO", - "design_description": "Design Description", - "experiment_alias": "", - "experiment_title": "Example project for ENA submission RELECOV", - "fastq_r1_md5": "a86f4fa0c92d76df34fd000a29d1cdd3", - "fastq_r2_md5": "8c4309dc00d725496c48bee6da0e4bbf", - "file_type": "fastq", - "geographic location (latitude)": "43.3200", - "geographic location (longitude)": "-1.9800", - "geographic_location_(country_and/or_sea)": "Spain", - "host_common_name": "Human", - "host_scientific_name": "Homo Sapiens", - "host_sex": "Female", - "instrument_model": "Illumina MiSeq", - "isolate": "1197685", - "isolation source host-associated": "Nasopharynx aspirate", - "isolation source non-host-associated": "Other", - "library_layout": "SINGLE", - "library_name": "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "library_selection": "RT-PCR", - "library_source": "RNA", - "library_strategy": "WGS", - "platform": "Illumina", - "purpose_sampling": "Whole Genome Sequencing", - "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R1_0010.fastq.gz", - "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220422ABC123_S1_L001_R2_0010.fastq.gz", - "receipt_date": "2022-01-26", - "run_alias": "", - "sample_description": "Sample for surveillance", - "sample_name": "1197685", - "sample_storage_conditions": " -80ºC", - "sample_title": "1197685", - "scientific_name": "Severe acute respiratory syndrome coronavirus 2", - "sequence_file_R1_fastq": "ABC123_S1_L001_R1_0010.fastq.gz", - "sequence_file_R2_fastq": "ABC123_S1_L001_R2_0010.fastq.gz", - "study_abstract": "RELECOV Spanish Network for genomics surveillance", - "study_alias": "RELECOV", - "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "Whole Genome Sequencing", - "taxon_id": "2697049" - } -] \ No newline at end of file From a347d05309c3dcd88644213a15c9e276026cbb35 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 19 Aug 2022 17:03:07 +0200 Subject: [PATCH 0811/1454] Added progress printouts during validation checks --- relecov_tools/__main__.py | 18 ++++++++++++------ relecov_tools/json_validation.py | 8 ++++++++ .../schema/institution_schemas/ISCIII.json | 4 ++-- 3 files changed, 22 insertions(+), 8 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 6092b0a2..721d6dec 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -24,13 +24,13 @@ log = logging.getLogger() +# Set up rich stderr console +stderr = rich.console.Console( + stderr=True, force_terminal=relecov_tools.utils.rich_force_colors() +) -def run_relecov_tools(): - # Set up rich stderr console - stderr = rich.console.Console( - stderr=True, force_terminal=relecov_tools.utils.rich_force_colors() - ) +def run_relecov_tools(): # Set up the rich traceback rich.traceback.install(console=stderr, width=200, word_wrap=True, extra_lines=1) @@ -205,8 +205,14 @@ def validate(json_file, json_schema, metadata, out_folder): ) = relecov_tools.json_validation.validate_json(json_file, json_schema, out_folder) if len(invalid_json) > 0: log.error("Some of the samples in json metadata were not validated") + stderr.print("[red] Some of the Samples are not validate") if not os.path.isfile(metadata): - log.error("Metadata file %s does not exists", metadata) + log.error("Metadata file %s does not exist", metadata) + stderr.print( + "[red] Unable to create excel file for invalid samples. Metadata file ", + metadata, + " does not exist", + ) exit(1) relecov_tools.json_validation.create_invalid_metadata( metadata, invalid_json, out_folder diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 7a769e30..18471db2 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -44,12 +44,14 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): if not os.path.isfile(json_data_file): stderr.print("[red] Json file does not exists") sys.exit(1) + stderr.print("[blue] Reading the json file") json_data = relecov_tools.utils.read_json_file(json_data_file) with open(json_data_file, "r") as fh: json_data = json.load(fh) validated_json_data = [] invalid_json = [] errors = {} + stderr.print("[blue] Start processing the json file") for item_row in json_data: try: validate(instance=item_row, schema=json_schema) @@ -59,6 +61,10 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): invalid_json.append(item_row) # Enviar los errores por correo # logging.handlers.SMTPHandler(mailhost=("smtp.gmail.com", 465), fromaddr=correo_isciii, toaddrs=correo_usuario, subject="Validation errors", credentials=(usurario,contraseña), secure=None, timeout=1.0) + if len(invalid_json) == 0: + stderr.print("[green] Sucessful validation") + else: + stderr.print("[red] Some samples are not validated") return validated_json_data, invalid_json, errors @@ -72,6 +78,7 @@ def create_invalid_metadata(metadata_file, invalid_json, out_folder): sample_list = [] # import pdb; pdb.set_trace() # json_data = relecov_tools.utils.read_json_file(invalid_json) + stderr.print("[red] Start preparation of invalid samples") for row in invalid_json: sample_list.append(str(row["collecting_lab_sample_id"])) wb = openpyxl.load_workbook(metadata_file) @@ -94,5 +101,6 @@ def create_invalid_metadata(metadata_file, invalid_json, out_folder): os.makedirs(out_folder, exist_ok=True) new_name = "invalid_" + os.path.basename(metadata_file) m_file = os.path.join(out_folder, new_name) + stderr.print("[red] Saving excel file with the invalid samples") wb.save(m_file) return diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 900056a6..77aa3391 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -2,7 +2,7 @@ "pyhon_file": "ISCIII.py", "required_files": { "meta_file": { - "file_name": "new_lab_metadata2022_07_20_13_35_38.xlsx", + "file_name": "new_lab_metadata.xlsx", "mapped_fields": { "Public Health sample id (SIVIES)": "Código SiViEs", "Sample ID given by originating laboratory": "Ref Hospital", @@ -113,4 +113,4 @@ "function": "None" } } -} \ No newline at end of file +} From 520e46c778cc1d28060baa626eff46ad383476fe Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 19 Aug 2022 17:34:38 +0200 Subject: [PATCH 0812/1454] including schema_name and schema_version in the request --- relecov_tools/conf/configuration.json | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index b27d883f..21c631e6 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -149,6 +149,8 @@ "r1_fastq_filepath", "r2_fastq_filepath", "collecting_lab_sample_id", + "schema_name", + "schema_version", "sequence_file_R1_fastq", "sequence_file_R2_fastq", "sequencing_sample_id", From c1c302994c18e7f64e52af7b6d29919fbb2f1f2e Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 22 Aug 2022 09:44:38 +0200 Subject: [PATCH 0813/1454] linitn --- relecov_tools/ena_upload.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 920ece66..90b87a5a 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -433,6 +433,7 @@ def create_structure_to_ena(self): schema_dataframe = update_table( schema_dataframe, schema_targets, schema_update ) + ###### def upload(self): """Create the required files and upload to ENA""" From 5222813c76a77a295e1858191b3b0c2c0747f826 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 22 Aug 2022 16:14:09 +0200 Subject: [PATCH 0814/1454] add broker name in templates --- relecov_tools/templates/ENA_template_experiments.xml | 2 +- relecov_tools/templates/ENA_template_runs.xml | 2 +- relecov_tools/templates/ENA_template_samples_ERC000033.xml | 2 +- relecov_tools/templates/ENA_template_studies.xml | 2 +- relecov_tools/templates/ENA_template_submission.xml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/relecov_tools/templates/ENA_template_experiments.xml b/relecov_tools/templates/ENA_template_experiments.xml index 87fe6359..7d4cf7a8 100755 --- a/relecov_tools/templates/ENA_template_experiments.xml +++ b/relecov_tools/templates/ENA_template_experiments.xml @@ -12,7 +12,7 @@ def attributetest(row, column): xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_6/SRA.experiment.xsd"> - + ${row.title} diff --git a/relecov_tools/templates/ENA_template_runs.xml b/relecov_tools/templates/ENA_template_runs.xml index b8f8cc0f..d788c8d1 100755 --- a/relecov_tools/templates/ENA_template_runs.xml +++ b/relecov_tools/templates/ENA_template_runs.xml @@ -12,7 +12,7 @@ def attributetest(row, column): xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_6/SRA.run.xsd"> - + diff --git a/relecov_tools/templates/ENA_template_samples_ERC000033.xml b/relecov_tools/templates/ENA_template_samples_ERC000033.xml index acb0003b..efc27593 100644 --- a/relecov_tools/templates/ENA_template_samples_ERC000033.xml +++ b/relecov_tools/templates/ENA_template_samples_ERC000033.xml @@ -11,7 +11,7 @@ def attributetest(row, column): xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_6/SRA.sample.xsd"> - + ${row.title} ${row.taxon_id} diff --git a/relecov_tools/templates/ENA_template_studies.xml b/relecov_tools/templates/ENA_template_studies.xml index 5c466259..072b450a 100755 --- a/relecov_tools/templates/ENA_template_studies.xml +++ b/relecov_tools/templates/ENA_template_studies.xml @@ -12,7 +12,7 @@ def attributetest(row, column): xsi:noNamespaceSchemaLocation="ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_6/SRA.study.xsd"> + broker_name="${center}"> ${row.title} diff --git a/relecov_tools/templates/ENA_template_submission.xml b/relecov_tools/templates/ENA_template_submission.xml index d3cec42e..86f1c567 100644 --- a/relecov_tools/templates/ENA_template_submission.xml +++ b/relecov_tools/templates/ENA_template_submission.xml @@ -2,7 +2,7 @@ - + From a976d9aeadec34bb5697053479587761aee9c661 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 22 Aug 2022 16:17:22 +0200 Subject: [PATCH 0815/1454] lintin --- relecov_tools/ena_upload.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 90b87a5a..992f6bf8 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -367,6 +367,7 @@ def create_structure_to_ena(self): # print(chec) # when ADD/MODIFY, + # # requires source XMLs for 'run', 'experiment', 'sample', 'experiment' # schema_xmls record XMLs for all these schema and following 'submission' From cce9b23b70004a4b833ed29053383c671fa583d5 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 22 Aug 2022 16:56:10 +0200 Subject: [PATCH 0816/1454] Changed Ciudad de Ceuta by Ceuta, the same for Melilla --- relecov_tools/conf/geo_loc_cities.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/geo_loc_cities.json b/relecov_tools/conf/geo_loc_cities.json index 13bb8f09..2eca59a6 100644 --- a/relecov_tools/conf/geo_loc_cities.json +++ b/relecov_tools/conf/geo_loc_cities.json @@ -365,12 +365,12 @@ "geo_loc_longitude": "2.0417" }, { - "geo_loc_city": "Ciudad de Ceuta", + "geo_loc_city": "Ceuta", "geo_loc_latitude": "35.8867", "geo_loc_longitude": "-5.3000" }, { - "geo_loc_city": "Ciudad de Melilla", + "geo_loc_city": "Melilla", "geo_loc_latitude": "35.2919", "geo_loc_longitude": "-2.93848" }, From 3fe3b9a75e5362eb4704b31d6573d27c0ce9b4b0 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 22 Aug 2022 18:09:54 +0200 Subject: [PATCH 0817/1454] Do not get printout when error code is 500 --- relecov_tools/rest_api.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/relecov_tools/rest_api.py b/relecov_tools/rest_api.py index 058b553b..6d8278b4 100644 --- a/relecov_tools/rest_api.py +++ b/relecov_tools/rest_api.py @@ -60,7 +60,8 @@ def put_request(self, data, credentials, url): "Unable to post parameters. Received error code %s", req.status_code, ) - stderr.print(f"[red] Unable to post data because {req.text}") + if req.status_code != 500: + stderr.print(f"[red] Unable to post data because {req.text}") stderr.print(f"[red] Received error {req.status_code}") return {"ERROR": req.status_code} return {"Success": req.text} @@ -84,9 +85,12 @@ def post_request(self, data, credentials, url, file=None): "Unable to post parameters. Received error code %s", req.status_code, ) - stderr.print(f"[red] Unable to post data because {req.text}") stderr.print(f"[red] Received error {req.status_code}") - return {"ERROR": req.status_code} + if req.status_code != 500: + stderr.print(f"[red] Unable to post data because {req.text}") + return {"ERROR": req.status_code, "ERROR_TEST": req.text} + else: + return {"ERROR": req.status_code, "ERROR_TEST": ""} return {"Success": req.text} except requests.ConnectionError: log.error("Unable to open connection towards %s", self.request_url) From 42d7d98c30322d49ad7e741acee1d539ba00b3d0 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 22 Aug 2022 18:10:49 +0200 Subject: [PATCH 0818/1454] change city Vitoria-Gazteiz to only Vitoria --- relecov_tools/conf/geo_loc_cities.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/geo_loc_cities.json b/relecov_tools/conf/geo_loc_cities.json index 13bb8f09..7cd8925d 100644 --- a/relecov_tools/conf/geo_loc_cities.json +++ b/relecov_tools/conf/geo_loc_cities.json @@ -80,7 +80,7 @@ "geo_loc_longitude": "-5.7000" }, { - "geo_loc_city": "Vitoria-Gasteiz", + "geo_loc_city": "Vitoria", "geo_loc_latitude": "42.8500", "geo_loc_longitude": "-2.6833" }, From 5ea40f52869e14ebafda3327410ee34f70fdaa62 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 22 Aug 2022 18:11:36 +0200 Subject: [PATCH 0819/1454] allow to continue if sample is already defined --- relecov_tools/feed_database.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 6f0fe329..8955b412 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -236,10 +236,12 @@ def update_database(self, field_values, post_url): stderr.print( f"[blue] sending request for sample {chunk['sample_name']}" ) + req_sample = chunk['sample_name'] elif "sequencing_sample_id" in chunk: stderr.print( f"[blue] sending request for sample {chunk['sequencing_sample_id']}" ) + req_sample = chunk['sequencing_sample_id'] result = self.database_rest_api.post_request( json.dumps(chunk), {"user": self.user, "pass": self.passwd}, @@ -264,6 +266,12 @@ def update_database(self, field_values, post_url): "[red] Unable to sent the request to remote server" ) sys.exit(1) + elif "already defined" in result["ERROR_TEST"].lower(): + log.warning("Request to %s for %s was not accepted", self.database_server, req_sample) + stderr.print( + f"[yellow] Warning request for {req_sample} already defined" + ) + continue else: log.error("Request to %s was not accepted", self.database_server) stderr.print( From ffa8e463ea6ffd590f4d4e6a5e979cc270a2b960 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 22 Aug 2022 18:13:28 +0200 Subject: [PATCH 0820/1454] fix liting --- relecov_tools/feed_database.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 8955b412..a2364ec0 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -236,12 +236,12 @@ def update_database(self, field_values, post_url): stderr.print( f"[blue] sending request for sample {chunk['sample_name']}" ) - req_sample = chunk['sample_name'] + req_sample = chunk["sample_name"] elif "sequencing_sample_id" in chunk: stderr.print( f"[blue] sending request for sample {chunk['sequencing_sample_id']}" ) - req_sample = chunk['sequencing_sample_id'] + req_sample = chunk["sequencing_sample_id"] result = self.database_rest_api.post_request( json.dumps(chunk), {"user": self.user, "pass": self.passwd}, @@ -267,7 +267,11 @@ def update_database(self, field_values, post_url): ) sys.exit(1) elif "already defined" in result["ERROR_TEST"].lower(): - log.warning("Request to %s for %s was not accepted", self.database_server, req_sample) + log.warning( + "Request to %s for %s was not accepted", + self.database_server, + req_sample, + ) stderr.print( f"[yellow] Warning request for {req_sample} already defined" ) From 8d0f3fab08e0863cb5d7fc0396f2260a2bf035a4 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 22 Aug 2022 20:23:27 +0200 Subject: [PATCH 0821/1454] added a successful counter of the request to get at the end of execution --- relecov_tools/feed_database.py | 32 ++++++++++++++++++++------------ 1 file changed, 20 insertions(+), 12 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index a2364ec0..543e8e88 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -231,7 +231,11 @@ def map_relecov_bioinfo_data(self): def update_database(self, field_values, post_url): """Send the request to update database""" + suces_count = 0 + request_count = 0 for chunk in field_values: + req_sample = "" + request_count += 1 if "sample_name" in chunk: stderr.print( f"[blue] sending request for sample {chunk['sample_name']}" @@ -282,18 +286,22 @@ def update_database(self, field_values, post_url): f"[red] Error {result['ERROR']} when sending request to {self.database_server}" ) sys.exit(1) - if "sampleName" in chunk: - log.info("stored data in iskylims for sample %s", chunk["sampleName"]) - elif "sequencing_sample_id" in chunk: - log.info( - "stored data in relecov for sample %s", - chunk["sequencing_sample_id"], - ) - else: - log.info("stored data in relecov") - stderr.print( - f"[gren] All information was sent sucessfuly to {self.server_type}" - ) + log.info( + "stored data in %s iskylims for sample %s", + self.database_server, + req_sample, + ) + stderr.print(f"[green] Successful request for {req_sample}") + suces_count += 1 + if request_count == suces_count: + stderr.print( + f"[gren] All information was sent sucessfuly to {self.server_type}" + ) + else: + stderr.print( + "[yellow] Some of your requests were not successful stored in database" + ) + stderr.print(f"[yellow] {suces_count} of the {request_count} were done ok") return def store_data(self): From 765d8fbd4db45dd7fad869addec4eeb87d0cb447 Mon Sep 17 00:00:00 2001 From: birbi Date: Mon, 22 Aug 2022 20:25:54 +0200 Subject: [PATCH 0822/1454] before merge upstream --- relecov_tools/feed_database.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index bbbc8eee..3b5983ec 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -302,11 +302,9 @@ def store_data(self): # post_url = "sample" map_fields = self.map_relecov_sample_data() else: -<<<<<<< HEAD + # sample_fields, s_project_fields = self.get_iskylims_fields_sample() -======= stderr.print("[blue] Selecting sample fields") ->>>>>>> 81811ac73801f69cf3f726a3173373ad2850da45 map_fields = self.map_relecov_sample_data() post_url = "store_samples" From 93dda0a2f156b475c41236755a3569ade65e6204 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 23 Aug 2022 09:58:24 +0200 Subject: [PATCH 0823/1454] adding missing email field for collectin institution --- relecov_tools/conf/laboratory_address.json | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 5e2b2314..e35b7c68 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -314,6 +314,7 @@ { "collecting_institution": "Banc de Sang i Teixits Catalunya", "collecting_institution_address": "Passeig del Taulat, 116", + "collecting_institution_email": "", "geo_loc_state": "Cataluña", "geo_loc_city": "Barcelona", "geo_loc_country": "Spain" @@ -321,6 +322,7 @@ { "collecting_institution": "Laboratorio Echevarne Sant Cugat del Vallès", "collecting_institution_address": "Carrer de Martorell,20 Sant Cugat del Vallès", + "collecting_institution_email": "", "geo_loc_state": "Cataluña", "geo_loc_city": "Barcelona", "geo_loc_country": "Spain" From ebac70c31cb373cb4a2812eac51b7db1892e960a Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 23 Aug 2022 10:41:53 +0200 Subject: [PATCH 0824/1454] deleted commas in gisaid_schema.json --- relecov_tools/schema/gisaid_schema.json | 60 ++++++++++++------------- 1 file changed, 30 insertions(+), 30 deletions(-) diff --git a/relecov_tools/schema/gisaid_schema.json b/relecov_tools/schema/gisaid_schema.json index 430e5f25..5ddecb0f 100644 --- a/relecov_tools/schema/gisaid_schema.json +++ b/relecov_tools/schema/gisaid_schema.json @@ -14,7 +14,7 @@ "covv_seq_technology", "covv_subm_lab", "covv_subm_lab_addr", - "covv_authors", + "covv_authors" ], "type": "object", "properties": { @@ -23,7 +23,7 @@ "ontology": "NCIT:C25284", "type": "string", "description": "default must remain 'betacoronavirus'", - "clasification": "Database Identifiers", + "clasification": "Database Identifiers" }, "sample_name": { "examples": ["prov_rona_99"], @@ -31,7 +31,7 @@ "type": "string", "description": "The user-defined name for the sample.", "clasification": "Database Identifiers", - "label": "Collecting Sample id", + "label": "Collecting Sample id" }, "covv_virus_name": { "examples": ["hCoV-19/Canada/prov_rona_99/2020"], @@ -39,7 +39,7 @@ "type": "string", "description": "The user-defined GISAID virus name assigned to the sequence.", "clasification": "Database Identifiers", - "label": "GISAID Virus Name", + "label": "GISAID Virus Name" }, "submitter": { "examples": [""], @@ -47,14 +47,14 @@ "type": "string", "description": "", "clasification": "enter your GISAID-Username", - "label": "GISAID Id", + "label": "GISAID Id" }, "covv_orig_lab": { "examples": ["Public Health Agency of Canada"], "ontology": "GENEPIO:0001153", "type": "string", "description": "The name of the agency that collected the original sample.", - "label": "Originating Laboratory", + "label": "Originating Laboratory" }, "covv_orig_lab_addr": { "examples": ["655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada"], @@ -62,7 +62,7 @@ "type": "string", "description": "The mailing address of the agency submitting the sample.", "clasification": "Sample collection and processing", - "label": "Originating Laboratory Address", + "label": "Originating Laboratory Address" }, "covv_subm_lab_addr": { "examples": ["123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"], @@ -70,7 +70,7 @@ "type": "string", "description": "The mailing address of the agency submitting the sequence.", "clasification": "Sample collection and processing", - "label": "Submitting Institution Address", + "label": "Submitting Institution Address" }, "covv_collection_date": { "examples": ["3/19/2020"], @@ -79,7 +79,7 @@ "description": "The date on which the sample was collected.", "format": "date", "classification": "Sample collection and processing", - "label": "Sample Collection Date", + "label": "Sample Collection Date" }, "covv_location": { "examples": ["e.g. Europe / Germany / Bavaria / Munich"], @@ -87,7 +87,7 @@ "type": "string", "description": "The country of origin of the sample.", "clasification": "Sample collection and processing", - "label": "Geo Loc Autonomic Country", + "label": "Geo Loc Autonomic Country" }, "covv_host": { "examples": [ @@ -97,14 +97,14 @@ "type": "string", "description": "The taxonomic, or scientific name of the host.", "clasification": "Host information", - "label": "Host Scientific Name", + "label": "Host Scientific Name" }, "covv_patient_age": { "ontology": "GENEPIO:0001392", "anyOf": [{"type": "integer"}, {"pattern": "\\d+-\\d+", "type": "string"}], "description": "Age of host at the time of sampling.", "examples": [79], - "label": "Host Age", + "label": "Host Age" }, "covv_specimen": { "Enums": [ @@ -121,14 +121,14 @@ "Not Collected [GENEPIO:0001620]", "Not Provided [GENEPIO:0001668]", "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]", + "Restricted Access [GENEPIO:0001810]" ], "ontology": "GENEPIO:0001211", "type": "string", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", "examples": ["Blood [UBERON:0000178]"], "classification": "Sample collection and processing", - "label": "Organism Substance", + "label": "Organism Substance" }, "covv_assembly_method": { "examples": ["Ivar"], @@ -136,7 +136,7 @@ "type": "string", "description": "The name of software used to generate the consensus sequence.", "clasification": "Bioinformatics and QC metrics", - "label": "Consensus sequence software name", + "label": "Consensus sequence software name" }, "covv_gender": { "Enums": [ @@ -150,13 +150,13 @@ "Not Collected [GENEPIO:0001620]", "Not Provided [GENEPIO:0001668]", "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]", + "Restricted Access [GENEPIO:0001810]" ], "examples": ["Male [NCIT:C46109]"], "ontology": "GENEPIO:0001395", "type": "string", "description": "The gender of the host at the time of sample collection.", - "clasification": "Host information", + "clasification": "Host information" }, "covv_seq_technology": { "examples": [ @@ -166,7 +166,7 @@ "type": "string", "description": "The model of the sequencing instrument used.", "classification": "Sequencing", - "label": "Sequencing Instrument Model", + "label": "Sequencing Instrument Model" }, "covv_authors": { "examples": [""], @@ -174,7 +174,7 @@ "type": "string", "description": "", "clasification": "Contributor Acknowledgement", - "label": "Authors", + "label": "Authors" }, "covv_coverage": { "examples": ["400x"], @@ -182,14 +182,14 @@ "type": "string", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", "clasification": "Bioinformatics and QC metrics", - "label": "Depth of coverage value ", + "label": "Depth of coverage value " }, "covv_fasta_filename": { "examples": [""], "ontology": "GENEPIO:0001460", "type": "string", "description": "Filename that contains the sequence without path", - "clasification": "Bioinformatics and QC metrics", + "clasification": "Bioinformatics and QC metrics" }, "covv_add_host_info": { "examples": ["e.g. Patient infected while traveling in …."], @@ -197,7 +197,7 @@ "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", "clasification": "Host information", - "label": "Additional Host Information", + "label": "Additional Host Information" }, "covv_last_vaccinated": { "examples": ["e.g. 04/09/2021"], @@ -205,7 +205,7 @@ "type": "string", "description": "The date the host received their last dose of vaccine.", "format": "date", - "clasification": "Host information", + "clasification": "Host information" }, "covv_outbreak": { "examples": ["Date, Location e.g. type of gathering, Family cluster, etc."], @@ -213,7 +213,7 @@ "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", "clasification": "Host information", - "label": "Outbreak Exposure Event Location", + "label": "Outbreak Exposure Event Location" }, "covv_sampling_strategy": { "examples": [ @@ -223,21 +223,21 @@ "type": "string", "description": "The reason that the sample was sequenced.", "classification": "Sequencing", - "label": "Purpose of Sequencing", + "label": "Purpose of Sequencing" }, "submitting_lab_sequence_id": { "examples": [""], "ontology": "0", "type": "string", "description": "Sample ID given by the submitting laboratory", - "clasification": "Database Identifiers", + "clasification": "Database Identifiers" }, "covv_subm_lab": { "examples": ["Centers for Disease Control and Prevention"], "ontology": "GENEPIO:0001159", "type": "string", "description": "The name of the agency that generated the sequence.", - "label": "Submitting Institution", + "label": "Submitting Institution" }, "covv_subm_sample_id": { "examples": ["prov_rona_99"], @@ -246,7 +246,7 @@ "description": "The user-defined name for the sample.", "classification": "Database Identifiers", "label": "Sample ID given by originating laboratory", - "fill_mode": "sample", - }, - }, + "fill_mode": "sample" + } + } } From 83f3415033686f99516628335e3d559e313625e9 Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Tue, 23 Aug 2022 10:54:16 +0200 Subject: [PATCH 0825/1454] update-db --- relecov_tools/conf/configuration.json | 9 --------- relecov_tools/feed_database.py | 1 + 2 files changed, 1 insertion(+), 9 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 000cc82c..288dcd8d 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -126,15 +126,6 @@ "long_table": "longtableData", "sftp_info": "sftpInfo", "token": "" - }, - "relecov_local": { - "server": "127.0.0.1:8000", - "url": "/api/", - "store_samples": "createSampleData", - "analysis": "bioinfoData", - "long_table": "longtableData", - "sftp_info": "sftpInfo", - "token": "" } }, "iskylims_fixed_values": { diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index f6f27801..101a7e88 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -331,6 +331,7 @@ def store_data(self): elif self.type_of_info == "longtable": post_url = "long_table" + map_fields = self.json_data else: stderr.print("[red] Invalid type to upload to database") sys.exit(1) From 1dfc8dbb681fe9274b21b4b4dd29125e2f388930 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 23 Aug 2022 12:12:39 +0200 Subject: [PATCH 0826/1454] corrected spelling mistake --- relecov_tools/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 721d6dec..854d4ac9 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -272,7 +272,7 @@ def upload_to_ena(user, password, center, ena_json, dev, study, action, output_p @click.option("-p", "--password", help="password for the user to login") @click.option("-c", "--client_id", help="client-ID provided by clisupport@gisaid.org") @click.option("-t", "--token", help="path to athentication token") -@click.option("-e", "--gisaid_json", help="patch validated json mapped to GISAID") +@click.option("-e", "--gisaid_json", help="path to validated json mapped to GISAID") @click.option( "-i", "--input_path", From 3f451cea5ad81258efab0329bf080528237165a3 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 23 Aug 2022 12:27:36 +0200 Subject: [PATCH 0827/1454] creates output path, gisaid_upload.py --- relecov_tools/gisaid_upload.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 0c0cb075..ff4dc1c5 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -152,6 +152,8 @@ def metadata_to_csv(self): df_data_comp = self.complete_mand_fields(df_data) df_data_path = os.path.join(self.output_path, "meta_gisaid.csv") + if not os.path.exists(self.output_path): + os.mkdir(self.output_path) df_data_comp.to_csv(df_data_path, index=False) metagisaid = df_data_path return metagisaid From fcf73685a2fb83fb69ef34fd146950fbb0507fdf Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Tue, 23 Aug 2022 12:32:06 +0200 Subject: [PATCH 0828/1454] modified:relecov_tools/long_table_parse.py-> corrected nucleotide -> alt --- relecov_tools/feed_database.py | 9 +++------ relecov_tools/long_table_parse.py | 4 ++-- 2 files changed, 5 insertions(+), 8 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index a870e1c3..765cf7b0 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -251,7 +251,7 @@ def update_database(self, field_values, post_url): {"user": self.user, "pass": self.passwd}, self.database_settings[post_url], ) - + if "ERROR" in result: if result["ERROR"] == "Server not available": # retry to connect to server @@ -318,11 +318,11 @@ def store_data(self): map_fields = self.map_iskylims_sample_fields_values( sample_fields, s_project_fields ) - + elif self.server_type == "relecov_local": post_url = "analysis" map_fields = self.map_relecov_sample_data() - + else: stderr.print("[blue] Selecting sample fields") map_fields = self.map_relecov_sample_data() @@ -333,8 +333,6 @@ def store_data(self): post_url = "analysis" map_fields = self.map_relecov_bioinfo_data() - - # sample_fields, s_project_fields = self.get_iskylims_fields_sample() # map_fields = self.map_iskylims_sample_fields_values( # sample_fields, s_project_fields @@ -348,7 +346,6 @@ def store_data(self): # post_url = "analysis" # map_fields = self.map_relecov_bioinfo_data() - elif self.type_of_info == "longtable": post_url = "long_table" map_fields = self.json_data diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index ca3652a7..fc9977fc 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -76,7 +76,7 @@ def parse_file(self): """_summary_ This function generates a json file from the csv file entered by the user (long_table.csv). - - Checks if expected headers match with file headers + - Checks if expected headers match with file headers Returns: dictionary with key as sample and value the list of variants """ @@ -104,7 +104,7 @@ def parse_file(self): variant_dict["Position"] = { "pos": line_s[heading_index["POS"]], - "nucleotide": line_s[heading_index["ALT"]], + "alt": line_s[heading_index["ALT"]], } variant_dict["Filter"] = {"filter": line_s[heading_index["FILTER"]]} From 54d3fe491f8065a98338324fd9fae694e60e1788 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 23 Aug 2022 12:37:50 +0200 Subject: [PATCH 0829/1454] improved create_multifasta function in gisaid_upload.py --- relecov_tools/gisaid_upload.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index ff4dc1c5..406f10ef 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -180,8 +180,9 @@ def metadata_to_csv(self): def create_multifasta(self): """Create multifasta from single fastas (if --single)""" if self.single: + gather_fastas_path = os.path.join(self.fasta_path, "*.fa*") os.system( - "cat %s > %s/multifasta.fasta" % (self.fasta_path, self.output_path) + "cat %s > %s/multifasta.fasta" % (gather_fastas_path, self.output_path) ) multifasta = "%s/multifasta.fasta" % self.output_path else: From f352dfcf824aa15e476aa088d6b40e622b61a013 Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Tue, 23 Aug 2022 12:40:16 +0200 Subject: [PATCH 0830/1454] modified:relecov_tools/long_table_parse.py-> corrected nucleotide -> alt, lintinOK --- relecov_tools/conf/configuration.json | 2 +- relecov_tools/feed_database.py | 18 ++++++------------ 2 files changed, 7 insertions(+), 13 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 288dcd8d..21c631e6 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -119,7 +119,7 @@ "token": "" }, "relecov": { - "server": "http://relecov-platform.isciiides.es:8000", + "server": "http://relecov-platform.isciiides.es", "url": "/api/", "store_samples": "createSampleData", "analysis": "bioinfoData", diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 765cf7b0..2327cbd9 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -333,18 +333,12 @@ def store_data(self): post_url = "analysis" map_fields = self.map_relecov_bioinfo_data() - # sample_fields, s_project_fields = self.get_iskylims_fields_sample() - # map_fields = self.map_iskylims_sample_fields_values( - # sample_fields, s_project_fields - # ) - """ - elif self.server_type == "relecov_local": - post_url = "analysis" - map_fields = self.map_relecov_bioinfo_data() - # post_url = "analysis" - """ - # post_url = "analysis" - # map_fields = self.map_relecov_bioinfo_data() +# sample_fields, s_project_fields = self.get_iskylims_fields_sample() +# map_fields = self.map_iskylims_sample_fields_values( +# sample_fields, s_project_fields +# ) +# post_url = "analysis" +# map_fields = self.map_relecov_bioinfo_data() elif self.type_of_info == "longtable": post_url = "long_table" From b9adc90d4be195a81d575c7f87f5e4d98749e6f8 Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Tue, 23 Aug 2022 12:41:52 +0200 Subject: [PATCH 0831/1454] modified:relecov_tools/long_table_parse.py-> corrected nucleotide -> alt, lintinOK2 --- relecov_tools/feed_database.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 2327cbd9..09d49e30 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -333,12 +333,12 @@ def store_data(self): post_url = "analysis" map_fields = self.map_relecov_bioinfo_data() -# sample_fields, s_project_fields = self.get_iskylims_fields_sample() -# map_fields = self.map_iskylims_sample_fields_values( -# sample_fields, s_project_fields -# ) -# post_url = "analysis" -# map_fields = self.map_relecov_bioinfo_data() + # sample_fields, s_project_fields = self.get_iskylims_fields_sample() + # map_fields = self.map_iskylims_sample_fields_values( + # sample_fields, s_project_fields + # ) + # post_url = "analysis" + # map_fields = self.map_relecov_bioinfo_data() elif self.type_of_info == "longtable": post_url = "long_table" From d0665e3a8995eeb0e18a2c2da99967b7b6185c16 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 24 Aug 2022 00:43:21 +0200 Subject: [PATCH 0832/1454] Changing json output for dictionnary to a list oc dictionaries --- relecov_tools/conf/configuration.json | 4 ++-- relecov_tools/read_bioinfo_metadata.py | 22 ++++++++++++---------- 2 files changed, 14 insertions(+), 12 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 21c631e6..ceae9520 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -109,7 +109,7 @@ }, "external_url": { "iskylims": { - "server": "http://relecov-iskylims.isciiides.es", + "server": "http://relecov-iskylims.isciiides.es:8000", "url": "/wetlab/api/", "store_samples": "createSampleData", "url_project_fields": "sampleProjectFields", @@ -119,7 +119,7 @@ "token": "" }, "relecov": { - "server": "http://relecov-platform.isciiides.es", + "server": "http://relecov-platform.isciiides.es:8000", "url": "/api/", "store_samples": "createSampleData", "analysis": "bioinfoData", diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 20b3aa1e..c56a32af 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -150,11 +150,12 @@ def bioinfo_parse(self, file_name): # FUNCTION fill_bioinfo_dict """Iterating through each row and each loaded file the values of the bioinfo_dict are filled""" - bioinfo_list = {} + bioinfo_list = [] for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): - # row = ws_metadata_lab[5] - sample_name = row[5] + if row[6] is None: + continue + sample_name = row[6] print(sample_name) fastq_r1 = row[47] @@ -259,13 +260,13 @@ def bioinfo_parse(self, file_name): # FUNCTION software_data # fields from software version file bioinfo_dict["dehosting_method_software_version"] = str( - list(software_versions["KRAKEN2_KRAKEN2"].values())[0] + software_versions["KRAKEN2_KRAKEN2"]["kraken2"] ) bioinfo_dict["variant_calling_software_version"] = str( - list(software_versions["IVAR_VARIANTS"].values())[0] + software_versions["IVAR_VARIANTS"]["ivar"] ) bioinfo_dict["consensus_sequence_software_version"] = str( - list(software_versions["BCFTOOLS_CONSENSUS"].values())[0] + software_versions["BCFTOOLS_CONSENSUS"]["bcftools"] ) bioinfo_dict["bioinformatics_protocol_software_version"] = str( @@ -273,11 +274,12 @@ def bioinfo_parse(self, file_name): ) bioinfo_dict["preprocessing_software_version"] = str( - list(software_versions["FASTP"].values())[0] + software_versions["FASTP"]["fastp"] ) bioinfo_dict["mapping_software_version"] = str( - list(software_versions["BOWTIE2_ALIGN"].values())[0] + software_versions["BOWTIE2_ALIGN"]["bowtie2"] ) + # FUNCTION pangolin_data # files from pangolin.csv file @@ -309,8 +311,8 @@ def bioinfo_parse(self, file_name): bioinfo_dict["lineage_identification_date"] = str( pango_last_modified_date ) - - bioinfo_list[str(sample_name)] = bioinfo_dict + bioinfo_list.append(bioinfo_dict) + # bioinfo_list[str(sample_name)] = bioinfo_dict c = c + 1 # adding schema_name and schema_version bioinfo_dict["schema_name"] = self.schema_name From 24b3723dd4642d13c90b708d36c18667a09d8685 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 24 Aug 2022 00:44:40 +0200 Subject: [PATCH 0833/1454] Changing json output for dictionnary to a list oc dictionaries --- relecov_tools/conf/configuration.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index ceae9520..21c631e6 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -109,7 +109,7 @@ }, "external_url": { "iskylims": { - "server": "http://relecov-iskylims.isciiides.es:8000", + "server": "http://relecov-iskylims.isciiides.es", "url": "/wetlab/api/", "store_samples": "createSampleData", "url_project_fields": "sampleProjectFields", @@ -119,7 +119,7 @@ "token": "" }, "relecov": { - "server": "http://relecov-platform.isciiides.es:8000", + "server": "http://relecov-platform.isciiides.es", "url": "/api/", "store_samples": "createSampleData", "analysis": "bioinfoData", From 8e4e7ee605318ab247d5d6e1a5a6f3ea9faa651f Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 24 Aug 2022 00:46:36 +0200 Subject: [PATCH 0834/1454] fixing bugs for uploading bioinfo data to relecov --- relecov_tools/__main__.py | 2 +- relecov_tools/conf/configuration.json | 4 ++-- relecov_tools/feed_database.py | 29 +++++------------------- relecov_tools/schema/relecov_schema.json | 2 +- 4 files changed, 10 insertions(+), 27 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 721d6dec..4f84b986 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -340,7 +340,7 @@ def launch(user): @click.option( "-t", "--type", - type=click.Choice(["sample", "analysis"]), + type=click.Choice(["sample", "bioinfodata", "variantdata"]), multiple=False, help="Select the type of information to upload to database", ) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 21c631e6..6d2d2c3a 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -122,8 +122,8 @@ "server": "http://relecov-platform.isciiides.es", "url": "/api/", "store_samples": "createSampleData", - "analysis": "bioinfoData", - "long_table": "longtableData", + "bioinfodata": "createBioinfoData", + "variantdata": "createVariantData", "sftp_info": "sftpInfo", "token": "" } diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 543e8e88..0d210372 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -75,7 +75,7 @@ def __init__( if type_of_info is None: type_of_info = relecov_tools.utils.prompt_selection( "Select:", - ["sample", "analysis", "longtable"], + ["sample", "bioinfodata", "variantdata"], ) self.type_of_info = type_of_info @@ -212,23 +212,6 @@ def map_relecov_sample_data(self): field_values.append(s_dict) return field_values - def map_relecov_bioinfo_data(self): - # Select the values from self.json_data - field_values = [] - - for row in self.json_data: - s_dict = {} - for r_field in self.json_data[row]: - if r_field in self.json_data[row]: - s_dict[r_field] = self.json_data[row][r_field] - if r_field == "sample_name": - s_dict[r_field] = row - else: - s_dict[r_field] = None - field_values.append(s_dict) - - return field_values - def update_database(self, field_values, post_url): """Send the request to update database""" suces_count = 0 @@ -321,12 +304,12 @@ def store_data(self): stderr.print("[blue] Selecting sample fields") map_fields = self.map_relecov_sample_data() post_url = "store_samples" - elif self.type_of_info == "analysis": - post_url = "analysis" - map_fields = self.map_relecov_bioinfo_data() + elif self.type_of_info == "bioinfodata": + post_url = "bioinfodata" + map_fields = self.json_data - elif self.type_of_info == "longtable": - post_url = "long_table" + elif self.type_of_info == "variantdata": + post_url = "variantdata" else: stderr.print("[red] Invalid type to upload to database") sys.exit(1) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 0cba8df3..4b429f7f 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1874,7 +1874,7 @@ "type": "string", "description": "", "classification": "Bioinformatics and QC metrics fields", - "label": "% genome greater 10x", + "label": "% genome greater 10x", "fill_mode": "batch" }, "per_Ns": { From 3ad36a03602c5281d767a1645bf6ada654f062e6 Mon Sep 17 00:00:00 2001 From: birbi Date: Wed, 24 Aug 2022 10:01:11 +0200 Subject: [PATCH 0835/1454] both modified: relecov_tools/feed_database.py. after merge --- relecov_tools/feed_database.py | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 74c608c6..230939da 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -308,27 +308,9 @@ def store_data(self): stderr.print("[blue] Selecting sample fields") map_fields = self.map_relecov_sample_data() post_url = "store_samples" -<<<<<<< HEAD - elif self.type_of_info == "analysis": - - if self.server_type == "relecov": - post_url = "analysis" - map_fields = self.map_relecov_bioinfo_data() - - # sample_fields, s_project_fields = self.get_iskylims_fields_sample() - # map_fields = self.map_iskylims_sample_fields_values( - # sample_fields, s_project_fields - # ) - # post_url = "analysis" - # map_fields = self.map_relecov_bioinfo_data() - - elif self.type_of_info == "longtable": - post_url = "long_table" -======= elif self.type_of_info == "bioinfodata": post_url = "bioinfodata" ->>>>>>> de48b8f4f9e7050df1b6e98da55ac231982d220b map_fields = self.json_data elif self.type_of_info == "variantdata": From 5df3c2a681e967d642379e0ed3cb081cd26709e6 Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Wed, 24 Aug 2022 12:06:45 +0200 Subject: [PATCH 0836/1454] api-> long table hanling.py, lintin OK3 --- relecov_tools/conf/configuration.json | 230 -------------------------- 1 file changed, 230 deletions(-) delete mode 100644 relecov_tools/conf/configuration.json diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json deleted file mode 100644 index 21c631e6..00000000 --- a/relecov_tools/conf/configuration.json +++ /dev/null @@ -1,230 +0,0 @@ -{ - "metadata_lab_heading": [ - "Public Health sample id (SIVIES)", - "Sample ID given by originating laboratory", - "Sample ID given by the submitting laboratory", - "Sample ID given in the microbiology lab", - "Sample ID given if multiple rna-extraction or passages", - "Sample ID given for sequencing", - "ENA Sample ID", - "GISAID Virus Name", - "GISAID id", - "Originating Laboratory", - "Submitting Institution", - "Sample Collection Date", - "Sample Received Date", - "Purpose of sampling", - "Biological Sample Storage Condition", - "Specimen source", - "Environmental Material", - "Environmental System", - "Collection Device", - "Host", - "Host Age", - "Host Gender", - "Sequencing Date", - "Rna Extraction Protocol", - "Commercial All-in-one library kit", - "Library Preparation Kit", - "Enrichment Protocol", - "If Enrichment Protocol Is Other, Specify", - "Enrichment panel/assay", - "If Enrichment panel/assay Is Other, Specify", - "Enrichment panel/assay version", - "Number Of Samples In Run", - "Runid", - "Sequencing Instrument Model", - "Flowcell Kit", - "Source material", - "Capture method", - "Sequencing technique", - "Library Layout", - "Gene Name 1", - "Diagnostic Pcr Ct Value 1", - "Gene Name 2", - "Diagnostic Pcr Ct Value-2", - "Analysis Authors", - "Author Submitter", - "Authors", - "Sequence file R1 fastq", - "Sequence file R2 fastq" - ], - "gisaid_csv_headers": [ - "submitter", - "covv_virus_name", - "covv_type", - "covv_passage", - "covv_collection_date", - "covv_location", - "covv_add_location", - "covv_host", - "covv_add_host_info", - "covv_sampling_strategy", - "covv_gender", - "covv_patient_age", - "covv_patient_status", - "covv_specimen", - "covv_outbreak", - "covv_last_vaccinated", - "covv_treatment", - "covv_seq_technology", - "covv_assembly_method", - "covv_coverage", - "covv_orig_lab", - "covv_orig_lab_addr", - "covv_provider_sample_id", - "covv_subm_lab", - "covv_subm_lab_addr", - "covv_subm_sample_id", - "covv_authors" - ], - "json_schemas": { - "relecov_schema": "relecov_schema.json", - "ena_schema": "ena_schema.json", - "gisaid_schema": "gisaid_schema.json" - }, - "sftp_connection": { - "sftp_server": "sftprelecov.isciii.es", - "sftp_port": "22" - }, - "abort_if_md5_mismatch": "False", - "storage_local_folder": "/tmp/relecov", - "tmp_folder_for_metadata": "/tmp/relecov/tmp", - "allowed_sample_extensions": [ - "fastq.gz", - "fasta" - ], - "laboratory_data": "laboratory_address.json", - "geo_location_data": "geo_loc_cities.json", - "ENA_configuration": { - "study_alias": "RELECOV", - "design_description": "Design Description", - "experiment_title": "Example project for ENA submission RELECOV", - "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "", - "study_id": "ERP137164" - }, - "GISATD_configuration": { - "submitter": "GISAID_ID" - }, - "external_url": { - "iskylims": { - "server": "http://relecov-iskylims.isciiides.es", - "url": "/wetlab/api/", - "store_samples": "createSampleData", - "url_project_fields": "sampleProjectFields", - "url_sample_fields": "sampleFields", - "param_sample_project": "project", - "project_name": "relecov", - "token": "" - }, - "relecov": { - "server": "http://relecov-platform.isciiides.es", - "url": "/api/", - "store_samples": "createSampleData", - "analysis": "bioinfoData", - "long_table": "longtableData", - "sftp_info": "sftpInfo", - "token": "" - } - }, - "iskylims_fixed_values": { - "patientCore": "", - "sampleProject": "Relecov", - "onlyRecorded": "Yes", - "sampleLocation": "Not defined" - }, - "relecov_sample_metadata": [ - "author_submitter", - "authors", - "bioproject_accession_ENA", - "bioproject_umbrella_accession_ENA", - "biosample_accession_ENA", - "fastq_r1_md5", - "fastq_r2_md5", - "GenBank_ENA_DDBJ_accession", - "GISAID_accession", - "gisaid_id", - "microbiology_lab_sample_id", - "r1_fastq_filepath", - "r2_fastq_filepath", - "collecting_lab_sample_id", - "schema_name", - "schema_version", - "sequence_file_R1_fastq", - "sequence_file_R2_fastq", - "sequencing_sample_id", - "submitting_lab_sample_id", - "virus_name" - ], - "relecov_bioinfo_metadata": { - "dehosting_method_software_name": "KRAKEN2_KRAKEN2", - "assembly": "None", - "if_assembly_other": "None", - "assembly_params": "None", - "variant_calling_software_name": "IVAR_VARIANTS", - "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", - "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", - "if_consensus_other": "None", - "consensus_params": "-p vcf -f", - "depth_of_coverage_threshold": ">10x", - "bioinformatics_protocol_software_name": "nf-core/viralrecon", - "if_bioinformatic_protocol_is_other_specify": "None", - "commercial_open_source_both": "open-source", - "preprocessing_software_name": "FASTP", - "if_preprocessing_other": "None", - "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", - "mapping_software_name": "BOWTIE2_ALIGN", - "if_mapping_other": "None", - "mapping_params": "--seed 1", - "lineage_analysis_software_name": "pangolin", - "if_lineage_identification_other": "None" - }, - "mapping_illumina_tab_field_list": { - "lineage_name": "Lineage", - "per_genome_greater_10x": "Coverage>10x(%)", - "per_reads_host": "%readshost", - "per_reads_virus": "%readsvirus", - "per_unmapped": "%unmapedreads", - "per_Ns": "%Ns10x", - "depth_of_coverage_value": "medianDPcoveragevirus", - "number_of_variants_in_consensus": "Variantsinconsensusx10", - "number_of_variants_with_effect": "MissenseVariants" - }, - "files_read_bioinfo_metadata": { - "mapping_illumina.tab": "mapping_illumina_tab_path", - "summary_variants_metrics_mqc.csv": "summary_variants_metrics_path ", - "variants_long_table.csv": "variants_long_table_path", - "consensus_genome_length.csv": "consensus_genome_length_path", - "software_versions.yml": "software_versions_path" - }, - "tool": { - "tool_name": "ena-upload-cli", - "tool_version": "0.5.3" - }, - "md5_file_name": "md5_check_file.csv", - "checklist": "ERC000033", - "long_table_heading": [ - "SAMPLE", - "CHROM", - "POS", - "REF", - "ALT", - "FILTER", - "DP", - "REF_DP", - "ALT_DP", - "AF", - "GENE", - "EFFECT", - "HGVS_C", - "HGVS_P", - "HGVS_P_1LETTER", - "CALLER", - "LINEAGE" - ], - "mapping_file": { - "ISCIII": "ISCIII.json", - "HUGTiP": "HUGTiP.json" - } -} From 165c880e897ccdb272a7768caace01c6f38711a2 Mon Sep 17 00:00:00 2001 From: birbi Date: Wed, 24 Aug 2022 13:06:20 +0200 Subject: [PATCH 0837/1454] fixed relecov_tools/feed_database.py --- relecov_tools/feed_database.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 230939da..81121b94 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -289,6 +289,8 @@ def update_database(self, field_values, post_url): return def store_data(self): + import pdb + """Collect data from json file and split them to store data in iSkyLIMS and in Relecov Platform """ @@ -315,8 +317,11 @@ def store_data(self): elif self.type_of_info == "variantdata": post_url = "variantdata" + map_fields = self.json_data else: stderr.print("[red] Invalid type to upload to database") sys.exit(1) + + pdb.set_trace() self.update_database(map_fields, post_url) stderr.print(f"[green] Upload process to {self.server_type} completed") From ca66fe24b166c2824027a2f9374d4031ee0b8216 Mon Sep 17 00:00:00 2001 From: birbi Date: Wed, 24 Aug 2022 13:07:59 +0200 Subject: [PATCH 0838/1454] fixed relecov_tools/feed_database.py, config --- relecov_tools/conf/configuration.json | 13 ++----------- 1 file changed, 2 insertions(+), 11 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 8f5f2640..02275a1b 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -119,19 +119,10 @@ "token": "" }, "relecov": { - "server": "http://relecov-platform.isciiides.es:8000", + "server": "http://relecov-platform.isciiides.es", "url": "/api/", "store_samples": "createSampleData", - "analysis": "bioinfoData", - "long_table": "longtableData", - "sftp_info": "sftpInfo", - "token": "" - }, - "relecov_local": { - "server": "http://127.0.0.1:8000", - "url": "/api/", - "store_samples": "createSampleData", - "bioinfodata": "createBioinfoData", + "analysis": "createBioinfoData", "variantdata": "createVariantData", "sftp_info": "sftpInfo", "token": "" From 1db3d3343fd2e1f99375c8bedd6937933b5274d5 Mon Sep 17 00:00:00 2001 From: birbi Date: Wed, 24 Aug 2022 13:16:55 +0200 Subject: [PATCH 0839/1454] fixed relecov_tools/feed_database.py, deleted pdb --- relecov_tools/feed_database.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 81121b94..2d93896a 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -289,8 +289,6 @@ def update_database(self, field_values, post_url): return def store_data(self): - import pdb - """Collect data from json file and split them to store data in iSkyLIMS and in Relecov Platform """ @@ -322,6 +320,5 @@ def store_data(self): stderr.print("[red] Invalid type to upload to database") sys.exit(1) - pdb.set_trace() self.update_database(map_fields, post_url) stderr.print(f"[green] Upload process to {self.server_type} completed") From 0b6d9ca5980c5cc80c4ef774ae01dd26c875a8c6 Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Fri, 26 Aug 2022 12:35:53 +0200 Subject: [PATCH 0840/1454] deleted wrong configuration JSON --- ...n~3ad36a03602c5281d767a1645bf6ada654f062e6 | 239 ------------------ 1 file changed, 239 deletions(-) delete mode 100644 relecov_tools/conf/configuration.json~3ad36a03602c5281d767a1645bf6ada654f062e6 diff --git a/relecov_tools/conf/configuration.json~3ad36a03602c5281d767a1645bf6ada654f062e6 b/relecov_tools/conf/configuration.json~3ad36a03602c5281d767a1645bf6ada654f062e6 deleted file mode 100644 index 8f5f2640..00000000 --- a/relecov_tools/conf/configuration.json~3ad36a03602c5281d767a1645bf6ada654f062e6 +++ /dev/null @@ -1,239 +0,0 @@ -{ - "metadata_lab_heading": [ - "Public Health sample id (SIVIES)", - "Sample ID given by originating laboratory", - "Sample ID given by the submitting laboratory", - "Sample ID given in the microbiology lab", - "Sample ID given if multiple rna-extraction or passages", - "Sample ID given for sequencing", - "ENA Sample ID", - "GISAID Virus Name", - "GISAID id", - "Originating Laboratory", - "Submitting Institution", - "Sample Collection Date", - "Sample Received Date", - "Purpose of sampling", - "Biological Sample Storage Condition", - "Specimen source", - "Environmental Material", - "Environmental System", - "Collection Device", - "Host", - "Host Age", - "Host Gender", - "Sequencing Date", - "Rna Extraction Protocol", - "Commercial All-in-one library kit", - "Library Preparation Kit", - "Enrichment Protocol", - "If Enrichment Protocol Is Other, Specify", - "Enrichment panel/assay", - "If Enrichment panel/assay Is Other, Specify", - "Enrichment panel/assay version", - "Number Of Samples In Run", - "Runid", - "Sequencing Instrument Model", - "Flowcell Kit", - "Source material", - "Capture method", - "Sequencing technique", - "Library Layout", - "Gene Name 1", - "Diagnostic Pcr Ct Value 1", - "Gene Name 2", - "Diagnostic Pcr Ct Value-2", - "Analysis Authors", - "Author Submitter", - "Authors", - "Sequence file R1 fastq", - "Sequence file R2 fastq" - ], - "gisaid_csv_headers": [ - "submitter", - "covv_virus_name", - "covv_type", - "covv_passage", - "covv_collection_date", - "covv_location", - "covv_add_location", - "covv_host", - "covv_add_host_info", - "covv_sampling_strategy", - "covv_gender", - "covv_patient_age", - "covv_patient_status", - "covv_specimen", - "covv_outbreak", - "covv_last_vaccinated", - "covv_treatment", - "covv_seq_technology", - "covv_assembly_method", - "covv_coverage", - "covv_orig_lab", - "covv_orig_lab_addr", - "covv_provider_sample_id", - "covv_subm_lab", - "covv_subm_lab_addr", - "covv_subm_sample_id", - "covv_authors" - ], - "json_schemas": { - "relecov_schema": "relecov_schema.json", - "ena_schema": "ena_schema.json", - "gisaid_schema": "gisaid_schema.json" - }, - "sftp_connection": { - "sftp_server": "sftprelecov.isciii.es", - "sftp_port": "22" - }, - "abort_if_md5_mismatch": "False", - "storage_local_folder": "/tmp/relecov", - "tmp_folder_for_metadata": "/tmp/relecov/tmp", - "allowed_sample_extensions": [ - "fastq.gz", - "fasta" - ], - "laboratory_data": "laboratory_address.json", - "geo_location_data": "geo_loc_cities.json", - "ENA_configuration": { - "study_alias": "RELECOV", - "design_description": "Design Description", - "experiment_title": "Example project for ENA submission RELECOV", - "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "", - "study_id": "ERP137164" - }, - "GISATD_configuration": { - "submitter": "GISAID_ID" - }, - "external_url": { - "iskylims": { - "server": "http://relecov-iskylims.isciiides.es", - "url": "/wetlab/api/", - "store_samples": "createSampleData", - "url_project_fields": "sampleProjectFields", - "url_sample_fields": "sampleFields", - "param_sample_project": "project", - "project_name": "relecov", - "token": "" - }, - "relecov": { - "server": "http://relecov-platform.isciiides.es:8000", - "url": "/api/", - "store_samples": "createSampleData", - "analysis": "bioinfoData", - "long_table": "longtableData", - "sftp_info": "sftpInfo", - "token": "" - }, - "relecov_local": { - "server": "http://127.0.0.1:8000", - "url": "/api/", - "store_samples": "createSampleData", - "bioinfodata": "createBioinfoData", - "variantdata": "createVariantData", - "sftp_info": "sftpInfo", - "token": "" - } - }, - "iskylims_fixed_values": { - "patientCore": "", - "sampleProject": "Relecov", - "onlyRecorded": "Yes", - "sampleLocation": "Not defined" - }, - "relecov_sample_metadata": [ - "author_submitter", - "authors", - "bioproject_accession_ENA", - "bioproject_umbrella_accession_ENA", - "biosample_accession_ENA", - "fastq_r1_md5", - "fastq_r2_md5", - "GenBank_ENA_DDBJ_accession", - "GISAID_accession", - "gisaid_id", - "microbiology_lab_sample_id", - "r1_fastq_filepath", - "r2_fastq_filepath", - "collecting_lab_sample_id", - "schema_name", - "schema_version", - "sequence_file_R1_fastq", - "sequence_file_R2_fastq", - "sequencing_sample_id", - "submitting_lab_sample_id", - "virus_name" - ], - "relecov_bioinfo_metadata": { - "dehosting_method_software_name": "KRAKEN2_KRAKEN2", - "assembly": "None", - "if_assembly_other": "None", - "assembly_params": "None", - "variant_calling_software_name": "IVAR_VARIANTS", - "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", - "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", - "if_consensus_other": "None", - "consensus_params": "-p vcf -f", - "depth_of_coverage_threshold": ">10x", - "bioinformatics_protocol_software_name": "nf-core/viralrecon", - "if_bioinformatic_protocol_is_other_specify": "None", - "commercial_open_source_both": "open-source", - "preprocessing_software_name": "FASTP", - "if_preprocessing_other": "None", - "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", - "mapping_software_name": "BOWTIE2_ALIGN", - "if_mapping_other": "None", - "mapping_params": "--seed 1", - "lineage_analysis_software_name": "pangolin", - "if_lineage_identification_other": "None" - }, - "mapping_illumina_tab_field_list": { - "lineage_name": "Lineage", - "per_genome_greater_10x": "Coverage>10x(%)", - "per_reads_host": "%readshost", - "per_reads_virus": "%readsvirus", - "per_unmapped": "%unmapedreads", - "per_Ns": "%Ns10x", - "depth_of_coverage_value": "medianDPcoveragevirus", - "number_of_variants_in_consensus": "Variantsinconsensusx10", - "number_of_variants_with_effect": "MissenseVariants" - }, - "files_read_bioinfo_metadata": { - "mapping_illumina.tab": "mapping_illumina_tab_path", - "summary_variants_metrics_mqc.csv": "summary_variants_metrics_path ", - "variants_long_table.csv": "variants_long_table_path", - "consensus_genome_length.csv": "consensus_genome_length_path", - "software_versions.yml": "software_versions_path" - }, - "tool": { - "tool_name": "ena-upload-cli", - "tool_version": "0.5.3" - }, - "md5_file_name": "md5_check_file.csv", - "checklist": "ERC000033", - "long_table_heading": [ - "SAMPLE", - "CHROM", - "POS", - "REF", - "ALT", - "FILTER", - "DP", - "REF_DP", - "ALT_DP", - "AF", - "GENE", - "EFFECT", - "HGVS_C", - "HGVS_P", - "HGVS_P_1LETTER", - "CALLER", - "LINEAGE" - ], - "mapping_file": { - "ISCIII": "ISCIII.json", - "HUGTiP": "HUGTiP.json" - } -} From 2d41676ec4950ee4f00c88badf91aa4b2b39dbb0 Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Fri, 26 Aug 2022 12:39:38 +0200 Subject: [PATCH 0841/1454] deleted wrong configuration JSON, fixed errors --- relecov_tools/conf/configuration.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 02275a1b..6d2d2c3a 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -122,7 +122,7 @@ "server": "http://relecov-platform.isciiides.es", "url": "/api/", "store_samples": "createSampleData", - "analysis": "createBioinfoData", + "bioinfodata": "createBioinfoData", "variantdata": "createVariantData", "sftp_info": "sftpInfo", "token": "" From 5126682f9137987f095d34d84847b0eedb6174c4 Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Fri, 26 Aug 2022 14:20:52 +0200 Subject: [PATCH 0842/1454] modified long_table_parse.py, changed sample to sample_name --- relecov_tools/conf/configuration.json | 2 +- relecov_tools/long_table_parse.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 6d2d2c3a..dda40a27 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -119,7 +119,7 @@ "token": "" }, "relecov": { - "server": "http://relecov-platform.isciiides.es", + "server": "http://relecov-platform.isciiides.es:8000", "url": "/api/", "store_samples": "createSampleData", "bioinfodata": "createBioinfoData", diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index fc9977fc..c70b9464 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -135,7 +135,7 @@ def convert_to_json(self, samp_dict): """ """ j_list = [] for key, values in samp_dict.items(): - j_dict = {"sample": key} + j_dict = {"sample_name": key} j_dict["variants"] = values j_list.append(j_dict) return j_list From 7bfa13f0df55c2fa25bdaeab35aa3a804d8dc839 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 29 Aug 2022 10:12:47 +0200 Subject: [PATCH 0843/1454] Reviewing relecov_schema --- relecov_tools/schema/relecov_schema.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 4b429f7f..37e3e275 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -22,7 +22,7 @@ ], "ontology": "GENEPIO:0001123", "type": "string", - "description": "The user-defined name for the sample.", + "description": "The name given for the sample by the collecting institution.", "classification": "Database Identifiers", "label": "Sample ID given by originating laboratory", "fill_mode": "sample" @@ -33,7 +33,7 @@ ], "ontology": "GENEPIO:0001153", "type": "string", - "description": "The name of the agency that collected the original sample.", + "description": "The name of the agency/institution that collected the sample.", "classification": "Sample collection and processing", "label": "Originating Laboratory", "fill_mode": "sample" @@ -44,7 +44,7 @@ ], "ontology": "GENEPIO:0001159", "type": "string", - "description": "The name of the agency that generated the sequence.", + "description": "The name of the agency that submitted the sequence to public databases.", "classification": "Sample collection and processing", "label": "Submitting Institution", "fill_mode": "sample" From 91baee81a2f689b02e044520293704d41931b8b7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 29 Aug 2022 12:08:30 +0200 Subject: [PATCH 0844/1454] Update relecov_schema.json --- relecov_tools/schema/relecov_schema.json | 240 +++++++++++------------ 1 file changed, 118 insertions(+), 122 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 37e3e275..ebcff5e7 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -37,6 +37,39 @@ "classification": "Sample collection and processing", "label": "Originating Laboratory", "fill_mode": "sample" + }, + "collecting_institution_email": { + "examples": [ + "johnnyblogs@lab.ca" + ], + "ontology": "OBI:0001890", + "type": "string", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "classification": "Sample collection and processing", + "label": "Originating Laboratory Email", + "fill_mode": "batch" + }, + "collecting_institution_address": { + "examples": [ + "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" + ], + "ontology": "GENEPIO:0001158", + "type": "string", + "description": "The mailing address of the agency submitting the sample.", + "classification": "Sample collection and processing", + "label": "Originating Laboratory Address", + "fill_mode": "batch" + }, + "submitting_lab_sample_id": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "Sample ID given by the submitting laboratory", + "classification": "Sequencing", + "label": "Sample ID given by the submitting laboratory", + "fill_mode": "sample" }, "submitting_institution": { "examples": [ @@ -49,6 +82,28 @@ "label": "Submitting Institution", "fill_mode": "sample" }, + "submitting_institution_email": { + "examples": [ + "RespLab@lab.ca" + ], + "ontology": "GENEPIO:0001165", + "type": "string", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "classification": "Sample collection and processing", + "label": "Submitting Institution Email", + "fill_mode": "batch" + }, + "submitting_institution_address": { + "examples": [ + "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" + ], + "ontology": "GENEPIO:0001167", + "type": "string", + "description": "The mailing address of the agency submitting the sequence.", + "classification": "Sample collection and processing", + "label": "Submitting Institution Address", + "fill_mode": "batch" + }, "sample_collection_date": { "examples": [ "3/19/2020" @@ -60,6 +115,29 @@ "classification": "Sample collection and processing", "label": "Sample Collection Date", "fill_mode": "sample" + }, + "sample_received_date": { + "examples": [ + "3/21/2020" + ], + "ontology": "GENEPIO:0001179", + "type": "string", + "description": "The date on which the sample was received.", + "format": "date", + "classification": "Sample collection and processing", + "label": "Sample Received Date", + "fill_mode": "sample" + }, + "sample_storage_conditions": { + "examples": [ + "24 degrees celsius" + ], + "ontology": "NCIT_C115535", + "type": "string", + "description": "The name and version of a particular protocol used for sampling.", + "classification": "Sample collection and processing", + "label": "Biological Sample Storage Condition", + "fill_mode": "batch" }, "geo_loc_country": { "Enums": [ @@ -387,12 +465,9 @@ ], "ontology": "GENEPIO:0001398", "type": "string", - "description": "a unique identifier by which each subject can be referred to, de-identified.", - "clasification": "Host information", + "description": "An unique identifier by which each subject can be referred to, de-identified.", + "classification": "Host information", "label": "Host Subject Id", - "table": [ - "sample" - ] }, "host_health_state": { "examples": [ @@ -401,11 +476,8 @@ "ontology": "GENEPIO:0001388", "type": "string", "description": " Status of the host", - "clasification": "Host information", + "classification": "Host health state information", "label": "Host health state", - "table": [ - "sample" - ] }, "host_scientific_name": { "Enums": [ @@ -460,6 +532,41 @@ "label": "Host disease", "fill_mode": "batch" }, + "host_age": { + "ontology": "GENEPIO:0001392", + "type": "string", + "description": "Age of host at the time of sampling.", + "examples": [ + "79" + ], + "classification": "Host information", + "label": "Host Age", + "fill_mode": "sample" + }, + "host_gender": { + "Enums": [ + "Female [NCIT:C46110]", + "Male [NCIT:C46109]", + "Non-binary Gender [GSSO:000132]", + "Transgender (assigned male at birth) [GSSO:004004]", + "Transgender (assigned female at birth) [GSSO:004005]", + "Undeclared [NCIT:C110959]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001395", + "type": "string", + "description": "The gender of the host at the time of sample collection.", + "examples": [ + "Male [NCIT:C46109]" + ], + "classification": "Host information", + "label": "Host Gender", + "fill_mode": "sample" + }, "sequencing_instrument_model": { "Enums": [ "Illumina sequencing instrument [GENEPIO:0100105]", @@ -524,17 +631,7 @@ "label": "Sequencing Instrument Model", "fill_mode": "batch" }, - "submitting_lab_sample_id": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "Sample ID given by the submitting laboratory", - "classification": "Sequencing", - "label": "Sample ID given by the submitting laboratory", - "fill_mode": "sample" - }, + "biosample_accession_ENA": { "examples": [ "SAMN14180202" @@ -557,108 +654,7 @@ "label": "GISAID Virus Name", "fill_mode": "sample" }, - "collecting_institution_email": { - "examples": [ - "johnnyblogs@lab.ca" - ], - "ontology": "OBI:0001890", - "type": "string", - "description": "The email address of the contact responsible for follow-up regarding the sample.", - "classification": "Sample collection and processing", - "label": "Originating Laboratory Email", - "fill_mode": "batch" - }, - "collecting_institution_address": { - "examples": [ - "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" - ], - "ontology": "GENEPIO:0001158", - "type": "string", - "description": "The mailing address of the agency submitting the sample.", - "classification": "Sample collection and processing", - "label": "Originating Laboratory Address", - "fill_mode": "batch" - }, - "submitting_institution_email": { - "examples": [ - "RespLab@lab.ca" - ], - "ontology": "GENEPIO:0001165", - "type": "string", - "description": "The email address of the contact responsible for follow-up regarding the sequence.", - "classification": "Sample collection and processing", - "label": "Submitting Institution Email", - "fill_mode": "batch" - }, - "submitting_institution_address": { - "examples": [ - "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" - ], - "ontology": "GENEPIO:0001167", - "type": "string", - "description": "The mailing address of the agency submitting the sequence.", - "classification": "Sample collection and processing", - "label": "Submitting Institution Address", - "fill_mode": "batch" - }, - "sample_received_date": { - "examples": [ - "3/21/2020" - ], - "ontology": "GENEPIO:0001179", - "type": "string", - "description": "The date on which the sample was received.", - "format": "date", - "classification": "Sample collection and processing", - "label": "Sample Received Date", - "fill_mode": "sample" - }, - "sample_storage_conditions": { - "examples": [ - "24 degrees celsius" - ], - "ontology": "NCIT_C115535", - "type": "string", - "description": "The name and version of a particular protocol used for sampling.", - "classification": "Sample collection and processing", - "label": "Biological Sample Storage Condition", - "fill_mode": "batch" - }, - "host_age": { - "ontology": "GENEPIO:0001392", - "type": "string", - "description": "Age of host at the time of sampling.", - "examples": [ - "79" - ], - "classification": "Host information", - "label": "Host Age", - "fill_mode": "sample" - }, - "host_gender": { - "Enums": [ - "Female [NCIT:C46110]", - "Male [NCIT:C46109]", - "Non-binary Gender [GSSO:000132]", - "Transgender (assigned male at birth) [GSSO:004004]", - "Transgender (assigned female at birth) [GSSO:004005]", - "Undeclared [NCIT:C110959]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001395", - "type": "string", - "description": "The gender of the host at the time of sample collection.", - "examples": [ - "Male [NCIT:C46109]" - ], - "classification": "Host information", - "label": "Host Gender", - "fill_mode": "sample" - }, + "microbiology_lab_sample_id": { "examples": [ "" From bcf6b5a56c9a417ce1c99db8a7f097204647263d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 29 Aug 2022 13:25:11 +0200 Subject: [PATCH 0845/1454] Update relecov_schema.json --- relecov_tools/schema/relecov_schema.json | 744 +++++++++++------------ 1 file changed, 366 insertions(+), 378 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index ebcff5e7..771d9937 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -16,6 +16,17 @@ ], "type": "object", "properties": { + "public_health_sample_id_sivies": { + "examples": [ + "2022CEU03926" + ], + "ontology": "0", + "type": "string", + "description": "", + "classification": "Sample collection and processing", + "label": "Public Health sample id (SIVIES)", + "fill_mode": "sample" + }, "collecting_lab_sample_id": { "examples": [ "prov_rona_99" @@ -59,6 +70,28 @@ "classification": "Sample collection and processing", "label": "Originating Laboratory Address", "fill_mode": "batch" + }, + "microbiology_lab_sample_id": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "classification": "Sample collection and processing", + "label": "Sample ID given in the microbiology lab", + "fill_mode": "sample" + }, + "sequencing_sample_id": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0000079", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "classification": "Database Identifiers", + "label": "Sample ID given for sequencing", + "fill_mode": "sample" }, "submitting_lab_sample_id": { "examples": [ @@ -116,7 +149,7 @@ "label": "Sample Collection Date", "fill_mode": "sample" }, - "sample_received_date": { + "sample_received_date": { "examples": [ "3/21/2020" ], @@ -439,245 +472,7 @@ "label": "Autonomic Community", "fill_mode": "batch" }, - "organism": { - "Enums": [ - "Coronaviridae [NCBITaxon:11118]", - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001191", - "type": "string", - "description": "Taxonomic name of the organism.", - "examples": [ - "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]" - ], - "classification": "Sample collection and processing", - "label": "Organism", - "fill_mode": "batch" - }, - "host_subject_id": { - "examples": [ - "e.g. #131" - ], - "ontology": "GENEPIO:0001398", - "type": "string", - "description": "An unique identifier by which each subject can be referred to, de-identified.", - "classification": "Host information", - "label": "Host Subject Id", - }, - "host_health_state": { - "examples": [ - "" - ], - "ontology": "GENEPIO:0001388", - "type": "string", - "description": " Status of the host", - "classification": "Host health state information", - "label": "Host health state", - }, - "host_scientific_name": { - "Enums": [ - "Bos taurus [NCBITaxon:9913]", - "Canis lupus familiaris [NCBITaxon:9615]", - "Chiroptera [NCBITaxon:9397]", - "Columbidae [NCBITaxon:8930]", - "Felis catus [NCBITaxon:9685]", - "Gallus gallus [NCBITaxon:9031]", - "Homo sapiens [NCBITaxon:9606]", - "Manis [NCBITaxon:9973]", - "Manis javanica [NCBITaxon:9974]", - "Neovison vison [NCBITaxon:452646]", - "Panthera leo [NCBITaxon:9689]", - "Panthera tigris [NCBITaxon:9694]", - "Rhinolophidae [NCBITaxon:58055]", - "Rhinolophus affinis [NCBITaxon:59477]", - "Sus scrofa domesticus [NCBITaxon:9825]", - "Viverridae [NCBITaxon:9673]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001387", - "type": "string", - "description": "The taxonomic, or scientific name of the host.", - "examples": [ - "Homo sapiens [NCBITaxon:9606]" - ], - "classification": "Host information", - "label": "Host Scientific Name", - "fill_mode": "batch" - }, - "host_disease": { - "Enums": [ - "COVID-19 [MONDO:0100096]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001391", - "type": "string", - "description": "The name of the disease experienced by the host.", - "examples": [ - "COVID-19 [MONDO:0100096]" - ], - "classification": "Host information", - "label": "Host disease", - "fill_mode": "batch" - }, - "host_age": { - "ontology": "GENEPIO:0001392", - "type": "string", - "description": "Age of host at the time of sampling.", - "examples": [ - "79" - ], - "classification": "Host information", - "label": "Host Age", - "fill_mode": "sample" - }, - "host_gender": { - "Enums": [ - "Female [NCIT:C46110]", - "Male [NCIT:C46109]", - "Non-binary Gender [GSSO:000132]", - "Transgender (assigned male at birth) [GSSO:004004]", - "Transgender (assigned female at birth) [GSSO:004005]", - "Undeclared [NCIT:C110959]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001395", - "type": "string", - "description": "The gender of the host at the time of sample collection.", - "examples": [ - "Male [NCIT:C46109]" - ], - "classification": "Host information", - "label": "Host Gender", - "fill_mode": "sample" - }, - "sequencing_instrument_model": { - "Enums": [ - "Illumina sequencing instrument [GENEPIO:0100105]", - "Illumina Genome Analyzer [GENEPIO:0100106]", - "Illumina Genome Analyzer II [GENEPIO:0100107]", - "Illumina Genome Analyzer IIx [GENEPIO:0100108]", - "Illumina HiScanSQ [GENEPIO:0100109]", - "Illumina HiSeq [GENEPIO:0100110]", - "Illumina HiSeq X [GENEPIO:0100111]", - "Illumina HiSeq X Five [GENEPIO:0100112]", - "Illumina HiSeq X Ten [GENEPIO:0100113]", - "Illumina HiSeq 1000 [GENEPIO:0100114]", - "Illumina HiSeq 1500 [GENEPIO:0100115]", - "Illumina HiSeq 2000 [GENEPIO:0100116]", - "Illumina HiSeq 2500 [GENEPIO:0100117]", - "Illumina HiSeq 3000 [GENEPIO:0100118]", - "Illumina HiSeq 4000 [GENEPIO:0100119]", - "Illumina iSeq [GENEPIO:0100120]", - "Illumina iSeq 100 [GENEPIO:0100121]", - "Illumina NovaSeq [GENEPIO:0100122]", - "Illumina NovaSeq 6000 [GENEPIO:0100123]", - "Illumina MiniSeq [GENEPIO:0100124]", - "Illumina MiSeq [GENEPIO:0100125]", - "Illumina NextSeq [GENEPIO:0100126]", - "Illumina NextSeq 500 [GENEPIO:0100127]", - "Illumina NextSeq 550 [GENEPIO:0100128]", - "Illumina NextSeq 2000 [GENEPIO:0100129]", - "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", - "PacBio RS [GENEPIO:0100131]", - "PacBio RS II [GENEPIO:0100132]", - "PacBio Sequel [GENEPIO:0100133]", - "PacBio Sequel II [GENEPIO:0100134]", - "Ion Torrent sequencing instrument [GENEPIO:0100135]", - "Ion Torrent PGM [GENEPIO:0100136]", - "Ion Torrent Proton [GENEPIO:0100137]", - "Ion Torrent S5 XL [GENEPIO:0100138]", - "Ion Torrent S5 [GENEPIO:0100139]", - "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", - "Oxford Nanopore GridION [GENEPIO:0100141]", - "Oxford Nanopore MinION [GENEPIO:0100142]", - "Oxford Nanopore PromethION [GENEPIO:0100143]", - "BGI Genomics sequencing instrument [GENEPIO:0100144]", - "BGI SEQ-500 [GENEPIO:0100145]", - "MGI sequencing instrument [GENEPIO:0100146]", - "MGI DNBSEQ-T7 [GENEPIO:0100147]", - "MGI DNBSEQ-G400 [GENEPIO:0100148]", - "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", - "MGI DNBSEQ-G50 [GENEPIO:0100150]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001452", - "type": "string", - "description": "The model of the sequencing instrument used.", - "examples": [ - "Oxford Nanopore MinION [GENEPIO:0100142]" - ], - "classification": "Sequencing", - "label": "Sequencing Instrument Model", - "fill_mode": "batch" - }, - - "biosample_accession_ENA": { - "examples": [ - "SAMN14180202" - ], - "ontology": "GENEPIO:0001139", - "type": "string", - "description": "The identifier assigned to a BioSample in INSDC archives.", - "classification": "Database Identifiers", - "label": "ENA Sample ID", - "fill_mode": "sample" - }, - "virus_name": { - "examples": [ - "hCoV-19/Canada/prov_rona_99/2020" - ], - "ontology": "GENEPIO:0100282", - "type": "string", - "description": "The user-defined GISAID virus name assigned to the sequence.", - "classification": "Database Identifiers", - "label": "GISAID Virus Name", - "fill_mode": "sample" - }, - - "microbiology_lab_sample_id": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Sample collection and processing", - "label": "Sample ID given in the microbiology lab", - "fill_mode": "sample" - }, - "public_health_sample_id_sivies": { - "examples": [ - "2022CEU03926" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Sample collection and processing", - "label": "Public Health sample id (SIVIES)", - "fill_mode": "sample" - }, - "geo_loc_region": { + "geo_loc_region": { "examples": [ "Derbyshire" ], @@ -721,6 +516,29 @@ "label": "Geo Loc Longitude", "fill_mode": "batch" }, + "purpose_sampling": { + "Enums": [ + "Cluster/Outbreak Investigation [GENEPIO:0100001]", + "Diagnostic Testing [GENEPIO:0100002]", + "Research [GENEPIO:0100003]", + "Protocol Testing [GENEPIO:0100024]", + "Surveillance [GENEPIO:0100004]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "NCIT_C146997", + "type": "string", + "description": "The reason that the sample was collected.", + "examples": [ + "Diagnostic Testing [GENEPIO:0100002]" + ], + "classification": "Sample collection and processing", + "label": "Purpose of sampling", + "fill_mode": "batch" + }, "anatomical_material": { "Enums": [ "Blood [UBERON:0000178]", @@ -828,102 +646,248 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "GENEPIO:0001232", + "ontology": "GENEPIO:0001232", + "type": "string", + "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", + "examples": [ + "Hospital [ENVO:00002173]" + ], + "classification": "Sample collection and processing", + "label": "Environmental System", + "fill_mode": "batch" + }, + "organism": { + "Enums": [ + "Coronaviridae [NCBITaxon:11118]", + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001191", + "type": "string", + "description": "Taxonomic name of the organism.", + "examples": [ + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]" + ], + "classification": "Sample collection and processing", + "label": "Organism", + "fill_mode": "batch" + }, + "tax_id": { + "examples": [ + "probably 2697049 in all cases" + ], + "ontology": "GENEPIO_0001724", + "type": "string", + "description": "The NCBITaxon identifier for the organism being sequenced.", + "classification": "Sample collection and processing", + "label": "Tax ID", + "fill_mode": "batch" + }, + "host_subject_id": { + "examples": [ + "e.g. #131" + ], + "ontology": "GENEPIO:0001398", + "type": "string", + "description": "An unique identifier by which each subject can be referred to, de-identified.", + "classification": "Host information", + "label": "Host Subject Id", + }, + "host_health_state": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001388", + "type": "string", + "description": " Status of the host", + "classification": "Host health state information", + "label": "Host health state", + }, + "host_common_name": { + "Enums": [ + "Human [NCBITaxon:9606]", + "Bat [NCBITaxon:9397]", + "Cat [NCBITaxon:9685]", + "Chicken [NCBITaxon:9031]", + "Civet [NCBITaxon:9673]", + "Cow [NCBITaxon:9913]", + "Dog [NCBITaxon:9615]", + "Lion [NCBITaxon:9689]", + "Mink [NCBITaxon:452646]", + "Pangolin [NCBITaxon:9973]", + "Pig [NCBITaxon:9825]", + "Pigeon [NCBITaxon:8930]", + "Tiger [NCBITaxon:9694]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001386", + "type": "string", + "description": "The commonly used name of the host.", + "examples": [ + "Human [NCBITaxon:9606]" + ], + "classification": "Host information", + "label": "Host", + "fill_mode": "batch" + }, + "host_scientific_name": { + "Enums": [ + "Bos taurus [NCBITaxon:9913]", + "Canis lupus familiaris [NCBITaxon:9615]", + "Chiroptera [NCBITaxon:9397]", + "Columbidae [NCBITaxon:8930]", + "Felis catus [NCBITaxon:9685]", + "Gallus gallus [NCBITaxon:9031]", + "Homo sapiens [NCBITaxon:9606]", + "Manis [NCBITaxon:9973]", + "Manis javanica [NCBITaxon:9974]", + "Neovison vison [NCBITaxon:452646]", + "Panthera leo [NCBITaxon:9689]", + "Panthera tigris [NCBITaxon:9694]", + "Rhinolophidae [NCBITaxon:58055]", + "Rhinolophus affinis [NCBITaxon:59477]", + "Sus scrofa domesticus [NCBITaxon:9825]", + "Viverridae [NCBITaxon:9673]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "GENEPIO:0001387", "type": "string", - "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", + "description": "The taxonomic, or scientific name of the host.", "examples": [ - "Hospital [ENVO:00002173]" + "Homo sapiens [NCBITaxon:9606]" ], - "classification": "Sample collection and processing", - "label": "Environmental System", + "classification": "Host information", + "label": "Host Scientific Name", "fill_mode": "batch" }, - "collection_device": { + "host_disease": { "Enums": [ - "Air filter [ENVO:00003968]", - "Blood Collection Tube [OBI:0002859]", - "Bronchoscope [OBI:0002826]", - "Collection Container [OBI:0002088]", - "Collection Cup [GENEPIO:0100026]", - "Fibrobronchoscope Brush [OBI:0002825]", - "Filter [GENEPIO:0100103]", - "Fine Needle [OBI:0002827]", - "Microcapillary tube [OBI:0002858]", - "Micropipette [OBI:0001128]", - "Needle [OBI:0000436]", - "Serum Collection Tube [OBI:0002860]", - "Sputum Collection Tube [OBI:0002861]", - "Suction Catheter [OBI:0002831]", - "Swab [GENEPIO:0100027]", - "Urine Collection Tube [OBI:0002862]", - "Virus Transport Medium [OBI:0002866]", + "COVID-19 [MONDO:0100096]", "Not Applicable [GENEPIO:0001619]", "Not Collected [GENEPIO:0001620]", "Not Provided [GENEPIO:0001668]", "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "GENEPIO:0001234", + "ontology": "GENEPIO:0001391", "type": "string", - "description": "The instrument or container used to collect the sample e.g. swab.", + "description": "The name of the disease experienced by the host.", "examples": [ - "Swab [GENEPIO:0100027]" + "COVID-19 [MONDO:0100096]" ], - "classification": "Sample collection and processing", - "label": "Collection Device", + "classification": "Host information", + "label": "Host disease", "fill_mode": "batch" }, - "tax_id": { + "host_age": { + "ontology": "GENEPIO:0001392", + "type": "string", + "description": "Age of host at the time of sampling.", "examples": [ - "probably 2697049 in all cases" + "79" ], - "ontology": "GENEPIO_0001724", - "type": "string", - "description": "The NCBITaxon identifier for the organism being sequenced.", - "classification": "Sample collection and processing", - "label": "Tax ID", - "fill_mode": "batch" + "classification": "Host information", + "label": "Host Age", + "fill_mode": "sample" }, - "center_name": { - "examples": [ - " KAROLINSKA INSITUTET" + "host_gender": { + "Enums": [ + "Female [NCIT:C46110]", + "Male [NCIT:C46109]", + "Non-binary Gender [GSSO:000132]", + "Transgender (assigned male at birth) [GSSO:004004]", + "Transgender (assigned female at birth) [GSSO:004005]", + "Undeclared [NCIT:C110959]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" ], - "ontology": "NCIT_C19983", + "ontology": "GENEPIO:0001395", "type": "string", - "description": "The name of the institution", - "classification": "Sample collection and processing", - "label": "Center Name", - "fill_mode": "batch" + "description": "The gender of the host at the time of sample collection.", + "examples": [ + "Male [NCIT:C46109]" + ], + "classification": "Host information", + "label": "Host Gender", + "fill_mode": "sample" }, - "host_common_name": { + "sequencing_instrument_model": { "Enums": [ - "Human [NCBITaxon:9606]", - "Bat [NCBITaxon:9397]", - "Cat [NCBITaxon:9685]", - "Chicken [NCBITaxon:9031]", - "Civet [NCBITaxon:9673]", - "Cow [NCBITaxon:9913]", - "Dog [NCBITaxon:9615]", - "Lion [NCBITaxon:9689]", - "Mink [NCBITaxon:452646]", - "Pangolin [NCBITaxon:9973]", - "Pig [NCBITaxon:9825]", - "Pigeon [NCBITaxon:8930]", - "Tiger [NCBITaxon:9694]", + "Illumina sequencing instrument [GENEPIO:0100105]", + "Illumina Genome Analyzer [GENEPIO:0100106]", + "Illumina Genome Analyzer II [GENEPIO:0100107]", + "Illumina Genome Analyzer IIx [GENEPIO:0100108]", + "Illumina HiScanSQ [GENEPIO:0100109]", + "Illumina HiSeq [GENEPIO:0100110]", + "Illumina HiSeq X [GENEPIO:0100111]", + "Illumina HiSeq X Five [GENEPIO:0100112]", + "Illumina HiSeq X Ten [GENEPIO:0100113]", + "Illumina HiSeq 1000 [GENEPIO:0100114]", + "Illumina HiSeq 1500 [GENEPIO:0100115]", + "Illumina HiSeq 2000 [GENEPIO:0100116]", + "Illumina HiSeq 2500 [GENEPIO:0100117]", + "Illumina HiSeq 3000 [GENEPIO:0100118]", + "Illumina HiSeq 4000 [GENEPIO:0100119]", + "Illumina iSeq [GENEPIO:0100120]", + "Illumina iSeq 100 [GENEPIO:0100121]", + "Illumina NovaSeq [GENEPIO:0100122]", + "Illumina NovaSeq 6000 [GENEPIO:0100123]", + "Illumina MiniSeq [GENEPIO:0100124]", + "Illumina MiSeq [GENEPIO:0100125]", + "Illumina NextSeq [GENEPIO:0100126]", + "Illumina NextSeq 500 [GENEPIO:0100127]", + "Illumina NextSeq 550 [GENEPIO:0100128]", + "Illumina NextSeq 2000 [GENEPIO:0100129]", + "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", + "PacBio RS [GENEPIO:0100131]", + "PacBio RS II [GENEPIO:0100132]", + "PacBio Sequel [GENEPIO:0100133]", + "PacBio Sequel II [GENEPIO:0100134]", + "Ion Torrent sequencing instrument [GENEPIO:0100135]", + "Ion Torrent PGM [GENEPIO:0100136]", + "Ion Torrent Proton [GENEPIO:0100137]", + "Ion Torrent S5 XL [GENEPIO:0100138]", + "Ion Torrent S5 [GENEPIO:0100139]", + "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", + "Oxford Nanopore GridION [GENEPIO:0100141]", + "Oxford Nanopore MinION [GENEPIO:0100142]", + "Oxford Nanopore PromethION [GENEPIO:0100143]", + "BGI Genomics sequencing instrument [GENEPIO:0100144]", + "BGI SEQ-500 [GENEPIO:0100145]", + "MGI sequencing instrument [GENEPIO:0100146]", + "MGI DNBSEQ-T7 [GENEPIO:0100147]", + "MGI DNBSEQ-G400 [GENEPIO:0100148]", + "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", + "MGI DNBSEQ-G50 [GENEPIO:0100150]", "Not Applicable [GENEPIO:0001619]", "Not Collected [GENEPIO:0001620]", "Not Provided [GENEPIO:0001668]", "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "GENEPIO:0001386", + "ontology": "GENEPIO:0001452", "type": "string", - "description": "The commonly used name of the host.", + "description": "The model of the sequencing instrument used.", "examples": [ - "Human [NCBITaxon:9606]" + "Oxford Nanopore MinION [GENEPIO:0100142]" ], - "classification": "Host information", - "label": "Host", + "classification": "Sequencing", + "label": "Sequencing Instrument Model", "fill_mode": "batch" }, "purpose_of_sequencing": { @@ -968,40 +932,6 @@ "label": "Purpose of Sequencing", "fill_mode": "batch" }, - "purpose_sampling": { - "Enums": [ - "Cluster/Outbreak Investigation [GENEPIO:0100001]", - "Diagnostic Testing [GENEPIO:0100002]", - "Research [GENEPIO:0100003]", - "Protocol Testing [GENEPIO:0100024]", - "Surveillance [GENEPIO:0100004]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "NCIT_C146997", - "type": "string", - "description": "The reason that the sample was collected.", - "examples": [ - "Diagnostic Testing [GENEPIO:0100002]" - ], - "classification": "Sample collection and processing", - "label": "Purpose of sampling", - "fill_mode": "batch" - }, - "sequencing_sample_id": { - "examples": [ - "" - ], - "ontology": "GENEPIO:0000079", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "classification": "Database Identifiers", - "label": "Sample ID given for sequencing", - "fill_mode": "sample" - }, "sequencing_date": { "examples": [ "4/26/2021" @@ -1014,20 +944,30 @@ "label": "Sequencing Date", "fill_mode": "batch" }, - "rna_extraction_protocol": { + "extraction_protocol": { "examples": [ - "" + "Opentrons custom protocol" ], "ontology": "OBI_0302884", "type": "string", - "description": "", + "description": "DNA/RNA extraction protocol", "classification": "Sequencing", - "label": "Rna Extraction Protocol", + "label": "Extraction Protocol", "fill_mode": "batch" }, - "library_kit": { + "all_in_one_library_kit": { + "Enums": [ + "Ion Xpress", + "ABL_DeepChek NGS", + "Ion AmpliSeq Kit for Chef DL8", + "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", + "NEBNext® ARTIC SARS-CoV-2 FS", + "Illumina COVIDSeq Test", + "ABL DeepChek® Assay WG SC2 V1", + "Other" + ], "examples": [ - "" + "Illumina COVIDSeq Test" ], "ontology": "GENEPIO_0000085", "type": "string", @@ -1036,9 +976,46 @@ "label": "Commercial All-in-one library kit", "fill_mode": "batch" }, + "library_preparation_kit": { + "Enums": [ + "Illumina DNA PCR-Free Prep", + "Illumina DNA Prep", + "Illumina Stranded mRNA Prep", + "Nextera XT DNA Library Preparation Kit", + "TruSeq DNA Nano", + "TruSeq DNA Nano Library Prep Kit for NeoPrep", + "TruSeq DNA PCR-Free", + "TruSeq RNA Library Prep Kit v2", + "TruSeq Stranded Total RNA", + "TruSeq Stranded mRNA", + "Nextera XT", + "NEBNex Fast DNA Library Prep Set for Ion Torrent", + "Nextera DNA Flex", + "Ion AmpliSeq Kit Library Kit Plus", + "Ion AmpliSeq Kit Library Kit Plus", + "Ion AmpliSeq Library Kit 2.0", + "Ion Xpress Plus Fragment Library Kit", + "Oxford Nanopore Sequencing Kit", + "SQK-RBK110-96", + "Nanopore COVID Maxi: 9216 samples", + "Nanopore COVID Midi: 2304 samples", + "Nanopore COVID Mini: 576 samples", + "Vela Diagnostics:ViroKey SQ FLEX Library Prep Reagents", + "Other", + ] + "examples": [ + "Illumina DNA Prep Tagmentation" + ], + "ontology": "GENEPIO:0001450", + "type": "string", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "classification": "Sequencing", + "label": "Library Preparation Kit", + "fill_mode": "batch" + }, "enrichment_protocol": { "examples": [ - "" + "AMPLICON" ], "ontology": "EFO_0009089", "type": "string", @@ -1058,37 +1035,37 @@ "label": "If Enrichment Protocol Is Other, Specify", "fill_mode": "batch" }, - "amplicon_protocol": { + "enrichment_panel": { "examples": [ - "" + "ARTIC" ], - "ontology": "EFO_0003747", + "ontology": "0", "type": "string", "description": "", "classification": "Sequencing", "label": "Enrichment panel/assay", "fill_mode": "batch" }, - "if_amplicon_protocol_if_other_specify": { + "enrichment_panel_version": { "examples": [ - "" + "ARTIC v4" ], "ontology": "0", "type": "string", "description": "", "classification": "Sequencing", - "label": "If Enrichment panel/assay Is Other, Specify", + "label": "Enrichment panel/assay version", "fill_mode": "batch" }, - "amplicon_version": { + "amplicon_pcr_primer_scheme": { "examples": [ - "" + "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv" ], - "ontology": "0", + "ontology": "GENEPIO:0001456", "type": "string", - "description": "", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", "classification": "Sequencing", - "label": "Enrichment panel/assay version", + "label": "Amplicon Pcr Primer Scheme", "fill_mode": "batch" }, "number_of_samples_in_run": { @@ -1135,28 +1112,6 @@ "label": "Sequencing Instrument Platform", "fill_mode": "batch" }, - "library_preparation_kit": { - "examples": [ - "Nextera XT" - ], - "ontology": "GENEPIO:0001450", - "type": "string", - "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", - "classification": "Sequencing", - "label": "Library Preparation Kit", - "fill_mode": "batch" - }, - "amplicon_pcr_primer_scheme": { - "examples": [ - "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv" - ], - "ontology": "GENEPIO:0001456", - "type": "string", - "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", - "classification": "Sequencing", - "label": "Amplicon Pcr Primer Scheme", - "fill_mode": "batch" - }, "library_selection": { "examples": [ "RANDOM PCR" @@ -2537,6 +2492,39 @@ "classification": "Database Identifiers", "label": "Type", "fill_mode": "batch" - } + }, + "biosample_accession_ENA": { + "examples": [ + "SAMN14180202" + ], + "ontology": "GENEPIO:0001139", + "type": "string", + "description": "The identifier assigned to a BioSample in INSDC archives.", + "classification": "Database Identifiers", + "label": "ENA Sample ID", + "fill_mode": "sample" + }, + "virus_name": { + "examples": [ + "hCoV-19/Canada/prov_rona_99/2020" + ], + "ontology": "GENEPIO:0100282", + "type": "string", + "description": "The user-defined GISAID virus name assigned to the sequence.", + "classification": "Database Identifiers", + "label": "GISAID Virus Name", + "fill_mode": "sample" + }, + "center_name": { + "examples": [ + " KAROLINSKA INSITUTET" + ], + "ontology": "NCIT_C19983", + "type": "string", + "description": "The name of the institution", + "classification": "Sample collection and processing", + "label": "Center Name", + "fill_mode": "batch" + }, } } From 2b882bafce25155a3b1b5d54b20b33782b824f92 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 29 Aug 2022 13:30:25 +0200 Subject: [PATCH 0846/1454] new functionality to have a list of parameters --- relecov_tools/rest_api.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/relecov_tools/rest_api.py b/relecov_tools/rest_api.py index 6d8278b4..a5374519 100644 --- a/relecov_tools/rest_api.py +++ b/relecov_tools/rest_api.py @@ -20,9 +20,16 @@ def __init__(self, server, url): self.request_url = server + url self.headers = {"content-type": "application/json"} - def get_request(self, request_info, parameter, value, safe=True): + def get_request(self, request_info, parameter, value=None, safe=True): if parameter == "" or parameter is None: url_http = str(self.request_url + request_info) + elif isinstance(parameter, dict): + param_value = [] + for key, value in parameter.items(): + param_value.append(key + "=" + value) + url_http = str( + self.request_url + request_info + "?" + "?".join(param_value) + ) else: url_http = str( self.request_url + request_info + "?" + parameter + "=" + value From b860b5d30dda08841e7fd48a40a06ff0cefbcc89 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 30 Aug 2022 10:51:43 +0200 Subject: [PATCH 0847/1454] fixed some bugs --- relecov_tools/conf/configuration.json | 4 ++-- relecov_tools/feed_database.py | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 6d2d2c3a..b85bdf89 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -109,7 +109,7 @@ }, "external_url": { "iskylims": { - "server": "http://relecov-iskylims.isciiides.es", + "server": "http://relecov-iskylims.isciiides.es:8001", "url": "/wetlab/api/", "store_samples": "createSampleData", "url_project_fields": "sampleProjectFields", @@ -119,7 +119,7 @@ "token": "" }, "relecov": { - "server": "http://relecov-platform.isciiides.es", + "server": "http://relecov-platform.isciiides.es:8000", "url": "/api/", "store_samples": "createSampleData", "bioinfodata": "createBioinfoData", diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index ddc4bc24..5eeac883 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -316,6 +316,7 @@ def store_data(self): elif self.type_of_info == "variantdata": post_url = "variantdata" + map_fields = self.json_data else: stderr.print("[red] Invalid type to upload to database") sys.exit(1) From 9deccdf26b715084edf6b707eaa49f5dbd6732b3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 30 Aug 2022 14:25:35 +0200 Subject: [PATCH 0848/1454] fixes relecov schema --- relecov_tools/schema/relecov_schema.json | 1704 ++++++++++------------ 1 file changed, 741 insertions(+), 963 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 771d9937..00a11f6a 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1,6 +1,6 @@ { "schema": "RELECOV", - "version": "0.1.0", + "version": "1.0.0", "required": [ "collecting_lab_sample_id", "collecting_institution", @@ -82,6 +82,17 @@ "label": "Sample ID given in the microbiology lab", "fill_mode": "sample" }, + "isolate_sample_id": { + "examples": [ + "" + ], + "ontology": "NCIT:C53471", + "type": "string", + "description": "", + "classification": "Database Identifiers", + "label": "Sample ID given if multiple rna-extraction or passages", + "fill_mode": "sample" + }, "sequencing_sample_id": { "examples": [ "" @@ -617,7 +628,7 @@ "label": "Environmental Material", "fill_mode": "batch" }, - "environmental_site": { + "environmental_system": { "Enums": [ "Acute care facility [ENVO:03501135]", "Animal house [ENVO:00003040]", @@ -678,7 +689,7 @@ }, "tax_id": { "examples": [ - "probably 2697049 in all cases" + "2697049" ], "ontology": "GENEPIO_0001724", "type": "string", @@ -695,7 +706,7 @@ "type": "string", "description": "An unique identifier by which each subject can be referred to, de-identified.", "classification": "Host information", - "label": "Host Subject Id", + "label": "Host Subject Id" }, "host_health_state": { "examples": [ @@ -705,7 +716,7 @@ "type": "string", "description": " Status of the host", "classification": "Host health state information", - "label": "Host health state", + "label": "Host health state" }, "host_common_name": { "Enums": [ @@ -1001,8 +1012,8 @@ "Nanopore COVID Midi: 2304 samples", "Nanopore COVID Mini: 576 samples", "Vela Diagnostics:ViroKey SQ FLEX Library Prep Reagents", - "Other", - ] + "Other" + ], "examples": [ "Illumina DNA Prep Tagmentation" ], @@ -1014,12 +1025,20 @@ "fill_mode": "batch" }, "enrichment_protocol": { + "Enums":[ + "Amplicon", + "Probes", + "Custom probes", + "Custom amplicon", + "No enrichment", + "Other" + ], "examples": [ "AMPLICON" ], "ontology": "EFO_0009089", "type": "string", - "description": "", + "description": "Type of enrichment protocol", "classification": "Sequencing", "label": "Enrichment Protocol", "fill_mode": "batch" @@ -1036,17 +1055,43 @@ "fill_mode": "batch" }, "enrichment_panel": { + "Enums":[ + "ARTIC", + "Illumina respiratory Virus Oligo Panel", + "Illumina AmpliSeq Community panel", + "Illumina AmpliSeq SARS-CoV-2 Research Panel for Illumina", + "Ion AmpliSeq SARS‑CoV‑2 Research Panel", + "xGen SC2 Midnight1200 Amplicon Panel", + "ViroKey SQ FLEX SARS-CoV-2 Primer Set", + "NEBNext VarSkip Short SARS-CoV-2 primers", + "Other" + ], "examples": [ "ARTIC" ], "ontology": "0", "type": "string", - "description": "", + "description": "Commercial or custom panel/assay used for enrichment.", "classification": "Sequencing", "label": "Enrichment panel/assay", "fill_mode": "batch" }, "enrichment_panel_version": { + "Enums":[ + "ARTIC v1", + "ARTIC v2", + "ARTIC v3", + "ARTIC v4", + "Illumina AmpliSeq Community panel", + "Illumina AmpliSeq SARS-CoV-2 Research Panel for Illumina", + "Illumina Respiratory Virus Oligos Panel V1", + "Illumina Respiratory Virus Oligos Panel V2", + "Ion AmpliSeq SARS-CoV-2 Insight", + "xGen SC2 Midnight1200 Amplicon Panel", + "ViroKey SQ FLEX SARS-CoV-2 Primer Set",  + "NEBNext VarSkip Short SARS-CoV-2 primers", + "Other" + ], "examples": [ "ARTIC v4" ], @@ -1080,30 +1125,164 @@ "fill_mode": "batch" }, "flowcell_kit": { + "Enums":[ + "HiSeq 3000/4000 PE Cluster Kit", + "HiSeq 3000/4000 SBS Kit (50 cycles)", + "HiSeq 3000/4000 SBS Kit (150 cycles)", + "HiSeq 3000/4000 SBS Kit (300 cycles)", + "HiSeq 3000/4000 SBS Kit", + "HiSeq 3000/4000 SR Cluster Kit", + "TG HiSeq 3000/4000 SBS Kit (50 cycles)", + "TG HiSeq 3000/4000 SBS Kit (150 cycles)", + "TG HiSeq 3000/4000 SBS Kit (300 cycles)", + "TG HiSeq 3000/4000 PE ClusterKit", + "TG HiSeq 3000/4000 SR ClusterKit", + "HiSeq PE Cluster Kit v4 cBot", + "HiSeq SR Rapid Cluster Kit v2", + "HiSeq PE Rapid Cluster Kit v2", + "TG HiSeq Rapid PE Cluster Kit v2", + "HiSeq Rapid Duo cBot Sample Loading Kit", + "TG TruSeq Rapid Duo cBot Sample Loading Kit", + "HiSeq Rapid SBS Kit v2 (50 cycles)", + "HiSeq Rapid SBS Kit v2 (200 cycles)", + "HiSeq Rapid SBS Kit v2 (500 cycles)", + "TG HiSeq Rapid SBS Kit v2 (200 Cycle)", + "TG HiSeq Rapid SBS Kit v2 (50 Cycle)", + "HiSeq SR Cluster Kit v4 cBot", + "TG HiSeq SR Cluster Kit v4 - cBot", + "TG HiSeq PE Cluster Kit v4 – cBot", + "HiSeq X Ten Reagent Kit v2.5", + "HiSeq X Ten Reagent Kit v2.5 - 10 pack", + "HiSeq X Five Reagent Kit v2.5", + "MiSeq Reagent Kit v3 (150-cycle)", + "MiSeq Reagent Kit v3 (600-cycle)", + "TG MiSeq Reagent Kit v3 (600 cycle)", + "TG MiSeq Reagent Kit v3 (150 cycle)", + "MiSeq Reagent Kit v3 (150-cycle)", + "MiSeq Reagent Kit v3 (600-cycle)", + "TG MiSeq Reagent Kit v3 (600 cycle)", + "TG MiSeq Reagent Kit v3 (150 cycle)", + "MiSeq Reagent Kit v3 (150-cycle)", + "MiSeq Reagent Kit v3 (600-cycle)", + "TG MiSeq Reagent Kit v3 (600 cycle)", + "TG MiSeq Reagent Kit v3 (150 cycle)", + "MiSeq Reagent Kit v2 (50-cycles)", + "MiSeq Reagent Kit v2 (300-cycles)", + "MiSeq Reagent Kit v2 (500-cycles)", + "MiniSeq Rapid Reagent Kit (100 cycles)", + "MiniSeq High Output Reagent Kit (75-cycles)", + "MiniSeq High Output Reagent Kit (150-cycles)", + "NextSeq 1000/2000 P1 Reagents (300 Cycles)", + "NextSeq 1000/2000 P2 Reagents (100 Cycles) v3", + "NextSeq 1000/2000 P2 Reagents (200 Cycles) v3", + "NextSeq 1000/2000 P2 Reagents (300 Cycles) v3", + "NextSeq 2000 P3 Reagents (50 Cycles)",  + "NextSeq 2000 P3 Reagents (100 Cycles)", + "NextSeq 2000 P3 Reagents (200 Cycles)",  + "NextSeq 2000 P3 Reagents (300 Cycles)", + "NextSeq 1000/2000 Read and Index Primers",  + "NextSeq 1000/2000 Index Primer Kit", + "NextSeq 1000/2000 Read Primer Kit",  + "NextSeq 500/550 High Output Kit v2.5 (75 Cycles)", + "NextSeq 500/550 High Output Kit v2.5 (150 Cycles)", + "NextSeq 500/550 High Output Kit v2.5 (300 Cycles)", + "NextSeq 500/550 Mid Output Kit v2.5 (150 Cycles)", + "NextSeq 500/550 Mid Output Kit v2.5 (300 Cycles)", + "TG NextSeq 500/550 High Output Kit v2.5 (75 Cycles)",  + "TG NextSeq 500/550 High Output Kit v2.5 (150 Cycles)", + "TG NextSeq 500/550 High Output Kit v2.5 (300 Cycles)", + "TG NextSeq 500/550 Mid Output Kit v2.5 (150 Cycles)", + "TG NextSeq 500/550 Mid Output Kit v2.5 (300 Cycles)", + "NovaSeq 6000 S4 Reagent Kit v1.5 (300 cycles)", + "NovaSeq 6000 S4 Reagent Kit v1.5 (200 cycles)", + "NovaSeq 6000 S4 Reagent Kit v1.5 (35 cycles)", + "NovaSeq 6000 S2 Reagent Kit v1.5 (300 cycles)", + "NovaSeq 6000 S2 Reagent Kit v1.5 (200 cycles)", + "NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles)", + "NovaSeq 6000 S1 Reagent Kit v1.5 (300 cycles)", + "NovaSeq 6000 S1 Reagent Kit v1.5 (200 cycles)",  + "NovaSeq 6000 S1 Reagent Kit v1.5 (100 cycles)",  + "NovaSeq 6000 SP Reagent Kit v1.5 (500 cycles)", + "NovaSeq 6000 SP Reagent Kit v1.5 (300 cycles)", + "NovaSeq 6000 SP Reagent Kit v1.5 (200 cycles)",  + "NovaSeq 6000 SP Reagent Kit v1.5 (100 cycles)", + "NovaSeq 6000 SP Reagent Kit (100 cycles)",  + "NovaSeq 6000 SP Reagent Kit (200 cycles)",  + "NovaSeq 6000 SP Reagent Kit (300 cycles)", + "NovaSeq 6000 SP Reagent Kit (500 cycles)", + "NovaSeq 6000 S1 Reagent Kit (100 cycles)", + "NovaSeq 6000 S1 Reagent Kit (200 cycles)", + "NovaSeq 6000 S1 Reagent Kit (300 cycles)", + "NovaSeq 6000 S2 Reagent Kit (100 cycles)", + "NovaSeq 6000 S2 Reagent Kit (200 cycles)",  + "NovaSeq 6000 S2 Reagent Kit (300 cycles)",  + "NovaSeq 6000 S4 Reagent Kit (200 cycles)", + "NovaSeq 6000 S4 Reagent Kit (300 cycles)",  + "NovaSeq 6000 S4 Reagent Kit (300 Cycles) – 10 pack", + "NovaSeq 6000 S4 Reagent Kit (300 Cycles) – 20 pack", + "NovaSeq 6000 S4 Reagent Kit (300 Cycles) – 40 pack", + "NovaSeq Library Tubes Accessory Pack (24 tubes)", + "NovaSeq XP 4-Lane Kit v1.5",  + "NovaSeq XP 2-Lane Kit v1.5", + "NovaSeq XP 2-Lane Kit", + "NovaSeq Xp 4-Lane Kit", + "NovaSeq Xp Flow Cell Dock", + "NovaSeq Xp 2-Lane Manifold Pack", + "NovaSeq Xp 4-Lane Manifold Pack", + "PhiX Control v3", + "TG PhiX Control Kit v3", + "NextSeq PhiX Control Kit", + "TruSeq Dual Index Sequencing Primer Box, Single-Read", + "TruSeq Dual Index Sequencing Primer Box, Paired-End", + "TruSeq PE Cluster Kit v3-cBot-HS", + "TruSeq PE Cluster Kit v5-CS-GA", + "HiSeq SR Rapid Cluster Kit v2", + "HiSeq PE Rapid Cluster Kit v2", + "TG HiSeq Rapid PE Cluster Kit v2", + "HiSeq SR Rapid Cluster Kit v2", + "HiSeq PE Rapid Cluster Kit v2", + "TG HiSeq Rapid PE Cluster Kit v2", + "TruSeq SBS Kit v3-HS (200 cycles)", + "TruSeq SBS Kit v3-HS (50 cycles)", + "TG TruSeq SBS Kit v3 - HS (200-cycles)", + "TruSeq SBS Kit v5-GA", + "TruSeq SR Cluster Kit v3-cBot-HS", + "TG TruSeq SR Cluster Kit v1–cBot - HS", + "iSeq 100 i1 Reagent v2 (300-cycle)", + "iSeq 100 i1 Reagent v2 (300-cycle) 4 pack", + "iSeq 100 i1 Reagent v2 (300-cycle) 8 pack", + "Other" + ], "examples": [ - "" + "iSeq 100 i1 Reagent v2 (300-cycle) 8 pack" ], "ontology": "0", "type": "string", - "description": "", + "description": "Flowcell sequencer used for sequencing the sample", "classification": "Sequencing", "label": "Flowcell Kit", "fill_mode": "batch" }, "runID": { "examples": [ - "" + "NextSeq_GEN_320" ], "ontology": "NCIT_C117058", "type": "string", - "description": "", + "description": "Unique sequencing run identifier.", "classification": "Sequencing", "label": "Runid", "fill_mode": "batch" }, "sequencing_instrument_platform": { + "Enums":[ + "Oxford Nanopore", + "Illumina", + "Ion Torrent", + "Other" + ], "examples": [ - "" + "Illumina" ], "ontology": "0", "type": "string", @@ -1112,7 +1291,55 @@ "label": "Sequencing Instrument Platform", "fill_mode": "batch" }, + "library_source": { + "Enums": [ + "GENOMIC", + "TRANSCRIPTOMIC", + "METAGENOMIC", + "METATRANSCRIPTOMIC", + "SYNTHETIC", + "VIRAL RNA", + "OTHER" + ], + "examples": [ + "METAGENOMIC" + ], + "ontology": "GENEPIO_0001965", + "type": "string", + "description": "Molecule type used to make the library.", + "classification": "Sequencing", + "label": "Source material", + "fill_mode": "batch" + }, "library_selection": { + "Enums":[ + "RANDOM", + "PCR", + "RANDOM PCR", + "RT-PCR", + "HMPR", + "MF", + "repeat fractionation", + "size fractionation", + "MSLL", + "cDNA", + "ChIP", + "MNase", + "DNase", + "Hybrid Selection", + "Reduced Representation", + "Restriction Digest", + "5-methylcytidine antibody", + "MBD2 protein methyl-CpG binding domain", + "CAGE", + "RACE", + "MDA", + "padlock probes capture method", + "Oligo-dT", + "Inverse rRNA selection", + "ChIP-Seq", + "Other" + ], "examples": [ "RANDOM PCR" ], @@ -1157,669 +1384,535 @@ "fill_mode": "batch" }, "library_layout": { + "Enums":[ + "SINGLE", + "PAIRED" + ], "examples": [ - "PAIRED end" + "PAIRED" ], "ontology": "NCIT:C175894", "type": "string", - "description": "Single or paired.", + "description": "Single or paired sequencing configuration", "classification": "Sequencing", "label": "Library Layout", "fill_mode": "batch" }, - "dehosting_method_software_name": { + "sequence_file_R1_fastq": { "examples": [ - "Nanostripper" + "ABC123_S1_L001_R1_001.fastq.gz" ], - "ontology": "GENEPIO:0001459", + "ontology": "GENEPIO:0001476", "type": "string", - "description": "The method used to remove host reads from the pathogen sequence.", - "classification": "Bioinformatic Analysis fields", - "label": "Dehosting Method", - "fill_mode": "batch" + "description": "The user-specified filename of the r1 FASTQ file.", + "classification": "Bioinformatics and QC metrics fields", + "label": "Sequence file R1 fastq", + "fill_mode": "sample" }, - "dehosting_method_software_version": { + "sequence_file_R2_fastq": { "examples": [ - "2.4.1" + "ABC123_S1_L001_R2_002.fastq.gz" ], - "ontology": "0", + "ontology": "GENEPIO:0001477", "type": "string", - "description": "The method version used to remove host reads from the pathogen sequence.", - "classification": "Bioinformatic Analysis fields", - "label": "Dehosting Method Version", - "fill_mode": "batch" + "description": "The user-specified filename of the r2 FASTQ file.", + "classification": "Bioinformatics and QC metrics fields", + "label": "Sequence file R2 fastq", + "fill_mode": "sample" }, - "assembly": { + "r1_fastq_filepath": { "examples": [ - "" + "/User/Documents/RespLab/Data/" ], - "ontology": "NCIT_C63548", + "ontology": "GENEPIO:0001478", "type": "string", - "description": "", - "classification": "Bioinformatic Analysis fields", - "label": "Assembly", + "description": "The filepath of the r1 FASTQ file.", + "classification": "Files info", + "label": "Filepath R1 fastq", "fill_mode": "batch" }, - "if_assembly_other": { + "r2_fastq_filepath": { "examples": [ - "" + "/User/Documents/RespLab/Data/" ], - "ontology": "0", + "ontology": "GENEPIO:0001479", "type": "string", - "description": "", - "classification": "Bioinformatic Analysis fields", - "label": "If assembly Is Other, Specify", + "description": "The filepath of the r2 FASTQ file.", + "classification": "Files info", + "label": "Filepath R2 fastq", "fill_mode": "batch" }, - "assembly_params": { + "fast5_filename": { "examples": [ - "" + "batch1a_sequences.fast5" ], - "ontology": "0", + "ontology": "GENEPIO:0001480", "type": "string", - "description": "", - "classification": "Bioinformatic Analysis fields", - "label": "Assambly params", + "description": "The user-specified filename of the FAST5 file.", + "classification": "Files info", + "label": "Filename fast5", "fill_mode": "batch" }, - "variant_calling_software_name": { + "fast5_filepath": { "examples": [ - "" + "/User/Documents/RespLab/Data/" ], - "ontology": "operation_3227", + "ontology": "GENEPIO:0001481", "type": "string", - "description": "", - "classification": "Bioinformatic Variants", - "label": "Variant Calling", + "description": "The filepath of the FAST5 file.", + "classification": "Files info", + "label": "Filepath fast5", "fill_mode": "batch" }, - "variant_calling_software_version": { + "analysis_date": { "examples": [ - "" + "e.g 2020-08-07" ], "ontology": "0", "type": "string", + "format": "date", "description": "", - "classification": "Bioinformatic Variants", - "label": "Variant Calling Version", + "classification": "Bioinformatics and QC metrics fields", + "label": "Analysis date", "fill_mode": "batch" }, - "if_variant_calling_other": { + "dehosting_method_software_name": { "examples": [ - "" + "Nanostripper" ], - "ontology": "0", + "ontology": "GENEPIO:0001459", "type": "string", - "description": "", - "classification": "Bioinformatic Variants", - "label": "If variant calling Is Other, Specify", + "description": "The method used to remove host reads from the pathogen sequence.", + "classification": "Bioinformatic Analysis fields", + "label": "Dehosting Method", "fill_mode": "batch" }, - "variant_calling_params": { + "dehosting_method_software_version": { "examples": [ - "" + "2.4.1" ], "ontology": "0", "type": "string", - "description": "", - "classification": "Bioinformatic Variants", - "label": "Variant Calling params", - "fill_mode": "batch" - }, - "consensus_sequence_R1_name": { - "ontology": "GENEPIO:0001461", - "type": "string", - "description": "The name of the consensus sequence.", - "examples": [ - "ncov123assembly3" - ], + "description": "The method version used to remove host reads from the pathogen sequence.", "classification": "Bioinformatic Analysis fields", - "label": "Consensus sequence name", + "label": "Dehosting Method Version", "fill_mode": "batch" }, - "consensus_sequence_R2_name": { - "ontology": "GENEPIO:0001460", - "type": "string", - "description": "The name of the consensus sequence.", + "reference_genome_accession": { "examples": [ - "ncov123assembly3" + "NC_045512.2" ], - "classification": "Bioinformatic Analysis fields", - "label": "Consensus sequence name", + "ontology": "GENEPIO:0001485", + "type": "string", + "description": "A persistent, unique identifier of a genome database entry.", + "classification": "Bioinformatics and QC metrics fields", + "label": "Reference genome accession", "fill_mode": "batch" }, - "consensus_sequence_R1_md5": { - "ontology": "NMR:1000568", - "type": "string", - "description": "The name of the consensus sequence.", + "bioinformatics_protocol_software_name": { "examples": [ - "ncov123assembly3" + "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" ], + "ontology": "GENEPIO:0001489", + "type": "string", + "description": "The name of the bioinformatics protocol used.", "classification": "Bioinformatic Analysis fields", - "label": "Consensus sequence name md5", + "label": "Bioinformatics protocol", "fill_mode": "batch" }, - "consensus_sequence_R2_md5": { - "ontology": "NMR:1000569", - "type": "string", - "description": "The name of the consensus sequence.", + "if_bioinformatic_protocol_is_other_specify": { "examples": [ - "ncov123assembly3" + "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" ], + "ontology": "0", + "type": "string", + "description": "The name of the bioinformatics protocol used.", "classification": "Bioinformatic Analysis fields", - "label": "Consensus sequence name md5", + "label": "If bioinformatic protocol Is Other, Specify", "fill_mode": "batch" }, - "consensus_sequence_filepath": { + "bioinformatics_protocol_software_version": { "examples": [ - "/User/Documents/RespLab/Data/ncov123assembly.fasta" + "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" ], - "ontology": "GENEPIO:0001462", + "ontology": "NCIT:C93490", "type": "string", - "description": "The filepath of the consesnsus sequence file.", + "description": "The version number of the bioinformatics protocol used.", "classification": "Bioinformatic Analysis fields", - "label": "Consensus sequence filepath", + "label": "bioinformatics protocol version", "fill_mode": "batch" }, - "long_table_path": { + "commercial_open_source_both": { + "Enums":[ + "Commercial", + "Open Source", + "Both" + ], "examples": [ - "1.3" + "" ], "ontology": "0", "type": "string", - "description": "The path where the long table is ", + "description": "", "classification": "Bioinformatic Analysis fields", - "label": "Long table path", + "label": "Commercial/Open-source/both", "fill_mode": "batch" }, - "consensus_sequence_software_name": { + "preprocessing_software_name": { "examples": [ - "Ivar" + "fastp" ], - "ontology": "GENEPIO:0001463", + "ontology": "MS_1002386", "type": "string", - "description": "The name of software used to generate the consensus sequence.", + "description": "Software used for preprocessing step.", "classification": "Bioinformatic Analysis fields", - "label": "Consensus sequence software name", + "label": "Preprocessing", "fill_mode": "batch" }, - "if_consensus_other": { + "preprocessing_software_version": { "examples": [ - "1.3" + "v5.3.1" ], "ontology": "0", "type": "string", - "description": "The version of the software used to generate the consensus sequence.", + "description": "Version of the preprocessing software used.", "classification": "Bioinformatic Analysis fields", - "label": "If consensus Is Other, Specify", + "label": "Preprocessing Version", "fill_mode": "batch" }, - "consensus_sequence_software_version": { + "if_preprocessing_other": { "examples": [ - "1.3" + "" ], - "ontology": "GENEPIO:0001469", + "ontology": "0", "type": "string", - "description": "The version of the software used to generate the consensus sequence.", + "description": "", "classification": "Bioinformatic Analysis fields", - "label": "Consensus sequence software version", + "label": "If preprocessing Is Other, Specify", "fill_mode": "batch" }, - "consensus_params": { + "preprocessing_params": { "examples": [ "" ], "ontology": "0", "type": "string", - "description": "", + "description": "Preprocessing parameters used.", "classification": "Bioinformatic Analysis fields", - "label": "Consensus Params", + "label": "Preprocessing params", "fill_mode": "batch" }, - "depth_of_coverage_value": { + "mapping_software_name": { "examples": [ - "400x" + "bowtie2" ], - "ontology": "GENEPIO:0001474", + "ontology": "topic:0102", "type": "string", - "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "classification": "Bioinformatics and QC metrics fields", - "label": "Depth of coverage value ", + "description": "Software used for mapping step.", + "classification": "Bioinformatic Analysis fields", + "label": "Mapping", "fill_mode": "batch" }, - "sample_name": { + "mapping_software_version": { "examples": [ - "234546" + "v7.0.1" ], "ontology": "0", "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics fields", - "label": "Sample Name", + "description": "Version of the mapper used.", + "classification": "Bioinformatic Analysis fields", + "label": "Mapping Version", "fill_mode": "batch" }, - "depth_of_coverage_threshold": { + "if_mapping_other": { "examples": [ - "100x" + "" ], - "ontology": "GENEPIO:0001475", + "ontology": "0", "type": "string", - "description": "The threshold used as a cut-off for the depth of coverage.", - "classification": "Bioinformatics and QC metrics fields", - "label": "Depth of coverage threshold", + "description": "", + "classification": "Bioinformatic Analysis fields", + "label": "If mapping Is Other, Specify", "fill_mode": "batch" }, - "sequence_file_R1_fastq": { + "mapping_params": { "examples": [ - "ABC123_S1_L001_R1_001.fastq.gz" + "" ], - "ontology": "GENEPIO:0001476", + "ontology": "0", "type": "string", - "description": "The user-specified filename of the r1 FASTQ file.", - "classification": "Bioinformatics and QC metrics fields", - "label": "Sequence file R1 fastq", - "fill_mode": "sample" + "description": "Parameters used for mapping step.", + "classification": "Bioinformatic Analysis fields", + "label": "Mapping params", + "fill_mode": "batch" }, - "sequence_file_R2_fastq": { + "assembly": { "examples": [ - "ABC123_S1_L001_R2_002.fastq.gz" + "Spades" ], - "ontology": "GENEPIO:0001477", + "ontology": "NCIT_C63548", "type": "string", - "description": "The user-specified filename of the r2 FASTQ file.", - "classification": "Bioinformatics and QC metrics fields", - "label": "Sequence file R2 fastq", - "fill_mode": "sample" + "description": "Software used for assembly of the pathogen genome.", + "classification": "Bioinformatic Analysis fields", + "label": "Assembly", + "fill_mode": "batch" }, - "r1_fastq_filepath": { + "if_assembly_other": { "examples": [ - "/User/Documents/RespLab/Data/" + "v3.1" ], - "ontology": "GENEPIO:0001478", + "ontology": "0", "type": "string", - "description": "The filepath of the r1 FASTQ file.", - "classification": "Files info", - "label": "Filepath R1 fastq", + "description": "Assembly software version", + "classification": "Bioinformatic Analysis fields", + "label": "If assembly Is Other, Specify", "fill_mode": "batch" }, - "r2_fastq_filepath": { + "assembly_params": { "examples": [ - "/User/Documents/RespLab/Data/" + "-k 127,56,27" ], - "ontology": "GENEPIO:0001479", + "ontology": "0", "type": "string", - "description": "The filepath of the r2 FASTQ file.", - "classification": "Files info", - "label": "Filepath R2 fastq", + "description": "Params used for genome assembly.", + "classification": "Bioinformatic Analysis fields", + "label": "Assambly params", "fill_mode": "batch" }, - "fast5_filename": { + "variant_calling_software_name": { "examples": [ - "batch1a_sequences.fast5" + "Ivar" ], - "ontology": "GENEPIO:0001480", + "ontology": "operation_3227", "type": "string", - "description": "The user-specified filename of the FAST5 file.", - "classification": "Files info", - "label": "Filename fast5", + "description": "Software used for variant calling.", + "classification": "Bioinformatic Variants", + "label": "Variant Calling", "fill_mode": "batch" }, - "fast5_filepath": { + "variant_calling_software_version": { "examples": [ - "/User/Documents/RespLab/Data/" + "v4.1" ], - "ontology": "GENEPIO:0001481", + "ontology": "0", "type": "string", - "description": "The filepath of the FAST5 file.", - "classification": "Files info", - "label": "Filepath fast5", + "description": "Variant calling software version", + "classification": "Bioinformatic Variants", + "label": "Variant Calling Version", "fill_mode": "batch" }, - "number_of_base_pairs_sequenced": { + "if_variant_calling_other": { "examples": [ - "387566" + "" ], - "ontology": "GENEPIO:0001482", + "ontology": "0", "type": "string", - "description": "The number of total base pairs generated by the sequencing process.", - "classification": "Bioinformatics and QC metrics fields", - "label": "Number of base pairs sequenced ", + "description": "", + "classification": "Bioinformatic Variants", + "label": "If variant calling Is Other, Specify", "fill_mode": "batch" }, - "consensus_genome_length": { + "variant_calling_params": { "examples": [ - "38677" + "-t 0.5 -Q 20" ], - "ontology": "GENEPIO:0001483", + "ontology": "0", "type": "string", - "description": "Size of the assembled genome described as the number of base pairs.", - "classification": "Bioinformatics and QC metrics fields", - "label": "Consensus genome length", + "description": "Params used for variant calling", + "classification": "Bioinformatic Variants", + "label": "Variant Calling params", "fill_mode": "batch" }, - "ns_per_100_kbp": { + "consensus_sequence_name": { + "ontology": "GENEPIO:0001460", + "type": "string", + "description": "The name of the consensus sequence.", "examples": [ - "300" + "ncov123assembly3" ], - "ontology": "GENEPIO:0001484", - "type": "string", - "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", - "classification": "Bioinformatics and QC metrics fields", - "label": "Ns per 100 kbp", + "classification": "Bioinformatic Analysis fields", + "label": "Consensus sequence name", "fill_mode": "batch" }, - "reference_genome_accession": { + "consensus_sequence_filename": { + "ontology": "GENEPIO:0001461", + "type": "string", + "description": "The name of the consensus sequence filename", "examples": [ - "NC_045512.2" + "ncov123assembly3" ], - "ontology": "GENEPIO:0001485", + "classification": "Bioinformatic Analysis fields", + "label": "Consensus sequence name", + "fill_mode": "batch" + }, + "consensus_sequence_md5": { + "ontology": "0", "type": "string", - "description": "A persistent, unique identifier of a genome database entry.", - "classification": "Bioinformatics and QC metrics fields", - "label": "Reference genome accession", + "description": "The name of the consensus sequence.", + "examples": [ + "5gaskañlkdak3143242ñlkas" + ], + "classification": "Bioinformatic Analysis fields", + "label": "Consensus sequence name md5", "fill_mode": "batch" }, - "bioinformatics_protocol_software_name": { + "consensus_sequence_filepath": { "examples": [ - "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" + "/User/Documents/RespLab/Data/ncov123assembly.fasta" ], - "ontology": "GENEPIO:0001489", + "ontology": "GENEPIO:0001462", "type": "string", - "description": "The name of the bioinformatics protocol used.", + "description": "The filepath of the consesnsus sequence file.", "classification": "Bioinformatic Analysis fields", - "label": "Bioinformatics protocol", + "label": "Consensus sequence filepath", "fill_mode": "batch" }, - "if_bioinformatic_protocol_is_other_specify": { + "long_table_path": { "examples": [ - "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" + "/User/Documents/RespLab/ncov123_longtable.tsv" ], "ontology": "0", "type": "string", - "description": "The name of the bioinformatics protocol used.", + "description": "The path where the long table including all variants and annotations is.", "classification": "Bioinformatic Analysis fields", - "label": "If bioinformatic protocol Is Other, Specify", + "label": "Long table path", "fill_mode": "batch" }, - "bioinformatics_protocol_software_version": { + "consensus_sequence_software_name": { "examples": [ - "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" + "Ivar" ], - "ontology": "NCIT:C93490", + "ontology": "GENEPIO:0001463", "type": "string", - "description": "The version number of the bioinformatics protocol used.", + "description": "The name of software used to generate the consensus sequence.", "classification": "Bioinformatic Analysis fields", - "label": "bioinformatics protocol version", + "label": "Consensus sequence software name", "fill_mode": "batch" }, - "commercial_open_source_both": { + "if_consensus_other": { "examples": [ - "" + "v1.3" ], "ontology": "0", "type": "string", - "description": "", + "description": "The version of the software used to generate the consensus sequence.", "classification": "Bioinformatic Analysis fields", - "label": "Commercial/Open-source/both", + "label": "If consensus Is Other, Specify", "fill_mode": "batch" }, - "preprocessing_software_name": { + "consensus_sequence_software_version": { "examples": [ - "" + "1.3" ], - "ontology": "MS_1002386", + "ontology": "GENEPIO:0001469", "type": "string", - "description": "", + "description": "The version of the software used to generate the consensus sequence.", "classification": "Bioinformatic Analysis fields", - "label": "Preprocessing", + "label": "Consensus sequence software version", "fill_mode": "batch" }, - "preprocessing_software_version": { + "consensus_params": { "examples": [ - "" + "AF > 0.75" ], "ontology": "0", "type": "string", - "description": "", + "description": "Parameters used for consensus generation", "classification": "Bioinformatic Analysis fields", - "label": "Preprocessing Version", + "label": "Consensus Params", "fill_mode": "batch" }, - "if_preprocessing_other": { + "consensus_genome_length": { "examples": [ - "" + "38677" ], - "ontology": "0", + "ontology": "GENEPIO:0001483", "type": "string", - "description": "", - "classification": "Bioinformatic Analysis fields", - "label": "If preprocessing Is Other, Specify", + "description": "Size of the assembled genome described as the number of base pairs.", + "classification": "Bioinformatics and QC metrics fields", + "label": "Consensus genome length", "fill_mode": "batch" }, - "preprocessing_params": { + "depth_of_coverage_threshold": { "examples": [ - "" + "10x" ], - "ontology": "0", + "ontology": "GENEPIO:0001475", "type": "string", - "description": "", - "classification": "Bioinformatic Analysis fields", - "label": "Preprocessing params", + "description": "The threshold used as a cut-off for the depth of coverage.", + "classification": "Bioinformatics and QC metrics fields", + "label": "Depth of coverage threshold", "fill_mode": "batch" }, - "mapping_software_name": { + "number_of_base_pairs_sequenced": { + "examples": [ + "387566" + ], + "ontology": "GENEPIO:0001482", + "type": "string", + "description": "The number of total base pairs generated by the sequencing process.", + "classification": "Bioinformatics and QC metrics fields", + "label": "Number of base pairs sequenced ", + "fill_mode": "batch" + }, + "qc_filtered": { "examples": [ "" ], - "ontology": "topic:0102", + "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatic Analysis fields", - "label": "Mapping", + "classification": "Bioinformatics and QC metrics fields", + "label": "%qc filtered", "fill_mode": "batch" }, - "mapping_software_version": { + "per_reads_host": { "examples": [ "" ], "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatic Analysis fields", - "label": "Mapping Version", + "classification": "Bioinformatics and QC metrics fields", + "label": "%reads host", "fill_mode": "batch" }, - "if_mapping_other": { + "per_reads_virus": { "examples": [ "" ], "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatic Analysis fields", - "label": "If mapping Is Other, Specify", + "classification": "Bioinformatics and QC metrics fields", + "label": "%reads virus", "fill_mode": "batch" }, - "mapping_params": { + "per_unmapped": { "examples": [ "" ], "ontology": "0", "type": "string", "description": "", - "classification": "Bioinformatic Analysis fields", - "label": "Mapping params", + "classification": "Bioinformatics and QC metrics fields", + "label": "%unmapped", "fill_mode": "batch" }, - "lineage_name": { + "depth_of_coverage_value": { "examples": [ - "B.1.1.7" + "400x" ], - "ontology": "GENEPIO:0001500", + "ontology": "GENEPIO:0001474", "type": "string", - "description": "The name of the lineage or clade.", - "classification": "Lineage fields", - "label": "Lineage/clade name", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "classification": "Bioinformatics and QC metrics fields", + "label": "Depth of coverage value ", "fill_mode": "batch" }, - "lineage_analysis_software_name": { + "per_genome_greater_10x": { "examples": [ - "Pangolin" - ], - "ontology": "GENEPIO:0001501", - "type": "string", - "description": "The name of the software used to determine the lineage/clade.", - "classification": "Lineage fields", - "label": "lineage/clade analysis software name", - "fill_mode": "batch" - }, - "if_lineage_identification_other": { - "examples": [ - "Other than Pangolin" - ], - "ontology": "0", - "type": "string", - "description": "The name of the software used to determine the lineage/clade.", - "classification": "Lineage fields", - "label": "If lineage identification Is Other, Specify", - "fill_mode": "batch" - }, - "lineage_analysis_software_version": { - "examples": [ - "2.1.10" - ], - "ontology": "GENEPIO:0001502", - "type": "string", - "description": "The version of the software used to determine the lineage/clade.", - "classification": "Lineage fields", - "label": "Lineage/clade analysis software version", - "fill_mode": "batch" - }, - "isolate_sample_id": { - "examples": [ - "" - ], - "ontology": "NCIT:C53471", - "type": "string", - "description": "", - "classification": "Database Identifiers", - "label": "Sample ID given if multiple rna-extraction or passages", - "fill_mode": "sample" - }, - "variant_designation": { - "Enums": [ - "Variant of Interest (VOI) [GENEPIO:0100082]", - "Variant of Concern (VOC) [GENEPIO:0100083]", - "Variant Under Monitoring (VUM) [GENEPIO:0100279]" - ], - "ontology": "GENEPIO:0001503", - "type": "string", - "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", - "examples": [ - "Variant of Concern (VOC) [GENEPIO:0100083]" - ], - "classification": "Bioinformatic Variants", - "label": "Variant designation", - "fill_mode": "batch" - }, - "gene_name_1": { - "Enums": [ - "E gene (orf4) [GENEPIO:0100151]", - "M gene (orf5) [GENEPIO:0100152]", - "N gene (orf9) [GENEPIO:0100153]", - "Spike gene (orf2) [GENEPIO:0100154]", - "orf1ab (rep) [GENEPIO:0100155]", - "orf1a (pp1a) [GENEPIO:0100156]", - "nsp11 [GENEPIO:0100157]", - "nsp1 [GENEPIO:0100158]", - "nsp2 [GENEPIO:0100159]", - "nsp3 [GENEPIO:0100160]", - "nsp4 [GENEPIO:0100161]", - "nsp5 [GENEPIO:0100162]", - "nsp6 [GENEPIO:0100163]", - "nsp7 [GENEPIO:0100164]", - "nsp8 [GENEPIO:0100165]", - "nsp9 [GENEPIO:0100166]", - "nsp10 [GENEPIO:0100167]", - "RdRp gene (nsp12) [GENEPIO:0100168]", - "hel gene (nsp13) [GENEPIO:0100169]", - "exoN gene (nsp14) [GENEPIO:0100170]", - "nsp15 [GENEPIO:0100171]", - "nsp16 [GENEPIO:0100172]", - "orf3a [GENEPIO:0100173]", - "orf3b [GENEPIO:0100174]", - "orf6 (ns6) [GENEPIO:0100175]", - "orf7a [GENEPIO:0100176]", - "orf7b (ns7b) [GENEPIO:0100177]", - "orf8 (ns8) [GENEPIO:0100178]", - "orf9b [GENEPIO:0100179]", - "orf9c [GENEPIO:0100180]", - "orf10 [GENEPIO:0100181]", - "orf14 [GENEPIO:0100182]", - "SARS-COV-2 5' UTR [GENEPIO:0100183]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001507", - "type": "string", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "examples": [ - "E gene (orf4) [GENEPIO:0100151]" - ], - "classification": "Pathogen diagnostic testing", - "label": "Gene Name 1", - "fill_mode": "batch" - }, - "qc_filtered": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics fields", - "label": "%qc filtered", - "fill_mode": "batch" - }, - "per_reads_host": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics fields", - "label": "%reads host", - "fill_mode": "batch" - }, - "per_reads_virus": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics fields", - "label": "%reads virus", - "fill_mode": "batch" - }, - "per_unmapped": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics fields", - "label": "%unmapped", - "fill_mode": "batch" - }, - "per_genome_greater_10x": { - "examples": [ - "" + "" ], "ontology": "0", "type": "string", @@ -1839,638 +1932,367 @@ "label": "%Ns", "fill_mode": "batch" }, - "number_of_variants_in_consensus": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatic Variants", - "label": "Number of variants (AF greater 75%)", - "fill_mode": "batch" - }, - "number_of_variants_with_effect": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Bioinformatic Variants", - "label": "Number of variants with effect", - "fill_mode": "batch" - }, - "diagnostic_pcr_Ct_value_1": { - "examples": [ - "21" - ], - "ontology": "GENEPIO:0001509", - "type": "string", - "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "classification": "Pathogen diagnostic testing", - "label": "Diagnostic Pcr Ct Value 1", - "fill_mode": "batch" - }, - "gene_name_2": { - "Enums": [ - "E gene (orf4) [GENEPIO:0100151]", - "M gene (orf5) [GENEPIO:0100152]", - "N gene (orf9) [GENEPIO:0100153]", - "Spike gene (orf2) [GENEPIO:0100154]", - "orf1ab (rep) [GENEPIO:0100155]", - "orf1a (pp1a) [GENEPIO:0100156]", - "nsp11 [GENEPIO:0100157]", - "nsp1 [GENEPIO:0100158]", - "nsp2 [GENEPIO:0100159]", - "nsp3 [GENEPIO:0100160]", - "nsp4 [GENEPIO:0100161]", - "nsp5 [GENEPIO:0100162]", - "nsp6 [GENEPIO:0100163]", - "nsp7 [GENEPIO:0100164]", - "nsp8 [GENEPIO:0100165]", - "nsp9 [GENEPIO:0100166]", - "nsp10 [GENEPIO:0100167]", - "RdRp gene (nsp12) [GENEPIO:0100168]", - "hel gene (nsp13) [GENEPIO:0100169]", - "exoN gene (nsp14) [GENEPIO:0100170]", - "nsp15 [GENEPIO:0100171]", - "nsp16 [GENEPIO:0100172]", - "orf3a [GENEPIO:0100173]", - "orf3b [GENEPIO:0100174]", - "orf6 (ns6) [GENEPIO:0100175]", - "orf7a [GENEPIO:0100176]", - "orf7b (ns7b) [GENEPIO:0100177]", - "orf8 (ns8) [GENEPIO:0100178]", - "orf9b [GENEPIO:0100179]", - "orf9c [GENEPIO:0100180]", - "orf10 [GENEPIO:0100181]", - "orf14 [GENEPIO:0100182]", - "SARS-COV-2 5' UTR [GENEPIO:0100183]", - "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", - "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]" - ], - "ontology": "GENEPIO:0001510", - "type": "string", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "examples": [ - "RdRp gene (nsp12) [GENEPIO:0100168]" - ], - "classification": "Pathogen diagnostic testing", - "label": "Gene Name 2", - "fill_mode": "batch" - }, - "analysis_date": { - "examples": [ - "e.g 2020-08-07" - ], - "ontology": "0", - "type": "string", - "format": "date", - "description": "", - "classification": "Bioinformatics and QC metrics fields", - "label": "Analysis date", - "fill_mode": "batch" - }, - "lineage_identification_date": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "format": "date", - "description": "", - "classification": "Lineage fields", - "label": "Lineage identification date", - "fill_mode": "batch" - }, - "diagnostic_pcr_Ct_value_2": { - "examples": [ - "36" - ], - "ontology": "GENEPIO:0001512", - "type": "string", - "description": "The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "classification": "Pathogen diagnostic testing", - "label": "Diagnostic Pcr Ct Value-2", - "fill_mode": "batch" - }, - "analysis_authors": { - "examples": [ - "" - ], - "ontology": "NCIT:C42781", - "type": "string", - "description": "", - "classification": "Contributor Acknowledgement", - "label": "Analysis Authors", - "fill_mode": "batch" - }, - "author_submitter": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Contributor Acknowledgement", - "label": "Author Submitter", - "fill_mode": "batch" - }, - "gisaid_id": { - "examples": [ - "" - ], - "ontology": "NCIT:C54269", - "type": "string", - "description": "enter your GISAID-Username", - "classification": "Database Identifiers", - "label": "GISAID id", - "fill_mode": "sample" - }, - "authors": { - "examples": [ - "" - ], - "ontology": "GENEPIO:0001517", - "type": "string", - "description": "", - "classification": "Contributor Acknowledgement", - "label": "Authors", - "fill_mode": "batch" - }, - "common_name": { - "examples": [ - "" - ], - "ontology": "NCIT:C164471", - "type": "string", - "description": "The common name of the organism.", - "classification": "Sample collection and processing", - "label": "Common name", - "fill_mode": "batch" - }, - "collector_name": { - "examples": [ - "John Smith" - ], - "ontology": "GENEPIO:0001797", - "type": "string", - "description": "Name of the person who collected the specimen", - "classification": "Sample collection and processing", - "label": "Sample collector name", - "table": "sample", - "fill_mode": "batch" - }, - "library_source": { - "Enums": [ - "5-methycytidine antibody method [GENPIO:0001941]", - "CAGE method [GENPIO:0001942]", - "CF-H method [GENPIO:0001943]", - "CF-M method ]GENPIO:0001944]", - "CF-S method [GENPIO:0001945]", - "CF-T method [GENPIO:0001946]", - "ChIP method ]GENPIO:0001947]", - "DNAse method [GENPIO:0001948]", - "HMPR method [GENPIO:0001949]", - "Hybrid Selection Method [GENPIO:0001950]", - "MBD2 protein methyl-CpG binding domain method [GENPIO:0001951]", - "MF method [GENPIO:0001952]", - "MNase method [GENPIO:0001953]", - "MSLL method [GENPIO:0001954]", - "PCR method [GENPIO:0001955]", - "RACE method [GENPIO:0001956]", - "RANDOM PCR method [GENPIO:0001957]", - "RANDOM method [GENPIO:0001958]", - "RT-PCR method [GENPIO:0001959]", - "Reduced Representation method [GENPIO:0001960]", - "Resctriction Digest method [GENPIO:0001961]", - "cDNA method [GENPIO:0001962]", - "other library method [GENPIO:0001964]", - "size fractionation method [GENPIO:0001963]" - ], - "examples": [ - "METAGENOMIC" - ], - "ontology": "GENEPIO_0001965", - "type": "string", - "description": "Molecule type used to make the library.", - "classification": "Sequencing", - "label": "Source material", - "fill_mode": "batch" - }, - "analysis_accession": { - "examples": [ - "" - ], - "ontology": "GENEPIO_0001145", - "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Analysis Accession", - "fill_mode": "batch" - }, - "study_accession": { - "examples": [ - "e.g PRJEB39632" - ], - "ontology": "GENEPIO_0001136", - "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Study accession", - "fill_mode": "batch" - }, - "secondary_study_accession": { - "examples": [ - "e.g ERP123173" - ], - "ontology": "BU_ISCIII:012", - "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Secondary study accession", - "fill_mode": "batch" - }, - "sample_accession": { - "examples": [ - "e.g SAMEA7098096" - ], - "ontology": "GENEPIO_0001139", - "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Sample accession", - "fill_mode": "batch" - }, - "secondary_sample_accession": { - "examples": [ - "e.g ERS4858671" - ], - "ontology": "BU_ISCIII:014", - "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Secondary sample accession", - "fill_mode": "batch" - }, - "experiment_accession": { - "examples": [ - "e.g ERX4331406" - ], - "ontology": "BU_ISCIII:015", - "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Experiment Accession", - "fill_mode": "batch" - }, - "run_accession": { - "examples": [ - "e.g ERX4331406" - ], - "ontology": "BU_ISCIII:016", - "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Run Accession", - "fill_mode": "batch" - }, - "submission_accession": { - "examples": [ - "e.g ERA2794974" - ], - "ontology": "BU_ISCIII:017", - "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Submission Accession", - "fill_mode": "batch" - }, - "read_count": { - "examples": [ - "e.g 837055" - ], - "ontology": "STATO_0000064", - "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Read count", - "fill_mode": "batch" - }, - "read_length": { - "examples": [ - "" - ], - "ontology": "STATO_0000064", - "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Read length", - "fill_mode": "batch" - }, - "base_count": { - "examples": [ - "e.g 503907110" - ], - "ontology": "UO_0000244", - "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Base count", - "fill_mode": "batch" - }, - "first_public": { + "ns_per_100_kbp": { "examples": [ - "e.g 2020-08-07" + "300" ], - "ontology": "NCIT_C142711", + "ontology": "GENEPIO:0001484", "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "First Public date", + "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", + "classification": "Bioinformatics and QC metrics fields", + "label": "Ns per 100 kbp", "fill_mode": "batch" }, - "last_updated": { + "number_of_variants_in_consensus": { "examples": [ - "e.g 2020-07-29" + "" ], - "ontology": "OMIABIS_0001005", + "ontology": "0", "type": "string", "description": "", - "classification": "Submission ENA", - "format": "date", - "label": "Last Updated", + "classification": "Bioinformatic Variants", + "label": "Number of variants (AF greater 75%)", "fill_mode": "batch" }, - "experiment_title": { + "number_of_variants_with_effect": { "examples": [ - "e.g Illumina MiSeq paired end sequencing" + "" ], - "ontology": "ORNASEQ_0000004", + "ontology": "0", "type": "string", "description": "", - "classification": "Submission ENA", - "label": "Experiment title", + "classification": "Bioinformatic Variants", + "label": "Number of variants with effect", "fill_mode": "batch" }, - "study_title": { + "lineage_name": { "examples": [ - "e.g SARS-CoV-2 genomes from late April in Stockholm" + "B.1.1.7" ], - "ontology": "OPMI_0000380", + "ontology": "GENEPIO:0001500", "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Study title", + "description": "The name of the lineage or clade.", + "classification": "Lineage fields", + "label": "Lineage/clade name", "fill_mode": "batch" }, - "study_alias": { + "lineage_analysis_software_name": { "examples": [ - "e.g Sweden" + "Pangolin" ], - "ontology": "SIO_001066", + "ontology": "GENEPIO:0001501", "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Study alias", + "description": "The name of the software used to determine the lineage/clade.", + "classification": "Lineage fields", + "label": "lineage/clade analysis software name", "fill_mode": "batch" }, - "experiment_alias": { + "if_lineage_identification_other": { "examples": [ - "e.g ena-STUDY-KAROLINSKA INSITUTET-29-07-2020-14:18:07:925-2092" + "Nextclade" ], - "ontology": "NCIT_C42790", + "ontology": "0", "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Experiment alias", + "description": "The name of the software used to determine the lineage/clade.", + "classification": "Lineage fields", + "label": "If lineage identification Is Other, Specify", "fill_mode": "batch" }, - "run_alias": { + "lineage_analysis_software_version": { "examples": [ - "e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1" + "2.1.10" ], - "ontology": "NCIT_C47911", + "ontology": "GENEPIO:0001502", "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Run Alias", + "description": "The version of the software used to determine the lineage/clade.", + "classification": "Lineage fields", + "label": "Lineage/clade analysis software version", "fill_mode": "batch" }, - "fastq_bytes": { - "examples": [ - "e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1" + "variant_designation": { + "Enums": [ + "Variant of Interest (VOI) [GENEPIO:0100082]", + "Variant of Concern (VOC) [GENEPIO:0100083]", + "Variant Under Monitoring (VUM) [GENEPIO:0100279]" ], - "ontology": "NCIT_C48047", + "ontology": "GENEPIO:0001503", "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Fastq bytes", + "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", + "examples": [ + "Variant of Concern (VOC) [GENEPIO:0100083]" + ], + "classification": "Lineage fields", + "label": "Variant designation", "fill_mode": "batch" }, - "fastq_md5_r1": { - "examples": [ - "" + "gene_name_1": { + "Enums": [ + "E gene (orf4) [GENEPIO:0100151]", + "M gene (orf5) [GENEPIO:0100152]", + "N gene (orf9) [GENEPIO:0100153]", + "Spike gene (orf2) [GENEPIO:0100154]", + "orf1ab (rep) [GENEPIO:0100155]", + "orf1a (pp1a) [GENEPIO:0100156]", + "nsp11 [GENEPIO:0100157]", + "nsp1 [GENEPIO:0100158]", + "nsp2 [GENEPIO:0100159]", + "nsp3 [GENEPIO:0100160]", + "nsp4 [GENEPIO:0100161]", + "nsp5 [GENEPIO:0100162]", + "nsp6 [GENEPIO:0100163]", + "nsp7 [GENEPIO:0100164]", + "nsp8 [GENEPIO:0100165]", + "nsp9 [GENEPIO:0100166]", + "nsp10 [GENEPIO:0100167]", + "RdRp gene (nsp12) [GENEPIO:0100168]", + "hel gene (nsp13) [GENEPIO:0100169]", + "exoN gene (nsp14) [GENEPIO:0100170]", + "nsp15 [GENEPIO:0100171]", + "nsp16 [GENEPIO:0100172]", + "orf3a [GENEPIO:0100173]", + "orf3b [GENEPIO:0100174]", + "orf6 (ns6) [GENEPIO:0100175]", + "orf7a [GENEPIO:0100176]", + "orf7b (ns7b) [GENEPIO:0100177]", + "orf8 (ns8) [GENEPIO:0100178]", + "orf9b [GENEPIO:0100179]", + "orf9c [GENEPIO:0100180]", + "orf10 [GENEPIO:0100181]", + "orf14 [GENEPIO:0100182]", + "SARS-COV-2 5' UTR [GENEPIO:0100183]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" ], - "ontology": "MS_1000568", + "ontology": "GENEPIO:0001507", "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Fastq md5 r1", + "description": "The name of the gene used in the diagnostic RT-PCR test.", + "examples": [ + "E gene (orf4) [GENEPIO:0100151]" + ], + "classification": "Pathogen diagnostic testing", + "label": "Gene Name 1", "fill_mode": "batch" }, - "fastq_md5_r2": { + "diagnostic_pcr_Ct_value_1": { "examples": [ - "" + "21" ], - "ontology": "MS_1000568", + "ontology": "GENEPIO:0001509", "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Fastq md5 r2", + "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "classification": "Pathogen diagnostic testing", + "label": "Diagnostic Pcr Ct Value 1", "fill_mode": "batch" }, - "fastq_ftp": { - "examples": [ - "" + "gene_name_2": { + "Enums": [ + "E gene (orf4) [GENEPIO:0100151]", + "M gene (orf5) [GENEPIO:0100152]", + "N gene (orf9) [GENEPIO:0100153]", + "Spike gene (orf2) [GENEPIO:0100154]", + "orf1ab (rep) [GENEPIO:0100155]", + "orf1a (pp1a) [GENEPIO:0100156]", + "nsp11 [GENEPIO:0100157]", + "nsp1 [GENEPIO:0100158]", + "nsp2 [GENEPIO:0100159]", + "nsp3 [GENEPIO:0100160]", + "nsp4 [GENEPIO:0100161]", + "nsp5 [GENEPIO:0100162]", + "nsp6 [GENEPIO:0100163]", + "nsp7 [GENEPIO:0100164]", + "nsp8 [GENEPIO:0100165]", + "nsp9 [GENEPIO:0100166]", + "nsp10 [GENEPIO:0100167]", + "RdRp gene (nsp12) [GENEPIO:0100168]", + "hel gene (nsp13) [GENEPIO:0100169]", + "exoN gene (nsp14) [GENEPIO:0100170]", + "nsp15 [GENEPIO:0100171]", + "nsp16 [GENEPIO:0100172]", + "orf3a [GENEPIO:0100173]", + "orf3b [GENEPIO:0100174]", + "orf6 (ns6) [GENEPIO:0100175]", + "orf7a [GENEPIO:0100176]", + "orf7b (ns7b) [GENEPIO:0100177]", + "orf8 (ns8) [GENEPIO:0100178]", + "orf9b [GENEPIO:0100179]", + "orf9c [GENEPIO:0100180]", + "orf10 [GENEPIO:0100181]", + "orf14 [GENEPIO:0100182]", + "SARS-COV-2 5' UTR [GENEPIO:0100183]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" ], - "ontology": "PRIDE_0000469", + "ontology": "GENEPIO:0001510", "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Fastq ftp", + "description": "The name of the gene used in the diagnostic RT-PCR test.", + "examples": [ + "RdRp gene (nsp12) [GENEPIO:0100168]" + ], + "classification": "Pathogen diagnostic testing", + "label": "Gene Name 2", "fill_mode": "batch" }, - "fastq_aspera": { + "diagnostic_pcr_Ct_value_2": { "examples": [ - "e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz" + "36" ], - "ontology": "BU_ISCIII:032", + "ontology": "GENEPIO:0001512", "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Fastq aspera", + "description": "The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "classification": "Pathogen diagnostic testing", + "label": "Diagnostic Pcr Ct Value-2", "fill_mode": "batch" }, - "fastq_galaxy": { + "authors": { "examples": [ - "e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz" + "" ], - "ontology": "ENVO_01000807", + "ontology": "GENEPIO:0001517", "type": "string", "description": "", - "classification": "Submission ENA", - "label": "Fastq galaxy", + "classification": "Public databases", + "label": "Authors", "fill_mode": "batch" }, - "submitted_bytes": { + "gisaid_submitter_id": { "examples": [ - "e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz" + "" ], - "ontology": "NCIT_C172872", + "ontology": "NCIT:C54269", "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Submitted bytes ", - "fill_mode": "batch" + "description": "GISAID sequence ID.", + "classification": "Public Databases", + "label": "GISAID id", + "fill_mode": "sample" }, - "submitted_md5": { + "gisaid_accession_id": { "examples": [ - "e.g 139853010;166270048" + "NCIT:C180324" ], - "ontology": "BU_ISCIII:035", + "ontology": "", "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Submitted md5", - "fill_mode": "batch" + "description": "GISAID sequence ID.", + "classification": "Public Databases", + "label": "GISAID id", + "fill_mode": "sample" }, - "submitted_ftp": { + "gisaid_virus_name": { "examples": [ - "e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a" + "hCoV-19/Canada/prov_rona_99/2020" ], - "ontology": "BU_ISCIII:036", + "ontology": "GENEPIO:0100282", "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Submitted ftp", - "fill_mode": "batch" + "description": "The user-defined GISAID virus name assigned to the sequence.", + "classification": "Public Databases", + "label": "GISAID Virus Name", + "fill_mode": "sample" }, - "submitted_aspera": { + "ena_analysis_accession": { "examples": [ - "e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz" + "" ], - "ontology": "BU_ISCIII:037", + "ontology": "GENEPIO_0001145", "type": "string", "description": "", - "classification": "Submission ENA", - "label": "Submitted aspera", + "classification": "Public databases", + "label": "Analysis Accession", "fill_mode": "batch" }, - "submitted_galaxy": { + "ena_study_accession": { "examples": [ - "e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz" + "e.g PRJEB39632" ], - "ontology": "BU_ISCIII:038", + "ontology": "GENEPIO_0001136", "type": "string", "description": "", - "classification": "Submission ENA", - "label": "Submitted Galaxy", + "classification": "Public databases", + "label": "Study accession", "fill_mode": "batch" }, - "submitted_format": { + "ena_sample_accession": { "examples": [ - "e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz" + "e.g SAMEA7098096" ], - "ontology": "BU_ISCIII:039", + "ontology": "GENEPIO_0001139", "type": "string", "description": "", - "classification": "Submission ENA", - "label": "Submitted Format", + "classification": "Public databases", + "label": "Sample accession", "fill_mode": "batch" }, - "sra_bytes": { + "ena_experiment_accession": { "examples": [ - "e.g FASTQ;FASTQ" + "e.g ERX4331406" ], - "ontology": "BU_ISCIII:040", + "ontology": "BU_ISCIII:015", "type": "string", "description": "", - "classification": "Submission ENA", - "label": "SRA bytes", + "classification": "Public databases", + "label": "Experiment Accession", "fill_mode": "batch" }, - "sra_md5": { + "ena_run_accession": { "examples": [ - "e.g 260236789" + "e.g ERX4331406" ], - "ontology": "BU_ISCIII:041", + "ontology": "BU_ISCIII:016", "type": "string", "description": "", - "classification": "Submission ENA", - "label": "SRA md5", + "classification": "Public databases", + "label": "Run Accession", "fill_mode": "batch" }, - "sra_ftp": { + "ena_submission_accession": { "examples": [ - "e.g 2cf0d467d6dc4ae0a5473774d54c059c" + "e.g ERA2794974" ], - "ontology": "BU_ISCIII:042", + "ontology": "BU_ISCIII:017", "type": "string", "description": "", - "classification": "Submission ENA", - "label": "SRA ftp", + "classification": "Public databases", + "label": "Submission Accession", "fill_mode": "batch" }, - "sra_aspera": { + "ena_experiment_title": { "examples": [ - "e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385" + "e.g Illumina MiSeq paired end sequencing" ], - "ontology": "BU_ISCIII:043", + "ontology": "ORNASEQ_0000004", "type": "string", "description": "", - "classification": "Submission ENA", - "label": "SRA aspera", + "classification": "Public Databases", + "label": "Experiment title", "fill_mode": "batch" }, - "sra_galaxy": { + "ena_study_title": { "examples": [ - "e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385" + "e.g SARS-CoV-2 genomes from late April in Stockholm" ], - "ontology": "BU_ISCIII:044", + "ontology": "OPMI_0000380", "type": "string", "description": "", - "classification": "Submission ENA", - "label": "SRA galaxy", + "classification": "Public Databases", + "label": "Study title", "fill_mode": "batch" }, - "broker_name": { + "ena_broker_name": { "examples": [ "P17157_1007" ], "ontology": "BU_ISCIII:045", "type": "string", "description": "", - "classification": "Submission ENA", + "classification": "Public Databases", "label": "Broker Name", "fill_mode": "batch" }, - "nominal_sdev": { - "examples": [ - "" - ], - "ontology": "STATO_0000237", - "type": "string", - "description": "", - "classification": "Submission ENA", - "label": "Nominal sdev", - "fill_mode": "batch" - }, - "first_created_date": { + "ena_first_created_date": { "examples": [ "e.g 2020-08-07" ], @@ -2478,53 +2300,9 @@ "type": "string", "format": "date", "description": "", - "classification": "Submission ENA", + "classification": "Public Databases", "label": "First created date", "fill_mode": "batch" - }, - "type": { - "examples": [ - "betacoronavirus" - ], - "ontology": "NCIT:C25284", - "type": "string", - "description": "default must remain 'betacoronavirus'", - "classification": "Database Identifiers", - "label": "Type", - "fill_mode": "batch" - }, - "biosample_accession_ENA": { - "examples": [ - "SAMN14180202" - ], - "ontology": "GENEPIO:0001139", - "type": "string", - "description": "The identifier assigned to a BioSample in INSDC archives.", - "classification": "Database Identifiers", - "label": "ENA Sample ID", - "fill_mode": "sample" - }, - "virus_name": { - "examples": [ - "hCoV-19/Canada/prov_rona_99/2020" - ], - "ontology": "GENEPIO:0100282", - "type": "string", - "description": "The user-defined GISAID virus name assigned to the sequence.", - "classification": "Database Identifiers", - "label": "GISAID Virus Name", - "fill_mode": "sample" - }, - "center_name": { - "examples": [ - " KAROLINSKA INSITUTET" - ], - "ontology": "NCIT_C19983", - "type": "string", - "description": "The name of the institution", - "classification": "Sample collection and processing", - "label": "Center Name", - "fill_mode": "batch" - }, + } } } From 6fcede0629507b17446f1ce1b462b11a4360ee8a Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 31 Aug 2022 09:44:57 +0200 Subject: [PATCH 0849/1454] deleted the fields related to GISAID, ENA from the data to be included in relecov-palatform sample --- relecov_tools/__main__.py | 2 +- relecov_tools/conf/configuration.json | 12 ++---------- 2 files changed, 3 insertions(+), 11 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 840681bc..e96c4761 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -406,10 +406,10 @@ def read_bioinfo_metadata(metadata_file, input_folder, metadata_out, mapping_ill ) @click.option("-o", "--output", type=click.Path(), help="Path to save json output") def long_table_parse(longtable_file, output): - """Create Json file from long table""" new_json_parse = relecov_tools.long_table_parse.LongTableParse( longtable_file, output ) + """Create Json file from long table""" new_json_parse.parsing_csv() diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index b85bdf89..c724d298 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -109,7 +109,7 @@ }, "external_url": { "iskylims": { - "server": "http://relecov-iskylims.isciiides.es:8001", + "server": "http://relecov-iskylims.isciiides.es", "url": "/wetlab/api/", "store_samples": "createSampleData", "url_project_fields": "sampleProjectFields", @@ -119,7 +119,7 @@ "token": "" }, "relecov": { - "server": "http://relecov-platform.isciiides.es:8000", + "server": "http://relecov-platform.isciiides.es", "url": "/api/", "store_samples": "createSampleData", "bioinfodata": "createBioinfoData", @@ -135,16 +135,8 @@ "sampleLocation": "Not defined" }, "relecov_sample_metadata": [ - "author_submitter", - "authors", - "bioproject_accession_ENA", - "bioproject_umbrella_accession_ENA", - "biosample_accession_ENA", "fastq_r1_md5", "fastq_r2_md5", - "GenBank_ENA_DDBJ_accession", - "GISAID_accession", - "gisaid_id", "microbiology_lab_sample_id", "r1_fastq_filepath", "r2_fastq_filepath", From 33bd5bd5514404cdb9fc822a47f5a6f067f0f2c4 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 31 Aug 2022 09:55:23 +0200 Subject: [PATCH 0850/1454] Modify long table output json file --- relecov_tools/long_table_parse.py | 21 ++++++++++----------- 1 file changed, 10 insertions(+), 11 deletions(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index c70b9464..d6ab2499 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -63,13 +63,15 @@ def __init__(self, file_path=None, output_directory=None): config_json = ConfigJson() self.long_table_heading = config_json.get_configuration("long_table_heading") - def valid_file(self, heading): + def validate_file(self, heading): """Check if long table file has all mandatory fields defined in configuration file """ for field in self.long_table_heading: if field not in heading: - return False + log.error("Incorrect format file. %s is missing", field) + stderr.print(f"[red]Incorrect Format. {field} is missing in file") + sys.exit(1) return True def parse_file(self): @@ -83,9 +85,7 @@ def parse_file(self): with open(self.file_path) as fh: lines = fh.readlines() - if not self.valid_file(lines[0].strip().split(",")): - stderr.print("[red]Incorrect Format, fields don't match") - sys.exit(1) + self.validate_file(lines[0].strip().split(",")) heading_index = {} headings_from_csv = lines[0].strip().split(",") @@ -100,14 +100,15 @@ def parse_file(self): if sample not in samp_dict: samp_dict[sample] = [] variant_dict = {} - variant_dict["Chromosome"] = {"chromosome": line_s[heading_index["CHROM"]]} + variant_dict["Chromosome"] = line_s[heading_index["CHROM"]] - variant_dict["Position"] = { + variant_dict["Variant"] = { "pos": line_s[heading_index["POS"]], "alt": line_s[heading_index["ALT"]], + "ref": line_s[heading_index["REF"]], } - variant_dict["Filter"] = {"filter": line_s[heading_index["FILTER"]]} + variant_dict["Filter"] = line_s[heading_index["FILTER"]] variant_dict["VariantInSample"] = { "dp": line_s[heading_index["DP"]], @@ -116,7 +117,7 @@ def parse_file(self): "af": line_s[heading_index["AF"]], } - variant_dict["Gene"] = {"gene": line_s[heading_index["GENE"]]} + variant_dict["Gene"] = line_s[heading_index["GENE"]] variant_dict["Effect"] = { "effect": line_s[heading_index["EFFECT"]], @@ -125,8 +126,6 @@ def parse_file(self): "hgvs_p_1_letter": line_s[heading_index["HGVS_P_1LETTER"]], } - variant_dict["Variant"] = {"ref": line_s[heading_index["REF"]]} - samp_dict[sample].append(variant_dict) return samp_dict From eeec9910b683873d64a8852b79b1c68dad54c9ae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 31 Aug 2022 10:17:45 +0200 Subject: [PATCH 0851/1454] passing tests --- relecov_tools/config_json.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/config_json.py b/relecov_tools/config_json.py index 4d2a2922..56a38f48 100644 --- a/relecov_tools/config_json.py +++ b/relecov_tools/config_json.py @@ -2,7 +2,7 @@ import json import os - +# class ConfigJson: def __init__( self, From b423da412a76b9b000e57d5ae95d7e942e8a6cfd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 31 Aug 2022 10:18:59 +0200 Subject: [PATCH 0852/1454] passing tests --- relecov_tools/config_json.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/config_json.py b/relecov_tools/config_json.py index 56a38f48..793c5694 100644 --- a/relecov_tools/config_json.py +++ b/relecov_tools/config_json.py @@ -2,7 +2,8 @@ import json import os -# + +# pass test class ConfigJson: def __init__( self, From 34e7b8e13c00e911d565f4c96ac984f789eb3e19 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 31 Aug 2022 12:25:33 +0200 Subject: [PATCH 0853/1454] fixed that VariantAnnotation field was missing and added progressing text --- relecov_tools/long_table_parse.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index d6ab2499..eb11f8e3 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -86,7 +86,8 @@ def parse_file(self): lines = fh.readlines() self.validate_file(lines[0].strip().split(",")) - + stderr.print("[green]Successful checking heading fields") + stderr.print("[blue]Parsing the input file") heading_index = {} headings_from_csv = lines[0].strip().split(",") for heading in self.long_table_heading: @@ -119,15 +120,15 @@ def parse_file(self): variant_dict["Gene"] = line_s[heading_index["GENE"]] - variant_dict["Effect"] = { - "effect": line_s[heading_index["EFFECT"]], + variant_dict["Effect"] = line_s[heading_index["EFFECT"]] + variant_dict["VariantAnnotation"] = { "hgvs_c": line_s[heading_index["HGVS_C"]], "hgvs_p": line_s[heading_index["HGVS_P"]], "hgvs_p_1_letter": line_s[heading_index["HGVS_P_1LETTER"]], } samp_dict[sample].append(variant_dict) - + stderr.print("[green]Successful parsing data") return samp_dict def convert_to_json(self, samp_dict): @@ -144,6 +145,7 @@ def saving_file(self, j_list): Transform the p0arsed data into a jsonf file, naming as "long_table_" + "current date" + ".json" """ + stderr.print("[blue]Saving parsed data to file") date_now = datetime.now().strftime("%Y_%m_%d_%H_%M_%S") file_name = "long_table_" + date_now + ".json" file_path = os.path.join(self.output_directory, file_name) @@ -156,6 +158,8 @@ def parsing_csv(self): """ function called when using the relecov-tools long-table-parse function. """ + stderr.print("[blue]Starting reading the input file") parsed_data = self.parse_file() j_list = self.convert_to_json(parsed_data) self.saving_file(j_list) + stderr.print("[green]Process completed") From 8f2a131b10e4241bf0fb317d3a215f766a67a1cc Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 31 Aug 2022 14:09:17 +0200 Subject: [PATCH 0854/1454] fixes relecov schema --- relecov_tools/read_lab_metadata.py | 2 +- relecov_tools/schema/relecov_schema.json | 559 ++++++++++++++++------- 2 files changed, 393 insertions(+), 168 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 9341fa9f..582792a4 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -162,7 +162,7 @@ def include_processed_data(self, metadata): "Illumina NextSeq", "Illumina NovaSeq 6000", ], - "MinION": ["Oxford Nanopore"], + "Oxford Nanopore": ["MinION"], "Ion Torrent": ["Ion Torrent S5", "Ion Torrent PGM"], } for key, values in p_data.items(): diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 00a11f6a..e3d7d027 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -25,7 +25,8 @@ "description": "", "classification": "Sample collection and processing", "label": "Public Health sample id (SIVIES)", - "fill_mode": "sample" + "fill_mode": "sample", + "required": "No" }, "collecting_lab_sample_id": { "examples": [ @@ -36,7 +37,8 @@ "description": "The name given for the sample by the collecting institution.", "classification": "Database Identifiers", "label": "Sample ID given by originating laboratory", - "fill_mode": "sample" + "fill_mode": "sample", + "required": "No" }, "collecting_institution": { "examples": [ @@ -47,9 +49,10 @@ "description": "The name of the agency/institution that collected the sample.", "classification": "Sample collection and processing", "label": "Originating Laboratory", - "fill_mode": "sample" + "fill_mode": "sample", + "required": "No" }, - "collecting_institution_email": { + "collecting_institution_email": { "examples": [ "johnnyblogs@lab.ca" ], @@ -58,7 +61,8 @@ "description": "The email address of the contact responsible for follow-up regarding the sample.", "classification": "Sample collection and processing", "label": "Originating Laboratory Email", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "collecting_institution_address": { "examples": [ @@ -69,9 +73,10 @@ "description": "The mailing address of the agency submitting the sample.", "classification": "Sample collection and processing", "label": "Originating Laboratory Address", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, - "microbiology_lab_sample_id": { + "microbiology_lab_sample_id": { "examples": [ "" ], @@ -80,7 +85,8 @@ "description": "", "classification": "Sample collection and processing", "label": "Sample ID given in the microbiology lab", - "fill_mode": "sample" + "fill_mode": "sample", + "required": "No" }, "isolate_sample_id": { "examples": [ @@ -91,7 +97,8 @@ "description": "", "classification": "Database Identifiers", "label": "Sample ID given if multiple rna-extraction or passages", - "fill_mode": "sample" + "fill_mode": "sample", + "required": "No" }, "sequencing_sample_id": { "examples": [ @@ -102,9 +109,10 @@ "description": "If the information is unknown or can not be shared, leave blank.", "classification": "Database Identifiers", "label": "Sample ID given for sequencing", - "fill_mode": "sample" + "fill_mode": "sample", + "required": "No" }, - "submitting_lab_sample_id": { + "submitting_lab_sample_id": { "examples": [ "" ], @@ -113,7 +121,8 @@ "description": "Sample ID given by the submitting laboratory", "classification": "Sequencing", "label": "Sample ID given by the submitting laboratory", - "fill_mode": "sample" + "fill_mode": "sample", + "required": "No" }, "submitting_institution": { "examples": [ @@ -124,7 +133,8 @@ "description": "The name of the agency that submitted the sequence to public databases.", "classification": "Sample collection and processing", "label": "Submitting Institution", - "fill_mode": "sample" + "fill_mode": "sample", + "required": "No" }, "submitting_institution_email": { "examples": [ @@ -135,7 +145,8 @@ "description": "The email address of the contact responsible for follow-up regarding the sequence.", "classification": "Sample collection and processing", "label": "Submitting Institution Email", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "submitting_institution_address": { "examples": [ @@ -146,7 +157,8 @@ "description": "The mailing address of the agency submitting the sequence.", "classification": "Sample collection and processing", "label": "Submitting Institution Address", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "sample_collection_date": { "examples": [ @@ -158,7 +170,8 @@ "format": "date", "classification": "Sample collection and processing", "label": "Sample Collection Date", - "fill_mode": "sample" + "fill_mode": "sample", + "required": "No" }, "sample_received_date": { "examples": [ @@ -170,7 +183,8 @@ "format": "date", "classification": "Sample collection and processing", "label": "Sample Received Date", - "fill_mode": "sample" + "fill_mode": "sample", + "required": "No" }, "sample_storage_conditions": { "examples": [ @@ -181,10 +195,11 @@ "description": "The name and version of a particular protocol used for sampling.", "classification": "Sample collection and processing", "label": "Biological Sample Storage Condition", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "geo_loc_country": { - "Enums": [ + "enum": [ "Afghanistan [GAZ:00006882]", "Albania [GAZ:00002953]", "Algeria [GAZ:00000563]", @@ -470,7 +485,8 @@ ], "classification": "Sample collection and processing", "label": "Country", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "geo_loc_state": { "examples": [ @@ -481,9 +497,10 @@ "description": "The state/province/territory of origin of the sample.", "classification": "Sample collection and processing", "label": "Autonomic Community", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, - "geo_loc_region": { + "geo_loc_region": { "examples": [ "Derbyshire" ], @@ -492,7 +509,8 @@ "description": "The county/region of origin of the sample.", "classification": "Sample collection and processing", "label": "Province", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "geo_loc_city": { "examples": [ @@ -503,7 +521,8 @@ "description": "The city of origin of the sample.", "classification": "Sample collection and processing", "label": "City", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "geo_loc_latitude": { "examples": [ @@ -514,7 +533,8 @@ "description": "The latitude coordinates of the geographical location of sample collection.", "classification": "Sample collection and processing", "label": "Geo Loc Latitude", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "geo_loc_longitude": { "examples": [ @@ -525,10 +545,11 @@ "description": "The longitude coordinates of the geographical location of sample collection.", "classification": "Sample collection and processing", "label": "Geo Loc Longitude", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "purpose_sampling": { - "Enums": [ + "enum": [ "Cluster/Outbreak Investigation [GENEPIO:0100001]", "Diagnostic Testing [GENEPIO:0100002]", "Research [GENEPIO:0100003]", @@ -548,17 +569,13 @@ ], "classification": "Sample collection and processing", "label": "Purpose of sampling", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "anatomical_material": { - "Enums": [ + "enum": [ "Blood [UBERON:0000178]", - "Fluid [UBERON:0006314]", "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", - "Fluid (Pericardial) [UBERON:0002409]", - "Fluid (Pleural) [UBERON:0001087]", - "Fluid (Vaginal) [UBERON:0036243]", - "Fluid (Amniotic) [UBERON:0000173]", "Saliva [UBERON:0001836]", "Tissue [UBERON:0000479]", "Not Applicable [GENEPIO:0001619]", @@ -575,10 +592,117 @@ ], "classification": "Sample collection and processing", "label": "Specimen source", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" + }, + "anatomical_part": { + "enum": [ + "Lower respiratory tract [UBERON:0001558]", + "Bronchus [UBERON:0002185]", + "Lung [UBERON:0002048]", + "Bronchiole [UBERON:0002186]", + "Alveolar sac [UBERON:0002169]", + "Pleural sac [UBERON:0009778]", + "Pleural cavity [UBERON:0002402]", + "Trachea [UBERON:0003126]", + "Rectum [UBERON:0001052]", + "Skin [UBERON:0001052]", + "Stomach [UBERON:0000945]", + "Upper respiratory tract [UBERON:0001557]", + "Anterior Nares [UBERON:2001427]", + "Esophagus [UBERON:0001043]", + "Ethmoid sinus [UBERON:0002453]", + "Nasal Cavity [UBERON:0001707]", + "Middle Nasal Turbinate [UBERON:0001762]", + "Anus [UBERON:0001245]", + "Duodenum [UBERON:0002114]", + "Nasopharynx (NP) [UBERON:0001728]", + "Oropharynx (OP) [UBERON:0001729]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]", + ], + "ontology": "", + "type": "string", + "description": "", + "examples": [ + "" + ], + "classification": "Sample collection and processing", + "label": "Specimen source", + "fill_mode": "batch", + "required": "No" + }, + "collection_device": { + "enum": [ + "Swab [GENEPIO:0100027]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "", + "type": "string", + "description": "", + "examples": [ + "" + ], + "classification": "Sample collection and processing", + "label": "Specimen source", + "fill_mode": "batch", + "required": "No" + }, + "collection_method": { + "enum": [ + "Aspiration [NCIT:C15631]", + "Biopsy [NCIT:C15189]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], + "ontology": "", + "type": "string", + "description": "", + "examples": [ + "" + ], + "classification": "Sample collection and processing", + "label": "Specimen source", + "fill_mode": "batch", + "required": "No" + }, + "body_product": { + "enum": [ + "Feces UBERON:0001988]", + "Mucus UBERON:0000912]", + "Sputum UBERON:0007311]", + "Sweat UBERON:0001089]", + "Tear UBERON:0001827]", + "Urine UBERON:0001088]", + "Not Applicable GENEPIO:0001619]", + "Not Collected GENEPIO:0001620]", + "Not Provided GENEPIO:0001668]", + "Missing GENEPIO:0001618]", + "Restricted Access GENEPIO:0001810]" + ], + "ontology": "", + "type": "string", + "description": "", + "examples": [ + "" + ], + "classification": "Sample collection and processing", + "label": "Specimen source", + "fill_mode": "batch", + "required": "No" }, "environmental_material": { - "Enums": [ + "enum": [ "Air vent [ENVO:03501208]", "Banknote [ENVO:00003896]", "Bed rail [ENVO:03501209]", @@ -626,10 +750,11 @@ ], "classification": "Sample collection and processing", "label": "Environmental Material", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "environmental_system": { - "Enums": [ + "enum": [ "Acute care facility [ENVO:03501135]", "Animal house [ENVO:00003040]", "Bathroom [ENVO:01000422]", @@ -665,10 +790,11 @@ ], "classification": "Sample collection and processing", "label": "Environmental System", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "organism": { - "Enums": [ + "enum": [ "Coronaviridae [NCBITaxon:11118]", "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", "Not Applicable [GENEPIO:0001619]", @@ -685,7 +811,8 @@ ], "classification": "Sample collection and processing", "label": "Organism", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "tax_id": { "examples": [ @@ -696,7 +823,8 @@ "description": "The NCBITaxon identifier for the organism being sequenced.", "classification": "Sample collection and processing", "label": "Tax ID", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "host_subject_id": { "examples": [ @@ -706,7 +834,7 @@ "type": "string", "description": "An unique identifier by which each subject can be referred to, de-identified.", "classification": "Host information", - "label": "Host Subject Id" + "label": "Host Subject Id""required": "No" }, "host_health_state": { "examples": [ @@ -716,10 +844,10 @@ "type": "string", "description": " Status of the host", "classification": "Host health state information", - "label": "Host health state" + "label": "Host health state""required": "No" }, "host_common_name": { - "Enums": [ + "enum": [ "Human [NCBITaxon:9606]", "Bat [NCBITaxon:9397]", "Cat [NCBITaxon:9685]", @@ -747,10 +875,11 @@ ], "classification": "Host information", "label": "Host", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "host_scientific_name": { - "Enums": [ + "enum": [ "Bos taurus [NCBITaxon:9913]", "Canis lupus familiaris [NCBITaxon:9615]", "Chiroptera [NCBITaxon:9397]", @@ -781,10 +910,11 @@ ], "classification": "Host information", "label": "Host Scientific Name", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "host_disease": { - "Enums": [ + "enum": [ "COVID-19 [MONDO:0100096]", "Not Applicable [GENEPIO:0001619]", "Not Collected [GENEPIO:0001620]", @@ -800,7 +930,8 @@ ], "classification": "Host information", "label": "Host disease", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "host_age": { "ontology": "GENEPIO:0001392", @@ -811,10 +942,11 @@ ], "classification": "Host information", "label": "Host Age", - "fill_mode": "sample" + "fill_mode": "sample", + "required": "No" }, "host_gender": { - "Enums": [ + "enum": [ "Female [NCIT:C46110]", "Male [NCIT:C46109]", "Non-binary Gender [GSSO:000132]", @@ -835,10 +967,11 @@ ], "classification": "Host information", "label": "Host Gender", - "fill_mode": "sample" + "fill_mode": "sample", + "required": "No" }, "sequencing_instrument_model": { - "Enums": [ + "enum": [ "Illumina sequencing instrument [GENEPIO:0100105]", "Illumina Genome Analyzer [GENEPIO:0100106]", "Illumina Genome Analyzer II [GENEPIO:0100107]", @@ -899,10 +1032,11 @@ ], "classification": "Sequencing", "label": "Sequencing Instrument Model", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "purpose_of_sequencing": { - "Enums": [ + "enum": [ "Baseline surveillance (random sampling) [GENEPIO:0100005]", "Targeted surveillance (non-random sampling) [GENEPIO:0100006]", "Priority surveillance projects [GENEPIO:0100007]", @@ -941,7 +1075,8 @@ ], "classification": "Sequencing", "label": "Purpose of Sequencing", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "sequencing_date": { "examples": [ @@ -953,7 +1088,8 @@ "format": "date", "classification": "Sequencing", "label": "Sequencing Date", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "extraction_protocol": { "examples": [ @@ -964,10 +1100,11 @@ "description": "DNA/RNA extraction protocol", "classification": "Sequencing", "label": "Extraction Protocol", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "all_in_one_library_kit": { - "Enums": [ + "enum": [ "Ion Xpress", "ABL_DeepChek NGS", "Ion AmpliSeq Kit for Chef DL8", @@ -985,10 +1122,11 @@ "description": "", "classification": "Sequencing", "label": "Commercial All-in-one library kit", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "library_preparation_kit": { - "Enums": [ + "enum": [ "Illumina DNA PCR-Free Prep", "Illumina DNA Prep", "Illumina Stranded mRNA Prep", @@ -1022,10 +1160,11 @@ "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "classification": "Sequencing", "label": "Library Preparation Kit", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "enrichment_protocol": { - "Enums":[ + "enum": [ "Amplicon", "Probes", "Custom probes", @@ -1041,7 +1180,8 @@ "description": "Type of enrichment protocol", "classification": "Sequencing", "label": "Enrichment Protocol", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "if_enrichment_protocol_is_other_specify": { "examples": [ @@ -1052,10 +1192,11 @@ "description": "", "classification": "Sequencing", "label": "If Enrichment Protocol Is Other, Specify", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "enrichment_panel": { - "Enums":[ + "enum": [ "ARTIC", "Illumina respiratory Virus Oligo Panel", "Illumina AmpliSeq Community panel", @@ -1074,10 +1215,11 @@ "description": "Commercial or custom panel/assay used for enrichment.", "classification": "Sequencing", "label": "Enrichment panel/assay", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "enrichment_panel_version": { - "Enums":[ + "enum": [ "ARTIC v1", "ARTIC v2", "ARTIC v3", @@ -1100,9 +1242,10 @@ "description": "", "classification": "Sequencing", "label": "Enrichment panel/assay version", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, - "amplicon_pcr_primer_scheme": { + "amplicon_pcr_primer_scheme": { "examples": [ "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv" ], @@ -1111,7 +1254,8 @@ "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", "classification": "Sequencing", "label": "Amplicon Pcr Primer Scheme", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "number_of_samples_in_run": { "examples": [ @@ -1122,10 +1266,11 @@ "description": "", "classification": "Sequencing", "label": "Number Of Samples In Run", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "flowcell_kit": { - "Enums":[ + "enum": [ "HiSeq 3000/4000 PE Cluster Kit", "HiSeq 3000/4000 SBS Kit (50 cycles)", "HiSeq 3000/4000 SBS Kit (150 cycles)", @@ -1261,7 +1406,8 @@ "description": "Flowcell sequencer used for sequencing the sample", "classification": "Sequencing", "label": "Flowcell Kit", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "runID": { "examples": [ @@ -1272,10 +1418,11 @@ "description": "Unique sequencing run identifier.", "classification": "Sequencing", "label": "Runid", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "sequencing_instrument_platform": { - "Enums":[ + "enum": [ "Oxford Nanopore", "Illumina", "Ion Torrent", @@ -1289,10 +1436,11 @@ "description": "", "classification": "Sequencing", "label": "Sequencing Instrument Platform", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "library_source": { - "Enums": [ + "enum": [ "GENOMIC", "TRANSCRIPTOMIC", "METAGENOMIC", @@ -1309,10 +1457,11 @@ "description": "Molecule type used to make the library.", "classification": "Sequencing", "label": "Source material", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "library_selection": { - "Enums":[ + "enum": [ "RANDOM", "PCR", "RANDOM PCR", @@ -1348,10 +1497,11 @@ "description": "Library capture method.", "classification": "Sequencing", "label": "Capture method", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "library_strategy": { - "Enums": [ + "enum": [ "Bisultife-Seq strategy [GENPIO:0001975]", "CTS strategy [GENPIO:0001978]", "ChIP-Seq strategy [GENPIO:0001979]", @@ -1381,12 +1531,13 @@ "description": "Overall sequencing strategy or approach.", "classification": "Sequencing", "label": "Sequencing technique", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "library_layout": { - "Enums":[ - "SINGLE", - "PAIRED" + "enum": [ + "SINGLE", + "PAIRED" ], "examples": [ "PAIRED" @@ -1396,7 +1547,8 @@ "description": "Single or paired sequencing configuration", "classification": "Sequencing", "label": "Library Layout", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "sequence_file_R1_fastq": { "examples": [ @@ -1407,7 +1559,8 @@ "description": "The user-specified filename of the r1 FASTQ file.", "classification": "Bioinformatics and QC metrics fields", "label": "Sequence file R1 fastq", - "fill_mode": "sample" + "fill_mode": "sample", + "required": "No" }, "sequence_file_R2_fastq": { "examples": [ @@ -1418,7 +1571,8 @@ "description": "The user-specified filename of the r2 FASTQ file.", "classification": "Bioinformatics and QC metrics fields", "label": "Sequence file R2 fastq", - "fill_mode": "sample" + "fill_mode": "sample", + "required": "No" }, "r1_fastq_filepath": { "examples": [ @@ -1429,7 +1583,8 @@ "description": "The filepath of the r1 FASTQ file.", "classification": "Files info", "label": "Filepath R1 fastq", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "r2_fastq_filepath": { "examples": [ @@ -1440,7 +1595,8 @@ "description": "The filepath of the r2 FASTQ file.", "classification": "Files info", "label": "Filepath R2 fastq", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "fast5_filename": { "examples": [ @@ -1451,7 +1607,8 @@ "description": "The user-specified filename of the FAST5 file.", "classification": "Files info", "label": "Filename fast5", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "fast5_filepath": { "examples": [ @@ -1462,7 +1619,8 @@ "description": "The filepath of the FAST5 file.", "classification": "Files info", "label": "Filepath fast5", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "analysis_date": { "examples": [ @@ -1474,7 +1632,8 @@ "description": "", "classification": "Bioinformatics and QC metrics fields", "label": "Analysis date", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "dehosting_method_software_name": { "examples": [ @@ -1485,7 +1644,8 @@ "description": "The method used to remove host reads from the pathogen sequence.", "classification": "Bioinformatic Analysis fields", "label": "Dehosting Method", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "dehosting_method_software_version": { "examples": [ @@ -1496,7 +1656,8 @@ "description": "The method version used to remove host reads from the pathogen sequence.", "classification": "Bioinformatic Analysis fields", "label": "Dehosting Method Version", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "reference_genome_accession": { "examples": [ @@ -1507,7 +1668,8 @@ "description": "A persistent, unique identifier of a genome database entry.", "classification": "Bioinformatics and QC metrics fields", "label": "Reference genome accession", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "bioinformatics_protocol_software_name": { "examples": [ @@ -1518,7 +1680,8 @@ "description": "The name of the bioinformatics protocol used.", "classification": "Bioinformatic Analysis fields", "label": "Bioinformatics protocol", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "if_bioinformatic_protocol_is_other_specify": { "examples": [ @@ -1529,7 +1692,8 @@ "description": "The name of the bioinformatics protocol used.", "classification": "Bioinformatic Analysis fields", "label": "If bioinformatic protocol Is Other, Specify", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "bioinformatics_protocol_software_version": { "examples": [ @@ -1540,10 +1704,11 @@ "description": "The version number of the bioinformatics protocol used.", "classification": "Bioinformatic Analysis fields", "label": "bioinformatics protocol version", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "commercial_open_source_both": { - "Enums":[ + "enum": [ "Commercial", "Open Source", "Both" @@ -1556,7 +1721,8 @@ "description": "", "classification": "Bioinformatic Analysis fields", "label": "Commercial/Open-source/both", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "preprocessing_software_name": { "examples": [ @@ -1567,7 +1733,8 @@ "description": "Software used for preprocessing step.", "classification": "Bioinformatic Analysis fields", "label": "Preprocessing", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "preprocessing_software_version": { "examples": [ @@ -1578,7 +1745,8 @@ "description": "Version of the preprocessing software used.", "classification": "Bioinformatic Analysis fields", "label": "Preprocessing Version", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "if_preprocessing_other": { "examples": [ @@ -1589,7 +1757,8 @@ "description": "", "classification": "Bioinformatic Analysis fields", "label": "If preprocessing Is Other, Specify", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "preprocessing_params": { "examples": [ @@ -1600,7 +1769,8 @@ "description": "Preprocessing parameters used.", "classification": "Bioinformatic Analysis fields", "label": "Preprocessing params", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "mapping_software_name": { "examples": [ @@ -1611,7 +1781,8 @@ "description": "Software used for mapping step.", "classification": "Bioinformatic Analysis fields", "label": "Mapping", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "mapping_software_version": { "examples": [ @@ -1622,7 +1793,8 @@ "description": "Version of the mapper used.", "classification": "Bioinformatic Analysis fields", "label": "Mapping Version", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "if_mapping_other": { "examples": [ @@ -1633,7 +1805,8 @@ "description": "", "classification": "Bioinformatic Analysis fields", "label": "If mapping Is Other, Specify", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "mapping_params": { "examples": [ @@ -1644,7 +1817,8 @@ "description": "Parameters used for mapping step.", "classification": "Bioinformatic Analysis fields", "label": "Mapping params", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "assembly": { "examples": [ @@ -1655,7 +1829,8 @@ "description": "Software used for assembly of the pathogen genome.", "classification": "Bioinformatic Analysis fields", "label": "Assembly", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "if_assembly_other": { "examples": [ @@ -1666,7 +1841,8 @@ "description": "Assembly software version", "classification": "Bioinformatic Analysis fields", "label": "If assembly Is Other, Specify", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "assembly_params": { "examples": [ @@ -1677,7 +1853,8 @@ "description": "Params used for genome assembly.", "classification": "Bioinformatic Analysis fields", "label": "Assambly params", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "variant_calling_software_name": { "examples": [ @@ -1688,7 +1865,8 @@ "description": "Software used for variant calling.", "classification": "Bioinformatic Variants", "label": "Variant Calling", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "variant_calling_software_version": { "examples": [ @@ -1699,7 +1877,8 @@ "description": "Variant calling software version", "classification": "Bioinformatic Variants", "label": "Variant Calling Version", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "if_variant_calling_other": { "examples": [ @@ -1710,7 +1889,8 @@ "description": "", "classification": "Bioinformatic Variants", "label": "If variant calling Is Other, Specify", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "variant_calling_params": { "examples": [ @@ -1721,7 +1901,8 @@ "description": "Params used for variant calling", "classification": "Bioinformatic Variants", "label": "Variant Calling params", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "consensus_sequence_name": { "ontology": "GENEPIO:0001460", @@ -1732,7 +1913,8 @@ ], "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence name", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "consensus_sequence_filename": { "ontology": "GENEPIO:0001461", @@ -1743,7 +1925,8 @@ ], "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence name", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "consensus_sequence_md5": { "ontology": "0", @@ -1754,7 +1937,8 @@ ], "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence name md5", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "consensus_sequence_filepath": { "examples": [ @@ -1765,7 +1949,8 @@ "description": "The filepath of the consesnsus sequence file.", "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence filepath", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "long_table_path": { "examples": [ @@ -1776,7 +1961,8 @@ "description": "The path where the long table including all variants and annotations is.", "classification": "Bioinformatic Analysis fields", "label": "Long table path", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "consensus_sequence_software_name": { "examples": [ @@ -1787,7 +1973,8 @@ "description": "The name of software used to generate the consensus sequence.", "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence software name", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "if_consensus_other": { "examples": [ @@ -1798,7 +1985,8 @@ "description": "The version of the software used to generate the consensus sequence.", "classification": "Bioinformatic Analysis fields", "label": "If consensus Is Other, Specify", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "consensus_sequence_software_version": { "examples": [ @@ -1809,7 +1997,8 @@ "description": "The version of the software used to generate the consensus sequence.", "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence software version", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "consensus_params": { "examples": [ @@ -1820,7 +2009,8 @@ "description": "Parameters used for consensus generation", "classification": "Bioinformatic Analysis fields", "label": "Consensus Params", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "consensus_genome_length": { "examples": [ @@ -1831,7 +2021,8 @@ "description": "Size of the assembled genome described as the number of base pairs.", "classification": "Bioinformatics and QC metrics fields", "label": "Consensus genome length", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "depth_of_coverage_threshold": { "examples": [ @@ -1842,7 +2033,8 @@ "description": "The threshold used as a cut-off for the depth of coverage.", "classification": "Bioinformatics and QC metrics fields", "label": "Depth of coverage threshold", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "number_of_base_pairs_sequenced": { "examples": [ @@ -1853,7 +2045,8 @@ "description": "The number of total base pairs generated by the sequencing process.", "classification": "Bioinformatics and QC metrics fields", "label": "Number of base pairs sequenced ", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "qc_filtered": { "examples": [ @@ -1864,7 +2057,8 @@ "description": "", "classification": "Bioinformatics and QC metrics fields", "label": "%qc filtered", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "per_reads_host": { "examples": [ @@ -1875,7 +2069,8 @@ "description": "", "classification": "Bioinformatics and QC metrics fields", "label": "%reads host", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "per_reads_virus": { "examples": [ @@ -1886,7 +2081,8 @@ "description": "", "classification": "Bioinformatics and QC metrics fields", "label": "%reads virus", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "per_unmapped": { "examples": [ @@ -1897,7 +2093,8 @@ "description": "", "classification": "Bioinformatics and QC metrics fields", "label": "%unmapped", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "depth_of_coverage_value": { "examples": [ @@ -1908,7 +2105,8 @@ "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", "classification": "Bioinformatics and QC metrics fields", "label": "Depth of coverage value ", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "per_genome_greater_10x": { "examples": [ @@ -1919,7 +2117,8 @@ "description": "", "classification": "Bioinformatics and QC metrics fields", "label": "% genome greater 10x", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "per_Ns": { "examples": [ @@ -1930,7 +2129,8 @@ "description": "", "classification": "Bioinformatics and QC metrics fields", "label": "%Ns", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "ns_per_100_kbp": { "examples": [ @@ -1941,7 +2141,8 @@ "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", "classification": "Bioinformatics and QC metrics fields", "label": "Ns per 100 kbp", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "number_of_variants_in_consensus": { "examples": [ @@ -1952,7 +2153,8 @@ "description": "", "classification": "Bioinformatic Variants", "label": "Number of variants (AF greater 75%)", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "number_of_variants_with_effect": { "examples": [ @@ -1963,7 +2165,8 @@ "description": "", "classification": "Bioinformatic Variants", "label": "Number of variants with effect", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "lineage_name": { "examples": [ @@ -1974,7 +2177,8 @@ "description": "The name of the lineage or clade.", "classification": "Lineage fields", "label": "Lineage/clade name", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "lineage_analysis_software_name": { "examples": [ @@ -1985,7 +2189,8 @@ "description": "The name of the software used to determine the lineage/clade.", "classification": "Lineage fields", "label": "lineage/clade analysis software name", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "if_lineage_identification_other": { "examples": [ @@ -1996,7 +2201,8 @@ "description": "The name of the software used to determine the lineage/clade.", "classification": "Lineage fields", "label": "If lineage identification Is Other, Specify", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "lineage_analysis_software_version": { "examples": [ @@ -2007,10 +2213,11 @@ "description": "The version of the software used to determine the lineage/clade.", "classification": "Lineage fields", "label": "Lineage/clade analysis software version", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "variant_designation": { - "Enums": [ + "enum": [ "Variant of Interest (VOI) [GENEPIO:0100082]", "Variant of Concern (VOC) [GENEPIO:0100083]", "Variant Under Monitoring (VUM) [GENEPIO:0100279]" @@ -2023,10 +2230,11 @@ ], "classification": "Lineage fields", "label": "Variant designation", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "gene_name_1": { - "Enums": [ + "enum": [ "E gene (orf4) [GENEPIO:0100151]", "M gene (orf5) [GENEPIO:0100152]", "N gene (orf9) [GENEPIO:0100153]", @@ -2074,7 +2282,8 @@ ], "classification": "Pathogen diagnostic testing", "label": "Gene Name 1", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "diagnostic_pcr_Ct_value_1": { "examples": [ @@ -2085,10 +2294,11 @@ "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "classification": "Pathogen diagnostic testing", "label": "Diagnostic Pcr Ct Value 1", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "gene_name_2": { - "Enums": [ + "enum": [ "E gene (orf4) [GENEPIO:0100151]", "M gene (orf5) [GENEPIO:0100152]", "N gene (orf9) [GENEPIO:0100153]", @@ -2136,7 +2346,8 @@ ], "classification": "Pathogen diagnostic testing", "label": "Gene Name 2", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "diagnostic_pcr_Ct_value_2": { "examples": [ @@ -2147,7 +2358,8 @@ "description": "The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.", "classification": "Pathogen diagnostic testing", "label": "Diagnostic Pcr Ct Value-2", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "authors": { "examples": [ @@ -2158,7 +2370,8 @@ "description": "", "classification": "Public databases", "label": "Authors", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "gisaid_submitter_id": { "examples": [ @@ -2169,7 +2382,8 @@ "description": "GISAID sequence ID.", "classification": "Public Databases", "label": "GISAID id", - "fill_mode": "sample" + "fill_mode": "sample", + "required": "No" }, "gisaid_accession_id": { "examples": [ @@ -2180,7 +2394,8 @@ "description": "GISAID sequence ID.", "classification": "Public Databases", "label": "GISAID id", - "fill_mode": "sample" + "fill_mode": "sample", + "required": "No" }, "gisaid_virus_name": { "examples": [ @@ -2191,7 +2406,8 @@ "description": "The user-defined GISAID virus name assigned to the sequence.", "classification": "Public Databases", "label": "GISAID Virus Name", - "fill_mode": "sample" + "fill_mode": "sample", + "required": "No" }, "ena_analysis_accession": { "examples": [ @@ -2202,7 +2418,8 @@ "description": "", "classification": "Public databases", "label": "Analysis Accession", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "ena_study_accession": { "examples": [ @@ -2213,7 +2430,8 @@ "description": "", "classification": "Public databases", "label": "Study accession", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "ena_sample_accession": { "examples": [ @@ -2224,7 +2442,8 @@ "description": "", "classification": "Public databases", "label": "Sample accession", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "ena_experiment_accession": { "examples": [ @@ -2235,7 +2454,8 @@ "description": "", "classification": "Public databases", "label": "Experiment Accession", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "ena_run_accession": { "examples": [ @@ -2246,7 +2466,8 @@ "description": "", "classification": "Public databases", "label": "Run Accession", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "ena_submission_accession": { "examples": [ @@ -2257,7 +2478,8 @@ "description": "", "classification": "Public databases", "label": "Submission Accession", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "ena_experiment_title": { "examples": [ @@ -2268,7 +2490,8 @@ "description": "", "classification": "Public Databases", "label": "Experiment title", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "ena_study_title": { "examples": [ @@ -2279,7 +2502,8 @@ "description": "", "classification": "Public Databases", "label": "Study title", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "ena_broker_name": { "examples": [ @@ -2290,7 +2514,8 @@ "description": "", "classification": "Public Databases", "label": "Broker Name", - "fill_mode": "batch" + "fill_mode": "batch", + "required": "No" }, "ena_first_created_date": { "examples": [ @@ -2302,7 +2527,7 @@ "description": "", "classification": "Public Databases", "label": "First created date", - "fill_mode": "batch" + "fill_mode": "batch", } } -} +} \ No newline at end of file From 7f79d7c40f6c2778985aeae5ab8fa20d6991d46b Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 31 Aug 2022 17:14:28 +0200 Subject: [PATCH 0855/1454] fixes in relecov schema 2 --- relecov_tools/schema/relecov_schema.json | 64 ++++++++++++++++++------ 1 file changed, 50 insertions(+), 14 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index e3d7d027..4164e694 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -576,6 +576,10 @@ "enum": [ "Blood [UBERON:0000178]", "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", + "Fluid (Pericardial) [UBERON:0002409]", + "Fluid (Pleural) [UBERON:0001087]", + "Fluid (Vaginal) [UBERON:0036243]", + "Fluid (Amniotic) [UBERON:0000173]", "Saliva [UBERON:0001836]", "Tissue [UBERON:0000479]", "Not Applicable [GENEPIO:0001619]", @@ -597,6 +601,8 @@ }, "anatomical_part": { "enum": [ + "Eye [UBERON:0000970]", + "Intestine [UBERON:0000160]", "Lower respiratory tract [UBERON:0001558]", "Bronchus [UBERON:0002185]", "Lung [UBERON:0002048]", @@ -624,7 +630,7 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]", ], - "ontology": "", + "ontology": "GENEPIO:0001214", "type": "string", "description": "", "examples": [ @@ -637,6 +643,16 @@ }, "collection_device": { "enum": [ + "Air filter [GENEPIO:0100031]", + "Blood Collection Tube [GENEPIO:0100031]", + "Bronchoscope [NCIT:C17611]", + "Collection Container [NCIT:C43446]", + "Collection Cup [GENEPIO:0100026]", + "Filter [NCIT:C45801]", + "Needle [NCIT:C69013]", + "Serum Collection Tube [NCIT:C113675]", + "Sputum Collection Tube [GENEPIO:0002115]", + "Suction Catheter [58253008]", "Swab [GENEPIO:0100027]", "Not Applicable [GENEPIO:0001619]", "Not Collected [GENEPIO:0001620]", @@ -644,7 +660,7 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "", + "ontology": "GENEPIO:0001234", "type": "string", "description": "", "examples": [ @@ -657,6 +673,25 @@ }, "collection_method": { "enum": [ + "Amniocentesis [NCIT:C52009]", + "Suprapublic Aspiration [GENEPIO:0100028]", + "Tracheal Aspiration [GENEPIO:0100029]", + "Vacuum Aspiration [GENEPIO:0100030]", + "Needle Biopsy [OBI:0002654]", + "Filtration [NCIT:C16583]", + "Lavage [NCIT:C38068]", + "Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]", + "Gastric Lavage [GENEPIO:0100033]", + "Lumbar Puncture [NCIT:C15327]", + "Necropsy [NCIT:C166270]", + "Phlebotomy [NCIT:C28221]", + "Rinsing [GENEPIO:0002116]", + "Scraping [GENEPIO:0100035]", + "Swabbing [NCIT:C17627]", + "Finger Pick [GENEPIO:0100036]", + "Wash [NCIT:C65077]", + "Washout Tear Collection [GENEPIO:0100038]", + "Inferior Nasal Turbinate [NCIT:C32794]", "Aspiration [NCIT:C15631]", "Biopsy [NCIT:C15189]", "Not Applicable [GENEPIO:0001619]", @@ -665,7 +700,7 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "", + "ontology": "GENEPIO:0001241", "type": "string", "description": "", "examples": [ @@ -678,17 +713,18 @@ }, "body_product": { "enum": [ - "Feces UBERON:0001988]", - "Mucus UBERON:0000912]", - "Sputum UBERON:0007311]", - "Sweat UBERON:0001089]", - "Tear UBERON:0001827]", - "Urine UBERON:0001088]", - "Not Applicable GENEPIO:0001619]", - "Not Collected GENEPIO:0001620]", - "Not Provided GENEPIO:0001668]", - "Missing GENEPIO:0001618]", - "Restricted Access GENEPIO:0001810]" + "Breast Milk [UBERON:0001913]", + "Feces [UBERON:0001988]", + "Mucus [UBERON:0000912]", + "Sputum [UBERON:0007311]", + "Sweat [UBERON:0001089]", + "Tear [UBERON:0001827]", + "Urine [UBERON:0001088]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" ], "ontology": "", "type": "string", From af03fb74b87f0e699324998dd468c17134d4b521 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 1 Sep 2022 11:22:01 +0200 Subject: [PATCH 0856/1454] changes in schema --- relecov_tools/schema/relecov_schema.json | 426 ++++++++--------------- 1 file changed, 149 insertions(+), 277 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 4164e694..9a5d1b39 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -25,8 +25,7 @@ "description": "", "classification": "Sample collection and processing", "label": "Public Health sample id (SIVIES)", - "fill_mode": "sample", - "required": "No" + "fill_mode": "sample" }, "collecting_lab_sample_id": { "examples": [ @@ -37,8 +36,7 @@ "description": "The name given for the sample by the collecting institution.", "classification": "Database Identifiers", "label": "Sample ID given by originating laboratory", - "fill_mode": "sample", - "required": "No" + "fill_mode": "sample" }, "collecting_institution": { "examples": [ @@ -49,8 +47,7 @@ "description": "The name of the agency/institution that collected the sample.", "classification": "Sample collection and processing", "label": "Originating Laboratory", - "fill_mode": "sample", - "required": "No" + "fill_mode": "sample" }, "collecting_institution_email": { "examples": [ @@ -61,8 +58,7 @@ "description": "The email address of the contact responsible for follow-up regarding the sample.", "classification": "Sample collection and processing", "label": "Originating Laboratory Email", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "collecting_institution_address": { "examples": [ @@ -73,8 +69,7 @@ "description": "The mailing address of the agency submitting the sample.", "classification": "Sample collection and processing", "label": "Originating Laboratory Address", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "microbiology_lab_sample_id": { "examples": [ @@ -85,8 +80,7 @@ "description": "", "classification": "Sample collection and processing", "label": "Sample ID given in the microbiology lab", - "fill_mode": "sample", - "required": "No" + "fill_mode": "sample" }, "isolate_sample_id": { "examples": [ @@ -97,8 +91,7 @@ "description": "", "classification": "Database Identifiers", "label": "Sample ID given if multiple rna-extraction or passages", - "fill_mode": "sample", - "required": "No" + "fill_mode": "sample" }, "sequencing_sample_id": { "examples": [ @@ -109,8 +102,7 @@ "description": "If the information is unknown or can not be shared, leave blank.", "classification": "Database Identifiers", "label": "Sample ID given for sequencing", - "fill_mode": "sample", - "required": "No" + "fill_mode": "sample" }, "submitting_lab_sample_id": { "examples": [ @@ -121,8 +113,7 @@ "description": "Sample ID given by the submitting laboratory", "classification": "Sequencing", "label": "Sample ID given by the submitting laboratory", - "fill_mode": "sample", - "required": "No" + "fill_mode": "sample" }, "submitting_institution": { "examples": [ @@ -133,8 +124,7 @@ "description": "The name of the agency that submitted the sequence to public databases.", "classification": "Sample collection and processing", "label": "Submitting Institution", - "fill_mode": "sample", - "required": "No" + "fill_mode": "sample" }, "submitting_institution_email": { "examples": [ @@ -145,8 +135,7 @@ "description": "The email address of the contact responsible for follow-up regarding the sequence.", "classification": "Sample collection and processing", "label": "Submitting Institution Email", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "submitting_institution_address": { "examples": [ @@ -157,8 +146,7 @@ "description": "The mailing address of the agency submitting the sequence.", "classification": "Sample collection and processing", "label": "Submitting Institution Address", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "sample_collection_date": { "examples": [ @@ -170,8 +158,7 @@ "format": "date", "classification": "Sample collection and processing", "label": "Sample Collection Date", - "fill_mode": "sample", - "required": "No" + "fill_mode": "sample" }, "sample_received_date": { "examples": [ @@ -183,8 +170,7 @@ "format": "date", "classification": "Sample collection and processing", "label": "Sample Received Date", - "fill_mode": "sample", - "required": "No" + "fill_mode": "sample" }, "sample_storage_conditions": { "examples": [ @@ -195,8 +181,7 @@ "description": "The name and version of a particular protocol used for sampling.", "classification": "Sample collection and processing", "label": "Biological Sample Storage Condition", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "geo_loc_country": { "enum": [ @@ -485,8 +470,7 @@ ], "classification": "Sample collection and processing", "label": "Country", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "geo_loc_state": { "examples": [ @@ -497,8 +481,7 @@ "description": "The state/province/territory of origin of the sample.", "classification": "Sample collection and processing", "label": "Autonomic Community", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "geo_loc_region": { "examples": [ @@ -509,8 +492,7 @@ "description": "The county/region of origin of the sample.", "classification": "Sample collection and processing", "label": "Province", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "geo_loc_city": { "examples": [ @@ -521,8 +503,7 @@ "description": "The city of origin of the sample.", "classification": "Sample collection and processing", "label": "City", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "geo_loc_latitude": { "examples": [ @@ -533,8 +514,7 @@ "description": "The latitude coordinates of the geographical location of sample collection.", "classification": "Sample collection and processing", "label": "Geo Loc Latitude", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "geo_loc_longitude": { "examples": [ @@ -545,8 +525,7 @@ "description": "The longitude coordinates of the geographical location of sample collection.", "classification": "Sample collection and processing", "label": "Geo Loc Longitude", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "purpose_sampling": { "enum": [ @@ -569,8 +548,7 @@ ], "classification": "Sample collection and processing", "label": "Purpose of sampling", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "anatomical_material": { "enum": [ @@ -596,8 +574,7 @@ ], "classification": "Sample collection and processing", "label": "Specimen source", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "anatomical_part": { "enum": [ @@ -628,7 +605,7 @@ "Not Collected [GENEPIO:0001620]", "Not Provided [GENEPIO:0001668]", "Missing [GENEPIO:0001618]", - "Restricted Access [GENEPIO:0001810]", + "Restricted Access [GENEPIO:0001810]" ], "ontology": "GENEPIO:0001214", "type": "string", @@ -638,8 +615,7 @@ ], "classification": "Sample collection and processing", "label": "Specimen source", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "collection_device": { "enum": [ @@ -668,8 +644,7 @@ ], "classification": "Sample collection and processing", "label": "Specimen source", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "collection_method": { "enum": [ @@ -708,8 +683,7 @@ ], "classification": "Sample collection and processing", "label": "Specimen source", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "body_product": { "enum": [ @@ -734,8 +708,7 @@ ], "classification": "Sample collection and processing", "label": "Specimen source", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "environmental_material": { "enum": [ @@ -786,8 +759,7 @@ ], "classification": "Sample collection and processing", "label": "Environmental Material", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "environmental_system": { "enum": [ @@ -826,8 +798,7 @@ ], "classification": "Sample collection and processing", "label": "Environmental System", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "organism": { "enum": [ @@ -847,8 +818,7 @@ ], "classification": "Sample collection and processing", "label": "Organism", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "tax_id": { "examples": [ @@ -859,8 +829,7 @@ "description": "The NCBITaxon identifier for the organism being sequenced.", "classification": "Sample collection and processing", "label": "Tax ID", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "host_subject_id": { "examples": [ @@ -870,7 +839,7 @@ "type": "string", "description": "An unique identifier by which each subject can be referred to, de-identified.", "classification": "Host information", - "label": "Host Subject Id""required": "No" + "label": "Host Subject Id" }, "host_health_state": { "examples": [ @@ -879,8 +848,8 @@ "ontology": "GENEPIO:0001388", "type": "string", "description": " Status of the host", - "classification": "Host health state information", - "label": "Host health state""required": "No" + "classification": "Host information", + "label": "Host health state" }, "host_common_name": { "enum": [ @@ -911,8 +880,7 @@ ], "classification": "Host information", "label": "Host", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "host_scientific_name": { "enum": [ @@ -946,8 +914,7 @@ ], "classification": "Host information", "label": "Host Scientific Name", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "host_disease": { "enum": [ @@ -966,8 +933,7 @@ ], "classification": "Host information", "label": "Host disease", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "host_age": { "ontology": "GENEPIO:0001392", @@ -978,8 +944,7 @@ ], "classification": "Host information", "label": "Host Age", - "fill_mode": "sample", - "required": "No" + "fill_mode": "sample" }, "host_gender": { "enum": [ @@ -1003,8 +968,7 @@ ], "classification": "Host information", "label": "Host Gender", - "fill_mode": "sample", - "required": "No" + "fill_mode": "sample" }, "sequencing_instrument_model": { "enum": [ @@ -1068,8 +1032,7 @@ ], "classification": "Sequencing", "label": "Sequencing Instrument Model", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "purpose_of_sequencing": { "enum": [ @@ -1111,8 +1074,7 @@ ], "classification": "Sequencing", "label": "Purpose of Sequencing", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "sequencing_date": { "examples": [ @@ -1124,8 +1086,7 @@ "format": "date", "classification": "Sequencing", "label": "Sequencing Date", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "extraction_protocol": { "examples": [ @@ -1136,8 +1097,7 @@ "description": "DNA/RNA extraction protocol", "classification": "Sequencing", "label": "Extraction Protocol", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "all_in_one_library_kit": { "enum": [ @@ -1158,8 +1118,7 @@ "description": "", "classification": "Sequencing", "label": "Commercial All-in-one library kit", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "library_preparation_kit": { "enum": [ @@ -1196,8 +1155,7 @@ "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "classification": "Sequencing", "label": "Library Preparation Kit", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "enrichment_protocol": { "enum": [ @@ -1216,8 +1174,7 @@ "description": "Type of enrichment protocol", "classification": "Sequencing", "label": "Enrichment Protocol", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "if_enrichment_protocol_is_other_specify": { "examples": [ @@ -1228,8 +1185,7 @@ "description": "", "classification": "Sequencing", "label": "If Enrichment Protocol Is Other, Specify", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "enrichment_panel": { "enum": [ @@ -1251,8 +1207,7 @@ "description": "Commercial or custom panel/assay used for enrichment.", "classification": "Sequencing", "label": "Enrichment panel/assay", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "enrichment_panel_version": { "enum": [ @@ -1261,12 +1216,12 @@ "ARTIC v3", "ARTIC v4", "Illumina AmpliSeq Community panel", - "Illumina AmpliSeq SARS-CoV-2 Research Panel for Illumina", + "Illumina AmpliSeq SARS-CoV-2 Research Panel for Illumina", "Illumina Respiratory Virus Oligos Panel V1", "Illumina Respiratory Virus Oligos Panel V2", "Ion AmpliSeq SARS-CoV-2 Insight", "xGen SC2 Midnight1200 Amplicon Panel", - "ViroKey SQ FLEX SARS-CoV-2 Primer Set",  + "ViroKey SQ FLEX SARS-CoV-2 Primer Set", "NEBNext VarSkip Short SARS-CoV-2 primers", "Other" ], @@ -1278,8 +1233,7 @@ "description": "", "classification": "Sequencing", "label": "Enrichment panel/assay version", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "amplicon_pcr_primer_scheme": { "examples": [ @@ -1290,8 +1244,7 @@ "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", "classification": "Sequencing", "label": "Amplicon Pcr Primer Scheme", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "number_of_samples_in_run": { "examples": [ @@ -1302,8 +1255,7 @@ "description": "", "classification": "Sequencing", "label": "Number Of Samples In Run", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "flowcell_kit": { "enum": [ @@ -1357,19 +1309,19 @@ "NextSeq 1000/2000 P2 Reagents (100 Cycles) v3", "NextSeq 1000/2000 P2 Reagents (200 Cycles) v3", "NextSeq 1000/2000 P2 Reagents (300 Cycles) v3", - "NextSeq 2000 P3 Reagents (50 Cycles)",  + "NextSeq 2000 P3 Reagents (50 Cycles)", "NextSeq 2000 P3 Reagents (100 Cycles)", - "NextSeq 2000 P3 Reagents (200 Cycles)",  + "NextSeq 2000 P3 Reagents (200 Cycles)", "NextSeq 2000 P3 Reagents (300 Cycles)", - "NextSeq 1000/2000 Read and Index Primers",  + "NextSeq 1000/2000 Read and Index Primers", "NextSeq 1000/2000 Index Primer Kit", - "NextSeq 1000/2000 Read Primer Kit",  + "NextSeq 1000/2000 Read Primer Kit", "NextSeq 500/550 High Output Kit v2.5 (75 Cycles)", "NextSeq 500/550 High Output Kit v2.5 (150 Cycles)", "NextSeq 500/550 High Output Kit v2.5 (300 Cycles)", "NextSeq 500/550 Mid Output Kit v2.5 (150 Cycles)", "NextSeq 500/550 Mid Output Kit v2.5 (300 Cycles)", - "TG NextSeq 500/550 High Output Kit v2.5 (75 Cycles)",  + "TG NextSeq 500/550 High Output Kit v2.5 (75 Cycles)", "TG NextSeq 500/550 High Output Kit v2.5 (150 Cycles)", "TG NextSeq 500/550 High Output Kit v2.5 (300 Cycles)", "TG NextSeq 500/550 Mid Output Kit v2.5 (150 Cycles)", @@ -1381,29 +1333,29 @@ "NovaSeq 6000 S2 Reagent Kit v1.5 (200 cycles)", "NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles)", "NovaSeq 6000 S1 Reagent Kit v1.5 (300 cycles)", - "NovaSeq 6000 S1 Reagent Kit v1.5 (200 cycles)",  - "NovaSeq 6000 S1 Reagent Kit v1.5 (100 cycles)",  + "NovaSeq 6000 S1 Reagent Kit v1.5 (200 cycles)", + "NovaSeq 6000 S1 Reagent Kit v1.5 (100 cycles)", "NovaSeq 6000 SP Reagent Kit v1.5 (500 cycles)", "NovaSeq 6000 SP Reagent Kit v1.5 (300 cycles)", - "NovaSeq 6000 SP Reagent Kit v1.5 (200 cycles)",  + "NovaSeq 6000 SP Reagent Kit v1.5 (200 cycles)", "NovaSeq 6000 SP Reagent Kit v1.5 (100 cycles)", - "NovaSeq 6000 SP Reagent Kit (100 cycles)",  - "NovaSeq 6000 SP Reagent Kit (200 cycles)",  + "NovaSeq 6000 SP Reagent Kit (100 cycles)", + "NovaSeq 6000 SP Reagent Kit (200 cycles)", "NovaSeq 6000 SP Reagent Kit (300 cycles)", "NovaSeq 6000 SP Reagent Kit (500 cycles)", "NovaSeq 6000 S1 Reagent Kit (100 cycles)", "NovaSeq 6000 S1 Reagent Kit (200 cycles)", "NovaSeq 6000 S1 Reagent Kit (300 cycles)", "NovaSeq 6000 S2 Reagent Kit (100 cycles)", - "NovaSeq 6000 S2 Reagent Kit (200 cycles)",  - "NovaSeq 6000 S2 Reagent Kit (300 cycles)",  + "NovaSeq 6000 S2 Reagent Kit (200 cycles)", + "NovaSeq 6000 S2 Reagent Kit (300 cycles)", "NovaSeq 6000 S4 Reagent Kit (200 cycles)", - "NovaSeq 6000 S4 Reagent Kit (300 cycles)",  + "NovaSeq 6000 S4 Reagent Kit (300 cycles)", "NovaSeq 6000 S4 Reagent Kit (300 Cycles) – 10 pack", "NovaSeq 6000 S4 Reagent Kit (300 Cycles) – 20 pack", "NovaSeq 6000 S4 Reagent Kit (300 Cycles) – 40 pack", "NovaSeq Library Tubes Accessory Pack (24 tubes)", - "NovaSeq XP 4-Lane Kit v1.5",  + "NovaSeq XP 4-Lane Kit v1.5", "NovaSeq XP 2-Lane Kit v1.5", "NovaSeq XP 2-Lane Kit", "NovaSeq Xp 4-Lane Kit", @@ -1442,8 +1394,7 @@ "description": "Flowcell sequencer used for sequencing the sample", "classification": "Sequencing", "label": "Flowcell Kit", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "runID": { "examples": [ @@ -1454,8 +1405,7 @@ "description": "Unique sequencing run identifier.", "classification": "Sequencing", "label": "Runid", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "sequencing_instrument_platform": { "enum": [ @@ -1472,8 +1422,7 @@ "description": "", "classification": "Sequencing", "label": "Sequencing Instrument Platform", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "library_source": { "enum": [ @@ -1493,8 +1442,7 @@ "description": "Molecule type used to make the library.", "classification": "Sequencing", "label": "Source material", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "library_selection": { "enum": [ @@ -1533,8 +1481,7 @@ "description": "Library capture method.", "classification": "Sequencing", "label": "Capture method", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "library_strategy": { "enum": [ @@ -1567,8 +1514,7 @@ "description": "Overall sequencing strategy or approach.", "classification": "Sequencing", "label": "Sequencing technique", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "library_layout": { "enum": [ @@ -1583,8 +1529,7 @@ "description": "Single or paired sequencing configuration", "classification": "Sequencing", "label": "Library Layout", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "sequence_file_R1_fastq": { "examples": [ @@ -1595,8 +1540,7 @@ "description": "The user-specified filename of the r1 FASTQ file.", "classification": "Bioinformatics and QC metrics fields", "label": "Sequence file R1 fastq", - "fill_mode": "sample", - "required": "No" + "fill_mode": "sample" }, "sequence_file_R2_fastq": { "examples": [ @@ -1607,8 +1551,7 @@ "description": "The user-specified filename of the r2 FASTQ file.", "classification": "Bioinformatics and QC metrics fields", "label": "Sequence file R2 fastq", - "fill_mode": "sample", - "required": "No" + "fill_mode": "sample" }, "r1_fastq_filepath": { "examples": [ @@ -1619,8 +1562,7 @@ "description": "The filepath of the r1 FASTQ file.", "classification": "Files info", "label": "Filepath R1 fastq", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "r2_fastq_filepath": { "examples": [ @@ -1631,8 +1573,7 @@ "description": "The filepath of the r2 FASTQ file.", "classification": "Files info", "label": "Filepath R2 fastq", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "fast5_filename": { "examples": [ @@ -1643,8 +1584,7 @@ "description": "The user-specified filename of the FAST5 file.", "classification": "Files info", "label": "Filename fast5", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "fast5_filepath": { "examples": [ @@ -1655,8 +1595,7 @@ "description": "The filepath of the FAST5 file.", "classification": "Files info", "label": "Filepath fast5", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "analysis_date": { "examples": [ @@ -1668,8 +1607,7 @@ "description": "", "classification": "Bioinformatics and QC metrics fields", "label": "Analysis date", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "dehosting_method_software_name": { "examples": [ @@ -1680,8 +1618,7 @@ "description": "The method used to remove host reads from the pathogen sequence.", "classification": "Bioinformatic Analysis fields", "label": "Dehosting Method", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "dehosting_method_software_version": { "examples": [ @@ -1692,8 +1629,7 @@ "description": "The method version used to remove host reads from the pathogen sequence.", "classification": "Bioinformatic Analysis fields", "label": "Dehosting Method Version", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "reference_genome_accession": { "examples": [ @@ -1704,8 +1640,7 @@ "description": "A persistent, unique identifier of a genome database entry.", "classification": "Bioinformatics and QC metrics fields", "label": "Reference genome accession", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "bioinformatics_protocol_software_name": { "examples": [ @@ -1716,8 +1651,7 @@ "description": "The name of the bioinformatics protocol used.", "classification": "Bioinformatic Analysis fields", "label": "Bioinformatics protocol", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "if_bioinformatic_protocol_is_other_specify": { "examples": [ @@ -1728,8 +1662,7 @@ "description": "The name of the bioinformatics protocol used.", "classification": "Bioinformatic Analysis fields", "label": "If bioinformatic protocol Is Other, Specify", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "bioinformatics_protocol_software_version": { "examples": [ @@ -1740,8 +1673,7 @@ "description": "The version number of the bioinformatics protocol used.", "classification": "Bioinformatic Analysis fields", "label": "bioinformatics protocol version", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "commercial_open_source_both": { "enum": [ @@ -1757,8 +1689,7 @@ "description": "", "classification": "Bioinformatic Analysis fields", "label": "Commercial/Open-source/both", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "preprocessing_software_name": { "examples": [ @@ -1769,8 +1700,7 @@ "description": "Software used for preprocessing step.", "classification": "Bioinformatic Analysis fields", "label": "Preprocessing", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "preprocessing_software_version": { "examples": [ @@ -1781,8 +1711,7 @@ "description": "Version of the preprocessing software used.", "classification": "Bioinformatic Analysis fields", "label": "Preprocessing Version", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "if_preprocessing_other": { "examples": [ @@ -1793,8 +1722,7 @@ "description": "", "classification": "Bioinformatic Analysis fields", "label": "If preprocessing Is Other, Specify", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "preprocessing_params": { "examples": [ @@ -1805,8 +1733,7 @@ "description": "Preprocessing parameters used.", "classification": "Bioinformatic Analysis fields", "label": "Preprocessing params", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "mapping_software_name": { "examples": [ @@ -1817,8 +1744,7 @@ "description": "Software used for mapping step.", "classification": "Bioinformatic Analysis fields", "label": "Mapping", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "mapping_software_version": { "examples": [ @@ -1829,8 +1755,7 @@ "description": "Version of the mapper used.", "classification": "Bioinformatic Analysis fields", "label": "Mapping Version", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "if_mapping_other": { "examples": [ @@ -1841,8 +1766,7 @@ "description": "", "classification": "Bioinformatic Analysis fields", "label": "If mapping Is Other, Specify", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "mapping_params": { "examples": [ @@ -1853,8 +1777,7 @@ "description": "Parameters used for mapping step.", "classification": "Bioinformatic Analysis fields", "label": "Mapping params", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "assembly": { "examples": [ @@ -1865,8 +1788,7 @@ "description": "Software used for assembly of the pathogen genome.", "classification": "Bioinformatic Analysis fields", "label": "Assembly", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "if_assembly_other": { "examples": [ @@ -1877,8 +1799,7 @@ "description": "Assembly software version", "classification": "Bioinformatic Analysis fields", "label": "If assembly Is Other, Specify", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "assembly_params": { "examples": [ @@ -1889,8 +1810,7 @@ "description": "Params used for genome assembly.", "classification": "Bioinformatic Analysis fields", "label": "Assambly params", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "variant_calling_software_name": { "examples": [ @@ -1901,8 +1821,7 @@ "description": "Software used for variant calling.", "classification": "Bioinformatic Variants", "label": "Variant Calling", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "variant_calling_software_version": { "examples": [ @@ -1913,8 +1832,7 @@ "description": "Variant calling software version", "classification": "Bioinformatic Variants", "label": "Variant Calling Version", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "if_variant_calling_other": { "examples": [ @@ -1925,8 +1843,7 @@ "description": "", "classification": "Bioinformatic Variants", "label": "If variant calling Is Other, Specify", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "variant_calling_params": { "examples": [ @@ -1937,8 +1854,7 @@ "description": "Params used for variant calling", "classification": "Bioinformatic Variants", "label": "Variant Calling params", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "consensus_sequence_name": { "ontology": "GENEPIO:0001460", @@ -1949,8 +1865,7 @@ ], "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence name", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "consensus_sequence_filename": { "ontology": "GENEPIO:0001461", @@ -1961,8 +1876,7 @@ ], "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence name", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "consensus_sequence_md5": { "ontology": "0", @@ -1973,8 +1887,7 @@ ], "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence name md5", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "consensus_sequence_filepath": { "examples": [ @@ -1985,8 +1898,7 @@ "description": "The filepath of the consesnsus sequence file.", "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence filepath", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "long_table_path": { "examples": [ @@ -1997,8 +1909,7 @@ "description": "The path where the long table including all variants and annotations is.", "classification": "Bioinformatic Analysis fields", "label": "Long table path", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "consensus_sequence_software_name": { "examples": [ @@ -2009,8 +1920,7 @@ "description": "The name of software used to generate the consensus sequence.", "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence software name", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "if_consensus_other": { "examples": [ @@ -2021,8 +1931,7 @@ "description": "The version of the software used to generate the consensus sequence.", "classification": "Bioinformatic Analysis fields", "label": "If consensus Is Other, Specify", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "consensus_sequence_software_version": { "examples": [ @@ -2033,8 +1942,7 @@ "description": "The version of the software used to generate the consensus sequence.", "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence software version", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "consensus_params": { "examples": [ @@ -2045,8 +1953,7 @@ "description": "Parameters used for consensus generation", "classification": "Bioinformatic Analysis fields", "label": "Consensus Params", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "consensus_genome_length": { "examples": [ @@ -2057,8 +1964,7 @@ "description": "Size of the assembled genome described as the number of base pairs.", "classification": "Bioinformatics and QC metrics fields", "label": "Consensus genome length", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "depth_of_coverage_threshold": { "examples": [ @@ -2069,8 +1975,7 @@ "description": "The threshold used as a cut-off for the depth of coverage.", "classification": "Bioinformatics and QC metrics fields", "label": "Depth of coverage threshold", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "number_of_base_pairs_sequenced": { "examples": [ @@ -2081,8 +1986,7 @@ "description": "The number of total base pairs generated by the sequencing process.", "classification": "Bioinformatics and QC metrics fields", "label": "Number of base pairs sequenced ", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "qc_filtered": { "examples": [ @@ -2093,8 +1997,7 @@ "description": "", "classification": "Bioinformatics and QC metrics fields", "label": "%qc filtered", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "per_reads_host": { "examples": [ @@ -2105,8 +2008,7 @@ "description": "", "classification": "Bioinformatics and QC metrics fields", "label": "%reads host", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "per_reads_virus": { "examples": [ @@ -2117,8 +2019,7 @@ "description": "", "classification": "Bioinformatics and QC metrics fields", "label": "%reads virus", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "per_unmapped": { "examples": [ @@ -2129,8 +2030,7 @@ "description": "", "classification": "Bioinformatics and QC metrics fields", "label": "%unmapped", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "depth_of_coverage_value": { "examples": [ @@ -2141,8 +2041,7 @@ "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", "classification": "Bioinformatics and QC metrics fields", "label": "Depth of coverage value ", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "per_genome_greater_10x": { "examples": [ @@ -2153,8 +2052,7 @@ "description": "", "classification": "Bioinformatics and QC metrics fields", "label": "% genome greater 10x", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "per_Ns": { "examples": [ @@ -2165,8 +2063,7 @@ "description": "", "classification": "Bioinformatics and QC metrics fields", "label": "%Ns", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "ns_per_100_kbp": { "examples": [ @@ -2177,8 +2074,7 @@ "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", "classification": "Bioinformatics and QC metrics fields", "label": "Ns per 100 kbp", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "number_of_variants_in_consensus": { "examples": [ @@ -2189,8 +2085,7 @@ "description": "", "classification": "Bioinformatic Variants", "label": "Number of variants (AF greater 75%)", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "number_of_variants_with_effect": { "examples": [ @@ -2201,8 +2096,7 @@ "description": "", "classification": "Bioinformatic Variants", "label": "Number of variants with effect", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "lineage_name": { "examples": [ @@ -2213,8 +2107,7 @@ "description": "The name of the lineage or clade.", "classification": "Lineage fields", "label": "Lineage/clade name", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "lineage_analysis_software_name": { "examples": [ @@ -2225,8 +2118,7 @@ "description": "The name of the software used to determine the lineage/clade.", "classification": "Lineage fields", "label": "lineage/clade analysis software name", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "if_lineage_identification_other": { "examples": [ @@ -2237,8 +2129,7 @@ "description": "The name of the software used to determine the lineage/clade.", "classification": "Lineage fields", "label": "If lineage identification Is Other, Specify", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "lineage_analysis_software_version": { "examples": [ @@ -2249,8 +2140,7 @@ "description": "The version of the software used to determine the lineage/clade.", "classification": "Lineage fields", "label": "Lineage/clade analysis software version", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "variant_designation": { "enum": [ @@ -2266,8 +2156,7 @@ ], "classification": "Lineage fields", "label": "Variant designation", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "gene_name_1": { "enum": [ @@ -2318,8 +2207,7 @@ ], "classification": "Pathogen diagnostic testing", "label": "Gene Name 1", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "diagnostic_pcr_Ct_value_1": { "examples": [ @@ -2330,8 +2218,7 @@ "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "classification": "Pathogen diagnostic testing", "label": "Diagnostic Pcr Ct Value 1", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "gene_name_2": { "enum": [ @@ -2382,8 +2269,7 @@ ], "classification": "Pathogen diagnostic testing", "label": "Gene Name 2", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "diagnostic_pcr_Ct_value_2": { "examples": [ @@ -2394,8 +2280,7 @@ "description": "The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.", "classification": "Pathogen diagnostic testing", "label": "Diagnostic Pcr Ct Value-2", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "authors": { "examples": [ @@ -2406,8 +2291,7 @@ "description": "", "classification": "Public databases", "label": "Authors", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "gisaid_submitter_id": { "examples": [ @@ -2418,8 +2302,7 @@ "description": "GISAID sequence ID.", "classification": "Public Databases", "label": "GISAID id", - "fill_mode": "sample", - "required": "No" + "fill_mode": "sample" }, "gisaid_accession_id": { "examples": [ @@ -2430,8 +2313,7 @@ "description": "GISAID sequence ID.", "classification": "Public Databases", "label": "GISAID id", - "fill_mode": "sample", - "required": "No" + "fill_mode": "sample" }, "gisaid_virus_name": { "examples": [ @@ -2442,8 +2324,7 @@ "description": "The user-defined GISAID virus name assigned to the sequence.", "classification": "Public Databases", "label": "GISAID Virus Name", - "fill_mode": "sample", - "required": "No" + "fill_mode": "sample" }, "ena_analysis_accession": { "examples": [ @@ -2454,8 +2335,7 @@ "description": "", "classification": "Public databases", "label": "Analysis Accession", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "ena_study_accession": { "examples": [ @@ -2466,8 +2346,7 @@ "description": "", "classification": "Public databases", "label": "Study accession", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "ena_sample_accession": { "examples": [ @@ -2478,8 +2357,7 @@ "description": "", "classification": "Public databases", "label": "Sample accession", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "ena_experiment_accession": { "examples": [ @@ -2490,8 +2368,7 @@ "description": "", "classification": "Public databases", "label": "Experiment Accession", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "ena_run_accession": { "examples": [ @@ -2502,8 +2379,7 @@ "description": "", "classification": "Public databases", "label": "Run Accession", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "ena_submission_accession": { "examples": [ @@ -2514,8 +2390,7 @@ "description": "", "classification": "Public databases", "label": "Submission Accession", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "ena_experiment_title": { "examples": [ @@ -2526,8 +2401,7 @@ "description": "", "classification": "Public Databases", "label": "Experiment title", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "ena_study_title": { "examples": [ @@ -2538,8 +2412,7 @@ "description": "", "classification": "Public Databases", "label": "Study title", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "ena_broker_name": { "examples": [ @@ -2550,8 +2423,7 @@ "description": "", "classification": "Public Databases", "label": "Broker Name", - "fill_mode": "batch", - "required": "No" + "fill_mode": "batch" }, "ena_first_created_date": { "examples": [ @@ -2563,7 +2435,7 @@ "description": "", "classification": "Public Databases", "label": "First created date", - "fill_mode": "batch", + "fill_mode": "batch" } } } \ No newline at end of file From 6f27bca495d0afc531d61fc574b0053e62856e89 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 1 Sep 2022 11:23:04 +0200 Subject: [PATCH 0857/1454] changes in schema --- relecov_tools/gisaid_upload.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 406f10ef..947a8f81 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -23,6 +23,8 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) +# + class GisaidUpload: def __init__( From 6f029806d4fa7fca6f14e848ebf4506838a4bc3b Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 1 Sep 2022 13:18:16 +0200 Subject: [PATCH 0858/1454] changes in relecov schema --- relecov_tools/gisaid_upload.py | 2 - relecov_tools/schema/relecov_schema.json | 60 ++++++++++++++++-------- 2 files changed, 40 insertions(+), 22 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 947a8f81..406f10ef 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -23,8 +23,6 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) -# - class GisaidUpload: def __init__( diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 9a5d1b39..2a22febc 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -25,7 +25,8 @@ "description": "", "classification": "Sample collection and processing", "label": "Public Health sample id (SIVIES)", - "fill_mode": "sample" + "fill_mode": "sample", + "minLenght": "1" }, "collecting_lab_sample_id": { "examples": [ @@ -36,7 +37,8 @@ "description": "The name given for the sample by the collecting institution.", "classification": "Database Identifiers", "label": "Sample ID given by originating laboratory", - "fill_mode": "sample" + "fill_mode": "sample", + "minLenght": "1" }, "collecting_institution": { "examples": [ @@ -47,7 +49,8 @@ "description": "The name of the agency/institution that collected the sample.", "classification": "Sample collection and processing", "label": "Originating Laboratory", - "fill_mode": "sample" + "fill_mode": "sample", + "minLenght": "1" }, "collecting_institution_email": { "examples": [ @@ -80,7 +83,8 @@ "description": "", "classification": "Sample collection and processing", "label": "Sample ID given in the microbiology lab", - "fill_mode": "sample" + "fill_mode": "sample", + "minLenght": "1" }, "isolate_sample_id": { "examples": [ @@ -91,7 +95,8 @@ "description": "", "classification": "Database Identifiers", "label": "Sample ID given if multiple rna-extraction or passages", - "fill_mode": "sample" + "fill_mode": "sample", + "minLenght": "1" }, "sequencing_sample_id": { "examples": [ @@ -102,7 +107,8 @@ "description": "If the information is unknown or can not be shared, leave blank.", "classification": "Database Identifiers", "label": "Sample ID given for sequencing", - "fill_mode": "sample" + "fill_mode": "sample", + "minLenght": "1" }, "submitting_lab_sample_id": { "examples": [ @@ -113,7 +119,8 @@ "description": "Sample ID given by the submitting laboratory", "classification": "Sequencing", "label": "Sample ID given by the submitting laboratory", - "fill_mode": "sample" + "fill_mode": "sample", + "minLenght": "1" }, "submitting_institution": { "examples": [ @@ -124,7 +131,8 @@ "description": "The name of the agency that submitted the sequence to public databases.", "classification": "Sample collection and processing", "label": "Submitting Institution", - "fill_mode": "sample" + "fill_mode": "sample", + "minLenght": "1" }, "submitting_institution_email": { "examples": [ @@ -158,7 +166,8 @@ "format": "date", "classification": "Sample collection and processing", "label": "Sample Collection Date", - "fill_mode": "sample" + "fill_mode": "sample", + "minLenght": "1" }, "sample_received_date": { "examples": [ @@ -470,7 +479,8 @@ ], "classification": "Sample collection and processing", "label": "Country", - "fill_mode": "batch" + "fill_mode": "batch", + "minLenght": "1" }, "geo_loc_state": { "examples": [ @@ -481,7 +491,8 @@ "description": "The state/province/territory of origin of the sample.", "classification": "Sample collection and processing", "label": "Autonomic Community", - "fill_mode": "batch" + "fill_mode": "batch", + "minLenght": "1" }, "geo_loc_region": { "examples": [ @@ -818,7 +829,8 @@ ], "classification": "Sample collection and processing", "label": "Organism", - "fill_mode": "batch" + "fill_mode": "batch", + "minLenght": "1" }, "tax_id": { "examples": [ @@ -829,7 +841,8 @@ "description": "The NCBITaxon identifier for the organism being sequenced.", "classification": "Sample collection and processing", "label": "Tax ID", - "fill_mode": "batch" + "fill_mode": "batch", + "minLenght": "1" }, "host_subject_id": { "examples": [ @@ -839,7 +852,8 @@ "type": "string", "description": "An unique identifier by which each subject can be referred to, de-identified.", "classification": "Host information", - "label": "Host Subject Id" + "label": "Host Subject Id", + "minLenght": "1" }, "host_health_state": { "examples": [ @@ -914,7 +928,8 @@ ], "classification": "Host information", "label": "Host Scientific Name", - "fill_mode": "batch" + "fill_mode": "batch", + "minLenght": "1" }, "host_disease": { "enum": [ @@ -1032,7 +1047,8 @@ ], "classification": "Sequencing", "label": "Sequencing Instrument Model", - "fill_mode": "batch" + "fill_mode": "batch", + "minLenght": "1" }, "purpose_of_sequencing": { "enum": [ @@ -1422,7 +1438,8 @@ "description": "", "classification": "Sequencing", "label": "Sequencing Instrument Platform", - "fill_mode": "batch" + "fill_mode": "batch", + "minLenght": "1" }, "library_source": { "enum": [ @@ -1607,7 +1624,8 @@ "description": "", "classification": "Bioinformatics and QC metrics fields", "label": "Analysis date", - "fill_mode": "batch" + "fill_mode": "batch", + "minLenght": "1" }, "dehosting_method_software_name": { "examples": [ @@ -1662,7 +1680,8 @@ "description": "The name of the bioinformatics protocol used.", "classification": "Bioinformatic Analysis fields", "label": "If bioinformatic protocol Is Other, Specify", - "fill_mode": "batch" + "fill_mode": "batch", + "minLenght": "1" }, "bioinformatics_protocol_software_version": { "examples": [ @@ -1673,7 +1692,8 @@ "description": "The version number of the bioinformatics protocol used.", "classification": "Bioinformatic Analysis fields", "label": "bioinformatics protocol version", - "fill_mode": "batch" + "fill_mode": "batch", + "minLenght": "1" }, "commercial_open_source_both": { "enum": [ From f1f977d07b005ffa22025f2787144e139e14f91a Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 1 Sep 2022 15:42:09 +0200 Subject: [PATCH 0859/1454] added to config anatomical part and collection method --- relecov_tools/conf/configuration.json | 622 +++++++++++++++++++++++++- 1 file changed, 620 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index c724d298..b52a5032 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -218,5 +218,623 @@ "mapping_file": { "ISCIII": "ISCIII.json", "HUGTiP": "HUGTiP.json" - } -} + }, + "anatomical_part_collection_method_list": [ + [ + "Bronchus", + "Aspiration" + ], + [ + "Lung", + "Aspiration" + ], + [ + "Bronchiole", + "Aspiration" + ], + [ + "Alveolar sac", + "Aspiration" + ], + [ + "Pleural sac", + "Aspiration" + ], + [ + "Pleural cavity", + "Aspiration" + ], + [ + "Trachea", + "Aspiration" + ], + [ + "Upper respiratory tract", + "Aspiration" + ], + [ + "Anterior Nares", + "Aspiration" + ], + [ + "Esophagus", + "Aspiration" + ], + [ + "Ethmoid sinus", + "Aspiration" + ], + [ + "Nasal Cavity", + "Aspiration" + ], + [ + "Middle Nasal Turbinate", + "Aspiration" + ], + [ + "Nasopharynx", + "Aspiration" + ], + [ + "Oropharynx", + "Aspiration" + ], + [ + "Lower respiratory tract", + "Vacuum Aspiration" + ], + [ + "Bronchus", + "Vacuum Aspiration" + ], + [ + "Lung", + "Vacuum Aspiration" + ], + [ + "Bronchiole", + "Vacuum Aspiration" + ], + [ + "Alveolar sac", + "Vacuum Aspiration" + ], + [ + "Pleural sac", + "Vacuum Aspiration" + ], + [ + "Pleural cavity", + "Vacuum Aspiration" + ], + [ + "Trachea", + "Vacuum Aspiration" + ], + [ + "Upper respiratory tract", + "Vacuum Aspiration" + ], + [ + "Anterior Nares", + "Vacuum Aspiration" + ], + [ + "Esophagus", + "Vacuum Aspiration" + ], + [ + "Ethmoid sinus", + "Vacuum Aspiration" + ], + [ + "Nasal Cavity", + "Vacuum Aspiration" + ], + [ + "Middle Nasal Turbinate", + "Vacuum Aspiration" + ], + [ + "Nasopharynx", + "Vacuum Aspiration" + ], + [ + "Oropharynx", + "Vacuum Aspiration" + ], + [ + "Lower respiratory tract", + "Biopsy" + ], + [ + "Bronchus", + "Biopsy" + ], + [ + "Lung", + "Biopsy" + ], + [ + "Bronchiole", + "Biopsy" + ], + [ + "Alveolar sac", + "Biopsy" + ], + [ + "Pleural sac", + "Biopsy" + ], + [ + "Pleural cavity", + "Biopsy" + ], + [ + "Trachea", + "Biopsy" + ], + [ + "Rectum", + "Biopsy" + ], + [ + "Skin", + "Biopsy" + ], + [ + "Stomach", + "Biopsy" + ], + [ + "Upper respiratory tract", + "Biopsy" + ], + [ + "Anterior Nares", + "Biopsy" + ], + [ + "Esophagus", + "Biopsy" + ], + [ + "Ethmoid sinus", + "Biopsy" + ], + [ + "Nasal Cavity", + "Biopsy" + ], + [ + "Middle Nasal Turbinate", + "Biopsy" + ], + [ + "Duodenum", + "Biopsy" + ], + [ + "Nasopharynx", + "Biopsy" + ], + [ + "Oropharynx", + "Biopsy" + ], + [ + "Lower respiratory tract", + "Needle Biopsy" + ], + [ + "Bronchus", + "Needle Biopsy" + ], + [ + "Lung", + "Needle Biopsy" + ], + [ + "Bronchiole", + "Needle Biopsy" + ], + [ + "Alveolar sac", + "Needle Biopsy" + ], + [ + "Pleural sac", + "Needle Biopsy" + ], + [ + "Pleural cavity", + "Needle Biopsy" + ], + [ + "Trachea", + "Needle Biopsy" + ], + [ + "Rectum", + "Needle Biopsy" + ], + [ + "Skin", + "Needle Biopsy" + ], + [ + "Stomach", + "Needle Biopsy" + ], + [ + "Upper respiratory tract", + "Needle Biopsy" + ], + [ + "Anterior Nares", + "Needle Biopsy" + ], + [ + "Esophagus", + "Needle Biopsy" + ], + [ + "Ethmoid sinus", + "Needle Biopsy" + ], + [ + "Nasal Cavity", + "Needle Biopsy" + ], + [ + "Middle Nasal Turbinate", + "Needle Biopsy" + ], + [ + "Duodenum", + "Needle Biopsy" + ], + [ + "Nasopharynx", + "Needle Biopsy" + ], + [ + "Oropharynx", + "Needle Biopsy" + ], + [ + "Lower respiratory tract", + "Lavage" + ], + [ + "Bronchus", + "Lavage" + ], + [ + "Lung", + "Lavage" + ], + [ + "Pleural sac", + "Lavage" + ], + [ + "Pleural cavity", + "Lavage" + ], + [ + "Trachea", + "Lavage" + ], + [ + "Upper respiratory tract", + "Lavage" + ], + [ + "Anterior Nares", + "Lavage" + ], + [ + "Esophagus", + "Lavage" + ], + [ + "Ethmoid sinus", + "Lavage" + ], + [ + "Nasal Cavity", + "Lavage" + ], + [ + "Middle Nasal Turbinate", + "Lavage" + ], + [ + "Nasopharynx", + "Lavage" + ], + [ + "Oropharynx", + "Lavage" + ], + [ + "Bronchoalveolar", + "Lavage" + ], + [ + "Gastric", + "Lavage" + ], + [ + "Lower respiratory tract", + "Necropsy" + ], + [ + "Bronchus", + "Necropsy" + ], + [ + "Lung", + "Necropsy" + ], + [ + "Bronchiole", + "Necropsy" + ], + [ + "Alveolar sac", + "Necropsy" + ], + [ + "Pleural sac", + "Necropsy" + ], + [ + "Pleural cavity", + "Necropsy" + ], + [ + "Trachea", + "Necropsy" + ], + [ + "Rectum", + "Necropsy" + ], + [ + "Skin", + "Necropsy" + ], + [ + "Stomach", + "Necropsy" + ], + [ + "Upper respiratory tract", + "Necropsy" + ], + [ + "Anterior Nares", + "Necropsy" + ], + [ + "Esophagus", + "Necropsy" + ], + [ + "Ethmoid sinus", + "Necropsy" + ], + [ + "Nasal Cavity", + "Necropsy" + ], + [ + "Middle Nasal Turbinate", + "Necropsy" + ], + [ + "Duodenum", + "Necropsy" + ], + [ + "Nasopharynx", + "Necropsy" + ], + [ + "Oropharynx", + "Necropsy" + ], + [ + "Lower respiratory tract", + "Rinsing" + ], + [ + "Bronchus", + "Rinsing" + ], + [ + "Lung", + "Rinsing" + ], + [ + "Bronchiole", + "Rinsing" + ], + [ + "Alveolar sac", + "Rinsing" + ], + [ + "Pleural sac", + "Rinsing" + ], + [ + "Pleural cavity", + "Rinsing" + ], + [ + "Trachea", + "Rinsing" + ], + [ + "Upper respiratory tract", + "Rinsing" + ], + [ + "Anterior Nares", + "Rinsing" + ], + [ + "Esophagus", + "Rinsing" + ], + [ + "Ethmoid sinus", + "Rinsing" + ], + [ + "Nasal Cavity", + "Rinsing" + ], + [ + "Middle Nasal Turbinate", + "Rinsing" + ], + [ + "Nasopharynx", + "Rinsing" + ], + [ + "Oropharynx", + "Rinsing" + ], + [ + "Bronchiole", + "Scraping" + ], + [ + "Alveolar sac", + "Scraping" + ], + [ + "Pleural sac", + "Scraping" + ], + [ + "Pleural cavity", + "Scraping" + ], + [ + "Trachea", + "Scraping" + ], + [ + "Upper respiratory tract", + "Scraping" + ], + [ + "Anterior Nares", + "Scraping" + ], + [ + "Esophagus", + "Scraping" + ], + [ + "Ethmoid sinus", + "Scraping" + ], + [ + "Nasal Cavity", + "Scraping" + ], + [ + "Middle Nasal Turbinate", + "Scraping" + ], + [ + "Nasopharynx", + "Scraping" + ], + [ + "Oropharynx", + "Scraping" + ], + [ + "Nasopharynx", + "Swabbing" + ], + [ + "Oropharynx", + "Swabbing" + ], + [ + "Lower respiratory tract", + "Wash" + ], + [ + "Bronchus", + "Wash" + ], + [ + "Lung", + "Wash" + ], + [ + "Bronchiole", + "Wash" + ], + [ + "Alveolar sac", + "Wash" + ], + [ + "Pleural sac", + "Wash" + ], + [ + "Pleural cavity", + "Wash" + ], + [ + "Trachea", + "Wash" + ], + [ + "Upper respiratory tract", + "Wash" + ], + [ + "Anterior Nares", + "Wash" + ], + [ + "Esophagus", + "Wash" + ], + [ + "Ethmoid sinus", + "Wash" + ], + [ + "Nasal Cavity", + "Wash" + ], + [ + "Middle Nasal Turbinate", + "Wash" + ], + [ + "Nasopharynx", + "Wash" + ], + [ + "Oropharynx", + "Wash" + ] + ] +} \ No newline at end of file From 9f2b6a869c4ec670e2e1fe37a2c01a8cf1beb99f Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 1 Sep 2022 16:03:10 +0200 Subject: [PATCH 0860/1454] changes for instrumnet_platform in template --- relecov_tools/map_schema.py | 9 +++++---- relecov_tools/templates/ENA_template_PLATFORM.xml | 12 ++++++------ 2 files changed, 11 insertions(+), 10 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index fe5623f8..61664969 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -204,7 +204,7 @@ def additional_formating(self, mapped_json_data): mapped_json_data[idx][ "sequencing_instrument_platform" ] = self.json_data[idx]["sequencing_instrument_platform"].upper() - + """ if ( "nextseq" in self.json_data[idx]["sequencing_instrument_model"].lower() @@ -235,9 +235,10 @@ def additional_formating(self, mapped_json_data): ): mapped_json_data[idx]["instrument_model"] = "NextSeq 550" else: - mapped_json_data[idx]["instrument_model"] = self.json_data[idx][ - "sequencing_instrument_model" - ] + """ + mapped_json_data[idx]["instrument_model"] = self.json_data[idx][ + "sequencing_instrument_model" + ] mapped_json_data[idx]["host health state"] = "not provided" mapped_json_data[idx]["center_name"] = mapped_json_data[idx][ diff --git a/relecov_tools/templates/ENA_template_PLATFORM.xml b/relecov_tools/templates/ENA_template_PLATFORM.xml index 4e514c5e..7cd494b1 100644 --- a/relecov_tools/templates/ENA_template_PLATFORM.xml +++ b/relecov_tools/templates/ENA_template_PLATFORM.xml @@ -9,8 +9,8 @@ unspecified - HiSeq X Five - HiSeq X Ten + HiSeq X Five + HiSeq X Ten Illumina Genome Analyzer Illumina Genome Analyzer II Illumina Genome Analyzer IIx @@ -26,10 +26,10 @@ Illumina MiSeq Illumina MiniSeq Illumina NovaSeq 6000 - NextSeq 500 - NextSeq 550 - NextSeq 1000 - NextSeq 2000 + NextSeq 500 + NextSeq 550 + NextSeq 1000 + NextSeq 2000 unspecified From 76248365abe7eaa4715bc4bf92f70024fd698d82 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 1 Sep 2022 17:03:58 +0200 Subject: [PATCH 0861/1454] fixing schemas --- relecov_tools/ena_upload.py | 29 ++++++++++--------- .../schema/institution_schemas/ISCIII.json | 4 +-- 2 files changed, 16 insertions(+), 17 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 992f6bf8..6d35e55b 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -133,6 +133,7 @@ def create_structure_to_ena(self): 0 Hospital Clínic de Barcelona 2021-05-10 Inmaculada Casas ... RELECOV Spanish Network for genomics surveillance Surveillance 2697049 1 Hospital Clínic de Barcelona 2021-05-07 Inmaculada Casas ... RELECOV Spanish Network for genomics surveillance Surveillance 2697049 + """ """ df_study = df_schemas[ ["study_alias", "study_title", "study_type", "study_abstract"] @@ -140,9 +141,16 @@ def create_structure_to_ena(self): df_study = df_study.rename(columns={"study_alias": "alias"}) df_study = df_study.rename(columns={"study_title": "title"}) + + + """ + df_study = df_schemas[["study_type", "study_abstract"]] + df_study["alias"] = df_study["study_abstract"][0].rsplit(" ", 5)[0] + df_study["title"] = df_study["study_abstract"] df_study.insert(3, "status", self.action) - # df_study + """ + # df_study alias title study_type status study_abstract 0 RELECOV RELECOV Spanish Network for genomics surveillance Surveillance ADD RELECOV Spanish Network for genomics surveillance 1 RELECOV RELECOV Spanish Network for genomics surveillance Surveillance ADD RELECOV Spanish Network for genomics surveillance @@ -206,6 +214,9 @@ def create_structure_to_ena(self): 1 212163777 212163777 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212163777 2 212153091 212153091 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212153091 """ + import pdb + + pdb.set_trace() df_run = df_schemas[ [ "experiment_alias", @@ -341,7 +352,8 @@ def create_structure_to_ena(self): # submit data to webin ftp server. It should only upload fastq files in case the action is ADD. # When the action is MODIFY rthe fastq are already submitted. - + """ + if self.action == "ADD" or self.action == "add": session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) @@ -361,6 +373,7 @@ def create_structure_to_ena(self): g2 = session.quit() print(g2) + """ # THE ENA_UPLOAD_CLI METHOD DOES NOT WORK (below) # chec = submit_data(file_paths, self.passwd, self.user) @@ -396,18 +409,6 @@ def create_structure_to_ena(self): files.set("checksum", H) # print(files.attrib["checksum"]) tree.write(schema_xmls["run"]) - """ - tree = ET.parse(schema_xmls["sample"]) - root = tree.getroot() - for files in root.iter("SAMPLE_ATTRIBUTES"): - tag = ET.SubElement(files, "SAMPLE_ATTRIBUTE") - tag_2 = ET.SubElement(tag, "TAG") - tag_2.text = str("ENA-CHECKLIST") - tag_3 = ET.SubElement(tag, "VALUE") - tag_3.text = str("ERC000033") - - tree.write(schema_xmls["sample"]) - """ if self.dev: url = "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 77aa3391..2b719028 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -23,8 +23,6 @@ "Biological Sample Storage Condition": "-80 C", "Rna Extraction Protocol": "RT-PCR", "Purpose of sampling": "Surveillance", - "Specimen source": "Nasopharyngeal exudate", - "Environmental System": "Swab", "Host": "Human", "Library Preparation Kit": "Illumina DNA Prep", "Enrichment Protocol": "Amplicon", @@ -113,4 +111,4 @@ "function": "None" } } -} +} \ No newline at end of file From 5ee212046ff20c88a8de58a49ab805bb688df91c Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 1 Sep 2022 23:07:34 +0200 Subject: [PATCH 0862/1454] Incorrect string value: '\xE2\x80\x91CoV... --- relecov_tools/schema/relecov_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 2a22febc..2950817f 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1209,7 +1209,7 @@ "Illumina respiratory Virus Oligo Panel", "Illumina AmpliSeq Community panel", "Illumina AmpliSeq SARS-CoV-2 Research Panel for Illumina", - "Ion AmpliSeq SARS‑CoV‑2 Research Panel", + "Ion AmpliSeq SARS-CoV-2 Research Panel", "xGen SC2 Midnight1200 Amplicon Panel", "ViroKey SQ FLEX SARS-CoV-2 Primer Set", "NEBNext VarSkip Short SARS-CoV-2 primers", @@ -2458,4 +2458,4 @@ "fill_mode": "batch" } } -} \ No newline at end of file +} From 0a47803cc105f827821f5544db4f796cd06a8028 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 2 Sep 2022 11:44:50 +0200 Subject: [PATCH 0863/1454] changes in schema placenta and config --- relecov_tools/conf/configuration.json | 1610 ++++++++++++------- relecov_tools/institution_scripts/ISCIII.py | 6 +- relecov_tools/schema/relecov_schema.json | 1 + 3 files changed, 995 insertions(+), 622 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index b52a5032..8d93a355 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -219,622 +219,994 @@ "ISCIII": "ISCIII.json", "HUGTiP": "HUGTiP.json" }, - "anatomical_part_collection_method_list": [ - [ - "Bronchus", - "Aspiration" - ], - [ - "Lung", - "Aspiration" - ], - [ - "Bronchiole", - "Aspiration" - ], - [ - "Alveolar sac", - "Aspiration" - ], - [ - "Pleural sac", - "Aspiration" - ], - [ - "Pleural cavity", - "Aspiration" - ], - [ - "Trachea", - "Aspiration" - ], - [ - "Upper respiratory tract", - "Aspiration" - ], - [ - "Anterior Nares", - "Aspiration" - ], - [ - "Esophagus", - "Aspiration" - ], - [ - "Ethmoid sinus", - "Aspiration" - ], - [ - "Nasal Cavity", - "Aspiration" - ], - [ - "Middle Nasal Turbinate", - "Aspiration" - ], - [ - "Nasopharynx", - "Aspiration" - ], - [ - "Oropharynx", - "Aspiration" - ], - [ - "Lower respiratory tract", - "Vacuum Aspiration" - ], - [ - "Bronchus", - "Vacuum Aspiration" - ], - [ - "Lung", - "Vacuum Aspiration" - ], - [ - "Bronchiole", - "Vacuum Aspiration" - ], - [ - "Alveolar sac", - "Vacuum Aspiration" - ], - [ - "Pleural sac", - "Vacuum Aspiration" - ], - [ - "Pleural cavity", - "Vacuum Aspiration" - ], - [ - "Trachea", - "Vacuum Aspiration" - ], - [ - "Upper respiratory tract", - "Vacuum Aspiration" - ], - [ - "Anterior Nares", - "Vacuum Aspiration" - ], - [ - "Esophagus", - "Vacuum Aspiration" - ], - [ - "Ethmoid sinus", - "Vacuum Aspiration" - ], - [ - "Nasal Cavity", - "Vacuum Aspiration" - ], - [ - "Middle Nasal Turbinate", - "Vacuum Aspiration" - ], - [ - "Nasopharynx", - "Vacuum Aspiration" - ], - [ - "Oropharynx", - "Vacuum Aspiration" - ], - [ - "Lower respiratory tract", - "Biopsy" - ], - [ - "Bronchus", - "Biopsy" - ], - [ - "Lung", - "Biopsy" - ], - [ - "Bronchiole", - "Biopsy" - ], - [ - "Alveolar sac", - "Biopsy" - ], - [ - "Pleural sac", - "Biopsy" - ], - [ - "Pleural cavity", - "Biopsy" - ], - [ - "Trachea", - "Biopsy" - ], - [ - "Rectum", - "Biopsy" - ], - [ - "Skin", - "Biopsy" - ], - [ - "Stomach", - "Biopsy" - ], - [ - "Upper respiratory tract", - "Biopsy" - ], - [ - "Anterior Nares", - "Biopsy" - ], - [ - "Esophagus", - "Biopsy" - ], - [ - "Ethmoid sinus", - "Biopsy" - ], - [ - "Nasal Cavity", - "Biopsy" - ], - [ - "Middle Nasal Turbinate", - "Biopsy" - ], - [ - "Duodenum", - "Biopsy" - ], - [ - "Nasopharynx", - "Biopsy" - ], - [ - "Oropharynx", - "Biopsy" - ], - [ - "Lower respiratory tract", - "Needle Biopsy" - ], - [ - "Bronchus", - "Needle Biopsy" - ], - [ - "Lung", - "Needle Biopsy" - ], - [ - "Bronchiole", - "Needle Biopsy" - ], - [ - "Alveolar sac", - "Needle Biopsy" - ], - [ - "Pleural sac", - "Needle Biopsy" - ], - [ - "Pleural cavity", - "Needle Biopsy" - ], - [ - "Trachea", - "Needle Biopsy" - ], - [ - "Rectum", - "Needle Biopsy" - ], - [ - "Skin", - "Needle Biopsy" - ], - [ - "Stomach", - "Needle Biopsy" - ], - [ - "Upper respiratory tract", - "Needle Biopsy" - ], - [ - "Anterior Nares", - "Needle Biopsy" - ], - [ - "Esophagus", - "Needle Biopsy" - ], - [ - "Ethmoid sinus", - "Needle Biopsy" - ], - [ - "Nasal Cavity", - "Needle Biopsy" - ], - [ - "Middle Nasal Turbinate", - "Needle Biopsy" - ], - [ - "Duodenum", - "Needle Biopsy" - ], - [ - "Nasopharynx", - "Needle Biopsy" - ], - [ - "Oropharynx", - "Needle Biopsy" - ], - [ - "Lower respiratory tract", - "Lavage" - ], - [ - "Bronchus", - "Lavage" - ], - [ - "Lung", - "Lavage" - ], - [ - "Pleural sac", - "Lavage" - ], - [ - "Pleural cavity", - "Lavage" - ], - [ - "Trachea", - "Lavage" - ], - [ - "Upper respiratory tract", - "Lavage" - ], - [ - "Anterior Nares", - "Lavage" - ], - [ - "Esophagus", - "Lavage" - ], - [ - "Ethmoid sinus", - "Lavage" - ], - [ - "Nasal Cavity", - "Lavage" - ], - [ - "Middle Nasal Turbinate", - "Lavage" - ], - [ - "Nasopharynx", - "Lavage" - ], - [ - "Oropharynx", - "Lavage" - ], - [ - "Bronchoalveolar", - "Lavage" - ], - [ - "Gastric", - "Lavage" - ], - [ - "Lower respiratory tract", - "Necropsy" - ], - [ - "Bronchus", - "Necropsy" - ], - [ - "Lung", - "Necropsy" - ], - [ - "Bronchiole", - "Necropsy" - ], - [ - "Alveolar sac", - "Necropsy" - ], - [ - "Pleural sac", - "Necropsy" - ], - [ - "Pleural cavity", - "Necropsy" - ], - [ - "Trachea", - "Necropsy" - ], - [ - "Rectum", - "Necropsy" - ], - [ - "Skin", - "Necropsy" - ], - [ - "Stomach", - "Necropsy" - ], - [ - "Upper respiratory tract", - "Necropsy" - ], - [ - "Anterior Nares", - "Necropsy" - ], - [ - "Esophagus", - "Necropsy" - ], - [ - "Ethmoid sinus", - "Necropsy" - ], - [ - "Nasal Cavity", - "Necropsy" - ], - [ - "Middle Nasal Turbinate", - "Necropsy" - ], - [ - "Duodenum", - "Necropsy" - ], - [ - "Nasopharynx", - "Necropsy" - ], - [ - "Oropharynx", - "Necropsy" - ], - [ - "Lower respiratory tract", - "Rinsing" - ], - [ - "Bronchus", - "Rinsing" - ], - [ - "Lung", - "Rinsing" - ], - [ - "Bronchiole", - "Rinsing" - ], - [ - "Alveolar sac", - "Rinsing" - ], - [ - "Pleural sac", - "Rinsing" - ], - [ - "Pleural cavity", - "Rinsing" - ], - [ - "Trachea", - "Rinsing" - ], - [ - "Upper respiratory tract", - "Rinsing" - ], - [ - "Anterior Nares", - "Rinsing" - ], - [ - "Esophagus", - "Rinsing" - ], - [ - "Ethmoid sinus", - "Rinsing" - ], - [ - "Nasal Cavity", - "Rinsing" - ], - [ - "Middle Nasal Turbinate", - "Rinsing" - ], - [ - "Nasopharynx", - "Rinsing" - ], - [ - "Oropharynx", - "Rinsing" - ], - [ - "Bronchiole", - "Scraping" - ], - [ - "Alveolar sac", - "Scraping" - ], - [ - "Pleural sac", - "Scraping" - ], - [ - "Pleural cavity", - "Scraping" - ], - [ - "Trachea", - "Scraping" - ], - [ - "Upper respiratory tract", - "Scraping" - ], - [ - "Anterior Nares", - "Scraping" - ], - [ - "Esophagus", - "Scraping" - ], - [ - "Ethmoid sinus", - "Scraping" - ], - [ - "Nasal Cavity", - "Scraping" - ], - [ - "Middle Nasal Turbinate", - "Scraping" - ], - [ - "Nasopharynx", - "Scraping" - ], - [ - "Oropharynx", - "Scraping" - ], - [ - "Nasopharynx", - "Swabbing" - ], - [ - "Oropharynx", - "Swabbing" - ], - [ - "Lower respiratory tract", - "Wash" - ], - [ - "Bronchus", - "Wash" - ], - [ - "Lung", - "Wash" - ], - [ - "Bronchiole", - "Wash" - ], - [ - "Alveolar sac", - "Wash" - ], - [ - "Pleural sac", - "Wash" - ], - [ - "Pleural cavity", - "Wash" - ], - [ - "Trachea", - "Wash" - ], - [ - "Upper respiratory tract", - "Wash" - ], - [ - "Anterior Nares", - "Wash" - ], - [ - "Esophagus", - "Wash" - ], - [ - "Ethmoid sinus", - "Wash" - ], - [ - "Nasal Cavity", - "Wash" - ], - [ - "Middle Nasal Turbinate", - "Wash" - ], - [ - "Nasopharynx", - "Wash" - ], - [ - "Oropharynx", - "Wash" - ] - ] -} \ No newline at end of file + "anatomical_material_collection_method": { + { + "Lower respiratory tract Aspiration": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Aspiration": { + "anatomical_part": "Bronchus", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Aspiration": { + "anatomical_part": "Lung", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Aspiration": { + "anatomical_part": "Bronchiole", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Aspiration": { + "anatomical_part": "Alveolar sac", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Aspiration": { + "anatomical_part": "Pleural sac", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Aspiration": { + "anatomical_part": "Pleural cavity", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Aspiration": { + "anatomical_part": "Trachea", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Aspiration": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Aspiration": { + "anatomical_part": "Anterior Nares", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Aspiration": { + "anatomical_part": "Esophagus", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Aspiration": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Aspiration": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Aspiration": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Aspiration": { + "anatomical_part": "Nasopharynx", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Aspiration": { + "anatomical_part": "Oropharynx", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Vacuum Aspiration": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Vacuum Aspiration": { + "anatomical_part": "Bronchus", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Vacuum Aspiration": { + "anatomical_part": "Lung", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Vacuum Aspiration": { + "anatomical_part": "Bronchiole", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Vacuum Aspiration": { + "anatomical_part": "Alveolar sac", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Vacuum Aspiration": { + "anatomical_part": "Pleural sac", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Vacuum Aspiration": { + "anatomical_part": "Pleural cavity", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Vacuum Aspiration": { + "anatomical_part": "Trachea", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Vacuum Aspiration": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Vacuum Aspiration": { + "anatomical_part": "Anterior Nares", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Vacuum Aspiration": { + "anatomical_part": "Esophagus", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Vacuum Aspiration": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Vacuum Aspiration": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Vacuum Aspiration": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Vacuum Aspiration": { + "anatomical_part": "Nasopharynx", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Vacuum Aspiration": { + "anatomical_part": "Oropharynx", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Biopsy": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Biopsy": { + "anatomical_part": "Bronchus", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Biopsy": { + "anatomical_part": "Lung", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Biopsy": { + "anatomical_part": "Bronchiole", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Biopsy": { + "anatomical_part": "Alveolar sac", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Biopsy": { + "anatomical_part": "Pleural sac", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Biopsy": { + "anatomical_part": "Pleural cavity", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Biopsy": { + "anatomical_part": "Trachea", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Rectum Biopsy": { + "anatomical_part": "Rectum", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Skin Biopsy": { + "anatomical_part": "Skin", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Stomach Biopsy": { + "anatomical_part": "Stomach", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Biopsy": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Biopsy": { + "anatomical_part": "Anterior Nares", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Biopsy": { + "anatomical_part": "Esophagus", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Biopsy": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Biopsy": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Biopsy": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Duodenum Biopsy": { + "anatomical_part": "Duodenum", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Biopsy": { + "anatomical_part": "Nasopharynx", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Biopsy": { + "anatomical_part": "Oropharynx", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Needle Biopsy": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Needle Biopsy": { + "anatomical_part": "Bronchus", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Needle Biopsy": { + "anatomical_part": "Lung", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Needle Biopsy": { + "anatomical_part": "Bronchiole", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Needle Biopsy": { + "anatomical_part": "Alveolar sac", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Needle Biopsy": { + "anatomical_part": "Pleural sac", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Needle Biopsy": { + "anatomical_part": "Pleural cavity", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Needle Biopsy": { + "anatomical_part": "Trachea", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Rectum Needle Biopsy": { + "anatomical_part": "Rectum", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Skin Needle Biopsy": { + "anatomical_part": "Skin", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Stomach Needle Biopsy": { + "anatomical_part": "Stomach", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Needle Biopsy": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Needle Biopsy": { + "anatomical_part": "Anterior Nares", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Needle Biopsy": { + "anatomical_part": "Esophagus", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Needle Biopsy": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Needle Biopsy": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Needle Biopsy": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Duodenum Needle Biopsy": { + "anatomical_part": "Duodenum", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Needle Biopsy": { + "anatomical_part": "Nasopharynx", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Needle Biopsy": { + "anatomical_part": "Oropharynx", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Lavage": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Lavage": { + "anatomical_part": "Bronchus", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Lavage": { + "anatomical_part": "Lung", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Lavage": { + "anatomical_part": "Pleural sac", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Lavage": { + "anatomical_part": "Pleural cavity", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Lavage": { + "anatomical_part": "Trachea", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Lavage": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Lavage": { + "anatomical_part": "Anterior Nares", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Lavage": { + "anatomical_part": "Esophagus", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Lavage": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Lavage": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Lavage": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Lavage": { + "anatomical_part": "Nasopharynx", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Lavage": { + "anatomical_part": "Oropharynx", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Necropsy": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Necropsy": { + "anatomical_part": "Bronchus", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Necropsy": { + "anatomical_part": "Lung", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Necropsy": { + "anatomical_part": "Bronchiole", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Necropsy": { + "anatomical_part": "Alveolar sac", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Necropsy": { + "anatomical_part": "Pleural sac", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Necropsy": { + "anatomical_part": "Pleural cavity", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Necropsy": { + "anatomical_part": "Trachea", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Rectum Necropsy": { + "anatomical_part": "Rectum", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Skin Necropsy": { + "anatomical_part": "Skin", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Stomach Necropsy": { + "anatomical_part": "Stomach", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Necropsy": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Necropsy": { + "anatomical_part": "Anterior Nares", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Necropsy": { + "anatomical_part": "Esophagus", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Necropsy": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Necropsy": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Necropsy": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Duodenum Necropsy": { + "anatomical_part": "Duodenum", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Necropsy": { + "anatomical_part": "Nasopharynx", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Necropsy": { + "anatomical_part": "Oropharynx", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Rinsing": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Rinsing": { + "anatomical_part": "Bronchus", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Rinsing": { + "anatomical_part": "Lung", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Rinsing": { + "anatomical_part": "Bronchiole", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Rinsing": { + "anatomical_part": "Alveolar sac", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Rinsing": { + "anatomical_part": "Pleural sac", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Rinsing": { + "anatomical_part": "Pleural cavity", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Rinsing": { + "anatomical_part": "Trachea", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Rinsing": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Rinsing": { + "anatomical_part": "Anterior Nares", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Rinsing": { + "anatomical_part": "Esophagus", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Rinsing": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Rinsing": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Rinsing": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Rinsing": { + "anatomical_part": "Nasopharynx", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Rinsing": { + "anatomical_part": "Oropharynx", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Scraping": { + "anatomical_part": "Bronchiole", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Scraping": { + "anatomical_part": "Alveolar sac", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Scraping": { + "anatomical_part": "Pleural sac", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Scraping": { + "anatomical_part": "Pleural cavity", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Scraping": { + "anatomical_part": "Trachea", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Scraping": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Scraping": { + "anatomical_part": "Anterior Nares", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Scraping": { + "anatomical_part": "Esophagus", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Scraping": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Scraping": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Scraping": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Scraping": { + "anatomical_part": "Nasopharynx", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Scraping": { + "anatomical_part": "Oropharynx", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Swabbing": { + "anatomical_part": "Nasopharynx", + "collection_device": "Swabbing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Swabbing": { + "anatomical_part": "Oropharynx", + "collection_device": "Swabbing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Wash": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Wash": { + "anatomical_part": "Bronchus", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Wash": { + "anatomical_part": "Lung", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Wash": { + "anatomical_part": "Bronchiole", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Wash": { + "anatomical_part": "Alveolar sac", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Wash": { + "anatomical_part": "Pleural sac", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Wash": { + "anatomical_part": "Pleural cavity", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Wash": { + "anatomical_part": "Trachea", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Wash": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Wash": { + "anatomical_part": "Anterior Nares", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Wash": { + "anatomical_part": "Esophagus", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Wash": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Wash": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Wash": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Wash": { + "anatomical_part": "Nasopharynx", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Wash": { + "anatomical_part": "Oropharynx", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchoalveolar Lavage": { + "anatomical_part": "Not Applicable", + "collection_device": "Bronchoalveolar Lavage" + }, + "Gastric Lavage": { + "anatomical_part": "Not Applicable", + "collection_device": "Gastric Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Feces": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Feces", + "anatomical_material": "Not Applicable" + }, + "Mucus": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Mucus", + "anatomical_material": "Not Applicable" + }, + "Sputum": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Sputum", + "anatomical_material": "Not Applicable" + }, + "Sweat": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Sweat", + "anatomical_material": "Not Applicable" + }, + "Tear": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Tear", + "anatomical_material": "Not Applicable" + }, + "Urine": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Urine", + "anatomical_material": "Not Applicable" + }, + "Blood": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Blood", + "anatomical_material": "Not Applicable" + }, + "Cerebrospinal Fluid": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Not Applicable", + "anatomical_material": "Cerebrospinal Fluid" + }, + "Saliva": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Not Applicable", + "anatomical_material": "Saliva" + }, + "Tissue": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Not Applicable", + "anatomical_material": "Tissue" + } + } \ No newline at end of file diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index 8ecccf83..0078999f 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -44,15 +44,15 @@ def added_seq_inst_model(metadata, f_data, mapped_fields, heading): stderr.print(f"[red] Value {e} does not exist") sys.exit(1) if "nextseq" in run_name: - row[m_idx] = "Illumina NextSeq" + row[m_idx] = "Illumina NextSeq 500" elif "next_seq" in run_name: - row[m_idx] = "Illumina NextSeq" + row[m_idx] = "Illumina NextSeq 500" elif "miseq" in run_name: row[m_idx] = "Illumina MiSeq" elif "miseaq" in run_name: row[m_idx] = "Illumina MiSeq" elif "novaseq" in run_name: - row[m_idx] = "Illumina NovaSeq" + row[m_idx] = "Illumina NovaSeq 6000" else: log.error("Value %s is not defined in the mapping ", run_name) stderr.print(f"[red] Value {run_name} is not defined in the mapping") diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 2a22febc..6336bee0 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -571,6 +571,7 @@ "Fluid (Amniotic) [UBERON:0000173]", "Saliva [UBERON:0001836]", "Tissue [UBERON:0000479]", + "Placenta [UBERON:0001987]", "Not Applicable [GENEPIO:0001619]", "Not Collected [GENEPIO:0001620]", "Not Provided [GENEPIO:0001668]", From c211fa91e7cd096b11862cb9434aa73e21f0ce43 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 2 Sep 2022 11:48:45 +0200 Subject: [PATCH 0864/1454] lintin --- relecov_tools/ena_upload.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 6d35e55b..98dd2031 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -14,7 +14,7 @@ import sys import os -import ftplib +# import ftplib import relecov_tools.utils from relecov_tools.config_json import ConfigJson @@ -141,14 +141,11 @@ def create_structure_to_ena(self): df_study = df_study.rename(columns={"study_alias": "alias"}) df_study = df_study.rename(columns={"study_title": "title"}) - - """ df_study = df_schemas[["study_type", "study_abstract"]] df_study["alias"] = df_study["study_abstract"][0].rsplit(" ", 5)[0] df_study["title"] = df_study["study_abstract"] df_study.insert(3, "status", self.action) - """ # df_study alias title study_type status study_abstract From 1152f6c87687c496241b8db356e154db1d74eba8 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 2 Sep 2022 11:50:59 +0200 Subject: [PATCH 0865/1454] lintin2 --- relecov_tools/conf/configuration.json | 1979 ++++++++++++------------- relecov_tools/ena_upload.py | 3 +- 2 files changed, 990 insertions(+), 992 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 8d93a355..4625655d 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -220,993 +220,992 @@ "HUGTiP": "HUGTiP.json" }, "anatomical_material_collection_method": { - { - "Lower respiratory tract Aspiration": { - "anatomical_part": "Lower respiratory tract", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Aspiration": { - "anatomical_part": "Bronchus", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Aspiration": { - "anatomical_part": "Lung", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Aspiration": { - "anatomical_part": "Bronchiole", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Aspiration": { - "anatomical_part": "Alveolar sac", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Aspiration": { - "anatomical_part": "Pleural sac", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Aspiration": { - "anatomical_part": "Pleural cavity", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Aspiration": { - "anatomical_part": "Trachea", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Aspiration": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Aspiration": { - "anatomical_part": "Anterior Nares", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Aspiration": { - "anatomical_part": "Esophagus", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Aspiration": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Aspiration": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Aspiration": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Aspiration": { - "anatomical_part": "Nasopharynx", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Aspiration": { - "anatomical_part": "Oropharynx", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Vacuum Aspiration": { - "anatomical_part": "Lower respiratory tract", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Vacuum Aspiration": { - "anatomical_part": "Bronchus", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Vacuum Aspiration": { - "anatomical_part": "Lung", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Vacuum Aspiration": { - "anatomical_part": "Bronchiole", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Vacuum Aspiration": { - "anatomical_part": "Alveolar sac", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Vacuum Aspiration": { - "anatomical_part": "Pleural sac", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Vacuum Aspiration": { - "anatomical_part": "Pleural cavity", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Vacuum Aspiration": { - "anatomical_part": "Trachea", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Vacuum Aspiration": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Vacuum Aspiration": { - "anatomical_part": "Anterior Nares", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Vacuum Aspiration": { - "anatomical_part": "Esophagus", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Vacuum Aspiration": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Vacuum Aspiration": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Vacuum Aspiration": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Vacuum Aspiration": { - "anatomical_part": "Nasopharynx", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Vacuum Aspiration": { - "anatomical_part": "Oropharynx", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Biopsy": { - "anatomical_part": "Lower respiratory tract", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Biopsy": { - "anatomical_part": "Bronchus", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Biopsy": { - "anatomical_part": "Lung", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Biopsy": { - "anatomical_part": "Bronchiole", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Biopsy": { - "anatomical_part": "Alveolar sac", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Biopsy": { - "anatomical_part": "Pleural sac", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Biopsy": { - "anatomical_part": "Pleural cavity", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Biopsy": { - "anatomical_part": "Trachea", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Rectum Biopsy": { - "anatomical_part": "Rectum", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Skin Biopsy": { - "anatomical_part": "Skin", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Stomach Biopsy": { - "anatomical_part": "Stomach", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Biopsy": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Biopsy": { - "anatomical_part": "Anterior Nares", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Biopsy": { - "anatomical_part": "Esophagus", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Biopsy": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Biopsy": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Biopsy": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Duodenum Biopsy": { - "anatomical_part": "Duodenum", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Biopsy": { - "anatomical_part": "Nasopharynx", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Biopsy": { - "anatomical_part": "Oropharynx", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Needle Biopsy": { - "anatomical_part": "Lower respiratory tract", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Needle Biopsy": { - "anatomical_part": "Bronchus", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Needle Biopsy": { - "anatomical_part": "Lung", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Needle Biopsy": { - "anatomical_part": "Bronchiole", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Needle Biopsy": { - "anatomical_part": "Alveolar sac", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Needle Biopsy": { - "anatomical_part": "Pleural sac", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Needle Biopsy": { - "anatomical_part": "Pleural cavity", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Needle Biopsy": { - "anatomical_part": "Trachea", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Rectum Needle Biopsy": { - "anatomical_part": "Rectum", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Skin Needle Biopsy": { - "anatomical_part": "Skin", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Stomach Needle Biopsy": { - "anatomical_part": "Stomach", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Needle Biopsy": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Needle Biopsy": { - "anatomical_part": "Anterior Nares", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Needle Biopsy": { - "anatomical_part": "Esophagus", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Needle Biopsy": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Needle Biopsy": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Needle Biopsy": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Duodenum Needle Biopsy": { - "anatomical_part": "Duodenum", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Needle Biopsy": { - "anatomical_part": "Nasopharynx", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Needle Biopsy": { - "anatomical_part": "Oropharynx", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Lavage": { - "anatomical_part": "Lower respiratory tract", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Lavage": { - "anatomical_part": "Bronchus", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Lavage": { - "anatomical_part": "Lung", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Lavage": { - "anatomical_part": "Pleural sac", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Lavage": { - "anatomical_part": "Pleural cavity", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Lavage": { - "anatomical_part": "Trachea", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Lavage": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Lavage": { - "anatomical_part": "Anterior Nares", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Lavage": { - "anatomical_part": "Esophagus", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Lavage": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Lavage": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Lavage": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Lavage": { - "anatomical_part": "Nasopharynx", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Lavage": { - "anatomical_part": "Oropharynx", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Necropsy": { - "anatomical_part": "Lower respiratory tract", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Necropsy": { - "anatomical_part": "Bronchus", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Necropsy": { - "anatomical_part": "Lung", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Necropsy": { - "anatomical_part": "Bronchiole", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Necropsy": { - "anatomical_part": "Alveolar sac", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Necropsy": { - "anatomical_part": "Pleural sac", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Necropsy": { - "anatomical_part": "Pleural cavity", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Necropsy": { - "anatomical_part": "Trachea", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Rectum Necropsy": { - "anatomical_part": "Rectum", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Skin Necropsy": { - "anatomical_part": "Skin", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Stomach Necropsy": { - "anatomical_part": "Stomach", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Necropsy": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Necropsy": { - "anatomical_part": "Anterior Nares", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Necropsy": { - "anatomical_part": "Esophagus", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Necropsy": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Necropsy": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Necropsy": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Duodenum Necropsy": { - "anatomical_part": "Duodenum", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Necropsy": { - "anatomical_part": "Nasopharynx", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Necropsy": { - "anatomical_part": "Oropharynx", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Rinsing": { - "anatomical_part": "Lower respiratory tract", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Rinsing": { - "anatomical_part": "Bronchus", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Rinsing": { - "anatomical_part": "Lung", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Rinsing": { - "anatomical_part": "Bronchiole", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Rinsing": { - "anatomical_part": "Alveolar sac", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Rinsing": { - "anatomical_part": "Pleural sac", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Rinsing": { - "anatomical_part": "Pleural cavity", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Rinsing": { - "anatomical_part": "Trachea", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Rinsing": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Rinsing": { - "anatomical_part": "Anterior Nares", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Rinsing": { - "anatomical_part": "Esophagus", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Rinsing": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Rinsing": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Rinsing": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Rinsing": { - "anatomical_part": "Nasopharynx", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Rinsing": { - "anatomical_part": "Oropharynx", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Scraping": { - "anatomical_part": "Bronchiole", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Scraping": { - "anatomical_part": "Alveolar sac", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Scraping": { - "anatomical_part": "Pleural sac", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Scraping": { - "anatomical_part": "Pleural cavity", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Scraping": { - "anatomical_part": "Trachea", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Scraping": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Scraping": { - "anatomical_part": "Anterior Nares", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Scraping": { - "anatomical_part": "Esophagus", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Scraping": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Scraping": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Scraping": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Scraping": { - "anatomical_part": "Nasopharynx", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Scraping": { - "anatomical_part": "Oropharynx", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Swabbing": { - "anatomical_part": "Nasopharynx", - "collection_device": "Swabbing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Swabbing": { - "anatomical_part": "Oropharynx", - "collection_device": "Swabbing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Wash": { - "anatomical_part": "Lower respiratory tract", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Wash": { - "anatomical_part": "Bronchus", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Wash": { - "anatomical_part": "Lung", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Wash": { - "anatomical_part": "Bronchiole", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Wash": { - "anatomical_part": "Alveolar sac", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Wash": { - "anatomical_part": "Pleural sac", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Wash": { - "anatomical_part": "Pleural cavity", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Wash": { - "anatomical_part": "Trachea", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Wash": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Wash": { - "anatomical_part": "Anterior Nares", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Wash": { - "anatomical_part": "Esophagus", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Wash": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Wash": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Wash": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Wash": { - "anatomical_part": "Nasopharynx", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Wash": { - "anatomical_part": "Oropharynx", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchoalveolar Lavage": { - "anatomical_part": "Not Applicable", - "collection_device": "Bronchoalveolar Lavage" - }, - "Gastric Lavage": { - "anatomical_part": "Not Applicable", - "collection_device": "Gastric Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Feces": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Feces", - "anatomical_material": "Not Applicable" - }, - "Mucus": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Mucus", - "anatomical_material": "Not Applicable" - }, - "Sputum": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Sputum", - "anatomical_material": "Not Applicable" - }, - "Sweat": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Sweat", - "anatomical_material": "Not Applicable" - }, - "Tear": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Tear", - "anatomical_material": "Not Applicable" - }, - "Urine": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Urine", - "anatomical_material": "Not Applicable" - }, - "Blood": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Blood", - "anatomical_material": "Not Applicable" - }, - "Cerebrospinal Fluid": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Not Applicable", - "anatomical_material": "Cerebrospinal Fluid" - }, - "Saliva": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Not Applicable", - "anatomical_material": "Saliva" - }, - "Tissue": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Not Applicable", - "anatomical_material": "Tissue" - } - } \ No newline at end of file + "Lower respiratory tract Aspiration": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Aspiration": { + "anatomical_part": "Bronchus", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Aspiration": { + "anatomical_part": "Lung", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Aspiration": { + "anatomical_part": "Bronchiole", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Aspiration": { + "anatomical_part": "Alveolar sac", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Aspiration": { + "anatomical_part": "Pleural sac", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Aspiration": { + "anatomical_part": "Pleural cavity", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Aspiration": { + "anatomical_part": "Trachea", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Aspiration": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Aspiration": { + "anatomical_part": "Anterior Nares", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Aspiration": { + "anatomical_part": "Esophagus", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Aspiration": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Aspiration": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Aspiration": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Aspiration": { + "anatomical_part": "Nasopharynx", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Aspiration": { + "anatomical_part": "Oropharynx", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Vacuum Aspiration": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Vacuum Aspiration": { + "anatomical_part": "Bronchus", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Vacuum Aspiration": { + "anatomical_part": "Lung", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Vacuum Aspiration": { + "anatomical_part": "Bronchiole", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Vacuum Aspiration": { + "anatomical_part": "Alveolar sac", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Vacuum Aspiration": { + "anatomical_part": "Pleural sac", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Vacuum Aspiration": { + "anatomical_part": "Pleural cavity", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Vacuum Aspiration": { + "anatomical_part": "Trachea", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Vacuum Aspiration": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Vacuum Aspiration": { + "anatomical_part": "Anterior Nares", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Vacuum Aspiration": { + "anatomical_part": "Esophagus", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Vacuum Aspiration": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Vacuum Aspiration": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Vacuum Aspiration": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Vacuum Aspiration": { + "anatomical_part": "Nasopharynx", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Vacuum Aspiration": { + "anatomical_part": "Oropharynx", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Biopsy": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Biopsy": { + "anatomical_part": "Bronchus", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Biopsy": { + "anatomical_part": "Lung", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Biopsy": { + "anatomical_part": "Bronchiole", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Biopsy": { + "anatomical_part": "Alveolar sac", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Biopsy": { + "anatomical_part": "Pleural sac", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Biopsy": { + "anatomical_part": "Pleural cavity", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Biopsy": { + "anatomical_part": "Trachea", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Rectum Biopsy": { + "anatomical_part": "Rectum", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Skin Biopsy": { + "anatomical_part": "Skin", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Stomach Biopsy": { + "anatomical_part": "Stomach", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Biopsy": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Biopsy": { + "anatomical_part": "Anterior Nares", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Biopsy": { + "anatomical_part": "Esophagus", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Biopsy": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Biopsy": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Biopsy": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Duodenum Biopsy": { + "anatomical_part": "Duodenum", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Biopsy": { + "anatomical_part": "Nasopharynx", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Biopsy": { + "anatomical_part": "Oropharynx", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Needle Biopsy": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Needle Biopsy": { + "anatomical_part": "Bronchus", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Needle Biopsy": { + "anatomical_part": "Lung", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Needle Biopsy": { + "anatomical_part": "Bronchiole", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Needle Biopsy": { + "anatomical_part": "Alveolar sac", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Needle Biopsy": { + "anatomical_part": "Pleural sac", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Needle Biopsy": { + "anatomical_part": "Pleural cavity", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Needle Biopsy": { + "anatomical_part": "Trachea", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Rectum Needle Biopsy": { + "anatomical_part": "Rectum", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Skin Needle Biopsy": { + "anatomical_part": "Skin", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Stomach Needle Biopsy": { + "anatomical_part": "Stomach", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Needle Biopsy": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Needle Biopsy": { + "anatomical_part": "Anterior Nares", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Needle Biopsy": { + "anatomical_part": "Esophagus", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Needle Biopsy": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Needle Biopsy": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Needle Biopsy": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Duodenum Needle Biopsy": { + "anatomical_part": "Duodenum", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Needle Biopsy": { + "anatomical_part": "Nasopharynx", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Needle Biopsy": { + "anatomical_part": "Oropharynx", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Lavage": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Lavage": { + "anatomical_part": "Bronchus", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Lavage": { + "anatomical_part": "Lung", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Lavage": { + "anatomical_part": "Pleural sac", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Lavage": { + "anatomical_part": "Pleural cavity", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Lavage": { + "anatomical_part": "Trachea", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Lavage": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Lavage": { + "anatomical_part": "Anterior Nares", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Lavage": { + "anatomical_part": "Esophagus", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Lavage": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Lavage": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Lavage": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Lavage": { + "anatomical_part": "Nasopharynx", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Lavage": { + "anatomical_part": "Oropharynx", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Necropsy": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Necropsy": { + "anatomical_part": "Bronchus", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Necropsy": { + "anatomical_part": "Lung", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Necropsy": { + "anatomical_part": "Bronchiole", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Necropsy": { + "anatomical_part": "Alveolar sac", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Necropsy": { + "anatomical_part": "Pleural sac", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Necropsy": { + "anatomical_part": "Pleural cavity", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Necropsy": { + "anatomical_part": "Trachea", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Rectum Necropsy": { + "anatomical_part": "Rectum", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Skin Necropsy": { + "anatomical_part": "Skin", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Stomach Necropsy": { + "anatomical_part": "Stomach", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Necropsy": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Necropsy": { + "anatomical_part": "Anterior Nares", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Necropsy": { + "anatomical_part": "Esophagus", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Necropsy": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Necropsy": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Necropsy": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Duodenum Necropsy": { + "anatomical_part": "Duodenum", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Necropsy": { + "anatomical_part": "Nasopharynx", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Necropsy": { + "anatomical_part": "Oropharynx", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Rinsing": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Rinsing": { + "anatomical_part": "Bronchus", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Rinsing": { + "anatomical_part": "Lung", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Rinsing": { + "anatomical_part": "Bronchiole", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Rinsing": { + "anatomical_part": "Alveolar sac", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Rinsing": { + "anatomical_part": "Pleural sac", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Rinsing": { + "anatomical_part": "Pleural cavity", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Rinsing": { + "anatomical_part": "Trachea", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Rinsing": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Rinsing": { + "anatomical_part": "Anterior Nares", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Rinsing": { + "anatomical_part": "Esophagus", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Rinsing": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Rinsing": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Rinsing": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Rinsing": { + "anatomical_part": "Nasopharynx", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Rinsing": { + "anatomical_part": "Oropharynx", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Scraping": { + "anatomical_part": "Bronchiole", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Scraping": { + "anatomical_part": "Alveolar sac", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Scraping": { + "anatomical_part": "Pleural sac", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Scraping": { + "anatomical_part": "Pleural cavity", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Scraping": { + "anatomical_part": "Trachea", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Scraping": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Scraping": { + "anatomical_part": "Anterior Nares", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Scraping": { + "anatomical_part": "Esophagus", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Scraping": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Scraping": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Scraping": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Scraping": { + "anatomical_part": "Nasopharynx", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Scraping": { + "anatomical_part": "Oropharynx", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Swabbing": { + "anatomical_part": "Nasopharynx", + "collection_device": "Swabbing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Swabbing": { + "anatomical_part": "Oropharynx", + "collection_device": "Swabbing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Wash": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Wash": { + "anatomical_part": "Bronchus", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Wash": { + "anatomical_part": "Lung", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Wash": { + "anatomical_part": "Bronchiole", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Wash": { + "anatomical_part": "Alveolar sac", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Wash": { + "anatomical_part": "Pleural sac", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Wash": { + "anatomical_part": "Pleural cavity", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Wash": { + "anatomical_part": "Trachea", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Wash": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Wash": { + "anatomical_part": "Anterior Nares", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Wash": { + "anatomical_part": "Esophagus", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Wash": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Wash": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Wash": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Wash": { + "anatomical_part": "Nasopharynx", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Wash": { + "anatomical_part": "Oropharynx", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchoalveolar Lavage": { + "anatomical_part": "Not Applicable", + "collection_device": "Bronchoalveolar Lavage" + }, + "Gastric Lavage": { + "anatomical_part": "Not Applicable", + "collection_device": "Gastric Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Feces": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Feces", + "anatomical_material": "Not Applicable" + }, + "Mucus": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Mucus", + "anatomical_material": "Not Applicable" + }, + "Sputum": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Sputum", + "anatomical_material": "Not Applicable" + }, + "Sweat": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Sweat", + "anatomical_material": "Not Applicable" + }, + "Tear": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Tear", + "anatomical_material": "Not Applicable" + }, + "Urine": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Urine", + "anatomical_material": "Not Applicable" + }, + "Blood": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Blood", + "anatomical_material": "Not Applicable" + }, + "Cerebrospinal Fluid": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Not Applicable", + "anatomical_material": "Cerebrospinal Fluid" + }, + "Saliva": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Not Applicable", + "anatomical_material": "Saliva" + }, + "Tissue": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Not Applicable", + "anatomical_material": "Tissue" + } + } \ No newline at end of file diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 98dd2031..c59365d4 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -348,9 +348,8 @@ def create_structure_to_ena(self): file_paths.update(file_paths_r2) # submit data to webin ftp server. It should only upload fastq files in case the action is ADD. - # When the action is MODIFY rthe fastq are already submitted. + # # When the action is MODIFY rthe fastq are already submitted """ - if self.action == "ADD" or self.action == "add": session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) From 0b76f96bdad7dc2c1064db905d9fcd8553a715e1 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 3 Sep 2022 11:06:22 +0200 Subject: [PATCH 0866/1454] moved read_metada (to read_excel), and write_file (to write_excel) to utils. Read metadata used handling_files, but skyping the process by calling mapping_metadata and return to the main function the info --- relecov_tools/metadata_homogeneizer.py | 206 ++++++++---------- .../schema/institution_schemas/ISCIII.json | 40 ++-- relecov_tools/utils.py | 48 ++++ 3 files changed, 154 insertions(+), 140 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index ea926f0a..97473d6b 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -3,8 +3,7 @@ import sys import logging import rich.console -import openpyxl -from itertools import islice + import relecov_tools.utils from relecov_tools.config_json import ConfigJson @@ -19,7 +18,6 @@ class MetadataHomogeneizer: """MetadataHomogeneizer object""" - def __init__(self, institution=None, directory=None, output_folder=None): self.config_json = ConfigJson() self.heading = self.config_json.get_configuration("metadata_lab_heading") @@ -50,7 +48,7 @@ def __init__(self, institution=None, directory=None, output_folder=None): self.mapping_json_data = relecov_tools.utils.read_json_file(mapping_json_file) try: - lab_metadata = self.mapping_json_data["required_files"]["meta_file"][ + lab_metadata = self.mapping_json_data["required_files"]["metadata_file"][ "file_name" ] except KeyError: @@ -62,7 +60,8 @@ def __init__(self, institution=None, directory=None, output_folder=None): log.error("Metadata File %s does not exists", metadata_path) stderr.print("[red] Metadata File " + metadata_path + "does not exists") sys.exit(1) - self.lab_metadata = metadata_path + self.lab_metadata = self.mapping_json_data["required_files"]["metadata_file"] + self.lab_metadata["file_name"] = metadata_path # Check if python file is defined function_file = self.mapping_json_data["pyhon_file"] if function_file == "": @@ -82,7 +81,7 @@ def __init__(self, institution=None, directory=None, output_folder=None): self.additional_files = [] if len(self.mapping_json_data["required_files"]) > 1: for key, values in self.mapping_json_data["required_files"].items(): - if key == "meta_file": + if key == "metadata_file": continue if values["file_name"] == "": self.additional_files.append(values) @@ -101,27 +100,8 @@ def __init__(self, institution=None, directory=None, output_folder=None): else: self.output_folder = output_folder - def read_metadata_file(self): - """Read the input metadata file""" - wb_file = openpyxl.load_workbook(self.lab_metadata, data_only=True) - ws_metadata_lab = wb_file["Sheet"] - heading = [i.value.strip() for i in ws_metadata_lab[1] if i.value] - ws_data = [] - for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row): - l_row = list(row) - data_row = {} - # Ignore the empty rows - # guessing that row 1 and 2 with no data are empty rows - if l_row[0] is None and l_row[1] is None: - continue - for idx in range(0, len(heading)): - data_row[heading[idx]] = l_row[idx] - ws_data.append(data_row) - # import pdb; pdb.set_trace() - return ws_data - def mapping_metadata(self, ws_data): - map_fields = self.mapping_json_data["required_files"]["meta_file"][ + map_fields = self.mapping_json_data["required_files"]["metadata_file"][ "mapped_fields" ] map_data = [] @@ -134,11 +114,9 @@ def mapping_metadata(self, ws_data): return map_data - def additional_fields(self, mapped_data): + def add_fixed_fields(self, mapped_data): add_data = [self.heading] - fixed_fields = self.mapping_json_data["required_files"]["meta_file"][ - "fixed_fields" - ] + fixed_fields = self.mapping_json_data["fixed_fields"] for row in mapped_data: new_row_data = [] for field in self.heading: @@ -152,110 +130,98 @@ def additional_fields(self, mapped_data): add_data.append(new_row_data) return add_data - def handling_additional_files(self, additional_data): - - for additional_file in self.additional_files: - if additional_file["file_name"] != "": - f_name = additional_file["file_name"] - stderr.print("[blue] Start processing additional file " + f_name) - if f_name.endswith(".json"): - data = relecov_tools.utils.read_json_file(f_name) - elif f_name.endswith(".tsv"): - data = relecov_tools.utils.read_csv_file_return_dict(f_name, "\t") - elif f_name.endswith(".csv"): - data = relecov_tools.utils.read_csv_file_return_dict(f_name, ",") - else: - log.error("Additional file extension %s is not supported ", f_name) + def handling_files(self, file_data, additional_data): + """Added information based on the required file configuration. + The first time this function is called is for mapping the laboratory + metadata to ISCIII. For this time mapping_metadata method is used. + and return the list that is going to be used later for adding/modifing + information + """ + if file_data["file_name"] != "": + f_name = file_data["file_name"] + stderr.print("[blue] Start processing additional file " + f_name) + if f_name.endswith(".json"): + data = relecov_tools.utils.read_json_file(f_name) + elif f_name.endswith(".tsv"): + data = relecov_tools.utils.read_csv_file_return_dict(f_name, "\t") + elif f_name.endswith(".csv"): + data = relecov_tools.utils.read_csv_file_return_dict(f_name, ",") + elif f_name.endswith(".xlsx"): + data = relecov_tools.utils.read_execl_file(f_name, "Sheet") + return self.mapping_metadata(data) + else: + log.error("Additional file extension %s is not supported ", f_name) + stderr.print( + "[red] Additional file extension " + f_name + " is not supported" + ) + sys.exit(1) + else: + data = "" + if file_data["function"] == "None": + mapping_idx = self.heading.index(file_data["mapped_key"]) + for row in additional_data[1:]: + # new_row_data = [] + s_value = str(row[mapping_idx]) + try: + item_data = data[s_value] + except KeyError: + log.error( + "Additional file %s does not have the information for %s ", + f_name, + s_value, + ) stderr.print( - "[red] Additional file extension " + "[yellow] Additional file " + f_name - + " is not supported" + + " does not have information for " + + str(s_value) ) - sys.exit(1) - - else: - data = "" - - if additional_file["function"] == "None": - mapping_idx = self.heading.index(additional_file["mapped_key"]) - for row in additional_data[1:]: - # new_row_data = [] - s_value = str(row[mapping_idx]) + continue + # sys.exit(1) + for m_field, f_field in file_data["mapped_fields"].items(): try: - item_data = data[s_value] - except KeyError: - log.error( - "Additional file %s does not have the information for %s ", - f_name, - s_value, - ) - stderr.print( - "[yellow] Additional file " - + f_name - + " does not have information for " - + str(s_value) - ) - continue - # sys.exit(1) - for m_field, f_field in additional_file["mapped_fields"].items(): - try: - meta_idx = self.heading.index(m_field) - except ValueError as e: - log.error("Field %s does not exist in Metadata ", e) - stderr.print(f"[red] Field {e} does not exist") - sys.exit(1) - row[meta_idx] = item_data[f_field] - - # import pdb; pdb.set_trace() - else: - func_name = additional_file["function"] - stderr.print("[yellow] Start processing function " + func_name) - exec( - "from relecov_tools.institution_scripts." - + self.institution - + " import " - + func_name - ) - eval( - func_name - + "(additional_data, data, additional_file['mapped_fields'], self.heading)" - ) + meta_idx = self.heading.index(m_field) + except ValueError as e: + log.error("Field %s does not exist in Metadata ", e) + stderr.print(f"[red] Field {e} does not exist") + sys.exit(1) + row[meta_idx] = item_data[f_field] + + # import pdb; pdb.set_trace() + else: + func_name = file_data["function"] + stderr.print("[yellow] Start processing function " + func_name) + exec( + "from relecov_tools.institution_scripts." + + self.institution + + " import " + + func_name + ) + eval( + func_name + + "(additional_data, data, file_data['mapped_fields'], self.heading)" + ) stderr.print("[green] Succesful processing of additional file ") return additional_data - def write_to_excel_file(self, data, f_name): - book = openpyxl.Workbook() - sheet = book.active - - for row in data: - sheet.append(row) - # adding one column with row number - sheet.insert_cols(1) - sheet["A1"] = "Campo" - counter = 1 - for i in range(len(data)): - idx = "A" + str(counter + 1) - sheet[idx] = counter - counter += 1 - # adding 3 empty rows - for x in range(3): - sheet.insert_rows(1) - sheet.title = "METADATA_LAB" - book.save(f_name) - return - def converting_metadata(self): stderr.print("[blue] Reading the metadata file to convert") - ws_data = self.read_metadata_file() - mapped_data = self.mapping_metadata(ws_data) + # ws_data = self.read_metadata_file() + # mapped_data = self.mapping_metadata(ws_data) + mapped_data = self.handling_files(self.lab_metadata, "") stderr.print("[green] Successful conversion mapping to ISCIII metadata") stderr.print("[blue] Adding fixed information") - additional_data = self.additional_fields(mapped_data) + additional_data = self.add_fixed_fields(mapped_data) # Fetch the additional files and include the information in metadata stderr.print("[blue] reading and mapping de information that are in files") - converted_data = self.handling_additional_files(additional_data) + for additional_file in self.additional_files: + additional_data = self.handling_files(additional_file, additional_data) f_name = os.path.join(self.output_folder, "converted_metadata_lab.xlsx") stderr.print("[blue] Dumping information to excel") - self.write_to_excel_file(converted_data, f_name) + post_process = {"insert_rows": 3, "insert_cols": 1} + relecov_tools.utils.write_to_excel_file( + additional_data, f_name, "METADATA_LAB", post_process + ) + stderr.print("[green] Complete process for mapping to ISCIII metadata") return diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 77aa3391..e7416018 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -1,7 +1,7 @@ { "pyhon_file": "ISCIII.py", "required_files": { - "meta_file": { + "metadata_file": { "file_name": "new_lab_metadata.xlsx", "mapped_fields": { "Public Health sample id (SIVIES)": "Código SiViEs", @@ -18,25 +18,6 @@ "Host Gender": "Sexo", "Diagnostic Pcr Ct Value 1": "PCR genE" }, - "fixed_fields": { - "Submitting Institution": "Instituto de Salud Carlos III", - "Biological Sample Storage Condition": "-80 C", - "Rna Extraction Protocol": "RT-PCR", - "Purpose of sampling": "Surveillance", - "Specimen source": "Nasopharyngeal exudate", - "Environmental System": "Swab", - "Host": "Human", - "Library Preparation Kit": "Illumina DNA Prep", - "Enrichment Protocol": "Amplicon", - "Enrichment panel/assay": "ARTIC", - "Source material": "Viral RNA", - "Capture method": "PCR", - "Sequencing technique": "Amplicon", - "Library Layout": "Paired", - "Gene Name 1": "ORF E", - "Diagnostic Pcr Ct Value 1": "", - "Authors": "" - }, "function": "None" }, "sample_file": { @@ -112,5 +93,24 @@ "mapped_key": "Sample ID given for sequencing", "function": "None" } + }, + "fixed_fields": { + "Submitting Institution": "Instituto de Salud Carlos III", + "Biological Sample Storage Condition": "-80 C", + "Rna Extraction Protocol": "RT-PCR", + "Purpose of sampling": "Surveillance", + "Specimen source": "Nasopharyngeal exudate", + "Environmental System": "Swab", + "Host": "Human", + "Library Preparation Kit": "Illumina DNA Prep", + "Enrichment Protocol": "Amplicon", + "Enrichment panel/assay": "ARTIC", + "Source material": "Viral RNA", + "Capture method": "PCR", + "Sequencing technique": "Amplicon", + "Library Layout": "Paired", + "Gene Name 1": "ORF E", + "Diagnostic Pcr Ct Value 1": "", + "Authors": "" } } diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 18c00a44..75c6a201 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -9,6 +9,8 @@ from rich.console import Console import questionary import json +import openpyxl +from itertools import islice log = logging.getLogger(__name__) @@ -32,6 +34,28 @@ def read_json_file(j_file): return data +def read_execl_file(f_name, sheet_name): + """Read the input excel file and give the information in a list + of dictionaries + """ + wb_file = openpyxl.load_workbook(f_name, data_only=True) + ws_metadata_lab = wb_file[sheet_name] + heading = [i.value.strip() for i in ws_metadata_lab[1] if i.value] + ws_data = [] + for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row): + l_row = list(row) + data_row = {} + # Ignore the empty rows + # guessing that row 1 and 2 with no data are empty rows + if l_row[0] is None and l_row[1] is None: + continue + for idx in range(0, len(heading)): + data_row[heading[idx]] = l_row[idx] + ws_data.append(data_row) + + return ws_data + + def read_csv_file_return_dict(file_name, sep): """Read csv or tsv file, according to separator, and return a dictionary where the main key is the first column @@ -103,6 +127,30 @@ def save_local_md5(file_name, md5_value): return True +def write_to_excel_file(data, f_name, sheet_name, post_process=None): + book = openpyxl.Workbook() + sheet = book.active + + for row in data: + sheet.append(row) + # adding one column with row number + if "insert_cols" in post_process: + sheet.insert_cols(post_process["insert_cols"]) + sheet["A1"] = "Campo" + counter = 1 + for i in range(len(data)): + idx = "A" + str(counter + 1) + sheet[idx] = counter + counter += 1 + # adding 3 empty rows + if "insert_rows" in post_process: + for x in range(post_process["insert_rows"]): + sheet.insert_rows(1) + sheet.title = sheet_name + book.save(f_name) + return + + def rich_force_colors(): """ Check if any environment variables are set to force Rich to use coloured output From 9d260fa9617c2f013dc1bbef6b099c483ab7c87d Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 3 Sep 2022 11:10:26 +0200 Subject: [PATCH 0867/1454] change pyhon by python in the ISCIII.json schema --- relecov_tools/metadata_homogeneizer.py | 2 +- relecov_tools/schema/institution_schemas/ISCIII.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 97473d6b..acd016fb 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -63,7 +63,7 @@ def __init__(self, institution=None, directory=None, output_folder=None): self.lab_metadata = self.mapping_json_data["required_files"]["metadata_file"] self.lab_metadata["file_name"] = metadata_path # Check if python file is defined - function_file = self.mapping_json_data["pyhon_file"] + function_file = self.mapping_json_data["python_file"] if function_file == "": self.function_file = None else: diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index e7416018..26e7283a 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -1,5 +1,5 @@ { - "pyhon_file": "ISCIII.py", + "python_file": "ISCIII.py", "required_files": { "metadata_file": { "file_name": "new_lab_metadata.xlsx", From c008d6272e2f3b9031226ad37f960955dacac41d Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 3 Sep 2022 11:12:04 +0200 Subject: [PATCH 0868/1454] fixing liting --- relecov_tools/metadata_homogeneizer.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index acd016fb..6f5404e9 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -18,6 +18,7 @@ class MetadataHomogeneizer: """MetadataHomogeneizer object""" + def __init__(self, institution=None, directory=None, output_folder=None): self.config_json = ConfigJson() self.heading = self.config_json.get_configuration("metadata_lab_heading") From 68b3dd9df6bae3a9a6d5f6c89409936732466cce Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 3 Sep 2022 11:59:26 +0200 Subject: [PATCH 0869/1454] create in configuration.json the topic headings, to include inside all headings that were split in configuration.json --- relecov_tools/conf/configuration.json | 143 +++++++++++++------------ relecov_tools/metadata_homogeneizer.py | 2 +- 2 files changed, 74 insertions(+), 71 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 4625655d..c1c49e48 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -1,54 +1,75 @@ { - "metadata_lab_heading": [ - "Public Health sample id (SIVIES)", - "Sample ID given by originating laboratory", - "Sample ID given by the submitting laboratory", - "Sample ID given in the microbiology lab", - "Sample ID given if multiple rna-extraction or passages", - "Sample ID given for sequencing", - "ENA Sample ID", - "GISAID Virus Name", - "GISAID id", - "Originating Laboratory", - "Submitting Institution", - "Sample Collection Date", - "Sample Received Date", - "Purpose of sampling", - "Biological Sample Storage Condition", - "Specimen source", - "Environmental Material", - "Environmental System", - "Collection Device", - "Host", - "Host Age", - "Host Gender", - "Sequencing Date", - "Rna Extraction Protocol", - "Commercial All-in-one library kit", - "Library Preparation Kit", - "Enrichment Protocol", - "If Enrichment Protocol Is Other, Specify", - "Enrichment panel/assay", - "If Enrichment panel/assay Is Other, Specify", - "Enrichment panel/assay version", - "Number Of Samples In Run", - "Runid", - "Sequencing Instrument Model", - "Flowcell Kit", - "Source material", - "Capture method", - "Sequencing technique", - "Library Layout", - "Gene Name 1", - "Diagnostic Pcr Ct Value 1", - "Gene Name 2", - "Diagnostic Pcr Ct Value-2", - "Analysis Authors", - "Author Submitter", - "Authors", - "Sequence file R1 fastq", - "Sequence file R2 fastq" - ], + "headings": { + "metadata_lab_heading": [ + "Public Health sample id (SIVIES)", + "Sample ID given by originating laboratory", + "Sample ID given by the submitting laboratory", + "Sample ID given in the microbiology lab", + "Sample ID given if multiple rna-extraction or passages", + "Sample ID given for sequencing", + "ENA Sample ID", + "GISAID Virus Name", + "GISAID id", + "Originating Laboratory", + "Submitting Institution", + "Sample Collection Date", + "Sample Received Date", + "Purpose of sampling", + "Biological Sample Storage Condition", + "Specimen source", + "Environmental Material", + "Environmental System", + "Collection Device", + "Host", + "Host Age", + "Host Gender", + "Sequencing Date", + "Rna Extraction Protocol", + "Commercial All-in-one library kit", + "Library Preparation Kit", + "Enrichment Protocol", + "If Enrichment Protocol Is Other, Specify", + "Enrichment panel/assay", + "If Enrichment panel/assay Is Other, Specify", + "Enrichment panel/assay version", + "Number Of Samples In Run", + "Runid", + "Sequencing Instrument Model", + "Flowcell Kit", + "Source material", + "Capture method", + "Sequencing technique", + "Library Layout", + "Gene Name 1", + "Diagnostic Pcr Ct Value 1", + "Gene Name 2", + "Diagnostic Pcr Ct Value-2", + "Analysis Authors", + "Author Submitter", + "Authors", + "Sequence file R1 fastq", + "Sequence file R2 fastq" + ], + "long_table_heading": [ + "SAMPLE", + "CHROM", + "POS", + "REF", + "ALT", + "FILTER", + "DP", + "REF_DP", + "ALT_DP", + "AF", + "GENE", + "EFFECT", + "HGVS_C", + "HGVS_P", + "HGVS_P_1LETTER", + "CALLER", + "LINEAGE" + ] + }, "gisaid_csv_headers": [ "submitter", "covv_virus_name", @@ -196,25 +217,6 @@ }, "md5_file_name": "md5_check_file.csv", "checklist": "ERC000033", - "long_table_heading": [ - "SAMPLE", - "CHROM", - "POS", - "REF", - "ALT", - "FILTER", - "DP", - "REF_DP", - "ALT_DP", - "AF", - "GENE", - "EFFECT", - "HGVS_C", - "HGVS_P", - "HGVS_P_1LETTER", - "CALLER", - "LINEAGE" - ], "mapping_file": { "ISCIII": "ISCIII.json", "HUGTiP": "HUGTiP.json" @@ -1208,4 +1210,5 @@ "body_product": "Not Applicable", "anatomical_material": "Tissue" } - } \ No newline at end of file + } +} diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 6f5404e9..e3a81f17 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -21,7 +21,7 @@ class MetadataHomogeneizer: def __init__(self, institution=None, directory=None, output_folder=None): self.config_json = ConfigJson() - self.heading = self.config_json.get_configuration("metadata_lab_heading") + self.heading = self.config_json.get_topic_data("headings", "metadata_lab_heading") if institution is None: self.institution = relecov_tools.utils.prompt_selection( From 3b0f96272e366f28f82c95ccce71b2437130997b Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 3 Sep 2022 12:02:01 +0200 Subject: [PATCH 0870/1454] moved long table heading inside headings --- relecov_tools/long_table_parse.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index eb11f8e3..f6ef4edf 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -61,7 +61,7 @@ def __init__(self, file_path=None, output_directory=None): Path(self.output_directory).mkdir(parents=True, exist_ok=True) config_json = ConfigJson() - self.long_table_heading = config_json.get_configuration("long_table_heading") + self.long_table_heading = config_json.get_topic_data("headings", "long_table_heading") def validate_file(self, heading): """Check if long table file has all mandatory fields defined in From 780220ab2c1ed5a9a3023536ba39cbade36e36e7 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 3 Sep 2022 12:02:55 +0200 Subject: [PATCH 0871/1454] liting --- relecov_tools/long_table_parse.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index f6ef4edf..4e4b79a7 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -61,7 +61,9 @@ def __init__(self, file_path=None, output_directory=None): Path(self.output_directory).mkdir(parents=True, exist_ok=True) config_json = ConfigJson() - self.long_table_heading = config_json.get_topic_data("headings", "long_table_heading") + self.long_table_heading = config_json.get_topic_data( + "headings", "long_table_heading" + ) def validate_file(self, heading): """Check if long table file has all mandatory fields defined in From a9a869d2ae19dbf11001b872d1777034ba34de46 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 3 Sep 2022 12:04:20 +0200 Subject: [PATCH 0872/1454] liting --- relecov_tools/metadata_homogeneizer.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index e3a81f17..29dde8b1 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -21,7 +21,9 @@ class MetadataHomogeneizer: def __init__(self, institution=None, directory=None, output_folder=None): self.config_json = ConfigJson() - self.heading = self.config_json.get_topic_data("headings", "metadata_lab_heading") + self.heading = self.config_json.get_topic_data( + "headings", "metadata_lab_heading" + ) if institution is None: self.institution = relecov_tools.utils.prompt_selection( From b386d002dd4c62636a63b837805d7cdc82b7e645 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 4 Sep 2022 09:27:56 +0200 Subject: [PATCH 0873/1454] defined processed_metadata function to do the first mapping --- relecov_tools/metadata_homogeneizer.py | 37 +++++++++++++++----------- 1 file changed, 21 insertions(+), 16 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 29dde8b1..eb402dbe 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -65,6 +65,22 @@ def __init__(self, institution=None, directory=None, output_folder=None): sys.exit(1) self.lab_metadata = self.mapping_json_data["required_files"]["metadata_file"] self.lab_metadata["file_name"] = metadata_path + + self.additional_files = [] + if len(self.mapping_json_data["required_files"]) > 1: + for key, values in self.mapping_json_data["required_files"].items(): + if key == "metadata_file": + continue + if values["file_name"] == "": + self.additional_files.append(values) + continue + f_path = os.path.join(directory, values["file_name"]) + if not os.path.isfile(f_path): + log.error("Additional file %s does not exist ", f_path) + stderr.print("[red] Additional file " + f_path + " does not exist") + sys.exit(1) + values["file_name"] = f_path + self.additional_files.append(values) # Check if python file is defined function_file = self.mapping_json_data["python_file"] if function_file == "": @@ -81,27 +97,13 @@ def __init__(self, institution=None, directory=None, output_folder=None): + " does not exist" ) sys.exit(1) - self.additional_files = [] - if len(self.mapping_json_data["required_files"]) > 1: - for key, values in self.mapping_json_data["required_files"].items(): - if key == "metadata_file": - continue - if values["file_name"] == "": - self.additional_files.append(values) - continue - f_path = os.path.join(directory, values["file_name"]) - if not os.path.isfile(f_path): - log.error("Additional file %s does not exist ", f_path) - stderr.print("[red] Additional file " + f_path + " does not exist") - sys.exit(1) - values["file_name"] = f_path - self.additional_files.append(values) if output_folder is None: self.output_folder = relecov_tools.utils.prompt_path( msg="Select the output folder" ) else: self.output_folder = output_folder + self.processed_metadata = False def mapping_metadata(self, ws_data): map_fields = self.mapping_json_data["required_files"]["metadata_file"][ @@ -151,7 +153,6 @@ def handling_files(self, file_data, additional_data): data = relecov_tools.utils.read_csv_file_return_dict(f_name, ",") elif f_name.endswith(".xlsx"): data = relecov_tools.utils.read_execl_file(f_name, "Sheet") - return self.mapping_metadata(data) else: log.error("Additional file extension %s is not supported ", f_name) stderr.print( @@ -160,6 +161,10 @@ def handling_files(self, file_data, additional_data): sys.exit(1) else: data = "" + if not self.processed_metadata: + self.processed_metadata = True + return self.mapping_metadata(data) + if file_data["function"] == "None": mapping_idx = self.heading.index(file_data["mapped_key"]) for row in additional_data[1:]: From 0bc86901de9185935338b94e7bb40696f3b86696 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 4 Sep 2022 09:28:48 +0200 Subject: [PATCH 0874/1454] split anatomical material in a separated file --- ...anatomical_material_collection_method.json | 990 ++++++++++++++++++ relecov_tools/conf/configuration.json | 990 ------------------ 2 files changed, 990 insertions(+), 990 deletions(-) create mode 100644 relecov_tools/conf/anatomical_material_collection_method.json diff --git a/relecov_tools/conf/anatomical_material_collection_method.json b/relecov_tools/conf/anatomical_material_collection_method.json new file mode 100644 index 00000000..a5060f9a --- /dev/null +++ b/relecov_tools/conf/anatomical_material_collection_method.json @@ -0,0 +1,990 @@ +{ + "Lower respiratory tract Aspiration": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Aspiration": { + "anatomical_part": "Bronchus", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Aspiration": { + "anatomical_part": "Lung", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Aspiration": { + "anatomical_part": "Bronchiole", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Aspiration": { + "anatomical_part": "Alveolar sac", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Aspiration": { + "anatomical_part": "Pleural sac", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Aspiration": { + "anatomical_part": "Pleural cavity", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Aspiration": { + "anatomical_part": "Trachea", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Aspiration": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Aspiration": { + "anatomical_part": "Anterior Nares", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Aspiration": { + "anatomical_part": "Esophagus", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Aspiration": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Aspiration": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Aspiration": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Aspiration": { + "anatomical_part": "Nasopharynx", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Aspiration": { + "anatomical_part": "Oropharynx", + "collection_device": "Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Vacuum Aspiration": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Vacuum Aspiration": { + "anatomical_part": "Bronchus", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Vacuum Aspiration": { + "anatomical_part": "Lung", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Vacuum Aspiration": { + "anatomical_part": "Bronchiole", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Vacuum Aspiration": { + "anatomical_part": "Alveolar sac", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Vacuum Aspiration": { + "anatomical_part": "Pleural sac", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Vacuum Aspiration": { + "anatomical_part": "Pleural cavity", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Vacuum Aspiration": { + "anatomical_part": "Trachea", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Vacuum Aspiration": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Vacuum Aspiration": { + "anatomical_part": "Anterior Nares", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Vacuum Aspiration": { + "anatomical_part": "Esophagus", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Vacuum Aspiration": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Vacuum Aspiration": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Vacuum Aspiration": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Vacuum Aspiration": { + "anatomical_part": "Nasopharynx", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Vacuum Aspiration": { + "anatomical_part": "Oropharynx", + "collection_device": "Vacuum Aspiration", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Biopsy": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Biopsy": { + "anatomical_part": "Bronchus", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Biopsy": { + "anatomical_part": "Lung", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Biopsy": { + "anatomical_part": "Bronchiole", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Biopsy": { + "anatomical_part": "Alveolar sac", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Biopsy": { + "anatomical_part": "Pleural sac", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Biopsy": { + "anatomical_part": "Pleural cavity", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Biopsy": { + "anatomical_part": "Trachea", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Rectum Biopsy": { + "anatomical_part": "Rectum", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Skin Biopsy": { + "anatomical_part": "Skin", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Stomach Biopsy": { + "anatomical_part": "Stomach", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Biopsy": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Biopsy": { + "anatomical_part": "Anterior Nares", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Biopsy": { + "anatomical_part": "Esophagus", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Biopsy": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Biopsy": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Biopsy": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Duodenum Biopsy": { + "anatomical_part": "Duodenum", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Biopsy": { + "anatomical_part": "Nasopharynx", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Biopsy": { + "anatomical_part": "Oropharynx", + "collection_device": "Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Needle Biopsy": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Needle Biopsy": { + "anatomical_part": "Bronchus", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Needle Biopsy": { + "anatomical_part": "Lung", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Needle Biopsy": { + "anatomical_part": "Bronchiole", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Needle Biopsy": { + "anatomical_part": "Alveolar sac", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Needle Biopsy": { + "anatomical_part": "Pleural sac", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Needle Biopsy": { + "anatomical_part": "Pleural cavity", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Needle Biopsy": { + "anatomical_part": "Trachea", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Rectum Needle Biopsy": { + "anatomical_part": "Rectum", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Skin Needle Biopsy": { + "anatomical_part": "Skin", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Stomach Needle Biopsy": { + "anatomical_part": "Stomach", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Needle Biopsy": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Needle Biopsy": { + "anatomical_part": "Anterior Nares", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Needle Biopsy": { + "anatomical_part": "Esophagus", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Needle Biopsy": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Needle Biopsy": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Needle Biopsy": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Duodenum Needle Biopsy": { + "anatomical_part": "Duodenum", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Needle Biopsy": { + "anatomical_part": "Nasopharynx", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Needle Biopsy": { + "anatomical_part": "Oropharynx", + "collection_device": "Needle Biopsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Lavage": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Lavage": { + "anatomical_part": "Bronchus", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Lavage": { + "anatomical_part": "Lung", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Lavage": { + "anatomical_part": "Pleural sac", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Lavage": { + "anatomical_part": "Pleural cavity", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Lavage": { + "anatomical_part": "Trachea", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Lavage": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Lavage": { + "anatomical_part": "Anterior Nares", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Lavage": { + "anatomical_part": "Esophagus", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Lavage": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Lavage": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Lavage": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Lavage": { + "anatomical_part": "Nasopharynx", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Lavage": { + "anatomical_part": "Oropharynx", + "collection_device": "Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Necropsy": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Necropsy": { + "anatomical_part": "Bronchus", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Necropsy": { + "anatomical_part": "Lung", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Necropsy": { + "anatomical_part": "Bronchiole", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Necropsy": { + "anatomical_part": "Alveolar sac", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Necropsy": { + "anatomical_part": "Pleural sac", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Necropsy": { + "anatomical_part": "Pleural cavity", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Necropsy": { + "anatomical_part": "Trachea", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Rectum Necropsy": { + "anatomical_part": "Rectum", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Skin Necropsy": { + "anatomical_part": "Skin", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Stomach Necropsy": { + "anatomical_part": "Stomach", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Necropsy": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Necropsy": { + "anatomical_part": "Anterior Nares", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Necropsy": { + "anatomical_part": "Esophagus", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Necropsy": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Necropsy": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Necropsy": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Duodenum Necropsy": { + "anatomical_part": "Duodenum", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Necropsy": { + "anatomical_part": "Nasopharynx", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Necropsy": { + "anatomical_part": "Oropharynx", + "collection_device": "Necropsy", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Rinsing": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Rinsing": { + "anatomical_part": "Bronchus", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Rinsing": { + "anatomical_part": "Lung", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Rinsing": { + "anatomical_part": "Bronchiole", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Rinsing": { + "anatomical_part": "Alveolar sac", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Rinsing": { + "anatomical_part": "Pleural sac", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Rinsing": { + "anatomical_part": "Pleural cavity", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Rinsing": { + "anatomical_part": "Trachea", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Rinsing": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Rinsing": { + "anatomical_part": "Anterior Nares", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Rinsing": { + "anatomical_part": "Esophagus", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Rinsing": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Rinsing": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Rinsing": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Rinsing": { + "anatomical_part": "Nasopharynx", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Rinsing": { + "anatomical_part": "Oropharynx", + "collection_device": "Rinsing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Scraping": { + "anatomical_part": "Bronchiole", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Scraping": { + "anatomical_part": "Alveolar sac", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Scraping": { + "anatomical_part": "Pleural sac", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Scraping": { + "anatomical_part": "Pleural cavity", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Scraping": { + "anatomical_part": "Trachea", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Scraping": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Scraping": { + "anatomical_part": "Anterior Nares", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Scraping": { + "anatomical_part": "Esophagus", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Scraping": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Scraping": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Scraping": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Scraping": { + "anatomical_part": "Nasopharynx", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Scraping": { + "anatomical_part": "Oropharynx", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Swabbing": { + "anatomical_part": "Nasopharynx", + "collection_device": "Swabbing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Swabbing": { + "anatomical_part": "Oropharynx", + "collection_device": "Swabbing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lower respiratory tract Wash": { + "anatomical_part": "Lower respiratory tract", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchus Wash": { + "anatomical_part": "Bronchus", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Lung Wash": { + "anatomical_part": "Lung", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchiole Wash": { + "anatomical_part": "Bronchiole", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Alveolar sac Wash": { + "anatomical_part": "Alveolar sac", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural sac Wash": { + "anatomical_part": "Pleural sac", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Pleural cavity Wash": { + "anatomical_part": "Pleural cavity", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Trachea Wash": { + "anatomical_part": "Trachea", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Upper respiratory tract Wash": { + "anatomical_part": "Upper respiratory tract", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Anterior Nares Wash": { + "anatomical_part": "Anterior Nares", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Esophagus Wash": { + "anatomical_part": "Esophagus", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Ethmoid sinus Wash": { + "anatomical_part": "Ethmoid sinus", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasal Cavity Wash": { + "anatomical_part": "Nasal Cavity", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Middle Nasal Turbinate Wash": { + "anatomical_part": "Middle Nasal Turbinate", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Nasopharynx Wash": { + "anatomical_part": "Nasopharynx", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Oropharynx Wash": { + "anatomical_part": "Oropharynx", + "collection_device": "Wash", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Bronchoalveolar Lavage": { + "anatomical_part": "Not Applicable", + "collection_device": "Bronchoalveolar Lavage" + }, + "Gastric Lavage": { + "anatomical_part": "Not Applicable", + "collection_device": "Gastric Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Feces": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Feces", + "anatomical_material": "Not Applicable" + }, + "Mucus": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Mucus", + "anatomical_material": "Not Applicable" + }, + "Sputum": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Sputum", + "anatomical_material": "Not Applicable" + }, + "Sweat": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Sweat", + "anatomical_material": "Not Applicable" + }, + "Tear": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Tear", + "anatomical_material": "Not Applicable" + }, + "Urine": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Urine", + "anatomical_material": "Not Applicable" + }, + "Blood": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Blood", + "anatomical_material": "Not Applicable" + }, + "Cerebrospinal Fluid": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Not Applicable", + "anatomical_material": "Cerebrospinal Fluid" + }, + "Saliva": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Not Applicable", + "anatomical_material": "Saliva" + }, + "Tissue": { + "anatomical_part": "Not Applicable", + "collection_device": "Not Applicable", + "body_product": "Not Applicable", + "anatomical_material": "Tissue" + } +} diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index c1c49e48..3aa05082 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -220,995 +220,5 @@ "mapping_file": { "ISCIII": "ISCIII.json", "HUGTiP": "HUGTiP.json" - }, - "anatomical_material_collection_method": { - "Lower respiratory tract Aspiration": { - "anatomical_part": "Lower respiratory tract", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Aspiration": { - "anatomical_part": "Bronchus", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Aspiration": { - "anatomical_part": "Lung", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Aspiration": { - "anatomical_part": "Bronchiole", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Aspiration": { - "anatomical_part": "Alveolar sac", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Aspiration": { - "anatomical_part": "Pleural sac", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Aspiration": { - "anatomical_part": "Pleural cavity", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Aspiration": { - "anatomical_part": "Trachea", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Aspiration": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Aspiration": { - "anatomical_part": "Anterior Nares", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Aspiration": { - "anatomical_part": "Esophagus", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Aspiration": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Aspiration": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Aspiration": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Aspiration": { - "anatomical_part": "Nasopharynx", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Aspiration": { - "anatomical_part": "Oropharynx", - "collection_device": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Vacuum Aspiration": { - "anatomical_part": "Lower respiratory tract", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Vacuum Aspiration": { - "anatomical_part": "Bronchus", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Vacuum Aspiration": { - "anatomical_part": "Lung", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Vacuum Aspiration": { - "anatomical_part": "Bronchiole", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Vacuum Aspiration": { - "anatomical_part": "Alveolar sac", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Vacuum Aspiration": { - "anatomical_part": "Pleural sac", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Vacuum Aspiration": { - "anatomical_part": "Pleural cavity", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Vacuum Aspiration": { - "anatomical_part": "Trachea", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Vacuum Aspiration": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Vacuum Aspiration": { - "anatomical_part": "Anterior Nares", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Vacuum Aspiration": { - "anatomical_part": "Esophagus", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Vacuum Aspiration": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Vacuum Aspiration": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Vacuum Aspiration": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Vacuum Aspiration": { - "anatomical_part": "Nasopharynx", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Vacuum Aspiration": { - "anatomical_part": "Oropharynx", - "collection_device": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Biopsy": { - "anatomical_part": "Lower respiratory tract", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Biopsy": { - "anatomical_part": "Bronchus", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Biopsy": { - "anatomical_part": "Lung", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Biopsy": { - "anatomical_part": "Bronchiole", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Biopsy": { - "anatomical_part": "Alveolar sac", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Biopsy": { - "anatomical_part": "Pleural sac", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Biopsy": { - "anatomical_part": "Pleural cavity", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Biopsy": { - "anatomical_part": "Trachea", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Rectum Biopsy": { - "anatomical_part": "Rectum", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Skin Biopsy": { - "anatomical_part": "Skin", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Stomach Biopsy": { - "anatomical_part": "Stomach", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Biopsy": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Biopsy": { - "anatomical_part": "Anterior Nares", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Biopsy": { - "anatomical_part": "Esophagus", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Biopsy": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Biopsy": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Biopsy": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Duodenum Biopsy": { - "anatomical_part": "Duodenum", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Biopsy": { - "anatomical_part": "Nasopharynx", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Biopsy": { - "anatomical_part": "Oropharynx", - "collection_device": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Needle Biopsy": { - "anatomical_part": "Lower respiratory tract", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Needle Biopsy": { - "anatomical_part": "Bronchus", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Needle Biopsy": { - "anatomical_part": "Lung", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Needle Biopsy": { - "anatomical_part": "Bronchiole", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Needle Biopsy": { - "anatomical_part": "Alveolar sac", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Needle Biopsy": { - "anatomical_part": "Pleural sac", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Needle Biopsy": { - "anatomical_part": "Pleural cavity", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Needle Biopsy": { - "anatomical_part": "Trachea", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Rectum Needle Biopsy": { - "anatomical_part": "Rectum", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Skin Needle Biopsy": { - "anatomical_part": "Skin", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Stomach Needle Biopsy": { - "anatomical_part": "Stomach", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Needle Biopsy": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Needle Biopsy": { - "anatomical_part": "Anterior Nares", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Needle Biopsy": { - "anatomical_part": "Esophagus", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Needle Biopsy": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Needle Biopsy": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Needle Biopsy": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Duodenum Needle Biopsy": { - "anatomical_part": "Duodenum", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Needle Biopsy": { - "anatomical_part": "Nasopharynx", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Needle Biopsy": { - "anatomical_part": "Oropharynx", - "collection_device": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Lavage": { - "anatomical_part": "Lower respiratory tract", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Lavage": { - "anatomical_part": "Bronchus", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Lavage": { - "anatomical_part": "Lung", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Lavage": { - "anatomical_part": "Pleural sac", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Lavage": { - "anatomical_part": "Pleural cavity", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Lavage": { - "anatomical_part": "Trachea", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Lavage": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Lavage": { - "anatomical_part": "Anterior Nares", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Lavage": { - "anatomical_part": "Esophagus", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Lavage": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Lavage": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Lavage": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Lavage": { - "anatomical_part": "Nasopharynx", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Lavage": { - "anatomical_part": "Oropharynx", - "collection_device": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Necropsy": { - "anatomical_part": "Lower respiratory tract", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Necropsy": { - "anatomical_part": "Bronchus", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Necropsy": { - "anatomical_part": "Lung", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Necropsy": { - "anatomical_part": "Bronchiole", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Necropsy": { - "anatomical_part": "Alveolar sac", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Necropsy": { - "anatomical_part": "Pleural sac", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Necropsy": { - "anatomical_part": "Pleural cavity", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Necropsy": { - "anatomical_part": "Trachea", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Rectum Necropsy": { - "anatomical_part": "Rectum", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Skin Necropsy": { - "anatomical_part": "Skin", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Stomach Necropsy": { - "anatomical_part": "Stomach", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Necropsy": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Necropsy": { - "anatomical_part": "Anterior Nares", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Necropsy": { - "anatomical_part": "Esophagus", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Necropsy": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Necropsy": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Necropsy": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Duodenum Necropsy": { - "anatomical_part": "Duodenum", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Necropsy": { - "anatomical_part": "Nasopharynx", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Necropsy": { - "anatomical_part": "Oropharynx", - "collection_device": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Rinsing": { - "anatomical_part": "Lower respiratory tract", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Rinsing": { - "anatomical_part": "Bronchus", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Rinsing": { - "anatomical_part": "Lung", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Rinsing": { - "anatomical_part": "Bronchiole", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Rinsing": { - "anatomical_part": "Alveolar sac", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Rinsing": { - "anatomical_part": "Pleural sac", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Rinsing": { - "anatomical_part": "Pleural cavity", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Rinsing": { - "anatomical_part": "Trachea", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Rinsing": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Rinsing": { - "anatomical_part": "Anterior Nares", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Rinsing": { - "anatomical_part": "Esophagus", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Rinsing": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Rinsing": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Rinsing": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Rinsing": { - "anatomical_part": "Nasopharynx", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Rinsing": { - "anatomical_part": "Oropharynx", - "collection_device": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Scraping": { - "anatomical_part": "Bronchiole", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Scraping": { - "anatomical_part": "Alveolar sac", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Scraping": { - "anatomical_part": "Pleural sac", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Scraping": { - "anatomical_part": "Pleural cavity", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Scraping": { - "anatomical_part": "Trachea", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Scraping": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Scraping": { - "anatomical_part": "Anterior Nares", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Scraping": { - "anatomical_part": "Esophagus", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Scraping": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Scraping": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Scraping": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Scraping": { - "anatomical_part": "Nasopharynx", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Scraping": { - "anatomical_part": "Oropharynx", - "collection_device": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Swabbing": { - "anatomical_part": "Nasopharynx", - "collection_device": "Swabbing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Swabbing": { - "anatomical_part": "Oropharynx", - "collection_device": "Swabbing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Wash": { - "anatomical_part": "Lower respiratory tract", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Wash": { - "anatomical_part": "Bronchus", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Wash": { - "anatomical_part": "Lung", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Wash": { - "anatomical_part": "Bronchiole", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Wash": { - "anatomical_part": "Alveolar sac", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Wash": { - "anatomical_part": "Pleural sac", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Wash": { - "anatomical_part": "Pleural cavity", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Wash": { - "anatomical_part": "Trachea", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Wash": { - "anatomical_part": "Upper respiratory tract", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Wash": { - "anatomical_part": "Anterior Nares", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Wash": { - "anatomical_part": "Esophagus", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Wash": { - "anatomical_part": "Ethmoid sinus", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Wash": { - "anatomical_part": "Nasal Cavity", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Wash": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Wash": { - "anatomical_part": "Nasopharynx", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Wash": { - "anatomical_part": "Oropharynx", - "collection_device": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchoalveolar Lavage": { - "anatomical_part": "Not Applicable", - "collection_device": "Bronchoalveolar Lavage" - }, - "Gastric Lavage": { - "anatomical_part": "Not Applicable", - "collection_device": "Gastric Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Feces": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Feces", - "anatomical_material": "Not Applicable" - }, - "Mucus": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Mucus", - "anatomical_material": "Not Applicable" - }, - "Sputum": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Sputum", - "anatomical_material": "Not Applicable" - }, - "Sweat": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Sweat", - "anatomical_material": "Not Applicable" - }, - "Tear": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Tear", - "anatomical_material": "Not Applicable" - }, - "Urine": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Urine", - "anatomical_material": "Not Applicable" - }, - "Blood": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Blood", - "anatomical_material": "Not Applicable" - }, - "Cerebrospinal Fluid": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Not Applicable", - "anatomical_material": "Cerebrospinal Fluid" - }, - "Saliva": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Not Applicable", - "anatomical_material": "Saliva" - }, - "Tissue": { - "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", - "body_product": "Not Applicable", - "anatomical_material": "Tissue" - } } } From 28f885a57dfb35d0a532abead3ac1b1f64dd11f7 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 4 Sep 2022 09:35:13 +0200 Subject: [PATCH 0875/1454] removed not used fecth_metadata_file function --- relecov_tools/read_lab_metadata.py | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 582792a4..15fbddeb 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -74,16 +74,6 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None self.schema_name = self.relecov_sch_json["schema"] self.schema_version = self.relecov_sch_json["version"] - def fetch_metadata_file(folder, file_name): - """Fetch the metadata file folder Directory to fetch metadata file - file_name metadata file name - """ - wb_file = openpyxl.load_workbook(file_name, data_only=True) - ws_metadata_lab = wb_file["METADATA_LAB"] - heading = [] - for cell in ws_metadata_lab[1]: - heading.append(cell.value) - def read_json_file(self, j_file): """Read json file.""" with open(j_file, "r") as fh: From 5a34f75909b4cf5ed0b860a91e249b3d5bc88abd Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 4 Sep 2022 16:41:26 +0200 Subject: [PATCH 0876/1454] new parameter to define from which line start reading the excel --- relecov_tools/metadata_homogeneizer.py | 5 ++++- relecov_tools/utils.py | 15 +++++++++++---- 2 files changed, 15 insertions(+), 5 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index eb402dbe..be04bc7c 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -152,7 +152,10 @@ def handling_files(self, file_data, additional_data): elif f_name.endswith(".csv"): data = relecov_tools.utils.read_csv_file_return_dict(f_name, ",") elif f_name.endswith(".xlsx"): - data = relecov_tools.utils.read_execl_file(f_name, "Sheet") + heading_row_number = 1 + data = relecov_tools.utils.read_excel_file( + f_name, "Sheet", heading_row_number + ) else: log.error("Additional file extension %s is not supported ", f_name) stderr.print( diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 75c6a201..8b7fb867 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -34,15 +34,15 @@ def read_json_file(j_file): return data -def read_execl_file(f_name, sheet_name): +def read_excel_file(f_name, sheet_name, heading_row): """Read the input excel file and give the information in a list of dictionaries """ wb_file = openpyxl.load_workbook(f_name, data_only=True) ws_metadata_lab = wb_file[sheet_name] - heading = [i.value.strip() for i in ws_metadata_lab[1] if i.value] + heading = [i.value.strip() for i in ws_metadata_lab[heading_row] if i.value] ws_data = [] - for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row): + for row in islice(ws_metadata_lab.values, heading_row, ws_metadata_lab.max_row): l_row = list(row) data_row = {} # Ignore the empty rows @@ -127,6 +127,13 @@ def save_local_md5(file_name, md5_value): return True +def write_json_fo_file(data, file_name): + """Write metadata to json file""" + with open(file_name, "w", encoding="utf-8") as fh: + fh.write(json.dumps(data, indent=4, sort_keys=True, ensure_ascii=False)) + return True + + def write_to_excel_file(data, f_name, sheet_name, post_process=None): book = openpyxl.Workbook() sheet = book.active @@ -138,7 +145,7 @@ def write_to_excel_file(data, f_name, sheet_name, post_process=None): sheet.insert_cols(post_process["insert_cols"]) sheet["A1"] = "Campo" counter = 1 - for i in range(len(data)): + for i in range(len(data) - 1): idx = "A" + str(counter + 1) sheet[idx] = counter counter += 1 From 6635e59c8db1f5e28a6231168eefe93337a26980 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 4 Sep 2022 17:49:09 +0200 Subject: [PATCH 0877/1454] moved json files inside lab_metadata_req_json --- relecov_tools/conf/configuration.json | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 3aa05082..3c48edb8 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -104,6 +104,15 @@ "ena_schema": "ena_schema.json", "gisaid_schema": "gisaid_schema.json" }, + "lab_metadata_req_json":{ + "laboratory_data": "laboratory_address.json", + "geo_location_data": "geo_loc_cities.json", + "anatomical_material": "anatomical_material_collection_method.json" + }, + "mapping_file": { + "ISCIII": "ISCIII.json", + "HUGTiP": "HUGTiP.json" + }, "sftp_connection": { "sftp_server": "sftprelecov.isciii.es", "sftp_port": "22" @@ -115,8 +124,6 @@ "fastq.gz", "fasta" ], - "laboratory_data": "laboratory_address.json", - "geo_location_data": "geo_loc_cities.json", "ENA_configuration": { "study_alias": "RELECOV", "design_description": "Design Description", @@ -216,9 +223,5 @@ "tool_version": "0.5.3" }, "md5_file_name": "md5_check_file.csv", - "checklist": "ERC000033", - "mapping_file": { - "ISCIII": "ISCIII.json", - "HUGTiP": "HUGTiP.json" - } + "checklist": "ERC000033" } From e1dbf0667c3eec6eba1e9f357ed9878ee7d64b69 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 4 Sep 2022 17:51:25 +0200 Subject: [PATCH 0878/1454] using read_excel from utils and modify the code to handle now on read_metadata rows based on dict instead of list --- relecov_tools/read_lab_metadata.py | 222 ++++++++++++----------------- 1 file changed, 89 insertions(+), 133 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 15fbddeb..09bf4465 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -1,15 +1,7 @@ #!/usr/bin/env python -from itertools import islice - import json import logging - -# from queue import Empty - -# from turtle import heading import rich.console - -import openpyxl import os import sys import re @@ -71,15 +63,10 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None self.label_prop_dict[values["label"]] = prop except KeyError: continue + self.json_files = config_json.get_configuration("lab_metadata_req_json") self.schema_name = self.relecov_sch_json["schema"] self.schema_version = self.relecov_sch_json["version"] - def read_json_file(self, j_file): - """Read json file.""" - with open(j_file, "r") as fh: - data = json.load(fh) - return data - def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): """Fetch the laboratory location and return a dictionary""" data = {} @@ -125,7 +112,6 @@ def include_fixed_data(self): def include_fields_already_set(self, row_sample): processed_data = {} - if row_sample["author_submitter"] == "": processed_data["collector_name"] = "unknown" else: @@ -171,7 +157,7 @@ def include_processed_data(self, metadata): return new_data - def add_additional_data(self, metadata, lab_json_file, geo_loc_file): + def add_additional_data(self, metadata, conf_json_data): """Add the additional information that must be included in final metadata metadata Origin metadata extra_data additional data to be included @@ -180,22 +166,16 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): lab_data = {} additional_metadata = [] - lab_json = self.read_json_file(lab_json_file) - geo_loc_json = self.read_json_file(geo_loc_file) - samples_json = self.read_json_file(self.sample_list_file) + samples_json = relecov_tools.utils.read_json_file(self.sample_list_file) for row_sample in metadata: """Include sample data from sample json""" try: - for key, value in samples_json[ - row_sample["microbiology_lab_sample_id"] - # row_sample["sequencing_sample_id"] - ].items(): - - row_sample[key] = value - except KeyError as e: - stderr.print( - "[red] ERROR fastq information not found in sample json. ", e + row_sample.update( + samples_json[row_sample["microbiology_lab_sample_id"]] ) + except KeyError as e: + + stderr.print(f"[red] ERROR fastq information not found for sample {e}") """ Fetch the information related to the laboratory. Info is stored in lab_data, to prevent to call get_laboratory_data @@ -204,7 +184,9 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): if row_sample["collecting_institution"] not in lab_data: # from collecting_institution find city, and geo location latitude and longitude l_data = self.get_laboratory_data( - lab_json, geo_loc_json, row_sample["collecting_institution"] + conf_json_data["laboratory_data"], + conf_json_data["geo_location_data"], + row_sample["collecting_institution"], ) row_sample.update(l_data) lab_data[row_sample["collecting_institution"]] = l_data @@ -216,23 +198,21 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): row_sample["submitting_institution"] = row_sample[ "submitting_institution" ].strip() - if row_sample["submitting_institution"] not in lab_json: + if row_sample["submitting_institution"] not in lab_data: + # Include in lab_data the submitting institution l_data = self.get_laboratory_data( - lab_json, geo_loc_json, row_sample["submitting_institution"] + conf_json_data["laboratory_data"], + conf_json_data["geo_location_data"], + row_sample["submitting_institution"], ) - # row_sample.update(l_data) - lab_data[row_sample["submitting_institution"]] = l_data - sub_data = {} - sub_data["submitting_institution_email"] = lab_data[ + lab_data[row_sample["submitting_institution"]] = l_data + row_sample["submitting_institution_email"] = lab_data[ row_sample["submitting_institution"] ]["collecting_institution_email"] - sub_data["submitting_institution_address"] = lab_data[ + row_sample["submitting_institution_address"] = lab_data[ row_sample["submitting_institution"] ]["collecting_institution_address"] - # else: - # sub_data = {"collecting_institution_email" : "", "collecting_institution_address": ""} - row_sample.update(sub_data) """ Add Fixed information """ @@ -240,17 +220,11 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): """ Add fields that are already in other fields """ - row_sample.update(self.include_fields_already_set(row_sample)) + # row_sample.update(self.include_fields_already_set(row_sample)) """Add information which requires processing """ - row_sample.update(self.include_processed_data(row_sample)) - """ - row["isolate"] = row["collecting_lab_sample_id"] - row["host_scientific_name"] = extra_data["host_scientific_name"][ - row["host_common_name"] - ] - row["sequencing_instrument_platform"] = "To change" - """ + # row_sample.update(self.include_processed_data(row_sample)) + # Add experiment_alias and run_alias row_sample["experiment_alias"] = str( row_sample["sequence_file_R1_fastq"] @@ -266,101 +240,83 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): return additional_metadata - def request_information(external_url, request): - """Get information from external database server using Rest API - - external_url - request + def read_configuration_json_files(self): + """Read json files defined in configuration lab_metadata_req_json + property """ - pass - - def store_information(external_url, request, data): - """Update information""" - pass + c_files = {} + for item, value in self.json_files.items(): + f_path = os.path.join( + os.path.dirname(os.path.realpath(__file__)), "conf", value + ) + c_files[item] = relecov_tools.utils.read_json_file(f_path) + return c_files def read_metadata_file(self): - """Read the input metadata file, changing the metadata heading with - their property name values defined in schema. + """Read the input metadata file from row 4, changes the metadata heading + with their property name values defined in schema. Convert the date colunms value to the dd/mm/yyyy format. Return list of dict with data, and errors """ - # exc_format_num = ["Sample ID given for sequencing"] - wb_file = openpyxl.load_workbook(self.metadata_file, data_only=True) - ws_metadata_lab = wb_file["METADATA_LAB"] - - # removing the None columns in excel heading row - heading = [i.value.strip() for i in ws_metadata_lab[4] if i.value] + heading_row_number = 4 + ws_metadata_lab = relecov_tools.utils.read_excel_file( + self.metadata_file, "METADATA_LAB", heading_row_number + ) - # heading = self.update_heading_to_json(heading_without_none, meta_map_json) metadata_values = [] errors = {} - for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): - sample_data_row = {} - # Ignore the empty rows - if row[2] is None: + row_number = heading_row_number + for row in ws_metadata_lab: + row_number += 1 + property_row = {} + try: + sample_number = row["Sample ID given for sequencing"] + except KeyError: + log.error( + "Sample ID given for sequencing not found in row %s", row_number + ) + stderr.print( + f"[red] Sample ID given for sequencing not found in row {row_number}" + ) continue - for idx in range(1, len(heading)): - if "date" in heading[idx].lower(): - try: - sample_data_row[self.label_prop_dict[heading[idx]]] = row[ - idx - ].strftime("%Y-%m-%d") - except AttributeError: - # check if date is in string format - str_date = re.search(r"(\d{4}-\d{2}-\d{2}).*", row[idx]) - if str_date: - sample_data_row[ - self.label_prop_dict[heading[idx]] - ] = str_date.group(1) - else: - if row[2] not in errors: - errors[row[2]] = {} - errors[row[2]][heading[idx]] = "Invalid date format" - log.error("Invalid date format in sample %s", row[2]) - stderr.print( - "[red] Invalid date format in sample", - row[2] + " column " + heading[idx], - ) - else: - - if isinstance(row[idx], float) or isinstance(row[idx], int): - val = str(int(row[idx])) - try: - sample_data_row[self.label_prop_dict[heading[idx]]] = val - except TypeError as e: - stderr.print("[red] Error when reading " + row[2] + e) - else: + for key in row.keys(): + # skip the first column of the Metadata lab file + if "Campo" in key: + continue + if "date" in key.lower(): + if row[key] is not None: try: - sample_data_row[self.label_prop_dict[heading[idx]]] = ( - row[idx] if row[idx] else "" - ) - except KeyError as e: - stderr.print( - "[red] Error when reading " + str(row[2]) + str(e) - ) - metadata_values.append(sample_data_row) - + row[key] = row[key].strftime("%Y-%m-%d") + except AttributeError: + # check if date is in string format + str_date = re.search(r"(\d{4}-\d{2}-\d{2}).*", row[key]) + if str_date: + row[key] = str_date.group(1) + else: + if sample_number not in errors: + errors[sample_number] = {} + errors[sample_number][key] = "Invalid date format" + log.error( + "Invalid date format in sample %s", row_number + ) + stderr.print( + f"[red] Invalid date format in sample {sample_number}, {key}" + ) + else: + if isinstance(row[key], float) or isinstance(row[key], int): + row[key] = str(int(row[key])) + try: + property_row[self.label_prop_dict[key]] = row[key] + except KeyError as e: + continue + stderr.print(f"[red] Error when reading {sample_number} {str(e)}") + + metadata_values.append(property_row) return metadata_values, errors - def write_json_fo_file(self, data, file_name): - """Write metadata to json file""" - os.makedirs(self.output_folder, exist_ok=True) - json_file = os.path.join(self.output_folder, file_name) - with open(json_file, "w", encoding="utf-8") as fh: - fh.write(json.dumps(data, indent=4, sort_keys=True, ensure_ascii=False)) - return True - def create_metadata_json(self): stderr.print("[blue] Reading configuration settings") - config_json = ConfigJson() - geo_loc_json = config_json.get_configuration("geo_location_data") - geo_loc_file = os.path.join( - os.path.dirname(os.path.realpath(__file__)), "conf", geo_loc_json - ) - lab_json = config_json.get_configuration("laboratory_data") - lab_json_file = os.path.join( - os.path.dirname(os.path.realpath(__file__)), "conf", lab_json - ) + conf_json_data = self.read_configuration_json_files() stderr.print("[blue] Reading Lab Metadata Excel File") valid_metadata_rows, errors = self.read_metadata_file() if len(errors) > 0: @@ -369,9 +325,7 @@ def create_metadata_json(self): # Continue by adding extra information stderr.print("[blue] Including additional information") completed_metadata = self.add_additional_data( - valid_metadata_rows, - lab_json_file, - geo_loc_file, + valid_metadata_rows, conf_json_data ) file_name = ( @@ -379,6 +333,8 @@ def create_metadata_json(self): + os.path.splitext(os.path.basename(self.metadata_file))[0] + ".json" ) - stderr.print("[blue] Creating Json file") - self.write_json_fo_file(completed_metadata, file_name) + stderr.print("[blue] Writting output json file") + os.makedirs(self.output_folder, exist_ok=True) + file_path = os.path.join(self.output_folder, file_name) + relecov_tools.utils.write_json_fo_file(completed_metadata, file_path) return True From 007c09a638ed90aa4a0ce887e3e7c461e8f084a4 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 4 Sep 2022 17:59:08 +0200 Subject: [PATCH 0879/1454] changed in configuration json mapping_file for institution_mapping_file --- relecov_tools/conf/configuration.json | 2 +- relecov_tools/metadata_homogeneizer.py | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 3c48edb8..8c66a064 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -109,7 +109,7 @@ "geo_location_data": "geo_loc_cities.json", "anatomical_material": "anatomical_material_collection_method.json" }, - "mapping_file": { + "institution_mapping_file": { "ISCIII": "ISCIII.json", "HUGTiP": "HUGTiP.json" }, diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index be04bc7c..8e3ff84c 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -36,7 +36,9 @@ def __init__(self, institution=None, directory=None, output_folder=None): os.path.dirname(__file__), "schema", "institution_schemas", - self.config_json.get_topic_data("mapping_file", self.institution), + self.config_json.get_topic_data( + "institution_mapping_file", self.institution + ), ) if directory is None: directory = relecov_tools.utils.prompt_path( From c393e4c274a6aa4ca2b4baab92c88788e0295c24 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 4 Sep 2022 18:01:31 +0200 Subject: [PATCH 0880/1454] start working on version 0.0.5 --- relecov_tools/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index e96c4761..0adb35a2 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -59,7 +59,7 @@ def run_relecov_tools(): ) # stderr.print("[green] `._,._,'\n", highlight=False) - __version__ = "0.0.4" + __version__ = "0.0.5" stderr.print( "\n" "[grey39] RELECOV-tools version {}".format(__version__), highlight=False ) From ce840d42b9729abb4c0e885ef0ef36a6a9526014 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 4 Sep 2022 18:43:28 +0200 Subject: [PATCH 0881/1454] Removed duplicates in enum relecov schema --- relecov_tools/schema/relecov_schema.json | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 9bcc0eec..88a5e8fe 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1153,7 +1153,6 @@ "NEBNex Fast DNA Library Prep Set for Ion Torrent", "Nextera DNA Flex", "Ion AmpliSeq Kit Library Kit Plus", - "Ion AmpliSeq Kit Library Kit Plus", "Ion AmpliSeq Library Kit 2.0", "Ion Xpress Plus Fragment Library Kit", "Oxford Nanopore Sequencing Kit", @@ -1308,14 +1307,6 @@ "MiSeq Reagent Kit v3 (600-cycle)", "TG MiSeq Reagent Kit v3 (600 cycle)", "TG MiSeq Reagent Kit v3 (150 cycle)", - "MiSeq Reagent Kit v3 (150-cycle)", - "MiSeq Reagent Kit v3 (600-cycle)", - "TG MiSeq Reagent Kit v3 (600 cycle)", - "TG MiSeq Reagent Kit v3 (150 cycle)", - "MiSeq Reagent Kit v3 (150-cycle)", - "MiSeq Reagent Kit v3 (600-cycle)", - "TG MiSeq Reagent Kit v3 (600 cycle)", - "TG MiSeq Reagent Kit v3 (150 cycle)", "MiSeq Reagent Kit v2 (50-cycles)", "MiSeq Reagent Kit v2 (300-cycles)", "MiSeq Reagent Kit v2 (500-cycles)", @@ -1386,12 +1377,6 @@ "TruSeq Dual Index Sequencing Primer Box, Paired-End", "TruSeq PE Cluster Kit v3-cBot-HS", "TruSeq PE Cluster Kit v5-CS-GA", - "HiSeq SR Rapid Cluster Kit v2", - "HiSeq PE Rapid Cluster Kit v2", - "TG HiSeq Rapid PE Cluster Kit v2", - "HiSeq SR Rapid Cluster Kit v2", - "HiSeq PE Rapid Cluster Kit v2", - "TG HiSeq Rapid PE Cluster Kit v2", "TruSeq SBS Kit v3-HS (200 cycles)", "TruSeq SBS Kit v3-HS (50 cycles)", "TG TruSeq SBS Kit v3 - HS (200-cycles)", From 59a38dd9f99e696fd93e70783c5ac7982ec9cf46 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 5 Sep 2022 11:55:26 +0200 Subject: [PATCH 0882/1454] fixed if_enrichment_panel_assay_if_other_especify --- relecov_tools/conf/configuration.json | 332 ++++++++++++----------- relecov_tools/schema/relecov_schema.json | 37 ++- 2 files changed, 191 insertions(+), 178 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 4625655d..9219673b 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -222,989 +222,991 @@ "anatomical_material_collection_method": { "Lower respiratory tract Aspiration": { "anatomical_part": "Lower respiratory tract", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchus Aspiration": { "anatomical_part": "Bronchus", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lung Aspiration": { "anatomical_part": "Lung", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchiole Aspiration": { "anatomical_part": "Bronchiole", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Alveolar sac Aspiration": { "anatomical_part": "Alveolar sac", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Aspiration": { "anatomical_part": "Pleural sac", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Aspiration": { "anatomical_part": "Pleural cavity", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Aspiration": { "anatomical_part": "Trachea", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Aspiration": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Aspiration": { "anatomical_part": "Anterior Nares", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Aspiration": { "anatomical_part": "Esophagus", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Aspiration": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Aspiration": { "anatomical_part": "Nasal Cavity", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Aspiration": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Aspiration": { "anatomical_part": "Nasopharynx", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Aspiration": { "anatomical_part": "Oropharynx", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lower respiratory tract Vacuum Aspiration": { "anatomical_part": "Lower respiratory tract", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchus Vacuum Aspiration": { "anatomical_part": "Bronchus", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lung Vacuum Aspiration": { "anatomical_part": "Lung", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchiole Vacuum Aspiration": { "anatomical_part": "Bronchiole", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Alveolar sac Vacuum Aspiration": { "anatomical_part": "Alveolar sac", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Vacuum Aspiration": { "anatomical_part": "Pleural sac", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Vacuum Aspiration": { "anatomical_part": "Pleural cavity", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Vacuum Aspiration": { "anatomical_part": "Trachea", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Vacuum Aspiration": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Vacuum Aspiration": { "anatomical_part": "Anterior Nares", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Vacuum Aspiration": { "anatomical_part": "Esophagus", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Vacuum Aspiration": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Vacuum Aspiration": { "anatomical_part": "Nasal Cavity", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Vacuum Aspiration": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Vacuum Aspiration": { "anatomical_part": "Nasopharynx", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Vacuum Aspiration": { "anatomical_part": "Oropharynx", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lower respiratory tract Biopsy": { "anatomical_part": "Lower respiratory tract", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchus Biopsy": { "anatomical_part": "Bronchus", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lung Biopsy": { "anatomical_part": "Lung", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchiole Biopsy": { "anatomical_part": "Bronchiole", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Alveolar sac Biopsy": { "anatomical_part": "Alveolar sac", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Biopsy": { "anatomical_part": "Pleural sac", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Biopsy": { "anatomical_part": "Pleural cavity", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Biopsy": { "anatomical_part": "Trachea", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Rectum Biopsy": { "anatomical_part": "Rectum", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Skin Biopsy": { "anatomical_part": "Skin", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Stomach Biopsy": { "anatomical_part": "Stomach", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Biopsy": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Biopsy": { "anatomical_part": "Anterior Nares", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Biopsy": { "anatomical_part": "Esophagus", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Biopsy": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Biopsy": { "anatomical_part": "Nasal Cavity", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Biopsy": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Duodenum Biopsy": { "anatomical_part": "Duodenum", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Biopsy": { "anatomical_part": "Nasopharynx", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Biopsy": { "anatomical_part": "Oropharynx", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lower respiratory tract Needle Biopsy": { "anatomical_part": "Lower respiratory tract", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchus Needle Biopsy": { "anatomical_part": "Bronchus", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lung Needle Biopsy": { "anatomical_part": "Lung", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchiole Needle Biopsy": { "anatomical_part": "Bronchiole", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Alveolar sac Needle Biopsy": { "anatomical_part": "Alveolar sac", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Needle Biopsy": { "anatomical_part": "Pleural sac", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Needle Biopsy": { "anatomical_part": "Pleural cavity", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Needle Biopsy": { "anatomical_part": "Trachea", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Rectum Needle Biopsy": { "anatomical_part": "Rectum", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Skin Needle Biopsy": { "anatomical_part": "Skin", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Stomach Needle Biopsy": { "anatomical_part": "Stomach", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Needle Biopsy": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Needle Biopsy": { "anatomical_part": "Anterior Nares", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Needle Biopsy": { "anatomical_part": "Esophagus", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Needle Biopsy": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Needle Biopsy": { "anatomical_part": "Nasal Cavity", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Needle Biopsy": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Duodenum Needle Biopsy": { "anatomical_part": "Duodenum", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Needle Biopsy": { "anatomical_part": "Nasopharynx", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Needle Biopsy": { "anatomical_part": "Oropharynx", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lower respiratory tract Lavage": { "anatomical_part": "Lower respiratory tract", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchus Lavage": { "anatomical_part": "Bronchus", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lung Lavage": { "anatomical_part": "Lung", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Lavage": { "anatomical_part": "Pleural sac", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Lavage": { "anatomical_part": "Pleural cavity", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Lavage": { "anatomical_part": "Trachea", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Lavage": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Lavage": { "anatomical_part": "Anterior Nares", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Lavage": { "anatomical_part": "Esophagus", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Lavage": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Lavage": { "anatomical_part": "Nasal Cavity", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Lavage": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Lavage": { "anatomical_part": "Nasopharynx", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Lavage": { "anatomical_part": "Oropharynx", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lower respiratory tract Necropsy": { "anatomical_part": "Lower respiratory tract", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchus Necropsy": { "anatomical_part": "Bronchus", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lung Necropsy": { "anatomical_part": "Lung", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchiole Necropsy": { "anatomical_part": "Bronchiole", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Alveolar sac Necropsy": { "anatomical_part": "Alveolar sac", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Necropsy": { "anatomical_part": "Pleural sac", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Necropsy": { "anatomical_part": "Pleural cavity", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Necropsy": { "anatomical_part": "Trachea", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Rectum Necropsy": { "anatomical_part": "Rectum", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Skin Necropsy": { "anatomical_part": "Skin", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Stomach Necropsy": { "anatomical_part": "Stomach", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Necropsy": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Necropsy": { "anatomical_part": "Anterior Nares", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Necropsy": { "anatomical_part": "Esophagus", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Necropsy": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Necropsy": { "anatomical_part": "Nasal Cavity", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Necropsy": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Duodenum Necropsy": { "anatomical_part": "Duodenum", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Necropsy": { "anatomical_part": "Nasopharynx", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Necropsy": { "anatomical_part": "Oropharynx", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lower respiratory tract Rinsing": { "anatomical_part": "Lower respiratory tract", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchus Rinsing": { "anatomical_part": "Bronchus", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lung Rinsing": { "anatomical_part": "Lung", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchiole Rinsing": { "anatomical_part": "Bronchiole", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Alveolar sac Rinsing": { "anatomical_part": "Alveolar sac", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Rinsing": { "anatomical_part": "Pleural sac", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Rinsing": { "anatomical_part": "Pleural cavity", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Rinsing": { "anatomical_part": "Trachea", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Rinsing": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Rinsing": { "anatomical_part": "Anterior Nares", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Rinsing": { "anatomical_part": "Esophagus", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Rinsing": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Rinsing": { "anatomical_part": "Nasal Cavity", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Rinsing": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Rinsing": { "anatomical_part": "Nasopharynx", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Rinsing": { "anatomical_part": "Oropharynx", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchiole Scraping": { "anatomical_part": "Bronchiole", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Alveolar sac Scraping": { "anatomical_part": "Alveolar sac", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Scraping": { "anatomical_part": "Pleural sac", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Scraping": { "anatomical_part": "Pleural cavity", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Scraping": { "anatomical_part": "Trachea", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Scraping": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Scraping": { "anatomical_part": "Anterior Nares", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Scraping": { "anatomical_part": "Esophagus", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Scraping": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Scraping": { "anatomical_part": "Nasal Cavity", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Scraping": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Scraping": { "anatomical_part": "Nasopharynx", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Scraping": { "anatomical_part": "Oropharynx", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Swabbing": { "anatomical_part": "Nasopharynx", - "collection_device": "Swabbing", + "collection_method": "Swabbing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Swabbing": { "anatomical_part": "Oropharynx", - "collection_device": "Swabbing", + "collection_method": "Swabbing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lower respiratory tract Wash": { "anatomical_part": "Lower respiratory tract", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchus Wash": { "anatomical_part": "Bronchus", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lung Wash": { "anatomical_part": "Lung", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchiole Wash": { "anatomical_part": "Bronchiole", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Alveolar sac Wash": { "anatomical_part": "Alveolar sac", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Wash": { "anatomical_part": "Pleural sac", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Wash": { "anatomical_part": "Pleural cavity", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Wash": { "anatomical_part": "Trachea", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Wash": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Wash": { "anatomical_part": "Anterior Nares", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Wash": { "anatomical_part": "Esophagus", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Wash": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Wash": { "anatomical_part": "Nasal Cavity", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Wash": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Wash": { "anatomical_part": "Nasopharynx", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Wash": { "anatomical_part": "Oropharynx", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchoalveolar Lavage": { "anatomical_part": "Not Applicable", - "collection_device": "Bronchoalveolar Lavage" + "collection_method": "Bronchoalveolar Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" }, "Gastric Lavage": { "anatomical_part": "Not Applicable", - "collection_device": "Gastric Lavage", + "collection_method": "Gastric Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Feces": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Feces", "anatomical_material": "Not Applicable" }, "Mucus": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Mucus", "anatomical_material": "Not Applicable" }, "Sputum": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Sputum", "anatomical_material": "Not Applicable" }, "Sweat": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Sweat", "anatomical_material": "Not Applicable" }, "Tear": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Tear", "anatomical_material": "Not Applicable" }, "Urine": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Urine", "anatomical_material": "Not Applicable" }, "Blood": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Blood", "anatomical_material": "Not Applicable" }, "Cerebrospinal Fluid": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Not Applicable", "anatomical_material": "Cerebrospinal Fluid" }, "Saliva": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Not Applicable", "anatomical_material": "Saliva" }, "Tissue": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Not Applicable", "anatomical_material": "Tissue" } diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 6336bee0..857debff 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1121,9 +1121,9 @@ "Ion Xpress", "ABL_DeepChek NGS", "Ion AmpliSeq Kit for Chef DL8", - "NEBNext® Fast DNA Library Prep Set for Ion Torrent™", - "NEBNext® ARTIC SARS-CoV-2 FS", - "Illumina COVIDSeq Test", + "NEBNext Fast DNA Library Prep Set for Ion Torrent", + "NEBNext ARTIC SARS-CoV-2 FS", + "Illumina COVIDSeq Test [CIDO:0020172]", "ABL DeepChek® Assay WG SC2 V1", "Other" ], @@ -1162,7 +1162,7 @@ "Nanopore COVID Midi: 2304 samples", "Nanopore COVID Mini: 576 samples", "Vela Diagnostics:ViroKey SQ FLEX Library Prep Reagents", - "Other" + "Other [NCIT:C17649]" ], "examples": [ "Illumina DNA Prep Tagmentation" @@ -1176,12 +1176,12 @@ }, "enrichment_protocol": { "enum": [ - "Amplicon", - "Probes", - "Custom probes", - "Custom amplicon", - "No enrichment", - "Other" + "Amplicon [GENEPIO:0001974]", + "Probes [OMIT:0016121]", + "Custom probes [OMIT:0016112]", + "Custom amplicon [OMIT:0016112]", + "No enrichment [NCIT:C154307]", + "Other [NCIT:C17649]" ], "examples": [ "AMPLICON" @@ -1252,6 +1252,17 @@ "label": "Enrichment panel/assay version", "fill_mode": "batch" }, + "if_enrichment_panel_assay_if_other_especify": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "classification": "Sequencing", + "label": "If Enrichment panel/assay If Other, Especify", + "fill_mode": "batch" + }, "amplicon_pcr_primer_scheme": { "examples": [ "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv" @@ -1426,8 +1437,8 @@ }, "sequencing_instrument_platform": { "enum": [ - "Oxford Nanopore", - "Illumina", + "Oxford Nanopore [OBI:0002750]", + "Illumina [OBI:0000759]", "Ion Torrent", "Other" ], @@ -1517,7 +1528,7 @@ "WCS strategy [GENPIO:0001991]", "WGS strategy [GENPIO:0001992]", "WXS strategy [GENPIO:0001993]", - "amplicon strategy [GENPIO:0001974]", + "amplicon [GENPIO:0001974]", "clone end strategy [GENPIO:0001976]", "clone strategy [GENPIO:0001977]", "finishing strategy [GENPIO:0001982]", From 67fbfe221798954ab8fa988586b453be9ec72c9c Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 5 Sep 2022 12:36:14 +0200 Subject: [PATCH 0883/1454] fixing relecov schema --- relecov_tools/schema/relecov_schema.json | 46 +++++++++++++++++++++++- 1 file changed, 45 insertions(+), 1 deletion(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 264b1966..fbde55a7 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2288,6 +2288,39 @@ "label": "Gene Name 2", "fill_mode": "batch" }, + "bioproject_umbrella_accession_ENA": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001133", + "type": "string", + "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", + "classification": "Sample collection and processing", + "label": "Bioproject umbrella accession ENA", + "fill_mode": "batch" + }, + "bioproject_accession_ENA": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001136", + "type": "string", + "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", + "classification": "Sample collection and processing", + "label": "Bioproject accession ENA", + "fill_mode": "batch" + }, + "biosample_accession_ENA": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001139", + "type": "string", + "description": "The identifier assigned to a BioSample in INSDC archives.", + "classification": "Sample collection and processing", + "label": "ENA Sample Id", + "fill_mode": "batch" + }, "diagnostic_pcr_Ct_value_2": { "examples": [ "36" @@ -2310,6 +2343,17 @@ "label": "Authors", "fill_mode": "batch" }, + "broker_name": { + "examples": [ + "" + ], + "ontology": "0", + "type": "string", + "description": "", + "classification": "Public databases", + "label": "Broker Name", + "fill_mode": "batch" + }, "gisaid_submitter_id": { "examples": [ "" @@ -2455,4 +2499,4 @@ "fill_mode": "batch" } } -} +} \ No newline at end of file From 3410f050d1d62deb7fd6707a1d1a375c435a323d Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 5 Sep 2022 12:37:53 +0200 Subject: [PATCH 0884/1454] fixing relecov schema --- relecov_tools/schema/relecov_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index fbde55a7..cf65d7f3 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1113,7 +1113,7 @@ "type": "string", "description": "DNA/RNA extraction protocol", "classification": "Sequencing", - "label": "Extraction Protocol", + "label": "Nucleic acid extraction protocol", "fill_mode": "batch" }, "all_in_one_library_kit": { From 02e73fa1064ba9648afbcd1c3d77fd7885e92dbb Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 5 Sep 2022 13:31:09 +0200 Subject: [PATCH 0885/1454] little changes --- relecov_tools/institution_scripts/ISCIII.py | 30 +++++++++++++++++++++ relecov_tools/read_lab_metadata.py | 19 ++++++++++++- 2 files changed, 48 insertions(+), 1 deletion(-) diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index 0078999f..dd1b2703 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -80,3 +80,33 @@ def translate_gender_to_english(metadata, f_data, mapped_fields, heading): else: row[m_idx] = "not applicable" return metadata + + +def translate_anatomical_part(metadata, f_data, mapped_fields, heading): + """Translate into english the "muestra" that is written in spanish""" + for row in metadata[1:]: + for key, val in mapped_fields.items(): + m_idx = heading.index(key) + if row[m_idx] is None: + row[m_idx] = "not provided" + elif "ASPIRADO NASOFARÍNGEO" in row[m_idx].lower(): + row[m_idx] = "Nasopharynx Aspiration" + elif "ASPIRADO BRONQUIAL" in row[m_idx].lower(): + row[m_idx] = "Bronchus Aspiration" + elif "ESPUTO" in row[m_idx].lower(): + row[m_idx] = "Sputum" + elif "EXTRACTO" in row[m_idx].lower(): + row[m_idx] = "Scraping" + elif "EXUDADO FARÍNGEO" in row[m_idx].lower(): + row[m_idx] = "Nasopharynx Swabbing" + elif "EXUDADO NASOFARÍNGEO" in row[m_idx].lower(): + row[m_idx] = "Nasopharynx Swabbing" + elif "EXUDADO OROFARINGEO" in row[m_idx].lower(): + row[m_idx] = "Oropharynx Swabbing" + elif "PLACENTA" in row[m_idx].lower(): + row[m_idx] = "Placenta" + elif "SALIVA" in row[m_idx].lower(): + row[m_idx] = "Saliva" + else: + row[m_idx] = "not applicable" + return metadata diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 09bf4465..1b509902 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -134,9 +134,26 @@ def include_processed_data(self, metadata): "Illumina": [ "Illumina iSeq 100", "Illumina MiSeq", + "Illumina Miniseq", "Illumina NextSeq 550", - "Illumina NextSeq", + "Illumina NextSeq 500", + "Illumina NextSeq 1000", + "Illumina NextSeq 2000", "Illumina NovaSeq 6000", + "Illumina Miniseq", + "Illumina Hiseq x five", + "Illumina Hiseq x ten", + "Illumina Hiseq x", + "Illumina Genome analyzer", + "Illumina Genome analyzer ii", + "Illumina Genome analyzer iix", + "Illumina Hiscansq", + "Illumina Hiseq 1000", + "Illumina Hiseq 1500", + "Illumina Hiseq 2000", + "Illumina Hiseq 2500", + "Illumina Hiseq 3000", + "Illumina Hiseq 4000", ], "Oxford Nanopore": ["MinION"], "Ion Torrent": ["Ion Torrent S5", "Ion Torrent PGM"], From e0a0600dc498bb8930a3baa55d4622efe05d40a1 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 5 Sep 2022 14:03:44 +0200 Subject: [PATCH 0886/1454] added specimen source --- relecov_tools/schema/institution_schemas/ISCIII.json | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 26e7283a..5e55de41 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -61,6 +61,14 @@ "mapped_key": "", "function": "translate_gender_to_english" }, + "specimen_source_file": { + "file_name": "", + "mapped_fields": { + "Specimen source": "" + }, + "mapped_key": "", + "function": "translate_specimen_source" + }, "authors_file": { "file_name": "gisaid_authors.tsv", "mapped_fields": { @@ -113,4 +121,4 @@ "Diagnostic Pcr Ct Value 1": "", "Authors": "" } -} +} \ No newline at end of file From 9570c72f4e137645db355892c0f2cbd894ec8abe Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 5 Sep 2022 14:23:06 +0200 Subject: [PATCH 0887/1454] collection device --- relecov_tools/schema/relecov_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 88a5e8fe..cec60a99 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -655,7 +655,7 @@ "" ], "classification": "Sample collection and processing", - "label": "Specimen source", + "label": "Collection device", "fill_mode": "batch" }, "collection_method": { From 7d1b2c6cc2e36a54f5518c354394e7efac751016 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 5 Sep 2022 15:10:14 +0200 Subject: [PATCH 0888/1454] Fixing errors in homogenizer module --- relecov_tools/conf/configuration.json | 1015 ----------------- relecov_tools/institution_scripts/ISCIII.py | 20 +- .../schema/institution_schemas/ISCIII.json | 5 +- 3 files changed, 13 insertions(+), 1027 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index d21623ea..6ba53182 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -223,1024 +223,9 @@ "tool_version": "0.5.3" }, "md5_file_name": "md5_check_file.csv", -<<<<<<< HEAD "checklist": "ERC000033", - "long_table_heading": [ - "SAMPLE", - "CHROM", - "POS", - "REF", - "ALT", - "FILTER", - "DP", - "REF_DP", - "ALT_DP", - "AF", - "GENE", - "EFFECT", - "HGVS_C", - "HGVS_P", - "HGVS_P_1LETTER", - "CALLER", - "LINEAGE" - ], "mapping_file": { "ISCIII": "ISCIII.json", "HUGTiP": "HUGTiP.json" - }, - "anatomical_material_collection_method": { - "Lower respiratory tract Aspiration": { - "anatomical_part": "Lower respiratory tract", - "collection_method": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Aspiration": { - "anatomical_part": "Bronchus", - "collection_method": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Aspiration": { - "anatomical_part": "Lung", - "collection_method": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Aspiration": { - "anatomical_part": "Bronchiole", - "collection_method": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Aspiration": { - "anatomical_part": "Alveolar sac", - "collection_method": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Aspiration": { - "anatomical_part": "Pleural sac", - "collection_method": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Aspiration": { - "anatomical_part": "Pleural cavity", - "collection_method": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Aspiration": { - "anatomical_part": "Trachea", - "collection_method": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Aspiration": { - "anatomical_part": "Upper respiratory tract", - "collection_method": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Aspiration": { - "anatomical_part": "Anterior Nares", - "collection_method": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Aspiration": { - "anatomical_part": "Esophagus", - "collection_method": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Aspiration": { - "anatomical_part": "Ethmoid sinus", - "collection_method": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Aspiration": { - "anatomical_part": "Nasal Cavity", - "collection_method": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Aspiration": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_method": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Aspiration": { - "anatomical_part": "Nasopharynx", - "collection_method": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Aspiration": { - "anatomical_part": "Oropharynx", - "collection_method": "Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Vacuum Aspiration": { - "anatomical_part": "Lower respiratory tract", - "collection_method": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Vacuum Aspiration": { - "anatomical_part": "Bronchus", - "collection_method": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Vacuum Aspiration": { - "anatomical_part": "Lung", - "collection_method": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Vacuum Aspiration": { - "anatomical_part": "Bronchiole", - "collection_method": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Vacuum Aspiration": { - "anatomical_part": "Alveolar sac", - "collection_method": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Vacuum Aspiration": { - "anatomical_part": "Pleural sac", - "collection_method": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Vacuum Aspiration": { - "anatomical_part": "Pleural cavity", - "collection_method": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Vacuum Aspiration": { - "anatomical_part": "Trachea", - "collection_method": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Vacuum Aspiration": { - "anatomical_part": "Upper respiratory tract", - "collection_method": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Vacuum Aspiration": { - "anatomical_part": "Anterior Nares", - "collection_method": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Vacuum Aspiration": { - "anatomical_part": "Esophagus", - "collection_method": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Vacuum Aspiration": { - "anatomical_part": "Ethmoid sinus", - "collection_method": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Vacuum Aspiration": { - "anatomical_part": "Nasal Cavity", - "collection_method": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Vacuum Aspiration": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_method": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Vacuum Aspiration": { - "anatomical_part": "Nasopharynx", - "collection_method": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Vacuum Aspiration": { - "anatomical_part": "Oropharynx", - "collection_method": "Vacuum Aspiration", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Biopsy": { - "anatomical_part": "Lower respiratory tract", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Biopsy": { - "anatomical_part": "Bronchus", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Biopsy": { - "anatomical_part": "Lung", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Biopsy": { - "anatomical_part": "Bronchiole", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Biopsy": { - "anatomical_part": "Alveolar sac", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Biopsy": { - "anatomical_part": "Pleural sac", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Biopsy": { - "anatomical_part": "Pleural cavity", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Biopsy": { - "anatomical_part": "Trachea", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Rectum Biopsy": { - "anatomical_part": "Rectum", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Skin Biopsy": { - "anatomical_part": "Skin", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Stomach Biopsy": { - "anatomical_part": "Stomach", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Biopsy": { - "anatomical_part": "Upper respiratory tract", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Biopsy": { - "anatomical_part": "Anterior Nares", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Biopsy": { - "anatomical_part": "Esophagus", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Biopsy": { - "anatomical_part": "Ethmoid sinus", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Biopsy": { - "anatomical_part": "Nasal Cavity", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Biopsy": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Duodenum Biopsy": { - "anatomical_part": "Duodenum", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Biopsy": { - "anatomical_part": "Nasopharynx", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Biopsy": { - "anatomical_part": "Oropharynx", - "collection_method": "Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Needle Biopsy": { - "anatomical_part": "Lower respiratory tract", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Needle Biopsy": { - "anatomical_part": "Bronchus", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Needle Biopsy": { - "anatomical_part": "Lung", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Needle Biopsy": { - "anatomical_part": "Bronchiole", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Needle Biopsy": { - "anatomical_part": "Alveolar sac", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Needle Biopsy": { - "anatomical_part": "Pleural sac", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Needle Biopsy": { - "anatomical_part": "Pleural cavity", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Needle Biopsy": { - "anatomical_part": "Trachea", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Rectum Needle Biopsy": { - "anatomical_part": "Rectum", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Skin Needle Biopsy": { - "anatomical_part": "Skin", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Stomach Needle Biopsy": { - "anatomical_part": "Stomach", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Needle Biopsy": { - "anatomical_part": "Upper respiratory tract", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Needle Biopsy": { - "anatomical_part": "Anterior Nares", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Needle Biopsy": { - "anatomical_part": "Esophagus", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Needle Biopsy": { - "anatomical_part": "Ethmoid sinus", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Needle Biopsy": { - "anatomical_part": "Nasal Cavity", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Needle Biopsy": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Duodenum Needle Biopsy": { - "anatomical_part": "Duodenum", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Needle Biopsy": { - "anatomical_part": "Nasopharynx", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Needle Biopsy": { - "anatomical_part": "Oropharynx", - "collection_method": "Needle Biopsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Lavage": { - "anatomical_part": "Lower respiratory tract", - "collection_method": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Lavage": { - "anatomical_part": "Bronchus", - "collection_method": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Lavage": { - "anatomical_part": "Lung", - "collection_method": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Lavage": { - "anatomical_part": "Pleural sac", - "collection_method": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Lavage": { - "anatomical_part": "Pleural cavity", - "collection_method": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Lavage": { - "anatomical_part": "Trachea", - "collection_method": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Lavage": { - "anatomical_part": "Upper respiratory tract", - "collection_method": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Lavage": { - "anatomical_part": "Anterior Nares", - "collection_method": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Lavage": { - "anatomical_part": "Esophagus", - "collection_method": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Lavage": { - "anatomical_part": "Ethmoid sinus", - "collection_method": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Lavage": { - "anatomical_part": "Nasal Cavity", - "collection_method": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Lavage": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_method": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Lavage": { - "anatomical_part": "Nasopharynx", - "collection_method": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Lavage": { - "anatomical_part": "Oropharynx", - "collection_method": "Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Necropsy": { - "anatomical_part": "Lower respiratory tract", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Necropsy": { - "anatomical_part": "Bronchus", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Necropsy": { - "anatomical_part": "Lung", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Necropsy": { - "anatomical_part": "Bronchiole", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Necropsy": { - "anatomical_part": "Alveolar sac", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Necropsy": { - "anatomical_part": "Pleural sac", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Necropsy": { - "anatomical_part": "Pleural cavity", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Necropsy": { - "anatomical_part": "Trachea", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Rectum Necropsy": { - "anatomical_part": "Rectum", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Skin Necropsy": { - "anatomical_part": "Skin", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Stomach Necropsy": { - "anatomical_part": "Stomach", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Necropsy": { - "anatomical_part": "Upper respiratory tract", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Necropsy": { - "anatomical_part": "Anterior Nares", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Necropsy": { - "anatomical_part": "Esophagus", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Necropsy": { - "anatomical_part": "Ethmoid sinus", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Necropsy": { - "anatomical_part": "Nasal Cavity", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Necropsy": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Duodenum Necropsy": { - "anatomical_part": "Duodenum", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Necropsy": { - "anatomical_part": "Nasopharynx", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Necropsy": { - "anatomical_part": "Oropharynx", - "collection_method": "Necropsy", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Rinsing": { - "anatomical_part": "Lower respiratory tract", - "collection_method": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Rinsing": { - "anatomical_part": "Bronchus", - "collection_method": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Rinsing": { - "anatomical_part": "Lung", - "collection_method": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Rinsing": { - "anatomical_part": "Bronchiole", - "collection_method": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Rinsing": { - "anatomical_part": "Alveolar sac", - "collection_method": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Rinsing": { - "anatomical_part": "Pleural sac", - "collection_method": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Rinsing": { - "anatomical_part": "Pleural cavity", - "collection_method": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Rinsing": { - "anatomical_part": "Trachea", - "collection_method": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Rinsing": { - "anatomical_part": "Upper respiratory tract", - "collection_method": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Rinsing": { - "anatomical_part": "Anterior Nares", - "collection_method": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Rinsing": { - "anatomical_part": "Esophagus", - "collection_method": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Rinsing": { - "anatomical_part": "Ethmoid sinus", - "collection_method": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Rinsing": { - "anatomical_part": "Nasal Cavity", - "collection_method": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Rinsing": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_method": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Rinsing": { - "anatomical_part": "Nasopharynx", - "collection_method": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Rinsing": { - "anatomical_part": "Oropharynx", - "collection_method": "Rinsing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Scraping": { - "anatomical_part": "Bronchiole", - "collection_method": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Scraping": { - "anatomical_part": "Alveolar sac", - "collection_method": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Scraping": { - "anatomical_part": "Pleural sac", - "collection_method": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Scraping": { - "anatomical_part": "Pleural cavity", - "collection_method": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Scraping": { - "anatomical_part": "Trachea", - "collection_method": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Scraping": { - "anatomical_part": "Upper respiratory tract", - "collection_method": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Scraping": { - "anatomical_part": "Anterior Nares", - "collection_method": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Scraping": { - "anatomical_part": "Esophagus", - "collection_method": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Scraping": { - "anatomical_part": "Ethmoid sinus", - "collection_method": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Scraping": { - "anatomical_part": "Nasal Cavity", - "collection_method": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Scraping": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_method": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Scraping": { - "anatomical_part": "Nasopharynx", - "collection_method": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Scraping": { - "anatomical_part": "Oropharynx", - "collection_method": "Scraping", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Swabbing": { - "anatomical_part": "Nasopharynx", - "collection_method": "Swabbing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Swabbing": { - "anatomical_part": "Oropharynx", - "collection_method": "Swabbing", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lower respiratory tract Wash": { - "anatomical_part": "Lower respiratory tract", - "collection_method": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchus Wash": { - "anatomical_part": "Bronchus", - "collection_method": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Lung Wash": { - "anatomical_part": "Lung", - "collection_method": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchiole Wash": { - "anatomical_part": "Bronchiole", - "collection_method": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Alveolar sac Wash": { - "anatomical_part": "Alveolar sac", - "collection_method": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural sac Wash": { - "anatomical_part": "Pleural sac", - "collection_method": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Pleural cavity Wash": { - "anatomical_part": "Pleural cavity", - "collection_method": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Trachea Wash": { - "anatomical_part": "Trachea", - "collection_method": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Upper respiratory tract Wash": { - "anatomical_part": "Upper respiratory tract", - "collection_method": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Anterior Nares Wash": { - "anatomical_part": "Anterior Nares", - "collection_method": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Esophagus Wash": { - "anatomical_part": "Esophagus", - "collection_method": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Ethmoid sinus Wash": { - "anatomical_part": "Ethmoid sinus", - "collection_method": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasal Cavity Wash": { - "anatomical_part": "Nasal Cavity", - "collection_method": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Middle Nasal Turbinate Wash": { - "anatomical_part": "Middle Nasal Turbinate", - "collection_method": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Nasopharynx Wash": { - "anatomical_part": "Nasopharynx", - "collection_method": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Oropharynx Wash": { - "anatomical_part": "Oropharynx", - "collection_method": "Wash", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Bronchoalveolar Lavage": { - "anatomical_part": "Not Applicable", - "collection_method": "Bronchoalveolar Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Gastric Lavage": { - "anatomical_part": "Not Applicable", - "collection_method": "Gastric Lavage", - "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" - }, - "Feces": { - "anatomical_part": "Not Applicable", - "collection_method": "Not Applicable", - "body_product": "Feces", - "anatomical_material": "Not Applicable" - }, - "Mucus": { - "anatomical_part": "Not Applicable", - "collection_method": "Not Applicable", - "body_product": "Mucus", - "anatomical_material": "Not Applicable" - }, - "Sputum": { - "anatomical_part": "Not Applicable", - "collection_method": "Not Applicable", - "body_product": "Sputum", - "anatomical_material": "Not Applicable" - }, - "Sweat": { - "anatomical_part": "Not Applicable", - "collection_method": "Not Applicable", - "body_product": "Sweat", - "anatomical_material": "Not Applicable" - }, - "Tear": { - "anatomical_part": "Not Applicable", - "collection_method": "Not Applicable", - "body_product": "Tear", - "anatomical_material": "Not Applicable" - }, - "Urine": { - "anatomical_part": "Not Applicable", - "collection_method": "Not Applicable", - "body_product": "Urine", - "anatomical_material": "Not Applicable" - }, - "Blood": { - "anatomical_part": "Not Applicable", - "collection_method": "Not Applicable", - "body_product": "Blood", - "anatomical_material": "Not Applicable" - }, - "Cerebrospinal Fluid": { - "anatomical_part": "Not Applicable", - "collection_method": "Not Applicable", - "body_product": "Not Applicable", - "anatomical_material": "Cerebrospinal Fluid" - }, - "Saliva": { - "anatomical_part": "Not Applicable", - "collection_method": "Not Applicable", - "body_product": "Not Applicable", - "anatomical_material": "Saliva" - }, - "Tissue": { - "anatomical_part": "Not Applicable", - "collection_method": "Not Applicable", - "body_product": "Not Applicable", - "anatomical_material": "Tissue" - } } -======= - "checklist": "ERC000033" } ->>>>>>> d8dc1ad3ffdb5cf522e417f9b88df4803dff563a diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index dd1b2703..9fc8386d 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -82,30 +82,30 @@ def translate_gender_to_english(metadata, f_data, mapped_fields, heading): return metadata -def translate_anatomical_part(metadata, f_data, mapped_fields, heading): +def translate_specimen_source(metadata, f_data, mapped_fields, heading): """Translate into english the "muestra" that is written in spanish""" for row in metadata[1:]: for key, val in mapped_fields.items(): m_idx = heading.index(key) if row[m_idx] is None: row[m_idx] = "not provided" - elif "ASPIRADO NASOFARÍNGEO" in row[m_idx].lower(): + elif "ASPIRADO NASOFARÍNGEO" in row[m_idx].upper(): row[m_idx] = "Nasopharynx Aspiration" - elif "ASPIRADO BRONQUIAL" in row[m_idx].lower(): + elif "ASPIRADO BRONQUIAL" in row[m_idx].upper(): row[m_idx] = "Bronchus Aspiration" - elif "ESPUTO" in row[m_idx].lower(): + elif "ESPUTO" in row[m_idx].upper(): row[m_idx] = "Sputum" - elif "EXTRACTO" in row[m_idx].lower(): + elif "EXTRACTO" in row[m_idx].upper(): row[m_idx] = "Scraping" - elif "EXUDADO FARÍNGEO" in row[m_idx].lower(): + elif "EXUDADO FARÍNGEO" in row[m_idx].upper(): row[m_idx] = "Nasopharynx Swabbing" - elif "EXUDADO NASOFARÍNGEO" in row[m_idx].lower(): + elif "EXUDADO NASOFARÍNGEO" in row[m_idx].upper(): row[m_idx] = "Nasopharynx Swabbing" - elif "EXUDADO OROFARINGEO" in row[m_idx].lower(): + elif "EXUDADO OROFARINGEO" in row[m_idx].upper(): row[m_idx] = "Oropharynx Swabbing" - elif "PLACENTA" in row[m_idx].lower(): + elif "PLACENTA" in row[m_idx].upper(): row[m_idx] = "Placenta" - elif "SALIVA" in row[m_idx].lower(): + elif "SALIVA" in row[m_idx].upper(): row[m_idx] = "Saliva" else: row[m_idx] = "not applicable" diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 5e55de41..48feec11 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -16,7 +16,8 @@ "Sample Received Date": "Fecha recepción", "Host Age": "Edad (años)", "Host Gender": "Sexo", - "Diagnostic Pcr Ct Value 1": "PCR genE" + "Diagnostic Pcr Ct Value 1": "PCR genE", + "Specimen source": "Muestra" }, "function": "None" }, @@ -121,4 +122,4 @@ "Diagnostic Pcr Ct Value 1": "", "Authors": "" } -} \ No newline at end of file +} From 27ab6782adf1eef1f529351deae2f9d0ab480bec Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 5 Sep 2022 16:23:06 +0200 Subject: [PATCH 0889/1454] modify excel heading and do not set Environmental System to swab --- relecov_tools/conf/configuration.json | 5 ++--- relecov_tools/read_lab_metadata.py | 4 +++- relecov_tools/schema/institution_schemas/ISCIII.json | 3 +-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 6ba53182..24f2a0cb 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -24,7 +24,7 @@ "Host Age", "Host Gender", "Sequencing Date", - "Rna Extraction Protocol", + "Nucleic acid extraction protocol", "Commercial All-in-one library kit", "Library Preparation Kit", "Enrichment Protocol", @@ -44,8 +44,7 @@ "Diagnostic Pcr Ct Value 1", "Gene Name 2", "Diagnostic Pcr Ct Value-2", - "Analysis Authors", - "Author Submitter", + "Broker Name", "Authors", "Sequence file R1 fastq", "Sequence file R2 fastq" diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 1b509902..fa3ef0af 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -121,7 +121,9 @@ def include_fields_already_set(self, row_sample): return processed_data def include_processed_data(self, metadata): - """Include the data that requires to be processed to set the value""" + """Include the data that requires to be processed to set the value. + This values are checked aginst the available options in the schema + """ new_data = {} p_data = { "host_common_name": {"Human": ["host_scientific_name", "Homo Sapiens"]}, diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 48feec11..01f74ebf 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -106,10 +106,9 @@ "fixed_fields": { "Submitting Institution": "Instituto de Salud Carlos III", "Biological Sample Storage Condition": "-80 C", - "Rna Extraction Protocol": "RT-PCR", + "Nucleic acid extraction protocol": "RT-PCR", "Purpose of sampling": "Surveillance", "Specimen source": "Nasopharyngeal exudate", - "Environmental System": "Swab", "Host": "Human", "Library Preparation Kit": "Illumina DNA Prep", "Enrichment Protocol": "Amplicon", From 2650a7ecfa9bc93706c0a62f9010d265cb7ab36c Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 5 Sep 2022 16:38:23 +0200 Subject: [PATCH 0890/1454] small changes relecov --- relecov_tools/institution_scripts/ISCIII.py | 5 +++-- relecov_tools/schema/relecov_schema.json | 1 + 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index dd1b2703..1a02bb15 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -82,7 +82,7 @@ def translate_gender_to_english(metadata, f_data, mapped_fields, heading): return metadata -def translate_anatomical_part(metadata, f_data, mapped_fields, heading): +def translate_specimen_source(metadata, f_data, mapped_fields, heading): """Translate into english the "muestra" that is written in spanish""" for row in metadata[1:]: for key, val in mapped_fields.items(): @@ -108,5 +108,6 @@ def translate_anatomical_part(metadata, f_data, mapped_fields, heading): elif "SALIVA" in row[m_idx].lower(): row[m_idx] = "Saliva" else: - row[m_idx] = "not applicable" + log.error("The field is not correctly written or is not filled") + stderr.print(f"The field is not correctly written or is not filled") return metadata diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index cf65d7f3..15bec7e4 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -611,6 +611,7 @@ "Middle Nasal Turbinate [UBERON:0001762]", "Anus [UBERON:0001245]", "Duodenum [UBERON:0002114]", + "Pharynx [UBERON:0006562]", "Nasopharynx (NP) [UBERON:0001728]", "Oropharynx (OP) [UBERON:0001729]", "Not Applicable [GENEPIO:0001619]", From 69d954f4a9d8b7672045535a4dc59452e76a40e5 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 5 Sep 2022 17:08:53 +0200 Subject: [PATCH 0891/1454] relecov schema --- relecov_tools/schema/relecov_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 5c984a2b..ac396eea 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1106,7 +1106,7 @@ "label": "Sequencing Date", "fill_mode": "batch" }, - "extraction_protocol": { + "nucleic_acid_extraction_protocol": { "examples": [ "Opentrons custom protocol" ], From cdc626373bf994ee61a4ba83fc8938e958305112 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 5 Sep 2022 17:29:47 +0200 Subject: [PATCH 0892/1454] linitn --- relecov_tools/institution_scripts/ISCIII.py | 4 ++-- relecov_tools/read_lab_metadata.py | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index 2a46a1b3..d0f9ce32 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -109,5 +109,5 @@ def translate_specimen_source(metadata, f_data, mapped_fields, heading): row[m_idx] = "Saliva" else: log.error("The field is not correctly written or is not filled") - stderr.print(f"The field is not correctly written or is not filled") - return metadata + stderr.print("The field is not correctly written or is not filled") + return metadata diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index fa3ef0af..3282f04c 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -16,6 +16,7 @@ highlight=False, force_terminal=relecov_tools.utils.rich_force_colors(), ) +# class RelecovMetadata: From fda0b9b5410c64be60097baca7b460ffce6fd4f6 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 5 Sep 2022 22:14:36 +0200 Subject: [PATCH 0893/1454] changed collection_device by collection_method, because collection_device is not in the schema --- ...anatomical_material_collection_method.json | 330 +++++++++--------- 1 file changed, 165 insertions(+), 165 deletions(-) diff --git a/relecov_tools/conf/anatomical_material_collection_method.json b/relecov_tools/conf/anatomical_material_collection_method.json index a5060f9a..6ee6ae7f 100644 --- a/relecov_tools/conf/anatomical_material_collection_method.json +++ b/relecov_tools/conf/anatomical_material_collection_method.json @@ -1,989 +1,989 @@ { "Lower respiratory tract Aspiration": { "anatomical_part": "Lower respiratory tract", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchus Aspiration": { "anatomical_part": "Bronchus", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lung Aspiration": { "anatomical_part": "Lung", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchiole Aspiration": { "anatomical_part": "Bronchiole", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Alveolar sac Aspiration": { "anatomical_part": "Alveolar sac", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Aspiration": { "anatomical_part": "Pleural sac", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Aspiration": { "anatomical_part": "Pleural cavity", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Aspiration": { "anatomical_part": "Trachea", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Aspiration": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Aspiration": { "anatomical_part": "Anterior Nares", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Aspiration": { "anatomical_part": "Esophagus", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Aspiration": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Aspiration": { "anatomical_part": "Nasal Cavity", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Aspiration": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Aspiration": { "anatomical_part": "Nasopharynx", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Aspiration": { "anatomical_part": "Oropharynx", - "collection_device": "Aspiration", + "collection_method": "Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lower respiratory tract Vacuum Aspiration": { "anatomical_part": "Lower respiratory tract", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchus Vacuum Aspiration": { "anatomical_part": "Bronchus", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lung Vacuum Aspiration": { "anatomical_part": "Lung", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchiole Vacuum Aspiration": { "anatomical_part": "Bronchiole", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Alveolar sac Vacuum Aspiration": { "anatomical_part": "Alveolar sac", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Vacuum Aspiration": { "anatomical_part": "Pleural sac", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Vacuum Aspiration": { "anatomical_part": "Pleural cavity", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Vacuum Aspiration": { "anatomical_part": "Trachea", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Vacuum Aspiration": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Vacuum Aspiration": { "anatomical_part": "Anterior Nares", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Vacuum Aspiration": { "anatomical_part": "Esophagus", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Vacuum Aspiration": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Vacuum Aspiration": { "anatomical_part": "Nasal Cavity", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Vacuum Aspiration": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Vacuum Aspiration": { "anatomical_part": "Nasopharynx", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Vacuum Aspiration": { "anatomical_part": "Oropharynx", - "collection_device": "Vacuum Aspiration", + "collection_method": "Vacuum Aspiration", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lower respiratory tract Biopsy": { "anatomical_part": "Lower respiratory tract", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchus Biopsy": { "anatomical_part": "Bronchus", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lung Biopsy": { "anatomical_part": "Lung", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchiole Biopsy": { "anatomical_part": "Bronchiole", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Alveolar sac Biopsy": { "anatomical_part": "Alveolar sac", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Biopsy": { "anatomical_part": "Pleural sac", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Biopsy": { "anatomical_part": "Pleural cavity", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Biopsy": { "anatomical_part": "Trachea", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Rectum Biopsy": { "anatomical_part": "Rectum", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Skin Biopsy": { "anatomical_part": "Skin", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Stomach Biopsy": { "anatomical_part": "Stomach", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Biopsy": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Biopsy": { "anatomical_part": "Anterior Nares", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Biopsy": { "anatomical_part": "Esophagus", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Biopsy": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Biopsy": { "anatomical_part": "Nasal Cavity", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Biopsy": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Duodenum Biopsy": { "anatomical_part": "Duodenum", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Biopsy": { "anatomical_part": "Nasopharynx", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Biopsy": { "anatomical_part": "Oropharynx", - "collection_device": "Biopsy", + "collection_method": "Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lower respiratory tract Needle Biopsy": { "anatomical_part": "Lower respiratory tract", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchus Needle Biopsy": { "anatomical_part": "Bronchus", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lung Needle Biopsy": { "anatomical_part": "Lung", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchiole Needle Biopsy": { "anatomical_part": "Bronchiole", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Alveolar sac Needle Biopsy": { "anatomical_part": "Alveolar sac", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Needle Biopsy": { "anatomical_part": "Pleural sac", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Needle Biopsy": { "anatomical_part": "Pleural cavity", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Needle Biopsy": { "anatomical_part": "Trachea", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Rectum Needle Biopsy": { "anatomical_part": "Rectum", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Skin Needle Biopsy": { "anatomical_part": "Skin", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Stomach Needle Biopsy": { "anatomical_part": "Stomach", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Needle Biopsy": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Needle Biopsy": { "anatomical_part": "Anterior Nares", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Needle Biopsy": { "anatomical_part": "Esophagus", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Needle Biopsy": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Needle Biopsy": { "anatomical_part": "Nasal Cavity", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Needle Biopsy": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Duodenum Needle Biopsy": { "anatomical_part": "Duodenum", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Needle Biopsy": { "anatomical_part": "Nasopharynx", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Needle Biopsy": { "anatomical_part": "Oropharynx", - "collection_device": "Needle Biopsy", + "collection_method": "Needle Biopsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lower respiratory tract Lavage": { "anatomical_part": "Lower respiratory tract", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchus Lavage": { "anatomical_part": "Bronchus", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lung Lavage": { "anatomical_part": "Lung", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Lavage": { "anatomical_part": "Pleural sac", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Lavage": { "anatomical_part": "Pleural cavity", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Lavage": { "anatomical_part": "Trachea", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Lavage": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Lavage": { "anatomical_part": "Anterior Nares", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Lavage": { "anatomical_part": "Esophagus", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Lavage": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Lavage": { "anatomical_part": "Nasal Cavity", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Lavage": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Lavage": { "anatomical_part": "Nasopharynx", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Lavage": { "anatomical_part": "Oropharynx", - "collection_device": "Lavage", + "collection_method": "Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lower respiratory tract Necropsy": { "anatomical_part": "Lower respiratory tract", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchus Necropsy": { "anatomical_part": "Bronchus", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lung Necropsy": { "anatomical_part": "Lung", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchiole Necropsy": { "anatomical_part": "Bronchiole", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Alveolar sac Necropsy": { "anatomical_part": "Alveolar sac", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Necropsy": { "anatomical_part": "Pleural sac", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Necropsy": { "anatomical_part": "Pleural cavity", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Necropsy": { "anatomical_part": "Trachea", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Rectum Necropsy": { "anatomical_part": "Rectum", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Skin Necropsy": { "anatomical_part": "Skin", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Stomach Necropsy": { "anatomical_part": "Stomach", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Necropsy": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Necropsy": { "anatomical_part": "Anterior Nares", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Necropsy": { "anatomical_part": "Esophagus", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Necropsy": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Necropsy": { "anatomical_part": "Nasal Cavity", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Necropsy": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Duodenum Necropsy": { "anatomical_part": "Duodenum", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Necropsy": { "anatomical_part": "Nasopharynx", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Necropsy": { "anatomical_part": "Oropharynx", - "collection_device": "Necropsy", + "collection_method": "Necropsy", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lower respiratory tract Rinsing": { "anatomical_part": "Lower respiratory tract", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchus Rinsing": { "anatomical_part": "Bronchus", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lung Rinsing": { "anatomical_part": "Lung", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchiole Rinsing": { "anatomical_part": "Bronchiole", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Alveolar sac Rinsing": { "anatomical_part": "Alveolar sac", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Rinsing": { "anatomical_part": "Pleural sac", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Rinsing": { "anatomical_part": "Pleural cavity", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Rinsing": { "anatomical_part": "Trachea", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Rinsing": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Rinsing": { "anatomical_part": "Anterior Nares", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Rinsing": { "anatomical_part": "Esophagus", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Rinsing": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Rinsing": { "anatomical_part": "Nasal Cavity", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Rinsing": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Rinsing": { "anatomical_part": "Nasopharynx", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Rinsing": { "anatomical_part": "Oropharynx", - "collection_device": "Rinsing", + "collection_method": "Rinsing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchiole Scraping": { "anatomical_part": "Bronchiole", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Alveolar sac Scraping": { "anatomical_part": "Alveolar sac", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Scraping": { "anatomical_part": "Pleural sac", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Scraping": { "anatomical_part": "Pleural cavity", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Scraping": { "anatomical_part": "Trachea", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Scraping": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Scraping": { "anatomical_part": "Anterior Nares", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Scraping": { "anatomical_part": "Esophagus", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Scraping": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Scraping": { "anatomical_part": "Nasal Cavity", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Scraping": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Scraping": { "anatomical_part": "Nasopharynx", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Scraping": { "anatomical_part": "Oropharynx", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Swabbing": { "anatomical_part": "Nasopharynx", - "collection_device": "Swabbing", + "collection_method": "Swabbing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Swabbing": { "anatomical_part": "Oropharynx", - "collection_device": "Swabbing", + "collection_method": "Swabbing", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lower respiratory tract Wash": { "anatomical_part": "Lower respiratory tract", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchus Wash": { "anatomical_part": "Bronchus", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Lung Wash": { "anatomical_part": "Lung", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchiole Wash": { "anatomical_part": "Bronchiole", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Alveolar sac Wash": { "anatomical_part": "Alveolar sac", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural sac Wash": { "anatomical_part": "Pleural sac", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Pleural cavity Wash": { "anatomical_part": "Pleural cavity", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Trachea Wash": { "anatomical_part": "Trachea", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Upper respiratory tract Wash": { "anatomical_part": "Upper respiratory tract", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Anterior Nares Wash": { "anatomical_part": "Anterior Nares", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Esophagus Wash": { "anatomical_part": "Esophagus", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Ethmoid sinus Wash": { "anatomical_part": "Ethmoid sinus", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasal Cavity Wash": { "anatomical_part": "Nasal Cavity", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Middle Nasal Turbinate Wash": { "anatomical_part": "Middle Nasal Turbinate", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Nasopharynx Wash": { "anatomical_part": "Nasopharynx", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Oropharynx Wash": { "anatomical_part": "Oropharynx", - "collection_device": "Wash", + "collection_method": "Wash", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Bronchoalveolar Lavage": { "anatomical_part": "Not Applicable", - "collection_device": "Bronchoalveolar Lavage" + "collection_method": "Bronchoalveolar Lavage" }, "Gastric Lavage": { "anatomical_part": "Not Applicable", - "collection_device": "Gastric Lavage", + "collection_method": "Gastric Lavage", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Feces": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Feces", "anatomical_material": "Not Applicable" }, "Mucus": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Mucus", "anatomical_material": "Not Applicable" }, "Sputum": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Sputum", "anatomical_material": "Not Applicable" }, "Sweat": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Sweat", "anatomical_material": "Not Applicable" }, "Tear": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Tear", "anatomical_material": "Not Applicable" }, "Urine": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Urine", "anatomical_material": "Not Applicable" }, "Blood": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Blood", "anatomical_material": "Not Applicable" }, "Cerebrospinal Fluid": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Not Applicable", "anatomical_material": "Cerebrospinal Fluid" }, "Saliva": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Not Applicable", "anatomical_material": "Saliva" }, "Tissue": { "anatomical_part": "Not Applicable", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Not Applicable", "anatomical_material": "Tissue" } From 149b23b0d51b8f4dc0a570296b55844cee0530a4 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 6 Sep 2022 09:30:25 +0200 Subject: [PATCH 0894/1454] removed villages from cities json --- relecov_tools/conf/geo_loc_cities.json | 12063 +---------------------- 1 file changed, 56 insertions(+), 12007 deletions(-) diff --git a/relecov_tools/conf/geo_loc_cities.json b/relecov_tools/conf/geo_loc_cities.json index 58ce5648..8ccdbc26 100644 --- a/relecov_tools/conf/geo_loc_cities.json +++ b/relecov_tools/conf/geo_loc_cities.json @@ -1,12226 +1,275 @@ -[ - { - "geo_loc_city": "Madrid", +{ + "Madrid": { "geo_loc_latitude": "40.4167", "geo_loc_longitude": "-3.7167" }, { - "geo_loc_city": "Barcelona", + "Barcelona": { "geo_loc_latitude": "41.3825", "geo_loc_longitude": "2.1769" }, { - "geo_loc_city": "Sevilla", + "Sevilla": { "geo_loc_latitude": "37.3900", "geo_loc_longitude": "-5.9900" }, { - "geo_loc_city": "Málaga", + "Málaga": { "geo_loc_latitude": "36.7194", "geo_loc_longitude": "-4.4200" }, { - "geo_loc_city": "Valencia", + "Valencia": { "geo_loc_latitude": "39.4700", "geo_loc_longitude": "-0.3764" }, { - "geo_loc_city": "Zaragoza", + "Zaragoza": { "geo_loc_latitude": "41.6483", "geo_loc_longitude": "-0.8830" }, { - "geo_loc_city": "Palma de Mallorca", + "Palma de Mallorca": { "geo_loc_latitude": "39.5667", "geo_loc_longitude": "2.6500" }, { - "geo_loc_city": "Murcia", + "Murcia": { "geo_loc_latitude": "37.9861", "geo_loc_longitude": "-1.1303" }, { - "geo_loc_city": "Las Palmas", + "Las Palmas": { "geo_loc_latitude": "28.1272", "geo_loc_longitude": "-15.4314" }, { - "geo_loc_city": "A Coruña", + "A Coruña": { "geo_loc_latitude": "43.3713", "geo_loc_longitude": "-8.4188" }, { - "geo_loc_city": "Bilbao", + "Bilbao": { "geo_loc_latitude": "43.2569", "geo_loc_longitude": "-2.9236" }, { - "geo_loc_city": "Alicante", + "Alicante": { "geo_loc_latitude": "38.3453", "geo_loc_longitude": "-0.4831" }, { - "geo_loc_city": "Córdoba", + "Córdoba": { "geo_loc_latitude": "37.8845", "geo_loc_longitude": "-4.7796" }, { - "geo_loc_city": "Valladolid", + "Valladolid": { "geo_loc_latitude": "41.6528", "geo_loc_longitude": "-4.7236" }, { - "geo_loc_city": "Vigo", + "Vigo": { "geo_loc_latitude": "42.2314", "geo_loc_longitude": "-8.7124" }, { - "geo_loc_city": "Gijón", + "Gijón": { "geo_loc_latitude": "43.5333", "geo_loc_longitude": "-5.7000" }, { - "geo_loc_city": "Vitoria", + "Vitoria": { "geo_loc_latitude": "42.8500", "geo_loc_longitude": "-2.6833" }, { - "geo_loc_city": "Elche", - "geo_loc_latitude": "38.2669", - "geo_loc_longitude": "-0.6983" - }, - { - "geo_loc_city": "Granada", + "Granada": { "geo_loc_latitude": "37.1781", "geo_loc_longitude": "-3.6008" }, { - "geo_loc_city": "Tarrasa", - "geo_loc_latitude": "41.5611", - "geo_loc_longitude": "2.0081" - }, - { - "geo_loc_city": "Badalona", - "geo_loc_latitude": "41.4333", - "geo_loc_longitude": "2.2333" - }, - { - "geo_loc_city": "Oviedo", + "Oviedo": { "geo_loc_latitude": "43.3600", "geo_loc_longitude": "-5.8450" }, { - "geo_loc_city": "Petrel", - "geo_loc_latitude": "38.4789", - "geo_loc_longitude": "-0.7967" - }, - { - "geo_loc_city": "Sabadell", - "geo_loc_latitude": "41.5483", - "geo_loc_longitude": "2.1075" - }, - { - "geo_loc_city": "Cartagena", - "geo_loc_latitude": "37.6000", - "geo_loc_longitude": "-0.9819" - }, - { - "geo_loc_city": "Jerez de la Frontera", - "geo_loc_latitude": "36.6817", - "geo_loc_longitude": "-6.1378" - }, - { - "geo_loc_city": "Santa Cruz de Tenerife", + "Santa Cruz de Tenerife": { "geo_loc_latitude": "28.4667", "geo_loc_longitude": "-16.2500" }, { - "geo_loc_city": "Pamplona", + "Pamplona": { "geo_loc_latitude": "42.8167", "geo_loc_longitude": "-1.6500" }, { - "geo_loc_city": "León", + "León": { "geo_loc_latitude": "42.6056", "geo_loc_longitude": "-5.5700" }, { - "geo_loc_city": "Almería", + "Almería": { "geo_loc_latitude": "36.8403", "geo_loc_longitude": "-2.4681" }, { - "geo_loc_city": "Logroño", + "Logroño": { "geo_loc_latitude": "42.4650", "geo_loc_longitude": "-2.4456" }, { - "geo_loc_city": "Fuenlabrada", - "geo_loc_latitude": "40.2833", - "geo_loc_longitude": "-3.8000" - }, - { - "geo_loc_city": "Leganés", - "geo_loc_latitude": "40.3281", - "geo_loc_longitude": "-3.7644" - }, - { - "geo_loc_city": "Donostia", + "Donostia": { "geo_loc_latitude": "43.3200", "geo_loc_longitude": "-1.9800" }, { - "geo_loc_city": "Mataró", - "geo_loc_latitude": "41.5421", - "geo_loc_longitude": "2.4445" - }, - { - "geo_loc_city": "Albacete", + "Albacete": { "geo_loc_latitude": "38.9956", "geo_loc_longitude": "-1.8558" }, { - "geo_loc_city": "Castellón de la Plana", + "Castellón de la Plana": { "geo_loc_latitude": "39.9831", "geo_loc_longitude": "-0.0331" }, { - "geo_loc_city": "Santander", + "Santander": { "geo_loc_latitude": "43.4628", "geo_loc_longitude": "-3.8050" }, { - "geo_loc_city": "Getafe", - "geo_loc_latitude": "40.3047", - "geo_loc_longitude": "-3.7311" - }, - { - "geo_loc_city": "Alcorcón", - "geo_loc_latitude": "40.3500", - "geo_loc_longitude": "-3.8333" - }, - { - "geo_loc_city": "Burgos", + "Burgos": { "geo_loc_latitude": "42.3500", "geo_loc_longitude": "-3.6822" }, { - "geo_loc_city": "Guadalajara", + "Guadalajara": { "geo_loc_latitude": "40.6337", "geo_loc_longitude": "-3.1674" }, { - "geo_loc_city": "La Laguna", - "geo_loc_latitude": "28.4853", - "geo_loc_longitude": "-16.3167" - }, - { - "geo_loc_city": "Badajoz", + "Badajoz": { "geo_loc_latitude": "38.8803", "geo_loc_longitude": "-6.9753" }, { - "geo_loc_city": "Marbella", - "geo_loc_latitude": "36.5167", - "geo_loc_longitude": "-4.8833" - }, - { - "geo_loc_city": "Salamanca", + "Salamanca": { "geo_loc_latitude": "40.9667", "geo_loc_longitude": "-5.6639" }, { - "geo_loc_city": "Huelva", + "Huelva": { "geo_loc_latitude": "37.2500", "geo_loc_longitude": "-6.9500" }, { - "geo_loc_city": "Ciudad de Melilla", + "Ciudad de Melilla": { "geo_loc_latitude": "35.2937", "geo_loc_longitude": "-2.9383" }, { - "geo_loc_city": "Tarragona", + "Tarragona": { "geo_loc_latitude": "41.1187", "geo_loc_longitude": "1.2453" }, { - "geo_loc_city": "Dos Hermanas", - "geo_loc_latitude": "37.2836", - "geo_loc_longitude": "-5.9222" - }, - { - "geo_loc_city": "Torrejón de Ardoz", - "geo_loc_latitude": "40.4614", - "geo_loc_longitude": "-3.4978" - }, - { - "geo_loc_city": "Algeciras", - "geo_loc_latitude": "36.1275", - "geo_loc_longitude": "-5.4539" - }, - { - "geo_loc_city": "Cádiz", + "Cádiz": { "geo_loc_latitude": "36.5350", "geo_loc_longitude": "-6.2975" }, { - "geo_loc_city": "Jaén", + "Jaén": { "geo_loc_latitude": "37.7667", "geo_loc_longitude": "-3.7711" }, { - "geo_loc_city": "Reus", - "geo_loc_latitude": "41.1549", - "geo_loc_longitude": "1.1087" - }, - { - "geo_loc_city": "Girona", + "Girona": { "geo_loc_latitude": "41.9833", "geo_loc_longitude": "2.8167" }, { - "geo_loc_city": "San Vicente de Baracaldo", - "geo_loc_latitude": "43.2972", - "geo_loc_longitude": "-2.9917" - }, - { - "geo_loc_city": "Lugo", + "Lugo": { "geo_loc_latitude": "43.0167", "geo_loc_longitude": "-7.5500" }, { - "geo_loc_city": "Roquetas de Mar", - "geo_loc_latitude": "36.7642", - "geo_loc_longitude": "-2.6147" - }, - { - "geo_loc_city": "Cáceres", + "Cáceres": { "geo_loc_latitude": "39.4833", "geo_loc_longitude": "-6.3667" }, { - "geo_loc_city": "Las Rozas de Madrid", - "geo_loc_latitude": "40.4917", - "geo_loc_longitude": "-3.8733" - }, - { - "geo_loc_city": "Lorca", - "geo_loc_latitude": "37.6798", - "geo_loc_longitude": "-1.6944" - }, - { - "geo_loc_city": "San Fernando", - "geo_loc_latitude": "36.4667", - "geo_loc_longitude": "-6.2000" - }, - { - "geo_loc_city": "San Cugat del Vallés", - "geo_loc_latitude": "41.4735", - "geo_loc_longitude": "2.0852" - }, - { - "geo_loc_city": "Santiago de Compostela", - "geo_loc_latitude": "42.8778", - "geo_loc_longitude": "-8.5444" - }, - { - "geo_loc_city": "San Sebastián de los Reyes", - "geo_loc_latitude": "40.5469", - "geo_loc_longitude": "-3.6258" - }, - { - "geo_loc_city": "Vaciamadrid", - "geo_loc_latitude": "40.3394", - "geo_loc_longitude": "-3.5181" - }, - { - "geo_loc_city": "El Puerto de Santa María", - "geo_loc_latitude": "36.6000", - "geo_loc_longitude": "-6.2167" - }, - { - "geo_loc_city": "Toledo", + "Toledo": { "geo_loc_latitude": "39.8567", "geo_loc_longitude": "-4.0244" }, { - "geo_loc_city": "Mijas", - "geo_loc_latitude": "36.6000", - "geo_loc_longitude": "-4.6333" - }, - { - "geo_loc_city": "Chiclana de la Frontera", - "geo_loc_latitude": "36.4167", - "geo_loc_longitude": "-6.1500" - }, - { - "geo_loc_city": "Torrevieja", - "geo_loc_latitude": "37.9778", - "geo_loc_longitude": "-0.6833" - }, - { - "geo_loc_city": "San Baudilio de Llobregat", - "geo_loc_latitude": "41.3458", - "geo_loc_longitude": "2.0417" - }, - { - "geo_loc_city": "Ceuta", + "Ceuta": { "geo_loc_latitude": "35.8867", "geo_loc_longitude": "-5.3000" }, { - "geo_loc_city": "Melilla", + "Melilla": { "geo_loc_latitude": "35.2919", "geo_loc_longitude": "-2.93848" }, { - "geo_loc_city": "Torrente", - "geo_loc_latitude": "39.4365", - "geo_loc_longitude": "-0.4679" - }, - { - "geo_loc_city": "El Ejido", - "geo_loc_latitude": "36.7831", - "geo_loc_longitude": "-2.8167" - }, - { - "geo_loc_city": "Pontevedra", - "geo_loc_latitude": "42.4333", - "geo_loc_longitude": "-8.6333" - }, - { - "geo_loc_city": "Fuengirola", - "geo_loc_latitude": "36.5417", - "geo_loc_longitude": "-4.6250" - }, - { - "geo_loc_city": "Arona", - "geo_loc_latitude": "28.0996", - "geo_loc_longitude": "-16.6809" - }, - { - "geo_loc_city": "Vélez-Málaga", - "geo_loc_latitude": "36.7833", - "geo_loc_longitude": "-4.1000" - }, - { - "geo_loc_city": "Rubí", - "geo_loc_latitude": "41.4933", - "geo_loc_longitude": "2.0325" - }, - { - "geo_loc_city": "Manresa", - "geo_loc_latitude": "41.7264", - "geo_loc_longitude": "1.8292" - }, - { - "geo_loc_city": "Avilés", - "geo_loc_latitude": "43.5561", - "geo_loc_longitude": "-5.9083" - }, - { - "geo_loc_city": "Valdemoro", - "geo_loc_latitude": "40.1908", - "geo_loc_longitude": "-3.6742" - }, - { - "geo_loc_city": "Gandía", - "geo_loc_latitude": "38.9667", - "geo_loc_longitude": "-0.1833" - }, - { - "geo_loc_city": "Alcalá de Guadaira", - "geo_loc_latitude": "37.3333", - "geo_loc_longitude": "-5.8500" - }, - { - "geo_loc_city": "Molina de Segura", - "geo_loc_latitude": "38.0548", - "geo_loc_longitude": "-1.2131" - }, - { - "geo_loc_city": "Majadahonda", - "geo_loc_latitude": "40.4728", - "geo_loc_longitude": "-3.8722" - }, - { - "geo_loc_city": "Paterna", - "geo_loc_latitude": "39.5028", - "geo_loc_longitude": "-0.4406" - }, - { - "geo_loc_city": "Benidorm", - "geo_loc_latitude": "38.5342", - "geo_loc_longitude": "-0.1314" - }, - { - "geo_loc_city": "Sanlúcar de Barrameda", - "geo_loc_latitude": "36.7667", - "geo_loc_longitude": "-6.3500" - }, - { - "geo_loc_city": "Torremolinos", - "geo_loc_latitude": "36.6218", - "geo_loc_longitude": "-4.5003" - }, - { - "geo_loc_city": "Benalmádena", - "geo_loc_latitude": "36.6000", - "geo_loc_longitude": "-4.5167" - }, - { - "geo_loc_city": "Villanueva y Geltrú", - "geo_loc_latitude": "41.2243", - "geo_loc_longitude": "1.7259" - }, - { - "geo_loc_city": "Castelldefels", - "geo_loc_latitude": "41.2800", - "geo_loc_longitude": "1.9767" - }, - { - "geo_loc_city": "Viladecáns", - "geo_loc_latitude": "41.3158", - "geo_loc_longitude": "2.0194" - }, - { - "geo_loc_city": "Sagunto", - "geo_loc_latitude": "39.6764", - "geo_loc_longitude": "-0.2733" - }, - { - "geo_loc_city": "Ferrol", - "geo_loc_latitude": "43.4844", - "geo_loc_longitude": "-8.2328" - }, - { - "geo_loc_city": "El Prat de Llobregat", - "geo_loc_latitude": "41.3246", - "geo_loc_longitude": "2.0953" - }, - { - "geo_loc_city": "Arrecife", - "geo_loc_latitude": "28.9625", - "geo_loc_longitude": "-13.5506" - }, - { - "geo_loc_city": "Collado-Villalba", - "geo_loc_latitude": "40.6333", - "geo_loc_longitude": "-4.0083" - }, - { - "geo_loc_city": "La Línea de la Concepción", - "geo_loc_latitude": "36.1611", - "geo_loc_longitude": "-5.3486" - }, - { - "geo_loc_city": "Irún", - "geo_loc_latitude": "43.3378", - "geo_loc_longitude": "-1.7888" - }, - { - "geo_loc_city": "Granollers", - "geo_loc_latitude": "41.6083", - "geo_loc_longitude": "2.2889" - }, - { - "geo_loc_city": "Zamora", + "Zamora": { "geo_loc_latitude": "41.5033", "geo_loc_longitude": "-5.7556" }, { - "geo_loc_city": "Mérida", - "geo_loc_latitude": "38.9000", - "geo_loc_longitude": "-6.3333" - }, - { - "geo_loc_city": "Alcoy", - "geo_loc_latitude": "38.6983", - "geo_loc_longitude": "-0.4736" - }, - { - "geo_loc_city": "San Vicente del Raspeig", - "geo_loc_latitude": "38.3964", - "geo_loc_longitude": "-0.5253" - }, - { - "geo_loc_city": "Motril", - "geo_loc_latitude": "36.7500", - "geo_loc_longitude": "-3.5167" - }, - { - "geo_loc_city": "Avila", + "Avila": { "geo_loc_latitude": "40.6500", "geo_loc_longitude": "-4.6833" }, { - "geo_loc_city": "Linares", - "geo_loc_latitude": "38.0833", - "geo_loc_longitude": "-3.6333" - }, - { - "geo_loc_city": "Cuenca", + "Cuenca": { "geo_loc_latitude": "40.0667", "geo_loc_longitude": "-2.1500" }, { - "geo_loc_city": "Huesca", + "Huesca": { "geo_loc_latitude": "42.1333", "geo_loc_longitude": "-0.4167" }, { - "geo_loc_city": "San Bartolomé", - "geo_loc_latitude": "27.9254", - "geo_loc_longitude": "-15.5726" - }, - { - "geo_loc_city": "Pinto", - "geo_loc_latitude": "40.2500", - "geo_loc_longitude": "-3.7000" - }, - { - "geo_loc_city": "Elda", - "geo_loc_latitude": "38.4789", - "geo_loc_longitude": "-0.7967" - }, - { - "geo_loc_city": "Colmenar Viejo", - "geo_loc_latitude": "40.6589", - "geo_loc_longitude": "-3.7658" - }, - { - "geo_loc_city": "Mollet", - "geo_loc_latitude": "41.5356", - "geo_loc_longitude": "2.2107" - }, - { - "geo_loc_city": "Torrelavega", - "geo_loc_latitude": "43.3531", - "geo_loc_longitude": "-4.0458" - }, - { - "geo_loc_city": "Pola de Siero", - "geo_loc_latitude": "43.3833", - "geo_loc_longitude": "-5.6500" - }, - { - "geo_loc_city": "Villareal", - "geo_loc_latitude": "39.9378", - "geo_loc_longitude": "-0.1014" - }, - { - "geo_loc_city": "Granadilla de Abona", - "geo_loc_latitude": "28.1167", - "geo_loc_longitude": "-16.5833" - }, - { - "geo_loc_city": "Ibiza", - "geo_loc_latitude": "38.9089", - "geo_loc_longitude": "1.4328" - }, - { - "geo_loc_city": "Utrera", - "geo_loc_latitude": "37.1830", - "geo_loc_longitude": "-5.7670" - }, - { - "geo_loc_city": "Adeje", - "geo_loc_latitude": "28.1167", - "geo_loc_longitude": "-16.7167" - }, - { - "geo_loc_city": "Rincón de la Victoria", - "geo_loc_latitude": "36.7167", - "geo_loc_longitude": "-4.2833" - }, - { - "geo_loc_city": "Figueras", - "geo_loc_latitude": "42.2667", - "geo_loc_longitude": "2.9650" - }, - { - "geo_loc_city": "Esplugas de Llobregat", - "geo_loc_latitude": "41.3767", - "geo_loc_longitude": "2.0858" - }, - { - "geo_loc_city": "Gavá", - "geo_loc_latitude": "41.3072", - "geo_loc_longitude": "2.0039" - }, - { - "geo_loc_city": "Puertollano", - "geo_loc_latitude": "38.6833", - "geo_loc_longitude": "-4.1167" - }, - { - "geo_loc_city": "Mairena del Aljarafe", - "geo_loc_latitude": "37.3333", - "geo_loc_longitude": "-6.0667" - }, - { - "geo_loc_city": "Santurce-Antiguo", - "geo_loc_latitude": "43.3303", - "geo_loc_longitude": "-3.0314" - }, - { - "geo_loc_city": "Portugalete", - 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"geo_loc_longitude": "-5.6667" - }, - { - "geo_loc_city": "Potríes", - "geo_loc_latitude": "38.9153", - "geo_loc_longitude": "-0.2044" - }, - { - "geo_loc_city": "Campaspero", - "geo_loc_latitude": "41.4917", - "geo_loc_longitude": "-4.1944" - }, - { - "geo_loc_city": "La Seca", - "geo_loc_latitude": "41.4150", - "geo_loc_longitude": "-4.9069" - }, - { - "geo_loc_city": "Nalda", - "geo_loc_latitude": "42.3297", - "geo_loc_longitude": "-2.4797" - }, - { - "geo_loc_city": "Santa Eulalia", - "geo_loc_latitude": "43.4167", - "geo_loc_longitude": "-5.4000" - }, - { - "geo_loc_city": "Benalúa de las Villas", - "geo_loc_latitude": "37.4333", - "geo_loc_longitude": "-3.6833" - }, - { - "geo_loc_city": "Algimia de Alfara", - "geo_loc_latitude": "39.7531", - "geo_loc_longitude": "-0.3617" - }, - { - "geo_loc_city": "Villabrágima", - "geo_loc_latitude": "41.8167", - "geo_loc_longitude": "-5.1167" - }, - { - "geo_loc_city": "El Robledo", - "geo_loc_latitude": "39.2167", - "geo_loc_longitude": "-4.2833" - }, - { - "geo_loc_city": "San Amaro", - "geo_loc_latitude": "42.3731", - "geo_loc_longitude": "-8.0731" - }, - { - "geo_loc_city": "Ayerbe", - "geo_loc_latitude": "42.2767", - "geo_loc_longitude": "-0.6892" - }, - { - "geo_loc_city": "Jayena", - "geo_loc_latitude": "36.9500", - "geo_loc_longitude": "-3.8167" - }, - { - "geo_loc_city": "Santa Eulalia", - "geo_loc_latitude": "40.5667", - "geo_loc_longitude": "-1.3167" - }, - { - "geo_loc_city": "Benlloch", - "geo_loc_latitude": "40.2106", - "geo_loc_longitude": "0.0269" - }, - { - "geo_loc_city": "Llanera de Ranes", - "geo_loc_latitude": "38.9944", - "geo_loc_longitude": "-0.5753" - }, - { - "geo_loc_city": "Viladrau", - "geo_loc_latitude": "41.8500", - "geo_loc_longitude": "2.4000" - }, - { - "geo_loc_city": "Valverde de Mérida", - "geo_loc_latitude": "38.9108", - "geo_loc_longitude": "-6.2203" - }, - { - "geo_loc_city": "Santa Elena de Jamuz", - "geo_loc_latitude": "42.2667", - "geo_loc_longitude": "-5.8833" - }, - { - "geo_loc_city": "Solórzano", - "geo_loc_latitude": "43.3869", - "geo_loc_longitude": "-3.5864" - }, - { - "geo_loc_city": "Calders", - "geo_loc_latitude": "41.7906", - "geo_loc_longitude": "1.9878" - }, - { - "geo_loc_city": "Folgoso de la Ribera", - "geo_loc_latitude": "42.6433", - "geo_loc_longitude": "-6.3192" - }, - { - "geo_loc_city": "Boltaña", - "geo_loc_latitude": "42.4500", - "geo_loc_longitude": "0.0667" - }, - { - "geo_loc_city": "Coreses", - "geo_loc_latitude": "41.5500", - "geo_loc_longitude": "-5.6167" - }, - { - "geo_loc_city": "Santa Bárbara de Casa", - "geo_loc_latitude": "37.8000", - "geo_loc_longitude": "-7.1833" - }, - { - "geo_loc_city": "Gabarda", - "geo_loc_latitude": "39.0917", - "geo_loc_longitude": "-0.5600" - }, - { - "geo_loc_city": "Torrecampo", - "geo_loc_latitude": "38.4667", - "geo_loc_longitude": "-4.6667" - }, - { - "geo_loc_city": "Hortaleza", - "geo_loc_latitude": "40.4667", - "geo_loc_longitude": "-3.6333" - }, - { - "geo_loc_city": "Arróniz", - "geo_loc_latitude": "42.5889", - "geo_loc_longitude": "-2.0914" - }, - { - "geo_loc_city": "Ademuz", - "geo_loc_latitude": "40.0667", - "geo_loc_longitude": "-1.2833" - }, - { - "geo_loc_city": "Nívar", - "geo_loc_latitude": "37.2667", - "geo_loc_longitude": "-3.5833" - }, - { - "geo_loc_city": "Bodonal de la Sierra", - "geo_loc_latitude": "38.1483", - "geo_loc_longitude": "-6.5600" - }, - { - "geo_loc_city": "Cañaveral", - "geo_loc_latitude": "39.7833", - "geo_loc_longitude": "-6.4000" - }, - { - "geo_loc_city": "Partaloa", - "geo_loc_latitude": "37.4000", - "geo_loc_longitude": "-2.2167" - }, - { - "geo_loc_city": "Matapozuelos", - "geo_loc_latitude": "41.4167", - "geo_loc_longitude": "-4.7833" - }, - { - "geo_loc_city": "Castañar de Ibor", - "geo_loc_latitude": "39.6167", - "geo_loc_longitude": "-5.4167" - }, - { - "geo_loc_city": "Aledo", - "geo_loc_latitude": "37.7958", - "geo_loc_longitude": "-1.5733" - }, - { - "geo_loc_city": "Montesquíu", - "geo_loc_latitude": "42.1111", - "geo_loc_longitude": "2.2106" - }, - { - "geo_loc_city": "Bonete", - "geo_loc_latitude": "38.8699", - "geo_loc_longitude": "-1.3538" - }, - { - "geo_loc_city": "Quintanilla de Onésimo", - "geo_loc_latitude": "41.6167", - "geo_loc_longitude": "-4.3500" - }, - { - "geo_loc_city": "Cuart de les Valls", - "geo_loc_latitude": "39.7411", - "geo_loc_longitude": "-0.2714" - }, - { - "geo_loc_city": "Santa María de Oló", - "geo_loc_latitude": "41.8747", - "geo_loc_longitude": "2.0349" - }, - { - "geo_loc_city": "Illas", - "geo_loc_latitude": "43.5000", - "geo_loc_longitude": "-5.9667" - }, - { - "geo_loc_city": "Fortaleny", - "geo_loc_latitude": "39.1833", - "geo_loc_longitude": "-0.3142" - }, - { - "geo_loc_city": "Macotera", - "geo_loc_latitude": "40.8333", - "geo_loc_longitude": "-5.2833" - }, - { - "geo_loc_city": "Palmera", - "geo_loc_latitude": "38.9417", - "geo_loc_longitude": "-0.1517" - }, - { - "geo_loc_city": "La Pesga", - "geo_loc_latitude": "40.3333", - "geo_loc_longitude": "-6.1667" - }, - { - "geo_loc_city": "Villanueva del Rey", - "geo_loc_latitude": "38.2000", - "geo_loc_longitude": "-5.1500" - }, - { - "geo_loc_city": "La Mezquita", - "geo_loc_latitude": "42.0114", - "geo_loc_longitude": "-7.0453" - }, - { - "geo_loc_city": "San José", - "geo_loc_latitude": "36.7578", - "geo_loc_longitude": "-2.1094" - }, - { - "geo_loc_city": "Alhama de Aragón", - "geo_loc_latitude": "41.3000", - "geo_loc_longitude": "-1.9000" - }, - { - "geo_loc_city": "Albanchez de Úbeda", - "geo_loc_latitude": "37.7917", - "geo_loc_longitude": "-3.4500" - }, - { - "geo_loc_city": "Otívar", - "geo_loc_latitude": "36.8167", - "geo_loc_longitude": "-3.6833" - }, - { - "geo_loc_city": "Arenas de San Juan", - "geo_loc_latitude": "39.2167", - "geo_loc_longitude": "-3.5000" - }, - { - "geo_loc_city": "Ruente", - "geo_loc_latitude": "43.2594", - "geo_loc_longitude": "-4.2661" - }, - { - "geo_loc_city": "San Cugat Sasgarrigas", - "geo_loc_latitude": "41.3661", - "geo_loc_longitude": "1.7542" - }, - { - "geo_loc_city": "Pinell de Bray", - "geo_loc_latitude": "41.0155", - "geo_loc_longitude": "0.5144" - }, - { - "geo_loc_city": "Bermillo de Sayago", - "geo_loc_latitude": "41.3669", - "geo_loc_longitude": "-6.1121" - }, - { - "geo_loc_city": "Albarracín", - "geo_loc_latitude": "40.4053", - "geo_loc_longitude": "-1.4440" - }, - { - "geo_loc_city": "Santibáñez de la Peña", - "geo_loc_latitude": "42.8167", - "geo_loc_longitude": "-4.7167" - }, - { - "geo_loc_city": "Elciego", - "geo_loc_latitude": "42.5167", - "geo_loc_longitude": "-2.6167" - }, - { - "geo_loc_city": "Báscara", - "geo_loc_latitude": "42.1622", - "geo_loc_longitude": "2.9111" - }, - { - "geo_loc_city": "Ourense", + "Ourense": { "geo_loc_latitude": "42.3364", "geo_loc_longitude": "-7.8633" }, { - "geo_loc_city": "Palencia", + "Palencia": { "geo_loc_latitude": "42.0167", "geo_loc_longitude": "-4.5333" }, { - "geo_loc_city": "Lleida", + "Lleida": { "geo_loc_latitude": "41.6167", "geo_loc_longitude": "0.6222" }, { - "geo_loc_city": "Segovia", + "Segovia": { "geo_loc_latitude": "40.9481", "geo_loc_longitude": "-4.1184" }, { - "geo_loc_city": "Ciudad Real", + "Ciudad Real": { "geo_loc_latitude": "38.9833", "geo_loc_longitude": "-3.9167" }, { - "geo_loc_city": "Soria", + "Soria": { "geo_loc_latitude": "41.7667", "geo_loc_longitude": "-2.4667" }, { - "geo_loc_city": "Caceres", + "Caceres": { "geo_loc_latitude": "39.4752671", "geo_loc_longitude": "-6.3722951" } From c902f86e2250be5834f4fb2531e39d8f50fe246c Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 6 Sep 2022 10:02:52 +0200 Subject: [PATCH 0895/1454] fixing schema anatomical material --- .../anatomical_material_collection_method.json | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/anatomical_material_collection_method.json b/relecov_tools/conf/anatomical_material_collection_method.json index a5060f9a..22861920 100644 --- a/relecov_tools/conf/anatomical_material_collection_method.json +++ b/relecov_tools/conf/anatomical_material_collection_method.json @@ -986,5 +986,17 @@ "collection_device": "Not Applicable", "body_product": "Not Applicable", "anatomical_material": "Tissue" + }, + "Scraping": { + "anatomical_part": "Not Applicable", + "collection_device": "Scraping", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, + "Placenta": { + "anatomical_part": "Placenta", + "collection_device": "Not Applicable", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" } -} +} \ No newline at end of file From 1720a39f5553c0d3d1cab4bd605df8c253c0ef95 Mon Sep 17 00:00:00 2001 From: Alema91 Date: Tue, 6 Sep 2022 10:39:37 +0200 Subject: [PATCH 0896/1454] Change two empty ontologies --- relecov_tools/schema/relecov_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 822f4fcc..786376e6 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -712,7 +712,7 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "", + "ontology": "SNOMED:364684009", "type": "string", "description": "", "examples": [ @@ -2369,7 +2369,7 @@ "examples": [ "NCIT:C180324" ], - "ontology": "", + "ontology": "NCIT:C180324", "type": "string", "description": "GISAID sequence ID.", "classification": "Public Databases", From d6a4cc4a4537685d5202569b9fa2f255a6a87018 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 6 Sep 2022 11:59:06 +0200 Subject: [PATCH 0897/1454] fixed bug --- relecov_tools/institution_scripts/ISCIII.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index d0f9ce32..d1260e88 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -110,4 +110,5 @@ def translate_specimen_source(metadata, f_data, mapped_fields, heading): else: log.error("The field is not correctly written or is not filled") stderr.print("The field is not correctly written or is not filled") - return metadata + + return metadata From db2c912e5bfd522027b27aa585b27ff1bfa46c5b Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 6 Sep 2022 12:02:17 +0200 Subject: [PATCH 0898/1454] fixing bugs --- relecov_tools/ena_upload.py | 14 +++++--------- relecov_tools/metadata_homogeneizer.py | 18 ++++++++++-------- 2 files changed, 15 insertions(+), 17 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index c59365d4..02843b80 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -211,12 +211,9 @@ def create_structure_to_ena(self): 1 212163777 212163777 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212163777 2 212153091 212153091 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212153091 """ - import pdb - pdb.set_trace() df_run = df_schemas[ [ - "experiment_alias", "r1_fastq_filepath", "r2_fastq_filepath", "file_type", @@ -237,6 +234,7 @@ def create_structure_to_ena(self): i, "sequence_file_R2_fastq" ] df_run.insert(3, "status", self.action) + df_run = df_run.rename(columns={"fastq_r1_md5": "file_checksum"}) for i in range(len(df_run)): @@ -269,9 +267,7 @@ def create_structure_to_ena(self): df_experiments = df_schemas[ [ - "experiment_alias", - "study_title", - "study_alias", + "study_abstract", "sample_name", "library_name", "library_strategy", @@ -289,7 +285,7 @@ def create_structure_to_ena(self): df_experiments["instrument_model"] = df_experiments[ "instrument_model" ].str.lower() - + df_experiments["study_alias"] = df_study["alias"] df_experiments.insert(3, "status", self.action) for i in range(len(df_experiments)): @@ -305,7 +301,7 @@ def create_structure_to_ena(self): df_experiments = df_experiments.rename( columns={"sequencing_instrument_platform": "platform"} ) - df_experiments = df_experiments.rename(columns={"study_title": "title"}) + df_experiments = df_experiments.rename(columns={"study_abstract": "title"}) df_experiments = df_experiments.rename(columns={"sample_name": "sample_alias"}) df_experiments = df_experiments.rename( columns={"collecting_institution": "collecting institution"} @@ -401,7 +397,7 @@ def create_structure_to_ena(self): H = df_run_final.loc[ df_run_final["sequence_file_R2_fastq"] == files.attrib["filename"] - ].values[0][9] + ].values[0][8] files.set("checksum", H) # print(files.attrib["checksum"]) tree.write(schema_xmls["run"]) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 8e3ff84c..8488c12c 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -32,14 +32,15 @@ def __init__(self, institution=None, directory=None, output_folder=None): ) else: self.institution = institution.upper() - mapping_json_file = os.path.join( - os.path.dirname(__file__), - "schema", - "institution_schemas", - self.config_json.get_topic_data( - "institution_mapping_file", self.institution - ), - ) + mapping_json_file = os.path.join( + os.path.dirname(__file__), + "schema", + "institution_schemas", + self.config_json.get_topic_data( + "institution_mapping_file", self.institution + ), + ) + if directory is None: directory = relecov_tools.utils.prompt_path( msg="Select the directory which contains additional files for metadata" @@ -50,6 +51,7 @@ def __init__(self, institution=None, directory=None, output_folder=None): "[red] Folder for additional files " + directory + " does not exist" ) sys.exit(1) + self.mapping_json_data = relecov_tools.utils.read_json_file(mapping_json_file) try: From dd21be4ba6df1d955da80d4cd045bb8c6d31e460 Mon Sep 17 00:00:00 2001 From: Alema91 Date: Tue, 6 Sep 2022 12:10:31 +0200 Subject: [PATCH 0899/1454] linting --- relecov_tools/read_bioinfo_metadata.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index c56a32af..f6d2f496 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -321,6 +321,8 @@ def bioinfo_parse(self, file_name): json_file = "bioinfo_metadata.json" output_path = os.path.join(self.output_folder, json_file) + """Create json""" + with open(output_path, "w", encoding="utf-8") as fh: fh.write( json.dumps(bioinfo_list, indent=4, sort_keys=True, ensure_ascii=False) From 81e779e235a9d384c36354e2628888ab299fa139 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 6 Sep 2022 12:28:08 +0200 Subject: [PATCH 0900/1454] checked that new anatomical translation part function works --- relecov_tools/institution_scripts/ISCIII.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index d0f9ce32..976981ac 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -85,7 +85,9 @@ def translate_gender_to_english(metadata, f_data, mapped_fields, heading): def translate_specimen_source(metadata, f_data, mapped_fields, heading): """Translate into english the "muestra" that is written in spanish""" for row in metadata[1:]: + for key, val in mapped_fields.items(): + m_idx = heading.index(key) if row[m_idx] is None: row[m_idx] = "not provided" @@ -110,4 +112,4 @@ def translate_specimen_source(metadata, f_data, mapped_fields, heading): else: log.error("The field is not correctly written or is not filled") stderr.print("The field is not correctly written or is not filled") - return metadata + return metadata From bf0c8d832f7575a8c974c45d03b221e67143786d Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 6 Sep 2022 13:31:52 +0200 Subject: [PATCH 0901/1454] opentrons modification --- relecov_tools/metadata_homogeneizer.py | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 8488c12c..680c5285 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -202,7 +202,6 @@ def handling_files(self, file_data, additional_data): sys.exit(1) row[meta_idx] = item_data[f_field] - # import pdb; pdb.set_trace() else: func_name = file_data["function"] stderr.print("[yellow] Start processing function " + func_name) From 1aa5c7ce051eb728c13f2b403d1fdaae9a5e0b1e Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 6 Sep 2022 13:52:58 +0200 Subject: [PATCH 0902/1454] review ontologies --- relecov_tools/institution_scripts/ISCIII.py | 1 - .../schema/institution_schemas/ISCIII.json | 4 +- relecov_tools/schema/relecov_schema.json | 44 +++++++++---------- 3 files changed, 24 insertions(+), 25 deletions(-) diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index 48dd0e70..976981ac 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -112,5 +112,4 @@ def translate_specimen_source(metadata, f_data, mapped_fields, heading): else: log.error("The field is not correctly written or is not filled") stderr.print("The field is not correctly written or is not filled") - return metadata diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 01f74ebf..06996bba 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -106,7 +106,7 @@ "fixed_fields": { "Submitting Institution": "Instituto de Salud Carlos III", "Biological Sample Storage Condition": "-80 C", - "Nucleic acid extraction protocol": "RT-PCR", + "Nucleic acid extraction protocol": "Opentrons custom rna extraction protocol", "Purpose of sampling": "Surveillance", "Specimen source": "Nasopharyngeal exudate", "Host": "Human", @@ -121,4 +121,4 @@ "Diagnostic Pcr Ct Value 1": "", "Authors": "" } -} +} \ No newline at end of file diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index dbc3c19d..e8fef802 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1461,31 +1461,31 @@ }, "library_selection": { "enum": [ - "RANDOM", - "PCR", - "RANDOM PCR", - "RT-PCR", - "HMPR", - "MF", + "RANDOM [NCIT:C60702]", + "PCR [GENEPIO:0001955]", + "RANDOM PCR [GENEPIO:0001957]", + "RT-PCR [GENEPIO:0001959]", + "HMPR [GENEPIO:0001949]", + "MF [GENEPIO:0001952]", "repeat fractionation", - "size fractionation", - "MSLL", - "cDNA", - "ChIP", - "MNase", - "DNase", - "Hybrid Selection", - "Reduced Representation", - "Restriction Digest", - "5-methylcytidine antibody", - "MBD2 protein methyl-CpG binding domain", - "CAGE", - "RACE", + "size fractionation [GENEPIO:0001963]", + "MSLL [GENEPIO:0001954]", + "cDNA [GENEPIO:0001962]", + "ChIP [GENEPIO:0001947]", + "MNase [GENEPIO:0001953]", + "DNase [GENEPIO:0001948]", + "Hybrid Selection [GENEPIO:0001950]", + "Reduced Representation [GENEPIO:0001960]", + "Restriction Digest [GENEPIO:0001961]", + "5-methylcytidine antibody [GENEPIO:0001941]", + "MBD2 protein methyl-CpG binding domain [GENEPIO:0001951]", + "CAGE [GENEPIO:0001942]", + "RACE [GENEPIO:0001956]", "MDA", "padlock probes capture method", "Oligo-dT", "Inverse rRNA selection", - "ChIP-Seq", + "ChIP-Seq [GENEPIO:0001947]", "Other" ], "examples": [ @@ -1533,8 +1533,8 @@ }, "library_layout": { "enum": [ - "SINGLE", - "PAIRED" + "SINGLE [OBI:0002481]", + "PAIRED [OBI:0001852]" ], "examples": [ "PAIRED" From 45f705bdc656b77230ccb319010e3b66da3473af Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 6 Sep 2022 14:54:03 +0200 Subject: [PATCH 0903/1454] Re-writing the code to handle additional processing from configuration file --- relecov_tools/conf/configuration.json | 35 ++++++- relecov_tools/conf/geo_loc_cities.json | 60 +----------- relecov_tools/conf/submitter_address.json | 7 ++ relecov_tools/read_lab_metadata.py | 107 ++++++++++++++-------- 4 files changed, 114 insertions(+), 95 deletions(-) create mode 100644 relecov_tools/conf/submitter_address.json diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 24f2a0cb..f5c37659 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -103,10 +103,37 @@ "ena_schema": "ena_schema.json", "gisaid_schema": "gisaid_schema.json" }, - "lab_metadata_req_json":{ - "laboratory_data": "laboratory_address.json", - "geo_location_data": "geo_loc_cities.json", - "anatomical_material": "anatomical_material_collection_method.json" + "lab_metadata_req_json": { + "laboratory_data": { + "file": "laboratory_address.json", + "map_field": "collecting_institution", + "adding_fields": "__all__" + }, + "geo_location_data": { + "file": "geo_loc_cities.json", + "map_field": "geo_loc_city", + "adding_fields": "__all__" + }, + "submitting_data": { + "file": "submitter_address.json", + "map_field": "submitting_institution", + "adding_fields": [ + "submitting_institution_address", + "submitting_institution_email" + ] + }, + "anatomical_material": { + "file": "anatomical_material_collection_method.json", + "map_field": { + "any_of": [ + "body_product", + "anatomical_part", + "collection_method", + "anatomical_material" + ] + }, + "adding_fields" : "__all__" + } }, "institution_mapping_file": { "ISCIII": "ISCIII.json", diff --git a/relecov_tools/conf/geo_loc_cities.json b/relecov_tools/conf/geo_loc_cities.json index 8ccdbc26..3a2e3d55 100644 --- a/relecov_tools/conf/geo_loc_cities.json +++ b/relecov_tools/conf/geo_loc_cities.json @@ -3,274 +3,224 @@ "geo_loc_latitude": "40.4167", "geo_loc_longitude": "-3.7167" }, - { "Barcelona": { "geo_loc_latitude": "41.3825", "geo_loc_longitude": "2.1769" }, - { "Sevilla": { "geo_loc_latitude": "37.3900", "geo_loc_longitude": "-5.9900" }, - { "Málaga": { "geo_loc_latitude": "36.7194", "geo_loc_longitude": "-4.4200" }, - { "Valencia": { "geo_loc_latitude": "39.4700", "geo_loc_longitude": "-0.3764" }, - { "Zaragoza": { "geo_loc_latitude": "41.6483", "geo_loc_longitude": "-0.8830" }, - { "Palma de Mallorca": { "geo_loc_latitude": "39.5667", "geo_loc_longitude": "2.6500" }, - { "Murcia": { "geo_loc_latitude": "37.9861", "geo_loc_longitude": "-1.1303" }, - { "Las Palmas": { "geo_loc_latitude": "28.1272", "geo_loc_longitude": "-15.4314" }, - { "A Coruña": { "geo_loc_latitude": "43.3713", "geo_loc_longitude": "-8.4188" }, - { "Bilbao": { "geo_loc_latitude": "43.2569", "geo_loc_longitude": "-2.9236" }, - { "Alicante": { "geo_loc_latitude": "38.3453", "geo_loc_longitude": "-0.4831" }, - { "Córdoba": { "geo_loc_latitude": "37.8845", "geo_loc_longitude": "-4.7796" }, - { "Valladolid": { "geo_loc_latitude": "41.6528", "geo_loc_longitude": "-4.7236" }, - { "Vigo": { "geo_loc_latitude": "42.2314", "geo_loc_longitude": "-8.7124" }, - { "Gijón": { "geo_loc_latitude": "43.5333", "geo_loc_longitude": "-5.7000" }, - { "Vitoria": { "geo_loc_latitude": "42.8500", "geo_loc_longitude": "-2.6833" }, - { "Granada": { "geo_loc_latitude": "37.1781", "geo_loc_longitude": "-3.6008" }, - { "Oviedo": { "geo_loc_latitude": "43.3600", "geo_loc_longitude": "-5.8450" }, - { "Santa Cruz de Tenerife": { "geo_loc_latitude": "28.4667", "geo_loc_longitude": "-16.2500" }, - { "Pamplona": { "geo_loc_latitude": "42.8167", "geo_loc_longitude": "-1.6500" }, - { "León": { "geo_loc_latitude": "42.6056", "geo_loc_longitude": "-5.5700" }, - { "Almería": { "geo_loc_latitude": "36.8403", "geo_loc_longitude": "-2.4681" }, - { "Logroño": { "geo_loc_latitude": "42.4650", "geo_loc_longitude": "-2.4456" }, - { "Donostia": { "geo_loc_latitude": "43.3200", "geo_loc_longitude": "-1.9800" }, - { "Albacete": { "geo_loc_latitude": "38.9956", "geo_loc_longitude": "-1.8558" }, - { "Castellón de la Plana": { "geo_loc_latitude": "39.9831", "geo_loc_longitude": "-0.0331" }, - { "Santander": { "geo_loc_latitude": "43.4628", "geo_loc_longitude": "-3.8050" }, - { "Burgos": { "geo_loc_latitude": "42.3500", "geo_loc_longitude": "-3.6822" }, - { "Guadalajara": { "geo_loc_latitude": "40.6337", "geo_loc_longitude": "-3.1674" }, - { "Badajoz": { "geo_loc_latitude": "38.8803", "geo_loc_longitude": "-6.9753" }, - { "Salamanca": { "geo_loc_latitude": "40.9667", "geo_loc_longitude": "-5.6639" }, - { "Huelva": { "geo_loc_latitude": "37.2500", "geo_loc_longitude": "-6.9500" }, - { "Ciudad de Melilla": { "geo_loc_latitude": "35.2937", "geo_loc_longitude": "-2.9383" }, - { "Tarragona": { "geo_loc_latitude": "41.1187", "geo_loc_longitude": "1.2453" }, - { "Cádiz": { "geo_loc_latitude": "36.5350", "geo_loc_longitude": "-6.2975" }, - { "Jaén": { "geo_loc_latitude": "37.7667", "geo_loc_longitude": "-3.7711" }, - { "Girona": { "geo_loc_latitude": "41.9833", "geo_loc_longitude": "2.8167" }, - { "Lugo": { "geo_loc_latitude": "43.0167", "geo_loc_longitude": "-7.5500" }, - { "Cáceres": { "geo_loc_latitude": "39.4833", "geo_loc_longitude": "-6.3667" }, - { "Toledo": { "geo_loc_latitude": "39.8567", "geo_loc_longitude": "-4.0244" }, - { "Ceuta": { "geo_loc_latitude": "35.8867", "geo_loc_longitude": "-5.3000" }, - { "Melilla": { "geo_loc_latitude": "35.2919", "geo_loc_longitude": "-2.93848" }, - { "Zamora": { "geo_loc_latitude": "41.5033", "geo_loc_longitude": "-5.7556" }, - { "Avila": { "geo_loc_latitude": "40.6500", "geo_loc_longitude": "-4.6833" }, - { "Cuenca": { "geo_loc_latitude": "40.0667", "geo_loc_longitude": "-2.1500" }, - { "Huesca": { "geo_loc_latitude": "42.1333", "geo_loc_longitude": "-0.4167" }, - { "Teruel": { "geo_loc_latitude": "40.3456", "geo_loc_longitude": "-1.1065" }, - { "Ourense": { "geo_loc_latitude": "42.3364", "geo_loc_longitude": "-7.8633" }, - { "Palencia": { "geo_loc_latitude": "42.0167", "geo_loc_longitude": "-4.5333" }, - { "Lleida": { "geo_loc_latitude": "41.6167", "geo_loc_longitude": "0.6222" }, - { "Segovia": { "geo_loc_latitude": "40.9481", "geo_loc_longitude": "-4.1184" }, - { "Ciudad Real": { "geo_loc_latitude": "38.9833", "geo_loc_longitude": "-3.9167" }, - { "Soria": { "geo_loc_latitude": "41.7667", "geo_loc_longitude": "-2.4667" }, - { "Caceres": { "geo_loc_latitude": "39.4752671", "geo_loc_longitude": "-6.3722951" + }, + "Pontevedra": { + "geo_loc_latitude": "42.4333", + "geo_loc_longitude": "-8.6333" } -] +} diff --git a/relecov_tools/conf/submitter_address.json b/relecov_tools/conf/submitter_address.json new file mode 100644 index 00000000..ddc86a8c --- /dev/null +++ b/relecov_tools/conf/submitter_address.json @@ -0,0 +1,7 @@ +[ + { + "submitting_institution": "Instituto de Salud Carlos III", + "submitting_institution_address": "Crta. Pozuelo Majadahonda S/N,", + "submitting_institution_email": "info@isciii.es" + } +] diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 3282f04c..7ed9b716 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -64,7 +64,7 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None self.label_prop_dict[values["label"]] = prop except KeyError: continue - self.json_files = config_json.get_configuration("lab_metadata_req_json") + self.json_req_files = config_json.get_configuration("lab_metadata_req_json") self.schema_name = self.relecov_sch_json["schema"] self.schema_version = self.relecov_sch_json["version"] @@ -133,34 +133,7 @@ def include_processed_data(self, metadata): metadata["sequencing_sample_id"], ], } - seq_inst_plat = { - "Illumina": [ - "Illumina iSeq 100", - "Illumina MiSeq", - "Illumina Miniseq", - "Illumina NextSeq 550", - "Illumina NextSeq 500", - "Illumina NextSeq 1000", - "Illumina NextSeq 2000", - "Illumina NovaSeq 6000", - "Illumina Miniseq", - "Illumina Hiseq x five", - "Illumina Hiseq x ten", - "Illumina Hiseq x", - "Illumina Genome analyzer", - "Illumina Genome analyzer ii", - "Illumina Genome analyzer iix", - "Illumina Hiscansq", - "Illumina Hiseq 1000", - "Illumina Hiseq 1500", - "Illumina Hiseq 2000", - "Illumina Hiseq 2500", - "Illumina Hiseq 3000", - "Illumina Hiseq 4000", - ], - "Oxford Nanopore": ["MinION"], - "Ion Torrent": ["Ion Torrent S5", "Ion Torrent PGM"], - } + for key, values in p_data.items(): v_data = metadata[key] if isinstance(values, dict): @@ -169,14 +142,70 @@ def include_processed_data(self, metadata): else: new_data[values[0]] = values[1] """New fields that required processing from other field """ - for key, values in seq_inst_plat.items(): - if metadata["sequencing_instrument_model"] in values: - - new_data["sequencing_instrument_platform"] = key - break return new_data + def process_from_json(self, m_data, json_fields): + """ """ + if isinstance(json_fields["map_field"], dict): + # Search for the value which contains data + + for m_field in json_fields["map_field"]["any_of"]: + try: + m_data[0][m_field] + map_field = m_field + except KeyError: + continue + else: + map_field = json_fields["map_field"] + json_data = json_fields["j_data"] + if isinstance(json_data, dict): + # import pdb; pdb.set_trace() + for idx in range(len(m_data)): + m_data[idx].update(json_data[m_data[idx][map_field]]) + elif isinstance(json_data, list): + # to avoid searching for data for each row, for the first time searchs + # it is stored temporary. + tmp_data = {} + for idx in range(len(m_data)): + if m_data[idx][map_field] not in tmp_data: + for item in json_data: + if m_data[idx][map_field] == item[map_field]: + if json_fields["adding_fields"] == "__all__": + m_data[idx].update(item) + tmp_data[m_data[idx][map_field]] = item + else: + tmp_data[m_data[idx][map_field]] = {} + for field in json_fields["adding_fields"]: + m_data[idx][field] = item[field] + tmp_data[m_data[idx][map_field]][field] = item[ + field + ] + break + else: + m_data[idx].update(tmp_data[m_data[idx][map_field]]) + return m_data + + def adding_fields(self, metadata): + """Add fields""" + + for key, values in self.json_req_files.items(): + stderr.print(f"[blue] Processing {key}") + f_path = os.path.join( + os.path.dirname(os.path.realpath(__file__)), "conf", values["file"] + ) + values["j_data"] = relecov_tools.utils.read_json_file(f_path) + metadata = self.process_from_json(metadata, values) + stderr.print(f"[green] Processed {key}") + stderr.print("[blue] Reading sample list file") + # Include Sample informatin data from sample json file + s_json = {} + s_json["map_field"] = "sequencing_sample_id" + s_json["adding_field"] = "__all__" + s_json["j_data"] = relecov_tools.utils.read_json_file(self.sample_list_file) + metadata = self.process_from_json(metadata, s_json) + return metadata + def add_additional_data(self, metadata, conf_json_data): """Add the additional information that must be included in final metadata metadata Origin metadata @@ -335,8 +364,8 @@ def read_metadata_file(self): return metadata_values, errors def create_metadata_json(self): - stderr.print("[blue] Reading configuration settings") - conf_json_data = self.read_configuration_json_files() + # stderr.print("[blue] Reading configuration settings") + # conf_json_data = self.read_configuration_json_files() stderr.print("[blue] Reading Lab Metadata Excel File") valid_metadata_rows, errors = self.read_metadata_file() if len(errors) > 0: @@ -344,6 +373,12 @@ def create_metadata_json(self): sys.exit(1) # Continue by adding extra information stderr.print("[blue] Including additional information") + + completed_metadata = self.adding_fields(valid_metadata_rows) + import pdb + + pdb.set_trace() + completed_metadata = self.add_additional_data( valid_metadata_rows, conf_json_data ) From 640cd42fa6c0d0826023a82adf38da72da46bf52 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 6 Sep 2022 15:24:57 +0200 Subject: [PATCH 0904/1454] remove not longer valid comments --- relecov_tools/metadata_homogeneizer.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 680c5285..01c00303 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -221,8 +221,7 @@ def handling_files(self, file_data, additional_data): def converting_metadata(self): stderr.print("[blue] Reading the metadata file to convert") - # ws_data = self.read_metadata_file() - # mapped_data = self.mapping_metadata(ws_data) + mapped_data = self.handling_files(self.lab_metadata, "") stderr.print("[green] Successful conversion mapping to ISCIII metadata") stderr.print("[blue] Adding fixed information") From d2ca038c2973f61bb48938a9675988c7e0380342 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 6 Sep 2022 15:25:44 +0200 Subject: [PATCH 0905/1454] modify version to 0.0.5 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index e30d8edf..91770d8f 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import setup, find_packages -version = "0.0.4" +version = "0.0.5" with open("README.md") as f: readme = f.read() From c71c02790210f9321c8ae1a20b0ea223a5de0309 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 6 Sep 2022 16:11:55 +0200 Subject: [PATCH 0906/1454] fixed terms to configuration json --- relecov_tools/conf/configuration.json | 51 +++++++++++++++++++-- relecov_tools/ena_upload.py | 65 ++++++--------------------- 2 files changed, 62 insertions(+), 54 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 24f2a0cb..4e7c8087 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -103,7 +103,7 @@ "ena_schema": "ena_schema.json", "gisaid_schema": "gisaid_schema.json" }, - "lab_metadata_req_json":{ + "lab_metadata_req_json": { "laboratory_data": "laboratory_address.json", "geo_location_data": "geo_loc_cities.json", "anatomical_material": "anatomical_material_collection_method.json" @@ -226,5 +226,50 @@ "mapping_file": { "ISCIII": "ISCIII.json", "HUGTiP": "HUGTiP.json" - } -} + }, + "df_study_fields": [ + "study_type", + "study_abstract" + ], + "df_samples_fields": [ + "sample_name", + "sample_title", + "taxon_id", + "collection_date", + "geographic_location_(country_and/or_sea)", + "host_common_name", + "host_scientific_name", + "host_sex", + "scientific_name", + "collector_name", + "collecting_institution", + "isolate", + "host_subject_id", + "host health state", + "authors", + "sample_description", + "address" + ], + "df_run_fields": [ + "r1_fastq_filepath", + "r2_fastq_filepath", + "file_type", + "fastq_r1_md5", + "fastq_r2_md5", + "collecting_institution" + ], + "df_experiment_fields": [ + "study_abstract", + "sample_name", + "library_name", + "library_strategy", + "library_source", + "library_selection", + "library_layout", + "instrument_model", + "design_description", + "collecting_institution", + "insert_size", + "sequencing_instrument_platform" + ] +} \ No newline at end of file diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 02843b80..27d1c7cc 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -124,6 +124,7 @@ def create_structure_to_ena(self): fh_squema = open(squema) squema_json = json.load(fh_squema) fh_squema.close() + config_json = ConfigJson() df_schemas = pd.DataFrame(squema_json) @@ -142,37 +143,24 @@ def create_structure_to_ena(self): df_study = df_study.rename(columns={"study_alias": "alias"}) df_study = df_study.rename(columns={"study_title": "title"}) """ - df_study = df_schemas[["study_type", "study_abstract"]] + fields_study = config_json.get_configuration("df_study_fields") + df_study = df_schemas[fields_study] df_study["alias"] = df_study["study_abstract"][0].rsplit(" ", 5)[0] df_study["title"] = df_study["study_abstract"] df_study.insert(3, "status", self.action) + """ # df_study alias title study_type status study_abstract 0 RELECOV RELECOV Spanish Network for genomics surveillance Surveillance ADD RELECOV Spanish Network for genomics surveillance 1 RELECOV RELECOV Spanish Network for genomics surveillance Surveillance ADD RELECOV Spanish Network for genomics surveillance """ - df_samples = df_schemas[ - [ - "sample_name", - "sample_title", - "taxon_id", - "collection_date", - "geographic_location_(country_and/or_sea)", - "host_common_name", - "host_scientific_name", - "host_sex", - "scientific_name", - "collector_name", - "collecting_institution", - "isolate", - "host_subject_id", - "host health state", - "authors", - "sample_description", - "address", - ] - ] + + fields_samples = config_json.get_configuration("df_samples_fields") + import pdb + + pdb.set_trace() + df_samples = df_schemas[fields_samples] df_samples["host_sex"].replace("unknown", "not provided", inplace=True) df_samples["host_sex"].replace("Unknown", "not provided", inplace=True) @@ -199,7 +187,6 @@ def create_structure_to_ena(self): df_samples.insert(3, "status", self.action) # df_samples.insert(3, "host subject id", df_schemas["host subject id"]) # df_samples.insert(3, "host health state", df_schemas["host health state"]) - config_json = ConfigJson() checklist = config_json.get_configuration("checklist") df_samples.insert(4, "ENA_CHECKLIST", checklist) # df_samples.insert(5, "sample_description", df_schemas["sample_description"]) @@ -211,17 +198,8 @@ def create_structure_to_ena(self): 1 212163777 212163777 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212163777 2 212153091 212153091 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212153091 """ - - df_run = df_schemas[ - [ - "r1_fastq_filepath", - "r2_fastq_filepath", - "file_type", - "fastq_r1_md5", - "fastq_r2_md5", - "collecting_institution", - ] - ] + fields_run = config_json.get_configuration("df_run_fields") + df_run = df_schemas[fields_run] df_run.insert(1, "sequence_file_R1_fastq", "None") df_run.insert(2, "sequence_file_R2_fastq", "None") @@ -264,23 +242,8 @@ def create_structure_to_ena(self): 2 214821_S12 214823_S1_R1_001.fastq.gz 214823_S1_R2_001.fastq.gz ... fastq c16bdbfc03c354496fcfb2c107e3cbf6 4d9b80b977a75bf7e2a4282ca910d94a """ - - df_experiments = df_schemas[ - [ - "study_abstract", - "sample_name", - "library_name", - "library_strategy", - "library_source", - "library_selection", - "library_layout", - "instrument_model", - "design_description", - "collecting_institution", - "insert_size", - "sequencing_instrument_platform", - ] - ] + fields_experiment = config_json.get_configuration("df_experiment_fields") + df_experiments = df_schemas[[fields_experiment]] df_experiments["instrument_model"] = df_experiments[ "instrument_model" From d9f7749ef1c851e74a400fdac22c6e0de783df09 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 6 Sep 2022 16:23:54 +0200 Subject: [PATCH 0907/1454] Change in the red excel that if fill is None change to empty --- relecov_tools/utils.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 8b7fb867..895f8371 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -50,7 +50,10 @@ def read_excel_file(f_name, sheet_name, heading_row): if l_row[0] is None and l_row[1] is None: continue for idx in range(0, len(heading)): - data_row[heading[idx]] = l_row[idx] + if l_row[idx] is None: + data_row[heading[idx]] = "" + else: + data_row[heading[idx]] = l_row[idx] ws_data.append(data_row) return ws_data From b7c590b79b8905b9e372b1ae13c7cd9e81ddd765 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 6 Sep 2022 16:24:33 +0200 Subject: [PATCH 0908/1454] re-organizing the configuration json --- relecov_tools/conf/configuration.json | 133 ++++++++++++------------ relecov_tools/metadata_homogeneizer.py | 2 +- relecov_tools/read_lab_metadata.py | 134 +------------------------ 3 files changed, 71 insertions(+), 198 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index f5c37659..b5fe7a3f 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -1,5 +1,11 @@ { - "headings": { + "lab_metadata": { + "fixed_fields": { + "host_disease": "COVID-19", + "type": "betacoronavirus", + "tax_id": "2697049", + "organism": "Severe acute respiratory syndrome coronavirus 2" + }, "metadata_lab_heading": [ "Public Health sample id (SIVIES)", "Sample ID given by originating laboratory", @@ -49,26 +55,66 @@ "Sequence file R1 fastq", "Sequence file R2 fastq" ], - "long_table_heading": [ - "SAMPLE", - "CHROM", - "POS", - "REF", - "ALT", - "FILTER", - "DP", - "REF_DP", - "ALT_DP", - "AF", - "GENE", - "EFFECT", - "HGVS_C", - "HGVS_P", - "HGVS_P_1LETTER", - "CALLER", - "LINEAGE" - ] + "fields_required_for_ENA": { + "study_alias": "RELECOV", + "design_description": "Design Description", + "experiment_title": "Example project for ENA submission RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", + "study_id": "ERP137164" + }, + "lab_metadata_req_json": { + "laboratory_data": { + "file": "laboratory_address.json", + "map_field": "collecting_institution", + "adding_fields": "__all__" + }, + "geo_location_data": { + "file": "geo_loc_cities.json", + "map_field": "geo_loc_city", + "adding_fields": "__all__" + }, + "submitting_data": { + "file": "submitter_address.json", + "map_field": "submitting_institution", + "adding_fields": [ + "submitting_institution_address", + "submitting_institution_email" + ] + }, + "anatomical_material": { + "file": "anatomical_material_collection_method.json", + "map_field": { + "any_of": [ + "body_product", + "anatomical_part", + "collection_method", + "anatomical_material" + ] + }, + "adding_fields" : "__all__" + } + } }, + "long_table_heading": [ + "SAMPLE", + "CHROM", + "POS", + "REF", + "ALT", + "FILTER", + "DP", + "REF_DP", + "ALT_DP", + "AF", + "GENE", + "EFFECT", + "HGVS_C", + "HGVS_P", + "HGVS_P_1LETTER", + "CALLER", + "LINEAGE" + ], "gisaid_csv_headers": [ "submitter", "covv_virus_name", @@ -103,38 +149,7 @@ "ena_schema": "ena_schema.json", "gisaid_schema": "gisaid_schema.json" }, - "lab_metadata_req_json": { - "laboratory_data": { - "file": "laboratory_address.json", - "map_field": "collecting_institution", - "adding_fields": "__all__" - }, - "geo_location_data": { - "file": "geo_loc_cities.json", - "map_field": "geo_loc_city", - "adding_fields": "__all__" - }, - "submitting_data": { - "file": "submitter_address.json", - "map_field": "submitting_institution", - "adding_fields": [ - "submitting_institution_address", - "submitting_institution_email" - ] - }, - "anatomical_material": { - "file": "anatomical_material_collection_method.json", - "map_field": { - "any_of": [ - "body_product", - "anatomical_part", - "collection_method", - "anatomical_material" - ] - }, - "adding_fields" : "__all__" - } - }, + "institution_mapping_file": { "ISCIII": "ISCIII.json", "HUGTiP": "HUGTiP.json" @@ -150,14 +165,6 @@ "fastq.gz", "fasta" ], - "ENA_configuration": { - "study_alias": "RELECOV", - "design_description": "Design Description", - "experiment_title": "Example project for ENA submission RELECOV", - "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "", - "study_id": "ERP137164" - }, "GISATD_configuration": { "submitter": "GISAID_ID" }, @@ -249,9 +256,5 @@ "tool_version": "0.5.3" }, "md5_file_name": "md5_check_file.csv", - "checklist": "ERC000033", - "mapping_file": { - "ISCIII": "ISCIII.json", - "HUGTiP": "HUGTiP.json" - } + "checklist": "ERC000033" } diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 01c00303..8916a4c3 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -22,7 +22,7 @@ class MetadataHomogeneizer: def __init__(self, institution=None, directory=None, output_folder=None): self.config_json = ConfigJson() self.heading = self.config_json.get_topic_data( - "headings", "metadata_lab_heading" + "lab_metadata", "metadata_lab_heading" ) if institution is None: diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 7ed9b716..536524e2 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -64,38 +64,10 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None self.label_prop_dict[values["label"]] = prop except KeyError: continue - self.json_req_files = config_json.get_configuration("lab_metadata_req_json") + self.json_req_files = config_json.get_topic_data("lab_metadata", "lab_metadata_req_json") self.schema_name = self.relecov_sch_json["schema"] self.schema_version = self.relecov_sch_json["version"] - def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): - """Fetch the laboratory location and return a dictionary""" - data = {} - if lab_name == "": - data["geo_loc_city"] = "" - data["geo_loc_latitude"] = "" - data["geo_loc_longitude"] = "" - data["geo_loc_country"] = "" - stderr.print("[red] Empty Originating Laboratory.") - log.error("Found empty Originating Laboratory") - return data - for lab in lab_json: - if lab_name == lab["collecting_institution"]: - for key, value in lab.items(): - data[key] = value - break - - for city in geo_loc_json: - try: - if city["geo_loc_city"] == lab["geo_loc_city"]: - data["geo_loc_latitude"] = city["geo_loc_latitude"] - data["geo_loc_longitude"] = city["geo_loc_longitude"] - data["geo_loc_country"] = data["geo_loc_country"] - break - except KeyError as e: - print(e) - return data - def include_fixed_data(self): """Include fixed data that are always the same for each samples""" fixed_data = { @@ -103,24 +75,12 @@ def include_fixed_data(self): "type": "betacoronavirus", "tax_id": "2697049", "organism": "Severe acute respiratory syndrome coronavirus 2", - "common_name": "Severe acute respiratory syndrome", - "sample_description": "Sample for surveillance", } - fixed_data.update(self.configuration.get_configuration("ENA_configuration")) + fixed_data.update(self.configuration.get_topic_data("lab_metadata", "fields_required_for_ENA")) fixed_data["schema_name"] = self.schema_name fixed_data["schema_version"] = self.schema_version return fixed_data - def include_fields_already_set(self, row_sample): - processed_data = {} - if row_sample["author_submitter"] == "": - processed_data["collector_name"] = "unknown" - else: - processed_data["collector_name"] = row_sample["author_submitter"] - processed_data["host_subject_id"] = row_sample["microbiology_lab_sample_id"] - - return processed_data - def include_processed_data(self, metadata): """Include the data that requires to be processed to set the value. This values are checked aginst the available options in the schema @@ -206,89 +166,6 @@ def adding_fields(self, metadata): metadata = self.process_from_json(metadata, s_json) return metadata - def add_additional_data(self, metadata, conf_json_data): - """Add the additional information that must be included in final metadata - metadata Origin metadata - extra_data additional data to be included - result_metadata final metadata after adding the additional data - """ - lab_data = {} - additional_metadata = [] - - samples_json = relecov_tools.utils.read_json_file(self.sample_list_file) - for row_sample in metadata: - """Include sample data from sample json""" - try: - row_sample.update( - samples_json[row_sample["microbiology_lab_sample_id"]] - ) - except KeyError as e: - - stderr.print(f"[red] ERROR fastq information not found for sample {e}") - - """ Fetch the information related to the laboratory. - Info is stored in lab_data, to prevent to call get_laboratory_data - each time for each sample that belongs to the same lab - """ - if row_sample["collecting_institution"] not in lab_data: - # from collecting_institution find city, and geo location latitude and longitude - l_data = self.get_laboratory_data( - conf_json_data["laboratory_data"], - conf_json_data["geo_location_data"], - row_sample["collecting_institution"], - ) - row_sample.update(l_data) - lab_data[row_sample["collecting_institution"]] = l_data - else: - row_sample.update(lab_data[row_sample["collecting_institution"]]) - - """ Fetch email and address for submitting_institution - """ - row_sample["submitting_institution"] = row_sample[ - "submitting_institution" - ].strip() - if row_sample["submitting_institution"] not in lab_data: - # Include in lab_data the submitting institution - l_data = self.get_laboratory_data( - conf_json_data["laboratory_data"], - conf_json_data["geo_location_data"], - row_sample["submitting_institution"], - ) - - lab_data[row_sample["submitting_institution"]] = l_data - row_sample["submitting_institution_email"] = lab_data[ - row_sample["submitting_institution"] - ]["collecting_institution_email"] - row_sample["submitting_institution_address"] = lab_data[ - row_sample["submitting_institution"] - ]["collecting_institution_address"] - - """ Add Fixed information - """ - row_sample.update(self.include_fixed_data()) - - """ Add fields that are already in other fields - """ - # row_sample.update(self.include_fields_already_set(row_sample)) - """Add information which requires processing - """ - # row_sample.update(self.include_processed_data(row_sample)) - - # Add experiment_alias and run_alias - row_sample["experiment_alias"] = str( - row_sample["sequence_file_R1_fastq"] - + "_" - + row_sample["sequence_file_R2_fastq"] - ) - row_sample["run_alias"] = str( - row_sample["sequence_file_R1_fastq"] - + "_" - + row_sample["sequence_file_R2_fastq"] - ) - additional_metadata.append(row_sample) - - return additional_metadata - def read_configuration_json_files(self): """Read json files defined in configuration lab_metadata_req_json property @@ -375,13 +252,6 @@ def create_metadata_json(self): stderr.print("[blue] Including additional information") completed_metadata = self.adding_fields(valid_metadata_rows) - import pdb - - pdb.set_trace() - - completed_metadata = self.add_additional_data( - valid_metadata_rows, conf_json_data - ) file_name = ( "processed_" From 47598bfea049185191bdd7f3abb836de4db380c6 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 6 Sep 2022 16:41:39 +0200 Subject: [PATCH 0909/1454] liting --- relecov_tools/conf/configuration.json | 18 ------------------ relecov_tools/read_lab_metadata.py | 8 ++++++-- 2 files changed, 6 insertions(+), 20 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 40f73ff4..6fa0454c 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -149,15 +149,6 @@ "ena_schema": "ena_schema.json", "gisaid_schema": "gisaid_schema.json" }, -<<<<<<< HEAD - -======= - "lab_metadata_req_json": { - "laboratory_data": "laboratory_address.json", - "geo_location_data": "geo_loc_cities.json", - "anatomical_material": "anatomical_material_collection_method.json" - }, ->>>>>>> c39c0ded483e5453088d6294d67dcb51d2ef9333 "institution_mapping_file": { "ISCIII": "ISCIII.json", "HUGTiP": "HUGTiP.json" @@ -264,15 +255,7 @@ "tool_version": "0.5.3" }, "md5_file_name": "md5_check_file.csv", -<<<<<<< HEAD - "checklist": "ERC000033" -} -======= "checklist": "ERC000033", - "mapping_file": { - "ISCIII": "ISCIII.json", - "HUGTiP": "HUGTiP.json" - }, "df_study_fields": [ "study_type", "study_abstract" @@ -319,4 +302,3 @@ "sequencing_instrument_platform" ] } ->>>>>>> c39c0ded483e5453088d6294d67dcb51d2ef9333 diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 536524e2..7a2897b4 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -64,7 +64,9 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None self.label_prop_dict[values["label"]] = prop except KeyError: continue - self.json_req_files = config_json.get_topic_data("lab_metadata", "lab_metadata_req_json") + self.json_req_files = config_json.get_topic_data( + "lab_metadata", "lab_metadata_req_json" + ) self.schema_name = self.relecov_sch_json["schema"] self.schema_version = self.relecov_sch_json["version"] @@ -76,7 +78,9 @@ def include_fixed_data(self): "tax_id": "2697049", "organism": "Severe acute respiratory syndrome coronavirus 2", } - fixed_data.update(self.configuration.get_topic_data("lab_metadata", "fields_required_for_ENA")) + fixed_data.update( + self.configuration.get_topic_data("lab_metadata", "fields_required_for_ENA") + ) fixed_data["schema_name"] = self.schema_name fixed_data["schema_version"] = self.schema_version return fixed_data From 3e7a94d75a8a3b5de24951975ce319f8dcef936e Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 6 Sep 2022 17:00:25 +0200 Subject: [PATCH 0910/1454] working on ena upload functions --- relecov_tools/ena_upload.py | 26 ++++++++++++++++++++++++-- 1 file changed, 24 insertions(+), 2 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 27d1c7cc..4a26a14c 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -117,6 +117,19 @@ def convert_input_json_to_ena(self): """Split the input ena json, in samples and runs json""" pass + def create_dataframe(self, dataframe_name, fields_config, df_schemas): + df_list = [] + config_json = ConfigJson() + for index in range(len(dataframe_name)): + fields = config_json.get_configuration(fields_config[index]) + dataframe_name[index] = df_schemas[fields] + import pdb + + pdb.set_trace() + df_list.append(dataframe_name[index]) + + return df_list + def create_structure_to_ena(self): """Convert json to dataframe required by ena-upload-cli package""" @@ -127,7 +140,18 @@ def create_structure_to_ena(self): config_json = ConfigJson() df_schemas = pd.DataFrame(squema_json) + dataframe_name_list = ["df_study", "df_samples", "df_run", "df_experiments"] + dataframe_fileds_config_list = [ + "df_study_fields", + "df_samples_fields", + "df_run_fields" "df_experiment_fields", + ] + self.create_dataframe( + dataframe_name_list, dataframe_fileds_config_list, df_schemas + ) + import pdb + pdb.set_trace() # df_schema """ collecting_institution collection_date collector_name ... study_title study_type taxon_id @@ -157,9 +181,7 @@ def create_structure_to_ena(self): """ fields_samples = config_json.get_configuration("df_samples_fields") - import pdb - pdb.set_trace() df_samples = df_schemas[fields_samples] df_samples["host_sex"].replace("unknown", "not provided", inplace=True) From cf0015e40094294be7bf9ad7d0d7a23689d85c00 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 6 Sep 2022 17:18:51 +0200 Subject: [PATCH 0911/1454] removed ENA fields when creating the process lab metadata json --- relecov_tools/conf/configuration.json | 8 -------- 1 file changed, 8 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 6fa0454c..f3552d19 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -55,14 +55,6 @@ "Sequence file R1 fastq", "Sequence file R2 fastq" ], - "fields_required_for_ENA": { - "study_alias": "RELECOV", - "design_description": "Design Description", - "experiment_title": "Example project for ENA submission RELECOV", - "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "", - "study_id": "ERP137164" - }, "lab_metadata_req_json": { "laboratory_data": { "file": "laboratory_address.json", From 8c077606527129d6ccfd72ec27805cb119b28c39 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 6 Sep 2022 17:25:14 +0200 Subject: [PATCH 0912/1454] new parameter on read_excel to write Not Provided instead of empty --- relecov_tools/read_lab_metadata.py | 2 +- relecov_tools/utils.py | 7 +++++-- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 7a2897b4..35df2a3f 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -190,7 +190,7 @@ def read_metadata_file(self): """ heading_row_number = 4 ws_metadata_lab = relecov_tools.utils.read_excel_file( - self.metadata_file, "METADATA_LAB", heading_row_number + self.metadata_file, "METADATA_LAB", heading_row_number, False ) metadata_values = [] diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 895f8371..527260ac 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -34,7 +34,7 @@ def read_json_file(j_file): return data -def read_excel_file(f_name, sheet_name, heading_row): +def read_excel_file(f_name, sheet_name, heading_row, empty_value=True): """Read the input excel file and give the information in a list of dictionaries """ @@ -51,7 +51,10 @@ def read_excel_file(f_name, sheet_name, heading_row): continue for idx in range(0, len(heading)): if l_row[idx] is None: - data_row[heading[idx]] = "" + if empty_value : + data_row[heading[idx]] = "" + else: + data_row[heading[idx]] = "Not Provided" else: data_row[heading[idx]] = l_row[idx] ws_data.append(data_row) From 995bb594a6880062708e4adfe9eb0bc554a9de82 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 6 Sep 2022 17:27:26 +0200 Subject: [PATCH 0913/1454] new parameter on read_excel to write Not Provided instead of empty --- relecov_tools/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 527260ac..ff99fae3 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -51,7 +51,7 @@ def read_excel_file(f_name, sheet_name, heading_row, empty_value=True): continue for idx in range(0, len(heading)): if l_row[idx] is None: - if empty_value : + if empty_value: data_row[heading[idx]] = "" else: data_row[heading[idx]] = "Not Provided" From fbd718356a4a7bc58d42092a791ea1d1eea856c1 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 7 Sep 2022 13:03:47 +0200 Subject: [PATCH 0914/1454] added rename function to ena upload --- relecov_tools/conf/configuration.json | 28 ++++++++- relecov_tools/ena_upload.py | 90 ++++++++++----------------- 2 files changed, 59 insertions(+), 59 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 6fa0454c..310101e7 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -92,7 +92,7 @@ "anatomical_material" ] }, - "adding_fields" : "__all__" + "adding_fields": "__all__" } } }, @@ -300,5 +300,29 @@ "collecting_institution", "insert_size", "sequencing_instrument_platform" + ], + "rename_sample_list_og": [ + "sample_name", + "sample_title", + "geographic_location_(country_and/or_sea)", + "host_subject_id", + "collection_date", + "host_common_name", + "host_sex", + "host_scientific_name", + "collector_name", + "collecting_institution" + ], + "rename_sample_list_final": [ + "alias", + "title", + "geographic location (country and/or sea)", + "host subject id", + "collection date", + "host common name", + "host sex", + "host scientific name", + "collector name", + "collecting institution" ] -} +} \ No newline at end of file diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 4a26a14c..af50cc59 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -123,13 +123,20 @@ def create_dataframe(self, dataframe_name, fields_config, df_schemas): for index in range(len(dataframe_name)): fields = config_json.get_configuration(fields_config[index]) dataframe_name[index] = df_schemas[fields] - import pdb - - pdb.set_trace() df_list.append(dataframe_name[index]) return df_list + def rename_cols_df(self, dataframe_name, dataframe, col_name_og, col_name_final): + col_dict = {} + + for index in range(len(col_name_og)): + col_dict[col_name_og[index]] = col_name_final[index] + + dataframe_name = dataframe.rename(columns=col_dict) + + return dataframe_name + def create_structure_to_ena(self): """Convert json to dataframe required by ena-upload-cli package""" @@ -144,31 +151,27 @@ def create_structure_to_ena(self): dataframe_fileds_config_list = [ "df_study_fields", "df_samples_fields", - "df_run_fields" "df_experiment_fields", + "df_run_fields", + "df_experiment_fields", ] - self.create_dataframe( + # Creating the dataframes df_Study, df_samples, df_run and df_experiment + df_list = self.create_dataframe( dataframe_name_list, dataframe_fileds_config_list, df_schemas ) - import pdb - pdb.set_trace() + df_study = df_list[0] + df_samples = df_list[1] + df_run = df_list[2] + df_experiments = df_list[3] + # df_schema """ collecting_institution collection_date collector_name ... study_title study_type taxon_id 0 Hospital Clínic de Barcelona 2021-05-10 Inmaculada Casas ... RELECOV Spanish Network for genomics surveillance Surveillance 2697049 1 Hospital Clínic de Barcelona 2021-05-07 Inmaculada Casas ... RELECOV Spanish Network for genomics surveillance Surveillance 2697049 - - """ """ - df_study = df_schemas[ - ["study_alias", "study_title", "study_type", "study_abstract"] - ] - - df_study = df_study.rename(columns={"study_alias": "alias"}) - df_study = df_study.rename(columns={"study_title": "title"}) - """ - fields_study = config_json.get_configuration("df_study_fields") - df_study = df_schemas[fields_study] + ###################### Parsing the dataframes specifically according to ENA requirements############# + # df_study df_study["alias"] = df_study["study_abstract"][0].rsplit(" ", 5)[0] df_study["title"] = df_study["study_abstract"] df_study.insert(3, "status", self.action) @@ -179,50 +182,28 @@ def create_structure_to_ena(self): 0 RELECOV RELECOV Spanish Network for genomics surveillance Surveillance ADD RELECOV Spanish Network for genomics surveillance 1 RELECOV RELECOV Spanish Network for genomics surveillance Surveillance ADD RELECOV Spanish Network for genomics surveillance """ - - fields_samples = config_json.get_configuration("df_samples_fields") - - df_samples = df_schemas[fields_samples] - + # df_samples df_samples["host_sex"].replace("unknown", "not provided", inplace=True) df_samples["host_sex"].replace("Unknown", "not provided", inplace=True) - - df_samples = df_samples.rename(columns={"sample_name": "alias"}) - df_samples = df_samples.rename(columns={"sample_title": "title"}) - df_samples = df_samples.rename( - columns={ - "geographic_location_(country_and/or_sea)": "geographic location (country and/or sea)" - } - ) - df_samples = df_samples.rename(columns={"host_subject_id": "host subject id"}) - df_samples = df_samples.rename(columns={"collection_date": "collection date"}) - df_samples = df_samples.rename(columns={"host_common_name": "host common name"}) - df_samples = df_samples.rename(columns={"host_common_name": "host common name"}) - df_samples = df_samples.rename(columns={"host_sex": "host sex"}) - df_samples = df_samples.rename( - columns={"host_scientific_name": "host scientific name"} - ) - df_samples = df_samples.rename(columns={"collector_name": "collector name"}) - df_samples = df_samples.rename( - columns={"collecting_institution": "collecting institution"} + df_samples_fileds_config = ["rename_sample_list_og", "rename_sample_list_final"] + df_samples = self.rename_cols_df( + "df_samples", + df_samples, + config_json.get_configuration(df_samples_fileds_config[0]), + config_json.get_configuration(df_samples_fileds_config[1]), ) df_samples.insert(3, "status", self.action) - # df_samples.insert(3, "host subject id", df_schemas["host subject id"]) - # df_samples.insert(3, "host health state", df_schemas["host health state"]) checklist = config_json.get_configuration("checklist") df_samples.insert(4, "ENA_CHECKLIST", checklist) - # df_samples.insert(5, "sample_description", df_schemas["sample_description"]) - # df_samples """ + # df_samples alias title taxon_id host health state ... scientific_name collector name collecting institution isolate 0 212164375 212164375 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212164375 1 212163777 212163777 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212163777 2 212153091 212153091 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212153091 """ - fields_run = config_json.get_configuration("df_run_fields") - df_run = df_schemas[fields_run] - + # df_run df_run.insert(1, "sequence_file_R1_fastq", "None") df_run.insert(2, "sequence_file_R2_fastq", "None") for i in range(len(df_schemas)): @@ -256,17 +237,15 @@ def create_structure_to_ena(self): df_run_final = pd.concat([df_run, df_run2]) df_run_final.reset_index() - # df_run """ + # df_run experiment_alias sequence_file_R1_fastq sequence_file_R2_fastq ... file_type file_checksum fastq_r2_md5 0 214821_S12 214821_S12_R1_001.fastq.gz 214821_S12_R2_001.fastq.gz ... fastq 372ca8b10a8eeb7a04107634baf340ab 7f5081eec1b64b171402b66f37fe640d 1 214821_S12 214822_S13_R1_001.fastq.gz 214822_S13_R2_001.fastq.gz ... fastq b268d7be80e80455bec0807b5961d23c a15be39feaf73eec9b2c026717878bba 2 214821_S12 214823_S1_R1_001.fastq.gz 214823_S1_R2_001.fastq.gz ... fastq c16bdbfc03c354496fcfb2c107e3cbf6 4d9b80b977a75bf7e2a4282ca910d94a """ - fields_experiment = config_json.get_configuration("df_experiment_fields") - df_experiments = df_schemas[[fields_experiment]] - + # df_experiments df_experiments["instrument_model"] = df_experiments[ "instrument_model" ].str.lower() @@ -279,9 +258,6 @@ def create_structure_to_ena(self): + "_" + str(df_run.loc[i, "sequence_file_R2_fastq"]) ) - # df_experiments.insert(5, "design_description", df_schemas["design_description"]) - # df_experiments.insert(5, "insert_size", df_schemas["insert_size"]) - # df_experiments.insert(5, "platform", df_schemas["sequencing_instrument_platform"]) df_experiments = df_experiments.rename( columns={"sequencing_instrument_platform": "platform"} @@ -292,8 +268,8 @@ def create_structure_to_ena(self): columns={"collecting_institution": "collecting institution"} ) - # df_experiments example """ + # df_experiments example experiment_alias title study_alias ... library_layout instrument_model alias 0 214821_S12 RELECOV Spanish Network for genomics surveillance RELECOV ... PAIRED Illumina MiSeq 214821_S12_R1_001.fastq.gz_214821_S12_R2_001.f... 1 214821_S12 RELECOV Spanish Network for genomics surveillance RELECOV ... PAIRED Illumina MiSeq 214822_S13_R1_001.fastq.gz_214822_S13_R2_001.f... From bc777750fead5ccef0fcf43e4161809f15cc174d Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 7 Sep 2022 13:11:04 +0200 Subject: [PATCH 0915/1454] linitn2 --- relecov_tools/ena_upload.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index af50cc59..b562d6da 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -170,7 +170,7 @@ def create_structure_to_ena(self): 0 Hospital Clínic de Barcelona 2021-05-10 Inmaculada Casas ... RELECOV Spanish Network for genomics surveillance Surveillance 2697049 1 Hospital Clínic de Barcelona 2021-05-07 Inmaculada Casas ... RELECOV Spanish Network for genomics surveillance Surveillance 2697049 """ - ###################### Parsing the dataframes specifically according to ENA requirements############# + # Parsing the dataframes specifically according to ENA requirements # # df_study df_study["alias"] = df_study["study_abstract"][0].rsplit(" ", 5)[0] df_study["title"] = df_study["study_abstract"] @@ -267,7 +267,6 @@ def create_structure_to_ena(self): df_experiments = df_experiments.rename( columns={"collecting_institution": "collecting institution"} ) - """ # df_experiments example experiment_alias title study_alias ... library_layout instrument_model alias From f8d0ee4fb581a6edf21f60f7faa796e6f23d5f15 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 7 Sep 2022 13:58:24 +0200 Subject: [PATCH 0916/1454] processed json is validate aginst schema --- relecov_tools/conf/configuration.json | 14 +++ relecov_tools/read_lab_metadata.py | 110 ++++++++++++------ .../schema/institution_schemas/ISCIII.json | 6 +- relecov_tools/schema/relecov_schema.json | 49 ++++---- 4 files changed, 118 insertions(+), 61 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index f3552d19..f2ef8053 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -86,6 +86,20 @@ }, "adding_fields" : "__all__" } + }, + "required_post_processing":{ + "host_common_name": { + "Human": "host_scientific_name::Homo sapiens" + }, + "sequencing_instrument_model":{ + "Illumina": "sequencing_instrument_platform::Illumina", + "PacBio": "sequencing_instrument_platform::PacBio", + "Ion Torrent": "sequencing_instrument_platform::Ion Torrent", + "Oxford Nanopore": "sequencing_instrument_platform::Oxford Nanopore" + } + }, + "required_copy_from_other_field": { + "isolate_sample_id": "sequencing_sample_id" } }, "long_table_heading": [ diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 35df2a3f..b4d50113 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -70,50 +70,81 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None self.schema_name = self.relecov_sch_json["schema"] self.schema_version = self.relecov_sch_json["version"] - def include_fixed_data(self): + def adding_fixed_fields(self, m_data): """Include fixed data that are always the same for each samples""" - fixed_data = { - "host_disease": "COVID-19", - "type": "betacoronavirus", - "tax_id": "2697049", - "organism": "Severe acute respiratory syndrome coronavirus 2", - } - fixed_data.update( - self.configuration.get_topic_data("lab_metadata", "fields_required_for_ENA") + p_data = self.configuration.get_topic_data("lab_metadata", "fixed_fields") + for idx in range(len(m_data)): + for key, value in p_data.items(): + m_data[idx][key] = value + m_data[idx]["schema_name"] = self.schema_name + m_data[idx]["schema_version"] = self.schema_version + return m_data + + def adding_copy_from_other_field(self, m_data): + """Add in a new field the information that is already set in another + field. + """ + p_data = self.configuration.get_topic_data( + "lab_metadata", "required_copy_from_other_field" ) - fixed_data["schema_name"] = self.schema_name - fixed_data["schema_version"] = self.schema_version - return fixed_data + for idx in range(len(m_data)): + for key, value in p_data.items(): + m_data[idx][key] = m_data[idx][value] + return m_data - def include_processed_data(self, metadata): - """Include the data that requires to be processed to set the value. - This values are checked aginst the available options in the schema + def adding_post_processing(self, m_data): + """Add the fields that requires to set based on the existing value + in other field """ - new_data = {} - p_data = { - "host_common_name": {"Human": ["host_scientific_name", "Homo Sapiens"]}, - "collecting_lab_sample_id": [ - "isolate_sample_id", - metadata["sequencing_sample_id"], - ], - } + p_data = self.configuration.get_topic_data( + "lab_metadata", "required_post_processing" + ) + for idx in range(len(m_data)): + for key, p_values in p_data.items(): + value = m_data[idx][key] + if value in p_values: + p_field, p_set = p_values[value].split("::") + m_data[idx][p_field] = p_set + else: + # Check if key p_values should match only part of the value + for reg_key, reg_value in p_values.items(): + if reg_key in value: + p_field, p_set = reg_value.split("::") + m_data[idx][p_field] = p_set + + return m_data - for key, values in p_data.items(): - v_data = metadata[key] - if isinstance(values, dict): - if v_data in values: - new_data[values[v_data][0]] = values[v_data][1] - else: - new_data[values[0]] = values[1] - """New fields that required processing from other field """ + def adding_ontology_to_enum(self, m_data): + """Read the schema to get the properties enum and for those fields + which has an enum property value then replace the value for the one it + is defined in the schema + """ + enum_dict = {} + for prop, values in self.relecov_sch_json["properties"].items(): + # import pdb; pdb.set_trace() + if "enum" in values: + enum_dict[prop] = {} + for enum in values["enum"]: + go_match = re.search(r"(.+) \[\w+:.*", enum) + if go_match: + enum_dict[prop][go_match.group(1)] = enum + else: + enum_dict[prop][enum] = enum - return new_data + for idx in range(len(m_data)): + for key, e_values in enum_dict.items(): + if key in m_data[idx]: + if m_data[idx][key] in e_values: + m_data[idx][key] = e_values[m_data[idx][key]] + else: + continue + # import pdb; pdb.set_trace() + return m_data def process_from_json(self, m_data, json_fields): """ """ if isinstance(json_fields["map_field"], dict): # Search for the value which contains data - for m_field in json_fields["map_field"]["any_of"]: try: m_data[0][m_field] @@ -151,7 +182,8 @@ def process_from_json(self, m_data, json_fields): return m_data def adding_fields(self, metadata): - """Add fields""" + """Add information that requires to handle json files to include in + the fields""" for key, values in self.json_req_files.items(): stderr.print(f"[blue] Processing {key}") @@ -162,6 +194,8 @@ def adding_fields(self, metadata): metadata = self.process_from_json(metadata, values) stderr.print(f"[green] Processed {key}") stderr.print("[blue] Reading sample list file") + # Because sample data file is comming in an input parameter it cannot + # be inside the configuration json file. # Include Sample informatin data from sample json file s_json = {} s_json["map_field"] = "sequencing_sample_id" @@ -255,8 +289,12 @@ def create_metadata_json(self): # Continue by adding extra information stderr.print("[blue] Including additional information") - completed_metadata = self.adding_fields(valid_metadata_rows) - + extended_metadata = self.adding_fields(valid_metadata_rows) + stderr.print("[blue] Including post processing information") + extended_metadata = self.adding_post_processing(extended_metadata) + extended_metadata = self.adding_copy_from_other_field(extended_metadata) + extended_metadata = self.adding_fixed_fields(extended_metadata) + completed_metadata = self.adding_ontology_to_enum(extended_metadata) file_name = ( "processed_" + os.path.splitext(os.path.basename(self.metadata_file))[0] diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 06996bba..6ad98698 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -113,12 +113,12 @@ "Library Preparation Kit": "Illumina DNA Prep", "Enrichment Protocol": "Amplicon", "Enrichment panel/assay": "ARTIC", - "Source material": "Viral RNA", + "Source material": "VIRAL RNA", "Capture method": "PCR", "Sequencing technique": "Amplicon", "Library Layout": "Paired", - "Gene Name 1": "ORF E", + "Gene Name 1": "E gene", "Diagnostic Pcr Ct Value 1": "", "Authors": "" } -} \ No newline at end of file +} diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index e8fef802..936a67f8 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -612,8 +612,8 @@ "Anus [UBERON:0001245]", "Duodenum [UBERON:0002114]", "Pharynx [UBERON:0006562]", - "Nasopharynx (NP) [UBERON:0001728]", - "Oropharynx (OP) [UBERON:0001729]", + "Nasopharynx [UBERON:0001728]", + "Oropharynx [UBERON:0001729]", "Not Applicable [GENEPIO:0001619]", "Not Collected [GENEPIO:0001620]", "Not Provided [GENEPIO:0001668]", @@ -1126,6 +1126,7 @@ "NEBNext ARTIC SARS-CoV-2 FS", "Illumina COVIDSeq Test [CIDO:0020172]", "ABL DeepChek® Assay WG SC2 V1", + "Not Provided [GENEPIO:0001668]", "Other" ], "examples": [ @@ -1398,6 +1399,7 @@ "iSeq 100 i1 Reagent v2 (300-cycle)", "iSeq 100 i1 Reagent v2 (300-cycle) 4 pack", "iSeq 100 i1 Reagent v2 (300-cycle) 8 pack", + "Not Provided [GENEPIO:0001668]", "Other" ], "examples": [ @@ -1425,7 +1427,10 @@ "enum": [ "Oxford Nanopore [OBI:0002750]", "Illumina [OBI:0000759]", - "Ion Torrent", + "Ion Torrent [GENEPIO:0002683]", + "PacBio [GENEPIO:0001927]", + "BGI", + "MGI", "Other" ], "examples": [ @@ -1514,12 +1519,12 @@ "WCS strategy [GENPIO:0001991]", "WGS strategy [GENPIO:0001992]", "WXS strategy [GENPIO:0001993]", - "amplicon [GENPIO:0001974]", - "clone end strategy [GENPIO:0001976]", - "clone strategy [GENPIO:0001977]", - "finishing strategy [GENPIO:0001982]", - "other library strategy [GENPIO:0001988]", - "pool clone strategy [GENPIO:0001989]" + "Amplicon [GENPIO:0001974]", + "Clone end strategy [GENPIO:0001976]", + "Clone strategy [GENPIO:0001977]", + "Finishing strategy [GENPIO:0001982]", + "Other library strategy [GENPIO:0001988]", + "Pool clone strategy [GENPIO:0001989]" ], "examples": [ "WGS" @@ -1533,11 +1538,11 @@ }, "library_layout": { "enum": [ - "SINGLE [OBI:0002481]", - "PAIRED [OBI:0001852]" + "Single [OBI:0002481]", + "Paired [OBI:0001852]" ], "examples": [ - "PAIRED" + "Paired" ], "ontology": "NCIT:C175894", "type": "string", @@ -2178,10 +2183,10 @@ }, "gene_name_1": { "enum": [ - "E gene (orf4) [GENEPIO:0100151]", - "M gene (orf5) [GENEPIO:0100152]", - "N gene (orf9) [GENEPIO:0100153]", - "Spike gene (orf2) [GENEPIO:0100154]", + "E gene [GENEPIO:0100151]", + "M gene [GENEPIO:0100152]", + "N gene [GENEPIO:0100153]", + "Spike gene [GENEPIO:0100154]", "orf1ab (rep) [GENEPIO:0100155]", "orf1a (pp1a) [GENEPIO:0100156]", "nsp11 [GENEPIO:0100157]", @@ -2221,7 +2226,7 @@ "type": "string", "description": "The name of the gene used in the diagnostic RT-PCR test.", "examples": [ - "E gene (orf4) [GENEPIO:0100151]" + "E gene [GENEPIO:0100151]" ], "classification": "Pathogen diagnostic testing", "label": "Gene Name 1", @@ -2240,10 +2245,10 @@ }, "gene_name_2": { "enum": [ - "E gene (orf4) [GENEPIO:0100151]", - "M gene (orf5) [GENEPIO:0100152]", - "N gene (orf9) [GENEPIO:0100153]", - "Spike gene (orf2) [GENEPIO:0100154]", + "E gene [GENEPIO:0100151]", + "M gene [GENEPIO:0100152]", + "N gene [GENEPIO:0100153]", + "Spike gene [GENEPIO:0100154]", "orf1ab (rep) [GENEPIO:0100155]", "orf1a (pp1a) [GENEPIO:0100156]", "nsp11 [GENEPIO:0100157]", @@ -2500,4 +2505,4 @@ "fill_mode": "batch" } } -} \ No newline at end of file +} From 591be49fb2c0c66828b6695b68c787f5a4e6d4b1 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 7 Sep 2022 14:56:37 +0200 Subject: [PATCH 0917/1454] change in configuration --- relecov_tools/conf/configuration.json | 150 +++++++++++++------------- relecov_tools/ena_upload.py | 11 ++ 2 files changed, 87 insertions(+), 74 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 310101e7..4feaaefe 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -250,79 +250,81 @@ "consensus_genome_length.csv": "consensus_genome_length_path", "software_versions.yml": "software_versions_path" }, - "tool": { - "tool_name": "ena-upload-cli", - "tool_version": "0.5.3" - }, "md5_file_name": "md5_check_file.csv", - "checklist": "ERC000033", - "df_study_fields": [ - "study_type", - "study_abstract" - ], - "df_samples_fields": [ - "sample_name", - "sample_title", - "taxon_id", - "collection_date", - "geographic_location_(country_and/or_sea)", - "host_common_name", - "host_scientific_name", - "host_sex", - "scientific_name", - "collector_name", - "collecting_institution", - "isolate", - "host_subject_id", - "host health state", - "authors", - "sample_description", - "address" - ], - "df_run_fields": [ - "r1_fastq_filepath", - "r2_fastq_filepath", - "file_type", - "fastq_r1_md5", - "fastq_r2_md5", - "collecting_institution" - ], - "df_experiment_fields": [ - "study_abstract", - "sample_name", - "library_name", - "library_strategy", - "library_source", - "library_selection", - "library_layout", - "instrument_model", - "design_description", - "collecting_institution", - "insert_size", - "sequencing_instrument_platform" - ], - "rename_sample_list_og": [ - "sample_name", - "sample_title", - "geographic_location_(country_and/or_sea)", - "host_subject_id", - "collection_date", - "host_common_name", - "host_sex", - "host_scientific_name", - "collector_name", - "collecting_institution" - ], - "rename_sample_list_final": [ - "alias", - "title", - "geographic location (country and/or sea)", - "host subject id", - "collection date", - "host common name", - "host sex", - "host scientific name", - "collector name", - "collecting institution" - ] + "ENA_fields": { + "tool": { + "tool_name": "ena-upload-cli", + "tool_version": "0.5.3" + }, + "checklist": "ERC000033", + "df_study_fields": [ + "study_type", + "study_abstract" + ], + "df_samples_fields": [ + "sample_name", + "sample_title", + "taxon_id", + "collection_date", + "geographic_location_(country_and/or_sea)", + "host_common_name", + "host_scientific_name", + "host_sex", + "scientific_name", + "collector_name", + "collecting_institution", + "isolate", + "host_subject_id", + "host health state", + "authors", + "sample_description", + "address" + ], + "df_run_fields": [ + "r1_fastq_filepath", + "r2_fastq_filepath", + "file_type", + "fastq_r1_md5", + "fastq_r2_md5", + "collecting_institution" + ], + "df_experiment_fields": [ + "study_abstract", + "sample_name", + "library_name", + "library_strategy", + "library_source", + "library_selection", + "library_layout", + "instrument_model", + "design_description", + "collecting_institution", + "insert_size", + "sequencing_instrument_platform" + ], + "rename_sample_list_og": [ + "sample_name", + "sample_title", + "geographic_location_(country_and/or_sea)", + "host_subject_id", + "collection_date", + "host_common_name", + "host_sex", + "host_scientific_name", + "collector_name", + "collecting_institution" + ], + "rename_sample_list_final": [ + "alias", + "title", + "geographic location (country and/or sea)", + "host subject id", + "collection date", + "host common name", + "host sex", + "host scientific name", + "collector name", + "collecting institution" + ] + } } \ No newline at end of file diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index b562d6da..a692954b 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -276,6 +276,17 @@ def create_structure_to_ena(self): """ + """ + "ENA_configuration": { + "study_alias": "RELECOV", + "design_description": "Design Description", + "experiment_title": "Example project for ENA submission RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", + "study_id": "ERP137164" + }, + """ + ena_config = config_json.get_configuration("ENA_configuration") schema_dataframe = {} schema_dataframe["sample"] = df_samples From 4a71af231ce13a56322c96a2a6159968651376ad Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 7 Sep 2022 15:36:41 +0200 Subject: [PATCH 0918/1454] added pharynx in the ISCIII.py funciton --- relecov_tools/institution_scripts/ISCIII.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index 976981ac..590ab7b1 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -100,7 +100,7 @@ def translate_specimen_source(metadata, f_data, mapped_fields, heading): elif "EXTRACTO" in row[m_idx].upper(): row[m_idx] = "Scraping" elif "EXUDADO FARÍNGEO" in row[m_idx].upper(): - row[m_idx] = "Nasopharynx Swabbing" + row[m_idx] = "Pharynx Swabbing" elif "EXUDADO NASOFARÍNGEO" in row[m_idx].upper(): row[m_idx] = "Nasopharynx Swabbing" elif "EXUDADO OROFARINGEO" in row[m_idx].upper(): From 7fd08973770ac697b75203af7ff562ca5ecbe9e2 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 7 Sep 2022 15:48:59 +0200 Subject: [PATCH 0919/1454] not applicable added error handling --- relecov_tools/institution_scripts/ISCIII.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index 590ab7b1..6adc1eed 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -71,6 +71,10 @@ def translate_gender_to_english(metadata, f_data, mapped_fields, heading): row[m_idx] = "Male" elif "mujer" in row[m_idx].lower(): row[m_idx] = "Female" + elif "genero no-binario" in row[m_idx].lower(): + row[m_idx] = "Non-binary Gender" + elif "genero no-binario" in row[m_idx].lower(): + row[m_idx] = "Non-binary Gender" elif "desconocido" in row[m_idx].lower(): row[m_idx] = "not provided" elif "Unknown" in row[m_idx].lower(): @@ -78,7 +82,9 @@ def translate_gender_to_english(metadata, f_data, mapped_fields, heading): elif "unknown" in row[m_idx].lower(): row[m_idx] = "not provided" else: - row[m_idx] = "not applicable" + log.error("The field is not correctly written or is not filled") + stderr.print("The field is not correctly written or is not filled") + return metadata From a802f9d7b02ffdc7487d85820359878101808474 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 7 Sep 2022 18:22:14 +0200 Subject: [PATCH 0920/1454] pharynx again --- relecov_tools/institution_scripts/ISCIII.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index 6adc1eed..7b893a0c 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -117,5 +117,5 @@ def translate_specimen_source(metadata, f_data, mapped_fields, heading): row[m_idx] = "Saliva" else: log.error("The field is not correctly written or is not filled") - stderr.print("The field is not correctly written or is not filled") + stderr.print("The field is not correctly written or not filled") return metadata From a134ff66d1d36f777541ec3a15d07042d894bba6 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 7 Sep 2022 21:23:05 +0200 Subject: [PATCH 0921/1454] Changes in capsletter of Public databases --- relecov_tools/schema/relecov_schema.json | 31 +++++++++--------------- 1 file changed, 11 insertions(+), 20 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 936a67f8..ede7f205 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -855,6 +855,7 @@ "description": "An unique identifier by which each subject can be referred to, de-identified.", "classification": "Host information", "label": "Host Subject Id", + "fill_mode": "sample", "minLenght": "1" }, "host_health_state": { @@ -865,7 +866,8 @@ "type": "string", "description": " Status of the host", "classification": "Host information", - "label": "Host health state" + "label": "Host health state", + "fill_mode": "sample" }, "host_common_name": { "enum": [ @@ -2349,17 +2351,6 @@ "label": "Authors", "fill_mode": "batch" }, - "broker_name": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Public databases", - "label": "Broker Name", - "fill_mode": "batch" - }, "gisaid_submitter_id": { "examples": [ "" @@ -2367,8 +2358,8 @@ "ontology": "NCIT:C54269", "type": "string", "description": "GISAID sequence ID.", - "classification": "Public Databases", - "label": "GISAID id", + "classification": "Public databases", + "label": "GISAID submitter id", "fill_mode": "sample" }, "gisaid_accession_id": { @@ -2378,7 +2369,7 @@ "ontology": "NCIT:C180324", "type": "string", "description": "GISAID sequence ID.", - "classification": "Public Databases", + "classification": "Public databases", "label": "GISAID id", "fill_mode": "sample" }, @@ -2389,7 +2380,7 @@ "ontology": "GENEPIO:0100282", "type": "string", "description": "The user-defined GISAID virus name assigned to the sequence.", - "classification": "Public Databases", + "classification": "Public databases", "label": "GISAID Virus Name", "fill_mode": "sample" }, @@ -2466,7 +2457,7 @@ "ontology": "ORNASEQ_0000004", "type": "string", "description": "", - "classification": "Public Databases", + "classification": "Public databases", "label": "Experiment title", "fill_mode": "batch" }, @@ -2477,7 +2468,7 @@ "ontology": "OPMI_0000380", "type": "string", "description": "", - "classification": "Public Databases", + "classification": "Public databases", "label": "Study title", "fill_mode": "batch" }, @@ -2488,7 +2479,7 @@ "ontology": "BU_ISCIII:045", "type": "string", "description": "", - "classification": "Public Databases", + "classification": "Public databases", "label": "Broker Name", "fill_mode": "batch" }, @@ -2500,7 +2491,7 @@ "type": "string", "format": "date", "description": "", - "classification": "Public Databases", + "classification": "Public databases", "label": "First created date", "fill_mode": "batch" } From 18c3b06d746af22c9e1fb97061b4a0a212fc2627 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 7 Sep 2022 23:23:42 +0200 Subject: [PATCH 0922/1454] Removed the conversion to integrer if number was float --- relecov_tools/conf/anatomical_material_collection_method.json | 2 +- relecov_tools/read_lab_metadata.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/anatomical_material_collection_method.json b/relecov_tools/conf/anatomical_material_collection_method.json index 5439a2cc..6e71d137 100644 --- a/relecov_tools/conf/anatomical_material_collection_method.json +++ b/relecov_tools/conf/anatomical_material_collection_method.json @@ -999,4 +999,4 @@ "body_product": "Not Applicable", "anatomical_material": "Not Applicable" } -} \ No newline at end of file +} diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index b4d50113..45ad2d9f 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -268,7 +268,7 @@ def read_metadata_file(self): ) else: if isinstance(row[key], float) or isinstance(row[key], int): - row[key] = str(int(row[key])) + row[key] = str(row[key]) try: property_row[self.label_prop_dict[key]] = row[key] except KeyError as e: From 6e5408be8420f3965f059ff89669fdafa1bfd896 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 8 Sep 2022 09:31:16 +0200 Subject: [PATCH 0923/1454] changed anatomical_material_config.json & collection device --- .../conf/anatomical_material_collection_method.json | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/anatomical_material_collection_method.json b/relecov_tools/conf/anatomical_material_collection_method.json index 5439a2cc..3baee050 100644 --- a/relecov_tools/conf/anatomical_material_collection_method.json +++ b/relecov_tools/conf/anatomical_material_collection_method.json @@ -809,6 +809,12 @@ "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, + "Pharynx Swabbing": { + "anatomical_part": "Pharynx", + "collection_method": "Swabbing", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" + }, "Nasopharynx Swabbing": { "anatomical_part": "Nasopharynx", "collection_method": "Swabbing", @@ -989,13 +995,13 @@ }, "Scraping": { "anatomical_part": "Not Applicable", - "collection_device": "Scraping", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Placenta": { "anatomical_part": "Placenta", - "collection_device": "Not Applicable", + "collection_method": "Not Applicable", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" } From be795d6712110d5c667c51fdc74f1eb002354569 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 8 Sep 2022 09:39:29 +0200 Subject: [PATCH 0924/1454] lintin --- relecov_tools/institution_scripts/ISCIII.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index 7b893a0c..a80adec3 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -88,6 +88,9 @@ def translate_gender_to_english(metadata, f_data, mapped_fields, heading): return metadata +# + + def translate_specimen_source(metadata, f_data, mapped_fields, heading): """Translate into english the "muestra" that is written in spanish""" for row in metadata[1:]: From f91d81fccd5093a8d32a917d89d0f8d50802c641 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Thu, 8 Sep 2022 10:30:47 +0200 Subject: [PATCH 0925/1454] added --gzip flag to gisaid_upload --- relecov_tools/gisaid_upload.py | 21 ++++++++++++++++++--- 1 file changed, 18 insertions(+), 3 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 406f10ef..251cdc55 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -10,6 +10,7 @@ import relecov_tools.utils from Bio import SeqIO from relecov_tools.config_json import ConfigJson +import gzip # import site @@ -37,6 +38,7 @@ def __init__( frameshift=None, proxy_config=None, single=False, + gzip=False ): if ( token is None @@ -96,6 +98,7 @@ def __init__( else: self.proxy_config = proxy_config self.single = single + self.gzip = gzip # Metadatos @@ -181,12 +184,24 @@ def create_multifasta(self): """Create multifasta from single fastas (if --single)""" if self.single: gather_fastas_path = os.path.join(self.fasta_path, "*.fa*") - os.system( + if self.gzip: + os.system( + "zcat %s > %s/multifasta.fasta" % (gather_fastas_path, self.output_path) + ) + else: + os.system( "cat %s > %s/multifasta.fasta" % (gather_fastas_path, self.output_path) - ) + ) multifasta = "%s/multifasta.fasta" % self.output_path + else: - multifasta = self.fasta_path + if self.gzip: + os.system( + "zcat %s > %s/multifasta.fasta" % (self.fasta_path, self.output_path + ) + multifasta = "%s/multifasta.fasta" % self.output_path + else: + multifasta = self.fasta_path return multifasta def change_headers(self, multifasta): From ae7fb94b0851c23fd875e89b1f95d07f4f2bfc0c Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 8 Sep 2022 10:35:14 +0200 Subject: [PATCH 0926/1454] tried the modification in ena upload are working --- relecov_tools/conf/configuration.json | 12 +++++++-- relecov_tools/ena_upload.py | 28 ++++++++------------- relecov_tools/institution_scripts/ISCIII.py | 3 --- 3 files changed, 20 insertions(+), 23 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 36ae0bfa..b7ee614a 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -87,11 +87,11 @@ "adding_fields": "__all__" } }, - "required_post_processing":{ + "required_post_processing": { "host_common_name": { "Human": "host_scientific_name::Homo sapiens" }, - "sequencing_instrument_model":{ + "sequencing_instrument_model": { "Illumina": "sequencing_instrument_platform::Illumina", "PacBio": "sequencing_instrument_platform::PacBio", "Ion Torrent": "sequencing_instrument_platform::Ion Torrent", @@ -258,6 +258,14 @@ }, "md5_file_name": "md5_check_file.csv", "ENA_fields": { + "ENA_configuration": { + "study_alias": "RELECOV", + "design_description": "Design Description", + "experiment_title": "Project for ENA submission RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "", + "study_id": "ERP137164" + }, "tool": { "tool_name": "ena-upload-cli", "tool_version": "0.5.3" diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index a692954b..58902277 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -121,7 +121,8 @@ def create_dataframe(self, dataframe_name, fields_config, df_schemas): df_list = [] config_json = ConfigJson() for index in range(len(dataframe_name)): - fields = config_json.get_configuration(fields_config[index]) + + fields = config_json.get_configuration("ENA_fields")[fields_config[index]] dataframe_name[index] = df_schemas[fields] df_list.append(dataframe_name[index]) @@ -147,6 +148,7 @@ def create_structure_to_ena(self): config_json = ConfigJson() df_schemas = pd.DataFrame(squema_json) + dataframe_name_list = ["df_study", "df_samples", "df_run", "df_experiments"] dataframe_fileds_config_list = [ "df_study_fields", @@ -182,18 +184,19 @@ def create_structure_to_ena(self): 0 RELECOV RELECOV Spanish Network for genomics surveillance Surveillance ADD RELECOV Spanish Network for genomics surveillance 1 RELECOV RELECOV Spanish Network for genomics surveillance Surveillance ADD RELECOV Spanish Network for genomics surveillance """ + # df_samples df_samples["host_sex"].replace("unknown", "not provided", inplace=True) df_samples["host_sex"].replace("Unknown", "not provided", inplace=True) - df_samples_fileds_config = ["rename_sample_list_og", "rename_sample_list_final"] + # df_samples_fileds_config = ["rename_sample_list_og", "rename_sample_list_final"] df_samples = self.rename_cols_df( "df_samples", df_samples, - config_json.get_configuration(df_samples_fileds_config[0]), - config_json.get_configuration(df_samples_fileds_config[1]), + config_json.get_configuration("ENA_fields")["rename_sample_list_og"], + config_json.get_configuration("ENA_fields")["rename_sample_list_final"], ) df_samples.insert(3, "status", self.action) - checklist = config_json.get_configuration("checklist") + checklist = config_json.get_configuration("ENA_fields")["checklist"] df_samples.insert(4, "ENA_CHECKLIST", checklist) """ @@ -276,18 +279,7 @@ def create_structure_to_ena(self): """ - """ - "ENA_configuration": { - "study_alias": "RELECOV", - "design_description": "Design Description", - "experiment_title": "Example project for ENA submission RELECOV", - "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "", - "study_id": "ERP137164" - }, - """ - - ena_config = config_json.get_configuration("ENA_configuration") + ena_config = config_json.get_configuration("ENA_fields")["ENA_configuration"] schema_dataframe = {} schema_dataframe["sample"] = df_samples schema_dataframe["run"] = df_run_final @@ -347,7 +339,7 @@ def create_structure_to_ena(self): # requires source XMLs for 'run', 'experiment', 'sample', 'experiment' # schema_xmls record XMLs for all these schema and following 'submission' - tool = config_json.get_configuration("tool") + tool = config_json.get_configuration("ENA_fields")["tool"] schema_xmls = run_construct( template_path, schema_targets, self.center, checklist, tool diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index a80adec3..7b893a0c 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -88,9 +88,6 @@ def translate_gender_to_english(metadata, f_data, mapped_fields, heading): return metadata -# - - def translate_specimen_source(metadata, f_data, mapped_fields, heading): """Translate into english the "muestra" that is written in spanish""" for row in metadata[1:]: From 66f0f4290532bcf62e44425b02094270718c5e93 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Thu, 8 Sep 2022 10:49:12 +0200 Subject: [PATCH 0927/1454] added --gzip flag to __main__, modified --single flag --- relecov_tools/__main__.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 854d4ac9..76217f63 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -276,7 +276,7 @@ def upload_to_ena(user, password, center, ena_json, dev, study, action, output_p @click.option( "-i", "--input_path", - help="path to fasta or multifasta file", + help="path to fastas folder or multifasta file", ) @click.option("-o", "--output_path", help="output folder for log") @click.option( @@ -295,7 +295,13 @@ def upload_to_ena(user, password, center, ena_json, dev, study, action, output_p "--single", is_flag=True, default=False, - help="Default input is a multifasta.", + help="input is a folder with several fasta files. Default: False", +) +@click.option( + "--gzip", + is_flag=True, + default=False, + help="input fasta is gziped. Default: False", ) def upload_to_gisaid( user, From 1c1725f1e4d7e7a6d78bcc33c93b88f9e73dce5a Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 8 Sep 2022 10:56:24 +0200 Subject: [PATCH 0928/1454] Change in translation to english not provided for Not Provided --- relecov_tools/institution_scripts/ISCIII.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index a80adec3..1033a82c 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -76,14 +76,12 @@ def translate_gender_to_english(metadata, f_data, mapped_fields, heading): elif "genero no-binario" in row[m_idx].lower(): row[m_idx] = "Non-binary Gender" elif "desconocido" in row[m_idx].lower(): - row[m_idx] = "not provided" - elif "Unknown" in row[m_idx].lower(): - row[m_idx] = "not provided" + row[m_idx] = "Not Provided" elif "unknown" in row[m_idx].lower(): - row[m_idx] = "not provided" + row[m_idx] = "Not Provided" else: - log.error("The field is not correctly written or is not filled") - stderr.print("The field is not correctly written or is not filled") + log.error("The '%s' is not a valid data for translation" , row[m_idx]) + stderr.print("f[red] The '{row[m_idx]}' is not a valid data for translation") return metadata From 275a6dafa9b99bd25ecccb573e121d6b55360d33 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 8 Sep 2022 11:10:23 +0200 Subject: [PATCH 0929/1454] placenta anatomical material in anatomical_material_collection_method.json --- .../conf/anatomical_material_collection_method.json | 6 +++--- relecov_tools/institution_scripts/ISCIII.py | 3 +++ 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/relecov_tools/conf/anatomical_material_collection_method.json b/relecov_tools/conf/anatomical_material_collection_method.json index 75b0f7fa..373f43bf 100644 --- a/relecov_tools/conf/anatomical_material_collection_method.json +++ b/relecov_tools/conf/anatomical_material_collection_method.json @@ -1000,9 +1000,9 @@ "anatomical_material": "Not Applicable" }, "Placenta": { - "anatomical_part": "Placenta", + "anatomical_part": "Not Applicable", "collection_method": "Not Applicable", "body_product": "Not Applicable", - "anatomical_material": "Not Applicable" + "anatomical_material": "Placenta" } -} +} \ No newline at end of file diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index 7b893a0c..a80adec3 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -88,6 +88,9 @@ def translate_gender_to_english(metadata, f_data, mapped_fields, heading): return metadata +# + + def translate_specimen_source(metadata, f_data, mapped_fields, heading): """Translate into english the "muestra" that is written in spanish""" for row in metadata[1:]: From 62e97fe5fc193418fb47f7f8f330b053e566b809 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Thu, 8 Sep 2022 11:46:25 +0200 Subject: [PATCH 0930/1454] added gzip to main --- relecov_tools/__main__.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 3ee0d8db..cae070ef 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -314,6 +314,7 @@ def upload_to_gisaid( frameshift, proxy_config, single, + gzip ): """parsed data to create files to upload to gisaid""" upload_gisaid = relecov_tools.gisaid_upload.GisaidUpload( @@ -327,6 +328,7 @@ def upload_to_gisaid( frameshift, proxy_config, single, + gzip ) upload_gisaid.gisaid_upload() From d251e29cd6f1bfb48d809f4a28610f5217e68976 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Thu, 8 Sep 2022 12:03:16 +0200 Subject: [PATCH 0931/1454] fixed bug in proxy gisaid_upload --- relecov_tools/gisaid_upload.py | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 251cdc55..fed84367 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -186,18 +186,21 @@ def create_multifasta(self): gather_fastas_path = os.path.join(self.fasta_path, "*.fa*") if self.gzip: os.system( - "zcat %s > %s/multifasta.fasta" % (gather_fastas_path, self.output_path) - ) + "zcat %s > %s/multifasta.fasta" % ( + gather_fastas_path, self.output_path) + ) else: os.system( - "cat %s > %s/multifasta.fasta" % (gather_fastas_path, self.output_path) + "cat %s > %s/multifasta.fasta" % (gather_fastas_path, + self.output_path) ) multifasta = "%s/multifasta.fasta" % self.output_path - + else: if self.gzip: os.system( - "zcat %s > %s/multifasta.fasta" % (self.fasta_path, self.output_path + "zcat %s > %s/multifasta.fasta" % (self.fasta_path, + self.output_path) ) multifasta = "%s/multifasta.fasta" % self.output_path else: @@ -247,7 +250,7 @@ def cli3_upload(self): % ( self.token, self.metadata_to_csv(), - self.change_headers(), + self.change_headers(self.create_multifasta()), self.frameshift, self.proxy_config, ) From b4d12b23a135c68d3d3b4ea54593e335fc616c4c Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 8 Sep 2022 12:51:41 +0200 Subject: [PATCH 0932/1454] fixed bug that out_folder was none --- relecov_tools/__main__.py | 1 + relecov_tools/json_validation.py | 25 ++++++++++++++++++------- 2 files changed, 19 insertions(+), 7 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 0adb35a2..ab2b86cc 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -202,6 +202,7 @@ def validate(json_file, json_schema, metadata, out_folder): validated_json_data, invalid_json, errors, + out_folder ) = relecov_tools.json_validation.validate_json(json_file, json_schema, out_folder) if len(invalid_json) > 0: log.error("Some of the samples in json metadata were not validated") diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 18471db2..6ea788cd 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -44,6 +44,10 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): if not os.path.isfile(json_data_file): stderr.print("[red] Json file does not exists") sys.exit(1) + if out_folder is None: + out_folder = relecov_tools.utils.prompt_path( + msg="Select the folder where to save excel with invalid data" + ) stderr.print("[blue] Reading the json file") json_data = relecov_tools.utils.read_json_file(json_data_file) with open(json_data_file, "r") as fh: @@ -65,7 +69,7 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): stderr.print("[green] Sucessful validation") else: stderr.print("[red] Some samples are not validated") - return validated_json_data, invalid_json, errors + return validated_json_data, invalid_json, errors, out_folder def create_invalid_metadata(metadata_file, invalid_json, out_folder): @@ -81,6 +85,7 @@ def create_invalid_metadata(metadata_file, invalid_json, out_folder): stderr.print("[red] Start preparation of invalid samples") for row in invalid_json: sample_list.append(str(row["collecting_lab_sample_id"])) + wb = openpyxl.load_workbook(metadata_file) ws_sheet = wb["METADATA_LAB"] row_to_del = [] @@ -89,15 +94,21 @@ def create_invalid_metadata(metadata_file, invalid_json, out_folder): # if not data on row 1 and 2 assume that no more data are in file # then start deleting rows if not row[2].value and not row[1].value: - if len(row_to_del) > 0: - row_to_del.sort(reverse=True) - for idx in row_to_del: - ws_sheet.delete_rows(idx) break - if str(row[2].value) not in sample_list: row_to_del.append(row[0].row) - + stderr.print("[red] Collected rows to create the excel file") + if len(row_to_del) > 0: + row_to_del.sort(reverse=True) + for idx in row_to_del: + try: + ws_sheet.delete_rows(idx) + except TypeError as e: + log.error( + "Unable to delete row %s from metadata file because of", idx, e + ) + stderr.print("f[red] Unable to delete row {idx} becuase of {e}") + sys.exit(1) os.makedirs(out_folder, exist_ok=True) new_name = "invalid_" + os.path.basename(metadata_file) m_file = os.path.join(out_folder, new_name) From fab5ddf4ae59f51d3e7dcc5926e0c3daee85a045 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 8 Sep 2022 12:52:42 +0200 Subject: [PATCH 0933/1454] Adding ARTIC v4.1 --- relecov_tools/schema/relecov_schema.json | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index ede7f205..191e6c75 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1235,6 +1235,7 @@ "ARTIC v2", "ARTIC v3", "ARTIC v4", + "ARTIC v4.1", "Illumina AmpliSeq Community panel", "Illumina AmpliSeq SARS-CoV-2 Research Panel for Illumina", "Illumina Respiratory Virus Oligos Panel V1", From 13fe0cf14aafc7dea4c7d397a115f0a50f8c9848 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Thu, 8 Sep 2022 13:00:51 +0200 Subject: [PATCH 0934/1454] modified reading of lab config file in gisaid_upload --- relecov_tools/gisaid_upload.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index fed84367..a4d922d6 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -136,9 +136,9 @@ def metadata_to_csv(self): df_data.insert(4, field, "") config_lab_json = ConfigJson() - lab_json_conf = config_lab_json.get_configuration("laboratory_data") + lab_json_conf = config_lab_json.get_topic_data("lab_metadata", "laboratory_data") lab_json_file = os.path.join( - os.path.dirname(os.path.realpath(__file__)), "conf", lab_json_conf + os.path.dirname(os.path.realpath(__file__)), "conf", lab_json_conf["file"] ) lab_json = relecov_tools.utils.read_json_file(lab_json_file) for lab in lab_json: From 40d2d14ab180f2d64961d1a2b24cf250a5f04bc6 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 8 Sep 2022 15:50:10 +0200 Subject: [PATCH 0935/1454] added region to lab and added city to geo loc --- relecov_tools/conf/geo_loc_cities.json | 79 +++++++++- relecov_tools/conf/laboratory_address.json | 162 +++++++++++++++------ 2 files changed, 195 insertions(+), 46 deletions(-) diff --git a/relecov_tools/conf/geo_loc_cities.json b/relecov_tools/conf/geo_loc_cities.json index 3a2e3d55..f4ec1fcd 100644 --- a/relecov_tools/conf/geo_loc_cities.json +++ b/relecov_tools/conf/geo_loc_cities.json @@ -71,7 +71,7 @@ "geo_loc_latitude": "37.1781", "geo_loc_longitude": "-3.6008" }, - "Oviedo": { + "Asturias": { "geo_loc_latitude": "43.3600", "geo_loc_longitude": "-5.8450" }, @@ -222,5 +222,82 @@ "Pontevedra": { "geo_loc_latitude": "42.4333", "geo_loc_longitude": "-8.6333" + }, + { + "Alcázar de San Juan": { + "geo_loc_latitude": "39.4056", + "geo_loc_longitude": "-3.2056" + }, + "Manzanares": { + "geo_loc_latitude": "38.9964", + "geo_loc_longitude": "-3.3731" + }, + "Valdepeñas": { + "geo_loc_latitude": "38.7667", + "geo_loc_longitude": "-3.4000" + }, + "Puertollano": { + "geo_loc_latitude": "38.6833", + "geo_loc_longitude": "-4.1167" + }, + "Talavera de la Reina": { + "geo_loc_latitude": "39.95", + "geo_loc_longitude": "-4.8333" + }, + "Badalona": { + "geo_loc_latitude": "41.4333", + "geo_loc_longitude": "2.2333" + }, + "L'Hospitalet de Llobregat": { + "geo_loc_latitude": "41.4217", + "geo_loc_longitude": "2.1897" + }, + "Sant Cugat del Vallès": { + "geo_loc_latitude": "41.4667", + "geo_loc_longitude": "2.0833" + }, + "Mostoles": { + "geo_loc_latitude": "40.3223", + "geo_loc_longitude": "-3.865" + }, + "Leganés": { + "geo_loc_latitude": "40.3281", + "geo_loc_longitude": "-3.7644" + }, + "Getafe": { + "geo_loc_latitude": "40.3047", + "geo_loc_longitude": "-3.7311" + }, + "Cartagena": { + "geo_loc_latitude": "37.6000", + "geo_loc_longitude": "-0.9819" + }, + "Pozo Aledo": { + "geo_loc_latitude": "37.8167", + "geo_loc_longitude": "-0.85" + }, + "Lorca": { + "geo_loc_latitude": "37.6798", + "geo_loc_longitude": "-1.6944" + }, + "Cieza": { + "geo_loc_latitude": "38.2392", + "geo_loc_longitude": "-1.4189" + }, + "Mérida": { + "geo_loc_latitude": "38.9000", + "geo_loc_longitude": "-6.3333" + }, + "Santiago de Compostela": { + "geo_loc_latitude": "42.8833", + "geo_loc_longitude": "-8.55" + }, + "Elche": { + "geo_loc_latitude": "38.2669", + "geo_loc_longitude": "-0.6983" + }, + "Gazteiz": { + "geo_loc_latitude": "42.85", + "geo_loc_longitude": "-2.6667" } } diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index e35b7c68..7410c1ec 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -4,6 +4,7 @@ "collecting_institution_address": "Crta. Pozuelo Majadahonda S/N,", "collecting_institution_email": "info@isciii.es", "geo_loc_state": "Madrid", + "geo_loc_region": "Madrid", "geo_loc_city": "Madrid", "geo_loc_country": "Spain" }, @@ -12,6 +13,7 @@ "collecting_institution_address": "Av. del Conocimiento S/N,", "collecting_institution_email": "fegarcia@ugr.es", "geo_loc_state": "Andalucia", + "geo_loc_region": "Granada", "geo_loc_city": "Granada", "geo_loc_country": "Spain" }, @@ -20,6 +22,7 @@ "collecting_institution_address": "Avenida Manuel Siurot s/n", "collecting_institution_email": "josea.lepe.sspa@juntadeandalucia.es", "geo_loc_state": "Andalucia", + "geo_loc_region": "Sevilla", "geo_loc_city": "Sevilla", "geo_loc_country": "Spain" }, @@ -27,7 +30,8 @@ "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", "collecting_institution_address": "S. Juan Bosco, 15", "collecting_institution_email": "rbenito@salud.aragon.es", - "geo_loc_state": "Aragon", + "geo_loc_state": "Aragón", + "geo_loc_region": "Zaragoza", "geo_loc_city": "Zaragoza", "geo_loc_country": "Spain" }, @@ -35,7 +39,8 @@ "collecting_institution": "Hospital Universitario Miguel Servet", "collecting_institution_address": "P.º Isabel la Católica, 1-3", "collecting_institution_email": "rbenito@salud.aragon.es", - "geo_loc_state": "Aragon", + "geo_loc_state": "Aragón", + "geo_loc_region": "Zaragoza", "geo_loc_city": "Zaragoza", "geo_loc_country": "Spain" }, @@ -43,7 +48,8 @@ "collecting_institution": "Centro de Investigación Biomédica de Aragón", "collecting_institution_address": "Avenida San Juan Bosco 13", "collecting_institution_email": "mhpstrunk.iacs@aragon.es", - "geo_loc_state": "Aragon", + "geo_loc_state": "Aragón", + "geo_loc_region": "Zaragoza", "geo_loc_city": "Zaragoza", "geo_loc_country": "Spain" }, @@ -52,14 +58,16 @@ "collecting_institution_address": " Av. Roma, s/n,", "collecting_institution_email": "santiago.melon@sespa.es", "geo_loc_state": "Asturias", - "geo_loc_city": "Oviedo", + "geo_loc_region": "Asturias", + "geo_loc_city": "Asturias", "geo_loc_country": "Spain" }, { "collecting_institution": "Servicio de Microbiologia HU Son Espases", "collecting_institution_address": " Ctra. Valldemossa 79", "collecting_institution_email": "antonio.oliver@ssib.es", - "geo_loc_state": "Baleares", + "geo_loc_state": "Islas Baleares", + "geo_loc_region": "Palma de Mallorca", "geo_loc_city": "Palma de Mallorca", "geo_loc_country": "Spain" }, @@ -67,7 +75,8 @@ "collecting_institution": "Hospital Universitario Ntra. Sra de Candelaria", "collecting_institution_address": "Carretera del Rosario 145", "collecting_institution_email": "jalcflo@gobiernodecanarias.org", - "geo_loc_state": "Canarias", + "geo_loc_state": "Islas Canarias", + "geo_loc_region": "Santa Cruz de Tenerife", "geo_loc_city": "Santa Cruz de Tenerife", "geo_loc_country": "Spain" }, @@ -75,7 +84,8 @@ "collecting_institution": "Instituto Tecnológico y de Energías Renovables", "collecting_institution_address": "Polígono Industrial de Granadilla, s/n", "collecting_institution_email": "jlorenzo@iter.es", - "geo_loc_state": "Canarias", + "geo_loc_state": "Islas Canarias", + "geo_loc_region": "Santa Cruz de Tenerife", "geo_loc_city": "Santa Cruz de Tenerife", "geo_loc_country": "Spain" }, @@ -83,7 +93,8 @@ "collecting_institution": "Hospital Universitario de Canarias", "collecting_institution_address": "Carretera Ofra S/N, La Laguna", "collecting_institution_email": "", - "geo_loc_state": "Canarias", + "geo_loc_state": "Islas Canarias", + "geo_loc_region": "Santa Cruz de Tenerife", "geo_loc_city": "Santa Cruz de Tenerife", "geo_loc_country": "Spain" }, @@ -91,7 +102,8 @@ "collecting_institution": "Hospital Universitario de Gran Canaria", "collecting_institution_address": "C. Pl. Barranco de la Ballena s/n", "collecting_institution_email": "", - "geo_loc_state": "Canarias", + "geo_loc_state": "Islas Canarias", + "geo_loc_region": "Las Palmas", "geo_loc_city": "Las Palmas", "geo_loc_country": "Spain" }, @@ -99,7 +111,8 @@ "collecting_institution": "Hospital Insular de Lanzarote", "collecting_institution_address": "C. Juan de Quesada, s/n, Arrecife", "collecting_institution_email": "", - "geo_loc_state": "Canarias", + "geo_loc_state": "Islas Canarias", + "geo_loc_region": "Las Palmas", "geo_loc_city": "Las Palmas", "geo_loc_country": "Spain" }, @@ -108,6 +121,7 @@ "collecting_institution_address": "Av. Valdecilla s/n", "collecting_institution_email": "", "geo_loc_state": "Cantabria", + "geo_loc_region": "Cantabria", "geo_loc_city": "Santander", "geo_loc_country": "Spain" }, @@ -116,6 +130,7 @@ "collecting_institution_address": "Bo. Ganzo, s/n, Torrelavega", "collecting_institution_email": "", "geo_loc_state": "Cantabria", + "geo_loc_region": "Cantabria", "geo_loc_city": "Santander", "geo_loc_country": "Spain" }, @@ -123,7 +138,8 @@ "collecting_institution": "Hospital General Universitario de Ciudad Real", "collecting_institution_address": "Calle Obispo Rafael Torija s/n", "collecting_institution_email": "", - "geo_loc_state": "Castilla la Mancha", + "geo_loc_state": "Castilla-La Mancha", + "geo_loc_region": "Ciudad Real", "geo_loc_city": "Ciudad Real", "geo_loc_country": "Spain" }, @@ -131,47 +147,53 @@ "collecting_institution": "Hospital General La Mancha Centro", "collecting_institution_address": "Av. Constitución, 3, Alcázar de San Juan", "collecting_institution_email": "", - "geo_loc_state": "Castilla la Mancha", - "geo_loc_city": "Ciudad Real", + "geo_loc_state": "Castilla-La Mancha", + "geo_loc_region": "Ciudad Real", + "geo_loc_city": "Alcázar de San Juan", "geo_loc_country": "Spain" }, { "collecting_institution": "Hospital Virgen de Altagracia", "collecting_institution_address": "Avda. D. Emiliano García Roldán, s/n, Manzanares,", "collecting_institution_email": "", - "geo_loc_state": "Castilla la Mancha", - "geo_loc_city": "Ciudad Real", + "geo_loc_state": "Castilla-La Mancha", + "geo_loc_region": "Ciudad Real", + "geo_loc_city": "Manzanares", "geo_loc_country": "Spain" }, { "collecting_institution": "Hospital General de Valdepeñas", "collecting_institution_address": "Av. de los Estudiantes, s/n, Valdepeñas", "collecting_institution_email": "", - "geo_loc_state": "Castilla la Mancha", - "geo_loc_city": "Ciudad Real", + "geo_loc_state": "Castilla-La Mancha", + "geo_loc_region": "Ciudad Real", + "geo_loc_city": "Valdepeñas", "geo_loc_country": "Spain" }, { "collecting_institution": "Hospital General Universitario de Ciudad Real", "collecting_institution_address": "C. Obispo Rafael Torija, s/n", "collecting_institution_email": "", - "geo_loc_state": "Castilla la Mancha", + "geo_loc_state": "Castilla-La Mancha", + "geo_loc_region": "Ciudad Real", "geo_loc_city": "Ciudad Real", "geo_loc_country": "Spain" }, { "collecting_institution": "Hospital Público Santa Bárbara", - "collecting_institution_address": "C. Obispo Rafael Torija, s/n", + "collecting_institution_address": "C. Malagón s/n", "collecting_institution_email": "", - "geo_loc_state": "Castilla la Mancha", - "geo_loc_city": "Ciudad Real", + "geo_loc_state": "Castilla-La Mancha", + "geo_loc_region": "Ciudad Real", + "geo_loc_city": "Puertollano", "geo_loc_country": "Spain" }, { "collecting_institution": "Hospital Virgen de la Luz", "collecting_institution_address": "Hermandad de Donantes de Sangre, 1", "collecting_institution_email": "", - "geo_loc_state": "Castilla la Mancha", + "geo_loc_state": "Castilla-La Mancha", + "geo_loc_region": "Cuenca", "geo_loc_city": "Cuenca", "geo_loc_country": "Spain" }, @@ -179,7 +201,8 @@ "collecting_institution": "Hospital Universitario de Guadalajara", "collecting_institution_address": "C. Donante de Sangre, S/N", "collecting_institution_email": "", - "geo_loc_state": "Castilla la Mancha", + "geo_loc_state": "Castilla-La Mancha", + "geo_loc_region": "Guadalajara", "geo_loc_city": "Guadalajara", "geo_loc_country": "Spain" }, @@ -187,7 +210,8 @@ "collecting_institution": "Hospital Virgen de la Salud", "collecting_institution_address": "Calle Barber 30", "collecting_institution_email": "", - "geo_loc_state": "Castilla la Mancha", + "geo_loc_state": "Castilla-La Mancha", + "geo_loc_region": "Toledo", "geo_loc_city": "Toledo", "geo_loc_country": "Spain" }, @@ -195,15 +219,17 @@ "collecting_institution": "Hospital General Nuestra Sra. del Prado", "collecting_institution_address": "CTRA. MADRID, Av. Extremadura, KM 114", "collecting_institution_email": "", - "geo_loc_state": "Castilla la Mancha", - "geo_loc_city": "Toledo", + "geo_loc_state": "Castilla-La Mancha", + "geo_loc_region": "Toledo", + "geo_loc_city": "Talavera de la Reina", "geo_loc_country": "Spain" }, { "collecting_institution": "Consejería de Sanidad", "collecting_institution_address": "Avda. de Francia, 4.", "collecting_institution_email": "", - "geo_loc_state": "Castilla la Mancha", + "geo_loc_state": "Castilla-La Mancha", + "geo_loc_region": "Toledo", "geo_loc_city": "Toledo", "geo_loc_country": "Spain" }, @@ -211,7 +237,8 @@ "collecting_institution": "Hospital General Universitario de Albacete", "collecting_institution_address": "Calle Hermanos Falcó 37", "collecting_institution_email": "", - "geo_loc_state": "Castilla la Mancha", + "geo_loc_state": "Castilla-La Mancha", + "geo_loc_region": "Albacete", "geo_loc_city": "Albacete", "geo_loc_country": "Spain" }, @@ -220,6 +247,7 @@ "collecting_institution_address": "Paseo de Belen 19", "collecting_institution_email": "", "geo_loc_state": "Castilla y León", + "geo_loc_region": "Valladolid", "geo_loc_city": "Valladolid", "geo_loc_country": "Spain" }, @@ -228,6 +256,7 @@ "collecting_institution_address": "P.º de San Vicente, 58", "collecting_institution_email": "", "geo_loc_state": "Castilla y León", + "geo_loc_region": "Salamanca", "geo_loc_city": "Salamanca", "geo_loc_country": "Spain" }, @@ -236,6 +265,7 @@ "collecting_institution_address": "P.º el Espolón", "collecting_institution_email": "", "geo_loc_state": "Castilla y León", + "geo_loc_region": "Soria", "geo_loc_city": "Soria", "geo_loc_country": "Spain" }, @@ -244,6 +274,7 @@ "collecting_institution_address": "Av. Donantes de Sangre, s/n", "collecting_institution_email": "", "geo_loc_state": "Castilla y León", + "geo_loc_region": "Palencia", "geo_loc_city": "Palencia", "geo_loc_country": "Spain" }, @@ -252,6 +283,7 @@ "collecting_institution_address": " Av. Juan Carlos I, s/n", "collecting_institution_email": "", "geo_loc_state": "Castilla y León", + "geo_loc_region": "Avila", "geo_loc_city": "Avila", "geo_loc_country": "Spain" }, @@ -260,6 +292,7 @@ "collecting_institution_address": "Av. Islas Baleares, 3", "collecting_institution_email": "", "geo_loc_state": "Castilla y León", + "geo_loc_region": "Burgos", "geo_loc_city": "Burgos", "geo_loc_country": "Spain" }, @@ -268,6 +301,7 @@ "collecting_institution_address": " Passeig de la Vall d’Hebron, 119-129", "collecting_institution_email": "", "geo_loc_state": "Cataluña", + "geo_loc_region": "Barcelona", "geo_loc_city": "Barcelona", "geo_loc_country": "Spain" }, @@ -276,7 +310,8 @@ "collecting_institution_address": " Crta del Canyet s/n", "collecting_institution_email": "", "geo_loc_state": "Cataluña", - "geo_loc_city": "Barcelona", + "geo_loc_region": "Barcelona", + "geo_loc_city": "Badalona", "geo_loc_country": "Spain" }, { @@ -284,6 +319,7 @@ "collecting_institution_address": "C/Villarroel 170", "collecting_institution_email": "", "geo_loc_state": "Cataluña", + "geo_loc_region": "Barcelona", "geo_loc_city": "Barcelona", "geo_loc_country": "Spain" }, @@ -292,7 +328,8 @@ "collecting_institution_address": "Carrer Feixa Llarga s/n ", "collecting_institution_email": "", "geo_loc_state": "Cataluña", - "geo_loc_city": "Barcelona", + "geo_loc_region": "Barcelona", + "geo_loc_city": "L'Hospitalet de Llobregat", "geo_loc_country": "Spain" }, { @@ -300,6 +337,7 @@ "collecting_institution_address": "c/ Dr. Mallafrè Guasch, 4,", "collecting_institution_email": "", "geo_loc_state": "Cataluña", + "geo_loc_region": "Tarragona", "geo_loc_city": "Tarragona", "geo_loc_country": "Spain" }, @@ -308,6 +346,7 @@ "collecting_institution_address": "Carrer de la Selva, 10", "collecting_institution_email": "", "geo_loc_state": "Cataluña", + "geo_loc_region": "Barcelona", "geo_loc_city": "Barcelona", "geo_loc_country": "Spain" }, @@ -316,6 +355,7 @@ "collecting_institution_address": "Passeig del Taulat, 116", "collecting_institution_email": "", "geo_loc_state": "Cataluña", + "geo_loc_region": "Barcelona", "geo_loc_city": "Barcelona", "geo_loc_country": "Spain" }, @@ -324,7 +364,8 @@ "collecting_institution_address": "Carrer de Martorell,20 Sant Cugat del Vallès", "collecting_institution_email": "", "geo_loc_state": "Cataluña", - "geo_loc_city": "Barcelona", + "geo_loc_region": "Barcelona", + "geo_loc_city": "Sant Cugat del Vallès", "geo_loc_country": "Spain" }, { @@ -332,6 +373,7 @@ "collecting_institution_address": "Avinguda de França, S/N,", "collecting_institution_email": "", "geo_loc_state": "Cataluña", + "geo_loc_region": "Girona", "geo_loc_city": "Girona", "geo_loc_country": "Spain" }, @@ -339,7 +381,8 @@ "collecting_institution": "Hospital Universitario San Jorge", "collecting_institution_address": "Av. Martínez de Velasco, 36", "collecting_institution_email": "", - "geo_loc_state": "Cataluña", + "geo_loc_state": "Aragón", + "geo_loc_region": "Huesca", "geo_loc_city": "Huesca", "geo_loc_country": "Spain" }, @@ -348,6 +391,7 @@ "collecting_institution_address": "Colmenar s/n", "collecting_institution_email": "", "geo_loc_state": "Ceuta", + "geo_loc_region": "Ceuta", "geo_loc_city": "Ceuta", "geo_loc_country": "Spain" }, @@ -356,6 +400,7 @@ "collecting_institution_address": "Remonta, 2", "collecting_institution_email": "", "geo_loc_state": "Melilla", + "geo_loc_region": "Melilla", "geo_loc_city": "Melilla", "geo_loc_country": "Spain" }, @@ -364,7 +409,8 @@ "collecting_institution_address": "C. Dr. Luis Montes, S/N", "collecting_institution_email": "", "geo_loc_state": "Madrid", - "geo_loc_city": "Madrid", + "geo_loc_region": "Madrid", + "geo_loc_city": "Mostoles", "geo_loc_country": "Spain" }, { @@ -372,6 +418,7 @@ "collecting_institution_address": "Calle del Prof Martín Lagos", "collecting_institution_email": "", "geo_loc_state": "Madrid", + "geo_loc_region": "Madrid", "geo_loc_city": "Madrid", "geo_loc_country": "Spain" }, @@ -380,6 +427,7 @@ "collecting_institution_address": "C. Darío Gazapo 3", "collecting_institution_email": "", "geo_loc_state": "Madrid", + "geo_loc_region": "Madrid", "geo_loc_city": "Madrid", "geo_loc_country": "Spain" }, @@ -388,7 +436,8 @@ "collecting_institution_address": "Av. de Orellana, s/n, Leganés", "collecting_institution_email": "", "geo_loc_state": "Madrid", - "geo_loc_city": "Madrid", + "geo_loc_region": "Madrid", + "geo_loc_city": "Leganés", "geo_loc_country": "Spain" }, { @@ -396,7 +445,8 @@ "collecting_institution_address": "Carr. Madrid - Toledo, Km 12,500, Getafe", "collecting_institution_email": "", "geo_loc_state": "Madrid", - "geo_loc_city": "Madrid", + "geo_loc_region": "Madrid", + "geo_loc_city": "Getafe", "geo_loc_country": "Spain" }, { @@ -404,6 +454,7 @@ "collecting_institution_address": "", "collecting_institution_email": "", "geo_loc_state": "Madrid", + "geo_loc_region": "Madrid", "geo_loc_city": "Madrid", "geo_loc_country": "Spain" }, @@ -412,6 +463,7 @@ "collecting_institution_address": "P.º del Prado, 18", "collecting_institution_email": "", "geo_loc_state": "Madrid", + "geo_loc_region": "Madrid", "geo_loc_city": "Madrid", "geo_loc_country": "Spain" }, @@ -420,6 +472,7 @@ "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", "collecting_institution_email": "", "geo_loc_state": "Murcia", + "geo_loc_region": "Murcia", "geo_loc_city": "Murcia", "geo_loc_country": "Spain" }, @@ -428,6 +481,7 @@ "collecting_institution_address": "Av. Intendente Jorge Palacios, 1", "collecting_institution_email": "", "geo_loc_state": "Murcia", + "geo_loc_region": "Murcia", "geo_loc_city": "Murcia", "geo_loc_country": "Spain" }, @@ -436,7 +490,8 @@ "collecting_institution_address": "C. Minarete, s/n", "collecting_institution_email": "", "geo_loc_state": "Murcia", - "geo_loc_city": "Murcia", + "geo_loc_region": "Murcia", + "geo_loc_city": "Cartagena", "geo_loc_country": "Spain" }, { @@ -444,7 +499,8 @@ "collecting_institution_address": "Paraje Torre Octavio, 54, Pozo Aledo", "collecting_institution_email": "", "geo_loc_state": "Murcia", - "geo_loc_city": "Murcia", + "geo_loc_region": "Murcia", + "geo_loc_city": "Pozo Aledo", "geo_loc_country": "Spain" }, { @@ -452,6 +508,7 @@ "collecting_institution_address": "Av. Marqués de Los Vélez, s/n", "collecting_institution_email": "", "geo_loc_state": "Murcia", + "geo_loc_region": "Murcia", "geo_loc_city": "Murcia", "geo_loc_country": "Spain" }, @@ -460,6 +517,7 @@ "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n, El Palmar", "collecting_institution_email": "", "geo_loc_state": "Murcia", + "geo_loc_region": "Murcia", "geo_loc_city": "Murcia", "geo_loc_country": "Spain" }, @@ -468,7 +526,8 @@ "collecting_institution_address": "Ctra.N-340, Lorca", "collecting_institution_email": "", "geo_loc_state": "Murcia", - "geo_loc_city": "Murcia", + "geo_loc_region": "Murcia", + "geo_loc_city": "Lorca", "geo_loc_country": "Spain" }, { @@ -476,14 +535,16 @@ "collecting_institution_address": "Vereda de Morcillo, s/n, Cieza", "collecting_institution_email": "", "geo_loc_state": "Murcia", - "geo_loc_city": "Murcia", + "geo_loc_region": "Murcia", + "geo_loc_city": "Cieza", "geo_loc_country": "Spain" }, { - "collecting_institution": "HU de Donostia", + "collecting_institution": "Hospital Univeristario Donostia", "collecting_institution_address": "Begiristain Doktorea Pasealekua, s/n", "collecting_institution_email": "", "geo_loc_state": "País Vasco", + "geo_loc_region": "Guipúzcoa", "geo_loc_city": "Donostia", "geo_loc_country": "Spain" }, @@ -492,6 +553,7 @@ "collecting_institution_address": "Av. de Elvas, s/n", "collecting_institution_email": "", "geo_loc_state": "Extremadura", + "geo_loc_region": "Badajoz", "geo_loc_city": "Badajoz", "geo_loc_country": "Spain" }, @@ -500,7 +562,8 @@ "collecting_institution_address": "Av. Don Antonio Campos Hoyos, 26, Mérida", "collecting_institution_email": "", "geo_loc_state": "Extremadura", - "geo_loc_city": "Badajoz", + "geo_loc_region": "Badajoz", + "geo_loc_city": "Mérida", "geo_loc_country": "Spain" }, { @@ -508,6 +571,7 @@ "collecting_institution_address": "Av. Pablo Naranjo Porras, s/n", "collecting_institution_email": "", "geo_loc_state": "Extremadura", + "geo_loc_region": "Caceres", "geo_loc_city": "Caceres", "geo_loc_country": "Spain" }, @@ -516,7 +580,8 @@ "collecting_institution_address": "Av. das Camelias, 109, Vigo", "collecting_institution_email": "", "geo_loc_state": "Galicia", - "geo_loc_city": "Pontevedra", + "geo_loc_region": "Pontevedra", + "geo_loc_city": "Vigo", "geo_loc_country": "Spain" }, { @@ -524,6 +589,7 @@ "collecting_institution_address": " Rúa Dr. Ulises Romero, 1", "collecting_institution_email": "", "geo_loc_state": "Galicia", + "geo_loc_region": "Lugp", "geo_loc_city": "Lugo", "geo_loc_country": "Spain" }, @@ -532,6 +598,7 @@ "collecting_institution_address": "As Xubias, 84", "collecting_institution_email": "", "geo_loc_state": "Galicia", + "geo_loc_region": "A Coruña", "geo_loc_city": "A Coruña", "geo_loc_country": "Spain" }, @@ -540,7 +607,8 @@ "collecting_institution_address": "Rúa da Choupana, s/n, Santiago de Compostela", "collecting_institution_email": "", "geo_loc_state": "Galicia", - "geo_loc_city": "A Coruña", + "geo_loc_region": "A Coruña", + "geo_loc_city": "Santiago de Compostela", "geo_loc_country": "Spain" }, { @@ -548,6 +616,7 @@ "collecting_institution_address": "C. de Irunlarrea, 3, Pamplona", "collecting_institution_email": "", "geo_loc_state": "Navarra", + "geo_loc_region": "Navarra", "geo_loc_city": "Pamplona", "geo_loc_country": "Spain" }, @@ -556,7 +625,8 @@ "collecting_institution_address": "Carrer Almazara, 11, Elche", "collecting_institution_email": "", "geo_loc_state": "Valenciana", - "geo_loc_city": "Alicante", + "geo_loc_region": "Alicante", + "geo_loc_city": "Elche", "geo_loc_country": "Spain" }, { @@ -564,6 +634,7 @@ "collecting_institution_address": "C. Piqueras, 98", "collecting_institution_email": "", "geo_loc_state": "La Rioja", + "geo_loc_region": "La Rioja", "geo_loc_city": "Logroño", "geo_loc_country": "Spain" }, @@ -572,7 +643,8 @@ "collecting_institution_address": " Jose Atxotegi Kalea, s/n", "collecting_institution_email": "", "geo_loc_state": "País Vasco", - "geo_loc_city": "Vitoria", + "geo_loc_region": "Alava", + "geo_loc_city": "Gasteiz", "geo_loc_country": "Spain" } ] From 4f81fbffa7248a864f76f745104da0b94d2a32d9 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 8 Sep 2022 15:51:00 +0200 Subject: [PATCH 0936/1454] Added sequence_fastq_Rx_md5 --- relecov_tools/schema/relecov_schema.json | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 191e6c75..8eb86246 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1576,6 +1576,30 @@ "label": "Sequence file R2 fastq", "fill_mode": "sample" }, + "sequence_file_R1_md5": { + "examples": [ + "b5242d60471e5a5a97b35531dbbe8c30" + ], + "ontology": "MS_1000568", + "type": "string", + "description": "Checksum value to validate successful file transmission", + "classification": "Bioinformatics and QC metrics fields", + "label": "Fastq md5 r1", + "fill_mode": "sample", + "minLenght": "1" + + }, + "sequence_file_R2_md5": { + "examples": [ + "b5242d60471e5a5a97b35531dbbe8c30" + ], + "ontology": "MS_1000569", + "type": "string", + "description": "Checksum value to validate successful file transmission", + "classification": "Bioinformatics and QC metrics fields"", + "label": "Sequence fastq R2 md5", + "fill_mode": "sample" + }, "r1_fastq_filepath": { "examples": [ "/User/Documents/RespLab/Data/" From b89f15985e5e1016413a46588afa07877ce22038 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 8 Sep 2022 16:52:42 +0200 Subject: [PATCH 0937/1454] review ena schema vs ena upload cli and relecov schema --- relecov_tools/long_table_parse.py | 1 + relecov_tools/schema/ena_schema.json | 164 +++++++++++------------ relecov_tools/schema/relecov_schema.json | 43 ++++-- 3 files changed, 114 insertions(+), 94 deletions(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index 4e4b79a7..3c81c521 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -18,6 +18,7 @@ highlight=False, force_terminal=relecov_tools.utils.rich_force_colors(), ) +# class LongTableParse: diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index b8b0dfd3..3e81567d 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -83,7 +83,7 @@ "examples": [ "" ], - "ontology": "0", + "ontology": "NCIT:C53471", "type": "string", "description": "", "clasification": "", @@ -125,7 +125,7 @@ "experiments" ] }, - "geographic_location_(country_and/or_sea)": { + "geographic location (country and/or sea)": { "Enums": [ "Afghanistan [GAZ:00006882]", "Albania [GAZ:00002953]", @@ -460,6 +460,18 @@ "examples": [ "Diagnostic testing" ], + "enum": [ + "Cluster/Outbreak Investigation [GENEPIO:0100001]", + "Diagnostic Testing [GENEPIO:0100002]", + "Research [GENEPIO:0100003]", + "Protocol Testing [GENEPIO:0100024]", + "Surveillance [GENEPIO:0100004]", + "Not Applicable [GENEPIO:0001619]", + "Not Collected [GENEPIO:0001620]", + "Not Provided [GENEPIO:0001668]", + "Missing [GENEPIO:0001618]", + "Restricted Access [GENEPIO:0001810]" + ], "ontology": "NCIT_C146997", "type": "string", "description": "The reason that the sample was collected.", @@ -746,16 +758,25 @@ ] }, "platform": { + "enum": [ + "Oxford Nanopore [OBI:0002750]", + "Illumina [OBI:0000759]", + "Ion Torrent [GENEPIO:0002683]", + "PacBio [GENEPIO:0001927]", + "BGI", + "MGI", + "Other" + ], "examples": [ - "MinIon" + "Illumina" ], "ontology": "GENEPIO_0000071", "type": "string", - "description": "The model of the sequencing instrument used.", - "label": "Sequencing Platforms ", - "table": [ - "experiments" - ] + "description": "", + "classification": "Sequencing", + "label": "Sequencing Instrument Platform", + "fill_mode": "batch", + "minLenght": "1" }, "sequence_file_R1_fastq": { "examples": [ @@ -810,19 +831,6 @@ "runs" ] }, - "fastq_md5_r1": { - "examples": [ - "3e69af1f875fab020aed82f5edbc1f03" - ], - "ontology": "MS_1000568", - "type": "string", - "description": "", - "clasification": "Bioinformatics and QC metrics", - "label": "file checksum", - "table": [ - "runs" - ] - }, "fastq_md5_r2": { "examples": [ "3e69af1f875fab020aed82f5edbc1f03" @@ -902,31 +910,16 @@ "label": "Biological Sample Storage Condition" }, "library_source": { - "Enums": [ - "5-methycytidine antibody method [GENPIO:0001941]", - "CAGE method [GENPIO:0001942]", - "CF-H method [GENPIO:0001943]", - "CF-M method ]GENPIO:0001944]", - "CF-S method [GENPIO:0001945]", - "CF-T method [GENPIO:0001946]", - "ChIP method ]GENPIO:0001947]", - "DNAse method [GENPIO:0001948]", - "HMPR method [GENPIO:0001949]", - "Hybrid Selection Method [GENPIO:0001950]", - "MBD2 protein methyl-CpG binding domain method [GENPIO:0001951]", - "MF method [GENPIO:0001952]", - "MNase method [GENPIO:0001953]", - "MSLL method [GENPIO:0001954]", - "PCR method [GENPIO:0001955]", - "RACE method [GENPIO:0001956]", - "RANDOM PCR method [GENPIO:0001957]", - "RANDOM method [GENPIO:0001958]", - "RT-PCR method [GENPIO:0001959]", - "Reduced Representation method [GENPIO:0001960]", - "Resctriction Digest method [GENPIO:0001961]", - "cDNA method [GENPIO:0001962]", - "other library method [GENPIO:0001964]", - "size fractionation method [GENPIO:0001963]" + "enum": [ + "genomic", + "genomic single cell", + "transcriptomic", + "transcriptomic single cell", + "metagenomic", + "metatranscriptomic", + "synthetic", + "viral rna", + "other" ], "examples": [ "METAGENOMIC" @@ -941,17 +934,43 @@ ] }, "library_selection": { + "enum": [ + "RANDOM [NCIT:C60702]", + "PCR [GENEPIO:0001955]", + "RANDOM PCR [GENEPIO:0001957]", + "RT-PCR [GENEPIO:0001959]", + "HMPR [GENEPIO:0001949]", + "MF [GENEPIO:0001952]", + "repeat fractionation", + "size fractionation [GENEPIO:0001963]", + "MSLL [GENEPIO:0001954]", + "cDNA [GENEPIO:0001962]", + "ChIP [GENEPIO:0001947]", + "MNase [GENEPIO:0001953]", + "DNase [GENEPIO:0001948]", + "Hybrid Selection [GENEPIO:0001950]", + "Reduced Representation [GENEPIO:0001960]", + "Restriction Digest [GENEPIO:0001961]", + "5-methylcytidine antibody [GENEPIO:0001941]", + "MBD2 protein methyl-CpG binding domain [GENEPIO:0001951]", + "CAGE [GENEPIO:0001942]", + "RACE [GENEPIO:0001956]", + "MDA", + "padlock probes capture method", + "Oligo-dT", + "Inverse rRNA selection", + "ChIP-Seq [GENEPIO:0001947]", + "Other" + ], "examples": [ "RANDOM PCR" ], "ontology": "GENPIO_0001940", "type": "string", "description": "Library capture method.", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Capture method", - "table": [ - "experiments" - ] + "fill_mode": "batch" }, "library_construction_protocol": { "examples": [ @@ -967,7 +986,7 @@ ] }, "library_strategy": { - "Enums": [ + "enum": [ "Bisultife-Seq strategy [GENPIO:0001975]", "CTS strategy [GENPIO:0001978]", "ChIP-Seq strategy [GENPIO:0001979]", @@ -982,12 +1001,12 @@ "WCS strategy [GENPIO:0001991]", "WGS strategy [GENPIO:0001992]", "WXS strategy [GENPIO:0001993]", - "amplicon strategy [GENPIO:0001974]", - "clone end strategy [GENPIO:0001976]", - "clone strategy [GENPIO:0001977]", - "finishing strategy [GENPIO:0001982]", - "other library strategy [GENPIO:0001988]", - "pool clone strategy [GENPIO:0001989]" + "Amplicon [GENPIO:0001974]", + "Clone end strategy [GENPIO:0001976]", + "Clone strategy [GENPIO:0001977]", + "Finishing strategy [GENPIO:0001982]", + "Other library strategy [GENPIO:0001988]", + "Pool clone strategy [GENPIO:0001989]" ], "examples": [ "WGS" @@ -995,11 +1014,9 @@ "ontology": "GENPIO_0001973", "type": "string", "description": "Overall sequencing strategy or approach.", - "clasification": "Sequencing", + "classification": "Sequencing", "label": "Sequencing technique", - "table": [ - "experiments" - ] + "fill_mode": "batch" }, "library_layout": { "examples": [ @@ -1051,7 +1068,7 @@ "examples": [ "" ], - "ontology": "STATO_0000064", + "ontology": "GENEPIO_0000076", "type": "string", "description": "", "clasification": "Submission ENA", @@ -1147,19 +1164,6 @@ "clasification": "Submission ENA", "label": "Base count" }, - "insert_size": { - "examples": [ - "250" - ], - "ontology": "0", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Insert size", - "table": [ - "experiments" - ] - }, "center_name": { "examples": [ " KAROLINSKA INSITUTET" @@ -1326,16 +1330,6 @@ "clasification": "Submission ENA", "label": "Fastq md5 r1" }, - "fastq_md5_r2": { - "examples": [ - "" - ], - "ontology": "MS_1000568", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Fastq md5 r1" - }, "fastq_ftp": { "examples": [ "" diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index ede7f205..5203c6d9 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1438,7 +1438,7 @@ "examples": [ "Illumina" ], - "ontology": "0", + "ontology": "GENEPIO_0000071", "type": "string", "description": "", "classification": "Sequencing", @@ -1448,13 +1448,15 @@ }, "library_source": { "enum": [ - "GENOMIC", - "TRANSCRIPTOMIC", - "METAGENOMIC", - "METATRANSCRIPTOMIC", - "SYNTHETIC", - "VIRAL RNA", - "OTHER" + "genomic", + "genomic single cell", + "transcriptomic", + "transcriptomic single cell", + "metagenomic", + "metatranscriptomic", + "synthetic", + "viral rna", + "other" ], "examples": [ "METAGENOMIC" @@ -1914,6 +1916,29 @@ "label": "Consensus sequence name md5", "fill_mode": "batch" }, + "fastq_md5_r2": { + "examples": [ + "3e69af1f875fab020aed82f5edbc1f03" + ], + "ontology": "MS_1000568", + "type": "string", + "description": "", + "clasification": "Bioinformatics and QC metrics", + "label": "file checksum", + "table": [ + "runs" + ] + }, + "fastq_md5_r1": { + "examples": [ + "" + ], + "ontology": "MS_1000568", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Fastq md5 r1" + }, "consensus_sequence_filepath": { "examples": [ "/User/Documents/RespLab/Data/ncov123assembly.fasta" @@ -2496,4 +2521,4 @@ "fill_mode": "batch" } } -} +} \ No newline at end of file From decfaecde6903156d98184db3687a1893dff9249 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 8 Sep 2022 18:10:39 +0200 Subject: [PATCH 0938/1454] Fixed bugs in the json files --- relecov_tools/conf/geo_loc_cities.json | 3 +-- relecov_tools/schema/relecov_schema.json | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/relecov_tools/conf/geo_loc_cities.json b/relecov_tools/conf/geo_loc_cities.json index f4ec1fcd..e4a10776 100644 --- a/relecov_tools/conf/geo_loc_cities.json +++ b/relecov_tools/conf/geo_loc_cities.json @@ -223,7 +223,6 @@ "geo_loc_latitude": "42.4333", "geo_loc_longitude": "-8.6333" }, - { "Alcázar de San Juan": { "geo_loc_latitude": "39.4056", "geo_loc_longitude": "-3.2056" @@ -296,7 +295,7 @@ "geo_loc_latitude": "38.2669", "geo_loc_longitude": "-0.6983" }, - "Gazteiz": { + "Gasteiz": { "geo_loc_latitude": "42.85", "geo_loc_longitude": "-2.6667" } diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 8eb86246..0fcb1a8f 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1587,7 +1587,6 @@ "label": "Fastq md5 r1", "fill_mode": "sample", "minLenght": "1" - }, "sequence_file_R2_md5": { "examples": [ @@ -1596,7 +1595,7 @@ "ontology": "MS_1000569", "type": "string", "description": "Checksum value to validate successful file transmission", - "classification": "Bioinformatics and QC metrics fields"", + "classification": "Bioinformatics and QC metrics fields", "label": "Sequence fastq R2 md5", "fill_mode": "sample" }, From 981fd3c933f8caf4087de3798e178542c03ac35e Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 8 Sep 2022 22:16:57 +0200 Subject: [PATCH 0939/1454] adding purpose of sequencing in headin excel --- relecov_tools/conf/configuration.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index b7ee614a..d53f34c6 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -2,7 +2,6 @@ "lab_metadata": { "fixed_fields": { "host_disease": "COVID-19", - "type": "betacoronavirus", "tax_id": "2697049", "organism": "Severe acute respiratory syndrome coronavirus 2" }, @@ -30,6 +29,7 @@ "Host Age", "Host Gender", "Sequencing Date", + "Purpose of Sequencing", "Nucleic acid extraction protocol", "Commercial All-in-one library kit", "Library Preparation Kit", @@ -341,4 +341,4 @@ "collecting institution" ] } -} \ No newline at end of file +} From 3b9fa08d09f54a5d9f58c58843d51be4e6386016 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 8 Sep 2022 22:17:41 +0200 Subject: [PATCH 0940/1454] adding function for purpose of sequencing --- relecov_tools/institution_scripts/ISCIII.py | 85 ++++++++++++++++----- 1 file changed, 64 insertions(+), 21 deletions(-) diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index 1033a82c..3f6ffe3d 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -62,39 +62,36 @@ def added_seq_inst_model(metadata, f_data, mapped_fields, heading): def translate_gender_to_english(metadata, f_data, mapped_fields, heading): """Translate into english the host gender that is written in spanish""" + map_dict = { + "hombre": "Male", + "mujer": "Female", + "genero no-binario": "Non-binary Gender", + "genero no-binario": "Non-binary Gender", + "desconocido": "Not Provided", + "unknown": "Not Provided", + } for row in metadata[1:]: for key, val in mapped_fields.items(): m_idx = heading.index(key) - if row[m_idx] is None: - row[m_idx] = "not provided" - elif "hombre" in row[m_idx].lower(): - row[m_idx] = "Male" - elif "mujer" in row[m_idx].lower(): - row[m_idx] = "Female" - elif "genero no-binario" in row[m_idx].lower(): - row[m_idx] = "Non-binary Gender" - elif "genero no-binario" in row[m_idx].lower(): - row[m_idx] = "Non-binary Gender" - elif "desconocido" in row[m_idx].lower(): - row[m_idx] = "Not Provided" - elif "unknown" in row[m_idx].lower(): + if row[m_idx] is None or row[m_idx] == "": row[m_idx] = "Not Provided" + continue + item = row[m_idx].lower() + if item in map_dict: + row[m_idx] = map_dict[item] else: - log.error("The '%s' is not a valid data for translation" , row[m_idx]) - stderr.print("f[red] The '{row[m_idx]}' is not a valid data for translation") - + log.error("The '%s' is not a valid data for translation", row[m_idx]) + stderr.print( + "f[red] The '{row[m_idx]}' is not a valid data for translation" + ) + sys.exit(1) return metadata -# - - def translate_specimen_source(metadata, f_data, mapped_fields, heading): """Translate into english the "muestra" that is written in spanish""" for row in metadata[1:]: - for key, val in mapped_fields.items(): - m_idx = heading.index(key) if row[m_idx] is None: row[m_idx] = "not provided" @@ -119,4 +116,50 @@ def translate_specimen_source(metadata, f_data, mapped_fields, heading): else: log.error("The field is not correctly written or is not filled") stderr.print("The field is not correctly written or not filled") + sys.exit(1) + return metadata + + +def translate_purpose_seq_to_english(metadata, f_data, mapped_fields, heading): + """Fetch the first words of the option to group them according the + schema + """ + map_dict = { + "estudio variante": "Targeted surveillance (non-random sampling)", + "trabajador/a granja visones": "Targeted surveillance (non-random sampling)", + "sospecha reinfección": "Re-infection surveillance", + "i-move-covid": "Research", + "irag": "Research", + "muestreo aleatorio": "Baseline surveillance (random sampling)", + "paciente vacunado": "Vaccine escape surveillance", + "posible variante": "Sample has epidemiological link to Variant of Concern (VoC)", + "no consta": "Not Collected", + "brote": "Cluster/Outbreak investigation", + "viaje": "Surveillance of international border crossing by air travel or ground transport", + "posible variante": "Sample has epidemiological link to Variant of Concern (VoC)", + } + for row in metadata[1:]: + for key, val in mapped_fields.items(): + m_idx = heading.index(key) + if row[m_idx] is None or row[m_idx] == "": + row[m_idx] = "Not Provided" + continue + item = row[m_idx].lower() + if item in map_dict: + row[m_idx] = map_dict[item] + elif "brote" in item: + row[m_idx] = map_dict["brote"] + elif "viaje" in item: + row[m_idx] = map_dict["viaje"] + elif "posible variante" in item: + row[m_idx] = map_dict["posible variante"] + else: + log.error("The '%s' is not a valid data for translation", row[m_idx]) + stderr.print( + "f[red] The {row[m_idx]} is not a valid data for translation" + ) + import pdb + + pdb.set_trace() + sys.exit(1) return metadata From f56ee8453d2b3f06931f3b5d21670337f4b3924a Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 8 Sep 2022 22:19:09 +0200 Subject: [PATCH 0941/1454] change log error to log info in case that not mapping the dictionary. It is related to the author field --- relecov_tools/metadata_homogeneizer.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 8916a4c3..dc31b1b9 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -180,7 +180,7 @@ def handling_files(self, file_data, additional_data): try: item_data = data[s_value] except KeyError: - log.error( + log.info( "Additional file %s does not have the information for %s ", f_name, s_value, From 777886c3646b9bfd868ba65951fcdf6b712dcda2 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 8 Sep 2022 22:31:11 +0200 Subject: [PATCH 0942/1454] adding parameter for purpose of sequencing --- relecov_tools/schema/institution_schemas/ISCIII.json | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 6ad98698..fda015dd 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -17,7 +17,8 @@ "Host Age": "Edad (años)", "Host Gender": "Sexo", "Diagnostic Pcr Ct Value 1": "PCR genE", - "Specimen source": "Muestra" + "Specimen source": "Muestra", + "Purpose of Sequencing": "Contexto" }, "function": "None" }, @@ -101,6 +102,12 @@ }, "mapped_key": "Sample ID given for sequencing", "function": "None" + }, + "purpose_of_sequencing": { + "file_name": "", + "mapped_fields" : {"Purpose of Sequencing" : "" }, + "mapped_key" : "", + "function": "translate_purpose_seq_to_english" } }, "fixed_fields": { From ddc2823786e818bdb28a7b253e1cc214facde42b Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 8 Sep 2022 22:32:07 +0200 Subject: [PATCH 0943/1454] fixing misspelling in label schema --- relecov_tools/schema/relecov_schema.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 0fcb1a8f..047a651b 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -656,7 +656,7 @@ "" ], "classification": "Sample collection and processing", - "label": "Collection device", + "label": "Collection Device", "fill_mode": "batch" }, "collection_method": { @@ -1256,7 +1256,7 @@ "label": "Enrichment panel/assay version", "fill_mode": "batch" }, - "if_enrichment_panel_assay_if_other_especify": { + "if_enrichment_panel_assay_is_other_specify": { "examples": [ "" ], @@ -1264,7 +1264,7 @@ "type": "string", "description": "", "classification": "Sequencing", - "label": "If Enrichment panel/assay If Other, Especify", + "label": "If Enrichment panel/assay Is Other, Specify", "fill_mode": "batch" }, "amplicon_pcr_primer_scheme": { @@ -2350,7 +2350,7 @@ "type": "string", "description": "The identifier assigned to a BioSample in INSDC archives.", "classification": "Sample collection and processing", - "label": "ENA Sample Id", + "label": "ENA Sample ID", "fill_mode": "batch" }, "diagnostic_pcr_Ct_value_2": { From b9fec960c8a0d7119cd4df1befa448cfb56fc173 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 8 Sep 2022 22:33:16 +0200 Subject: [PATCH 0944/1454] dump info to log when error mapping for label key --- relecov_tools/read_lab_metadata.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 45ad2d9f..0f9fb9a7 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -121,7 +121,6 @@ def adding_ontology_to_enum(self, m_data): """ enum_dict = {} for prop, values in self.relecov_sch_json["properties"].items(): - # import pdb; pdb.set_trace() if "enum" in values: enum_dict[prop] = {} for enum in values["enum"]: @@ -138,7 +137,7 @@ def adding_ontology_to_enum(self, m_data): m_data[idx][key] = e_values[m_data[idx][key]] else: continue - # import pdb; pdb.set_trace() + return m_data def process_from_json(self, m_data, json_fields): @@ -155,7 +154,6 @@ def process_from_json(self, m_data, json_fields): map_field = json_fields["map_field"] json_data = json_fields["j_data"] if isinstance(json_data, dict): - # import pdb; pdb.set_trace() for idx in range(len(m_data)): m_data[idx].update(json_data[m_data[idx][map_field]]) elif isinstance(json_data, list): @@ -226,7 +224,6 @@ def read_metadata_file(self): ws_metadata_lab = relecov_tools.utils.read_excel_file( self.metadata_file, "METADATA_LAB", heading_row_number, False ) - metadata_values = [] errors = {} row_number = heading_row_number @@ -272,8 +269,9 @@ def read_metadata_file(self): try: property_row[self.label_prop_dict[key]] = row[key] except KeyError as e: + log.error("Error when mapping the label %s", e) + stderr.print(f"[red] Error when mapping the label {str(e)}") continue - stderr.print(f"[red] Error when reading {sample_number} {str(e)}") metadata_values.append(property_row) return metadata_values, errors From 52c2b14c179fbd64f7dc22b878af9292c5d42721 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 8 Sep 2022 22:57:05 +0200 Subject: [PATCH 0945/1454] renamed the fastq_r1_md5 for the label that we agreed sequence_fastq_r1_md5, same for r2 --- relecov_tools/schema/relecov_schema.json | 25 +----------------------- 1 file changed, 1 insertion(+), 24 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index fad9fe0d..6433eac8 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1940,29 +1940,6 @@ "label": "Consensus sequence name md5", "fill_mode": "batch" }, - "fastq_md5_r2": { - "examples": [ - "3e69af1f875fab020aed82f5edbc1f03" - ], - "ontology": "MS_1000568", - "type": "string", - "description": "", - "clasification": "Bioinformatics and QC metrics", - "label": "file checksum", - "table": [ - "runs" - ] - }, - "fastq_md5_r1": { - "examples": [ - "" - ], - "ontology": "MS_1000568", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Fastq md5 r1" - }, "consensus_sequence_filepath": { "examples": [ "/User/Documents/RespLab/Data/ncov123assembly.fasta" @@ -2545,4 +2522,4 @@ "fill_mode": "batch" } } -} \ No newline at end of file +} From a688ec7e599e0366506129a3b75b5bb221408e6b Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 8 Sep 2022 22:57:31 +0200 Subject: [PATCH 0946/1454] adding , for liting --- relecov_tools/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index ab2b86cc..b60be377 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -202,7 +202,7 @@ def validate(json_file, json_schema, metadata, out_folder): validated_json_data, invalid_json, errors, - out_folder + out_folder, ) = relecov_tools.json_validation.validate_json(json_file, json_schema, out_folder) if len(invalid_json) > 0: log.error("Some of the samples in json metadata were not validated") From 39abba5cc5bfacba055ddab52299b8fa697d072a Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 9 Sep 2022 13:19:50 +0200 Subject: [PATCH 0947/1454] modifications done at isciii --- relecov_tools/read_bioinfo_metadata.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index f6d2f496..ffccaf97 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -158,13 +158,13 @@ def bioinfo_parse(self, file_name): sample_name = row[6] print(sample_name) - fastq_r1 = row[47] + # fastq_r1 = row[47] - fastq_r2 = row[48] + # fastq_r2 = row[48] bioinfo_dict = {} bioinfo_dict["sample_name"] = str(sample_name) - bioinfo_dict["sequence_file_R1_fastq"] = fastq_r1 - bioinfo_dict["sequence_file_R2_fastq"] = fastq_r2 + # bioinfo_dict["sequence_file_R1_fastq"] = fastq_r1 + # bioinfo_dict["sequence_file_R2_fastq"] = fastq_r2 # FUNCTION config_data """inserting all keys from configuration.json relecov_bioinfo_metadata into bioinfo_dict""" for key in relecov_bioinfo_metadata.keys(): From 7b2d52374a15acd043c19f9c5c5b141a4d27c803 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 9 Sep 2022 13:29:05 +0200 Subject: [PATCH 0948/1454] ena_schema.json vs relecov_schema.json y ena-upload-cli --- relecov_tools/schema/ena_schema.json | 29 +++++++++++++++++------- relecov_tools/schema/relecov_schema.json | 8 +++---- 2 files changed, 25 insertions(+), 12 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 3e81567d..75f5836f 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -501,7 +501,7 @@ "Blood [UBERON:0000178]" ], "classification": "Sample collection and processing", - "label": "Organism Substance" + "label": "Specimen source" }, "isolation source non-host-associated": { "Enums": [ @@ -685,7 +685,7 @@ "examples": [ "e.g. Patient infected while traveling in …." ], - "ontology": "GENEPIO_0001268", + "ontology": "NCIT:C83280", "type": "string", "description": "If the information is unknown or can not be shared, leave blank.", "clasification": "Host information", @@ -848,7 +848,7 @@ "examples": [ "probably 2697049 in all cases" ], - "ontology": "GENEPIO_0001724", + "ontology": "NCIT:C164641", "type": "string", "description": "The NCBITaxon identifier for the organism being sequenced.", "clasification": "Sample collection and processing", @@ -870,7 +870,7 @@ "examples": [ "" ], - "ontology": "GENEPIO:0001191", + "ontology": "NCIT:C43459", "type": "string", "description": "The taxonomic name of the organism.", "clasification": "Sample collection and processing", @@ -892,7 +892,7 @@ "examples": [ "" ], - "ontology": "GENEPIO:0001156", + "ontology": "sep:00196", "type": "string", "description": "Free text description of the sample.", "clasification": "Sample collection and processing", @@ -903,7 +903,7 @@ "examples": [ "24 degrees celsius" ], - "ontology": "NCIT_C115535", + "ontology": "NCIT:C115535", "type": "string", "description": "The name and version of a particular protocol used for sampling.", "clasification": "Sample collection and processing", @@ -1211,7 +1211,7 @@ "examples": [ "" ], - "ontology": "0", + "ontology": "GENEPIO:0001808", "type": "string", "description": "", "clasification": "Submission ENA", @@ -1237,7 +1237,7 @@ "examples": [ "" ], - "ontology": "OPMI_0000380", + "ontology": "GENEPIO:0000156", "type": "string", "description": "", "clasification": "Submission ENA", @@ -1270,6 +1270,19 @@ "study" ] }, + "sample_alias": { + "examples": [ + "s_20201007_026" + ], + "ontology": "0", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Sample alias", + "table": [ + "sample" + ] + }, "study_alias": { "examples": [ "e.g Sweden" diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 6433eac8..8b38427f 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -185,7 +185,7 @@ "examples": [ "24 degrees celsius" ], - "ontology": "NCIT_C115535", + "ontology": "NCIT:C115535", "type": "string", "description": "The name and version of a particular protocol used for sampling.", "classification": "Sample collection and processing", @@ -823,7 +823,7 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "GENEPIO:0001191", + "ontology": "NCIT:C43459", "type": "string", "description": "Taxonomic name of the organism.", "examples": [ @@ -838,7 +838,7 @@ "examples": [ "2697049" ], - "ontology": "GENEPIO_0001724", + "ontology": "NCIT:C164641", "type": "string", "description": "The NCBITaxon identifier for the organism being sequenced.", "classification": "Sample collection and processing", @@ -2522,4 +2522,4 @@ "fill_mode": "batch" } } -} +} \ No newline at end of file From 6008377f65e87d122913aaa15281e7b965020782 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 9 Sep 2022 13:34:40 +0200 Subject: [PATCH 0949/1454] lintin --- relecov_tools/json_validation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 6ea788cd..a843cf69 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -20,7 +20,7 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) - +# def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): """Validate json file against the schema""" if json_data_file is None: From 407f017268ff751096f18425b7a5cb3a44d65e02 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 9 Sep 2022 13:39:33 +0200 Subject: [PATCH 0950/1454] lintin --- relecov_tools/json_validation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index a843cf69..6ea788cd 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -20,7 +20,7 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) -# + def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): """Validate json file against the schema""" if json_data_file is None: From c39cb2de58b5a16704e0474d04944aa230feecf0 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 9 Sep 2022 13:42:13 +0200 Subject: [PATCH 0951/1454] lintin --- relecov_tools/ena_upload.py | 1 - relecov_tools/schema/ena_schema.json | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 58902277..a4fa3867 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -246,7 +246,6 @@ def create_structure_to_ena(self): 0 214821_S12 214821_S12_R1_001.fastq.gz 214821_S12_R2_001.fastq.gz ... fastq 372ca8b10a8eeb7a04107634baf340ab 7f5081eec1b64b171402b66f37fe640d 1 214821_S12 214822_S13_R1_001.fastq.gz 214822_S13_R2_001.fastq.gz ... fastq b268d7be80e80455bec0807b5961d23c a15be39feaf73eec9b2c026717878bba 2 214821_S12 214823_S1_R1_001.fastq.gz 214823_S1_R2_001.fastq.gz ... fastq c16bdbfc03c354496fcfb2c107e3cbf6 4d9b80b977a75bf7e2a4282ca910d94a - """ # df_experiments df_experiments["instrument_model"] = df_experiments[ diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 75f5836f..1d469abd 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -1274,7 +1274,7 @@ "examples": [ "s_20201007_026" ], - "ontology": "0", + "ontology": "GENEPIO:0000079", "type": "string", "description": "", "clasification": "Submission ENA", From 4ed833ae4edc37af21e62be511d48a30cf50f3f5 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 9 Sep 2022 14:18:44 +0200 Subject: [PATCH 0952/1454] ena_schema.json vs relecov_schema.json y ena-upload-cli --- relecov_tools/schema/ena_schema.json | 38 +++++++++++++++++++++++- relecov_tools/schema/relecov_schema.json | 36 ++++++++++++++++++++++ 2 files changed, 73 insertions(+), 1 deletion(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 1d469abd..d38873de 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -89,6 +89,16 @@ "clasification": "", "label": "Sample ID given if multiple rna-extraction or passages" }, + "subject_exposure_duration": { + "examples": [ + "" + ], + "ontology": "NCIT:C83280", + "type": "string", + "description": "", + "clasification": "", + "label": "Additional Host Information" + }, "collection_date": { "examples": [ "3/19/2020" @@ -646,6 +656,32 @@ "sample" ] }, + "type_exposure": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001417", + "type": "string", + "description": " Date, Location e.g. type of gathering, Family cluster, etc.", + "clasification": "Host information", + "label": "Outbreak Exposure Event Location", + "table": [ + "sample" + ] + }, + "personal_protective_equipment": { + "examples": [ + "" + ], + "ontology": "NCIT:C173748", + "type": "string", + "description": "Use of personal protective equipment, such as gloves, gowns, during any type of exposure. Example: mask", + "clasification": "Host information", + "label": "Personal protective equipment", + "table": [ + "sample" + ] + }, "host_sex": { "Enums": [ "Female [NCIT:C46110]", @@ -1211,7 +1247,7 @@ "examples": [ "" ], - "ontology": "GENEPIO:0001808", + "ontology": "GENEPIO:0000079", "type": "string", "description": "", "clasification": "Submission ENA", diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 8b38427f..3df576ae 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -858,6 +858,16 @@ "fill_mode": "sample", "minLenght": "1" }, + "additional_host_information": { + "examples": [ + "" + ], + "ontology": "NCIT:C83280", + "type": "string", + "description": "", + "clasification": "", + "label": "Additional Host Information" + }, "host_health_state": { "examples": [ "" @@ -1119,6 +1129,32 @@ "label": "Nucleic acid extraction protocol", "fill_mode": "batch" }, + "outbreak": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001417", + "type": "string", + "description": " Date, Location e.g. type of gathering, Family cluster, etc.", + "clasification": "Host information", + "label": "Outbreak Exposure Event Location", + "table": [ + "sample" + ] + }, + "personal_protective_equipment": { + "examples": [ + "" + ], + "ontology": "NCIT:C173748", + "type": "string", + "description": "Use of personal protective equipment, such as gloves, gowns, during any type of exposure. Example: mask", + "clasification": "Host information", + "label": "Personal protective equipment", + "table": [ + "sample" + ] + }, "all_in_one_library_kit": { "enum": [ "Ion Xpress", From 1217efd1ddd4a13f980c73f50d864a8c6959c701 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 9 Sep 2022 17:16:16 +0200 Subject: [PATCH 0953/1454] added Read Length --- relecov_tools/schema/relecov_schema.json | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 6433eac8..e2956642 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1110,7 +1110,7 @@ }, "nucleic_acid_extraction_protocol": { "examples": [ - "Opentrons custom protocol" + "Opentrons custom rna extraction protocol" ], "ontology": "OBI_0302884", "type": "string", @@ -1556,6 +1556,17 @@ "label": "Library Layout", "fill_mode": "batch" }, + "read_length": { + "examples": [ + "75" + ], + "ontology": "GENEPIO:0000076", + "type": "string", + "description": "number of base pairs per read", + "classification": "Sequencing", + "label": "Read Length", + "fill_mode": "batch" + }, "sequence_file_R1_fastq": { "examples": [ "ABC123_S1_L001_R1_001.fastq.gz" From f82d3c3f0c03411cc3e28f71f8383926462b66c3 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 9 Sep 2022 19:08:33 +0200 Subject: [PATCH 0954/1454] added Read Length in the lab metadata heading --- relecov_tools/conf/configuration.json | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index d53f34c6..dbcc8e54 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -46,6 +46,7 @@ "Capture method", "Sequencing technique", "Library Layout", + "Read Length", "Gene Name 1", "Diagnostic Pcr Ct Value 1", "Gene Name 2", From 2c90e1a51d57fe915f4efb6f12b6055124f887bf Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 9 Sep 2022 19:11:39 +0200 Subject: [PATCH 0955/1454] Added new functions for library layout and transalate OPENTRONS --- relecov_tools/institution_scripts/ISCIII.py | 40 +++++++++++++++++++-- 1 file changed, 38 insertions(+), 2 deletions(-) diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index 3f6ffe3d..7cedfad9 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -158,8 +158,44 @@ def translate_purpose_seq_to_english(metadata, f_data, mapped_fields, heading): stderr.print( "f[red] The {row[m_idx]} is not a valid data for translation" ) - import pdb + sys.exit(1) + return metadata + + +def translate_nucleic_acid_extract_prot(metadata, f_data, mapped_fields, heading): + """Fetch the short name given in the input laboratory file and change for + the one is allow according to schema + """ + for row in metadata[1:]: + for key, val in mapped_fields.items(): + m_idx = heading.index(key) + if "NA" in row[m_idx]: + row[m_idx] = "Not Applicable" + elif "opentrons" in row[m_idx].lower(): + row[m_idx] = "Opentrons custom rna extraction protocol" + else: + # allow from now on until more options are available + continue + return metadata - pdb.set_trace() + +def findout_library_layout(metadata, f_data, mapped_fields, heading): + """Read the file and by checking if read2_cycles is 0 set to Single otherwise + to paired""" + s_idx = heading.index("Sample ID given for sequencing") + for row in metadata[1:]: + + for key, val in mapped_fields.items(): + m_idx = heading.index(key) + try: + if f_data[str(row[s_idx])][val] == "0": + row[m_idx] = "Single" + else: + row[m_idx] = "Paired" + except KeyError as e: + log.error("The %s is not defined in function findout_library_layout", e) + stderr.print( + f"[red] {e} is not defined in function findout_library_layout" + ) sys.exit(1) return metadata From c522dcaff344b8e61fbc25fd6fe7d000ad570cd2 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 9 Sep 2022 19:13:18 +0200 Subject: [PATCH 0956/1454] added configuration for Nucleic acid extraction protocol and read length --- .../schema/institution_schemas/ISCIII.json | 34 ++++++++++++++----- 1 file changed, 26 insertions(+), 8 deletions(-) diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index fda015dd..1d228ea0 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -18,7 +18,8 @@ "Host Gender": "Sexo", "Diagnostic Pcr Ct Value 1": "PCR genE", "Specimen source": "Muestra", - "Purpose of Sequencing": "Contexto" + "Purpose of Sequencing": "Contexto", + "Nucleic acid extraction protocol": "Extracción" }, "function": "None" }, @@ -32,7 +33,7 @@ "mapped_key": "Sample ID given for sequencing" }, "run_id_file": { - "file_name": "samples_run_services.tsv", + "file_name": "samples_run_services_length.tsv", "mapped_fields": { "Runid": "run_name" }, @@ -48,7 +49,7 @@ "function": "replace_originating_lab" }, "sequencer_file": { - "file_name": "samples_run_services.tsv", + "file_name": "samples_run_services_length.tsv", "mapped_fields": { "Sequencing Instrument Model": "run_name" }, @@ -87,6 +88,14 @@ "mapped_key": "Runid", "function": "None" }, + "read_length": { + "file_name": "samples_run_services_length.tsv", + "mapped_fields": { + "Read Length" : "read1_cycles" + }, + "mapped_key": "Sample ID given for sequencing", + "function": "None" + }, "samples_in_run": { "file_name": "run_and_num_of_samples.csv", "mapped_fields": { @@ -108,24 +117,33 @@ "mapped_fields" : {"Purpose of Sequencing" : "" }, "mapped_key" : "", "function": "translate_purpose_seq_to_english" + }, + "nucleic_acid_extraction_protocol": { + "file_name": "", + "mapped_fields" : {"Nucleic acid extraction protocol" : "" }, + "mapped_key" : "", + "function": "translate_nucleic_acid_extract_prot" + }, + "library_layout": { + "file_name": "samples_run_services_length.tsv", + "mapped_fields" : {"Library Layout" : "read2_cycles" }, + "mapped_key" : "sample_name", + "function": "findout_library_layout" } }, "fixed_fields": { "Submitting Institution": "Instituto de Salud Carlos III", "Biological Sample Storage Condition": "-80 C", - "Nucleic acid extraction protocol": "Opentrons custom rna extraction protocol", "Purpose of sampling": "Surveillance", "Specimen source": "Nasopharyngeal exudate", "Host": "Human", "Library Preparation Kit": "Illumina DNA Prep", "Enrichment Protocol": "Amplicon", "Enrichment panel/assay": "ARTIC", - "Source material": "VIRAL RNA", + "Source material": "viral rna", "Capture method": "PCR", "Sequencing technique": "Amplicon", - "Library Layout": "Paired", "Gene Name 1": "E gene", - "Diagnostic Pcr Ct Value 1": "", - "Authors": "" + "Diagnostic Pcr Ct Value 1": "" } } From 501005f3b456095dd8cfe7378c2ccdaa939f387c Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 9 Sep 2022 19:15:27 +0200 Subject: [PATCH 0957/1454] modify the example metagenomic to be in lowercase --- relecov_tools/schema/relecov_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index e2956642..f0303c1c 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1460,7 +1460,7 @@ "other" ], "examples": [ - "METAGENOMIC" + "metagenomic" ], "ontology": "GENEPIO_0001965", "type": "string", From 92c51f8bbd9a32f8db3783f4e5499dd0700f9b9e Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 9 Sep 2022 19:16:23 +0200 Subject: [PATCH 0958/1454] Incorrect handled if file is not in right format --- relecov_tools/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index ff99fae3..d6a3a9c8 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -69,7 +69,7 @@ def read_csv_file_return_dict(file_name, sep): with open(file_name, "r") as fh: lines = fh.readlines() heading = lines[0].strip().split(sep) - if len(heading) == 0: + if len(heading) == 1: return {"ERROR": "not valid format"} file_data = {} for line in lines[1:]: From 3dc2a513f2c2f2c44593737a94054442f2a96957 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 10 Sep 2022 13:39:16 +0200 Subject: [PATCH 0959/1454] changes in parameters name for bioinfo metadata module --- relecov_tools/__main__.py | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index b60be377..b2e71e2b 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -370,31 +370,28 @@ def update_db(user, password, json, schema, type, databaseServer): # read metadata bioinformatics @relecov_tools_cli.command(help_priority=10) @click.option( - "-m", - "--metadata_file", + "-j", + "--json_file", type=click.Path(), - help="file containing metadata", -) -@click.option("-i", "--input-folder", type=click.Path(), help="Path to input files") -@click.option( - "-o", "--metadata-out", type=click.Path(), help="Path to save output metadata file" + help="json file containing lab metadata", ) +@click.option("-i", "--input_folder", type=click.Path(), help="Path to input files") +@click.option("-o", "--out_dir", type=click.Path(), help="Path to save output file") @click.option( "-p", "--mapping-illumina", type=click.Path(), help="Name of the mapping_illumina file", ) -def read_bioinfo_metadata(metadata_file, input_folder, metadata_out, mapping_illumina): +def read_bioinfo_metadata(json_file, input_folder, out_dir, mapping_illumina): """ Create the json compliant from the Bioinfo Metadata. """ - new_bioinfo_metadata = relecov_tools.read_bioinfo_metadata.BioinfoMetadata( - metadata_file, input_folder, metadata_out, mapping_illumina + json_file, input_folder, out_dir, mapping_illumina ) - new_bioinfo_metadata.bioinfo_parse(metadata_file) + new_bioinfo_metadata.create_bioinfo_file() # read metadata bioinformatics From 3210630d8f712af22b4b98bcdfe9acc53ee08c34 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 10 Sep 2022 13:40:00 +0200 Subject: [PATCH 0960/1454] added bioinfo_analysis configuration --- relecov_tools/conf/configuration.json | 99 ++++++++++++++++++--------- 1 file changed, 66 insertions(+), 33 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index dbcc8e54..84dc2c66 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -216,39 +216,72 @@ "submitting_lab_sample_id", "virus_name" ], - "relecov_bioinfo_metadata": { - "dehosting_method_software_name": "KRAKEN2_KRAKEN2", - "assembly": "None", - "if_assembly_other": "None", - "assembly_params": "None", - "variant_calling_software_name": "IVAR_VARIANTS", - "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", - "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", - "if_consensus_other": "None", - "consensus_params": "-p vcf -f", - "depth_of_coverage_threshold": ">10x", - "bioinformatics_protocol_software_name": "nf-core/viralrecon", - "if_bioinformatic_protocol_is_other_specify": "None", - "commercial_open_source_both": "open-source", - "preprocessing_software_name": "FASTP", - "if_preprocessing_other": "None", - "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", - "mapping_software_name": "BOWTIE2_ALIGN", - "if_mapping_other": "None", - "mapping_params": "--seed 1", - "lineage_analysis_software_name": "pangolin", - "if_lineage_identification_other": "None" - }, - "mapping_illumina_tab_field_list": { - "lineage_name": "Lineage", - "per_genome_greater_10x": "Coverage>10x(%)", - "per_reads_host": "%readshost", - "per_reads_virus": "%readsvirus", - "per_unmapped": "%unmapedreads", - "per_Ns": "%Ns10x", - "depth_of_coverage_value": "medianDPcoveragevirus", - "number_of_variants_in_consensus": "Variantsinconsensusx10", - "number_of_variants_with_effect": "MissenseVariants" + "bioinfo_analysis": { + "fixed_values": { + "assembly": "None", + "assembly_params": "None", + "bioinformatics_protocol_software_name": "nf-core/viralrecon", + "commercial_open_source_both": "open-source", + "consensus_params": "-p vcf -f", + "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", + "dehosting_method_software_name": "KRAKEN2_KRAKEN2", + "depth_of_coverage_threshold": ">10x", + "if_assembly_other": "None", + "if_bioinformatic_protocol_is_other_specify": "None", + "if_consensus_other": "None", + "if_lineage_identification_other": "None", + "if_mapping_other": "None", + "if_preprocessing_other": "None", + "lineage_analysis_software_name": "pangolin", + "mapping_params": "--seed 1", + "mapping_software_name": "BOWTIE2_ALIGN", + "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", + "preprocessing_software_name": "FASTP", + "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", + "variant_calling_software_name": "IVAR_VARIANTS" + }, + "required_file": { + "variants_metrics": "summary_variants_metrics_mqc.csv", + "versions": "software_versions.yml", + "pangoling": "pangolin_version.csv" + }, + "mapping_stats": { + "depth_of_coverage_value": "medianDPcoveragevirus", + "lineage_name": "Lineage", + "number_of_variants_in_consensus": "Variantsinconsensusx10", + "number_of_variants_with_effect": "MissenseVariants", + "per_genome_greater_10x": "Coverage>10x(%)", + "per_Ns": "%Ns10x", + "per_reads_host": "%readshost", + "per_reads_virus": "%readsvirus", + "per_unmapped": "%unmapedreads", + "qc_filtered": "totalreads", + "reference_genome_accession": "Virussequence" + }, + "required_fields_from_lab_json": { + "schema_name": "schema_name", + "schema_version": "schema_version", + "sequence_file_R1_fastq": "sequence_file_R1_fastq", + "sequence_file_R2_fastq": "sequence_file_R2_fastq", + "sequence_file_R1_md5": "sequence_file_R1_md5", + "sequence_file_R2_md5" : "sequence_file_R2_md5", + "sequencing_sample_id" : "sample_name" + }, + "version_mapping":{ + "dehosting_method_software_version": { + "KRAKEN2_KRAKEN2": "kraken2" + }, + "mapping_software_name": { + "BOWTIE2_ALIGN": "bowtie2" + }, + "preprocessing_software_version": { + "FASTP": "fastp" + }, + "variant_calling_software_version": { + "IVAR_VARIANTS": "ivar" + } + + } }, "files_read_bioinfo_metadata": { "mapping_illumina.tab": "mapping_illumina_tab_path", From e0edac61f6f9b45120f0697b977f73706b11c3a6 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 10 Sep 2022 13:45:41 +0200 Subject: [PATCH 0961/1454] working on bioinfo, done fixed, mapping illumina, version --- relecov_tools/read_bioinfo_metadata.py | 381 ++++++++----------------- 1 file changed, 112 insertions(+), 269 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index ffccaf97..7ebd6252 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -7,16 +7,17 @@ import re import rich.console -from itertools import islice -import pandas as pd -import yaml -import openpyxl +# import pandas as pd + + import os import sys import relecov_tools.utils from relecov_tools.config_json import ConfigJson -import relecov_tools.json_schema +from yaml import YAMLError + +# import relecov_tools.json_schema log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -30,23 +31,21 @@ class BioinfoMetadata: def __init__( self, - metadata_file=None, + json_file=None, input_folder=None, output_folder=None, mapping_illumina=None, ): - if metadata_file is None: - self.metadata_file = relecov_tools.utils.prompt_path( - msg="Select the excel file which contains metadata" - ) - else: - self.metadata_file = metadata_file - if not os.path.exists(self.metadata_file): - log.error("Metadata file %s does not exist ", self.metadata_file) - stderr.print( - "[red] Metadata file " + self.metadata_file + " does not exist" + if json_file is None: + json_file = relecov_tools.utils.prompt_path( + msg="Select the json file that was created by the read-lab-metadata" ) + if not os.path.isfile(json_file): + log.error("json file %s does not exist ", json_file) + stderr.print(f"[red] file {json_file} does not exist") sys.exit(1) + self.json_file = json_file + if input_folder is None: self.input_folder = relecov_tools.utils.prompt_path( msg="Select the input folder" @@ -65,265 +64,109 @@ def __init__( ) else: self.mapping_illumina = mapping_illumina + if not os.path.isfile(self.mapping_illumina): + log.error("%s does not exist", self.mapping_illumina) + stderr.print(f"[red] {self.mapping_illumina} does not exist") + sys.exit(1) config_json = ConfigJson() - relecov_schema = config_json.get_topic_data("json_schemas", "relecov_schema") - relecov_sch_path = os.path.join( - os.path.dirname(os.path.realpath(__file__)), "schema", relecov_schema - ) self.configuration = config_json - - with open(relecov_sch_path, "r") as fh: - self.relecov_sch_json = json.load(fh) - self.schema_name = self.relecov_sch_json["schema"] - self.schema_version = self.relecov_sch_json["version"] - - def bioinfo_parse(self, file_name): - """Fetch the metadata file folder Directory to fetch metadata file - file_name metadata file name - """ - # FUNCTION read_files - """ - Read all the files and create dataframes - """ - - wb_file = openpyxl.load_workbook(file_name, data_only=True) - ws_metadata_lab = wb_file["METADATA_LAB"] - config_json = ConfigJson() - relecov_bioinfo_metadata = config_json.get_configuration( - "relecov_bioinfo_metadata" - ) - c = 0 - self.files_read_bioinfo_metadata = config_json.get_configuration( - "files_read_bioinfo_metadata" + required_files = self.configuration.get_topic_data( + "bioinfo_analysis", "required_file" ) - - mapping_illumina_tab_path = os.path.join( - self.input_folder, self.mapping_illumina - ) - - summary_variants_metrics_path = os.path.join( - self.input_folder, "summary_variants_metrics_mqc.csv" - ) - variants_long_table_path = os.path.join( - self.input_folder, "variants_long_table.csv" - ) - consensus_genome_length_path = os.path.join( - self.input_folder, "consensus_genome_length.csv" - ) - software_versions_path = os.path.join( - self.input_folder, "software_versions.yml" + self.req_files = {} + for key, file in required_files.items(): + f_path = os.path.join(self.input_folder, file) + if not os.path.isfile(f_path): + log.error("File %s does not exist", file) + stderr.print(f"[red]File {file} does not exist") + sys.exit(1) + self.req_files[key] = f_path + + def add_fixed_values(self, j_data): + """include the fixed data defined in configuration""" + f_values = self.configuration.get_topic_data("bioinfo_analysis", "fixed_values") + for row in j_data: + for field, value in f_values.items(): + row[field] = value + return j_data + + def include_data_from_mapping_stats(self, j_data): + """By processing mapping stats file the following information is + included in schema properties: depth_of_coverage_value, lineage_name, + number_of_variants_in_consensus, number_of_variants_with_effect, + per_genome_greater_10x. per_Ns. per_reads_host, per_reads_virus. + per_unmapped, qc_filtered, reference_genome_accession + """ + # position of the aample columns inside mapping file + sample_position = 4 + map_data = relecov_tools.utils.read_csv_file_return_dict( + self.mapping_illumina, ",", sample_position ) - pangolin_versions_path = os.path.join(self.input_folder, "pangolin_version.csv") - self.md5_file_name = config_json.get_configuration("md5_file_name") - md5_info_path = os.path.join( - self.input_folder, - self.md5_file_name, # como hacer esto general para los servicios + mapping_fields = self.configuration.get_topic_data( + "bioinfo_analysis", "mapping_stats" ) - mapping_illumina_tab = pd.read_csv( - mapping_illumina_tab_path, sep=",", encoding="utf-8" - ) - summary_variants_metrics = pd.read_csv( - summary_variants_metrics_path, sep=",", encoding="utf-8" + for row in j_data: + for field, value in mapping_fields.items(): + try: + row[field] = map_data[row["sample_name"]][value] + except KeyError as e: + log.error("Field %s not found in mapping stats", e) + stderr.print(f"[red]Field {e} not found in mapping stats") + sys.exit(1) + return j_data + + def include_software_versions(self, j_data): + """Include versions from the yaml version file""" + version_fields = self.configuration.get_topic_data( + "bioinfo_analysis", "version_mapping" ) - variants_long_table = pd.read_csv( - variants_long_table_path, - sep=",", - encoding="utf-8", - dtype={"SAMPLE": "string"}, - ) - consensus_genome_length = pd.read_csv( - consensus_genome_length_path, header=None, sep="\t", encoding="utf-8" - ) - md5_info = pd.read_csv(md5_info_path, header=None, sep=",", encoding="utf-8") - pangolin_version_table = pd.read_csv( - pangolin_versions_path, header=None, sep="\t", encoding="utf-8" - ) - - with open(software_versions_path) as file: - software_versions = yaml.load(file, Loader=yaml.FullLoader) - - self.mapping_illumina_tab_field_list = config_json.get_configuration( - "mapping_illumina_tab_field_list" + try: + versions = relecov_tools.utils.read_yml_file(self.req_files["versions"]) + except YAMLError as e: + log.error("Unable to process version file return error %s", e) + stderr.print("[red]Unable to process version file") + stderr.print(f" {e}") + sys.exit(1) + for row in j_data: + for field, version_data in version_fields.items(): + for key, value in version_data.items(): + row[field] = versions[key][value] + return j_data + + def collect_info_from_lab_json(self): + """Craeate the list of dictionaries from the data that is on json lab + metadata file. Return j_data that is used to add the rest of the fields + """ + try: + json_lab_data = relecov_tools.utils.read_json_file(self.json_file) + except ValueError: + log.error("%s invalid json file", self.json_file) + stderr.print(f"[red] {self.json_file} invalid json file") + sys.exit(1) + j_data = [] + mapping_fields = self.configuration.get_topic_data( + "bioinfo_analysis", "required_fields_from_lab_json" ) - # FUNCTION fill_bioinfo_dict - """Iterating through each row and each loaded file the values of the bioinfo_dict are filled""" - - bioinfo_list = [] - - for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): - if row[6] is None: - continue - sample_name = row[6] - print(sample_name) - - # fastq_r1 = row[47] - - # fastq_r2 = row[48] - bioinfo_dict = {} - bioinfo_dict["sample_name"] = str(sample_name) - # bioinfo_dict["sequence_file_R1_fastq"] = fastq_r1 - # bioinfo_dict["sequence_file_R2_fastq"] = fastq_r2 - # FUNCTION config_data - """inserting all keys from configuration.json relecov_bioinfo_metadata into bioinfo_dict""" - for key in relecov_bioinfo_metadata.keys(): - bioinfo_dict[key] = relecov_bioinfo_metadata[key] - bioinfo_dict["consensus_sequence_filepath"] = self.input_folder - bioinfo_dict["long_table_path"] = self.input_folder - # FUNCTION mapping_illumina_data - # fields from mapping_illumina.tab - mapping_illumina_tab_sample = mapping_illumina_tab[ - mapping_illumina_tab["sample"].str.contains(bioinfo_dict["sample_name"]) - ] - config_keys = list(self.mapping_illumina_tab_field_list.keys()) - for i in config_keys: - bioinfo_dict[i] = str( - mapping_illumina_tab_sample[ - self.mapping_illumina_tab_field_list[i] - ].values[0] - ) - # FUNCTION summary_metrics_data - # fields from summary_variants_metrics_mqc.csv - bioinfo_dict["number_of_base_pairs_sequenced"] = str( - summary_variants_metrics.loc[ - summary_variants_metrics["Sample"].str.contains( - bioinfo_dict["sample_name"] - ) - ]["# Input reads"].values[0] - * 2 - ) - - bioinfo_dict["ns_per_100_kbp"] = str( - summary_variants_metrics.loc[ - summary_variants_metrics["Sample"].str.contains( - bioinfo_dict["sample_name"] - ) - ]["# Ns per 100kb consensus"].values[0] - ) - - bioinfo_dict["qc_filtered"] = str( - summary_variants_metrics.loc[ - summary_variants_metrics["Sample"].str.contains( - bioinfo_dict["sample_name"] - ) - ]["# Trimmed reads (fastp)"].values[0] - ) - # FUNCTION long_table_data - # fields from variants_long_table.csv - - if os.path.isfile( - self.input_folder + bioinfo_dict["sample_name"] + ".consensus.fa" - ): - chrom = variants_long_table.loc[ - variants_long_table["SAMPLE"].str.contains( - bioinfo_dict["sample_name"] - ) - ]["CHROM"] - bioinfo_dict["reference_genome_accession"] = str(chrom.values[0]) - else: - bioinfo_dict["reference_genome_accession"] = "NC_045512.2" - # FUNCTION genome_length_data - # fields from consensus_genome_length - cons_array = consensus_genome_length.loc[ - consensus_genome_length[0].str.contains(bioinfo_dict["sample_name"]) - ] - if len(cons_array) > 1: - for i in cons_array: - if cons_array.values[i, 1] != 0: - bioinfo_dict["consensus_genome_length"] = str( - cons_array.values[i, 1] - ) - # FUNCTION md5_data - # fields from md5 file - - for i in range(len(md5_info)): - if "-2" in bioinfo_dict["sequence_file_R1_fastq"]: - g = re.match( - str(bioinfo_dict["sequence_file_R1_fastq"][0:8]) + "$", - md5_info[0][i], - ) - elif "-B" in bioinfo_dict["sequence_file_R1_fastq"]: - - g = re.match( - str(bioinfo_dict["sequence_file_R1_fastq"][0:8]) + "$", - md5_info[0][i], - ) - else: - g = re.match(str(bioinfo_dict["sample_name"]) + "$", md5_info[0][i]) - if g is not None: - bioinfo_dict["consensus_sequence_R1_name"] = md5_info[2][i] - bioinfo_dict["consensus_sequence_R2_name"] = md5_info[2][i + 1] - bioinfo_dict["consensus_sequence_R1_md5"] = md5_info[1][i] - bioinfo_dict["consensus_sequence_R2_md5"] = md5_info[1][i + 1] - break - # FUNCTION software_data - # fields from software version file - bioinfo_dict["dehosting_method_software_version"] = str( - software_versions["KRAKEN2_KRAKEN2"]["kraken2"] - ) - bioinfo_dict["variant_calling_software_version"] = str( - software_versions["IVAR_VARIANTS"]["ivar"] - ) - bioinfo_dict["consensus_sequence_software_version"] = str( - software_versions["BCFTOOLS_CONSENSUS"]["bcftools"] - ) - - bioinfo_dict["bioinformatics_protocol_software_version"] = str( - software_versions["Workflow"]["nf-core/viralrecon"] - ) - - bioinfo_dict["preprocessing_software_version"] = str( - software_versions["FASTP"]["fastp"] - ) - bioinfo_dict["mapping_software_version"] = str( - software_versions["BOWTIE2_ALIGN"]["bowtie2"] - ) - - # FUNCTION pangolin_data - # files from pangolin.csv file - - bioinfo_dict["lineage_analysis_software_version"] = str( - pangolin_version_table.loc[ - pangolin_version_table[0].str.contains(bioinfo_dict["sample_name"]) - ].values[0][1] - ) - bioinfo_dict["variant_designation"] = str( - pangolin_version_table.loc[ - pangolin_version_table[0].str.contains(bioinfo_dict["sample_name"]) - ].values[0][2] - ) - - # get the date from pangolin files - string = re.split("(\d+)", self.mapping_illumina)[1] - year, month, day = int(string[:4]), int(string[4:6]), int(string[6:-1]) - x = datetime.datetime(year, month, day) - bioinfo_dict["analysis_date"] = x.strftime("%b %d %Y %H:%M:%S") - - pango_file_path = ( - self.input_folder + bioinfo_dict["sample_name"] + ".pangolin.csv" - ) - if os.path.isfile(pango_file_path): - pango_last_modified = os.path.getctime(pango_file_path) - pango_last_modified_date = datetime.datetime.fromtimestamp( - pango_last_modified - ) - bioinfo_dict["lineage_identification_date"] = str( - pango_last_modified_date - ) - bioinfo_list.append(bioinfo_dict) - # bioinfo_list[str(sample_name)] = bioinfo_dict - c = c + 1 - # adding schema_name and schema_version - bioinfo_dict["schema_name"] = self.schema_name - bioinfo_dict["schema_version"] = self.schema_version - - json_file = "bioinfo_metadata.json" - output_path = os.path.join(self.output_folder, json_file) - - """Create json""" - - with open(output_path, "w", encoding="utf-8") as fh: - fh.write( - json.dumps(bioinfo_list, indent=4, sort_keys=True, ensure_ascii=False) - ) + for row in json_lab_data: + j_data_dict = {} + for lab_field, bio_field in mapping_fields.items(): + j_data_dict[bio_field] = row[lab_field] + j_data.append(j_data_dict) + return j_data + + def create_bioinfo_file(self): + """Create the bioinfodata json with collecting information from lab + metadata json, mapping_stats, and more information from the files + inside input directory + """ + stderr.print("[blue]Reading lab metadata json") + j_data = self.collect_info_from_lab_json() + stderr.print("[blue]Adding fixed values") + j_data = self.add_fixed_values(j_data) + stderr.print("[blue]Adding data from mapping stats") + j_data = self.include_data_from_mapping_stats(j_data) + j_data = self.include_software_versions(j_data) + + return From d47f57c00f11e5147ce94e1d268b53ccc14778db Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 10 Sep 2022 13:46:17 +0200 Subject: [PATCH 0962/1454] new function to read ym files --- relecov_tools/utils.py | 37 ++++++++++++++++++++++++++++++------- 1 file changed, 30 insertions(+), 7 deletions(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index d6a3a9c8..981ce0c8 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -1,6 +1,6 @@ #!/usr/bin/env python """ -Common utility function for relecov_tools package. +Common utility function used for relecov_tools package. """ import os import glob @@ -10,6 +10,7 @@ import questionary import json import openpyxl +import yaml from itertools import islice log = logging.getLogger(__name__) @@ -30,7 +31,11 @@ def file_exists(file_to_check): def read_json_file(j_file): """Read json file.""" with open(j_file, "r") as fh: - data = json.load(fh) + try: + data = json.load(fh) + except (UnicodeDecodeError, ValueError): + raise + return data @@ -62,9 +67,10 @@ def read_excel_file(f_name, sheet_name, heading_row, empty_value=True): return ws_data -def read_csv_file_return_dict(file_name, sep): +def read_csv_file_return_dict(file_name, sep, key_position=None): """Read csv or tsv file, according to separator, and return a dictionary - where the main key is the first column + where the main key is the first column, if key position is None otherwise + the index value of the kwy position is used as key """ with open(file_name, "r") as fh: lines = fh.readlines() @@ -74,12 +80,29 @@ def read_csv_file_return_dict(file_name, sep): file_data = {} for line in lines[1:]: line_s = line.strip().split(sep) - file_data[line_s[0]] = {} - for idx in range(1, len(heading)): - file_data[line_s[0]][heading[idx]] = line_s[idx] + if key_position is None: + file_data[line_s[0]] = {} + for idx in range(1, len(heading)): + file_data[line_s[0]][heading[idx]] = line_s[idx] + else: + file_data[line_s[key_position]] = {} + for idx in range(len(heading)): + if idx == key_position: + continue + file_data[line_s[key_position]][heading[idx]] = line_s[idx] + return file_data +def read_yml_file(file_name): + """Read yml file""" + with open(file_name, "r") as fh: + try: + return yaml.safe_load(fh) + except yaml.YAMLError: + raise + + def get_md5_from_local_folder(local_folder): """Fetch the md5 values for each file in the file list""" md5_results = {} From 155130756afe87610a3b76695ec4da00d6db0283 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 10 Sep 2022 13:48:38 +0200 Subject: [PATCH 0963/1454] removed unnecesary import from bioinfo --- relecov_tools/read_bioinfo_metadata.py | 8 -------- 1 file changed, 8 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 7ebd6252..80d4a739 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -2,15 +2,7 @@ # from itertools import islice import logging -import json -import datetime -import re - import rich.console - -# import pandas as pd - - import os import sys import relecov_tools.utils From a76aa8e8f291c27e7f367b95df2c4471d5d6069b Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 10 Sep 2022 15:34:47 +0200 Subject: [PATCH 0964/1454] fixed bug for nf-core viralrecom --- relecov_tools/conf/configuration.json | 8 +++++++- relecov_tools/read_bioinfo_metadata.py | 2 +- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 84dc2c66..42e6fcb7 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -259,6 +259,7 @@ "reference_genome_accession": "Virussequence" }, "required_fields_from_lab_json": { + "read_length": "number_of_base_paired_sequence", "schema_name": "schema_name", "schema_version": "schema_version", "sequence_file_R1_fastq": "sequence_file_R1_fastq", @@ -268,6 +269,12 @@ "sequencing_sample_id" : "sample_name" }, "version_mapping":{ + "bioinformatics_protocol_software_version":{ + "Workflow": "nf-core/viralrecon" + }, + "consensus_sequence_software_version":{ + "BCFTOOLS_CONSENSUS": "bcftools" + }, "dehosting_method_software_version": { "KRAKEN2_KRAKEN2": "kraken2" }, @@ -280,7 +287,6 @@ "variant_calling_software_version": { "IVAR_VARIANTS": "ivar" } - } }, "files_read_bioinfo_metadata": { diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 80d4a739..a4db823e 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# from itertools import islice import logging import rich.console @@ -159,6 +158,7 @@ def create_bioinfo_file(self): j_data = self.add_fixed_values(j_data) stderr.print("[blue]Adding data from mapping stats") j_data = self.include_data_from_mapping_stats(j_data) + stderr.print("[blue]Adding software versions") j_data = self.include_software_versions(j_data) return From 00b106794981540d38bf1b3c7316f77c9601a56c Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 10 Sep 2022 16:32:58 +0200 Subject: [PATCH 0965/1454] Removed ontology data before sending to iSkyLIMS --- relecov_tools/feed_database.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 2d93896a..bd4c3f1f 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -1,6 +1,7 @@ #!/usr/bin/env python import sys import os +import re import jsonschema import json import logging @@ -108,15 +109,17 @@ def get_schema_ontology_values(self): return ontology_dict def map_iskylims_sample_fields_values(self, sample_fields, s_project_fields): - """Map the values to the properties send to dtabasee + """Map the values to the properties send to databasee in json schema based on label """ sample_list = [] s_fields = list(sample_fields.keys()) for row in self.json_data: s_dict = {} - for key, value in row.items(): + found_ontology = re.search(r"(.+) \[\w+:.*", value) + if found_ontology: + value = found_ontology.group(1) if key in s_project_fields: s_dict[key] = value elif key in s_fields: @@ -301,10 +304,7 @@ def store_data(self): map_fields = self.map_iskylims_sample_fields_values( sample_fields, s_project_fields ) - else: - - # sample_fields, s_project_fields = self.get_iskylims_fields_sample() stderr.print("[blue] Selecting sample fields") map_fields = self.map_relecov_sample_data() post_url = "store_samples" From 04f0725fd88a0081133726183d983ebd2d3e4ec3 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 12 Sep 2022 00:33:42 +0200 Subject: [PATCH 0966/1454] Update read_bioinfo, to take the json as base input. Added fields from mapping, versions.pangolin. missing consensun --- relecov_tools/conf/configuration.json | 37 +++++++++--------- relecov_tools/read_bioinfo_metadata.py | 53 +++++++++++++++++++++++++- relecov_tools/utils.py | 7 +++- 3 files changed, 75 insertions(+), 22 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 42e6fcb7..5844f72a 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -243,9 +243,14 @@ "required_file": { "variants_metrics": "summary_variants_metrics_mqc.csv", "versions": "software_versions.yml", - "pangoling": "pangolin_version.csv" + "pangoling": "pangolin_version.csv", + "variant_metrics": "summary_variants_metrics_mqc.csv" + }, + "mapping_pangolin":{ + "variant_designation": "scorpio_call" }, "mapping_stats": { + "analysis_date": "analysis date", "depth_of_coverage_value": "medianDPcoveragevirus", "lineage_name": "Lineage", "number_of_variants_in_consensus": "Variantsinconsensusx10", @@ -258,17 +263,10 @@ "qc_filtered": "totalreads", "reference_genome_accession": "Virussequence" }, - "required_fields_from_lab_json": { - "read_length": "number_of_base_paired_sequence", - "schema_name": "schema_name", - "schema_version": "schema_version", - "sequence_file_R1_fastq": "sequence_file_R1_fastq", - "sequence_file_R2_fastq": "sequence_file_R2_fastq", - "sequence_file_R1_md5": "sequence_file_R1_md5", - "sequence_file_R2_md5" : "sequence_file_R2_md5", - "sequencing_sample_id" : "sample_name" + "mapping_variant_metrics": { + "ns_per_100_kbp": "# Ns per 100kb consensus" }, - "version_mapping":{ + "mapping_version":{ "bioinformatics_protocol_software_version":{ "Workflow": "nf-core/viralrecon" }, @@ -287,15 +285,18 @@ "variant_calling_software_version": { "IVAR_VARIANTS": "ivar" } + }, + "required_fields_from_lab_json": { + "read_length": "number_of_base_paired_sequence", + "schema_name": "schema_name", + "schema_version": "schema_version", + "sequence_file_R1_fastq": "sequence_file_R1_fastq", + "sequence_file_R2_fastq": "sequence_file_R2_fastq", + "sequence_file_R1_md5": "sequence_file_R1_md5", + "sequence_file_R2_md5" : "sequence_file_R2_md5", + "sequencing_sample_id" : "sample_name" } }, - "files_read_bioinfo_metadata": { - "mapping_illumina.tab": "mapping_illumina_tab_path", - "summary_variants_metrics_mqc.csv": "summary_variants_metrics_path ", - "variants_long_table.csv": "variants_long_table_path", - "consensus_genome_length.csv": "consensus_genome_length_path", - "software_versions.yml": "software_versions_path" - }, "md5_file_name": "md5_check_file.csv", "ENA_fields": { "ENA_configuration": { diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index a4db823e..50ba8801 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -108,10 +108,46 @@ def include_data_from_mapping_stats(self, j_data): sys.exit(1) return j_data + def include_pangolin_data(self, j_data): + """Include pangolin data collecting form each file generated by pangolin + """ + mapping_fields = self.configuration.get_topic_data("bioinfo_analysis", "mapping_pangolin") + for row in j_data: + f_name = row["sample_name"] + ".pangolin." + row["analysis_date"] + ".csv" + f_path = os.path.join(self.input_folder, f_name) + try: + f_data = relecov_tools.utils.read_csv_file_return_dict(f_path, ",") + except FileNotFoundError as e: + log.error("File %s not found ", e) + stderr.print(f"[red]File {e} not found") + sys.exit(1) + pang_key = list(f_data.keys())[0] + for field, value in mapping_fields.items(): + row[field] = f_data[pang_key][value] + + return j_data + + def include_variant_metrics(self, j_data): + """Include the # Ns per 100kb consensus from the summary variant + metric file_exists + """ + map_data = relecov_tools.utils.read_csv_file_return_dict( + self.req_files["variant_metrics"], ",") + mapping_fields = self.configuration.get_topic_data("bioinfo_analysis", "mapping_variant_metrics") + for row in j_data: + for field, value in mapping_fields.items(): + try: + row[field] = map_data[row["sample_name"]][value] + except KeyError as e: + log.error("Field %s not found in mapping stats", e) + stderr.print(f"[red]Field {e} not found in mapping stats") + sys.exit(1) + return j_data + def include_software_versions(self, j_data): """Include versions from the yaml version file""" version_fields = self.configuration.get_topic_data( - "bioinfo_analysis", "version_mapping" + "bioinfo_analysis", "mapping_version" ) try: versions = relecov_tools.utils.read_yml_file(self.req_files["versions"]) @@ -160,5 +196,18 @@ def create_bioinfo_file(self): j_data = self.include_data_from_mapping_stats(j_data) stderr.print("[blue]Adding software versions") j_data = self.include_software_versions(j_data) + stderr.print("[blue]Adding summary variant metrics") + j_data = self.include_variant_metrics(j_data) + stderr.print("[blue]Adding pangolin informtion") + j_data = self.include_pangolin_data(j_data) - return + file_name = ( + "bioinfo_" + + os.path.splitext(os.path.basename(self.json_file))[0] + + ".json" + ) + stderr.print("[blue]Writting output json file") + os.makedirs(self.output_folder, exist_ok=True) + file_path = os.path.join(self.output_folder, file_name) + relecov_tools.utils.write_json_fo_file(j_data, file_path) + return True diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 981ce0c8..489ab73e 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -72,8 +72,11 @@ def read_csv_file_return_dict(file_name, sep, key_position=None): where the main key is the first column, if key position is None otherwise the index value of the kwy position is used as key """ - with open(file_name, "r") as fh: - lines = fh.readlines() + try: + with open(file_name, "r") as fh: + lines = fh.readlines() + except FileNotFoundError: + raise heading = lines[0].strip().split(sep) if len(heading) == 1: return {"ERROR": "not valid format"} From fa008cbbe13546155584ebec0bf8affa6b08905f Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 12 Sep 2022 00:37:21 +0200 Subject: [PATCH 0967/1454] Update read_bioinfo, to take the json as base input. Added fields from mapping, versions.pangolin. missing consensun --- relecov_tools/read_bioinfo_metadata.py | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 50ba8801..e0b59217 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -109,9 +109,10 @@ def include_data_from_mapping_stats(self, j_data): return j_data def include_pangolin_data(self, j_data): - """Include pangolin data collecting form each file generated by pangolin - """ - mapping_fields = self.configuration.get_topic_data("bioinfo_analysis", "mapping_pangolin") + """Include pangolin data collecting form each file generated by pangolin""" + mapping_fields = self.configuration.get_topic_data( + "bioinfo_analysis", "mapping_pangolin" + ) for row in j_data: f_name = row["sample_name"] + ".pangolin." + row["analysis_date"] + ".csv" f_path = os.path.join(self.input_folder, f_name) @@ -132,8 +133,11 @@ def include_variant_metrics(self, j_data): metric file_exists """ map_data = relecov_tools.utils.read_csv_file_return_dict( - self.req_files["variant_metrics"], ",") - mapping_fields = self.configuration.get_topic_data("bioinfo_analysis", "mapping_variant_metrics") + self.req_files["variant_metrics"], "," + ) + mapping_fields = self.configuration.get_topic_data( + "bioinfo_analysis", "mapping_variant_metrics" + ) for row in j_data: for field, value in mapping_fields.items(): try: @@ -202,9 +206,7 @@ def create_bioinfo_file(self): j_data = self.include_pangolin_data(j_data) file_name = ( - "bioinfo_" - + os.path.splitext(os.path.basename(self.json_file))[0] - + ".json" + "bioinfo_" + os.path.splitext(os.path.basename(self.json_file))[0] + ".json" ) stderr.print("[blue]Writting output json file") os.makedirs(self.output_folder, exist_ok=True) From 221b9bd17f5bec269a5fbfd6e251828bc137b896 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 12 Sep 2022 13:50:38 +0200 Subject: [PATCH 0968/1454] added consensus information --- relecov_tools/conf/configuration.json | 7 ++++ relecov_tools/read_bioinfo_metadata.py | 46 ++++++++++++++++++++++++-- relecov_tools/utils.py | 11 +++++- 3 files changed, 61 insertions(+), 3 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 5844f72a..3964e527 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -246,6 +246,13 @@ "pangoling": "pangolin_version.csv", "variant_metrics": "summary_variants_metrics_mqc.csv" }, + "mapping_consensus": [ + "consensus_genome_length", + "consensus_sequence_filename", + "consensus_sequence_filepath", + "consensus_sequence_md5", + "consensus_sequence_name" + ], "mapping_pangolin":{ "variant_designation": "scorpio_call" }, diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index e0b59217..27b7bccd 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -114,20 +114,60 @@ def include_pangolin_data(self, j_data): "bioinfo_analysis", "mapping_pangolin" ) for row in j_data: - f_name = row["sample_name"] + ".pangolin." + row["analysis_date"] + ".csv" + if "-" in row["sample_name"]: + sample_name = row["sample_name"].replace("-", "_") + else: + sample_name = row["sample_name"] + f_name = sample_name + ".pangolin." + row["analysis_date"] + ".csv" f_path = os.path.join(self.input_folder, f_name) try: f_data = relecov_tools.utils.read_csv_file_return_dict(f_path, ",") except FileNotFoundError as e: log.error("File %s not found ", e) stderr.print(f"[red]File {e} not found") - sys.exit(1) + # When file does not exist set all values to empty + for field, value in mapping_fields.items(): + row[field] = "" + continue + # sys.exit(1) pang_key = list(f_data.keys())[0] for field, value in mapping_fields.items(): row[field] = f_data[pang_key][value] return j_data + def include_consensus_data(self, j_data): + """Include genome length, name, file name, path and md5 by preprocessing + each file of consensus.fa + """ + + mapping_fields = self.configuration.get_topic_data( + "bioinfo_analysis", "mapping_consensus" + ) + for row in j_data: + if "-" in row["sample_name"]: + sample_name = row["sample_name"].replace("-", "_") + else: + sample_name = row["sample_name"] + f_name = sample_name + ".consensus.fa" + f_path = os.path.join(self.input_folder, f_name) + try: + record_fasta = relecov_tools.utils.read_fasta_return_SeqIO_instance( + f_path + ) + except FileNotFoundError as e: + log.error("File %s not found ", e) + stderr.print(f"[red]File {e} not found") + for item in mapping_fields: + row[item] = "" + continue + row["consensus_geneme_length"] = str(len(record_fasta)) + row["consensus_sequence_name"] = record_fasta.description + row["consensus_sequence_filepath"] = self.input_folder + row["consensus_file_name"] = f_name + row["consensus_sequence_md5"] = relecov_tools.utils.calculate_md5(f_path) + return j_data + def include_variant_metrics(self, j_data): """Include the # Ns per 100kb consensus from the summary variant metric file_exists @@ -204,6 +244,8 @@ def create_bioinfo_file(self): j_data = self.include_variant_metrics(j_data) stderr.print("[blue]Adding pangolin informtion") j_data = self.include_pangolin_data(j_data) + stderr.print("[blue]Adding consensus data") + j_data = self.include_consensus_data(j_data) file_name = ( "bioinfo_" + os.path.splitext(os.path.basename(self.json_file))[0] + ".json" diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 489ab73e..c68538c8 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -6,12 +6,13 @@ import glob import hashlib import logging -from rich.console import Console import questionary import json import openpyxl import yaml from itertools import islice +from Bio import SeqIO +from rich.console import Console log = logging.getLogger(__name__) @@ -97,6 +98,14 @@ def read_csv_file_return_dict(file_name, sep, key_position=None): return file_data +def read_fasta_return_SeqIO_instance(file_name): + """Read fasta and return SeqIO instance""" + try: + return SeqIO.read(file_name, "fasta") + except FileNotFoundError: + raise + + def read_yml_file(file_name): """Read yml file""" with open(file_name, "r") as fh: From a10586a145f4ffbd1fa197a0425e96f165d3c2f7 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 12 Sep 2022 15:20:27 +0200 Subject: [PATCH 0969/1454] changes in schemas --- relecov_tools/gisaid_upload.py | 1 + relecov_tools/schema/ena_schema.json | 190 +++++++++++++++++++---- relecov_tools/schema/relecov_schema.json | 132 +++++++++++++++- 3 files changed, 286 insertions(+), 37 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 406f10ef..8b60876b 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -11,6 +11,7 @@ from Bio import SeqIO from relecov_tools.config_json import ConfigJson +# # import site diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index d38873de..cad48375 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -2,11 +2,11 @@ "schema": "ENA", "required": [ "sample_name", - "collecting_institution", - "geographic_location_(country_and/or_sea)", + "collecting institution", + "geographic location (country and/or sea)", "isolate", - "host_scientific_name", - "host_common_name", + "host scientific name", + "host common name", "instrument_model", "taxon_id", "scientific_name", @@ -38,21 +38,35 @@ "experiments" ] }, - "collecting_institution": { + "virus identifier": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001123", + "type": "string", + "description": "Unique laboratory identifier assigned to the virus by the investigator. Strain name is not sufficient since it might not be unique due to various passsages of the same virus. Format: up to 50 alphanumeric characters", + "clasification": "Database Identifiers", + "label": "Sample ID given by originating laboratory", + "table": [ + "sample", + "experiments" + ] + }, + "collecting institution": { "examples": [ "Public Health Agency of Canada" ], - "ontology": "GENEPIO:0001153", + "ontology": "GENEPIO:0001797", "type": "string", "description": "Name of the institution to which the person collecting the specimen belongs. Format: Institute Name, Institute Address", "label": "Originating Laboratory", "table": "sample" }, - "collector_name": { + "collector name": { "examples": [ "John Smith" ], - "ontology": "GENEPIO:0001153", + "ontology": "GENEPIO:0001797", "type": "string", "description": "Name of the person who collected the specimen", "clasification": "Sample collection and processing", @@ -89,17 +103,7 @@ "clasification": "", "label": "Sample ID given if multiple rna-extraction or passages" }, - "subject_exposure_duration": { - "examples": [ - "" - ], - "ontology": "NCIT:C83280", - "type": "string", - "description": "", - "clasification": "", - "label": "Additional Host Information" - }, - "collection_date": { + "collection date": { "examples": [ "3/19/2020" ], @@ -111,11 +115,11 @@ "label": "Sample Collection Date", "table": "sample" }, - "receipt_date": { + "receipt date": { "examples": [ "3/21/2020" ], - "ontology": "GENEPIO:0001179", + "ontology": "NCIT:C93644", "type": "string", "description": "The date on which the sample was received.", "format": "date", @@ -425,7 +429,7 @@ "table": "sample" }, "geographic location (region and locality)": { - "ontology": "GENEPIO:0100280", + "ontology": "NCIT:C87189", "type": "string", "description": "The county/region of origin of the sample.", "examples": [ @@ -466,7 +470,7 @@ "label": "Sample ID given by originating laboratory", "table": "sample" }, - "purpose_sampling": { + "sample capture status": { "examples": [ "Diagnostic testing" ], @@ -482,7 +486,7 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "NCIT_C146997", + "ontology": "GENEPIO:0001198", "type": "string", "description": "The reason that the sample was collected.", "clasification": "Sample collection and processing" @@ -563,7 +567,7 @@ "clasification": "Sample collection and processing", "label": "Environmental Material" }, - "host_common_name": { + "host common name": { "Enums": [ "Human [NCBITaxon:9606]", "Bat [NCBITaxon:9397]", @@ -594,7 +598,7 @@ "label": "Host Common Name", "table": "sample" }, - "host_scientific_name": { + "host scientific name": { "Enums": [ "Bos taurus [NCBITaxon:9913]", "Canis lupus familiaris [NCBITaxon:9615]", @@ -630,7 +634,7 @@ "runs" ] }, - "host_subject_id": { + "host subject id": { "examples": [ "e.g. #131" ], @@ -643,7 +647,109 @@ "sample" ] }, - "host_health_state": { + "definition for seropositive sample": { + "examples": [ + "" + ], + "ontology": "NCIT:C159692", + "type": "string", + "description": " The cut off value used by an investigatior in determining that a sample was seropositive.", + "clasification": "Sample collection and processing", + "label": "Definition for seropositive sample", + "table": [ + "sample" + ] + }, + "serotype (required for a seropositive sample)": { + "examples": [ + "h1n1" + ], + "ontology": "NCIT:C88894", + "type": "string", + "description": " erological variety of a species characterised by its antigenic properties. For influenza, ha subtype should be the letter h followed by a number between 1-16 unless novel subtype is identified and the na subtype should be the letter n followed by a number between 1-9 unless novel subtype is identified. If only one of the subtypes have been tested then use the format h5nx or hxn1.", + "clasification": "Sample collection and processing", + "label": "Serotype (required for a seropositive sample)", + "table": [ + "sample" + ] + }, + "host habitat": { + "examples": [ + "" + ], + "ontology": "ENVO:00002036", + "type": "string", + "description": "Natural habitat of the avian or mammalian host.", + "clasification": "Sample collection and processing", + "label": "Host habitat", + "table": [ + "sample" + ] + }, + "host description": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0000009", + "type": "string", + "description": "Other descriptive information relating to the host.", + "clasification": "Host information", + "label": "Host description", + "table": [ + "sample" + ] + }, + "gravidity": { + "examples": [ + "" + ], + "ontology": "OMIT:0020000", + "type": "string", + "description": "Whether or not the subject is gravid. If so, report date due or date post-conception and specify which of these two dates is being reported.", + "clasification": "Host information", + "label": "Gravidity", + "table": [ + "sample" + ] + }, + "strain": { + "examples": [ + "" + ], + "ontology": "NCIT:C14419", + "type": "string", + "description": "Name of the strain from which the sample was obtained..", + "clasification": "Sample collection and processing", + "label": "Strain", + "table": [ + "sample" + ] + }, + "host_age": { + "ontology": "GENEPIO:0001392", + "type": "string", + "description": "Age of host at the time of sampling.", + "examples": [ + "79" + ], + "classification": "Host information", + "label": "Host Age", + "fill_mode": "sample" + }, + "host disease outcome": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001390", + "type": "string", + "description": "Disease outcome in the host.", + "clasification": "Host information", + "label": "Host disease outcome", + "table": [ + "sample" + ] + }, + "host health state": { "examples": [ "" ], @@ -682,7 +788,7 @@ "sample" ] }, - "host_sex": { + "host sex": { "Enums": [ "Female [NCIT:C46110]", "Male [NCIT:C46109]", @@ -924,9 +1030,29 @@ "clasification": "Sample collection and processing", "label": "Common name" }, + "hospitalisation": { + "examples": [], + "ontology": "NCIT:C25179", + "type": "string", + "description": " Was the subject confined to a hospital as a result of virus infection or problems occurring secondary to virus infection?", + "clasification": "Sample collection and processing", + "label": "Hospitalisation", + "table": "sample" + }, + "illness symptoms": { + "examples": [ + "cough, diarrhea, fever, headache, malaise, myalgia" + ], + "ontology": "GENEPIO:00015f23", + "type": "string", + "description": "The symptoms that have been reported in relation to the illness. If multiple exposures are applicable, please state them separated by semicolon.", + "clasification": "Sample collection and processing", + "label": "Illness symptoms", + "table": "sample" + }, "sample_description": { "examples": [ - "" + "Sample from Belgian Covid-19 patient. Sample was obtained at the Hospital AZ Rivierenland, in Antwerp, Belgium." ], "ontology": "sep:00196", "type": "string", @@ -935,7 +1061,7 @@ "label": "Sample Description", "table": "sample" }, - "sample_storage_conditions": { + "sample storage conditions": { "examples": [ "24 degrees celsius" ], @@ -1297,7 +1423,7 @@ "examples": [ "" ], - "ontology": "0", + "ontology": "NCIT:C93415", "type": "string", "description": "", "clasification": "Submission ENA", diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 3df576ae..a830b882 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -44,7 +44,7 @@ "examples": [ "Public Health Agency of Canada" ], - "ontology": "GENEPIO:0001153", + "ontology": "GENEPIO:0001797", "type": "string", "description": "The name of the agency/institution that collected the sample.", "classification": "Sample collection and processing", @@ -110,6 +110,37 @@ "fill_mode": "sample", "minLenght": "1" }, + "sample_description": { + "examples": [ + "Sample from Belgian Covid-19 patient. Sample was obtained at the Hospital AZ Rivierenland, in Antwerp, Belgium." + ], + "ontology": "sep:00196", + "type": "string", + "description": "Free text description of the sample.", + "clasification": "Sample collection and processing", + "label": "Sample Description", + "table": "sample" + }, + "illness_symptoms": { + "examples": [ + "cough, diarrhea, fever, headache, malaise, myalgia" + ], + "ontology": "GENEPIO:0001523", + "type": "string", + "description": "The symptoms that have been reported in relation to the illness. If multiple exposures are applicable, please state them separated by semicolon.", + "clasification": "Sample collection and processing", + "label": "Illness symptoms", + "table": "sample" + }, + "hospitalisation": { + "examples": [], + "ontology": "NCIT:C25179", + "type": "string", + "description": " Was the subject confined to a hospital as a result of virus infection or problems occurring secondary to virus infection?", + "clasification": "Sample collection and processing", + "label": "Hospitalisation", + "table": "sample" + }, "submitting_lab_sample_id": { "examples": [ "" @@ -173,7 +204,7 @@ "examples": [ "3/21/2020" ], - "ontology": "GENEPIO:0001179", + "ontology": "NCIT:C93644", "type": "string", "description": "The date on which the sample was received.", "format": "date", @@ -181,6 +212,58 @@ "label": "Sample Received Date", "fill_mode": "sample" }, + "definition for seropositive sample": { + "examples": [ + "" + ], + "ontology": "NCIT:C159692", + "type": "string", + "description": " The cut off value used by an investigatior in determining that a sample was seropositive.", + "clasification": "Sample collection and processing", + "label": "Definition for seropositive sample", + "table": [ + "sample" + ] + }, + "serotype (required for a seropositive sample)": { + "examples": [ + "h1n1" + ], + "ontology": "NCIT:C88894", + "type": "string", + "description": " erological variety of a species characterised by its antigenic properties. For influenza, ha subtype should be the letter h followed by a number between 1-16 unless novel subtype is identified and the na subtype should be the letter n followed by a number between 1-9 unless novel subtype is identified. If only one of the subtypes have been tested then use the format h5nx or hxn1.", + "clasification": "Sample collection and processing", + "label": "Serotype (required for a seropositive sample)", + "table": [ + "sample" + ] + }, + "strain": { + "examples": [ + "" + ], + "ontology": "NCIT:C14419", + "type": "string", + "description": "Name of the strain from which the sample was obtained..", + "clasification": "Sample collection and processing", + "label": "Strain", + "table": [ + "sample" + ] + }, + "host habitat": { + "examples": [ + "" + ], + "ontology": "ENVO:00002036", + "type": "string", + "description": "Natural habitat of the avian or mammalian host.", + "clasification": "Sample collection and processing", + "label": "Host habitat", + "table": [ + "sample" + ] + }, "sample_storage_conditions": { "examples": [ "24 degrees celsius" @@ -498,8 +581,8 @@ "examples": [ "Derbyshire" ], - "ontology": "GENEPIO:0100280", - "type": "string", + "ontology": "NCIT:C87189", + "type": "s tring", "description": "The county/region of origin of the sample.", "classification": "Sample collection and processing", "label": "Province", @@ -527,6 +610,19 @@ "label": "Geo Loc Latitude", "fill_mode": "batch" }, + "gravidity": { + "examples": [ + "" + ], + "ontology": "OBI:0002456", + "type": "string", + "description": "Whether or not the subject is gravid. If so, report date due or date post-conception and specify which of these two dates is being reported.", + "clasification": "Host information", + "label": "Gravidity", + "table": [ + "sample" + ] + }, "geo_loc_longitude": { "examples": [ "77.11 W" @@ -551,7 +647,7 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "NCIT_C146997", + "ontology": "GENEPIO:0001198", "type": "string", "description": "The reason that the sample was collected.", "examples": [ @@ -561,6 +657,32 @@ "label": "Purpose of sampling", "fill_mode": "batch" }, + "host disease outcome": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001390", + "type": "string", + "description": "Disease outcome in the host.", + "clasification": "Host information", + "label": "Host disease outcome", + "table": [ + "sample" + ] + }, + "host description": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0000009", + "type": "string", + "description": "Other descriptive information relating to the host.", + "clasification": "Host information", + "label": "Host description", + "table": [ + "sample" + ] + }, "anatomical_material": { "enum": [ "Blood [UBERON:0000178]", From 12f580df0f0a1f1a2129a9caf0f2f08cb5105d4e Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 12 Sep 2022 15:56:27 +0200 Subject: [PATCH 0970/1454] latest changes in schema --- relecov_tools/schema/ena_schema.json | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index cad48375..9ee5c31b 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -1138,7 +1138,7 @@ "examples": [ "library_construction_protocol_1" ], - "ontology": "0", + "ontology": "NCIT:C41111", "type": "string", "description": "", "clasification": "Sequencing", @@ -1214,7 +1214,7 @@ "type": "string", "description": "", "clasification": "Sequencing", - "label": "Nominal Length" + "label": "Insert size" }, "analysis_accession": { "examples": [ @@ -1472,6 +1472,19 @@ "experiments" ] }, + "file_format": { + "examples": [ + "BAM,CRAM,FASTQ" + ], + "ontology": "NMR:1001459", + "type": "string", + "description": "The run data file model.", + "clasification": "Submission ENA", + "label": "File format", + "table": [ + "experiments" + ] + }, "run_alias": { "examples": [ "e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1" From d124d06899b72fa9e1a3597818c28b98e258ceea Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 12 Sep 2022 16:36:03 +0200 Subject: [PATCH 0971/1454] fix ENA schema --- relecov_tools/schema/ena_schema.json | 421 +-------------------------- 1 file changed, 4 insertions(+), 417 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 9ee5c31b..c17ddc2e 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -1,7 +1,7 @@ { "schema": "ENA", "required": [ - "sample_name", + "sample_title", "collecting institution", "geographic location (country and/or sea)", "isolate", @@ -16,6 +16,7 @@ "library_selection", "library_strategy", "library_layout", + "sample_alias", "study_alias", "experiment_alias", "run_alias", @@ -24,20 +25,6 @@ ], "type": "object", "properties": { - "sample_name": { - "examples": [ - "prov_rona_99" - ], - "ontology": "GENEPIO:0001123", - "type": "string", - "description": "The user-defined name for the sample.", - "clasification": "Database Identifiers", - "label": "Sample ID given by originating laboratory", - "table": [ - "sample", - "experiments" - ] - }, "virus identifier": { "examples": [ "" @@ -73,36 +60,6 @@ "label": "Sample collector name", "table": "sample" }, - "public_health_sample_id_sivies": { - "examples": [ - "2022CEU03926" - ], - "ontology": "0", - "type": "string", - "description": "", - "clasification": "Sample collection and processing", - "label": "Public Health sample id (SIVIES)" - }, - "microbiology_lab_sample_id": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "clasification": "Sample collection and processing", - "label": "Sample ID given in the microbiology lab" - }, - "isolate_sample_id": { - "examples": [ - "" - ], - "ontology": "NCIT:C53471", - "type": "string", - "description": "", - "clasification": "", - "label": "Sample ID given if multiple rna-extraction or passages" - }, "collection date": { "examples": [ "3/19/2020" @@ -762,7 +719,7 @@ "sample" ] }, - "type_exposure": { + "type exposure": { "examples": [ "" ], @@ -813,16 +770,6 @@ "sample" ] }, - "type exposure": { - "examples": [ - "Date, Location e.g. type of gathering, Family cluster, etc." - ], - "ontology": "GENEPIO:0001417", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification": "Host information", - "label": "Outbreak Exposure Event Location" - }, "subject exposure duration": { "examples": [ "e.g. Patient infected while traveling in …." @@ -960,19 +907,6 @@ "clasification": "Bioinformatics and QC metrics", "label": "Filepath R2 fastq" }, - "file_type": { - "examples": [ - "fastq" - ], - "ontology": "0", - "type": "string", - "description": "", - "clasification": "Bioinformatics and QC metrics", - "label": "file type", - "table": [ - "runs" - ] - }, "fastq_md5_r2": { "examples": [ "3e69af1f875fab020aed82f5edbc1f03" @@ -986,19 +920,6 @@ "runs" ] }, - "taxon_id": { - "examples": [ - "probably 2697049 in all cases" - ], - "ontology": "NCIT:C164641", - "type": "string", - "description": "The NCBITaxon identifier for the organism being sequenced.", - "clasification": "Sample collection and processing", - "label": "Tax ID", - "table": [ - "sample" - ] - }, "scientific_name": { "Enums": [ "Coronaviridae [NCBITaxon:11118]", @@ -1020,16 +941,6 @@ "label": "Organism", "table": "sample" }, - "common_name": { - "examples": [ - "" - ], - "ontology": "NCIT:C164471", - "type": "string", - "description": "The common name of the organism.", - "clasification": "Sample collection and processing", - "label": "Common name" - }, "hospitalisation": { "examples": [], "ontology": "NCIT:C25179", @@ -1206,7 +1117,7 @@ "experiments" ] }, - "nominal_length ": { + "insert_size": { "examples": [ "350" ], @@ -1216,146 +1127,6 @@ "clasification": "Sequencing", "label": "Insert size" }, - "analysis_accession": { - "examples": [ - "" - ], - "ontology": "GENEPIO_0001145", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Analysis Accession" - }, - "read_length": { - "examples": [ - "" - ], - "ontology": "GENEPIO_0000076", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Read length" - }, - "study_accession": { - "examples": [ - "e.g PRJEB39632" - ], - "ontology": "GENEPIO_0001136", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Study accession" - }, - "secondary_study_accession": { - "examples": [ - "e.g ERP123173" - ], - "ontology": "BU_ISCIII:012", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Secondary study accession" - }, - "sample_accession": { - "examples": [ - "e.g SAMEA7098096" - ], - "ontology": "GENEPIO_0001139", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Sample accession" - }, - "secondary_sample_accession": { - "examples": [ - "e.g ERS4858671" - ], - "ontology": "BU_ISCIII:014", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Secondary sample accession" - }, - "experiment_accession": { - "examples": [ - "e.g ERX4331406" - ], - "ontology": "BU_ISCIII:015", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Experiment Accession" - }, - "run_accession": { - "examples": [ - "e.g ERX4331406" - ], - "ontology": "BU_ISCIII:016", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Run Accession" - }, - "submission_accession": { - "examples": [ - "e.g ERA2794974" - ], - "ontology": "BU_ISCIII:017", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Submission accession" - }, - "read_count": { - "examples": [ - "e.g 837055" - ], - "ontology": "STATO_0000064", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Read count" - }, - "base_count": { - "examples": [ - "e.g 503907110" - ], - "ontology": "UO_0000244", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Base count" - }, - "center_name": { - "examples": [ - " KAROLINSKA INSITUTET" - ], - "ontology": "NCIT_C19983", - "type": "string", - "description": "The name of the institution", - "clasification": "Sample collection and processing", - "label": "Center Name" - }, - "first_public_date": { - "examples": [ - "e.g 2020-08-07" - ], - "ontology": "NCIT_C142711", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "First Public date" - }, - "last_updated": { - "examples": [ - "e.g 2020-07-29" - ], - "ontology": "OMIABIS_0001005", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Last Updated" - }, "experiment_title": { "examples": [ "experiment_title_1" @@ -1406,19 +1177,6 @@ "label": "Study type", "table": "study" }, - "pubmed_id": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "pubmed id", - "table": [ - "study" - ] - }, "study_abstract": { "examples": [ "" @@ -1498,16 +1256,6 @@ "runs" ] }, - "fastq_bytes": { - "examples": [ - "e.g ena-RUN-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1" - ], - "ontology": "NCIT_C48047", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Fastq bytes" - }, "fastq_md5_r1": { "examples": [ "" @@ -1518,146 +1266,6 @@ "clasification": "Submission ENA", "label": "Fastq md5 r1" }, - "fastq_ftp": { - "examples": [ - "" - ], - "ontology": "PRIDE_0000469", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Fastq ftp" - }, - "fastq_aspera": { - "examples": [ - "e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz" - ], - "ontology": "BU_ISCIII:032", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Fastq aspera" - }, - "fastq_galaxy": { - "examples": [ - "e.g fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz" - ], - "ontology": "ENVO_01000807", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Fastq galaxy" - }, - "submitted_bytes": { - "examples": [ - "e.g ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/005/ERR4387385/ERR4387385_2.fastq.gz" - ], - "ontology": "NCIT_C172872", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Submitted bytes " - }, - "submitted_md5": { - "examples": [ - "e.g 139853010;166270048" - ], - "ontology": "BU_ISCIII:035", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Submitted md5" - }, - "submitted_ftp": { - "examples": [ - "e.g d726a9abc918e2b43bd68b24c7d01b3a;f01eba1b2bad974bdf61b81b1ae8ac2a" - ], - "ontology": "BU_ISCIII:036", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Submitted ftp" - }, - "submitted_aspera": { - "examples": [ - "e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz" - ], - "ontology": "BU_ISCIII:037", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Submitted aspera" - }, - "submitted_galaxy": { - "examples": [ - "e.g fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz" - ], - "ontology": "BU_ISCIII:038", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Submitted Galaxy" - }, - "submitted_format": { - "examples": [ - "e.g ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R1_001.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR438/ERR4387385/P17157_1007_S7_L001_R2_001.fastq.gz" - ], - "ontology": "BU_ISCIII:039", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Submitted Format" - }, - "sra_bytes": { - "examples": [ - "e.g FASTQ;FASTQ" - ], - "ontology": "BU_ISCIII:040", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "SRA bytes" - }, - "sra_md5": { - "examples": [ - "e.g 260236789" - ], - "ontology": "BU_ISCIII:041", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "SRA md5" - }, - "sra_ftp": { - "examples": [ - "e.g 2cf0d467d6dc4ae0a5473774d54c059c" - ], - "ontology": "BU_ISCIII:042", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "SRA ftp" - }, - "sra_aspera": { - "examples": [ - "e.g ftp.sra.ebi.ac.uk/vol1/err/ERR438/005/ERR4387385" - ], - "ontology": "BU_ISCIII:043", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "SRA aspera" - }, - "sra_galaxy": { - "examples": [ - "e.g fasp.sra.ebi.ac.uk:/vol1/err/ERR438/005/ERR4387385" - ], - "ontology": "BU_ISCIII:044", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "SRA galaxy" - }, "broker_name": { "examples": [ "P17157_1007" @@ -1667,27 +1275,6 @@ "description": "", "clasification": "Submission ENA", "label": "Broker Name" - }, - "nominal_sdev": { - "examples": [ - "" - ], - "ontology": "STATO_0000237", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Nominal sdev" - }, - "first_created_date": { - "examples": [ - "e.g 2020-08-07" - ], - "ontology": "NCIT_C164483", - "type": "string", - "format": "date", - "description": "", - "clasification": "Submission ENA", - "label": "First created date" } } } \ No newline at end of file From 2e46ba020e66f96f301eef4a407d3fbc184e0c4f Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 12 Sep 2022 16:46:17 +0200 Subject: [PATCH 0972/1454] mandatory fileds ena --- relecov_tools/schema/ena_schema.json | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index c17ddc2e..51f9c31f 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -5,12 +5,15 @@ "collecting institution", "geographic location (country and/or sea)", "isolate", + "collector name", "host scientific name", "host common name", "instrument_model", - "taxon_id", + "host subject id", + "host health state", + "host sex", + "host scientific name", "scientific_name", - "common_name", "sample_description", "library_source", "library_selection", @@ -21,7 +24,11 @@ "experiment_alias", "run_alias", "experiment_title", - "study_title" + "study_title", + "study_type", + "platform", + "file_format", + "file_name" ], "type": "object", "properties": { From b6919136462c53ae03fe576ef7823fb6b50cb65f Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 12 Sep 2022 17:02:18 +0200 Subject: [PATCH 0973/1454] added calculations for number_of bases --- relecov_tools/conf/configuration.json | 3 ++- relecov_tools/read_bioinfo_metadata.py | 6 ++++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 3964e527..625c7082 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -251,7 +251,8 @@ "consensus_sequence_filename", "consensus_sequence_filepath", "consensus_sequence_md5", - "consensus_sequence_name" + "consensus_sequence_name", + "number_of_base_pairs_sequenced" ], "mapping_pangolin":{ "variant_designation": "scorpio_call" diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 27b7bccd..42ebc469 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -166,6 +166,12 @@ def include_consensus_data(self, j_data): row["consensus_sequence_filepath"] = self.input_folder row["consensus_file_name"] = f_name row["consensus_sequence_md5"] = relecov_tools.utils.calculate_md5(f_path) + base_calculation = int(row["number_of_base_pairs_sequenced"]) * len(record_fasta) + if row["sequence_file_R2_fastq"] != "": + row["number_of_base_pairs_sequenced"] = str(base_calculation * 2) + else: + row["number_of_base_pairs_sequenced"] = str(base_calculation) + return j_data def include_variant_metrics(self, j_data): From 04fa7ea8082614133eb5d28c956e2555f43b08a9 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 12 Sep 2022 17:24:35 +0200 Subject: [PATCH 0974/1454] added long table path --- relecov_tools/read_bioinfo_metadata.py | 18 +++++++++++++++++- relecov_tools/utils.py | 5 +++++ 2 files changed, 22 insertions(+), 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 42ebc469..367f454f 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -174,6 +174,20 @@ def include_consensus_data(self, j_data): return j_data + def include_long_table_path(self, j_data): + """Include the variant long table path by searchin the in input folder + the file name that contains long_table.csv + """ + condition = os.path.join(self.input_folder, "*long_table.csv") + f_path = relecov_tools.utils.get_files_match_condition(condition) + if len(f_path) == 0: + long_table_path = "" + else: + long_table_path = f_path[0] + for row in j_data: + row["long_table_path"] = long_table_path + return j_data + def include_variant_metrics(self, j_data): """Include the # Ns per 100kb consensus from the summary variant metric file_exists @@ -252,7 +266,8 @@ def create_bioinfo_file(self): j_data = self.include_pangolin_data(j_data) stderr.print("[blue]Adding consensus data") j_data = self.include_consensus_data(j_data) - + stderr.print("[blue]Adding variant long table path") + j_data = self.include_long_table_path(j_data) file_name = ( "bioinfo_" + os.path.splitext(os.path.basename(self.json_file))[0] + ".json" ) @@ -260,4 +275,5 @@ def create_bioinfo_file(self): os.makedirs(self.output_folder, exist_ok=True) file_path = os.path.join(self.output_folder, file_name) relecov_tools.utils.write_json_fo_file(j_data, file_path) + stderr.print("[green]Sucessful creation of bioinfo analyis file") return True diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index c68538c8..d803238b 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -29,6 +29,11 @@ def file_exists(file_to_check): return False +def get_files_match_condition(condition): + """find all path names that matches with the condition""" + return glob.glob(condition) + + def read_json_file(j_file): """Read json file.""" with open(j_file, "r") as fh: From 4c49a6fd07fc26e2b5d0800ac8f2b8f27b4a5e54 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 12 Sep 2022 17:29:32 +0200 Subject: [PATCH 0975/1454] renamed number_of_base_paired_sequence to the right one number_of_base_pairs_sequence --- relecov_tools/conf/configuration.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 625c7082..b36c6d9a 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -295,7 +295,7 @@ } }, "required_fields_from_lab_json": { - "read_length": "number_of_base_paired_sequence", + "read_length": "number_of_base_pairs_sequence", "schema_name": "schema_name", "schema_version": "schema_version", "sequence_file_R1_fastq": "sequence_file_R1_fastq", From 4ba86479335c5b0298bc9e30dfbeee529f726f7e Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 12 Sep 2022 17:48:59 +0200 Subject: [PATCH 0976/1454] missing letter d in number_of_base_pairs_ sequenced --- relecov_tools/conf/configuration.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index b36c6d9a..c1c4b9c8 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -295,7 +295,7 @@ } }, "required_fields_from_lab_json": { - "read_length": "number_of_base_pairs_sequence", + "read_length": "number_of_base_pairs_sequenced", "schema_name": "schema_name", "schema_version": "schema_version", "sequence_file_R1_fastq": "sequence_file_R1_fastq", From 5bbcc92d9f9e78d6a3727ad1eee7d6cd3d60596d Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 13 Sep 2022 09:32:29 +0200 Subject: [PATCH 0977/1454] added body_product and anatomical_material missing on Bronchoalveolar Lavage --- .../conf/anatomical_material_collection_method.json | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/anatomical_material_collection_method.json b/relecov_tools/conf/anatomical_material_collection_method.json index 373f43bf..35385768 100644 --- a/relecov_tools/conf/anatomical_material_collection_method.json +++ b/relecov_tools/conf/anatomical_material_collection_method.json @@ -925,7 +925,9 @@ }, "Bronchoalveolar Lavage": { "anatomical_part": "Not Applicable", - "collection_method": "Bronchoalveolar Lavage" + "collection_method": "Bronchoalveolar Lavage", + "body_product": "Not Applicable", + "anatomical_material": "Not Applicable" }, "Gastric Lavage": { "anatomical_part": "Not Applicable", @@ -1005,4 +1007,4 @@ "body_product": "Not Applicable", "anatomical_material": "Placenta" } -} \ No newline at end of file +} From f8aacdbb1dcd92f6b04dc4fad0094f23baf5b07c Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 13 Sep 2022 09:33:38 +0200 Subject: [PATCH 0978/1454] processing fields to create sampleType --- relecov_tools/feed_database.py | 21 +++++++++++++-------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index bd4c3f1f..4a426d76 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -112,6 +112,8 @@ def map_iskylims_sample_fields_values(self, sample_fields, s_project_fields): """Map the values to the properties send to databasee in json schema based on label """ + anatomical_fields = ["anatomical_part", "collection_method", "body_product", "anatomical_material"] + # collection_method = self.get_sample_type() sample_list = [] s_fields = list(sample_fields.keys()) for row in self.json_data: @@ -127,14 +129,16 @@ def map_iskylims_sample_fields_values(self, sample_fields, s_project_fields): else: log.info("not key %s in iSkyLIMS", key) # include the fix value - if self.server_type == "iskylims": - fixed_value = self.config_json.get_configuration( - "iskylims_fixed_values" - ) - for prop, val in fixed_value.items(): - s_dict[prop] = val + fixed_value = self.config_json.get_configuration("iskylims_fixed_values") + for prop, val in fixed_value.items(): + s_dict[prop] = val + # Using tha anatomical field find out the sampleType + sample_type = [] + for item in anatomical_fields: + if s_dict[item] != "Not Applicable": + sample_type.append(s_dict[item]) + s_dict["sampleType"] = " ".join(sample_type) sample_list.append(s_dict) - return sample_list def get_iskylims_fields_sample(self): @@ -143,6 +147,7 @@ def get_iskylims_fields_sample(self): The second request is for getting the sample project fields. These are mapped using the label value. """ + sample_fields = {} s_project_fields = [] # get the ontology values for mapping values in sample fields @@ -178,7 +183,6 @@ def get_iskylims_fields_sample(self): # and the value is empty # sample_fields[key] = "" log.info("not ontology for item %s", values["field_name"]) - # fetch label for sample Project s_project_url = self.database_settings["url_project_fields"] param = self.database_settings["param_sample_project"] @@ -295,6 +299,7 @@ def store_data(self): """Collect data from json file and split them to store data in iSkyLIMS and in Relecov Platform """ + map_fields = {} # if self.type_of_info == "sample": if self.server_type == "iskylims": From a56b44de83849af64f591a4b39b1eba76df9b479 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 13 Sep 2022 09:35:03 +0200 Subject: [PATCH 0979/1454] rename Source Speciment that which had the same label for anatomical fields --- relecov_tools/schema/relecov_schema.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index f0303c1c..6c9161e3 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -585,7 +585,7 @@ "Blood [UBERON:0000178]" ], "classification": "Sample collection and processing", - "label": "Specimen source", + "label": "Anatomical Material", "fill_mode": "batch" }, "anatomical_part": { @@ -627,7 +627,7 @@ "" ], "classification": "Sample collection and processing", - "label": "Specimen source", + "label": "Anatomical Part", "fill_mode": "batch" }, "collection_device": { @@ -695,7 +695,7 @@ "" ], "classification": "Sample collection and processing", - "label": "Specimen source", + "label": "Collection Method", "fill_mode": "batch" }, "body_product": { @@ -720,7 +720,7 @@ "" ], "classification": "Sample collection and processing", - "label": "Specimen source", + "label": "Body Product", "fill_mode": "batch" }, "environmental_material": { From 85d89171cc658797c779cccee7ac39f2103f620c Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 13 Sep 2022 09:37:16 +0200 Subject: [PATCH 0980/1454] fixin liting --- relecov_tools/read_bioinfo_metadata.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 367f454f..40ea89af 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -166,7 +166,9 @@ def include_consensus_data(self, j_data): row["consensus_sequence_filepath"] = self.input_folder row["consensus_file_name"] = f_name row["consensus_sequence_md5"] = relecov_tools.utils.calculate_md5(f_path) - base_calculation = int(row["number_of_base_pairs_sequenced"]) * len(record_fasta) + base_calculation = int(row["number_of_base_pairs_sequenced"]) * len( + record_fasta + ) if row["sequence_file_R2_fastq"] != "": row["number_of_base_pairs_sequenced"] = str(base_calculation * 2) else: From c3f9874105da04007c8a4ce8d00068ea295d553b Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 13 Sep 2022 09:38:44 +0200 Subject: [PATCH 0981/1454] fixin liting --- relecov_tools/feed_database.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 4a426d76..4ff611a1 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -112,7 +112,12 @@ def map_iskylims_sample_fields_values(self, sample_fields, s_project_fields): """Map the values to the properties send to databasee in json schema based on label """ - anatomical_fields = ["anatomical_part", "collection_method", "body_product", "anatomical_material"] + anatomical_fields = [ + "anatomical_part", + "collection_method", + "body_product", + "anatomical_material", + ] # collection_method = self.get_sample_type() sample_list = [] s_fields = list(sample_fields.keys()) From 3425bcedd23235e670cc36be6aed87e346437d35 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 13 Sep 2022 11:18:48 +0200 Subject: [PATCH 0982/1454] latest changes in ena and relecov --- relecov_tools/schema/ena_schema.json | 25 +++- relecov_tools/schema/relecov_schema.json | 160 +---------------------- 2 files changed, 22 insertions(+), 163 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 51f9c31f..9ac3d544 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -50,7 +50,7 @@ "examples": [ "Public Health Agency of Canada" ], - "ontology": "GENEPIO:0001797", + "ontology": "GENEPIO:0001153", "type": "string", "description": "Name of the institution to which the person collecting the specimen belongs. Format: Institute Name, Institute Address", "label": "Originating Laboratory", @@ -58,7 +58,7 @@ }, "collector name": { "examples": [ - "John Smith" + "John Smith, unknown" ], "ontology": "GENEPIO:0001797", "type": "string", @@ -667,7 +667,7 @@ "examples": [ "" ], - "ontology": "OMIT:0020000", + "ontology": "OBI:0002456", "type": "string", "description": "Whether or not the subject is gravid. If so, report date due or date post-conception and specify which of these two dates is being reported.", "clasification": "Host information", @@ -961,7 +961,7 @@ "examples": [ "cough, diarrhea, fever, headache, malaise, myalgia" ], - "ontology": "GENEPIO:00015f23", + "ontology": "GENEPIO:0001523", "type": "string", "description": "The symptoms that have been reported in relation to the illness. If multiple exposures are applicable, please state them separated by semicolon.", "clasification": "Sample collection and processing", @@ -1177,6 +1177,23 @@ "examples": [ "" ], + "enum": [ + "Whole Genome Sequencing []", + "Metagenomics []", + "Transcriptome Analysis []", + "Resequencing []", + "Epigenetics [] ", + "Synthetic Genomics []", + "Forensic or Paleo-genomics []", + "Gene Regulation Study []", + "Cancer Genomics []", + "Population Genomics []", + "RNASeq []", + "Exome Sequencing []", + "Pooled Clone Sequencing []", + "Transcriptome Sequencing []", + "Other []" + ], "ontology": "GENEPIO:0000156", "type": "string", "description": "", diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index a830b882..2ec1fb7d 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -44,7 +44,7 @@ "examples": [ "Public Health Agency of Canada" ], - "ontology": "GENEPIO:0001797", + "ontology": "GENEPIO:0001153", "type": "string", "description": "The name of the agency/institution that collected the sample.", "classification": "Sample collection and processing", @@ -110,37 +110,6 @@ "fill_mode": "sample", "minLenght": "1" }, - "sample_description": { - "examples": [ - "Sample from Belgian Covid-19 patient. Sample was obtained at the Hospital AZ Rivierenland, in Antwerp, Belgium." - ], - "ontology": "sep:00196", - "type": "string", - "description": "Free text description of the sample.", - "clasification": "Sample collection and processing", - "label": "Sample Description", - "table": "sample" - }, - "illness_symptoms": { - "examples": [ - "cough, diarrhea, fever, headache, malaise, myalgia" - ], - "ontology": "GENEPIO:0001523", - "type": "string", - "description": "The symptoms that have been reported in relation to the illness. If multiple exposures are applicable, please state them separated by semicolon.", - "clasification": "Sample collection and processing", - "label": "Illness symptoms", - "table": "sample" - }, - "hospitalisation": { - "examples": [], - "ontology": "NCIT:C25179", - "type": "string", - "description": " Was the subject confined to a hospital as a result of virus infection or problems occurring secondary to virus infection?", - "clasification": "Sample collection and processing", - "label": "Hospitalisation", - "table": "sample" - }, "submitting_lab_sample_id": { "examples": [ "" @@ -212,58 +181,6 @@ "label": "Sample Received Date", "fill_mode": "sample" }, - "definition for seropositive sample": { - "examples": [ - "" - ], - "ontology": "NCIT:C159692", - "type": "string", - "description": " The cut off value used by an investigatior in determining that a sample was seropositive.", - "clasification": "Sample collection and processing", - "label": "Definition for seropositive sample", - "table": [ - "sample" - ] - }, - "serotype (required for a seropositive sample)": { - "examples": [ - "h1n1" - ], - "ontology": "NCIT:C88894", - "type": "string", - "description": " erological variety of a species characterised by its antigenic properties. For influenza, ha subtype should be the letter h followed by a number between 1-16 unless novel subtype is identified and the na subtype should be the letter n followed by a number between 1-9 unless novel subtype is identified. If only one of the subtypes have been tested then use the format h5nx or hxn1.", - "clasification": "Sample collection and processing", - "label": "Serotype (required for a seropositive sample)", - "table": [ - "sample" - ] - }, - "strain": { - "examples": [ - "" - ], - "ontology": "NCIT:C14419", - "type": "string", - "description": "Name of the strain from which the sample was obtained..", - "clasification": "Sample collection and processing", - "label": "Strain", - "table": [ - "sample" - ] - }, - "host habitat": { - "examples": [ - "" - ], - "ontology": "ENVO:00002036", - "type": "string", - "description": "Natural habitat of the avian or mammalian host.", - "clasification": "Sample collection and processing", - "label": "Host habitat", - "table": [ - "sample" - ] - }, "sample_storage_conditions": { "examples": [ "24 degrees celsius" @@ -610,19 +527,6 @@ "label": "Geo Loc Latitude", "fill_mode": "batch" }, - "gravidity": { - "examples": [ - "" - ], - "ontology": "OBI:0002456", - "type": "string", - "description": "Whether or not the subject is gravid. If so, report date due or date post-conception and specify which of these two dates is being reported.", - "clasification": "Host information", - "label": "Gravidity", - "table": [ - "sample" - ] - }, "geo_loc_longitude": { "examples": [ "77.11 W" @@ -657,32 +561,6 @@ "label": "Purpose of sampling", "fill_mode": "batch" }, - "host disease outcome": { - "examples": [ - "" - ], - "ontology": "GENEPIO:0001390", - "type": "string", - "description": "Disease outcome in the host.", - "clasification": "Host information", - "label": "Host disease outcome", - "table": [ - "sample" - ] - }, - "host description": { - "examples": [ - "" - ], - "ontology": "GENEPIO:0000009", - "type": "string", - "description": "Other descriptive information relating to the host.", - "clasification": "Host information", - "label": "Host description", - "table": [ - "sample" - ] - }, "anatomical_material": { "enum": [ "Blood [UBERON:0000178]", @@ -980,16 +858,6 @@ "fill_mode": "sample", "minLenght": "1" }, - "additional_host_information": { - "examples": [ - "" - ], - "ontology": "NCIT:C83280", - "type": "string", - "description": "", - "clasification": "", - "label": "Additional Host Information" - }, "host_health_state": { "examples": [ "" @@ -1251,32 +1119,6 @@ "label": "Nucleic acid extraction protocol", "fill_mode": "batch" }, - "outbreak": { - "examples": [ - "" - ], - "ontology": "GENEPIO:0001417", - "type": "string", - "description": " Date, Location e.g. type of gathering, Family cluster, etc.", - "clasification": "Host information", - "label": "Outbreak Exposure Event Location", - "table": [ - "sample" - ] - }, - "personal_protective_equipment": { - "examples": [ - "" - ], - "ontology": "NCIT:C173748", - "type": "string", - "description": "Use of personal protective equipment, such as gloves, gowns, during any type of exposure. Example: mask", - "clasification": "Host information", - "label": "Personal protective equipment", - "table": [ - "sample" - ] - }, "all_in_one_library_kit": { "enum": [ "Ion Xpress", From acb9611d268dfe11f59664f821907e878c1fd44c Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 13 Sep 2022 11:45:28 +0200 Subject: [PATCH 0983/1454] added enums --- relecov_tools/schema/ena_schema.json | 34 ++++++++++++------------ relecov_tools/schema/relecov_schema.json | 28 +++++++++++++++++++ 2 files changed, 45 insertions(+), 17 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 9ac3d544..c3e43788 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -1178,21 +1178,21 @@ "" ], "enum": [ - "Whole Genome Sequencing []", - "Metagenomics []", - "Transcriptome Analysis []", - "Resequencing []", - "Epigenetics [] ", - "Synthetic Genomics []", - "Forensic or Paleo-genomics []", - "Gene Regulation Study []", - "Cancer Genomics []", - "Population Genomics []", - "RNASeq []", - "Exome Sequencing []", - "Pooled Clone Sequencing []", - "Transcriptome Sequencing []", - "Other []" + "Whole Genome Sequencing [NCIT:C101294]", + "Metagenomics [NCIT:C153191]", + "Transcriptome Analysis [GENEPIO:0001111]", + "Resequencing [NCIT:C41254]", + "Epigenetics [OMIT:0027036] ", + "Synthetic Genomics [NCIT:C84343]", + "Forensic or Paleo-genomics [topic:3943]", + "Gene Regulation Study [topic:0204]", + "Cancer Genomics [NCIT:C18247]", + "Population Genomics [topic:3796]", + "RNASeq [OBI:0001177]", + "Exome Sequencing [OBI:0002118]", + "Pooled Clone Sequencing [OBI:2100402]", + "Transcriptome Sequencing [NCIT:C124261]", + "Other [NCIT:C124261]" ], "ontology": "GENEPIO:0000156", "type": "string", @@ -1203,11 +1203,11 @@ }, "study_abstract": { "examples": [ - "" + "Whole-genome sequences of SARS-CoV-2 from oro-pharyngeal swabs obtained from Belgian Covid-19 patients." ], "ontology": "NCIT:C93415", "type": "string", - "description": "", + "description": " Briefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be inherited from a referenced publication.", "clasification": "Submission ENA", "label": "Study abstract", "table": [ diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 499bdf47..377b92d3 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -527,6 +527,34 @@ "label": "Geo Loc Latitude", "fill_mode": "batch" }, + "study_type": { + "examples": [ + "" + ], + "enum": [ + "Whole Genome Sequencing [NCIT:C101294]", + "Metagenomics [NCIT:C153191]", + "Transcriptome Analysis [GENEPIO:0001111]", + "Resequencing [NCIT:C41254]", + "Epigenetics [OMIT:0027036] ", + "Synthetic Genomics [NCIT:C84343]", + "Forensic or Paleo-genomics [topic:3943]", + "Gene Regulation Study [topic:0204]", + "Cancer Genomics [NCIT:C18247]", + "Population Genomics [topic:3796]", + "RNASeq [OBI:0001177]", + "Exome Sequencing [OBI:0002118]", + "Pooled Clone Sequencing [OBI:2100402]", + "Transcriptome Sequencing [NCIT:C124261]", + "Other [NCIT:C124261]" + ], + "ontology": "GENEPIO:0000156", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Study type", + "table": "study" + }, "geo_loc_longitude": { "examples": [ "77.11 W" From 71c8413f7426e99a82970e153b4224bf6f4ceff2 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 13 Sep 2022 11:55:18 +0200 Subject: [PATCH 0984/1454] latest changes in schema relecov --- relecov_tools/schema/relecov_schema.json | 111 ----------------------- 1 file changed, 111 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 377b92d3..9d2735b0 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2361,39 +2361,6 @@ "label": "Gene Name 2", "fill_mode": "batch" }, - "bioproject_umbrella_accession_ENA": { - "examples": [ - "" - ], - "ontology": "GENEPIO:0001133", - "type": "string", - "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", - "classification": "Sample collection and processing", - "label": "Bioproject umbrella accession ENA", - "fill_mode": "batch" - }, - "bioproject_accession_ENA": { - "examples": [ - "" - ], - "ontology": "GENEPIO:0001136", - "type": "string", - "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", - "classification": "Sample collection and processing", - "label": "Bioproject accession ENA", - "fill_mode": "batch" - }, - "biosample_accession_ENA": { - "examples": [ - "" - ], - "ontology": "GENEPIO:0001139", - "type": "string", - "description": "The identifier assigned to a BioSample in INSDC archives.", - "classification": "Sample collection and processing", - "label": "ENA Sample ID", - "fill_mode": "batch" - }, "diagnostic_pcr_Ct_value_2": { "examples": [ "36" @@ -2449,72 +2416,6 @@ "label": "GISAID Virus Name", "fill_mode": "sample" }, - "ena_analysis_accession": { - "examples": [ - "" - ], - "ontology": "GENEPIO_0001145", - "type": "string", - "description": "", - "classification": "Public databases", - "label": "Analysis Accession", - "fill_mode": "batch" - }, - "ena_study_accession": { - "examples": [ - "e.g PRJEB39632" - ], - "ontology": "GENEPIO_0001136", - "type": "string", - "description": "", - "classification": "Public databases", - "label": "Study accession", - "fill_mode": "batch" - }, - "ena_sample_accession": { - "examples": [ - "e.g SAMEA7098096" - ], - "ontology": "GENEPIO_0001139", - "type": "string", - "description": "", - "classification": "Public databases", - "label": "Sample accession", - "fill_mode": "batch" - }, - "ena_experiment_accession": { - "examples": [ - "e.g ERX4331406" - ], - "ontology": "BU_ISCIII:015", - "type": "string", - "description": "", - "classification": "Public databases", - "label": "Experiment Accession", - "fill_mode": "batch" - }, - "ena_run_accession": { - "examples": [ - "e.g ERX4331406" - ], - "ontology": "BU_ISCIII:016", - "type": "string", - "description": "", - "classification": "Public databases", - "label": "Run Accession", - "fill_mode": "batch" - }, - "ena_submission_accession": { - "examples": [ - "e.g ERA2794974" - ], - "ontology": "BU_ISCIII:017", - "type": "string", - "description": "", - "classification": "Public databases", - "label": "Submission Accession", - "fill_mode": "batch" - }, "ena_experiment_title": { "examples": [ "e.g Illumina MiSeq paired end sequencing" @@ -2547,18 +2448,6 @@ "classification": "Public databases", "label": "Broker Name", "fill_mode": "batch" - }, - "ena_first_created_date": { - "examples": [ - "e.g 2020-08-07" - ], - "ontology": "NCIT_C164483", - "type": "string", - "format": "date", - "description": "", - "classification": "Public databases", - "label": "First created date", - "fill_mode": "batch" } } } \ No newline at end of file From 2eee34f8c6f9f6a08d4115603ee4e52342a14bd6 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 13 Sep 2022 12:24:57 +0200 Subject: [PATCH 0985/1454] Fixed typo in configuration file about mapping_software_version --- relecov_tools/conf/configuration.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index c1c4b9c8..f3e28834 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -284,7 +284,7 @@ "dehosting_method_software_version": { "KRAKEN2_KRAKEN2": "kraken2" }, - "mapping_software_name": { + "mapping_software_version": { "BOWTIE2_ALIGN": "bowtie2" }, "preprocessing_software_version": { From 9b310d67aab85674409ff78f4b1d920238a4fffb Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 13 Sep 2022 12:30:42 +0200 Subject: [PATCH 0986/1454] Fixing typo for consensus_genome_lenght and consensus_filename --- relecov_tools/read_bioinfo_metadata.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 40ea89af..3117d3dc 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -161,10 +161,10 @@ def include_consensus_data(self, j_data): for item in mapping_fields: row[item] = "" continue - row["consensus_geneme_length"] = str(len(record_fasta)) + row["consensus_genome_length"] = str(len(record_fasta)) row["consensus_sequence_name"] = record_fasta.description row["consensus_sequence_filepath"] = self.input_folder - row["consensus_file_name"] = f_name + row["consensus_filename"] = f_name row["consensus_sequence_md5"] = relecov_tools.utils.calculate_md5(f_path) base_calculation = int(row["number_of_base_pairs_sequenced"]) * len( record_fasta From e0eb6e0cc10388046d7de816e30e9cddfbd0c66f Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 13 Sep 2022 12:37:15 +0200 Subject: [PATCH 0987/1454] change sequence_name for sequencing_sample_id for better matching --- relecov_tools/conf/configuration.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index f3e28834..dc3a6ecc 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -302,7 +302,7 @@ "sequence_file_R2_fastq": "sequence_file_R2_fastq", "sequence_file_R1_md5": "sequence_file_R1_md5", "sequence_file_R2_md5" : "sequence_file_R2_md5", - "sequencing_sample_id" : "sample_name" + "sequencing_sample_id" : "sequencing_sample_id" } }, "md5_file_name": "md5_check_file.csv", From f715bac71f05e5be638a5d3102eb8978c6808de0 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 13 Sep 2022 12:50:23 +0200 Subject: [PATCH 0988/1454] add again ena fileds in relecov schema --- relecov_tools/schema/ena_schema.json | 5 ++ relecov_tools/schema/relecov_schema.json | 78 ++++++++++++++++++++++++ 2 files changed, 83 insertions(+) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index c3e43788..b6bf7f4f 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -1258,6 +1258,11 @@ "examples": [ "BAM,CRAM,FASTQ" ], + "enum": [ + "BAM [format:2572]", + "CRAM [format:3462]", + "FASTQ [format:1930]" + ], "ontology": "NMR:1001459", "type": "string", "description": "The run data file model.", diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 9d2735b0..f1e0ff8c 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2416,6 +2416,72 @@ "label": "GISAID Virus Name", "fill_mode": "sample" }, + "ena_analysis_accession": { + "examples": [ + "" + ], + "ontology": "GENEPIO_0001145", + "type": "string", + "description": "", + "classification": "Public databases", + "label": "Analysis Accession", + "fill_mode": "batch" + }, + "ena_study_accession": { + "examples": [ + "e.g PRJEB39632" + ], + "ontology": "GENEPIO_0001136", + "type": "string", + "description": "", + "classification": "Public databases", + "label": "Study accession", + "fill_mode": "batch" + }, + "ena_sample_accession": { + "examples": [ + "e.g SAMEA7098096" + ], + "ontology": "GENEPIO_0001139", + "type": "string", + "description": "", + "classification": "Public databases", + "label": "Sample accession", + "fill_mode": "batch" + }, + "ena_experiment_accession": { + "examples": [ + "e.g ERX4331406" + ], + "ontology": "BU_ISCIII:015", + "type": "string", + "description": "", + "classification": "Public databases", + "label": "Experiment Accession", + "fill_mode": "batch" + }, + "ena_run_accession": { + "examples": [ + "e.g ERX4331406" + ], + "ontology": "BU_ISCIII:016", + "type": "string", + "description": "", + "classification": "Public databases", + "label": "Run Accession", + "fill_mode": "batch" + }, + "ena_submission_accession": { + "examples": [ + "e.g ERA2794974" + ], + "ontology": "BU_ISCIII:017", + "type": "string", + "description": "", + "classification": "Public databases", + "label": "Submission Accession", + "fill_mode": "batch" + }, "ena_experiment_title": { "examples": [ "e.g Illumina MiSeq paired end sequencing" @@ -2448,6 +2514,18 @@ "classification": "Public databases", "label": "Broker Name", "fill_mode": "batch" + }, + "ena_first_created_date": { + "examples": [ + "e.g 2020-08-07" + ], + "ontology": "NCIT_C164483", + "type": "string", + "format": "date", + "description": "", + "classification": "Public databases", + "label": "First created date", + "fill_mode": "batch" } } } \ No newline at end of file From a74613c28c5c8e3bb610594c5bd588114f1affec Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Wed, 14 Sep 2022 10:40:31 +0200 Subject: [PATCH 0989/1454] gisaid submitter id is retrieved from configuration.json --- relecov_tools/gisaid_upload.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index a4d922d6..ca116d3b 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -120,8 +120,15 @@ def complete_mand_fields(self, dataframe): dataframe.loc[ dataframe["covv_patient_status"] == "", "covv_patient_status" ] = "unknown" + + config_json = ConfigJson() + gisaid_config = config_json.get_configuration("GISAID_configuration") + submitter_id = gisaid_config["submitter"] + dataframe.loc[dataframe["submitter"] == "", "submitter"] = submitter_id + return dataframe + def metadata_to_csv(self): """Transform metadata json to csv""" data = relecov_tools.utils.read_json_file(self.gisaid_json) From b84bf907e4e441545c2fbaa815aa6b729c3498f7 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 15 Sep 2022 09:49:00 +0200 Subject: [PATCH 0990/1454] latest cahnges --- relecov_tools/conf/configuration.json | 14 ++++----- relecov_tools/map_schema.py | 33 ++-------------------- relecov_tools/read_bioinfo_metadata.py | 2 +- relecov_tools/schema/relecov_schema.json | 36 ++++++++++++------------ 4 files changed, 28 insertions(+), 57 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index c1c4b9c8..cdba2345 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -254,7 +254,7 @@ "consensus_sequence_name", "number_of_base_pairs_sequenced" ], - "mapping_pangolin":{ + "mapping_pangolin": { "variant_designation": "scorpio_call" }, "mapping_stats": { @@ -274,11 +274,11 @@ "mapping_variant_metrics": { "ns_per_100_kbp": "# Ns per 100kb consensus" }, - "mapping_version":{ - "bioinformatics_protocol_software_version":{ + "mapping_version": { + "bioinformatics_protocol_software_version": { "Workflow": "nf-core/viralrecon" }, - "consensus_sequence_software_version":{ + "consensus_sequence_software_version": { "BCFTOOLS_CONSENSUS": "bcftools" }, "dehosting_method_software_version": { @@ -301,8 +301,8 @@ "sequence_file_R1_fastq": "sequence_file_R1_fastq", "sequence_file_R2_fastq": "sequence_file_R2_fastq", "sequence_file_R1_md5": "sequence_file_R1_md5", - "sequence_file_R2_md5" : "sequence_file_R2_md5", - "sequencing_sample_id" : "sample_name" + "sequence_file_R2_md5": "sequence_file_R2_md5", + "sequencing_sample_id": "sample_name" } }, "md5_file_name": "md5_check_file.csv", @@ -390,4 +390,4 @@ "collecting institution" ] } -} +} \ No newline at end of file diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 61664969..52a26daf 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -204,41 +204,12 @@ def additional_formating(self, mapped_json_data): mapped_json_data[idx][ "sequencing_instrument_platform" ] = self.json_data[idx]["sequencing_instrument_platform"].upper() - """ - if ( - "nextseq" - in self.json_data[idx]["sequencing_instrument_model"].lower() - ): - if ( - "500" - in self.json_data[idx]["sequencing_instrument_model"].lower() - ): - mapped_json_data[idx]["instrument_model"] = "NextSeq 500" - if ( - "1000" - in self.json_data[idx]["sequencing_instrument_model"].lower() - ): - mapped_json_data[idx]["instrument_model"] = "NextSeq 1000" - if ( - "2000" - in self.json_data[idx]["sequencing_instrument_model"].lower() - ): - mapped_json_data[idx]["instrument_model"] = "NextSeq 2000" - if ( - "550" - in self.json_data[idx]["sequencing_instrument_model"].lower() - ): - mapped_json_data[idx]["instrument_model"] = "NextSeq 550" - if ( - "illumina nextseq" - in self.json_data[idx]["sequencing_instrument_model"].lower() - ): - mapped_json_data[idx]["instrument_model"] = "NextSeq 550" - else: + """ mapped_json_data[idx]["instrument_model"] = self.json_data[idx][ "sequencing_instrument_model" ] + """ mapped_json_data[idx]["host health state"] = "not provided" mapped_json_data[idx]["center_name"] = mapped_json_data[idx][ diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 40ea89af..3dee8794 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -161,7 +161,7 @@ def include_consensus_data(self, j_data): for item in mapping_fields: row[item] = "" continue - row["consensus_geneme_length"] = str(len(record_fasta)) + row["consensus_genome_length"] = str(len(record_fasta)) row["consensus_sequence_name"] = record_fasta.description row["consensus_sequence_filepath"] = self.input_folder row["consensus_file_name"] = f_name diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index f1e0ff8c..ec7242ca 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -499,7 +499,7 @@ "Derbyshire" ], "ontology": "NCIT:C87189", - "type": "s tring", + "type": "string", "description": "The county/region of origin of the sample.", "classification": "Sample collection and processing", "label": "Province", @@ -1686,12 +1686,12 @@ }, "analysis_date": { "examples": [ - "e.g 2020-08-07" + "e.g 20220705" ], "ontology": "0", "type": "string", "format": "date", - "description": "", + "description": "The time of a sample analysis process", "classification": "Bioinformatics and QC metrics fields", "label": "Analysis date", "fill_mode": "batch", @@ -1699,7 +1699,7 @@ }, "dehosting_method_software_name": { "examples": [ - "Nanostripper" + "KRAKEN2_KRAKEN2 " ], "ontology": "GENEPIO:0001459", "type": "string", @@ -1776,7 +1776,7 @@ ], "ontology": "0", "type": "string", - "description": "", + "description": "If bioinformatics protocol used was open-source or commercial", "classification": "Bioinformatic Analysis fields", "label": "Commercial/Open-source/both", "fill_mode": "batch" @@ -1809,7 +1809,7 @@ ], "ontology": "0", "type": "string", - "description": "", + "description": "Preprocessing software name other", "classification": "Bioinformatic Analysis fields", "label": "If preprocessing Is Other, Specify", "fill_mode": "batch" @@ -1853,7 +1853,7 @@ ], "ontology": "0", "type": "string", - "description": "", + "description": "Mapping software used other ", "classification": "Bioinformatic Analysis fields", "label": "If mapping Is Other, Specify", "fill_mode": "batch" @@ -1951,7 +1951,7 @@ "type": "string", "description": "The name of the consensus sequence.", "examples": [ - "ncov123assembly3" + "2018086 NC_045512.2" ], "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence name", @@ -1962,7 +1962,7 @@ "type": "string", "description": "The name of the consensus sequence filename", "examples": [ - "ncov123assembly3" + "2018102.consensus.fa" ], "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence name", @@ -1971,7 +1971,7 @@ "consensus_sequence_md5": { "ontology": "0", "type": "string", - "description": "The name of the consensus sequence.", + "description": "The md5 of the consensus sequence.", "examples": [ "5gaskañlkdak3143242ñlkas" ], @@ -2084,7 +2084,7 @@ ], "ontology": "0", "type": "string", - "description": "", + "description": "Percentage of read that pass quality control threshold ", "classification": "Bioinformatics and QC metrics fields", "label": "%qc filtered", "fill_mode": "batch" @@ -2095,7 +2095,7 @@ ], "ontology": "0", "type": "string", - "description": "", + "description": "Percentage of reads mapped to host", "classification": "Bioinformatics and QC metrics fields", "label": "%reads host", "fill_mode": "batch" @@ -2106,7 +2106,7 @@ ], "ontology": "0", "type": "string", - "description": "", + "description": "Percentage of reads mapped to virus", "classification": "Bioinformatics and QC metrics fields", "label": "%reads virus", "fill_mode": "batch" @@ -2117,7 +2117,7 @@ ], "ontology": "0", "type": "string", - "description": "", + "description": "Percentage of reads unmapped to virus or to host", "classification": "Bioinformatics and QC metrics fields", "label": "%unmapped", "fill_mode": "batch" @@ -2139,7 +2139,7 @@ ], "ontology": "0", "type": "string", - "description": "", + "description": "Percentage of genome with coverage greater than 10x", "classification": "Bioinformatics and QC metrics fields", "label": "% genome greater 10x", "fill_mode": "batch" @@ -2150,7 +2150,7 @@ ], "ontology": "0", "type": "string", - "description": "", + "description": "Percentage of Ns", "classification": "Bioinformatics and QC metrics fields", "label": "%Ns", "fill_mode": "batch" @@ -2172,7 +2172,7 @@ ], "ontology": "0", "type": "string", - "description": "", + "description": "The number of variants found in consensus sequence", "classification": "Bioinformatic Variants", "label": "Number of variants (AF greater 75%)", "fill_mode": "batch" @@ -2183,7 +2183,7 @@ ], "ontology": "0", "type": "string", - "description": "", + "description": "The number of missense variants", "classification": "Bioinformatic Variants", "label": "Number of variants with effect", "fill_mode": "batch" From 6d86ce18fbd7170f1aef5a199885912a29c99733 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Thu, 15 Sep 2022 13:00:29 +0200 Subject: [PATCH 0991/1454] replaced 'not provided' with 'unknown' in gisaid metadata --- relecov_tools/gisaid_upload.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index ca116d3b..116e3c17 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -159,7 +159,8 @@ def metadata_to_csv(self): lab["geo_loc_city"], ] ) - + + df_data.replace("not provided", "unknown", inplace=True) df_data_comp = self.complete_mand_fields(df_data) df_data_path = os.path.join(self.output_path, "meta_gisaid.csv") if not os.path.exists(self.output_path): From ee8cb002374d341322ad0612d47ef3867ecbb5fe Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Thu, 15 Sep 2022 13:43:27 +0200 Subject: [PATCH 0992/1454] removed redundant lines in gisaid_upload --- relecov_tools/gisaid_upload.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 116e3c17..4e723b43 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -166,8 +166,7 @@ def metadata_to_csv(self): if not os.path.exists(self.output_path): os.mkdir(self.output_path) df_data_comp.to_csv(df_data_path, index=False) - metagisaid = df_data_path - return metagisaid + return df_data_path # generar template con cli3 # ADD TOKEN WARNING and file token .authtoken @@ -230,8 +229,7 @@ def change_headers(self, multifasta): record.id = name record.description = name SeqIO.write(record, new_fasta, "fasta") - fastagisaid = multi_gis_path - return fastagisaid + return multi_gis_path def cli3_auth(self): """Create authenticate token""" From 753d8a0f96c7ebabdc07f254a3351772df2cdd63 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 15 Sep 2022 16:00:00 +0200 Subject: [PATCH 0993/1454] changes in map module --- relecov_tools/conf/configuration.json | 21 +++++- relecov_tools/map_schema.py | 93 ++++++++++++--------------- relecov_tools/schema/ena_schema.json | 6 +- 3 files changed, 62 insertions(+), 58 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index cdba2345..efebc359 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -202,8 +202,8 @@ "sampleLocation": "Not defined" }, "relecov_sample_metadata": [ - "fastq_r1_md5", - "fastq_r2_md5", + "sequence_file_R1_md5", + "sequence_file_R2_md5", "microbiology_lab_sample_id", "r1_fastq_filepath", "r2_fastq_filepath", @@ -388,6 +388,23 @@ "host scientific name", "collector name", "collecting institution" + ], + "map_not_provided_fields": [ + "subject exposure", + "subject exposure duration", + "type exposure", + "personal protective equipment", + "hospitalisation", + "illness duration", + "illness symptoms", + "host disease outcome", + "definition for seropositive sample", + "serotype (required for a seropositive sample)", + "strain", + "host habitat", + "host description", + "gravidity", + "host behaviour" ] } } \ No newline at end of file diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 52a26daf..2d57e3fe 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -153,77 +153,64 @@ def additional_formating(self, mapped_json_data): """ if self.destination_schema == "ENA": for idx in range(len(self.json_data)): - mapped_json_data[idx]["fastq_r1_md5"] = self.json_data[idx][ - "fastq_r1_md5" - ] - mapped_json_data[idx]["fastq_r2_md5"] = self.json_data[idx][ - "fastq_r2_md5" + + mapped_json_data[idx]["collector_name"] = "unknown" + mapped_json_data[idx]["file_format"] = "FASTQ [format:1930]" + mapped_json_data[idx][ + "study_type" + ] = "Whole Genome Sequencing [NCIT:C101294]" + mapped_json_data[idx][ + "study_title" + ] = "RELECOV Spanish Network for genomics surveillance" + mapped_json_data[idx]["study_abstract"] = mapped_json_data[idx][ + "study_title" ] - mapped_json_data[idx]["r1_fastq_filepath"] = ( - self.json_data[idx]["r1_fastq_filepath"] - + "/" - + self.json_data[idx]["sequence_file_R1_fastq"] - ) - mapped_json_data[idx]["r2_fastq_filepath"] = ( - self.json_data[idx]["r2_fastq_filepath"] - + "/" - + self.json_data[idx]["sequence_file_R2_fastq"] - ) - mapped_json_data[idx]["collecting_institution"] = self.json_data[idx][ + mapped_json_data[idx]["broker_name"] = "Instituto de Salud Carlos III" + mapped_json_data[idx]["host health state"] = "not provided" + mapped_json_data[idx]["center_name"] = self.json_data[idx][ "collecting_institution" ] - mapped_json_data[idx]["collector_name"] = self.json_data[idx][ - "collector_name" - ] mapped_json_data[idx]["library_name"] = self.json_data[idx][ - "collecting_lab_sample_id" + "library_preparation_kit" ] mapped_json_data[idx]["sample_title"] = self.json_data[idx][ "sequencing_sample_id" ] - mapped_json_data[idx]["file_type"] = "fastq" - # mapped_json_data[idx]["collector_name"] = self.json_data[idx][ "author_submitter"] - mapped_json_data[idx]["library_name"] = self.json_data[idx][ - "library_kit" - ] mapped_json_data[idx]["sample_name"] = self.json_data[idx][ "sequencing_sample_id" ] - mapped_json_data[idx]["study_type"] = self.json_data[idx][ - "purpose_sampling" - ] - mapped_json_data[idx]["study_abstract"] = self.json_data[idx][ - "study_title" - ] - mapped_json_data[idx]["sample_description"] = self.json_data[idx][ - "sequence_file_R1_fastq" + mapped_json_data[idx]["study_alias"] = self.json_data[idx][ + "schema_name" ] + + mapped_json_data[idx]["sample_description"] = ( + self.json_data[idx]["anatomical_part"] + + " " + + self.json_data[idx]["collection_method"] + ) mapped_json_data[idx]["isolate"] = self.json_data[idx][ "isolate_sample_id" ] - mapped_json_data[idx][ + mapped_json_data[idx]["platform"] = self.json_data[idx][ "sequencing_instrument_platform" - ] = self.json_data[idx]["sequencing_instrument_platform"].upper() - - """ - mapped_json_data[idx]["instrument_model"] = self.json_data[idx][ - "sequencing_instrument_model" - ] - """ + ].upper() - mapped_json_data[idx]["host health state"] = "not provided" - mapped_json_data[idx]["center_name"] = mapped_json_data[idx][ - "collecting_institution" - ] mapped_json_data[idx]["authors"] = self.json_data[idx]["authors"] - mapped_json_data[idx]["sample_description"] = "" - mapped_json_data[idx]["design_description"] = "" - mapped_json_data[idx]["insert_size"] = "0" - mapped_json_data[idx]["address"] = ( - self.json_data[idx]["geo_loc_city"] - + ", " - + self.json_data[idx]["geo_loc_country"] + mapped_json_data[idx]["design_description"] = ( + self.json_data[idx]["library_layout"] + + " " + + self.json_data[idx]["library_preparation_kit"] + + " " + + self.json_data[idx]["library_selection"] + + " " + + self.json_data[idx]["library_source"] + + " " + + self.json_data[idx]["library_strategy"] ) + mapped_json_data[idx]["insert_size"] = "0" + mapped_json_data[idx]["address"] = self.json_data[idx][ + "collecting_institution_address" + ] return mapped_json_data @@ -245,7 +232,7 @@ def write_json_fo_file(self, mapped_json_data): return True def map_to_data_to_new_schema(self): - """Mapping the json data from phage plus schema to the requested one""" + """Mapping the json data from relecov schema to the requested one""" mapping_schema_dict = self.maping_schemas_based_on_geontology() mapped_json_data = self.mapping_json_data(mapping_schema_dict) updated_json_data = self.additional_formating(mapped_json_data) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index b6bf7f4f..1a82dcf3 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -914,11 +914,11 @@ "clasification": "Bioinformatics and QC metrics", "label": "Filepath R2 fastq" }, - "fastq_md5_r2": { + "sequence_file_R2_md5": { "examples": [ "3e69af1f875fab020aed82f5edbc1f03" ], - "ontology": "MS_1000568", + "ontology": "MS_1000569", "type": "string", "description": "", "clasification": "Bioinformatics and QC metrics", @@ -1285,7 +1285,7 @@ "runs" ] }, - "fastq_md5_r1": { + "sequence_file_R1_md5": { "examples": [ "" ], From f25420e62777bcb6d7e7a9fb4e00d11a49c71a3c Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 15 Sep 2022 17:03:10 +0200 Subject: [PATCH 0994/1454] remove ontology in value for map module --- relecov_tools/map_schema.py | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 2d57e3fe..655f0c14 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -141,6 +141,9 @@ def mapping_json_data(self, mapping_schema_dict): map_sample_dict = OrderedDict() for item, value in mapping_schema_dict.items(): try: + + data[value] = data[value].split(" [", 1)[0] + map_sample_dict[item] = data[value] except KeyError as e: log.warning("Property %s not set in the source data", e) @@ -155,10 +158,8 @@ def additional_formating(self, mapped_json_data): for idx in range(len(self.json_data)): mapped_json_data[idx]["collector_name"] = "unknown" - mapped_json_data[idx]["file_format"] = "FASTQ [format:1930]" - mapped_json_data[idx][ - "study_type" - ] = "Whole Genome Sequencing [NCIT:C101294]" + mapped_json_data[idx]["file_format"] = "FASTQ" + mapped_json_data[idx]["study_type"] = "Whole Genome Sequencing" mapped_json_data[idx][ "study_title" ] = "RELECOV Spanish Network for genomics surveillance" @@ -184,9 +185,9 @@ def additional_formating(self, mapped_json_data): ] mapped_json_data[idx]["sample_description"] = ( - self.json_data[idx]["anatomical_part"] + self.json_data[idx]["anatomical_part"].split(" [", 1)[0] + " " - + self.json_data[idx]["collection_method"] + + self.json_data[idx]["collection_method"].split(" [", 1)[0] ) mapped_json_data[idx]["isolate"] = self.json_data[idx][ "isolate_sample_id" @@ -197,15 +198,15 @@ def additional_formating(self, mapped_json_data): mapped_json_data[idx]["authors"] = self.json_data[idx]["authors"] mapped_json_data[idx]["design_description"] = ( - self.json_data[idx]["library_layout"] + self.json_data[idx]["library_layout"].split(" [", 1)[0] + " " - + self.json_data[idx]["library_preparation_kit"] + + self.json_data[idx]["library_preparation_kit"].split(" [", 1)[0] + " " - + self.json_data[idx]["library_selection"] + + self.json_data[idx]["library_selection"].split(" [", 1)[0] + " " - + self.json_data[idx]["library_source"] + + self.json_data[idx]["library_source"].split(" [", 1)[0] + " " - + self.json_data[idx]["library_strategy"] + + self.json_data[idx]["library_strategy"].split(" [", 1)[0] ) mapped_json_data[idx]["insert_size"] = "0" mapped_json_data[idx]["address"] = self.json_data[idx][ From 35ef7ad14cf22f38c50f836aa64d4f985dea3db7 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 16 Sep 2022 09:51:52 +0200 Subject: [PATCH 0995/1454] corrected spelling mistake on gisaid_id field --- relecov_tools/conf/configuration.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index c1c4b9c8..8bb20c87 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -171,7 +171,7 @@ "fastq.gz", "fasta" ], - "GISATD_configuration": { + "GISAID_configuration": { "submitter": "GISAID_ID" }, "external_url": { From bc38d6d63256ab6c369099ae1c18d4d26f50f0af Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 16 Sep 2022 09:55:20 +0200 Subject: [PATCH 0996/1454] lintin --- relecov_tools/gisaid_upload.py | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 4e723b43..fbfdaacb 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -6,13 +6,11 @@ import pandas as pd import os -# import ftplib import relecov_tools.utils from Bio import SeqIO from relecov_tools.config_json import ConfigJson import gzip - # import site @@ -38,7 +36,7 @@ def __init__( frameshift=None, proxy_config=None, single=False, - gzip=False + gzip=False, ): if ( token is None @@ -120,14 +118,13 @@ def complete_mand_fields(self, dataframe): dataframe.loc[ dataframe["covv_patient_status"] == "", "covv_patient_status" ] = "unknown" - + config_json = ConfigJson() gisaid_config = config_json.get_configuration("GISAID_configuration") submitter_id = gisaid_config["submitter"] dataframe.loc[dataframe["submitter"] == "", "submitter"] = submitter_id - - return dataframe + return dataframe def metadata_to_csv(self): """Transform metadata json to csv""" @@ -143,7 +140,9 @@ def metadata_to_csv(self): df_data.insert(4, field, "") config_lab_json = ConfigJson() - lab_json_conf = config_lab_json.get_topic_data("lab_metadata", "laboratory_data") + lab_json_conf = config_lab_json.get_topic_data( + "lab_metadata", "laboratory_data" + ) lab_json_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "conf", lab_json_conf["file"] ) @@ -159,7 +158,7 @@ def metadata_to_csv(self): lab["geo_loc_city"], ] ) - + df_data.replace("not provided", "unknown", inplace=True) df_data_comp = self.complete_mand_fields(df_data) df_data_path = os.path.join(self.output_path, "meta_gisaid.csv") @@ -193,21 +192,21 @@ def create_multifasta(self): gather_fastas_path = os.path.join(self.fasta_path, "*.fa*") if self.gzip: os.system( - "zcat %s > %s/multifasta.fasta" % ( - gather_fastas_path, self.output_path) + "zcat %s > %s/multifasta.fasta" + % (gather_fastas_path, self.output_path) ) else: os.system( - "cat %s > %s/multifasta.fasta" % (gather_fastas_path, - self.output_path) + "cat %s > %s/multifasta.fasta" + % (gather_fastas_path, self.output_path) ) multifasta = "%s/multifasta.fasta" % self.output_path else: if self.gzip: os.system( - "zcat %s > %s/multifasta.fasta" % (self.fasta_path, - self.output_path) + "zcat %s > %s/multifasta.fasta" + % (self.fasta_path, self.output_path) ) multifasta = "%s/multifasta.fasta" % self.output_path else: From e5913c9cc0d1d8ef0f550f1c6ffc6985160751ce Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Fri, 16 Sep 2022 10:05:12 +0200 Subject: [PATCH 0997/1454] lintin2 --- relecov_tools/__main__.py | 4 ++-- relecov_tools/gisaid_upload.py | 1 - 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 7e6b00da..5cffefcd 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -315,7 +315,7 @@ def upload_to_gisaid( frameshift, proxy_config, single, - gzip + gzip, ): """parsed data to create files to upload to gisaid""" upload_gisaid = relecov_tools.gisaid_upload.GisaidUpload( @@ -329,7 +329,7 @@ def upload_to_gisaid( frameshift, proxy_config, single, - gzip + gzip, ) upload_gisaid.gisaid_upload() diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index fbfdaacb..74d02e60 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -9,7 +9,6 @@ import relecov_tools.utils from Bio import SeqIO from relecov_tools.config_json import ConfigJson -import gzip # import site From a643459737cebfb10a6931891f695b1491418bc5 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 16 Sep 2022 10:21:39 +0200 Subject: [PATCH 0998/1454] added not provided config terms to mapped ENA json --- relecov_tools/map_schema.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 655f0c14..11a6196b 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -4,6 +4,7 @@ import json import jsonschema from jsonschema import Draft202012Validator +from relecov_tools.config_json import ConfigJson import logging import rich.console import os @@ -212,6 +213,13 @@ def additional_formating(self, mapped_json_data): mapped_json_data[idx]["address"] = self.json_data[idx][ "collecting_institution_address" ] + config_json = ConfigJson() + fields = config_json.get_configuration("ENA_fields")[ + "map_not_provided_fields" + ] + for i, j in enumerate(fields): + + mapped_json_data[idx][j] = "not provided" return mapped_json_data From b0471a45c27c09a59c20d9f2243a749bbeb63e25 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 16 Sep 2022 14:23:25 +0200 Subject: [PATCH 0999/1454] review --- relecov_tools/map_schema.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 11a6196b..fd8e187f 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -213,6 +213,7 @@ def additional_formating(self, mapped_json_data): mapped_json_data[idx]["address"] = self.json_data[idx][ "collecting_institution_address" ] + "Adding all the 'not provided' fields that are not being captured" config_json = ConfigJson() fields = config_json.get_configuration("ENA_fields")[ "map_not_provided_fields" From b4f5fa5faf8848405286a1a14396774f534bcf96 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 19 Sep 2022 13:44:50 +0200 Subject: [PATCH 1000/1454] review of ena_upload --- relecov_tools/conf/configuration.json | 50 ++++++++++++------------ relecov_tools/ena_upload.py | 50 +++++++++--------------- relecov_tools/map_schema.py | 3 ++ relecov_tools/schema/ena_schema.json | 12 ++++++ relecov_tools/schema/relecov_schema.json | 11 +++--- 5 files changed, 66 insertions(+), 60 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index efebc359..be2e6fca 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -59,7 +59,7 @@ "lab_metadata_req_json": { "laboratory_data": { "file": "laboratory_address.json", - "map_field": "collecting_institution", + "map_field": "collecting institution", "adding_fields": "__all__" }, "geo_location_data": { @@ -93,10 +93,10 @@ "Human": "host_scientific_name::Homo sapiens" }, "sequencing_instrument_model": { - "Illumina": "sequencing_instrument_platform::Illumina", - "PacBio": "sequencing_instrument_platform::PacBio", - "Ion Torrent": "sequencing_instrument_platform::Ion Torrent", - "Oxford Nanopore": "sequencing_instrument_platform::Oxford Nanopore" + "Illumina": "platform::Illumina", + "PacBio": "platform::PacBio", + "Ion Torrent": "platform::Ion Torrent", + "Oxford Nanopore": "platform::Oxford Nanopore" } }, "required_copy_from_other_field": { @@ -322,38 +322,38 @@ "checklist": "ERC000033", "df_study_fields": [ "study_type", - "study_abstract" + "study_abstract", + "study_alias", + "study_title" ], "df_samples_fields": [ "sample_name", "sample_title", - "taxon_id", - "collection_date", - "geographic_location_(country_and/or_sea)", - "host_common_name", - "host_scientific_name", - "host_sex", + "collection date", + "geographic location (country and/or sea)", + "host common name", + "host scientific name", + "host sex", "scientific_name", "collector_name", - "collecting_institution", + "collecting institution", "isolate", - "host_subject_id", + "host subject id", "host health state", "authors", + "taxon_id", "sample_description", "address" ], "df_run_fields": [ "r1_fastq_filepath", "r2_fastq_filepath", - "file_type", - "fastq_r1_md5", - "fastq_r2_md5", - "collecting_institution" + "file_format", + "sequence_file_R1_md5", + "sequence_file_R2_md5", + "collecting institution" ], "df_experiment_fields": [ - "study_abstract", - "sample_name", "library_name", "library_strategy", "library_source", @@ -361,9 +361,10 @@ "library_layout", "instrument_model", "design_description", - "collecting_institution", + "collecting institution", + "library_construction_protocol", "insert_size", - "sequencing_instrument_platform" + "platform" ], "rename_sample_list_og": [ "sample_name", @@ -372,10 +373,10 @@ "host_subject_id", "collection_date", "host_common_name", - "host_sex", + "host sex", "host_scientific_name", "collector_name", - "collecting_institution" + "collecting institution" ], "rename_sample_list_final": [ "alias", @@ -399,6 +400,7 @@ "illness symptoms", "host disease outcome", "definition for seropositive sample", + "library_construction_protocol", "serotype (required for a seropositive sample)", "strain", "host habitat", diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index a4fa3867..45183a6a 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -174,8 +174,8 @@ def create_structure_to_ena(self): """ # Parsing the dataframes specifically according to ENA requirements # # df_study - df_study["alias"] = df_study["study_abstract"][0].rsplit(" ", 5)[0] - df_study["title"] = df_study["study_abstract"] + df_study["alias"] = df_study["study_alias"] + df_study["title"] = df_study["study_title"] df_study.insert(3, "status", self.action) """ @@ -186,9 +186,6 @@ def create_structure_to_ena(self): """ # df_samples - df_samples["host_sex"].replace("unknown", "not provided", inplace=True) - df_samples["host_sex"].replace("Unknown", "not provided", inplace=True) - # df_samples_fileds_config = ["rename_sample_list_og", "rename_sample_list_final"] df_samples = self.rename_cols_df( "df_samples", df_samples, @@ -219,7 +216,7 @@ def create_structure_to_ena(self): ] df_run.insert(3, "status", self.action) - df_run = df_run.rename(columns={"fastq_r1_md5": "file_checksum"}) + df_run = df_run.rename(columns={"sequence_file_R1_md5": "file_checksum"}) for i in range(len(df_run)): df_run.loc[i, "alias"] = ( @@ -236,7 +233,7 @@ def create_structure_to_ena(self): df_run.insert(5, "file_name", df_run["sequence_file_R1_fastq"]) df_run2 = df_run.copy() df_run2["file_name"] = df_run["sequence_file_R2_fastq"] - df_run2["file_checksum"] = df_run["fastq_r2_md5"] + df_run2["file_checksum"] = df_run["sequence_file_R2_md5"] df_run_final = pd.concat([df_run, df_run2]) df_run_final.reset_index() @@ -248,9 +245,12 @@ def create_structure_to_ena(self): 2 214821_S12 214823_S1_R1_001.fastq.gz 214823_S1_R2_001.fastq.gz ... fastq c16bdbfc03c354496fcfb2c107e3cbf6 4d9b80b977a75bf7e2a4282ca910d94a """ # df_experiments + df_experiments["instrument_model"] = df_experiments[ "instrument_model" ].str.lower() + df_experiments["sample_alias"] = df_samples["alias"] + df_experiments["title"] = df_study["study_abstract"] df_experiments["study_alias"] = df_study["alias"] df_experiments.insert(3, "status", self.action) @@ -261,14 +261,6 @@ def create_structure_to_ena(self): + str(df_run.loc[i, "sequence_file_R2_fastq"]) ) - df_experiments = df_experiments.rename( - columns={"sequencing_instrument_platform": "platform"} - ) - df_experiments = df_experiments.rename(columns={"study_abstract": "title"}) - df_experiments = df_experiments.rename(columns={"sample_name": "sample_alias"}) - df_experiments = df_experiments.rename( - columns={"collecting_institution": "collecting institution"} - ) """ # df_experiments example experiment_alias title study_alias ... library_layout instrument_model alias @@ -305,8 +297,8 @@ def create_structure_to_ena(self): file_paths.update(file_paths_r2) - # submit data to webin ftp server. It should only upload fastq files in case the action is ADD. - # # When the action is MODIFY rthe fastq are already submitted + # Submit data to webin ftp server. It should only upload fastq files in case the action is ADD. + # When the action is MODIFY rthe fastq are already submitted """ if self.action == "ADD" or self.action == "add": session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) @@ -328,23 +320,20 @@ def create_structure_to_ena(self): g2 = session.quit() print(g2) """ - - # THE ENA_UPLOAD_CLI METHOD DOES NOT WORK (below) - # chec = submit_data(file_paths, self.passwd, self.user) - # print(chec) - - # when ADD/MODIFY, - # - # requires source XMLs for 'run', 'experiment', 'sample', 'experiment' - # schema_xmls record XMLs for all these schema and following 'submission' - + """ + THE ENA_UPLOAD_CLI METHOD DOES NOT WORK (below) + chec = submit_data(file_paths, self.passwd, self.user) + print(chec) + When ADD/MODIFY: + requires source XMLs for 'run', 'experiment', 'sample', 'experiment' + schema_xmls record XMLs for all these schema and following 'submission' + """ tool = config_json.get_configuration("ENA_fields")["tool"] schema_xmls = run_construct( template_path, schema_targets, self.center, checklist, tool ) - # submission_xml = construct_submission(template_path, self.action, schema_xmls, self.center, checklist, tool) submission_xml = construct_submission( template_path, self.action, schema_xmls, self.center, checklist, tool ) @@ -355,13 +344,13 @@ def create_structure_to_ena(self): for files in root.iter("FILE"): if "R2" in files.attrib["filename"]: - # print(files.attrib["filename"]) + H = df_run_final.loc[ df_run_final["sequence_file_R2_fastq"] == files.attrib["filename"] ].values[0][8] files.set("checksum", H) - # print(files.attrib["checksum"]) + tree.write(schema_xmls["run"]) if self.dev: @@ -389,7 +378,6 @@ def create_structure_to_ena(self): schema_dataframe = update_table( schema_dataframe, schema_targets, schema_update ) - ###### def upload(self): """Create the required files and upload to ENA""" diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index fd8e187f..267dafb6 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -181,6 +181,9 @@ def additional_formating(self, mapped_json_data): mapped_json_data[idx]["sample_name"] = self.json_data[idx][ "sequencing_sample_id" ] + mapped_json_data[idx]["host subject id"] = self.json_data[idx][ + "sequencing_sample_id" + ] mapped_json_data[idx]["study_alias"] = self.json_data[idx][ "schema_name" ] diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 1a82dcf3..64fd9967 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -611,6 +611,18 @@ "sample" ] }, + "taxon_id": { + "examples": [ + "2697049" + ], + "ontology": "NCIT:C164641", + "type": "string", + "description": "The NCBITaxon identifier for the organism being sequenced.", + "classification": "Sample collection and processing", + "label": "Tax ID", + "fill_mode": "batch", + "minLenght": "1" + }, "definition for seropositive sample": { "examples": [ "" diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index ec7242ca..0a3108d1 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -874,17 +874,18 @@ "fill_mode": "batch", "minLenght": "1" }, - "host_subject_id": { + "host subject id": { "examples": [ "e.g. #131" ], "ontology": "GENEPIO:0001398", "type": "string", - "description": "An unique identifier by which each subject can be referred to, de-identified.", - "classification": "Host information", + "description": "a unique identifier by which each subject can be referred to, de-identified.", + "clasification": "Host information", "label": "Host Subject Id", - "fill_mode": "sample", - "minLenght": "1" + "table": [ + "sample" + ] }, "host_health_state": { "examples": [ From 52e0360d719f8d1f3529338fc989add2cd27d637 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 19 Sep 2022 13:48:04 +0200 Subject: [PATCH 1001/1454] lintin --- relecov_tools/ena_upload.py | 1 - relecov_tools/map_schema.py | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 45183a6a..39c0042f 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -288,7 +288,6 @@ def create_structure_to_ena(self): ): file_paths = {} file_paths_r2 = {} - for path in df_schemas["r1_fastq_filepath"]: file_paths[os.path.basename(path)] = os.path.abspath(path) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 267dafb6..f19c71ba 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -12,7 +12,7 @@ # import jsonschema import relecov_tools.utils -from relecov_tools.config_json import ConfigJson + log = logging.getLogger(__name__) stderr = rich.console.Console( From afc5d38d1469598f6e48aabfe3785ee507298ba5 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 19 Sep 2022 13:50:04 +0200 Subject: [PATCH 1002/1454] lintin --- relecov_tools/ena_upload.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 39c0042f..b3463e80 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -327,6 +327,7 @@ def create_structure_to_ena(self): requires source XMLs for 'run', 'experiment', 'sample', 'experiment' schema_xmls record XMLs for all these schema and following 'submission' """ + # tool = config_json.get_configuration("ENA_fields")["tool"] schema_xmls = run_construct( From 6f489b212d1cf058b7f161533ced55fbe8843b4d Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 19 Sep 2022 13:51:03 +0200 Subject: [PATCH 1003/1454] lintin --- relecov_tools/ena_upload.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index b3463e80..39ab7216 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -322,7 +322,7 @@ def create_structure_to_ena(self): """ THE ENA_UPLOAD_CLI METHOD DOES NOT WORK (below) chec = submit_data(file_paths, self.passwd, self.user) - print(chec) + print(chec) When ADD/MODIFY: requires source XMLs for 'run', 'experiment', 'sample', 'experiment' schema_xmls record XMLs for all these schema and following 'submission' From d04685234105a7dd4ed90bbeb4aa1b4eadf8996f Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 19 Sep 2022 13:52:03 +0200 Subject: [PATCH 1004/1454] lintin --- relecov_tools/ena_upload.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 39ab7216..e5c25e62 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -322,7 +322,7 @@ def create_structure_to_ena(self): """ THE ENA_UPLOAD_CLI METHOD DOES NOT WORK (below) chec = submit_data(file_paths, self.passwd, self.user) - print(chec) + print(chec) When ADD/MODIFY: requires source XMLs for 'run', 'experiment', 'sample', 'experiment' schema_xmls record XMLs for all these schema and following 'submission' From ecc3fc8c7cd50d22bbf29c08730ab39fc5e181fc Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 20 Sep 2022 13:19:28 +0200 Subject: [PATCH 1005/1454] review of read bioinfo module and configuration --- relecov_tools/conf/configuration.json | 8 +++++--- relecov_tools/ena_upload.py | 6 +++--- relecov_tools/map_schema.py | 8 ++++++++ relecov_tools/read_bioinfo_metadata.py | 4 ++-- 4 files changed, 18 insertions(+), 8 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index be2e6fca..bcb76fb2 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -251,14 +251,13 @@ "consensus_sequence_filename", "consensus_sequence_filepath", "consensus_sequence_md5", - "consensus_sequence_name", "number_of_base_pairs_sequenced" ], "mapping_pangolin": { "variant_designation": "scorpio_call" }, "mapping_stats": { - "analysis_date": "analysis date", + "analysis date": "analysis date", "depth_of_coverage_value": "medianDPcoveragevirus", "lineage_name": "Lineage", "number_of_variants_in_consensus": "Variantsinconsensusx10", @@ -287,6 +286,9 @@ "mapping_software_name": { "BOWTIE2_ALIGN": "bowtie2" }, + "mapping_software_version": { + "BOWTIE2_ALIGN": "2.4.4" + }, "preprocessing_software_version": { "FASTP": "fastp" }, @@ -302,7 +304,7 @@ "sequence_file_R2_fastq": "sequence_file_R2_fastq", "sequence_file_R1_md5": "sequence_file_R1_md5", "sequence_file_R2_md5": "sequence_file_R2_md5", - "sequencing_sample_id": "sample_name" + "sequencing_sample_id": "sequencing_sample_id" } }, "md5_file_name": "md5_check_file.csv", diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index e5c25e62..d41df2b5 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -14,7 +14,7 @@ import sys import os -# import ftplib +import ftplib import relecov_tools.utils from relecov_tools.config_json import ConfigJson @@ -298,7 +298,7 @@ def create_structure_to_ena(self): # Submit data to webin ftp server. It should only upload fastq files in case the action is ADD. # When the action is MODIFY rthe fastq are already submitted - """ + if self.action == "ADD" or self.action == "add": session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) @@ -318,7 +318,7 @@ def create_structure_to_ena(self): g2 = session.quit() print(g2) - """ + """ THE ENA_UPLOAD_CLI METHOD DOES NOT WORK (below) chec = submit_data(file_paths, self.passwd, self.user) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index f19c71ba..97f016bc 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -221,6 +221,14 @@ def additional_formating(self, mapped_json_data): fields = config_json.get_configuration("ENA_fields")[ "map_not_provided_fields" ] + mapped_json_data[idx]["r1_fastq_filepath"] = ( + self.json_data[idx]["r1_fastq_filepath"] + + self.json_data[idx]["sequence_file_R1_fastq"] + ) + mapped_json_data[idx]["r2_fastq_filepath"] = ( + self.json_data[idx]["r2_fastq_filepath"] + + self.json_data[idx]["sequence_file_R2_fastq"] + ) for i, j in enumerate(fields): mapped_json_data[idx][j] = "not provided" diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 3dee8794..1c618fea 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -101,7 +101,7 @@ def include_data_from_mapping_stats(self, j_data): for row in j_data: for field, value in mapping_fields.items(): try: - row[field] = map_data[row["sample_name"]][value] + row[field] = map_data[row["sequencing_sample_id"]][value] except KeyError as e: log.error("Field %s not found in mapping stats", e) stderr.print(f"[red]Field {e} not found in mapping stats") @@ -118,7 +118,7 @@ def include_pangolin_data(self, j_data): sample_name = row["sample_name"].replace("-", "_") else: sample_name = row["sample_name"] - f_name = sample_name + ".pangolin." + row["analysis_date"] + ".csv" + f_name = sample_name + ".pangolin." + row["analysis date"] + ".csv" f_path = os.path.join(self.input_folder, f_name) try: f_data = relecov_tools.utils.read_csv_file_return_dict(f_path, ",") From 1363f00eb611a7c685bc3521b47a53a7a3d593d3 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 20 Sep 2022 14:02:40 +0200 Subject: [PATCH 1006/1454] changes in anatomical config based on maria correction --- ...anatomical_material_collection_method.json | 58 +++++++++---------- 1 file changed, 29 insertions(+), 29 deletions(-) diff --git a/relecov_tools/conf/anatomical_material_collection_method.json b/relecov_tools/conf/anatomical_material_collection_method.json index 35385768..adcce820 100644 --- a/relecov_tools/conf/anatomical_material_collection_method.json +++ b/relecov_tools/conf/anatomical_material_collection_method.json @@ -731,81 +731,81 @@ "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, - "Bronchiole Scraping": { + "Bronchiole Extract": { "anatomical_part": "Bronchiole", - "collection_method": "Scraping", + "collection_method": "Extract", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, - "Alveolar sac Scraping": { + "Alveolar sac Extract": { "anatomical_part": "Alveolar sac", - "collection_method": "Scraping", + "collection_method": "Extract", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, - "Pleural sac Scraping": { + "Pleural sac Extract": { "anatomical_part": "Pleural sac", - "collection_method": "Scraping", + "collection_method": "Extract", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, - "Pleural cavity Scraping": { + "Pleural cavity Extract": { "anatomical_part": "Pleural cavity", - "collection_method": "Scraping", + "collection_method": "Extract", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, - "Trachea Scraping": { + "Trachea Extract": { "anatomical_part": "Trachea", - "collection_method": "Scraping", + "collection_method": "Extract", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, - "Upper respiratory tract Scraping": { + "Upper respiratory tract Extract": { "anatomical_part": "Upper respiratory tract", - "collection_method": "Scraping", + "collection_method": "Extract", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, - "Anterior Nares Scraping": { + "Anterior Nares Extract": { "anatomical_part": "Anterior Nares", - "collection_method": "Scraping", + "collection_method": "Extract", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, - "Esophagus Scraping": { + "Esophagus Extract": { "anatomical_part": "Esophagus", - "collection_method": "Scraping", + "collection_method": "Extract", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, - "Ethmoid sinus Scraping": { + "Ethmoid sinus Extract": { "anatomical_part": "Ethmoid sinus", - "collection_method": "Scraping", + "collection_method": "Extract", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, - "Nasal Cavity Scraping": { + "Nasal Cavity Extract": { "anatomical_part": "Nasal Cavity", - "collection_method": "Scraping", + "collection_method": "Extract", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, - "Middle Nasal Turbinate Scraping": { + "Middle Nasal Turbinate Extract": { "anatomical_part": "Middle Nasal Turbinate", - "collection_method": "Scraping", + "collection_method": "Extract", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, - "Nasopharynx Scraping": { + "Nasopharynx Extract": { "anatomical_part": "Nasopharynx", - "collection_method": "Scraping", + "collection_method": "Extract", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, - "Oropharynx Scraping": { + "Oropharynx Extract": { "anatomical_part": "Oropharynx", - "collection_method": "Scraping", + "collection_method": "Extract", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, @@ -995,9 +995,9 @@ "body_product": "Not Applicable", "anatomical_material": "Tissue" }, - "Scraping": { + "Extract": { "anatomical_part": "Not Applicable", - "collection_method": "Scraping", + "collection_method": "Extract", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, @@ -1007,4 +1007,4 @@ "body_product": "Not Applicable", "anatomical_material": "Placenta" } -} +} \ No newline at end of file From 0cebbd704631a610f6f6a338aeab72ed7d9dc639 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 22 Sep 2022 09:41:02 +0200 Subject: [PATCH 1007/1454] working on lineage analysis software version --- relecov_tools/conf/configuration.json | 4 +--- relecov_tools/ena_upload.py | 1 + relecov_tools/read_bioinfo_metadata.py | 24 ++++++++++++++---------- relecov_tools/utils.py | 1 + 4 files changed, 17 insertions(+), 13 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index bcb76fb2..2b87c502 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -287,7 +287,7 @@ "BOWTIE2_ALIGN": "bowtie2" }, "mapping_software_version": { - "BOWTIE2_ALIGN": "2.4.4" + "BOWTIE2_ALIGN": "bowtie2" }, "preprocessing_software_version": { "FASTP": "fastp" @@ -300,8 +300,6 @@ "read_length": "number_of_base_pairs_sequenced", "schema_name": "schema_name", "schema_version": "schema_version", - "sequence_file_R1_fastq": "sequence_file_R1_fastq", - "sequence_file_R2_fastq": "sequence_file_R2_fastq", "sequence_file_R1_md5": "sequence_file_R1_md5", "sequence_file_R2_md5": "sequence_file_R2_md5", "sequencing_sample_id": "sequencing_sample_id" diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index d41df2b5..46432e4e 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,3 +1,4 @@ +from distutils.errors import LibError import logging # from re import template diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 1c618fea..ba033879 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -89,7 +89,7 @@ def include_data_from_mapping_stats(self, j_data): per_genome_greater_10x. per_Ns. per_reads_host, per_reads_virus. per_unmapped, qc_filtered, reference_genome_accession """ - # position of the aample columns inside mapping file + # position of the sample columns inside mapping file sample_position = 4 map_data = relecov_tools.utils.read_csv_file_return_dict( self.mapping_illumina, ",", sample_position @@ -114,12 +114,13 @@ def include_pangolin_data(self, j_data): "bioinfo_analysis", "mapping_pangolin" ) for row in j_data: - if "-" in row["sample_name"]: - sample_name = row["sample_name"].replace("-", "_") + if "-" in row["sequencing_sample_id"]: + sample_name = row["sequencing_sample_id"].replace("-", "_") else: - sample_name = row["sample_name"] + sample_name = row["sequencing_sample_id"] f_name = sample_name + ".pangolin." + row["analysis date"] + ".csv" f_path = os.path.join(self.input_folder, f_name) + try: f_data = relecov_tools.utils.read_csv_file_return_dict(f_path, ",") except FileNotFoundError as e: @@ -145,10 +146,10 @@ def include_consensus_data(self, j_data): "bioinfo_analysis", "mapping_consensus" ) for row in j_data: - if "-" in row["sample_name"]: - sample_name = row["sample_name"].replace("-", "_") + if "-" in row["sequencing_sample_id"]: + sample_name = row["sequencing_sample_id"].replace("-", "_") else: - sample_name = row["sample_name"] + sample_name = row["sequencing_sample_id"] f_name = sample_name + ".consensus.fa" f_path = os.path.join(self.input_folder, f_name) try: @@ -164,12 +165,12 @@ def include_consensus_data(self, j_data): row["consensus_genome_length"] = str(len(record_fasta)) row["consensus_sequence_name"] = record_fasta.description row["consensus_sequence_filepath"] = self.input_folder - row["consensus_file_name"] = f_name + row["consensus_sequence_filename"] = f_name row["consensus_sequence_md5"] = relecov_tools.utils.calculate_md5(f_path) base_calculation = int(row["number_of_base_pairs_sequenced"]) * len( record_fasta ) - if row["sequence_file_R2_fastq"] != "": + if row["sequencing_sample_id"] != "": row["number_of_base_pairs_sequenced"] = str(base_calculation * 2) else: row["number_of_base_pairs_sequenced"] = str(base_calculation) @@ -203,7 +204,7 @@ def include_variant_metrics(self, j_data): for row in j_data: for field, value in mapping_fields.items(): try: - row[field] = map_data[row["sample_name"]][value] + row[field] = map_data[row["sequencing_sample_id"]][value] except KeyError as e: log.error("Field %s not found in mapping stats", e) stderr.print(f"[red]Field {e} not found in mapping stats") @@ -215,6 +216,7 @@ def include_software_versions(self, j_data): version_fields = self.configuration.get_topic_data( "bioinfo_analysis", "mapping_version" ) + try: versions = relecov_tools.utils.read_yml_file(self.req_files["versions"]) except YAMLError as e: @@ -224,7 +226,9 @@ def include_software_versions(self, j_data): sys.exit(1) for row in j_data: for field, version_data in version_fields.items(): + for key, value in version_data.items(): + row[field] = versions[key][value] return j_data diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index d803238b..2d3a04b9 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -78,6 +78,7 @@ def read_csv_file_return_dict(file_name, sep, key_position=None): where the main key is the first column, if key position is None otherwise the index value of the kwy position is used as key """ + try: with open(file_name, "r") as fh: lines = fh.readlines() From 358335ce75c3846ad8f805f654071d5037549ccc Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 22 Sep 2022 10:51:29 +0200 Subject: [PATCH 1008/1454] lintin --- relecov_tools/ena_upload.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 46432e4e..cd507169 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,4 +1,4 @@ -from distutils.errors import LibError +# from distutils.errors import LibError import logging # from re import template From bfa743bd0495400b6f2af428f7dbaa5ce2c16077 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Mon, 26 Sep 2022 13:53:13 +0200 Subject: [PATCH 1009/1454] added default values for covv_type and covv_passage in gisaid_upload --- relecov_tools/gisaid_upload.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 74d02e60..7716d092 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -117,6 +117,8 @@ def complete_mand_fields(self, dataframe): dataframe.loc[ dataframe["covv_patient_status"] == "", "covv_patient_status" ] = "unknown" + dataframe.loc[dataframe["covv_type"] == "", "covv_type"] = "betacoronavirus" + dataframe.loc[dataframe["covv_passage"] =="", "covv_passage"] = "Original" config_json = ConfigJson() gisaid_config = config_json.get_configuration("GISAID_configuration") @@ -129,7 +131,6 @@ def metadata_to_csv(self): """Transform metadata json to csv""" data = relecov_tools.utils.read_json_file(self.gisaid_json) df_data = pd.DataFrame(data) - df_data.insert(4, "covv_passage", "Original") config_json = ConfigJson() fields = config_json.get_configuration("gisaid_csv_headers") @@ -164,6 +165,7 @@ def metadata_to_csv(self): if not os.path.exists(self.output_path): os.mkdir(self.output_path) df_data_comp.to_csv(df_data_path, index=False) + import pdb; pdb.set_trace() return df_data_path # generar template con cli3 From 1bd39d60eef1af96deaed58fddfa7eb4c05df10b Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 27 Sep 2022 09:11:45 +0200 Subject: [PATCH 1010/1454] assembly method is retrieved from config json (gisaid_upload) --- relecov_tools/gisaid_upload.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 7716d092..4a3d5cea 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -124,6 +124,10 @@ def complete_mand_fields(self, dataframe): gisaid_config = config_json.get_configuration("GISAID_configuration") submitter_id = gisaid_config["submitter"] dataframe.loc[dataframe["submitter"] == "", "submitter"] = submitter_id + + bioinfo_config = config_json.get_configuration("bioinfo_analysis") + assembly_method = bioinfo_config["fixed_values"]["bioinformatics_protocol_software_name"] + dataframe.loc[dataframe["covv_assembly_method"] == "", "covv_assembly_method"] = assembly_method return dataframe @@ -165,7 +169,6 @@ def metadata_to_csv(self): if not os.path.exists(self.output_path): os.mkdir(self.output_path) df_data_comp.to_csv(df_data_path, index=False) - import pdb; pdb.set_trace() return df_data_path # generar template con cli3 From e1f4156649591c16eec340a2ac35e0be45eea968 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 27 Sep 2022 09:29:55 +0200 Subject: [PATCH 1011/1454] changed default value of token argument (gisaid_upload) --- relecov_tools/gisaid_upload.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 4a3d5cea..b05d4af1 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -240,6 +240,7 @@ def cli3_auth(self): "cli3 authenticate --username %s --password %s --client_id %s" % (self.user, self.passwd, self.client_id) ) + self.token = "gisaid.authtoken" def cli3_upload(self): """Upload to GISAID""" From d9ffd4d7c40bf1059759909761cf9166515f9ebe Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 27 Sep 2022 09:49:14 +0200 Subject: [PATCH 1012/1454] added patient status field to gisaid_schema --- relecov_tools/schema/gisaid_schema.json | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/relecov_tools/schema/gisaid_schema.json b/relecov_tools/schema/gisaid_schema.json index 5ddecb0f..d32237b6 100644 --- a/relecov_tools/schema/gisaid_schema.json +++ b/relecov_tools/schema/gisaid_schema.json @@ -247,6 +247,15 @@ "classification": "Database Identifiers", "label": "Sample ID given by originating laboratory", "fill_mode": "sample" + }, + "covv_patient_status": { + "examples": ["Hospitalized", "Released", "Live", "Deceased"], + "ontology": "GENEPIO:0001388", + "type": "string", + "description": " Status of the host", + "classification": "Host information", + "label": "Host health state", + "fill_mode": "sample" } } } From efbe49fc77fbc0ba6bd087a9b76d194daaabc298 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 27 Sep 2022 10:06:09 +0200 Subject: [PATCH 1013/1454] added ontology of submitting_lab_sample_id to gisaid and relecov schemas --- relecov_tools/schema/gisaid_schema.json | 9 +++++++++ relecov_tools/schema/relecov_schema.json | 2 +- 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/relecov_tools/schema/gisaid_schema.json b/relecov_tools/schema/gisaid_schema.json index d32237b6..20c1ddcb 100644 --- a/relecov_tools/schema/gisaid_schema.json +++ b/relecov_tools/schema/gisaid_schema.json @@ -240,6 +240,15 @@ "label": "Submitting Institution" }, "covv_subm_sample_id": { + "examples": "", + "ontology": "GENEPIO:0001148", + "type": "string", + "description": "Sample ID given by the submitting laboratory", + "classification": "Database Identifiers", + "label": "Sample ID given by submitting laboratory", + "fill_mode": "sample" + }, + "covv_provider_sample_id": { "examples": ["prov_rona_99"], "ontology": "GENEPIO:0001123", "type": "string", diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 6c9161e3..e44f32a2 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -114,7 +114,7 @@ "examples": [ "" ], - "ontology": "0", + "ontology": "GENEPIO:0001148", "type": "string", "description": "Sample ID given by the submitting laboratory", "classification": "Sequencing", From 6aabbe7f47c88a7e8967b86275ffac37faa8c26e Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Tue, 27 Sep 2022 11:43:18 +0200 Subject: [PATCH 1014/1454] added error if author is empty or unknown (gisaid_upload) --- relecov_tools/gisaid_upload.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index b05d4af1..b9de793f 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -2,7 +2,7 @@ # from pyparsing import col import rich.console - +import sys import pandas as pd import os @@ -105,7 +105,13 @@ def complete_mand_fields(self, dataframe): dataframe.loc[ dataframe["covv_patient_age"] == "", "covv_patient_age" ] = "unknown" - dataframe.loc[dataframe["covv_authors"] == "", "covv_authors"] = "unknown" + + authors = [authors_field for authors_field in dataframe["covv_authors"]] + if "" in authors or "unknown" in authors: + log.error( "Invalid value for author. This field is required in full") + stderr.print("[red] Invalid value for authors. This field is required in full, 'unknown' is not allowed") + sys.exit(1) + dataframe.loc[ dataframe["covv_subm_lab_addr"] == "", "covv_subm_lab_addr" ] = "unknown" @@ -130,7 +136,7 @@ def complete_mand_fields(self, dataframe): dataframe.loc[dataframe["covv_assembly_method"] == "", "covv_assembly_method"] = assembly_method return dataframe - + def metadata_to_csv(self): """Transform metadata json to csv""" data = relecov_tools.utils.read_json_file(self.gisaid_json) From fea515d81ef9be073d1faab9956ce40d74a50677 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 3 Oct 2022 10:46:30 +0200 Subject: [PATCH 1015/1454] fix bug in long_table_parse, because of change in config heading --- relecov_tools/long_table_parse.py | 22 +++++++--------------- 1 file changed, 7 insertions(+), 15 deletions(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index 3c81c521..a16cc195 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -23,7 +23,6 @@ class LongTableParse: """ - - parse_a_list_of_dictionaries() : returns generated_JSON - saving_file(generated_JSON) - parsing_csv() : It manages all this proccess: @@ -62,9 +61,7 @@ def __init__(self, file_path=None, output_directory=None): Path(self.output_directory).mkdir(parents=True, exist_ok=True) config_json = ConfigJson() - self.long_table_heading = config_json.get_topic_data( - "headings", "long_table_heading" - ) + self.long_table_heading = config_json.get_configuration("long_table_heading") def validate_file(self, heading): """Check if long table file has all mandatory fields defined in @@ -78,12 +75,9 @@ def validate_file(self, heading): return True def parse_file(self): - """_summary_ - This function generates a json file from the csv file entered by the user - (long_table.csv). - - Checks if expected headers match with file headers - Returns: - dictionary with key as sample and value the list of variants + """This function generates a json file from the csv file entered by + the user (long_table.csv). + Validate the file by checking the header line """ with open(self.file_path) as fh: lines = fh.readlines() @@ -135,7 +129,6 @@ def parse_file(self): return samp_dict def convert_to_json(self, samp_dict): - """ """ j_list = [] for key, values in samp_dict.items(): j_dict = {"sample_name": key} @@ -143,9 +136,8 @@ def convert_to_json(self, samp_dict): j_list.append(j_dict) return j_list - def saving_file(self, j_list): - """ - Transform the p0arsed data into a jsonf file, naming as + def save_to_file(self, j_list): + """Transform the parsed data into a jsonf file, naming as "long_table_" + "current date" + ".json" """ stderr.print("[blue]Saving parsed data to file") @@ -164,5 +156,5 @@ def parsing_csv(self): stderr.print("[blue]Starting reading the input file") parsed_data = self.parse_file() j_list = self.convert_to_json(parsed_data) - self.saving_file(j_list) + self.save_to_file(j_list) stderr.print("[green]Process completed") From 53c239d96b3c94f1de027cfda29653026ca35921 Mon Sep 17 00:00:00 2001 From: Maria Lara Date: Wed, 5 Oct 2022 13:29:29 +0200 Subject: [PATCH 1016/1454] lintin --- relecov_tools/gisaid_upload.py | 24 +++++++++++++++--------- 1 file changed, 15 insertions(+), 9 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index b9de793f..1920a0e2 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -105,13 +105,15 @@ def complete_mand_fields(self, dataframe): dataframe.loc[ dataframe["covv_patient_age"] == "", "covv_patient_age" ] = "unknown" - + authors = [authors_field for authors_field in dataframe["covv_authors"]] if "" in authors or "unknown" in authors: - log.error( "Invalid value for author. This field is required in full") - stderr.print("[red] Invalid value for authors. This field is required in full, 'unknown' is not allowed") + log.error("Invalid value for author. This field is required in full") + stderr.print( + "[red] Invalid value for authors. This field is required in full, 'unknown' is not allowed" + ) sys.exit(1) - + dataframe.loc[ dataframe["covv_subm_lab_addr"] == "", "covv_subm_lab_addr" ] = "unknown" @@ -124,19 +126,23 @@ def complete_mand_fields(self, dataframe): dataframe["covv_patient_status"] == "", "covv_patient_status" ] = "unknown" dataframe.loc[dataframe["covv_type"] == "", "covv_type"] = "betacoronavirus" - dataframe.loc[dataframe["covv_passage"] =="", "covv_passage"] = "Original" + dataframe.loc[dataframe["covv_passage"] == "", "covv_passage"] = "Original" config_json = ConfigJson() gisaid_config = config_json.get_configuration("GISAID_configuration") submitter_id = gisaid_config["submitter"] dataframe.loc[dataframe["submitter"] == "", "submitter"] = submitter_id - + bioinfo_config = config_json.get_configuration("bioinfo_analysis") - assembly_method = bioinfo_config["fixed_values"]["bioinformatics_protocol_software_name"] - dataframe.loc[dataframe["covv_assembly_method"] == "", "covv_assembly_method"] = assembly_method + assembly_method = bioinfo_config["fixed_values"][ + "bioinformatics_protocol_software_name" + ] + dataframe.loc[ + dataframe["covv_assembly_method"] == "", "covv_assembly_method" + ] = assembly_method return dataframe - + def metadata_to_csv(self): """Transform metadata json to csv""" data = relecov_tools.utils.read_json_file(self.gisaid_json) From bdd147f9dc15f66b6730a22c149bba7cf579a291 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 6 Oct 2022 12:27:13 +0200 Subject: [PATCH 1017/1454] fix for working interactive --- relecov_tools/metadata_homogeneizer.py | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index dc31b1b9..35b5db38 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -29,17 +29,20 @@ def __init__(self, institution=None, directory=None, output_folder=None): self.institution = relecov_tools.utils.prompt_selection( msg="Select the available mapping institution", choices=["isciii", "hugtip", "hunsc-iter"], - ) + ).upper() else: self.institution = institution.upper() - mapping_json_file = os.path.join( - os.path.dirname(__file__), - "schema", - "institution_schemas", - self.config_json.get_topic_data( - "institution_mapping_file", self.institution - ), - ) + + mapping_json_file = os.path.join( + os.path.dirname(__file__), + "schema", + "institution_schemas", + self.config_json.get_topic_data( + "institution_mapping_file", self.institution + ), + ) + + self.mapping_json_data = relecov_tools.utils.read_json_file(mapping_json_file) if directory is None: directory = relecov_tools.utils.prompt_path( @@ -52,8 +55,6 @@ def __init__(self, institution=None, directory=None, output_folder=None): ) sys.exit(1) - self.mapping_json_data = relecov_tools.utils.read_json_file(mapping_json_file) - try: lab_metadata = self.mapping_json_data["required_files"]["metadata_file"][ "file_name" From 89604d47eb2446325a7162ffeb6546ee0fc67548 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 6 Oct 2022 14:35:51 +0200 Subject: [PATCH 1018/1454] linting --- relecov_tools/metadata_homogeneizer.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 35b5db38..aabf0548 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -63,7 +63,9 @@ def __init__(self, institution=None, directory=None, output_folder=None): log.error("Metadata File is not defined in schema") stderr.print("[red] Metadata File is not defined in schema") sys.exit(1) + metadata_path = os.path.join(directory, lab_metadata) + if not os.path.isfile(metadata_path): log.error("Metadata File %s does not exists", metadata_path) stderr.print("[red] Metadata File " + metadata_path + "does not exists") @@ -72,6 +74,7 @@ def __init__(self, institution=None, directory=None, output_folder=None): self.lab_metadata["file_name"] = metadata_path self.additional_files = [] + if len(self.mapping_json_data["required_files"]) > 1: for key, values in self.mapping_json_data["required_files"].items(): if key == "metadata_file": @@ -86,8 +89,10 @@ def __init__(self, institution=None, directory=None, output_folder=None): sys.exit(1) values["file_name"] = f_path self.additional_files.append(values) + # Check if python file is defined function_file = self.mapping_json_data["python_file"] + if function_file == "": self.function_file = None else: From 939ad1f2b789cd8c5e1702e48e46ab8192e1fcd7 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 7 Oct 2022 13:04:07 +0200 Subject: [PATCH 1019/1454] fixed issue 215. https://github.com/BU-ISCIII/relecov-tools/issues/215. Also replace clasification for classification. A 's' was missing --- relecov_tools/schema/relecov_schema.json | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 3abd6966..3849d449 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -551,9 +551,9 @@ "ontology": "GENEPIO:0000156", "type": "string", "description": "", - "clasification": "Submission ENA", + "classification": "Submission ENA", "label": "Study type", - "table": "study" + "fill_mode": "batch" }, "geo_loc_longitude": { "examples": [ @@ -874,18 +874,16 @@ "fill_mode": "batch", "minLenght": "1" }, - "host subject id": { + "host_subject_id": { "examples": [ "e.g. #131" ], "ontology": "GENEPIO:0001398", "type": "string", "description": "a unique identifier by which each subject can be referred to, de-identified.", - "clasification": "Host information", + "classification": "Host information", "label": "Host Subject Id", - "table": [ - "sample" - ] + "fill_mode": "sample" }, "host_health_state": { "examples": [ @@ -2529,4 +2527,4 @@ "fill_mode": "batch" } } -} \ No newline at end of file +} From ced02ba9c4d456127932a426fbc98bac501920d1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 7 Oct 2022 13:38:49 +0200 Subject: [PATCH 1020/1454] few comments in homogeneizer module --- relecov_tools/metadata_homogeneizer.py | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index aabf0548..e5c74cd6 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -20,11 +20,15 @@ class MetadataHomogeneizer: """MetadataHomogeneizer object""" def __init__(self, institution=None, directory=None, output_folder=None): + + # open config self.config_json = ConfigJson() + # read heading from config self.heading = self.config_json.get_topic_data( "lab_metadata", "metadata_lab_heading" ) + # handle institution if institution is None: self.institution = relecov_tools.utils.prompt_selection( msg="Select the available mapping institution", @@ -123,7 +127,6 @@ def mapping_metadata(self, ws_data): for row in ws_data: row_data = {} for dest_map, orig_map in map_fields.items(): - row_data[dest_map] = row[orig_map] map_data.append(row_data) @@ -145,7 +148,7 @@ def add_fixed_fields(self, mapped_data): add_data.append(new_row_data) return add_data - def handling_files(self, file_data, additional_data): + def handling_files(self, file_data, data_to_add): """Added information based on the required file configuration. The first time this function is called is for mapping the laboratory metadata to ISCIII. For this time mapping_metadata method is used. @@ -154,7 +157,7 @@ def handling_files(self, file_data, additional_data): """ if file_data["file_name"] != "": f_name = file_data["file_name"] - stderr.print("[blue] Start processing additional file " + f_name) + stderr.print("[blue] Starting processing file " + f_name) if f_name.endswith(".json"): data = relecov_tools.utils.read_json_file(f_name) elif f_name.endswith(".tsv"): @@ -180,7 +183,7 @@ def handling_files(self, file_data, additional_data): if file_data["function"] == "None": mapping_idx = self.heading.index(file_data["mapped_key"]) - for row in additional_data[1:]: + for row in data_to_add[1:]: # new_row_data = [] s_value = str(row[mapping_idx]) try: @@ -217,6 +220,7 @@ def handling_files(self, file_data, additional_data): + " import " + func_name ) + # somehow this overrides additional_data working as a pointer eval( func_name + "(additional_data, data, file_data['mapped_fields'], self.heading)" @@ -228,14 +232,20 @@ def handling_files(self, file_data, additional_data): def converting_metadata(self): stderr.print("[blue] Reading the metadata file to convert") + # metadata_file contains the primary source of information. First we map it. mapped_data = self.handling_files(self.lab_metadata, "") stderr.print("[green] Successful conversion mapping to ISCIII metadata") stderr.print("[blue] Adding fixed information") + + # Then we add the fixed data additional_data = self.add_fixed_fields(mapped_data) + # Fetch the additional files and include the information in metadata stderr.print("[blue] reading and mapping de information that are in files") for additional_file in self.additional_files: additional_data = self.handling_files(additional_file, additional_data) + + ## write to excel mapped data f_name = os.path.join(self.output_folder, "converted_metadata_lab.xlsx") stderr.print("[blue] Dumping information to excel") post_process = {"insert_rows": 3, "insert_cols": 1} From 07d23f1999adce5907cb0894bd2dff55cdbfd05d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 7 Oct 2022 13:44:45 +0200 Subject: [PATCH 1021/1454] fixed variable name in read lab metadata --- relecov_tools/read_lab_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 0f9fb9a7..573e8295 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -29,7 +29,7 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None self.metadata_file = metadata_file if not os.path.exists(self.metadata_file): log.error("Metadata file %s does not exist ", self.metadata_file) - stderr.print("[red] Metadata file " + self.meta_file + " does not exist") + stderr.print("[red] Metadata file " + self.metadata_file + " does not exist") sys.exit(1) if sample_list_file is None: self.sample_list_file = relecov_tools.utils.prompt_path( From c55e969a888634b0d22bff8683cec6e4337f75e2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 7 Oct 2022 13:53:12 +0200 Subject: [PATCH 1022/1454] removed wrong default --- relecov_tools/__main__.py | 5 ----- relecov_tools/read_lab_metadata.py | 7 ++++++- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 5cffefcd..b5175fc8 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -164,11 +164,6 @@ def download(user, password, conf_file, user_relecov, password_relecov): "-s", "--sample_list_file", type=click.Path(), - default=os.path.join( - os.path.dirname(os.path.realpath(__file__)), - "assets", - "additional_metadata.json", - ), help="Json with the additional metadata to add to the received user metadata", ) @click.option( diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 573e8295..bba4f390 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -27,28 +27,33 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None ) else: self.metadata_file = metadata_file + if not os.path.exists(self.metadata_file): log.error("Metadata file %s does not exist ", self.metadata_file) stderr.print("[red] Metadata file " + self.metadata_file + " does not exist") sys.exit(1) + if sample_list_file is None: self.sample_list_file = relecov_tools.utils.prompt_path( msg="Select the file which contains the sample information" ) else: self.sample_list_file = sample_list_file + if not os.path.exists(self.sample_list_file): - log.error("Sample information file %s does not exist ", self.metadata_file) + log.error("Sample information file %s does not exist ", self.sample_list_file) stderr.print( "[red] Sample information " + self.sample_list_file + " does not exist" ) sys.exit(1) + if output_folder is None: self.output_folder = relecov_tools.utils.prompt_path( msg="Select the output folder" ) else: self.output_folder = output_folder + config_json = ConfigJson() relecov_schema = config_json.get_topic_data("json_schemas", "relecov_schema") relecov_sch_path = os.path.join( From 46db0a9daf54e2733f88368ec821bbae173fb31e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 7 Oct 2022 14:01:50 +0200 Subject: [PATCH 1023/1454] fixed name in map field for lab metadata conversion --- relecov_tools/conf/configuration.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index e405a1bd..7db633a8 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -59,7 +59,7 @@ "lab_metadata_req_json": { "laboratory_data": { "file": "laboratory_address.json", - "map_field": "collecting institution", + "map_field": "collecting_institution", "adding_fields": "__all__" }, "geo_location_data": { @@ -409,4 +409,4 @@ "host behaviour" ] } -} \ No newline at end of file +} From dbb6cc05739ed6cdeb55073c503d52396a98394b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 7 Oct 2022 14:16:14 +0200 Subject: [PATCH 1024/1454] added warning message in except --- relecov_tools/read_lab_metadata.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index bba4f390..7c8631ef 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -68,6 +68,10 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None try: self.label_prop_dict[values["label"]] = prop except KeyError: + log.warning("Property %s does not have 'label' attribute", prop) + stderr.print( + "[orange] Property " + prop + " does not have 'label' attribute" + ) continue self.json_req_files = config_json.get_topic_data( "lab_metadata", "lab_metadata_req_json" From 1def424a6eb65d579e220c5b742662b86a7a5527 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 10 Oct 2022 14:13:56 +0200 Subject: [PATCH 1025/1454] added spaces for better reading --- relecov_tools/read_lab_metadata.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 7c8631ef..e1beca73 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -64,6 +64,7 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None with open(relecov_sch_path, "r") as fh: self.relecov_sch_json = json.load(fh) self.label_prop_dict = {} + for prop, values in self.relecov_sch_json["properties"].items(): try: self.label_prop_dict[values["label"]] = prop @@ -73,6 +74,7 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None "[orange] Property " + prop + " does not have 'label' attribute" ) continue + self.json_req_files = config_json.get_topic_data( "lab_metadata", "lab_metadata_req_json" ) From f5b9d441e5fece9ac03aeb5ba79b59b5b7d284ff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 10 Oct 2022 16:51:52 +0200 Subject: [PATCH 1026/1454] fixed specimen source splitting --- ...anatomical_material_collection_method.json | 6 +- relecov_tools/conf/configuration.json | 20 +- relecov_tools/read_lab_metadata.py | 25 ++- relecov_tools/schema/relecov_schema.json | 189 +++++++++++++++++- 4 files changed, 215 insertions(+), 25 deletions(-) diff --git a/relecov_tools/conf/anatomical_material_collection_method.json b/relecov_tools/conf/anatomical_material_collection_method.json index adcce820..2edc43d3 100644 --- a/relecov_tools/conf/anatomical_material_collection_method.json +++ b/relecov_tools/conf/anatomical_material_collection_method.json @@ -995,9 +995,9 @@ "body_product": "Not Applicable", "anatomical_material": "Tissue" }, - "Extract": { + "Scraping": { "anatomical_part": "Not Applicable", - "collection_method": "Extract", + "collection_method": "Scraping2", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, @@ -1007,4 +1007,4 @@ "body_product": "Not Applicable", "anatomical_material": "Placenta" } -} \ No newline at end of file +} diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 7db633a8..095cbd18 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -75,19 +75,17 @@ "submitting_institution_email" ] }, - "anatomical_material": { + "specimen_source_splitting": { "file": "anatomical_material_collection_method.json", - "map_field": { - "any_of": [ - "body_product", - "anatomical_part", - "collection_method", - "anatomical_material" - ] - }, - "adding_fields": "__all__" + "map_field": "specimen_source", + "adding_fields": [ + "anatomical_material", + "anatomical_part", + "body_product", + "collection_method" + ] } - }, + }, "required_post_processing": { "host_common_name": { "Human": "host_scientific_name::Homo sapiens" diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index e1beca73..68701004 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -153,17 +153,22 @@ def adding_ontology_to_enum(self, m_data): def process_from_json(self, m_data, json_fields): """ """ - if isinstance(json_fields["map_field"], dict): - # Search for the value which contains data - for m_field in json_fields["map_field"]["any_of"]: - try: - m_data[0][m_field] - map_field = m_field - except KeyError: - continue - else: - map_field = json_fields["map_field"] +# if isinstance(json_fields["map_field"], dict): +# # Search for the value which contains data +# for m_field in json_fields["map_field"]["any_of"]: +# try: +# #m_data[0][m_field] +# map_field = m_field +# except KeyError: +# continue +# else: + + map_field = json_fields["map_field"] + + import pdb; pdb.set_trace() + json_data = json_fields["j_data"] + if isinstance(json_data, dict): for idx in range(len(m_data)): m_data[idx].update(json_data[m_data[idx][map_field]]) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 3abd6966..3b197335 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -616,6 +616,193 @@ "label": "Anatomical Material", "fill_mode": "batch" }, + "specimen_source": { + "enum": [ + "Lower respiratory tract Aspiration", + "Bronchus Aspiration", + "Lung Aspiration", + "Bronchiole Aspiration", + "Alveolar sac Aspiration", + "Pleural sac Aspiration", + "Pleural cavity Aspiration", + "Trachea Aspiration", + "Upper respiratory tract Aspiration", + "Anterior Nares Aspiration", + "Esophagus Aspiration", + "Ethmoid sinus Aspiration", + "Nasal Cavity Aspiration", + "Middle Nasal Turbinate Aspiration", + "Pharynx Aspiration", + "Nasopharynx Aspiration", + "Oropharynx Aspiration", + "Lower respiratory tract Vacuum Aspiration", + "Bronchus Vacuum Aspiration", + "Lung Vacuum Aspiration", + "Bronchiole Vacuum Aspiration", + "Alveolar sac Vacuum Aspiration", + "Pleural sac Vacuum Aspiration", + "Pleural cavity Vacuum Aspiration", + "Trachea Vacuum Aspiration", + "Upper respiratory tract Vacuum Aspiration", + "Anterior Nares Vacuum Aspiration", + "Esophagus Vacuum Aspiration", + "Ethmoid sinus Vacuum Aspiration", + "Nasal Cavity Vacuum Aspiration", + "Middle Nasal Turbinate Vacuum Aspiration", + "Nasopharynx Vacuum Aspiration", + "Oropharynx Vacuum Aspiration", + "Lower respiratory tract Biopsy", + "Bronchus Biopsy", + "Lung Biopsy", + "Bronchiole Biopsy", + "Alveolar sac Biopsy", + "Pleural sac Biopsy", + "Pleural cavity Biopsy", + "Trachea Biopsy", + "Rectum Biopsy", + "Skin Biopsy", + "Stomach Biopsy", + "Upper respiratory tract Biopsy", + "Anterior Nares Biopsy", + "Esophagus Biopsy", + "Ethmoid sinus Biopsy", + "Nasal Cavity Biopsy", + "Middle Nasal Turbinate Biopsy", + "Anus Biopsy", + "Duodenum Biopsy", + "Nasopharynx Biopsy", + "Oropharynx Biopsy", + "Lower respiratory tract Needle Biopsy", + "Bronchus Needle Biopsy", + "Lung Needle Biopsy", + "Bronchiole Needle Biopsy", + "Alveolar sac Needle Biopsy", + "Pleural sac Needle Biopsy", + "Pleural cavity Needle Biopsy", + "Trachea Needle Biopsy", + "Rectum Needle Biopsy", + "Skin Needle Biopsy", + "Stomach Needle Biopsy", + "Upper respiratory tract Needle Biopsy", + "Anterior Nares Needle Biopsy", + "Esophagus Needle Biopsy", + "Ethmoid sinus Needle Biopsy", + "Nasal Cavity Needle Biopsy", + "Middle Nasal Turbinate Needle Biopsy", + "Anus Needle Biopsy", + "Duodenum Needle Biopsy", + "Nasopharynx Needle Biopsy", + "Oropharynx Needle Biopsy", + "Lower respiratory tract Lavage ", + "Pleural sac Lavage ", + "Pleural cavity Lavage ", + "Trachea Lavage ", + "Upper respiratory tract Lavage ", + "Anterior Nares Lavage ", + "Esophagus Lavage ", + "Ethmoid sinus Lavage ", + "Nasal Cavity Lavage ", + "Middle Nasal Turbinate Lavage ", + "Nasopharynx Lavage ", + "Oropharynx Lavage ", + "Bronchoalveolar Lavage", + "Gastric Lavage", + "Lower respiratory tract Necropsy", + "Bronchus Necropsy", + "Lung Necropsy", + "Bronchiole Necropsy", + "Alveolar sac Necropsy", + "Pleural sac Necropsy", + "Pleural cavity Necropsy", + "Trachea Necropsy", + "Rectum Necropsy", + "Skin Necropsy", + "Stomach Necropsy", + "Upper respiratory tract Necropsy", + "Anterior Nares Necropsy", + "Esophagus Necropsy", + "Ethmoid sinus Necropsy", + "Nasal Cavity Necropsy", + "Middle Nasal Turbinate Necropsy", + "Anus Necropsy", + "Duodenum Necropsy", + "Nasopharynx (NP) Necropsy", + "Oropharynx (OP) Necropsy", + "Lower respiratory tract Rinsing", + "Bronchus Rinsing", + "Lung Rinsing", + "Bronchiole Rinsing", + "Alveolar sac Rinsing", + "Pleural sac Rinsing", + "Pleural cavity Rinsing", + "Trachea Rinsing", + "Upper respiratory tract Rinsing", + "Anterior Nares Rinsing", + "Esophagus Rinsing", + "Ethmoid sinus Rinsing", + "Nasal Cavity Rinsing", + "Middle Nasal Turbinate Rinsing", + "Nasopharynx Rinsing", + "Oropharynx Rinsing", + "Bronchiole Scraping", + "Alveolar sac Scraping", + "Pleural sac Scraping", + "Pleural cavity Scraping", + "Trachea Scraping", + "Upper respiratory tract Scraping", + "Anterior Nares Scraping", + "Esophagus Scraping", + "Ethmoid sinus Scraping", + "Nasal Cavity Scraping", + "Middle Nasal Turbinate Scraping", + "Nasopharynx Scraping", + "Oropharynx Scraping", + "Nasopharynx Swabbing", + "Oropharynx Swabbing", + "Lower respiratory tract Wash", + "Bronchus Wash", + "Lung Wash", + "Bronchiole Wash", + "Alveolar sac Wash", + "Pleural sac Wash", + "Pleural cavity Wash", + "Trachea Wash", + "Upper respiratory tract Wash", + "Anterior Nares Wash", + "Esophagus Wash", + "Ethmoid sinus Wash", + "Nasal Cavity Wash", + "Middle Nasal Turbinate Wash", + "Nasopharynx Wash", + "Oropharynx Wash", + "Feces", + "Mucus", + "Sputum", + "Sweat", + "Tear", + "Urine", + "Blood", + "Fluid (Cerebrospinal (CSF))", + "Saliva", + "Tissue", + "Placenta", + "Scraping", + "Not Applicable", + "Not Collected", + "Not Provided", + "Missing", + "Restricted Access" + ], + "ontology": "0", + "type": "string", + "description": "", + "examples": [ + "" + ], + "classification": "Source of the specimen, merge of anatomical_part, anatomical_material, body_product and collection method.", + "label": "Specimen source", + "fill_mode": "batch" + }, "anatomical_part": { "enum": [ "Eye [UBERON:0000970]", @@ -2529,4 +2716,4 @@ "fill_mode": "batch" } } -} \ No newline at end of file +} From ab63894e9efee621402ca9d020c9235f4ef3061a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 10 Oct 2022 16:53:56 +0200 Subject: [PATCH 1027/1454] fixed samples id saved as floats, now they are written as strings --- relecov_tools/read_lab_metadata.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 68701004..e31b6946 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -279,6 +279,10 @@ def read_metadata_file(self): stderr.print( f"[red] Invalid date format in sample {sample_number}, {key}" ) + elif "sample id" in key.lower(): + if isinstance(row[key], float): + row[key] = str(int(row[key])) + else: if isinstance(row[key], float) or isinstance(row[key], int): row[key] = str(row[key]) From 1dfc19ed77c933965d9a0abe1fd09e321ab952d9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 10 Oct 2022 16:59:43 +0200 Subject: [PATCH 1028/1454] delete test code --- relecov_tools/read_lab_metadata.py | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index e31b6946..968f2135 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -153,20 +153,8 @@ def adding_ontology_to_enum(self, m_data): def process_from_json(self, m_data, json_fields): """ """ -# if isinstance(json_fields["map_field"], dict): -# # Search for the value which contains data -# for m_field in json_fields["map_field"]["any_of"]: -# try: -# #m_data[0][m_field] -# map_field = m_field -# except KeyError: -# continue -# else: - map_field = json_fields["map_field"] - import pdb; pdb.set_trace() - json_data = json_fields["j_data"] if isinstance(json_data, dict): From 2bd678e90c9e5c3a83ee273376856f9996ead4a3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 10 Oct 2022 17:00:10 +0200 Subject: [PATCH 1029/1454] black linting --- relecov_tools/read_lab_metadata.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 968f2135..cc73294d 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -30,7 +30,9 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None if not os.path.exists(self.metadata_file): log.error("Metadata file %s does not exist ", self.metadata_file) - stderr.print("[red] Metadata file " + self.metadata_file + " does not exist") + stderr.print( + "[red] Metadata file " + self.metadata_file + " does not exist" + ) sys.exit(1) if sample_list_file is None: @@ -41,7 +43,9 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None self.sample_list_file = sample_list_file if not os.path.exists(self.sample_list_file): - log.error("Sample information file %s does not exist ", self.sample_list_file) + log.error( + "Sample information file %s does not exist ", self.sample_list_file + ) stderr.print( "[red] Sample information " + self.sample_list_file + " does not exist" ) From 25ca3c6ac7ead52dac8928bb0f45c308f948e58b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 10 Oct 2022 17:03:15 +0200 Subject: [PATCH 1030/1454] fixed variable name homogeneizer --- relecov_tools/metadata_homogeneizer.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index e5c74cd6..f62f1d66 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -223,11 +223,11 @@ def handling_files(self, file_data, data_to_add): # somehow this overrides additional_data working as a pointer eval( func_name - + "(additional_data, data, file_data['mapped_fields'], self.heading)" + + "(data_to_add, data, file_data['mapped_fields'], self.heading)" ) stderr.print("[green] Succesful processing of additional file ") - return additional_data + return data_to_add def converting_metadata(self): stderr.print("[blue] Reading the metadata file to convert") From 05d4637d63342198c27731ae19267aced0772c2b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 10 Oct 2022 17:04:02 +0200 Subject: [PATCH 1031/1454] linting --- relecov_tools/metadata_homogeneizer.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index f62f1d66..e7d8a8ba 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -245,7 +245,7 @@ def converting_metadata(self): for additional_file in self.additional_files: additional_data = self.handling_files(additional_file, additional_data) - ## write to excel mapped data + # write to excel mapped data f_name = os.path.join(self.output_folder, "converted_metadata_lab.xlsx") stderr.print("[blue] Dumping information to excel") post_process = {"insert_rows": 3, "insert_cols": 1} From 0ba380867f557944cffb6ce95987e7726a8c1f86 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 10 Oct 2022 21:23:47 +0200 Subject: [PATCH 1032/1454] removed self.headers for the PUT request --- relecov_tools/rest_api.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/rest_api.py b/relecov_tools/rest_api.py index a5374519..c8618adc 100644 --- a/relecov_tools/rest_api.py +++ b/relecov_tools/rest_api.py @@ -57,7 +57,7 @@ def put_request(self, data, credentials, url): auth = (credentials["user"], credentials["pass"]) url_http = str(self.request_url + url) try: - req = requests.put(url_http, data=data, headers=self.headers, auth=auth) + req = requests.put(url_http, data=data, auth=auth) except requests.ConnectionError: log.error("Unable to open connection towards %s", self.request_url) stderr.print("[red] Unable to open connection towards ", self.request_url) From a5165717ebbba8f84b9b5127d54ca19f10464154 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 12:45:01 +0200 Subject: [PATCH 1033/1454] Fixed ena sample id label in schema, fixed conversion to str when sample id is an int besides a float --- relecov_tools/read_lab_metadata.py | 3 +-- relecov_tools/schema/relecov_schema.json | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index cc73294d..a7b655fd 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -160,7 +160,6 @@ def process_from_json(self, m_data, json_fields): map_field = json_fields["map_field"] json_data = json_fields["j_data"] - if isinstance(json_data, dict): for idx in range(len(m_data)): m_data[idx].update(json_data[m_data[idx][map_field]]) @@ -272,7 +271,7 @@ def read_metadata_file(self): f"[red] Invalid date format in sample {sample_number}, {key}" ) elif "sample id" in key.lower(): - if isinstance(row[key], float): + if isinstance(row[key], float) or isinstance(row[key], int): row[key] = str(int(row[key])) else: diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index a155be80..9384c9f7 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2632,7 +2632,7 @@ "type": "string", "description": "", "classification": "Public databases", - "label": "Sample accession", + "label": "ENA Sample ID", "fill_mode": "batch" }, "ena_experiment_accession": { From 1ed6c8de1504ad9713e5d1cfc96f57c3abebf0cb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 12:47:40 +0200 Subject: [PATCH 1034/1454] fixed comments --- relecov_tools/read_lab_metadata.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index a7b655fd..b3d84609 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -198,15 +198,17 @@ def adding_fields(self, metadata): values["j_data"] = relecov_tools.utils.read_json_file(f_path) metadata = self.process_from_json(metadata, values) stderr.print(f"[green] Processed {key}") - stderr.print("[blue] Reading sample list file") + # Because sample data file is comming in an input parameter it cannot # be inside the configuration json file. # Include Sample informatin data from sample json file + stderr.print("[blue] Processing sample data file") s_json = {} s_json["map_field"] = "sequencing_sample_id" s_json["adding_field"] = "__all__" s_json["j_data"] = relecov_tools.utils.read_json_file(self.sample_list_file) metadata = self.process_from_json(metadata, s_json) + stderr.print("[green] Processed sample data file.") return metadata def read_configuration_json_files(self): From 341b1aa1692fa8ebc36cb4d3d4f2d9ee8cc053a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 13:41:24 +0200 Subject: [PATCH 1035/1454] added recommended fields to relecov schema according to specs --- relecov_tools/schema/relecov_schema.json | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 9384c9f7..e5d536ad 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1,5 +1,8 @@ { - "schema": "RELECOV", + "schema": "https://json-schema.org/draft/2020-12/schema", + "id": "https://github.com/BU-ISCIII/relecov-tools/blob/develop/relecov_tools/schema/relecov_schema.json", + "title": "RELECOV schema", + "description":"Json schema including the ", "version": "1.0.0", "required": [ "collecting_lab_sample_id", From cd91688d9c117aab5c7bfd96c7eece442c353d55 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 14:00:45 +0200 Subject: [PATCH 1036/1454] modified validation for iterating between errors and only printing error message --- relecov_tools/json_validation.py | 42 ++++++++++++++++++++++---------- 1 file changed, 29 insertions(+), 13 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 6ea788cd..97f51f0c 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -23,46 +23,62 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): """Validate json file against the schema""" - if json_data_file is None: - json_data_file = relecov_tools.utils.prompt_path( - msg="Select the json file to validate" - ) + if json_schema_file is None: config_json = ConfigJson() schema_name = config_json.get_topic_data("json_schemas", "relecov_schema") json_schema_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", schema_name ) - # schema_file = open('/home/lchapado/Projects/Proyecto_ERA/relecov-tools/schema/phage_plus_V0.json') + with open(json_schema_file, "r") as fh: json_schema = json.load(fh) + try: Draft202012Validator.check_schema(json_schema) + draft_202012_validator = Draft202012Validator(json_schema) except jsonschema.ValidationError: - stderr.print("[red] Json schema does not fulfil Draft 202012 Validation") - sys.exit(1) - if not os.path.isfile(json_data_file): - stderr.print("[red] Json file does not exists") + stderr.print("[red] Json schema does not fulfill Draft 202012 Validation") sys.exit(1) + + if json_data_file is None: + json_data_file = relecov_tools.utils.prompt_path( + msg="Select the json file to validate" + ) + if out_folder is None: out_folder = relecov_tools.utils.prompt_path( msg="Select the folder where to save excel with invalid data" ) + + # Read and check json to validate file + if not os.path.isfile(json_data_file): + stderr.print("[red] Json file does not exists") + sys.exit(1) + stderr.print("[blue] Reading the json file") json_data = relecov_tools.utils.read_json_file(json_data_file) + with open(json_data_file, "r") as fh: json_data = json.load(fh) + validated_json_data = [] invalid_json = [] errors = {} stderr.print("[blue] Start processing the json file") for item_row in json_data: - try: - validate(instance=item_row, schema=json_schema) + #validate(instance=item_row, schema=json_schema) + if draft_202012_validator.is_valid(item_row): validated_json_data.append(item_row) - except jsonschema.ValidationError as e: - log.error("Invalid sample data %s", e) + else: + for error in draft_202012_validator.iter_errors(item_row): + #import pdb; pdb.set_trace() + stderr.print("[red] Invalid sample data " + error.message) + log.error("Invalid sample data %s", error.message) + + # append row with errors invalid_json.append(item_row) + # Enviar los errores por correo # logging.handlers.SMTPHandler(mailhost=("smtp.gmail.com", 465), fromaddr=correo_isciii, toaddrs=correo_usuario, subject="Validation errors", credentials=(usurario,contraseña), secure=None, timeout=1.0) if len(invalid_json) == 0: From 08f30743a09b5c545d282ef64201a01084861a8a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 14:01:19 +0200 Subject: [PATCH 1037/1454] Fixed column name: sequencing instrument platform instead of model --- relecov_tools/schema/institution_schemas/ISCIII.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index 1d228ea0..bb40362b 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -51,7 +51,7 @@ "sequencer_file": { "file_name": "samples_run_services_length.tsv", "mapped_fields": { - "Sequencing Instrument Model": "run_name" + "Sequencing Instrument Platform": "run_name" }, "mapped_key": "", "function": "added_seq_inst_model" From 068114b2cd4d81778a1155015a16e390288bb885 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 14:03:35 +0200 Subject: [PATCH 1038/1454] fixed column name also in conf file --- relecov_tools/conf/configuration.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 095cbd18..56b9e7e9 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -40,7 +40,7 @@ "Enrichment panel/assay version", "Number Of Samples In Run", "Runid", - "Sequencing Instrument Model", + "Sequencing Instrument Platform", "Flowcell Kit", "Source material", "Capture method", From 33034fb3d3e7a04debe080863fd12b37b524ddfa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 14:07:45 +0200 Subject: [PATCH 1039/1454] Revert "Fixed column name: sequencing instrument platform instead of model" This reverts commit 08f30743a09b5c545d282ef64201a01084861a8a. --- relecov_tools/schema/institution_schemas/ISCIII.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index bb40362b..1d228ea0 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -51,7 +51,7 @@ "sequencer_file": { "file_name": "samples_run_services_length.tsv", "mapped_fields": { - "Sequencing Instrument Platform": "run_name" + "Sequencing Instrument Model": "run_name" }, "mapped_key": "", "function": "added_seq_inst_model" From 53228821a6e8f3619ec0886ee8f545e5d0017a7e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 14:08:11 +0200 Subject: [PATCH 1040/1454] Revert "modified validation for iterating between errors and only printing error message" This reverts commit cd91688d9c117aab5c7bfd96c7eece442c353d55. --- relecov_tools/json_validation.py | 42 ++++++++++---------------------- 1 file changed, 13 insertions(+), 29 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 97f51f0c..6ea788cd 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -23,62 +23,46 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): """Validate json file against the schema""" - + if json_data_file is None: + json_data_file = relecov_tools.utils.prompt_path( + msg="Select the json file to validate" + ) if json_schema_file is None: config_json = ConfigJson() schema_name = config_json.get_topic_data("json_schemas", "relecov_schema") json_schema_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", schema_name ) - + # schema_file = open('/home/lchapado/Projects/Proyecto_ERA/relecov-tools/schema/phage_plus_V0.json') with open(json_schema_file, "r") as fh: json_schema = json.load(fh) - try: Draft202012Validator.check_schema(json_schema) - draft_202012_validator = Draft202012Validator(json_schema) except jsonschema.ValidationError: - stderr.print("[red] Json schema does not fulfill Draft 202012 Validation") + stderr.print("[red] Json schema does not fulfil Draft 202012 Validation") + sys.exit(1) + if not os.path.isfile(json_data_file): + stderr.print("[red] Json file does not exists") sys.exit(1) - - if json_data_file is None: - json_data_file = relecov_tools.utils.prompt_path( - msg="Select the json file to validate" - ) - if out_folder is None: out_folder = relecov_tools.utils.prompt_path( msg="Select the folder where to save excel with invalid data" ) - - # Read and check json to validate file - if not os.path.isfile(json_data_file): - stderr.print("[red] Json file does not exists") - sys.exit(1) - stderr.print("[blue] Reading the json file") json_data = relecov_tools.utils.read_json_file(json_data_file) - with open(json_data_file, "r") as fh: json_data = json.load(fh) - validated_json_data = [] invalid_json = [] errors = {} stderr.print("[blue] Start processing the json file") for item_row in json_data: - #validate(instance=item_row, schema=json_schema) - if draft_202012_validator.is_valid(item_row): + try: + validate(instance=item_row, schema=json_schema) validated_json_data.append(item_row) - else: - for error in draft_202012_validator.iter_errors(item_row): - #import pdb; pdb.set_trace() - stderr.print("[red] Invalid sample data " + error.message) - log.error("Invalid sample data %s", error.message) - - # append row with errors + except jsonschema.ValidationError as e: + log.error("Invalid sample data %s", e) invalid_json.append(item_row) - # Enviar los errores por correo # logging.handlers.SMTPHandler(mailhost=("smtp.gmail.com", 465), fromaddr=correo_isciii, toaddrs=correo_usuario, subject="Validation errors", credentials=(usurario,contraseña), secure=None, timeout=1.0) if len(invalid_json) == 0: From 513016345852af289ba7179ca8228bd385c579a7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 14:09:38 +0200 Subject: [PATCH 1041/1454] Revert "fixed column name also in conf file" This reverts commit 068114b2cd4d81778a1155015a16e390288bb885. --- relecov_tools/conf/configuration.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 56b9e7e9..095cbd18 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -40,7 +40,7 @@ "Enrichment panel/assay version", "Number Of Samples In Run", "Runid", - "Sequencing Instrument Platform", + "Sequencing Instrument Model", "Flowcell Kit", "Source material", "Capture method", From 7521e9724afe9330f007310d895a52f19f23fbdc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 14:10:06 +0200 Subject: [PATCH 1042/1454] Revert "Revert "modified validation for iterating between errors and only printing error message"" This reverts commit 53228821a6e8f3619ec0886ee8f545e5d0017a7e. --- relecov_tools/json_validation.py | 42 ++++++++++++++++++++++---------- 1 file changed, 29 insertions(+), 13 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 6ea788cd..97f51f0c 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -23,46 +23,62 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): """Validate json file against the schema""" - if json_data_file is None: - json_data_file = relecov_tools.utils.prompt_path( - msg="Select the json file to validate" - ) + if json_schema_file is None: config_json = ConfigJson() schema_name = config_json.get_topic_data("json_schemas", "relecov_schema") json_schema_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", schema_name ) - # schema_file = open('/home/lchapado/Projects/Proyecto_ERA/relecov-tools/schema/phage_plus_V0.json') + with open(json_schema_file, "r") as fh: json_schema = json.load(fh) + try: Draft202012Validator.check_schema(json_schema) + draft_202012_validator = Draft202012Validator(json_schema) except jsonschema.ValidationError: - stderr.print("[red] Json schema does not fulfil Draft 202012 Validation") - sys.exit(1) - if not os.path.isfile(json_data_file): - stderr.print("[red] Json file does not exists") + stderr.print("[red] Json schema does not fulfill Draft 202012 Validation") sys.exit(1) + + if json_data_file is None: + json_data_file = relecov_tools.utils.prompt_path( + msg="Select the json file to validate" + ) + if out_folder is None: out_folder = relecov_tools.utils.prompt_path( msg="Select the folder where to save excel with invalid data" ) + + # Read and check json to validate file + if not os.path.isfile(json_data_file): + stderr.print("[red] Json file does not exists") + sys.exit(1) + stderr.print("[blue] Reading the json file") json_data = relecov_tools.utils.read_json_file(json_data_file) + with open(json_data_file, "r") as fh: json_data = json.load(fh) + validated_json_data = [] invalid_json = [] errors = {} stderr.print("[blue] Start processing the json file") for item_row in json_data: - try: - validate(instance=item_row, schema=json_schema) + #validate(instance=item_row, schema=json_schema) + if draft_202012_validator.is_valid(item_row): validated_json_data.append(item_row) - except jsonschema.ValidationError as e: - log.error("Invalid sample data %s", e) + else: + for error in draft_202012_validator.iter_errors(item_row): + #import pdb; pdb.set_trace() + stderr.print("[red] Invalid sample data " + error.message) + log.error("Invalid sample data %s", error.message) + + # append row with errors invalid_json.append(item_row) + # Enviar los errores por correo # logging.handlers.SMTPHandler(mailhost=("smtp.gmail.com", 465), fromaddr=correo_isciii, toaddrs=correo_usuario, subject="Validation errors", credentials=(usurario,contraseña), secure=None, timeout=1.0) if len(invalid_json) == 0: From 3c3c905e564dcac2bfbda50cb9b5707d55e60127 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 14:11:36 +0200 Subject: [PATCH 1043/1454] fix column name: sequencing_instrument_platform instead of platform --- relecov_tools/conf/configuration.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 095cbd18..a37b8eec 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -91,10 +91,10 @@ "Human": "host_scientific_name::Homo sapiens" }, "sequencing_instrument_model": { - "Illumina": "platform::Illumina", - "PacBio": "platform::PacBio", - "Ion Torrent": "platform::Ion Torrent", - "Oxford Nanopore": "platform::Oxford Nanopore" + "Illumina": "sequencing_instrument_platform::Illumina", + "PacBio": "sequencing_instrument_platform::PacBio", + "Ion Torrent": "sequencing_instrument_platform::Ion Torrent", + "Oxford Nanopore": "sequencing_instrument_platform::Oxford Nanopore" } }, "required_copy_from_other_field": { From 23f96f29e2b1a7e4469723fe1ea5457b7c610680 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 14:13:45 +0200 Subject: [PATCH 1044/1454] comment logging for now --- relecov_tools/json_validation.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 97f51f0c..e740f803 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -72,9 +72,8 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): validated_json_data.append(item_row) else: for error in draft_202012_validator.iter_errors(item_row): - #import pdb; pdb.set_trace() stderr.print("[red] Invalid sample data " + error.message) - log.error("Invalid sample data %s", error.message) + #log.error("Invalid sample data %s", error.message) # append row with errors invalid_json.append(item_row) From dbf98baf7515106de20228d340ca0eb7dfc31a3f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 14:41:05 +0200 Subject: [PATCH 1045/1454] minor re-structure validate module --- relecov_tools/__main__.py | 23 +---------------------- relecov_tools/json_validation.py | 24 +++++++++++++++++++++--- 2 files changed, 22 insertions(+), 25 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index b5175fc8..c141ec7b 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -193,29 +193,8 @@ def read_lab_metadata(metadata_file, sample_list_file, metadata_out): @click.option("-o", "--out_folder", help="Path to save validate json file") def validate(json_file, json_schema, metadata, out_folder): """Validate json file against schema.""" - ( - validated_json_data, - invalid_json, - errors, - out_folder, - ) = relecov_tools.json_validation.validate_json(json_file, json_schema, out_folder) - if len(invalid_json) > 0: - log.error("Some of the samples in json metadata were not validated") - stderr.print("[red] Some of the Samples are not validate") - if not os.path.isfile(metadata): - log.error("Metadata file %s does not exist", metadata) - stderr.print( - "[red] Unable to create excel file for invalid samples. Metadata file ", - metadata, - " does not exist", - ) - exit(1) - relecov_tools.json_validation.create_invalid_metadata( - metadata, invalid_json, out_folder - ) + relecov_tools.json_validation.validate_json(json_file, json_schema, metadata, out_folder) - else: - log.info("All data in json were validated") # mapping to ENA schema diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index e740f803..9b841895 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -21,7 +21,7 @@ ) -def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): +def validate_json(json_data_file=None, json_schema_file=None, metadata=None, out_folder=None): """Validate json file against the schema""" if json_schema_file is None: @@ -83,9 +83,25 @@ def validate_json(json_data_file=None, json_schema_file=None, out_folder=None): if len(invalid_json) == 0: stderr.print("[green] Sucessful validation") else: - stderr.print("[red] Some samples are not validated") - return validated_json_data, invalid_json, errors, out_folder + log.error("Some of the samples in json metadata were not validated") + stderr.print("[red] Some of the Samples are not validate") + if metadata is None: + metadata = relecov_tools.utils.prompt_path( + msg="Select the metadata file to select those samples not validated." + ) + if not os.path.isfile(metadata): + log.error("Metadata file %s does not exist", metadata) + stderr.print( + "[red] Unable to create excel file for invalid samples. Metadata file ", + metadata, + " does not exist", + ) + exit(1) + relecov_tools.json_validation.create_invalid_metadata( + metadata, invalid_json, out_folder + ) + return def create_invalid_metadata(metadata_file, invalid_json, out_folder): """Create a new sub excel file having only the samples that were invalid. @@ -130,3 +146,5 @@ def create_invalid_metadata(metadata_file, invalid_json, out_folder): stderr.print("[red] Saving excel file with the invalid samples") wb.save(m_file) return + + From 3d1dd935423a48506310319ed0169851d1f3d6f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 16:26:28 +0200 Subject: [PATCH 1046/1454] more re-structuring, now the module is a class --- relecov_tools/__main__.py | 7 +- relecov_tools/json_validation.py | 118 +++++++++++++++++-------------- 2 files changed, 67 insertions(+), 58 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index c141ec7b..a9f47b82 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -192,10 +192,9 @@ def read_lab_metadata(metadata_file, sample_list_file, metadata_out): ) @click.option("-o", "--out_folder", help="Path to save validate json file") def validate(json_file, json_schema, metadata, out_folder): - """Validate json file against schema.""" - relecov_tools.json_validation.validate_json(json_file, json_schema, metadata, out_folder) - - + """ Validate json file against schema.""" + validation = relecov_tools.json_validation.SchemaValidation(json_file, json_schema, metadata, out_folder) + validation.validate() # mapping to ENA schema @relecov_tools_cli.command(help_priority=5) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 9b841895..a2e2fab0 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -2,7 +2,6 @@ import logging import rich.console import jsonschema -from jsonschema import validate from jsonschema import Draft202012Validator import json import sys @@ -21,67 +20,80 @@ ) -def validate_json(json_data_file=None, json_schema_file=None, metadata=None, out_folder=None): - """Validate json file against the schema""" +class SchemaValidation: - if json_schema_file is None: - config_json = ConfigJson() - schema_name = config_json.get_topic_data("json_schemas", "relecov_schema") - json_schema_file = os.path.join( - os.path.dirname(os.path.realpath(__file__)), "schema", schema_name - ) + def __init__(json_data_file=None, json_schema_file=None, metadata=None, out_folder=None): + """Validate json file against the schema""" - with open(json_schema_file, "r") as fh: - json_schema = json.load(fh) + if json_schema_file is None: + config_json = ConfigJson() + schema_name = config_json.get_topic_data("json_schemas", "relecov_schema") + json_schema_file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), "schema", schema_name + ) + + self.json_schema = relecov_tools.utils.read_json_file(json_schema_file) + + + if json_data_file is None: + json_data_file = relecov_tools.utils.prompt_path( + msg="Select the json file to validate" + ) - try: - Draft202012Validator.check_schema(json_schema) - draft_202012_validator = Draft202012Validator(json_schema) - except jsonschema.ValidationError: - stderr.print("[red] Json schema does not fulfill Draft 202012 Validation") - sys.exit(1) + if out_folder is None: + self.out_folder = relecov_tools.utils.prompt_path( + msg="Select the folder where to save excel with invalid data" + ) - if json_data_file is None: - json_data_file = relecov_tools.utils.prompt_path( - msg="Select the json file to validate" - ) + # Read and check json to validate file + if not os.path.isfile(json_data_file): + stderr.print("[red] Json file does not exists") + sys.exit(1) - if out_folder is None: - out_folder = relecov_tools.utils.prompt_path( - msg="Select the folder where to save excel with invalid data" - ) + stderr.print("[blue] Reading the json file") + self.json_data = relecov_tools.utils.read_json_file(json_data_file) - # Read and check json to validate file - if not os.path.isfile(json_data_file): - stderr.print("[red] Json file does not exists") - sys.exit(1) +def validate_schema(self): + """Validate json schema against draft""" + try: + Draft202012Validator.check_schema(self.json_schema) + except jsonschema.ValidationError: + stderr.print("[red] Json schema does not fulfill Draft 202012 Validation") + sys.exit(1) - stderr.print("[blue] Reading the json file") - json_data = relecov_tools.utils.read_json_file(json_data_file) +def validate_instances(self): + """ Validate data instances against a validated json schema """ - with open(json_data_file, "r") as fh: - json_data = json.load(fh) + # create validator + validator = Draft202012Validator(self.json_schema) validated_json_data = [] invalid_json = [] errors = {} stderr.print("[blue] Start processing the json file") - for item_row in json_data: + for item_row in self.json_data: #validate(instance=item_row, schema=json_schema) - if draft_202012_validator.is_valid(item_row): + if validator.is_valid(item_row): validated_json_data.append(item_row) else: - for error in draft_202012_validator.iter_errors(item_row): + for error in validator.iter_errors(item_row): stderr.print("[red] Invalid sample data " + error.message) #log.error("Invalid sample data %s", error.message) # append row with errors invalid_json.append(item_row) + return invalid_json - # Enviar los errores por correo - # logging.handlers.SMTPHandler(mailhost=("smtp.gmail.com", 465), fromaddr=correo_isciii, toaddrs=correo_usuario, subject="Validation errors", credentials=(usurario,contraseña), secure=None, timeout=1.0) + +def create_invalid_metadata(invalid_json, out_folder): + """Create a new sub excel file having only the samples that were invalid. + Samples name are checking the Sequencing sample id which are in + column B (index 1). + The rows that match the value collected from json file on tag + collecting_lab_sample_id are removed from excel + """ if len(invalid_json) == 0: - stderr.print("[green] Sucessful validation") + stderr.print("[green] Sucessful validation, no invalid file will be written.") else: log.error("Some of the samples in json metadata were not validated") stderr.print("[red] Some of the Samples are not validate") @@ -96,24 +108,12 @@ def validate_json(json_data_file=None, json_schema_file=None, metadata=None, out metadata, " does not exist", ) - exit(1) - relecov_tools.json_validation.create_invalid_metadata( - metadata, invalid_json, out_folder - ) + sys.exit(1) - return - -def create_invalid_metadata(metadata_file, invalid_json, out_folder): - """Create a new sub excel file having only the samples that were invalid. - Samples name are checking the Sequencing sample id which are in - column B (index 1). - The rows that match the value collected from json file on tag - collecting_lab_sample_id are removed from excel - """ sample_list = [] - # import pdb; pdb.set_trace() - # json_data = relecov_tools.utils.read_json_file(invalid_json) + stderr.print("[red] Start preparation of invalid samples") + for row in invalid_json: sample_list.append(str(row["collecting_lab_sample_id"])) @@ -128,6 +128,7 @@ def create_invalid_metadata(metadata_file, invalid_json, out_folder): break if str(row[2].value) not in sample_list: row_to_del.append(row[0].row) + stderr.print("[red] Collected rows to create the excel file") if len(row_to_del) > 0: row_to_del.sort(reverse=True) @@ -140,6 +141,7 @@ def create_invalid_metadata(metadata_file, invalid_json, out_folder): ) stderr.print("f[red] Unable to delete row {idx} becuase of {e}") sys.exit(1) + os.makedirs(out_folder, exist_ok=True) new_name = "invalid_" + os.path.basename(metadata_file) m_file = os.path.join(out_folder, new_name) @@ -147,4 +149,12 @@ def create_invalid_metadata(metadata_file, invalid_json, out_folder): wb.save(m_file) return +def validate(self): + """ Write invalid samples from metadata to excel """ + self.validate_schema() + self.validate_instances() + self.create_invalid_metadata(invalid_json, self.out_folder) + + # Enviar los errores por correo + # logging.handlers.SMTPHandler(mailhost=("smtp.gmail.com", 465), fromaddr=correo_isciii, toaddrs=correo_usuario, subject="Validation errors", credentials=(usurario,contraseña), secure=None, timeout=1.0) From 32dfc14c42ec06ee8572cbe592700a607ac18f85 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 16:32:59 +0200 Subject: [PATCH 1047/1454] bug fixed and black linting --- relecov_tools/__main__.py | 7 +++++-- relecov_tools/json_validation.py | 27 +++++++++++++++------------ 2 files changed, 20 insertions(+), 14 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index a9f47b82..b67e494f 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -192,10 +192,13 @@ def read_lab_metadata(metadata_file, sample_list_file, metadata_out): ) @click.option("-o", "--out_folder", help="Path to save validate json file") def validate(json_file, json_schema, metadata, out_folder): - """ Validate json file against schema.""" - validation = relecov_tools.json_validation.SchemaValidation(json_file, json_schema, metadata, out_folder) + """Validate json file against schema.""" + validation = relecov_tools.json_validation.SchemaValidation( + json_file, json_schema, metadata, out_folder + ) validation.validate() + # mapping to ENA schema @relecov_tools_cli.command(help_priority=5) @click.option("-p", "--origin_schema", help="File with the origin (relecov) schema") diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index a2e2fab0..59fcf15e 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -21,8 +21,9 @@ class SchemaValidation: - - def __init__(json_data_file=None, json_schema_file=None, metadata=None, out_folder=None): + def __init__( + json_data_file=None, json_schema_file=None, metadata=None, out_folder=None + ): """Validate json file against the schema""" if json_schema_file is None: @@ -34,7 +35,6 @@ def __init__(json_data_file=None, json_schema_file=None, metadata=None, out_fold self.json_schema = relecov_tools.utils.read_json_file(json_schema_file) - if json_data_file is None: json_data_file = relecov_tools.utils.prompt_path( msg="Select the json file to validate" @@ -53,16 +53,18 @@ def __init__(json_data_file=None, json_schema_file=None, metadata=None, out_fold stderr.print("[blue] Reading the json file") self.json_data = relecov_tools.utils.read_json_file(json_data_file) + def validate_schema(self): """Validate json schema against draft""" - try: - Draft202012Validator.check_schema(self.json_schema) - except jsonschema.ValidationError: - stderr.print("[red] Json schema does not fulfill Draft 202012 Validation") - sys.exit(1) + try: + Draft202012Validator.check_schema(self.json_schema) + except jsonschema.ValidationError: + stderr.print("[red] Json schema does not fulfill Draft 202012 Validation") + sys.exit(1) + def validate_instances(self): - """ Validate data instances against a validated json schema """ + """Validate data instances against a validated json schema""" # create validator validator = Draft202012Validator(self.json_schema) @@ -72,13 +74,13 @@ def validate_instances(self): errors = {} stderr.print("[blue] Start processing the json file") for item_row in self.json_data: - #validate(instance=item_row, schema=json_schema) + # validate(instance=item_row, schema=json_schema) if validator.is_valid(item_row): validated_json_data.append(item_row) else: for error in validator.iter_errors(item_row): stderr.print("[red] Invalid sample data " + error.message) - #log.error("Invalid sample data %s", error.message) + # log.error("Invalid sample data %s", error.message) # append row with errors invalid_json.append(item_row) @@ -149,8 +151,9 @@ def create_invalid_metadata(invalid_json, out_folder): wb.save(m_file) return + def validate(self): - """ Write invalid samples from metadata to excel """ + """Write invalid samples from metadata to excel""" self.validate_schema() self.validate_instances() From faeeae3bdbc2a2e9b9372216a54a4c3a3903c9cf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 16:45:27 +0200 Subject: [PATCH 1048/1454] bug fixing: variable names, wrong positional arguments and indentation in json validation module --- relecov_tools/json_validation.py | 206 ++++++++++++++++--------------- 1 file changed, 104 insertions(+), 102 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 59fcf15e..9222bb0e 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -22,7 +22,7 @@ class SchemaValidation: def __init__( - json_data_file=None, json_schema_file=None, metadata=None, out_folder=None + self, json_data_file=None, json_schema_file=None, metadata=None, out_folder=None ): """Validate json file against the schema""" @@ -44,6 +44,8 @@ def __init__( self.out_folder = relecov_tools.utils.prompt_path( msg="Select the folder where to save excel with invalid data" ) + else: + self.out_folder = out_folder # Read and check json to validate file if not os.path.isfile(json_data_file): @@ -53,111 +55,111 @@ def __init__( stderr.print("[blue] Reading the json file") self.json_data = relecov_tools.utils.read_json_file(json_data_file) + self.metadata = metadata -def validate_schema(self): - """Validate json schema against draft""" - try: - Draft202012Validator.check_schema(self.json_schema) - except jsonschema.ValidationError: - stderr.print("[red] Json schema does not fulfill Draft 202012 Validation") - sys.exit(1) - - -def validate_instances(self): - """Validate data instances against a validated json schema""" - - # create validator - validator = Draft202012Validator(self.json_schema) + def validate_schema(self): + """Validate json schema against draft""" + try: + Draft202012Validator.check_schema(self.json_schema) + except jsonschema.ValidationError: + stderr.print("[red] Json schema does not fulfill Draft 202012 Validation") + sys.exit(1) - validated_json_data = [] - invalid_json = [] - errors = {} - stderr.print("[blue] Start processing the json file") - for item_row in self.json_data: - # validate(instance=item_row, schema=json_schema) - if validator.is_valid(item_row): - validated_json_data.append(item_row) - else: - for error in validator.iter_errors(item_row): - stderr.print("[red] Invalid sample data " + error.message) - # log.error("Invalid sample data %s", error.message) - - # append row with errors - invalid_json.append(item_row) - return invalid_json - - -def create_invalid_metadata(invalid_json, out_folder): - """Create a new sub excel file having only the samples that were invalid. - Samples name are checking the Sequencing sample id which are in - column B (index 1). - The rows that match the value collected from json file on tag - collecting_lab_sample_id are removed from excel - """ - if len(invalid_json) == 0: - stderr.print("[green] Sucessful validation, no invalid file will be written.") - else: - log.error("Some of the samples in json metadata were not validated") - stderr.print("[red] Some of the Samples are not validate") - if metadata is None: - metadata = relecov_tools.utils.prompt_path( - msg="Select the metadata file to select those samples not validated." - ) - if not os.path.isfile(metadata): - log.error("Metadata file %s does not exist", metadata) + def validate_instances(self): + """Validate data instances against a validated json schema""" + + # create validator + validator = Draft202012Validator(self.json_schema) + + validated_json_data = [] + invalid_json = [] + errors = {} + stderr.print("[blue] Start processing the json file") + for item_row in self.json_data: + # validate(instance=item_row, schema=json_schema) + if validator.is_valid(item_row): + validated_json_data.append(item_row) + else: + for error in validator.iter_errors(item_row): + stderr.print("[red] Invalid sample data " + error.message) + # log.error("Invalid sample data %s", error.message) + + # append row with errors + invalid_json.append(item_row) + return invalid_json + + def create_invalid_metadata(self, invalid_json, metadata, out_folder): + """Create a new sub excel file having only the samples that were invalid. + Samples name are checking the Sequencing sample id which are in + column B (index 1). + The rows that match the value collected from json file on tag + collecting_lab_sample_id are removed from excel + """ + if len(invalid_json) == 0: stderr.print( - "[red] Unable to create excel file for invalid samples. Metadata file ", - metadata, - " does not exist", + "[green] Sucessful validation, no invalid file will be written." ) - sys.exit(1) - - sample_list = [] - - stderr.print("[red] Start preparation of invalid samples") - - for row in invalid_json: - sample_list.append(str(row["collecting_lab_sample_id"])) - - wb = openpyxl.load_workbook(metadata_file) - ws_sheet = wb["METADATA_LAB"] - row_to_del = [] - - for row in ws_sheet.iter_rows(min_row=5, max_row=ws_sheet.max_row): - # if not data on row 1 and 2 assume that no more data are in file - # then start deleting rows - if not row[2].value and not row[1].value: - break - if str(row[2].value) not in sample_list: - row_to_del.append(row[0].row) - - stderr.print("[red] Collected rows to create the excel file") - if len(row_to_del) > 0: - row_to_del.sort(reverse=True) - for idx in row_to_del: - try: - ws_sheet.delete_rows(idx) - except TypeError as e: - log.error( - "Unable to delete row %s from metadata file because of", idx, e + else: + log.error("Some of the samples in json metadata were not validated") + stderr.print("[red] Some of the Samples are not validate") + if metadata is None: + metadata = relecov_tools.utils.prompt_path( + msg="Select the metadata file to select those samples not validated." + ) + if not os.path.isfile(metadata): + log.error("Metadata file %s does not exist", metadata) + stderr.print( + "[red] Unable to create excel file for invalid samples. Metadata file ", + metadata, + " does not exist", ) - stderr.print("f[red] Unable to delete row {idx} becuase of {e}") sys.exit(1) - os.makedirs(out_folder, exist_ok=True) - new_name = "invalid_" + os.path.basename(metadata_file) - m_file = os.path.join(out_folder, new_name) - stderr.print("[red] Saving excel file with the invalid samples") - wb.save(m_file) - return - - -def validate(self): - """Write invalid samples from metadata to excel""" - - self.validate_schema() - self.validate_instances() - self.create_invalid_metadata(invalid_json, self.out_folder) - - # Enviar los errores por correo - # logging.handlers.SMTPHandler(mailhost=("smtp.gmail.com", 465), fromaddr=correo_isciii, toaddrs=correo_usuario, subject="Validation errors", credentials=(usurario,contraseña), secure=None, timeout=1.0) + sample_list = [] + + stderr.print("[red] Start preparation of invalid samples") + + for row in invalid_json: + sample_list.append(str(row["collecting_lab_sample_id"])) + + wb = openpyxl.load_workbook(metadata) + ws_sheet = wb["METADATA_LAB"] + row_to_del = [] + + for row in ws_sheet.iter_rows(min_row=5, max_row=ws_sheet.max_row): + # if not data on row 1 and 2 assume that no more data are in file + # then start deleting rows + if not row[2].value and not row[1].value: + break + if str(row[2].value) not in sample_list: + row_to_del.append(row[0].row) + + stderr.print("[red] Collected rows to create the excel file") + if len(row_to_del) > 0: + row_to_del.sort(reverse=True) + for idx in row_to_del: + try: + ws_sheet.delete_rows(idx) + except TypeError as e: + log.error( + "Unable to delete row %s from metadata file because of", idx, e + ) + stderr.print("f[red] Unable to delete row {idx} becuase of {e}") + sys.exit(1) + + os.makedirs(out_folder, exist_ok=True) + new_name = "invalid_" + os.path.basename(metadata) + m_file = os.path.join(out_folder, new_name) + stderr.print("[red] Saving excel file with the invalid samples") + wb.save(m_file) + return + + def validate(self): + """Write invalid samples from metadata to excel""" + + self.validate_schema() + invalid_json = self.validate_instances() + self.create_invalid_metadata(invalid_json, self.metadata, self.out_folder) + + # Enviar los errores por correo + # logging.handlers.SMTPHandler(mailhost=("smtp.gmail.com", 465), fromaddr=correo_isciii, toaddrs=correo_usuario, subject="Validation errors", credentials=(usurario,contraseña), secure=None, timeout=1.0) From 9e488296cd1778e66af365c4b805daec65bee2e4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 17:09:02 +0200 Subject: [PATCH 1049/1454] create summary of samples not passing validation --- relecov_tools/json_validation.py | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 9222bb0e..a76c7a59 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -80,12 +80,25 @@ def validate_instances(self): if validator.is_valid(item_row): validated_json_data.append(item_row) else: + # Count error types for error in validator.iter_errors(item_row): - stderr.print("[red] Invalid sample data " + error.message) - # log.error("Invalid sample data %s", error.message) + if error.message in errors.keys(): + errors[error.message] += 1 + else: + errors[error.message] = 1 + # log.error("Invalid sample data %s", error.message) # append row with errors invalid_json.append(item_row) + + # Summarize errors + stderr.print("[red] --------------------") + stderr.print("[red] VALIDATION SUMMARY") + stderr.print("[red] --------------------") + for error_type in errors.keys(): + stderr.print("[red]" + str(errors[error_type]) + " samples failed validation:\n" + error_type) + stderr.print("[red] --------------------") + return invalid_json def create_invalid_metadata(self, invalid_json, metadata, out_folder): From 41d8c655e5c948cf85b6d91cc37fa500dc338f94 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 17:15:26 +0200 Subject: [PATCH 1050/1454] fixed typo in conf json and added left enum in relecov schema --- relecov_tools/conf/anatomical_material_collection_method.json | 2 +- relecov_tools/schema/relecov_schema.json | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/anatomical_material_collection_method.json b/relecov_tools/conf/anatomical_material_collection_method.json index 2edc43d3..818a2963 100644 --- a/relecov_tools/conf/anatomical_material_collection_method.json +++ b/relecov_tools/conf/anatomical_material_collection_method.json @@ -997,7 +997,7 @@ }, "Scraping": { "anatomical_part": "Not Applicable", - "collection_method": "Scraping2", + "collection_method": "Scraping", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index e5d536ad..35a97b15 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -762,6 +762,7 @@ "Oropharynx Scraping", "Nasopharynx Swabbing", "Oropharynx Swabbing", + "Pharynx Swabbing", "Lower respiratory tract Wash", "Bronchus Wash", "Lung Wash", From 2c3c2352b5c71fe12846d18c6b6cf4e6ebcfcccf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 17:19:24 +0200 Subject: [PATCH 1051/1454] fixed indentation in json validation, minor color changes --- relecov_tools/json_validation.py | 82 ++++++++++++++++---------------- 1 file changed, 41 insertions(+), 41 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index a76c7a59..42a99ad8 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -92,9 +92,9 @@ def validate_instances(self): invalid_json.append(item_row) # Summarize errors - stderr.print("[red] --------------------") - stderr.print("[red] VALIDATION SUMMARY") - stderr.print("[red] --------------------") + stderr.print("[blue] --------------------") + stderr.print("[blue] VALIDATION SUMMARY") + stderr.print("[blue] --------------------") for error_type in errors.keys(): stderr.print("[red]" + str(errors[error_type]) + " samples failed validation:\n" + error_type) stderr.print("[red] --------------------") @@ -110,7 +110,7 @@ def create_invalid_metadata(self, invalid_json, metadata, out_folder): """ if len(invalid_json) == 0: stderr.print( - "[green] Sucessful validation, no invalid file will be written." + "[green] Sucessful validation, no invalid file will be written!!" ) else: log.error("Some of the samples in json metadata were not validated") @@ -128,43 +128,43 @@ def create_invalid_metadata(self, invalid_json, metadata, out_folder): ) sys.exit(1) - sample_list = [] - - stderr.print("[red] Start preparation of invalid samples") - - for row in invalid_json: - sample_list.append(str(row["collecting_lab_sample_id"])) - - wb = openpyxl.load_workbook(metadata) - ws_sheet = wb["METADATA_LAB"] - row_to_del = [] - - for row in ws_sheet.iter_rows(min_row=5, max_row=ws_sheet.max_row): - # if not data on row 1 and 2 assume that no more data are in file - # then start deleting rows - if not row[2].value and not row[1].value: - break - if str(row[2].value) not in sample_list: - row_to_del.append(row[0].row) - - stderr.print("[red] Collected rows to create the excel file") - if len(row_to_del) > 0: - row_to_del.sort(reverse=True) - for idx in row_to_del: - try: - ws_sheet.delete_rows(idx) - except TypeError as e: - log.error( - "Unable to delete row %s from metadata file because of", idx, e - ) - stderr.print("f[red] Unable to delete row {idx} becuase of {e}") - sys.exit(1) - - os.makedirs(out_folder, exist_ok=True) - new_name = "invalid_" + os.path.basename(metadata) - m_file = os.path.join(out_folder, new_name) - stderr.print("[red] Saving excel file with the invalid samples") - wb.save(m_file) + sample_list = [] + + stderr.print("[red] Start preparation of invalid samples") + + for row in invalid_json: + sample_list.append(str(row["collecting_lab_sample_id"])) + + wb = openpyxl.load_workbook(metadata) + ws_sheet = wb["METADATA_LAB"] + row_to_del = [] + + for row in ws_sheet.iter_rows(min_row=5, max_row=ws_sheet.max_row): + # if not data on row 1 and 2 assume that no more data are in file + # then start deleting rows + if not row[2].value and not row[1].value: + break + if str(row[2].value) not in sample_list: + row_to_del.append(row[0].row) + + stderr.print("[red] Collected rows to create the excel file") + if len(row_to_del) > 0: + row_to_del.sort(reverse=True) + for idx in row_to_del: + try: + ws_sheet.delete_rows(idx) + except TypeError as e: + log.error( + "Unable to delete row %s from metadata file because of", idx, e + ) + stderr.print("f[red] Unable to delete row {idx} becuase of {e}") + sys.exit(1) + + os.makedirs(out_folder, exist_ok=True) + new_name = "invalid_" + os.path.basename(metadata) + m_file = os.path.join(out_folder, new_name) + stderr.print("[red] Saving excel file with the invalid samples") + wb.save(m_file) return def validate(self): From d8334480b285740a28f9e88f20fd4e67be43579e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 17:24:10 +0200 Subject: [PATCH 1052/1454] black linting --- relecov_tools/json_validation.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 42a99ad8..4fa44989 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -96,7 +96,12 @@ def validate_instances(self): stderr.print("[blue] VALIDATION SUMMARY") stderr.print("[blue] --------------------") for error_type in errors.keys(): - stderr.print("[red]" + str(errors[error_type]) + " samples failed validation:\n" + error_type) + stderr.print( + "[red]" + + str(errors[error_type]) + + " samples failed validation:\n" + + error_type + ) stderr.print("[red] --------------------") return invalid_json @@ -155,7 +160,9 @@ def create_invalid_metadata(self, invalid_json, metadata, out_folder): ws_sheet.delete_rows(idx) except TypeError as e: log.error( - "Unable to delete row %s from metadata file because of", idx, e + "Unable to delete row %s from metadata file because of", + idx, + e, ) stderr.print("f[red] Unable to delete row {idx} becuase of {e}") sys.exit(1) From 9fd1f60cd431e9891a6fdee01e620f397171465a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 11 Oct 2022 17:31:19 +0200 Subject: [PATCH 1053/1454] linting: unused imports --- relecov_tools/__main__.py | 1 - relecov_tools/json_validation.py | 1 - 2 files changed, 2 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index b67e494f..f0c5113a 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -import os import logging # import re diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 4fa44989..b0b277ea 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -3,7 +3,6 @@ import rich.console import jsonschema from jsonschema import Draft202012Validator -import json import sys import os import openpyxl From cffea98ac66e9dac426e78b92dd12f6ba47646d7 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 11 Oct 2022 23:40:34 +0200 Subject: [PATCH 1054/1454] Remove the logic to get the sampleType. Now is fetching form specimen_source --- relecov_tools/feed_database.py | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 4ff611a1..1572b528 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -112,12 +112,6 @@ def map_iskylims_sample_fields_values(self, sample_fields, s_project_fields): """Map the values to the properties send to databasee in json schema based on label """ - anatomical_fields = [ - "anatomical_part", - "collection_method", - "body_product", - "anatomical_material", - ] # collection_method = self.get_sample_type() sample_list = [] s_fields = list(sample_fields.keys()) @@ -126,23 +120,22 @@ def map_iskylims_sample_fields_values(self, sample_fields, s_project_fields): for key, value in row.items(): found_ontology = re.search(r"(.+) \[\w+:.*", value) if found_ontology: + # remove the ontology data from item value value = found_ontology.group(1) if key in s_project_fields: s_dict[key] = value elif key in s_fields: s_dict[sample_fields[key]] = value else: + # just for debug loginng write the fields that will not + # be inlcuded in iSkyLIMS request log.info("not key %s in iSkyLIMS", key) # include the fix value fixed_value = self.config_json.get_configuration("iskylims_fixed_values") for prop, val in fixed_value.items(): s_dict[prop] = val - # Using tha anatomical field find out the sampleType - sample_type = [] - for item in anatomical_fields: - if s_dict[item] != "Not Applicable": - sample_type.append(s_dict[item]) - s_dict["sampleType"] = " ".join(sample_type) + # Adding tha specimen_source field for setting sampleType + s_dict["sampleType"] = row["specimen_source"] sample_list.append(s_dict) return sample_list From 42cb756f2b7dd2870ddde179f52bfbad4f65d6ae Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 11 Oct 2022 23:59:14 +0200 Subject: [PATCH 1055/1454] Removed the parameter to load a new schema. the one in the tools must be used --- relecov_tools/__main__.py | 5 ++--- relecov_tools/feed_database.py | 33 ++++++++------------------------- 2 files changed, 10 insertions(+), 28 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index f0c5113a..169d9ccf 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -320,7 +320,6 @@ def launch(user): # update_db @relecov_tools_cli.command(help_priority=9) @click.option("-j", "--json", help="data in json format") -@click.option("-s", "--schema", help="json schema if relecov is not used") @click.option( "-t", "--type", @@ -342,10 +341,10 @@ def launch(user): ) @click.option("-u", "--user", help="user name for login") @click.option("-p", "--password", help="password for the user to login") -def update_db(user, password, json, schema, type, databaseServer): +def update_db(user, password, json, type, databaseServer): """feed database with json""" feed_database = relecov_tools.feed_database.FeedDatabase( - user, password, json, schema, type, databaseServer + user, password, json, type, databaseServer ) feed_database.store_data() diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 1572b528..30700e15 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -2,19 +2,15 @@ import sys import os import re -import jsonschema import json import logging import rich.console -from jsonschema import Draft202012Validator import time import relecov_tools.utils from relecov_tools.config_json import ConfigJson from relecov_tools.rest_api import RestApi -# import relecov_tools.json_schema - log = logging.getLogger(__name__) stderr = rich.console.Console( stderr=True, @@ -30,7 +26,6 @@ def __init__( user=None, passwd=None, json_file=None, - schema=None, type_of_info=None, database_server=None, ): @@ -44,7 +39,6 @@ def __init__( self.passwd = passwd self.config_json = ConfigJson() if json_file is None: - self.config_json = ConfigJson() json_file = relecov_tools.utils.prompt_path( msg="Select the json file which have the data to map" ) @@ -54,25 +48,14 @@ def __init__( sys.exit(1) self.json_data = relecov_tools.utils.read_json_file(json_file) self.json_file = json_file - if schema is None: - schema = os.path.join( - os.path.dirname(os.path.realpath(__file__)), - "schema", - self.config_json.get_topic_data("json_schemas", "relecov_schema"), - ) - else: - if os.path.isfile(schema): - log.error("Relecov schema file %s does not exists", schema) - stderr.print(f"[red] Relecov schema {schema} does not exists") - sys.exit(1) - rel_schema_json = relecov_tools.utils.read_json_file(schema) - try: - Draft202012Validator.check_schema(rel_schema_json) - except jsonschema.ValidationError: - log.error("Schema does not fulfil Draft 202012 Validation ") - stderr.print("[red] Schema does not fulfil Draft 202012 Validation") - sys.exit(1) - self.schema = rel_schema_json + schema = os.path.join( + os.path.dirname(os.path.realpath(__file__)), + "schema", + self.config_json.get_topic_data("json_schemas", "relecov_schema"), + ) + + self.schema = relecov_tools.utils.read_json_file(schema) + if type_of_info is None: type_of_info = relecov_tools.utils.prompt_selection( "Select:", From 5610cf5d784da9ead057ed6e454154b6c6e30a89 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 12 Oct 2022 00:09:12 +0200 Subject: [PATCH 1056/1454] Change the schema name from the property schema to title --- relecov_tools/read_lab_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index b3d84609..96ba32b2 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -82,7 +82,7 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None self.json_req_files = config_json.get_topic_data( "lab_metadata", "lab_metadata_req_json" ) - self.schema_name = self.relecov_sch_json["schema"] + self.schema_name = self.relecov_sch_json["title"] self.schema_version = self.relecov_sch_json["version"] def adding_fixed_fields(self, m_data): From ff6db1d4568532dacdc56f5b31735144b1dc0a8a Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 12 Oct 2022 09:38:39 +0200 Subject: [PATCH 1057/1454] specimen_source, moved the classification text to description and set in classification Sample collection and processing --- relecov_tools/schema/relecov_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 35a97b15..f5726ceb 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -799,11 +799,11 @@ ], "ontology": "0", "type": "string", - "description": "", + "description": "Source of the specimen, merge of anatomical_part, anatomical_material, body_product and collection method.", "examples": [ "" ], - "classification": "Source of the specimen, merge of anatomical_part, anatomical_material, body_product and collection method.", + "classification": "Sample collection and processing", "label": "Specimen source", "fill_mode": "batch" }, From 05be122736d7a139b4f2aa7675e8c50c55bf7233 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 18 Oct 2022 16:46:58 +0200 Subject: [PATCH 1058/1454] fix schema removed two unselected fields --- relecov_tools/schema/relecov_schema.json | 22 ---------------------- 1 file changed, 22 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 35a97b15..02bc7a2d 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1065,28 +1065,6 @@ "fill_mode": "batch", "minLenght": "1" }, - "host_subject_id": { - "examples": [ - "e.g. #131" - ], - "ontology": "GENEPIO:0001398", - "type": "string", - "description": "a unique identifier by which each subject can be referred to, de-identified.", - "classification": "Host information", - "label": "Host Subject Id", - "fill_mode": "sample" - }, - "host_health_state": { - "examples": [ - "" - ], - "ontology": "GENEPIO:0001388", - "type": "string", - "description": " Status of the host", - "classification": "Host information", - "label": "Host health state", - "fill_mode": "sample" - }, "host_common_name": { "enum": [ "Human [NCBITaxon:9606]", From 84c7ebe3a47b95a1b70ccc2647a13f9c988de8fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 18 Oct 2022 16:47:31 +0200 Subject: [PATCH 1059/1454] modified configuration file for read bioinfo metadata --- relecov_tools/conf/configuration.json | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index a37b8eec..bad02f93 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -242,7 +242,7 @@ "variants_metrics": "summary_variants_metrics_mqc.csv", "versions": "software_versions.yml", "pangoling": "pangolin_version.csv", - "variant_metrics": "summary_variants_metrics_mqc.csv" + "mapping_stats": "mapping_illumina_stats.tab" }, "mapping_consensus": [ "consensus_genome_length", @@ -255,7 +255,7 @@ "variant_designation": "scorpio_call" }, "mapping_stats": { - "analysis date": "analysis date", + "analysis_date": "analysis date", "depth_of_coverage_value": "medianDPcoveragevirus", "lineage_name": "Lineage", "number_of_variants_in_consensus": "Variantsinconsensusx10", @@ -298,8 +298,6 @@ "read_length": "number_of_base_pairs_sequenced", "schema_name": "schema_name", "schema_version": "schema_version", - "sequence_file_R1_md5": "sequence_file_R1_md5", - "sequence_file_R2_md5": "sequence_file_R2_md5", "sequencing_sample_id": "sequencing_sample_id" } }, From 883d91eaed9466c02bda356da078c0fa611f520c Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 19 Oct 2022 01:03:23 +0200 Subject: [PATCH 1060/1454] Included collecting_institution, secuencing_data, GISAID and ENA fields. In case that they are given in the excel metadata lab --- relecov_tools/conf/configuration.json | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index a37b8eec..646f1217 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -200,19 +200,25 @@ "sampleLocation": "Not defined" }, "relecov_sample_metadata": [ - "sequence_file_R1_md5", - "sequence_file_R2_md5", + "authors", + "collecting_institution", + "collecting_lab_sample_id", + "ena_broker_name", + "ena_sample_accession", + "gisaid_accession_id", + "gisaid_virus_name", "microbiology_lab_sample_id", "r1_fastq_filepath", "r2_fastq_filepath", - "collecting_lab_sample_id", "schema_name", "schema_version", + "sequencing_date", + "sequence_file_R1_md5", + "sequence_file_R2_md5", "sequence_file_R1_fastq", "sequence_file_R2_fastq", "sequencing_sample_id", - "submitting_lab_sample_id", - "virus_name" + "submitting_lab_sample_id" ], "bioinfo_analysis": { "fixed_values": { From 4f1118c72833fee3b45fa9da0a04855170f1d956 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 19 Oct 2022 16:43:50 +0200 Subject: [PATCH 1061/1454] removed mapping stats input, now is an additional req data. Now bionfo metadata is added to the processed json. --- relecov_tools/__main__.py | 10 ++---- relecov_tools/read_bioinfo_metadata.py | 43 ++++++++++---------------- 2 files changed, 19 insertions(+), 34 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index f0c5113a..ebc6604d 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -360,18 +360,12 @@ def update_db(user, password, json, schema, type, databaseServer): ) @click.option("-i", "--input_folder", type=click.Path(), help="Path to input files") @click.option("-o", "--out_dir", type=click.Path(), help="Path to save output file") -@click.option( - "-p", - "--mapping-illumina", - type=click.Path(), - help="Name of the mapping_illumina file", -) -def read_bioinfo_metadata(json_file, input_folder, out_dir, mapping_illumina): +def read_bioinfo_metadata(json_file, input_folder, out_dir): """ Create the json compliant from the Bioinfo Metadata. """ new_bioinfo_metadata = relecov_tools.read_bioinfo_metadata.BioinfoMetadata( - json_file, input_folder, out_dir, mapping_illumina + json_file, input_folder, out_dir ) new_bioinfo_metadata.create_bioinfo_file() diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index ba033879..139b8228 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -25,7 +25,6 @@ def __init__( json_file=None, input_folder=None, output_folder=None, - mapping_illumina=None, ): if json_file is None: json_file = relecov_tools.utils.prompt_path( @@ -49,16 +48,6 @@ def __init__( ) else: self.output_folder = output_folder - if mapping_illumina is None: - self.mapping_illumina = relecov_tools.utils.prompt_path( - msg="Select the mapping illumina file" - ) - else: - self.mapping_illumina = mapping_illumina - if not os.path.isfile(self.mapping_illumina): - log.error("%s does not exist", self.mapping_illumina) - stderr.print(f"[red] {self.mapping_illumina} does not exist") - sys.exit(1) config_json = ConfigJson() self.configuration = config_json @@ -92,8 +81,9 @@ def include_data_from_mapping_stats(self, j_data): # position of the sample columns inside mapping file sample_position = 4 map_data = relecov_tools.utils.read_csv_file_return_dict( - self.mapping_illumina, ",", sample_position + self.req_files["mapping_stats"], "\t", sample_position ) + mapping_fields = self.configuration.get_topic_data( "bioinfo_analysis", "mapping_stats" ) @@ -118,7 +108,7 @@ def include_pangolin_data(self, j_data): sample_name = row["sequencing_sample_id"].replace("-", "_") else: sample_name = row["sequencing_sample_id"] - f_name = sample_name + ".pangolin." + row["analysis date"] + ".csv" + f_name = sample_name + ".pangolin." + row["analysis_date"] + ".csv" f_path = os.path.join(self.input_folder, f_name) try: @@ -167,7 +157,7 @@ def include_consensus_data(self, j_data): row["consensus_sequence_filepath"] = self.input_folder row["consensus_sequence_filename"] = f_name row["consensus_sequence_md5"] = relecov_tools.utils.calculate_md5(f_path) - base_calculation = int(row["number_of_base_pairs_sequenced"]) * len( + base_calculation = int(row["read_length"]) * len( record_fasta ) if row["sequencing_sample_id"] != "": @@ -196,7 +186,7 @@ def include_variant_metrics(self, j_data): metric file_exists """ map_data = relecov_tools.utils.read_csv_file_return_dict( - self.req_files["variant_metrics"], "," + self.req_files["variants_metrics"], "," ) mapping_fields = self.configuration.get_topic_data( "bioinfo_analysis", "mapping_variant_metrics" @@ -233,7 +223,7 @@ def include_software_versions(self, j_data): return j_data def collect_info_from_lab_json(self): - """Craeate the list of dictionaries from the data that is on json lab + """Create the list of dictionaries from the data that is on json lab metadata file. Return j_data that is used to add the rest of the fields """ try: @@ -242,16 +232,17 @@ def collect_info_from_lab_json(self): log.error("%s invalid json file", self.json_file) stderr.print(f"[red] {self.json_file} invalid json file") sys.exit(1) - j_data = [] - mapping_fields = self.configuration.get_topic_data( - "bioinfo_analysis", "required_fields_from_lab_json" - ) - for row in json_lab_data: - j_data_dict = {} - for lab_field, bio_field in mapping_fields.items(): - j_data_dict[bio_field] = row[lab_field] - j_data.append(j_data_dict) - return j_data + import pdb; pdb.set_trace() +# j_data = [] +# mapping_fields = self.configuration.get_topic_data( +# "bioinfo_analysis", "required_fields_from_lab_json" +# ) +# for row in json_lab_data: +# j_data_dict = {} +# for lab_field, bio_field in mapping_fields.items(): +# j_data_dict[bio_field] = row[lab_field] +# j_data.append(j_data_dict) + return json_lab_data def create_bioinfo_file(self): """Create the bioinfodata json with collecting information from lab From fb5ae1a3e0f1d16cea4fbf27b8f848f0ec9aabd2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 19 Oct 2022 16:44:08 +0200 Subject: [PATCH 1062/1454] black linting --- relecov_tools/read_bioinfo_metadata.py | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 139b8228..bb58de8d 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -157,9 +157,7 @@ def include_consensus_data(self, j_data): row["consensus_sequence_filepath"] = self.input_folder row["consensus_sequence_filename"] = f_name row["consensus_sequence_md5"] = relecov_tools.utils.calculate_md5(f_path) - base_calculation = int(row["read_length"]) * len( - record_fasta - ) + base_calculation = int(row["read_length"]) * len(record_fasta) if row["sequencing_sample_id"] != "": row["number_of_base_pairs_sequenced"] = str(base_calculation * 2) else: @@ -232,16 +230,18 @@ def collect_info_from_lab_json(self): log.error("%s invalid json file", self.json_file) stderr.print(f"[red] {self.json_file} invalid json file") sys.exit(1) - import pdb; pdb.set_trace() -# j_data = [] -# mapping_fields = self.configuration.get_topic_data( -# "bioinfo_analysis", "required_fields_from_lab_json" -# ) -# for row in json_lab_data: -# j_data_dict = {} -# for lab_field, bio_field in mapping_fields.items(): -# j_data_dict[bio_field] = row[lab_field] -# j_data.append(j_data_dict) + import pdb + + pdb.set_trace() + # j_data = [] + # mapping_fields = self.configuration.get_topic_data( + # "bioinfo_analysis", "required_fields_from_lab_json" + # ) + # for row in json_lab_data: + # j_data_dict = {} + # for lab_field, bio_field in mapping_fields.items(): + # j_data_dict[bio_field] = row[lab_field] + # j_data.append(j_data_dict) return json_lab_data def create_bioinfo_file(self): From a018ac44f1113679fb29e0259205e34349c294e4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 19 Oct 2022 17:22:02 +0200 Subject: [PATCH 1063/1454] minor format change --- relecov_tools/read_bioinfo_metadata.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index bb58de8d..3ac3e7e7 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -108,6 +108,7 @@ def include_pangolin_data(self, j_data): sample_name = row["sequencing_sample_id"].replace("-", "_") else: sample_name = row["sequencing_sample_id"] + f_name = sample_name + ".pangolin." + row["analysis_date"] + ".csv" f_path = os.path.join(self.input_folder, f_name) From 85a1289929fd7ca60d1bd615c43eefa4aacf4fb5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 20 Oct 2022 13:21:42 +0200 Subject: [PATCH 1064/1454] Added new field, lineage analysis date --- relecov_tools/schema/relecov_schema.json | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index a099f846..1ffe4036 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2400,6 +2400,17 @@ "label": "Lineage/clade analysis software version", "fill_mode": "batch" }, + "lineage_analysis_date": { + "examples": [ + "2022/10/24" + ], + "ontology": "0", + "type": "date", + "description": "Date when the lineage analysis was performed", + "classification": "Lineage fields", + "label": "lineage/clade analysis date", + "fill_mode": "batch" + }, "variant_designation": { "enum": [ "Variant of Interest (VOI) [GENEPIO:0100082]", From 0ccbabd52ebaa3f374298c1a896e7cb17295f08f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 20 Oct 2022 13:22:12 +0200 Subject: [PATCH 1065/1454] lineage is gotten from pangolin file instead of mapping stats --- relecov_tools/conf/configuration.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 2a6129c1..a06353a2 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -258,12 +258,12 @@ "number_of_base_pairs_sequenced" ], "mapping_pangolin": { - "variant_designation": "scorpio_call" + "variant_designation": "scorpio_call", + "lineage_name": "lineage" }, "mapping_stats": { "analysis_date": "analysis date", "depth_of_coverage_value": "medianDPcoveragevirus", - "lineage_name": "Lineage", "number_of_variants_in_consensus": "Variantsinconsensusx10", "number_of_variants_with_effect": "MissenseVariants", "per_genome_greater_10x": "Coverage>10x(%)", From fe24d6e3efb3be0e7ee3c7958949f09762d55eb5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 21 Oct 2022 13:47:32 +0200 Subject: [PATCH 1066/1454] added date to lineage analysis --- relecov_tools/read_bioinfo_metadata.py | 68 +++++++++++++++++--------- 1 file changed, 46 insertions(+), 22 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 3ac3e7e7..c56f4e1e 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -1,12 +1,16 @@ #!/usr/bin/env python -import logging -import rich.console import os import sys +import re +import logging +import glob +import rich.console +from datetime import datetime +from yaml import YAMLError + import relecov_tools.utils from relecov_tools.config_json import ConfigJson -from yaml import YAMLError # import relecov_tools.json_schema @@ -109,22 +113,45 @@ def include_pangolin_data(self, j_data): else: sample_name = row["sequencing_sample_id"] - f_name = sample_name + ".pangolin." + row["analysis_date"] + ".csv" - f_path = os.path.join(self.input_folder, f_name) + f_name_regex = sample_name + ".pangolin.*.csv" + f_path = os.path.join(self.input_folder, f_name_regex) + pangolin_sample_file = glob.glob(f_path) + if pangolin_sample_file: + if len(pangolin_sample_file) == 1: + try: + result_regex = re.search( + "(.*)\.pangolin\.(.*)\.csv", pangolin_sample_file[0] + ) + row["lineage_analysis_date"] = result_regex.group(2) + row["lineage_analysis_date"] = datetime.strptime( row["lineage_analysis_date"], + "%Y%m%d" + ).strftime("%Y-%m-%d") + except Exception as e: + stderr.print(f"[red] Pattern not found in file name.") + import pdb;pdb.set_trace() + try: + f_data = relecov_tools.utils.read_csv_file_return_dict(result_regex + .group(), ",") + except FileNotFoundError as e: + log.error("File %s not found ", e) + stderr.print(f"[red]File {e} not found") + # When file does not exist set all values to empty + for field, value in mapping_fields.items(): + row[field] = "" + continue + # sys.exit(1) + pang_key = list(f_data.keys())[0] + for field, value in mapping_fields.items(): + row[field] = f_data[pang_key][value] + else: + ## We need to handle this when more than one analysis in the folder. How can we do this? Use the last one? + stderr.print( + f"[red] More than one pangolin file found for the same sample " + ) + sys.exit(1) + else: + stderr.print(f"[yellow] No pangolin file for sample: " + sample_name) - try: - f_data = relecov_tools.utils.read_csv_file_return_dict(f_path, ",") - except FileNotFoundError as e: - log.error("File %s not found ", e) - stderr.print(f"[red]File {e} not found") - # When file does not exist set all values to empty - for field, value in mapping_fields.items(): - row[field] = "" - continue - # sys.exit(1) - pang_key = list(f_data.keys())[0] - for field, value in mapping_fields.items(): - row[field] = f_data[pang_key][value] return j_data @@ -231,9 +258,6 @@ def collect_info_from_lab_json(self): log.error("%s invalid json file", self.json_file) stderr.print(f"[red] {self.json_file} invalid json file") sys.exit(1) - import pdb - - pdb.set_trace() # j_data = [] # mapping_fields = self.configuration.get_topic_data( # "bioinfo_analysis", "required_fields_from_lab_json" @@ -260,7 +284,7 @@ def create_bioinfo_file(self): j_data = self.include_software_versions(j_data) stderr.print("[blue]Adding summary variant metrics") j_data = self.include_variant_metrics(j_data) - stderr.print("[blue]Adding pangolin informtion") + stderr.print("[blue]Adding pangolin information") j_data = self.include_pangolin_data(j_data) stderr.print("[blue]Adding consensus data") j_data = self.include_consensus_data(j_data) From df06dbc42e8e8f233f941c82320c89e647a7ec56 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 21 Oct 2022 13:56:11 +0200 Subject: [PATCH 1067/1454] added study type as fixed field for lab metadata --- relecov_tools/conf/configuration.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index a06353a2..c27bf61e 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -3,7 +3,8 @@ "fixed_fields": { "host_disease": "COVID-19", "tax_id": "2697049", - "organism": "Severe acute respiratory syndrome coronavirus 2" + "organism": "Severe acute respiratory syndrome coronavirus 2", + "study_type": "Whole Genome Sequencing" }, "metadata_lab_heading": [ "Public Health sample id (SIVIES)", From d0b78adf4cae61b5318443ac78e4774cd6a76c3a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 24 Oct 2022 16:14:28 +0200 Subject: [PATCH 1068/1454] fixed required files bioinfo parser --- relecov_tools/conf/configuration.json | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index c27bf61e..38461375 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -248,7 +248,6 @@ "required_file": { "variants_metrics": "summary_variants_metrics_mqc.csv", "versions": "software_versions.yml", - "pangoling": "pangolin_version.csv", "mapping_stats": "mapping_illumina_stats.tab" }, "mapping_consensus": [ From 2de9ee23c88a24d785aace646e528cbeafe2ec0c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 24 Oct 2022 16:14:45 +0200 Subject: [PATCH 1069/1454] added versions for lineage software analysis to schema --- relecov_tools/schema/relecov_schema.json | 33 ++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 1ffe4036..41ab74ca 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2389,6 +2389,17 @@ "label": "If lineage identification Is Other, Specify", "fill_mode": "batch" }, + "lineage_algorithm_software_version": { + "examples": [ + "2.1.10" + ], + "ontology": "GENEPIO:0001502", + "type": "string", + "description": "The version of the software used to determine the lineage/clade.", + "classification": "Lineage fields", + "label": "Lineage/clade analysis software version", + "fill_mode": "batch" + }, "lineage_analysis_software_version": { "examples": [ "2.1.10" @@ -2400,6 +2411,28 @@ "label": "Lineage/clade analysis software version", "fill_mode": "batch" }, + "lineage_analysis_scorpio_version": { + "examples": [ + "2.1.10" + ], + "ontology": "GENEPIO:0001502", + "type": "string", + "description": "The version of the scorpio data used to determine the lineage/clade.", + "classification": "Lineage fields", + "label": "Lineage/clade analysis software version", + "fill_mode": "batch" + }, + "lineage_analysis_constellation_version": { + "examples": [ + "2.1.10" + ], + "ontology": "GENEPIO:0001502", + "type": "string", + "description": "The version of the constellations databases used to determine the lineage/clade.", + "classification": "Lineage fields", + "label": "Lineage/clade analysis software version", + "fill_mode": "batch" + }, "lineage_analysis_date": { "examples": [ "2022/10/24" From 9c3cbf45fd3e3436340f656acc92882829caeeb4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 24 Oct 2022 16:18:22 +0200 Subject: [PATCH 1070/1454] added more mapping fields from pangolin file --- relecov_tools/conf/configuration.json | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 38461375..3e578784 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -259,7 +259,11 @@ ], "mapping_pangolin": { "variant_designation": "scorpio_call", - "lineage_name": "lineage" + "lineage_name": "lineage", + "lineage_algorithm_software_version": "version", + "lineage_analysis_software_version": "pangolin_version", + "lineage_analysis_scorpio_version": "scorpio_version", + "lineage_analysis_constellation_version": "constellation_version" }, "mapping_stats": { "analysis_date": "analysis date", From 6e7b549d61f8b96dfb7fd863d27fa623d9cbd41d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 24 Oct 2022 16:23:03 +0200 Subject: [PATCH 1071/1454] fixed type and format date in schema for lineage analysis date field --- relecov_tools/schema/relecov_schema.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 41ab74ca..1ceff33f 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2438,7 +2438,8 @@ "2022/10/24" ], "ontology": "0", - "type": "date", + "type": "string", + "format": "date", "description": "Date when the lineage analysis was performed", "classification": "Lineage fields", "label": "lineage/clade analysis date", From f1ab9c5c84b205b411233db100ee629394d886ac Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 24 Oct 2022 16:50:10 +0200 Subject: [PATCH 1072/1454] black linting --- relecov_tools/read_bioinfo_metadata.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index c56f4e1e..a251cafb 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -123,15 +123,15 @@ def include_pangolin_data(self, j_data): "(.*)\.pangolin\.(.*)\.csv", pangolin_sample_file[0] ) row["lineage_analysis_date"] = result_regex.group(2) - row["lineage_analysis_date"] = datetime.strptime( row["lineage_analysis_date"], - "%Y%m%d" + row["lineage_analysis_date"] = datetime.strptime( + row["lineage_analysis_date"], "%Y%m%d" ).strftime("%Y-%m-%d") except Exception as e: stderr.print(f"[red] Pattern not found in file name.") - import pdb;pdb.set_trace() try: - f_data = relecov_tools.utils.read_csv_file_return_dict(result_regex - .group(), ",") + f_data = relecov_tools.utils.read_csv_file_return_dict( + result_regex.group(), "," + ) except FileNotFoundError as e: log.error("File %s not found ", e) stderr.print(f"[red]File {e} not found") @@ -152,7 +152,6 @@ def include_pangolin_data(self, j_data): else: stderr.print(f"[yellow] No pangolin file for sample: " + sample_name) - return j_data def include_consensus_data(self, j_data): From 4085d4e800ef9a9ad0a7e11091db6875cef8f7fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 25 Oct 2022 17:00:15 +0200 Subject: [PATCH 1073/1454] fixed validation errors schema --- relecov_tools/conf/configuration.json | 4 ++-- relecov_tools/schema/relecov_schema.json | 16 ++++++++++++++++ 2 files changed, 18 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 3e578784..58793eca 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -226,7 +226,7 @@ "assembly": "None", "assembly_params": "None", "bioinformatics_protocol_software_name": "nf-core/viralrecon", - "commercial_open_source_both": "open-source", + "commercial_open_source_both": "Open Source", "consensus_params": "-p vcf -f", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", @@ -258,7 +258,7 @@ "number_of_base_pairs_sequenced" ], "mapping_pangolin": { - "variant_designation": "scorpio_call", + "variant_name": "scorpio_call", "lineage_name": "lineage", "lineage_algorithm_software_version": "version", "lineage_analysis_software_version": "pangolin_version", diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 1ceff33f..c5caf113 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2445,6 +2445,22 @@ "label": "lineage/clade analysis date", "fill_mode": "batch" }, + "variant_name": { + "enum": [ + "Variant of Interest (VOI) [GENEPIO:0100082]", + "Variant of Concern (VOC) [GENEPIO:0100083]", + "Variant Under Monitoring (VUM) [GENEPIO:0100279]" + ], + "ontology": "GENEPIO:0001503", + "type": "string", + "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", + "examples": [ + "Variant of Concern (VOC) [GENEPIO:0100083]" + ], + "classification": "Lineage fields", + "label": "Variant designation", + "fill_mode": "batch" + }, "variant_designation": { "enum": [ "Variant of Interest (VOI) [GENEPIO:0100082]", From 61a06995e50be34541cfa818bedbfc3ac5f3d2ac Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 25 Oct 2022 17:01:23 +0200 Subject: [PATCH 1074/1454] fixed schema new field variant_name --- relecov_tools/schema/relecov_schema.json | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index c5caf113..888524dd 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2446,14 +2446,12 @@ "fill_mode": "batch" }, "variant_name": { - "enum": [ - "Variant of Interest (VOI) [GENEPIO:0100082]", - "Variant of Concern (VOC) [GENEPIO:0100083]", - "Variant Under Monitoring (VUM) [GENEPIO:0100279]" + "examples": [ + "Alpha" ], - "ontology": "GENEPIO:0001503", + "ontology": "", "type": "string", - "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", + "description": "The variant classification of the lineage/clade i.e. alpha, beta, etc.", "examples": [ "Variant of Concern (VOC) [GENEPIO:0100083]" ], From 3a64d79037295db101e2764acdce665adb5c12a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 27 Oct 2022 13:30:04 +0200 Subject: [PATCH 1075/1454] linting --- relecov_tools/read_bioinfo_metadata.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index a251cafb..35967002 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -127,7 +127,7 @@ def include_pangolin_data(self, j_data): row["lineage_analysis_date"], "%Y%m%d" ).strftime("%Y-%m-%d") except Exception as e: - stderr.print(f"[red] Pattern not found in file name.") + stderr.print(f"[red] Pattern not found in file name. Error: {e}") try: f_data = relecov_tools.utils.read_csv_file_return_dict( result_regex.group(), "," @@ -144,13 +144,13 @@ def include_pangolin_data(self, j_data): for field, value in mapping_fields.items(): row[field] = f_data[pang_key][value] else: - ## We need to handle this when more than one analysis in the folder. How can we do this? Use the last one? + # We need to handle this when more than one analysis in the folder. How can we do this? Use the last one? stderr.print( - f"[red] More than one pangolin file found for the same sample " + "[red] More than one pangolin file found for the same sample " ) sys.exit(1) else: - stderr.print(f"[yellow] No pangolin file for sample: " + sample_name) + stderr.print(f"[yellow] No pangolin file for sample: {sample_name}") return j_data From 2fc36299c164e544c8bfd72bb660383b1c6e56f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 27 Oct 2022 13:30:58 +0200 Subject: [PATCH 1076/1454] black linting --- relecov_tools/read_bioinfo_metadata.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 35967002..b32a6508 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -127,7 +127,9 @@ def include_pangolin_data(self, j_data): row["lineage_analysis_date"], "%Y%m%d" ).strftime("%Y-%m-%d") except Exception as e: - stderr.print(f"[red] Pattern not found in file name. Error: {e}") + stderr.print( + f"[red] Pattern not found in file name. Error: {e}" + ) try: f_data = relecov_tools.utils.read_csv_file_return_dict( result_regex.group(), "," From d3f9ae58ede0f52d3c4125795635e6c0382f9e76 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 2 Nov 2022 16:28:23 +0100 Subject: [PATCH 1077/1454] fix label for variant designation in schema --- relecov_tools/schema/relecov_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 888524dd..4835d608 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2456,7 +2456,7 @@ "Variant of Concern (VOC) [GENEPIO:0100083]" ], "classification": "Lineage fields", - "label": "Variant designation", + "label": "Variant Name", "fill_mode": "batch" }, "variant_designation": { From c80e996a3af96673fac23f6df23865418bf9ec4b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 3 Nov 2022 17:10:50 +0100 Subject: [PATCH 1078/1454] Do not stop if sample is not define for variant data upload --- relecov_tools/feed_database.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 30700e15..231754ad 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -242,6 +242,17 @@ def update_database(self, field_values, post_url): "[red] Unable to sent the request to remote server" ) sys.exit(1) + + elif "is not defined" in result["ERROR_TEST"].lower(): + log.warning( + "Request to %s for %s was not accepted", + self.database_server, + req_sample, + ) + stderr.print( + f"[yellow] Warning: {req_sample} is not defined" + ) + continue elif "already defined" in result["ERROR_TEST"].lower(): log.warning( "Request to %s for %s was not accepted", From e397109195b01a239447748ec37c3d67e48c5c68 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 4 Nov 2022 11:45:54 +0100 Subject: [PATCH 1079/1454] added analysis date to long table json --- relecov_tools/long_table_parse.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index a16cc195..b0a96d08 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -79,6 +79,7 @@ def parse_file(self): the user (long_table.csv). Validate the file by checking the header line """ + with open(self.file_path) as fh: lines = fh.readlines() @@ -130,8 +131,12 @@ def parse_file(self): def convert_to_json(self, samp_dict): j_list = [] + # Grab date from filename + result_regex = re.search( + "variants_long_table_(.*).csv", os.path.basename(self.file_path) + ) for key, values in samp_dict.items(): - j_dict = {"sample_name": key} + j_dict = {"sample_name": key, "analysis_date": result_regex.group(1)} j_dict["variants"] = values j_list.append(j_dict) return j_list From 14c060b22d984fe8672998124a48701bd43e0ab3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 4 Nov 2022 14:01:22 +0100 Subject: [PATCH 1080/1454] duplicate lines if Gene contains multiple genes separated with & --- relecov_tools/long_table_parse.py | 25 +++++++++++++++++++------ 1 file changed, 19 insertions(+), 6 deletions(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index b0a96d08..cd64252b 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -1,10 +1,13 @@ -from datetime import datetime import json +import re import logging -import os.path import sys -from pathlib import Path import rich +import os.path + +from pathlib import Path +from datetime import datetime + import relecov_tools from relecov_tools.config_json import ConfigJson @@ -116,8 +119,6 @@ def parse_file(self): "af": line_s[heading_index["AF"]], } - variant_dict["Gene"] = line_s[heading_index["GENE"]] - variant_dict["Effect"] = line_s[heading_index["EFFECT"]] variant_dict["VariantAnnotation"] = { "hgvs_c": line_s[heading_index["HGVS_C"]], @@ -125,7 +126,19 @@ def parse_file(self): "hgvs_p_1_letter": line_s[heading_index["HGVS_P_1LETTER"]], } - samp_dict[sample].append(variant_dict) + if re.search("&",line_s[heading_index["GENE"]]): + # Example + # 215184,NC_045512.2,27886,AAACGAACATGAAATT,A,PASS,1789,1756,1552,0.87,ORF7b&ORF8,gene_fusion,n.27887_27901delAACGAACATGAAATT,.,.,ivar,B.1.1.318 + # This only occurs (for now) as gene fusion, so we just duplicate lines with same values + genes = re.split("&",line_s[heading_index["GENE"]]) + for gene in genes: + variant_dict_copy = variant_dict.copy() + variant_dict_copy["Gene"] = gene + samp_dict[sample].append(variant_dict_copy) + else: + variant_dict["Gene"] = line_s[heading_index["GENE"]] + samp_dict[sample].append(variant_dict) + stderr.print("[green]Successful parsing data") return samp_dict From 667b6379c032d95b57d0cd43b4079c2ff0ff1ad7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 4 Nov 2022 14:02:59 +0100 Subject: [PATCH 1081/1454] black linting --- relecov_tools/feed_database.py | 4 +--- relecov_tools/long_table_parse.py | 4 ++-- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 231754ad..3c359902 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -249,9 +249,7 @@ def update_database(self, field_values, post_url): self.database_server, req_sample, ) - stderr.print( - f"[yellow] Warning: {req_sample} is not defined" - ) + stderr.print(f"[yellow] Warning: {req_sample} is not defined") continue elif "already defined" in result["ERROR_TEST"].lower(): log.warning( diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index cd64252b..6189a579 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -126,11 +126,11 @@ def parse_file(self): "hgvs_p_1_letter": line_s[heading_index["HGVS_P_1LETTER"]], } - if re.search("&",line_s[heading_index["GENE"]]): + if re.search("&", line_s[heading_index["GENE"]]): # Example # 215184,NC_045512.2,27886,AAACGAACATGAAATT,A,PASS,1789,1756,1552,0.87,ORF7b&ORF8,gene_fusion,n.27887_27901delAACGAACATGAAATT,.,.,ivar,B.1.1.318 # This only occurs (for now) as gene fusion, so we just duplicate lines with same values - genes = re.split("&",line_s[heading_index["GENE"]]) + genes = re.split("&", line_s[heading_index["GENE"]]) for gene in genes: variant_dict_copy = variant_dict.copy() variant_dict_copy["Gene"] = gene From c89531c3cac7c93442e6fb4ddd81502ecb7e92ce Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 25 Nov 2022 00:45:35 +0100 Subject: [PATCH 1082/1454] fixed error when sending several parameters via API --- relecov_tools/rest_api.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/rest_api.py b/relecov_tools/rest_api.py index c8618adc..d1fb45ee 100644 --- a/relecov_tools/rest_api.py +++ b/relecov_tools/rest_api.py @@ -28,7 +28,7 @@ def get_request(self, request_info, parameter, value=None, safe=True): for key, value in parameter.items(): param_value.append(key + "=" + value) url_http = str( - self.request_url + request_info + "?" + "?".join(param_value) + self.request_url + request_info + "?" + "&".join(param_value) ) else: url_http = str( From 37bb33bed22451a2ac01b7303f80126c7a2c9cae Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 17 Feb 2023 12:06:59 +0100 Subject: [PATCH 1083/1454] Introduced new option to download in __main__.py --- relecov_tools/__main__.py | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 17cabb74..6a13917b 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -143,10 +143,18 @@ def relecov_tools_cli(verbose, log_file): "--conf_file", help="Configuration file (no params file)", ) -def download(user, password, conf_file, user_relecov, password_relecov): +@click.option( + "-t", + "--target_folders", + is_flag=False, + flag_value="ALL", + default=None, + help="Flag: Select which folders will be downloaded giving [paths] or via prompt" +) +def download(user, password, conf_file, user_relecov, password_relecov, target_folders): """Download files located in sftp server.""" sftp_connection = relecov_tools.sftp_handle.SftpHandle( - user, password, conf_file, user_relecov, password_relecov + user, password, conf_file, user_relecov, password_relecov, target_folders ) sftp_connection.download() @@ -166,7 +174,7 @@ def download(user, password, conf_file, user_relecov, password_relecov): help="Json with the additional metadata to add to the received user metadata", ) @click.option( - "-o", "--metadata-out", type=click.Path(), help="Path to save output metadata file" + "-o", "--metadata-out", type=click.Path(), help="Path to save output metadata file" ) def read_lab_metadata(metadata_file, sample_list_file, metadata_out): """ From be32bf4cafc4501855fe27ed3a37b9eb7bea4435 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 17 Feb 2023 12:07:46 +0100 Subject: [PATCH 1084/1454] Introduced new aux function to utils.py --- relecov_tools/utils.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 2d3a04b9..5e40aef5 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -214,7 +214,7 @@ def rich_force_colors(): or os.getenv("FORCE_COLOR") or os.getenv("PY_COLORS") ): - return True + return TrueS return None @@ -258,3 +258,8 @@ def prompt_skip_folder_creation(): stderr.print("Do you want to skip folder creation? (Y/N)") confirmation = questionary.confirm("Skip?", default=False).unsafe_ask() return confirmation + + +def prompt_checkbox(msg, choices): + selected_options = questionary.checkbox(msg, choices=choices).unsafe_ask() + return selected_options From 79dfe758cc74f7061d05cf1852429094d2e287cb Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 17 Feb 2023 12:08:40 +0100 Subject: [PATCH 1085/1454] Changed download function in sftp_handle.py to support folder selection --- relecov_tools/sftp_handle.py | 68 +++++++++++++++++++++++++++++++++--- 1 file changed, 64 insertions(+), 4 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index d623fdc4..4f14dc2b 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -33,6 +33,7 @@ def __init__( conf_file=None, user_relecov=None, password_relecov=None, + target_folders=None ): """Initializes the sftp object""" config_json = ConfigJson() @@ -41,6 +42,7 @@ def __init__( ) self.sftp_user = user self.sftp_passwd = passwd + self.target_folders = target_folders if conf_file is None: self.sftp_server = config_json.get_topic_data( "sftp_connection", "sftp_server" @@ -69,6 +71,7 @@ def __init__( try: self.sftp_server = config["sftp_server"] self.sftp_port = config["sftp_port"] + self.target_folders = config["target_folders"] try: self.storage_local_folder = config["storage_local_folder"] except KeyError: @@ -105,6 +108,7 @@ def __init__( self.sftp_passwd = relecov_tools.utils.prompt_password( msg="Enter your password" ) + self.client = None external_servers = config_json.get_topic_data("external_url", "relecov") self.relecov_server = external_servers["server"] @@ -331,6 +335,48 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): ] return sample_file_list + def validate_fetched_files(self, fetched_folder): + """Check if the files in the fetched folder are the ones defined in metadata file""" + try: + files_list = self.client.listdir(fetched_folder) + except FileNotFoundError as e: + log.error("Invalid folder at remote sftp %s", e) + return False + meta_files = [fi for fi in files_list if fi.endswith(".xlsx")] + if len(meta_files) == 0: + log.error("Excel file for metadata does not exist on %s", fetched_folder) + stderr.print("[red] Metadata file does not exist on " + fetched_folder) + return False + if len(meta_files) > 1: + log.error("Too many Excel files on folder %s", fetched_folder) + stderr.print("[red] Metadata file does not exist on " + fetched_folder) + return False + target_meta_file = os.path.join(fetched_folder, meta_files[0]) + temp_folder = "/tmp/metadata_validation_file/" + os.makedirs(temp_folder, exist_ok=True) + local_meta_file = os.path.join(temp_folder, os.path.basename(target_meta_file)) + try: + self.client.get( + target_meta_file, + local_meta_file, + ) + except FileNotFoundError as e: + log.error("Unable to fetch metadata file %s ", e) + samples_files_list = self.get_sample_fastq_file_names(temp_folder, local_meta_file) + samples_files_list = sorted(sum([list(fi.values()) for sample, fi in samples_files_list.items()], [])) + filtered_files_list = sorted([fi for fi in files_list if fi.endswith('fastq.gz')]) + self.delete_local_folder(temp_folder) + stderr.print("files in metadata") + stderr.print(samples_files_list) + stderr.print("files in fetch") + stderr.print(filtered_files_list) + if samples_files_list == filtered_files_list: + return True + else: + log.info("Files in %s do not match metadata file", fetched_folder) + stderr.print("Files in " + fetched_folder + " do not match the ones described in metadata") + return False + def validate_download_files(self, sample_file_list, local_folder): """Check if download sample files are the ones defined on metadata file""" if not sample_file_list: @@ -394,25 +440,39 @@ def download(self): log.error("Unable to establish connection towards sftp server") stderr.print("[red] Unable to establish sftp connection") sys.exit(1) - root_directory_list = self.list_folders(".") if not root_directory_list: - log.error("There is no folders under root directory") + log.error("There are no folders under root directory") + sys.exit(1) + if self.target_folders == "ALL": + target_folders = relecov_tools.utils.prompt_checkbox( + msg="Select the folders that will be downloaded", + choices=sorted(root_directory_list) + ) + elif self.target_folders is None: + target_folders = root_directory_list + else: + target_folders = [tf for tf in root_directory_list if tf in self.target_folders] + if not target_folders: + log.error("There are no folders that match selection") sys.exit(1) folders_to_download = {} # create_main_folders(root_directory_list) - for folder in root_directory_list: + for folder in target_folders: list_files = self.get_file_list(folder) if len(list_files) > 0: folders_to_download[folder] = list_files if len(folders_to_download) == 0: - log.info("Exiting download. There is no files on sftp to dowload") + log.info("Exiting download. There are no files on sftp to dowload") self.close_connection() sys.exit(0) for folder, files in folders_to_download.items(): log.info("Processing folder %s", folder) stderr.print("Processing folder " + folder) + # Validate that the files are the ones described in metadata. + if not self.validate_fetched_files(folder): + continue # get the files in each folder result_data = self.get_files_from_sftp_folder(folder, files) md5_files, req_retransmition = self.verify_md5_checksum( From 75cb15a7113509b8b830fd147341018024d99fa7 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 17 Feb 2023 12:21:49 +0100 Subject: [PATCH 1086/1454] linting --- relecov_tools/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 5e40aef5..df6d448f 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -214,7 +214,7 @@ def rich_force_colors(): or os.getenv("FORCE_COLOR") or os.getenv("PY_COLORS") ): - return TrueS + return True return None From e5327f78231c693da1b12e866f051ac869d45a1e Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 17 Feb 2023 13:42:00 +0100 Subject: [PATCH 1087/1454] black linting --- relecov_tools/metadata_homogeneizer.py | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index e7d8a8ba..9c05e7b0 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -20,7 +20,6 @@ class MetadataHomogeneizer: """MetadataHomogeneizer object""" def __init__(self, institution=None, directory=None, output_folder=None): - # open config self.config_json = ConfigJson() # read heading from config From fa1426cc2f82858a715c56289947fb65996c10ab Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 17 Feb 2023 13:43:35 +0100 Subject: [PATCH 1088/1454] black linting --- relecov_tools/read_bioinfo_metadata.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index b32a6508..0affd7ca 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -243,9 +243,7 @@ def include_software_versions(self, j_data): sys.exit(1) for row in j_data: for field, version_data in version_fields.items(): - for key, value in version_data.items(): - row[field] = versions[key][value] return j_data From 3cab812780274a565fcf7717eb2bb6deaf7c51bc Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 17 Feb 2023 13:43:53 +0100 Subject: [PATCH 1089/1454] black linting --- relecov_tools/map_schema.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 97f016bc..afbcc76e 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -142,7 +142,6 @@ def mapping_json_data(self, mapping_schema_dict): map_sample_dict = OrderedDict() for item, value in mapping_schema_dict.items(): try: - data[value] = data[value].split(" [", 1)[0] map_sample_dict[item] = data[value] @@ -157,7 +156,6 @@ def additional_formating(self, mapped_json_data): """ if self.destination_schema == "ENA": for idx in range(len(self.json_data)): - mapped_json_data[idx]["collector_name"] = "unknown" mapped_json_data[idx]["file_format"] = "FASTQ" mapped_json_data[idx]["study_type"] = "Whole Genome Sequencing" @@ -230,7 +228,6 @@ def additional_formating(self, mapped_json_data): + self.json_data[idx]["sequence_file_R2_fastq"] ) for i, j in enumerate(fields): - mapped_json_data[idx][j] = "not provided" return mapped_json_data From 32f510fa294148f79bf6fcc43a52b107d5071304 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 17 Feb 2023 13:44:12 +0100 Subject: [PATCH 1090/1454] black linting --- relecov_tools/ena_upload.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index cd507169..5c3fceaa 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -122,7 +122,6 @@ def create_dataframe(self, dataframe_name, fields_config, df_schemas): df_list = [] config_json = ConfigJson() for index in range(len(dataframe_name)): - fields = config_json.get_configuration("ENA_fields")[fields_config[index]] dataframe_name[index] = df_schemas[fields] df_list.append(dataframe_name[index]) @@ -304,7 +303,6 @@ def create_structure_to_ena(self): session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) for filename, path in file_paths.items(): - print("Uploading path " + path + " and filename: " + filename) try: @@ -313,7 +311,6 @@ def create_structure_to_ena(self): print(g) # send the file file.close() # close file and FTP except BaseException as err: - print(f"ERROR: {err}") # print("ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000.") @@ -345,7 +342,6 @@ def create_structure_to_ena(self): for files in root.iter("FILE"): if "R2" in files.attrib["filename"]: - H = df_run_final.loc[ df_run_final["sequence_file_R2_fastq"] == files.attrib["filename"] From 5af6b0b7a2889f3979ceddb7e06e5327127a4b3f Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 17 Feb 2023 13:44:21 +0100 Subject: [PATCH 1091/1454] black linting --- relecov_tools/__main__.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 6a13917b..08aa2429 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -30,7 +30,6 @@ def run_relecov_tools(): - # Set up the rich traceback rich.traceback.install(console=stderr, width=200, word_wrap=True, extra_lines=1) @@ -116,7 +115,6 @@ def decorator(f): "-l", "--log-file", help="Save a verbose log to a file.", metavar="" ) def relecov_tools_cli(verbose, log_file): - # Set the base logger to output DEBUG log.setLevel(logging.DEBUG) @@ -144,12 +142,12 @@ def relecov_tools_cli(verbose, log_file): help="Configuration file (no params file)", ) @click.option( - "-t", - "--target_folders", + "-t", + "--target_folders", is_flag=False, flag_value="ALL", default=None, - help="Flag: Select which folders will be downloaded giving [paths] or via prompt" + help="Flag: Select which folders will be downloaded giving [paths] or via prompt", ) def download(user, password, conf_file, user_relecov, password_relecov, target_folders): """Download files located in sftp server.""" From dcb39803940aa580f5477f5ef52deacd1c134041 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 17 Feb 2023 13:44:29 +0100 Subject: [PATCH 1092/1454] black linting --- relecov_tools/sftp_handle.py | 30 +++++++++++++++++++++--------- 1 file changed, 21 insertions(+), 9 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 4f14dc2b..8b553abc 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -33,7 +33,7 @@ def __init__( conf_file=None, user_relecov=None, password_relecov=None, - target_folders=None + target_folders=None, ): """Initializes the sftp object""" config_json = ConfigJson() @@ -359,12 +359,18 @@ def validate_fetched_files(self, fetched_folder): self.client.get( target_meta_file, local_meta_file, - ) + ) except FileNotFoundError as e: log.error("Unable to fetch metadata file %s ", e) - samples_files_list = self.get_sample_fastq_file_names(temp_folder, local_meta_file) - samples_files_list = sorted(sum([list(fi.values()) for sample, fi in samples_files_list.items()], [])) - filtered_files_list = sorted([fi for fi in files_list if fi.endswith('fastq.gz')]) + samples_files_list = self.get_sample_fastq_file_names( + temp_folder, local_meta_file + ) + samples_files_list = sorted( + sum([list(fi.values()) for sample, fi in samples_files_list.items()], []) + ) + filtered_files_list = sorted( + [fi for fi in files_list if fi.endswith("fastq.gz")] + ) self.delete_local_folder(temp_folder) stderr.print("files in metadata") stderr.print(samples_files_list) @@ -374,8 +380,12 @@ def validate_fetched_files(self, fetched_folder): return True else: log.info("Files in %s do not match metadata file", fetched_folder) - stderr.print("Files in " + fetched_folder + " do not match the ones described in metadata") - return False + stderr.print( + "Files in " + + fetched_folder + + " do not match the ones described in metadata" + ) + return False def validate_download_files(self, sample_file_list, local_folder): """Check if download sample files are the ones defined on metadata file""" @@ -447,12 +457,14 @@ def download(self): if self.target_folders == "ALL": target_folders = relecov_tools.utils.prompt_checkbox( msg="Select the folders that will be downloaded", - choices=sorted(root_directory_list) + choices=sorted(root_directory_list), ) elif self.target_folders is None: target_folders = root_directory_list else: - target_folders = [tf for tf in root_directory_list if tf in self.target_folders] + target_folders = [ + tf for tf in root_directory_list if tf in self.target_folders + ] if not target_folders: log.error("There are no folders that match selection") sys.exit(1) From 758c858f0b4ef232ff0ecbefd83e1b7c3c0a959e Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 17 Feb 2023 13:47:20 +0100 Subject: [PATCH 1093/1454] black linting --- relecov_tools/institution_scripts/ISCIII.py | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index 7cedfad9..de84bf53 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -36,7 +36,6 @@ def added_seq_inst_model(metadata, f_data, mapped_fields, heading): for row in metadata[1:]: for key, val in mapped_fields.items(): m_idx = heading.index(key) - try: run_name = f_data[str(row[s_idx])][val].lower() except KeyError as e: From 89ec5907735e6c4d1a52885dc8a9b563927e558d Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 17 Feb 2023 13:50:47 +0100 Subject: [PATCH 1094/1454] black linting --- relecov_tools/institution_scripts/ISCIII.py | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/institution_scripts/ISCIII.py b/relecov_tools/institution_scripts/ISCIII.py index de84bf53..17235c63 100644 --- a/relecov_tools/institution_scripts/ISCIII.py +++ b/relecov_tools/institution_scripts/ISCIII.py @@ -183,7 +183,6 @@ def findout_library_layout(metadata, f_data, mapped_fields, heading): to paired""" s_idx = heading.index("Sample ID given for sequencing") for row in metadata[1:]: - for key, val in mapped_fields.items(): m_idx = heading.index(key) try: From b8f81ddfc700ebf1ac07149c54857ec4c902a4ee Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 20 Feb 2023 23:24:31 +0100 Subject: [PATCH 1095/1454] Introduced new changes to sftp_handle.py --- relecov_tools/sftp_handle.py | 61 ++++++++++++++++-------------------- 1 file changed, 27 insertions(+), 34 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 8b553abc..65a49f1b 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -110,10 +110,6 @@ def __init__( ) self.client = None - external_servers = config_json.get_topic_data("external_url", "relecov") - self.relecov_server = external_servers["server"] - self.relecov_url = external_servers["url"] - self.relecov_post_url = external_servers["sftp_info"] def open_connection(self): """Establish sftp connection""" @@ -279,7 +275,7 @@ def create_main_folders(self, root_directory_list): full_folder = os.path.join(self.storage_local_folder, folder) os.makedirs(full_folder, exist_ok=True) return True - + def find_metadata_file(self, local_folder): """Find excel extension file which contains metatada""" reg_for_xlsx = os.path.join(local_folder, "*.xlsx") @@ -334,25 +330,30 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): index_fastq_r2 ] return sample_file_list - - def validate_fetched_files(self, fetched_folder): - """Check if the files in the fetched folder are the ones defined in metadata file""" + + def list_fetched_files(self, fetched_folder): + """Check if the metadata file exists""" try: - files_list = self.client.listdir(fetched_folder) + fetched_files_list = self.client.listdir(fetched_folder) except FileNotFoundError as e: log.error("Invalid folder at remote sftp %s", e) return False - meta_files = [fi for fi in files_list if fi.endswith(".xlsx")] + return fetched_files_list + + def validate_metadata_file(self, fetched_folder): + """Check if the metadata file exists""" + fetched_files_list = self.list_fetched_files(fetched_folder) + meta_files = [fi for fi in fetched_files_list if fi.endswith(".xlsx")] if len(meta_files) == 0: log.error("Excel file for metadata does not exist on %s", fetched_folder) stderr.print("[red] Metadata file does not exist on " + fetched_folder) return False if len(meta_files) > 1: log.error("Too many Excel files on folder %s", fetched_folder) - stderr.print("[red] Metadata file does not exist on " + fetched_folder) + stderr.print("[red] Too many metadata files on " + fetched_folder) return False target_meta_file = os.path.join(fetched_folder, meta_files[0]) - temp_folder = "/tmp/metadata_validation_file/" + temp_folder = self.metadata_tmp_folder os.makedirs(temp_folder, exist_ok=True) local_meta_file = os.path.join(temp_folder, os.path.basename(target_meta_file)) try: @@ -362,20 +363,27 @@ def validate_fetched_files(self, fetched_folder): ) except FileNotFoundError as e: log.error("Unable to fetch metadata file %s ", e) + return local_meta_file + + def validate_fetched_files(self, fetched_folder): + """Check if the files in the fetched folder are the ones defined in metadata file""" + local_meta_file = self.validate_metadata_file(fetched_folder) + temp_folder = self.metadata_tmp_folder + if not local_meta_file: + log.error("Excel file for metadata not found %s", fetched_folder) + stderr.print("[red] Metadata file could not be obtained from " + fetched_folder) + return False + allowed_extensions = self.allowed_sample_ext samples_files_list = self.get_sample_fastq_file_names( temp_folder, local_meta_file ) samples_files_list = sorted( sum([list(fi.values()) for sample, fi in samples_files_list.items()], []) ) + fetched_files_list = self.list_fetched_files(fetched_folder) filtered_files_list = sorted( - [fi for fi in files_list if fi.endswith("fastq.gz")] + [fi for fi in fetched_files_list if fi.endswith(tuple(allowed_extensions))] ) - self.delete_local_folder(temp_folder) - stderr.print("files in metadata") - stderr.print(samples_files_list) - stderr.print("files in fetch") - stderr.print(filtered_files_list) if samples_files_list == filtered_files_list: return True else: @@ -385,6 +393,7 @@ def validate_fetched_files(self, fetched_folder): + fetched_folder + " do not match the ones described in metadata" ) + self.delete_local_folder(temp_folder) return False def validate_download_files(self, sample_file_list, local_folder): @@ -418,22 +427,6 @@ def create_json_with_downloaded_samples(self, sample_file_list, folder): sample_dict[sample] = {"folder": folder} return json.dumps(sample_dict, indent=4, sort_keys=True, ensure_ascii=False) - def send_info_to_server(self, json_data): - rest_api = RestApi(self.database_server, self.database_url) - error_counts = 0 - for item in json_data: - result = rest_api.post_request(item, "", self.relecov_post_url) - if "ERROR" in result: - error_counts += 1 - log.error("Request was not accepted %s", result["ERROR"]) - stderr.print( - "[red] Error " + result["ERROR"] + " when sending request}" - ) - if error_counts == 0: - log.info("Request was not accepted %s", result["ERROR"]) - stderr.print("[green] Successful upload information to server") - return - def delete_local_folder(self, local_folder): """Delete download folder because files does not complain requisites""" shutil.rmtree(local_folder, ignore_errors=True) From 393cef44fc11f39d262247df22aa28faec74d158 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 20 Feb 2023 23:44:26 +0100 Subject: [PATCH 1096/1454] linting --- relecov_tools/sftp_handle.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 65a49f1b..1fea62a5 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -14,7 +14,7 @@ import openpyxl import relecov_tools.utils from relecov_tools.config_json import ConfigJson -from relecov_tools.rest_api import RestApi +#from relecov_tools.rest_api import RestApi log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -400,7 +400,6 @@ def validate_download_files(self, sample_file_list, local_folder): """Check if download sample files are the ones defined on metadata file""" if not sample_file_list: return False - for sample, files in sample_file_list.items(): for file in files.values(): if not os.path.isfile(os.path.join(local_folder, file)): From fee856768479fafb0bee550c4b28b2ab23e219fb Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 20 Feb 2023 23:50:09 +0100 Subject: [PATCH 1097/1454] linting --- relecov_tools/sftp_handle.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 1fea62a5..9d10759f 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -14,7 +14,7 @@ import openpyxl import relecov_tools.utils from relecov_tools.config_json import ConfigJson -#from relecov_tools.rest_api import RestApi +# from relecov_tools.rest_api import RestApi log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -108,7 +108,6 @@ def __init__( self.sftp_passwd = relecov_tools.utils.prompt_password( msg="Enter your password" ) - self.client = None def open_connection(self): From 9da69ac123f2fab51fc78d7a061e167257121f62 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 20 Feb 2023 23:54:42 +0100 Subject: [PATCH 1098/1454] black linting --- relecov_tools/sftp_handle.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 9d10759f..575e1e89 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -14,6 +14,7 @@ import openpyxl import relecov_tools.utils from relecov_tools.config_json import ConfigJson + # from relecov_tools.rest_api import RestApi log = logging.getLogger(__name__) @@ -274,7 +275,7 @@ def create_main_folders(self, root_directory_list): full_folder = os.path.join(self.storage_local_folder, folder) os.makedirs(full_folder, exist_ok=True) return True - + def find_metadata_file(self, local_folder): """Find excel extension file which contains metatada""" reg_for_xlsx = os.path.join(local_folder, "*.xlsx") @@ -329,7 +330,7 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): index_fastq_r2 ] return sample_file_list - + def list_fetched_files(self, fetched_folder): """Check if the metadata file exists""" try: @@ -370,7 +371,9 @@ def validate_fetched_files(self, fetched_folder): temp_folder = self.metadata_tmp_folder if not local_meta_file: log.error("Excel file for metadata not found %s", fetched_folder) - stderr.print("[red] Metadata file could not be obtained from " + fetched_folder) + stderr.print( + "[red] Metadata file could not be obtained from " + fetched_folder + ) return False allowed_extensions = self.allowed_sample_ext samples_files_list = self.get_sample_fastq_file_names( From 90dc994afa8ad6db0e8e116bbeb7de58a0e76457 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 21 Feb 2023 10:29:38 +0100 Subject: [PATCH 1099/1454] Included a bunch of log prints for debugging --- relecov_tools/sftp_handle.py | 24 ++++++++++++++++++++---- 1 file changed, 20 insertions(+), 4 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 575e1e89..91f6b55a 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -113,6 +113,7 @@ def __init__( def open_connection(self): """Establish sftp connection""" + log.info("Setting credentials for SFTP connection with remote server") self.client = paramiko.SSHClient() self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) self.client.connect( @@ -124,6 +125,7 @@ def open_connection(self): look_for_keys=False, ) try: + log.info("Trying to stablish SFTP connection") self.client = self.client.open_sftp() return True except paramiko.SSHException as e: @@ -132,11 +134,13 @@ def open_connection(self): def close_connection(self): """Closes SFTP connection""" + log.info("Closing SFTP connection") self.client.close() return True def list_folders(self, folder_name): """Creates a directories list from the given path""" + log.info("Listing directories in %s", folder_name) directory_list = [] try: content_list = self.client.listdir(folder_name) @@ -155,6 +159,7 @@ def list_folders(self, folder_name): def get_file_list(self, folder_name): """Return a tuple with file name and directory path""" + log.info("Listing files in %s", folder_name) file_list = [] content_list = self.client.listdir(folder_name) for content in content_list: @@ -173,6 +178,7 @@ def get_files_from_sftp_folder(self, folder, files_list): """Create the subfolder with the present date and fetch all files from the sftp server """ + log.info("Creating folder %s to download files", folder) result_data = {"unable_to_fetch": [], "fetched_files": []} date = datetime.today().strftime("%Y%m%d") local_folder_path = os.path.join(self.storage_local_folder, folder, date) @@ -180,7 +186,7 @@ def get_files_from_sftp_folder(self, folder, files_list): os.makedirs(local_folder_path, exist_ok=True) log.info("created the folder to download files %s", local_folder_path) self.open_connection() - + log.info("Trying to fetch files in remote server") for file_list in files_list: try: self.client.get( @@ -201,9 +207,11 @@ def verify_md5_checksum(self, local_folder, file_list): required_retransmition = [] successful_files = [] # fetch the md5 file if exists + log.info("Searching for local md5 file") sftp_md5 = relecov_tools.utils.get_md5_from_local_folder(local_folder) if len(sftp_md5) > 0: # check md5 checksum for eac file + log.info("md5 file was not found in local, trying to fetch from SFTP") for f_name, values in sftp_md5.items(): f_path_name = os.path.join(local_folder, f_name) # Checksum value is stored in the index 1 @@ -266,7 +274,7 @@ def create_tmp_files_with_metadata_info( pass with open(sample_data_path, "w", encoding="utf-8") as fh: fh.write(json.dumps(data, indent=4, sort_keys=True, ensure_ascii=False)) - + log.info("Successfully created file with sample names list %s", sample_data_path) return True def create_main_folders(self, root_directory_list): @@ -274,6 +282,7 @@ def create_main_folders(self, root_directory_list): for folder in root_directory_list: full_folder = os.path.join(self.storage_local_folder, folder) os.makedirs(full_folder, exist_ok=True) + log.info("Created main folder for process %s", full_folder) return True def find_metadata_file(self, local_folder): @@ -334,6 +343,7 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): def list_fetched_files(self, fetched_folder): """Check if the metadata file exists""" try: + log.info("List files in fetched folder %s", fetched_folder) fetched_files_list = self.client.listdir(fetched_folder) except FileNotFoundError as e: log.error("Invalid folder at remote sftp %s", e) @@ -363,6 +373,8 @@ def validate_metadata_file(self, fetched_folder): ) except FileNotFoundError as e: log.error("Unable to fetch metadata file %s ", e) + return False + log.info(f"Obtained metadata file {local_meta_file} from {fetched folder}") return local_meta_file def validate_fetched_files(self, fetched_folder): @@ -387,9 +399,10 @@ def validate_fetched_files(self, fetched_folder): [fi for fi in fetched_files_list if fi.endswith(tuple(allowed_extensions))] ) if samples_files_list == filtered_files_list: + log.info("Files in %s match with metadata file", fetched_folder) return True else: - log.info("Files in %s do not match metadata file", fetched_folder) + log.error("Files in %s do not match metadata file", fetched_folder) stderr.print( "Files in " + fetched_folder @@ -430,6 +443,7 @@ def create_json_with_downloaded_samples(self, sample_file_list, folder): def delete_local_folder(self, local_folder): """Delete download folder because files does not complain requisites""" + log.info("Deleting local folder %s", local_folder) shutil.rmtree(local_folder, ignore_errors=True) return True @@ -449,6 +463,7 @@ def download(self): log.error("There are no folders under root directory") sys.exit(1) if self.target_folders == "ALL": + log.info("Showing folders from remote sftp for selection") target_folders = relecov_tools.utils.prompt_checkbox( msg="Select the folders that will be downloaded", choices=sorted(root_directory_list), @@ -469,7 +484,8 @@ def download(self): if len(list_files) > 0: folders_to_download[folder] = list_files if len(folders_to_download) == 0: - log.info("Exiting download. There are no files on sftp to dowload") + log.info("Exiting download.") + log.error("There are no files on sftp to dowload") self.close_connection() sys.exit(0) From c4226056758982b23ca8a53d7e044a71fa89fc0e Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 21 Feb 2023 10:42:51 +0100 Subject: [PATCH 1100/1454] linting --- relecov_tools/sftp_handle.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 91f6b55a..93c9cc89 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -274,7 +274,9 @@ def create_tmp_files_with_metadata_info( pass with open(sample_data_path, "w", encoding="utf-8") as fh: fh.write(json.dumps(data, indent=4, sort_keys=True, ensure_ascii=False)) - log.info("Successfully created file with sample names list %s", sample_data_path) + log.info( + "Successfully created file with sample names list %s", sample_data_path + ) return True def create_main_folders(self, root_directory_list): @@ -374,7 +376,11 @@ def validate_metadata_file(self, fetched_folder): except FileNotFoundError as e: log.error("Unable to fetch metadata file %s ", e) return False - log.info(f"Obtained metadata file {local_meta_file} from {fetched folder}") + log.info( + "Obtained metadata file %s from %s", + local_meta_file, + fetched_folder, + ) return local_meta_file def validate_fetched_files(self, fetched_folder): From d63ad04507d3f06db5c6851047ffc0171faaaebf Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 1 Mar 2023 12:05:49 +0100 Subject: [PATCH 1101/1454] Included new addresses --- relecov_tools/conf/laboratory_address.json | 38 +++++++++++++++++++++- 1 file changed, 37 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 7410c1ec..7f2bdf56 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -8,9 +8,45 @@ "geo_loc_city": "Madrid", "geo_loc_country": "Spain" }, + { + "collecting_institution": "Hospital Puerta del Mar", + "collecting_institution_address": "Av. Ana de Viya, 21", + "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Cadiz", + "geo_loc_city": "Cadiz", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Costa del Sol", + "collecting_institution_address": "A-7, Km 187", + "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Malaga", + "geo_loc_city": "Marbella", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Hospital Virgen de la Victoria", + "collecting_institution_address": "Campus de Teatinos, S/N", + "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Malaga", + "geo_loc_city": "Malaga", + "geo_loc_country": "Spain" + }, + { + "collecting_institution": "Complejo Hospitalario Torrecardenas", + "collecting_institution_address": "C. Hermandad de Donantes de Sangre, s/n", + "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Almeria", + "geo_loc_city": "Almeria", + "geo_loc_country": "Spain" + }, { "collecting_institution": "Microbiología HUC San Cecilio", - "collecting_institution_address": "Av. del Conocimiento S/N,", + "collecting_institution_address": "Av. del Conocimiento S/N", "collecting_institution_email": "fegarcia@ugr.es", "geo_loc_state": "Andalucia", "geo_loc_region": "Granada", From 1cc442ecd4049b5422a7bf4d5ed409b6644090bf Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 1 Mar 2023 12:06:35 +0100 Subject: [PATCH 1102/1454] Fixed a lot of bugs --- relecov_tools/read_lab_metadata.py | 52 ++++++++++++++++++------------ 1 file changed, 32 insertions(+), 20 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 96ba32b2..59ea9d84 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -130,9 +130,9 @@ def adding_post_processing(self, m_data): return m_data def adding_ontology_to_enum(self, m_data): - """Read the schema to get the properties enum and for those fields - which has an enum property value then replace the value for the one it - is defined in the schema + """Read the schema to get the properties enum and, for those fields + which have an enum property value, replace the value for the one + that is defined in the schema """ enum_dict = {} for prop, values in self.relecov_sch_json["properties"].items(): @@ -151,21 +151,29 @@ def adding_ontology_to_enum(self, m_data): if m_data[idx][key] in e_values: m_data[idx][key] = e_values[m_data[idx][key]] else: + log.error("No ontology could be added") continue return m_data def process_from_json(self, m_data, json_fields): - """ """ + """Find the labels that are missing in the file to match the given schema.""" map_field = json_fields["map_field"] - json_data = json_fields["j_data"] if isinstance(json_data, dict): for idx in range(len(m_data)): - m_data[idx].update(json_data[m_data[idx][map_field]]) + try: + m_data[idx].update(json_data[m_data[idx][map_field]]) + except KeyError as error: + if str(error).lower() == "not provided": + log.error("Label was not provided, auto-completing columns") + else: + log.error(f"Unknown map_field value for json data: \ + {str(map_field)}. Set as not provided") + fields_to_add = {x:"Not Provided" for x in json_fields["adding_fields"]} + m_data[idx].update(fields_to_add) elif isinstance(json_data, list): - # to avoid searching for data for each row, for the first time searchs - # it is stored temporary. + # to avoid searching for data for each row, its stored temporarily. tmp_data = {} for idx in range(len(m_data)): if m_data[idx][map_field] not in tmp_data: @@ -188,7 +196,7 @@ def process_from_json(self, m_data, json_fields): def adding_fields(self, metadata): """Add information that requires to handle json files to include in - the fields""" + the fields""" for key, values in self.json_req_files.items(): stderr.print(f"[blue] Processing {key}") @@ -199,12 +207,12 @@ def adding_fields(self, metadata): metadata = self.process_from_json(metadata, values) stderr.print(f"[green] Processed {key}") - # Because sample data file is comming in an input parameter it cannot + # As sample data file is comming in an input parameter, it cannot # be inside the configuration json file. - # Include Sample informatin data from sample json file + # Include Sample information data from sample json file stderr.print("[blue] Processing sample data file") s_json = {} - s_json["map_field"] = "sequencing_sample_id" + s_json["map_field"] = "collecting_lab_sample_id" s_json["adding_field"] = "__all__" s_json["j_data"] = relecov_tools.utils.read_json_file(self.sample_list_file) metadata = self.process_from_json(metadata, s_json) @@ -233,7 +241,7 @@ def read_metadata_file(self): ws_metadata_lab = relecov_tools.utils.read_excel_file( self.metadata_file, "METADATA_LAB", heading_row_number, False ) - metadata_values = [] + valid_metadata_rows = [] errors = {} row_number = heading_row_number for row in ws_metadata_lab: @@ -251,10 +259,16 @@ def read_metadata_file(self): continue for key in row.keys(): # skip the first column of the Metadata lab file - if "Campo" in key: + if "campo" in key.lower(): continue if "date" in key.lower(): - if row[key] is not None: + if row[key] is None or str(row[key]).lower() == "not provided": + log.info("Date was not provided") + row[key] = "Not Provided" + elif isinstance(row[key], int) or isinstance(row[key], float): + log.info("Date given as an integer. Understood as a year") + row[key] = str(row[key]) + else: try: row[key] = row[key].strftime("%Y-%m-%d") except AttributeError: @@ -286,16 +300,14 @@ def read_metadata_file(self): stderr.print(f"[red] Error when mapping the label {str(e)}") continue - metadata_values.append(property_row) - return metadata_values, errors + valid_metadata_rows.append(property_row) + return valid_metadata_rows, errors def create_metadata_json(self): - # stderr.print("[blue] Reading configuration settings") - # conf_json_data = self.read_configuration_json_files() stderr.print("[blue] Reading Lab Metadata Excel File") valid_metadata_rows, errors = self.read_metadata_file() if len(errors) > 0: - stderr.print("[red] Stopped executing because the errors found") + stderr.print("[red] Stopped executing because errors were found") sys.exit(1) # Continue by adding extra information stderr.print("[blue] Including additional information") From 19545a609bb081ff69450c11deab05a34dc79dfc Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 1 Mar 2023 12:07:48 +0100 Subject: [PATCH 1103/1454] Included a bunch of logs and comment fixing --- relecov_tools/sftp_handle.py | 73 ++++++++++++++++-------------------- 1 file changed, 32 insertions(+), 41 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 93c9cc89..5674a95e 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -101,7 +101,7 @@ def __init__( self.pp = config["allowed_sample_extensions"] except KeyError as e: log.error("Invalid configuration file %s", e) - stderr.print("[red] Invalide configuration file {e} !") + stderr.print("[red] Invalid configuration file {e} !") sys.exit(1) if self.sftp_user is None: self.sftp_user = relecov_tools.utils.prompt_text(msg="Enter the userid") @@ -112,7 +112,7 @@ def __init__( self.client = None def open_connection(self): - """Establish sftp connection""" + """Establishing sftp connection""" log.info("Setting credentials for SFTP connection with remote server") self.client = paramiko.SSHClient() self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) @@ -125,7 +125,7 @@ def open_connection(self): look_for_keys=False, ) try: - log.info("Trying to stablish SFTP connection") + log.info("Trying to establish SFTP connection") self.client = self.client.open_sftp() return True except paramiko.SSHException as e: @@ -261,7 +261,7 @@ def create_tmp_files_with_metadata_info( return False data = copy.deepcopy(file_list) for s_name, values in file_list.items(): - for f_type, f_name in values.items(): + for _, f_name in values.items(): if not f_name.endswith(tuple(self.allowed_sample_ext)): stderr.print("[red] " + f_name + " has a not valid extension") if "_R1_" in f_name: @@ -311,11 +311,10 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): ws_metadata_lab = wb_file["METADATA_LAB"] sample_file_list = {} # find out the index for file names - for col in ws_metadata_lab[4]: - if "Sequence file R1 fastq" == col.value: - index_fastq_r1 = col.column - 1 - elif "Sequence file R2 fastq" == col.value: - index_fastq_r2 = col.column - 1 + config_json = ConfigJson() + meta_column_list = config_json.get_topic_data("lab_metadata","metadata_lab_heading") + index_fastq_r1 = meta_column_list.index("Sequence file R1 fastq") + index_fastq_r2 = meta_column_list.index("Sequence file R2 fastq") for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): if row[2] is not None: try: @@ -398,7 +397,7 @@ def validate_fetched_files(self, fetched_folder): temp_folder, local_meta_file ) samples_files_list = sorted( - sum([list(fi.values()) for sample, fi in samples_files_list.items()], []) + sum([list(fi.values()) for _, fi in samples_files_list.items()], []) ) fetched_files_list = self.list_fetched_files(fetched_folder) filtered_files_list = sorted( @@ -406,6 +405,7 @@ def validate_fetched_files(self, fetched_folder): ) if samples_files_list == filtered_files_list: log.info("Files in %s match with metadata file", fetched_folder) + stderr.print("Successfully validated files based on metadata") return True else: log.error("Files in %s do not match metadata file", fetched_folder) @@ -414,27 +414,25 @@ def validate_fetched_files(self, fetched_folder): + fetched_folder + " do not match the ones described in metadata" ) + set_list = set(filtered_files_list) + mismatch_files = [fi for fi in samples_files_list if fi not in set_list] + if len(mismatch_files) < 10: + stderr.print(f"Files that mismatch: {str(mismatch_files)}") + else: + stderr.print( + "Showing some of the mismatches, check logs to see all of them: %s", + str(mismatch_files[0:9]), + ) + log.error(f"List of files that mismatch: {str(mismatch_files)}") self.delete_local_folder(temp_folder) return False - def validate_download_files(self, sample_file_list, local_folder): - """Check if download sample files are the ones defined on metadata file""" - if not sample_file_list: - return False - for sample, files in sample_file_list.items(): - for file in files.values(): - if not os.path.isfile(os.path.join(local_folder, file)): - log.error("File %s does not exist", file) - stderr.print("[red] File " + file + " does not exist") - return False - return True - - def delete_remote_files(self, folder, files): + def delete_remote_files(self, fetched_folder, files): """Delete files from remote server""" self.open_connection() for file in files: try: - self.client.remove(file) + self.client.remove(os.path.join(fetched_folder, os.path.basename(file))) log.info("%s Deleted from remote server", file) except FileNotFoundError: continue @@ -469,7 +467,7 @@ def download(self): log.error("There are no folders under root directory") sys.exit(1) if self.target_folders == "ALL": - log.info("Showing folders from remote sftp for selection") + log.info("Showing folders from remote SFTP for user selection") target_folders = relecov_tools.utils.prompt_checkbox( msg="Select the folders that will be downloaded", choices=sorted(root_directory_list), @@ -525,21 +523,14 @@ def download(self): sample_file_list = self.get_sample_fastq_file_names( result_data["local_folder"], meta_file ) - if self.validate_download_files( - sample_file_list, result_data["local_folder"] - ): - self.create_tmp_files_with_metadata_info( - result_data["local_folder"], sample_file_list, md5_files, meta_file - ) - # Collect data to send the request to relecov_platform - json_sample_data = self.create_json_with_downloaded_samples( - sample_file_list, folder - ) - for record in json_sample_data: - pass - else: - log.info("Deleting local folder %s", result_data["local_folder"]) - self.delete_local_folder(result_data["local_folder"]) - + self.create_tmp_files_with_metadata_info( + result_data["local_folder"], sample_file_list, md5_files, meta_file + ) + # Collect data to send the request to relecov_platform + json_sample_data = self.create_json_with_downloaded_samples( + sample_file_list, folder + ) + for record in json_sample_data: + pass self.close_connection() return From 92ae55d1895f4bead45937565ca6cdc0e6aa4067 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 1 Mar 2023 12:09:11 +0100 Subject: [PATCH 1104/1454] Fixed read_excel_file method --- relecov_tools/utils.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index df6d448f..c6d112f7 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -57,9 +57,6 @@ def read_excel_file(f_name, sheet_name, heading_row, empty_value=True): l_row = list(row) data_row = {} # Ignore the empty rows - # guessing that row 1 and 2 with no data are empty rows - if l_row[0] is None and l_row[1] is None: - continue for idx in range(0, len(heading)): if l_row[idx] is None: if empty_value: From fd6443ec05370c0eb5b60e50343f6dcad941abf5 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 1 Mar 2023 12:30:38 +0100 Subject: [PATCH 1105/1454] linting --- relecov_tools/read_lab_metadata.py | 14 +++++++++----- relecov_tools/sftp_handle.py | 4 +++- 2 files changed, 12 insertions(+), 6 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 59ea9d84..bee04670 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -130,8 +130,8 @@ def adding_post_processing(self, m_data): return m_data def adding_ontology_to_enum(self, m_data): - """Read the schema to get the properties enum and, for those fields - which have an enum property value, replace the value for the one + """Read the schema to get the properties enum and, for those fields + which have an enum property value, replace the value for the one that is defined in the schema """ enum_dict = {} @@ -168,9 +168,13 @@ def process_from_json(self, m_data, json_fields): if str(error).lower() == "not provided": log.error("Label was not provided, auto-completing columns") else: - log.error(f"Unknown map_field value for json data: \ - {str(map_field)}. Set as not provided") - fields_to_add = {x:"Not Provided" for x in json_fields["adding_fields"]} + log.error( + f"Unknown map_field value for json data: \ + {str(map_field)}. Set as not provided" + ) + fields_to_add = { + x: "Not Provided" for x in json_fields["adding_fields"] + } m_data[idx].update(fields_to_add) elif isinstance(json_data, list): # to avoid searching for data for each row, its stored temporarily. diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 5674a95e..dbd57de4 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -312,7 +312,9 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): sample_file_list = {} # find out the index for file names config_json = ConfigJson() - meta_column_list = config_json.get_topic_data("lab_metadata","metadata_lab_heading") + meta_column_list = config_json.get_topic_data( + "lab_metadata", "metadata_lab_heading" + ) index_fastq_r1 = meta_column_list.index("Sequence file R1 fastq") index_fastq_r2 = meta_column_list.index("Sequence file R2 fastq") for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): From 6060d4917bd3f38cec66e9b731b34c4a0d55c470 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 1 Mar 2023 12:43:44 +0100 Subject: [PATCH 1106/1454] Small fix --- relecov_tools/read_lab_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index bee04670..71055493 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -271,7 +271,7 @@ def read_metadata_file(self): row[key] = "Not Provided" elif isinstance(row[key], int) or isinstance(row[key], float): log.info("Date given as an integer. Understood as a year") - row[key] = str(row[key]) + row[key] = str(int(row[key])) else: try: row[key] = row[key].strftime("%Y-%m-%d") From d1a005b2909c9a77f9c5023a31b1dab7af375c77 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 2 Mar 2023 17:24:11 +0100 Subject: [PATCH 1107/1454] Included 'Not Provided' as a possible field --- .../conf/anatomical_material_collection_method.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/relecov_tools/conf/anatomical_material_collection_method.json b/relecov_tools/conf/anatomical_material_collection_method.json index 818a2963..bdd273ad 100644 --- a/relecov_tools/conf/anatomical_material_collection_method.json +++ b/relecov_tools/conf/anatomical_material_collection_method.json @@ -1006,5 +1006,11 @@ "collection_method": "Not Applicable", "body_product": "Not Applicable", "anatomical_material": "Placenta" + }, + "Not Provided": { + "anatomical_part": "Not Provided", + "collection_method": "Not Provided", + "body_product": "Not Provided", + "anatomical_material": "Not Provided" } } From d5f4135a4ff469668af51adc933a7be0aaee2598 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 2 Mar 2023 17:24:41 +0100 Subject: [PATCH 1108/1454] Included several locations --- relecov_tools/conf/geo_loc_cities.json | 34 +++++++++++++++++++------- 1 file changed, 25 insertions(+), 9 deletions(-) diff --git a/relecov_tools/conf/geo_loc_cities.json b/relecov_tools/conf/geo_loc_cities.json index e4a10776..7678c393 100644 --- a/relecov_tools/conf/geo_loc_cities.json +++ b/relecov_tools/conf/geo_loc_cities.json @@ -47,7 +47,7 @@ "geo_loc_latitude": "38.3453", "geo_loc_longitude": "-0.4831" }, - "Córdoba": { + "Cordoba": { "geo_loc_latitude": "37.8845", "geo_loc_longitude": "-4.7796" }, @@ -59,7 +59,7 @@ "geo_loc_latitude": "42.2314", "geo_loc_longitude": "-8.7124" }, - "Gijón": { + "Gijon": { "geo_loc_latitude": "43.5333", "geo_loc_longitude": "-5.7000" }, @@ -103,7 +103,7 @@ "geo_loc_latitude": "38.9956", "geo_loc_longitude": "-1.8558" }, - "Castellón de la Plana": { + "Castellon de la Plana": { "geo_loc_latitude": "39.9831", "geo_loc_longitude": "-0.0331" }, @@ -143,7 +143,7 @@ "geo_loc_latitude": "36.5350", "geo_loc_longitude": "-6.2975" }, - "Jaén": { + "Jaen": { "geo_loc_latitude": "37.7667", "geo_loc_longitude": "-3.7711" }, @@ -155,7 +155,7 @@ "geo_loc_latitude": "43.0167", "geo_loc_longitude": "-7.5500" }, - "Cáceres": { + "Caceres": { "geo_loc_latitude": "39.4833", "geo_loc_longitude": "-6.3667" }, @@ -223,7 +223,7 @@ "geo_loc_latitude": "42.4333", "geo_loc_longitude": "-8.6333" }, - "Alcázar de San Juan": { + "Alcazar de San Juan": { "geo_loc_latitude": "39.4056", "geo_loc_longitude": "-3.2056" }, @@ -251,7 +251,7 @@ "geo_loc_latitude": "41.4217", "geo_loc_longitude": "2.1897" }, - "Sant Cugat del Vallès": { + "Sant Cugat del Valles": { "geo_loc_latitude": "41.4667", "geo_loc_longitude": "2.0833" }, @@ -259,7 +259,7 @@ "geo_loc_latitude": "40.3223", "geo_loc_longitude": "-3.865" }, - "Leganés": { + "Leganes": { "geo_loc_latitude": "40.3281", "geo_loc_longitude": "-3.7644" }, @@ -283,7 +283,7 @@ "geo_loc_latitude": "38.2392", "geo_loc_longitude": "-1.4189" }, - "Mérida": { + "Merida": { "geo_loc_latitude": "38.9000", "geo_loc_longitude": "-6.3333" }, @@ -295,8 +295,24 @@ "geo_loc_latitude": "38.2669", "geo_loc_longitude": "-0.6983" }, + "Cadiz": { + "geo_loc_latitude": "36.52672", + "geo_loc_longitude": "-6.2891" + }, "Gasteiz": { "geo_loc_latitude": "42.85", "geo_loc_longitude": "-2.6667" + }, + "Marbella": { + "geo_loc_latitude": "36.51543", + "geo_loc_longitude": "-4.88583" + }, + "Malaga": { + "geo_loc_latitude": "36.72016", + "geo_loc_longitude": "-4.42034" + }, + "Almeria": { + "geo_loc_latitude": "36.72016", + "geo_loc_longitude": "-4.42034" } } From b85370093ed868b003a7f9cc99d32c3eab8d7410 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 2 Mar 2023 17:26:18 +0100 Subject: [PATCH 1109/1454] changed format to dictionary --- relecov_tools/conf/submitter_address.json | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/relecov_tools/conf/submitter_address.json b/relecov_tools/conf/submitter_address.json index ddc86a8c..2d469de9 100644 --- a/relecov_tools/conf/submitter_address.json +++ b/relecov_tools/conf/submitter_address.json @@ -1,7 +1,6 @@ -[ - { - "submitting_institution": "Instituto de Salud Carlos III", +{ + "Instituto de Salud Carlos III": { "submitting_institution_address": "Crta. Pozuelo Majadahonda S/N,", "submitting_institution_email": "info@isciii.es" } -] +} \ No newline at end of file From 23ac89b734b00585e164bc185f86a80c197920bf Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 2 Mar 2023 17:27:48 +0100 Subject: [PATCH 1110/1454] Changed format to dictionary of dictionaries instead of list of dictionaries. Also included 3 new fields related to submitter info --- relecov_tools/conf/laboratory_address.json | 655 +++++++++++++-------- 1 file changed, 409 insertions(+), 246 deletions(-) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 7f2bdf56..0f2ea6d3 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -1,686 +1,849 @@ -[ - { - "collecting_institution": "Instituto de Salud Carlos III", +{ + "Instituto de Salud Carlos III": { "collecting_institution_address": "Crta. Pozuelo Majadahonda S/N,", "collecting_institution_email": "info@isciii.es", "geo_loc_state": "Madrid", "geo_loc_region": "Madrid", "geo_loc_city": "Madrid", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Instituto de Salud Carlos III", + "submitting_institution_address": "Crta. Pozuelo Majadahonda S/N,", + "submitting_institution_email": "info@isciii.es" }, - { - "collecting_institution": "Hospital Puerta del Mar", + "Hospital Puerta del Mar": { "collecting_institution_address": "Av. Ana de Viya, 21", "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", "geo_loc_state": "Andalucia", "geo_loc_region": "Cadiz", "geo_loc_city": "Cadiz", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Puerta del Mar", + "submitting_institution_address": "Av. Ana de Viya, 21", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" }, - { - "collecting_institution": "Hospital Costa del Sol", + "Hospital Costa del Sol": { "collecting_institution_address": "A-7, Km 187", "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", "geo_loc_state": "Andalucia", "geo_loc_region": "Malaga", "geo_loc_city": "Marbella", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Costa del Sol", + "submitting_institution_address": "A-7, Km 187", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" }, - { - "collecting_institution": "Hospital Virgen de la Victoria", + "Hospital Virgen de la Victoria": { "collecting_institution_address": "Campus de Teatinos, S/N", "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", "geo_loc_state": "Andalucia", "geo_loc_region": "Malaga", "geo_loc_city": "Malaga", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Virgen de la Victoria", + "submitting_institution_address": "Campus de Teatinos, S/N", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" }, - { - "collecting_institution": "Complejo Hospitalario Torrecardenas", + "Complejo Hospitalario Torrecardenas": { "collecting_institution_address": "C. Hermandad de Donantes de Sangre, s/n", "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", "geo_loc_state": "Andalucia", "geo_loc_region": "Almeria", "geo_loc_city": "Almeria", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Complejo Hospitalario Torrecardenas", + "submitting_institution_address": "C. Hermandad de Donantes de Sangre, s/n", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" }, - { - "collecting_institution": "Microbiología HUC San Cecilio", + "Hospital Universitario San Cecilio": { "collecting_institution_address": "Av. del Conocimiento S/N", "collecting_institution_email": "fegarcia@ugr.es", "geo_loc_state": "Andalucia", "geo_loc_region": "Granada", "geo_loc_city": "Granada", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario San Cecilio", + "submitting_institution_address": "Av. del Conocimiento S/N", + "submitting_institution_email": "fegarcia@ugr.es" }, - { - "collecting_institution": "Microbiología. Hospital Universitario Virgen del Rocio", + "Microbiología HUC San Cecilio": { + "collecting_institution_address": "Av. del Conocimiento S/N", + "collecting_institution_email": "fegarcia@ugr.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Granada", + "geo_loc_city": "Granada", + "geo_loc_country": "Spain", + "submitting_institution": "Microbiología HUC San Cecilio", + "submitting_institution_address": "Av. del Conocimiento S/N", + "submitting_institution_email": "fegarcia@ugr.es" + }, + "Microbiología. Hospital Universitario Virgen del Rocio": { "collecting_institution_address": "Avenida Manuel Siurot s/n", "collecting_institution_email": "josea.lepe.sspa@juntadeandalucia.es", "geo_loc_state": "Andalucia", "geo_loc_region": "Sevilla", "geo_loc_city": "Sevilla", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Microbiología. Hospital Universitario Virgen del Rocio", + "submitting_institution_address": "Avenida Manuel Siurot s/n", + "submitting_institution_email": "josea.lepe.sspa@juntadeandalucia.es" }, - { - "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", + "Hospital Universitario Virgen del Rocio": { + "collecting_institution_address": "Avenida Manuel Siurot s/n", + "collecting_institution_email": "josea.lepe.sspa@juntadeandalucia.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Sevilla", + "geo_loc_city": "Sevilla", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Virgen del Rocio", + "submitting_institution_address": "Avenida Manuel Siurot s/n", + "submitting_institution_email": "josea.lepe.sspa@juntadeandalucia.es" + }, + "Hospital Clínico Universitario Lozano Blesa": { "collecting_institution_address": "S. Juan Bosco, 15", "collecting_institution_email": "rbenito@salud.aragon.es", - "geo_loc_state": "Aragón", + "geo_loc_state": "Aragon", "geo_loc_region": "Zaragoza", "geo_loc_city": "Zaragoza", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Clínico Universitario Lozano Blesa", + "submitting_institution_address": "S. Juan Bosco, 15", + "submitting_institution_email": "rbenito@salud.aragon.es" }, - { - "collecting_institution": "Hospital Universitario Miguel Servet", + "Hospital Universitario Miguel Servet": { "collecting_institution_address": "P.º Isabel la Católica, 1-3", "collecting_institution_email": "rbenito@salud.aragon.es", - "geo_loc_state": "Aragón", + "geo_loc_state": "Aragon", "geo_loc_region": "Zaragoza", "geo_loc_city": "Zaragoza", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Miguel Servet", + "submitting_institution_address": "P.º Isabel la Católica, 1-3", + "submitting_institution_email": "rbenito@salud.aragon.es" }, - { - "collecting_institution": "Centro de Investigación Biomédica de Aragón", + "Centro de Investigación Biomédica de Aragón": { "collecting_institution_address": "Avenida San Juan Bosco 13", "collecting_institution_email": "mhpstrunk.iacs@aragon.es", - "geo_loc_state": "Aragón", + "geo_loc_state": "Aragon", "geo_loc_region": "Zaragoza", "geo_loc_city": "Zaragoza", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Centro de Investigación Biomédica de Aragón", + "submitting_institution_address": "Avenida San Juan Bosco 13", + "submitting_institution_email": "mhpstrunk.iacs@aragon.es" }, - { - "collecting_institution": "Hospital Universitario Central de Asturias", + "Hospital Universitario Central de Asturias": { "collecting_institution_address": " Av. Roma, s/n,", "collecting_institution_email": "santiago.melon@sespa.es", "geo_loc_state": "Asturias", "geo_loc_region": "Asturias", "geo_loc_city": "Asturias", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Central de Asturias", + "submitting_institution_address": " Av. Roma, s/n,", + "submitting_institution_email": "santiago.melon@sespa.es" }, - { - "collecting_institution": "Servicio de Microbiologia HU Son Espases", + "Servicio de Microbiologia HU Son Espases": { "collecting_institution_address": " Ctra. Valldemossa 79", "collecting_institution_email": "antonio.oliver@ssib.es", "geo_loc_state": "Islas Baleares", "geo_loc_region": "Palma de Mallorca", "geo_loc_city": "Palma de Mallorca", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Servicio de Microbiologia HU Son Espases", + "submitting_institution_address": " Ctra. Valldemossa 79", + "submitting_institution_email": "antonio.oliver@ssib.es" }, - { - "collecting_institution": "Hospital Universitario Ntra. Sra de Candelaria", + "Hospital Universitario Ntra. Sra de Candelaria": { "collecting_institution_address": "Carretera del Rosario 145", "collecting_institution_email": "jalcflo@gobiernodecanarias.org", "geo_loc_state": "Islas Canarias", "geo_loc_region": "Santa Cruz de Tenerife", "geo_loc_city": "Santa Cruz de Tenerife", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Ntra. Sra de Candelaria", + "submitting_institution_address": "Carretera del Rosario 145", + "submitting_institution_email": "jalcflo@gobiernodecanarias.org" }, - { - "collecting_institution": "Instituto Tecnológico y de Energías Renovables", + "Instituto Tecnológico y de Energías Renovables": { "collecting_institution_address": "Polígono Industrial de Granadilla, s/n", "collecting_institution_email": "jlorenzo@iter.es", "geo_loc_state": "Islas Canarias", "geo_loc_region": "Santa Cruz de Tenerife", "geo_loc_city": "Santa Cruz de Tenerife", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Instituto Tecnológico y de Energías Renovables", + "submitting_institution_address": "Polígono Industrial de Granadilla, s/n", + "submitting_institution_email": "jlorenzo@iter.es" }, - { - "collecting_institution": "Hospital Universitario de Canarias", + "Hospital Universitario de Canarias": { "collecting_institution_address": "Carretera Ofra S/N, La Laguna", "collecting_institution_email": "", "geo_loc_state": "Islas Canarias", "geo_loc_region": "Santa Cruz de Tenerife", "geo_loc_city": "Santa Cruz de Tenerife", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario de Canarias", + "submitting_institution_address": "Carretera Ofra S/N, La Laguna", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Universitario de Gran Canaria", + "Hospital Universitario de Gran Canaria": { "collecting_institution_address": "C. Pl. Barranco de la Ballena s/n", "collecting_institution_email": "", "geo_loc_state": "Islas Canarias", "geo_loc_region": "Las Palmas", "geo_loc_city": "Las Palmas", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario de Gran Canaria", + "submitting_institution_address": "C. Pl. Barranco de la Ballena s/n", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Insular de Lanzarote", + "Hospital Insular de Lanzarote": { "collecting_institution_address": "C. Juan de Quesada, s/n, Arrecife", "collecting_institution_email": "", "geo_loc_state": "Islas Canarias", "geo_loc_region": "Las Palmas", "geo_loc_city": "Las Palmas", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Insular de Lanzarote", + "submitting_institution_address": "C. Juan de Quesada, s/n, Arrecife", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Universitario Marqués de Valdecilla", + "Hospital Universitario Marqués de Valdecilla": { "collecting_institution_address": "Av. Valdecilla s/n", "collecting_institution_email": "", "geo_loc_state": "Cantabria", "geo_loc_region": "Cantabria", "geo_loc_city": "Santander", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Marqués de Valdecilla", + "submitting_institution_address": "Av. Valdecilla s/n", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Sierrallana", + "Hospital Sierrallana": { "collecting_institution_address": "Bo. Ganzo, s/n, Torrelavega", "collecting_institution_email": "", "geo_loc_state": "Cantabria", "geo_loc_region": "Cantabria", "geo_loc_city": "Santander", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Sierrallana", + "submitting_institution_address": "Bo. Ganzo, s/n, Torrelavega", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital General Universitario de Ciudad Real", - "collecting_institution_address": "Calle Obispo Rafael Torija s/n", + "Hospital General Universitario de Ciudad Real": { + "collecting_institution_address": "C. Obispo Rafael Torija, s/n", "collecting_institution_email": "", "geo_loc_state": "Castilla-La Mancha", "geo_loc_region": "Ciudad Real", "geo_loc_city": "Ciudad Real", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital General Universitario de Ciudad Real", + "submitting_institution_address": "C. Obispo Rafael Torija, s/n", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital General La Mancha Centro", + "Hospital General La Mancha Centro": { "collecting_institution_address": "Av. Constitución, 3, Alcázar de San Juan", "collecting_institution_email": "", "geo_loc_state": "Castilla-La Mancha", "geo_loc_region": "Ciudad Real", "geo_loc_city": "Alcázar de San Juan", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital General La Mancha Centro", + "submitting_institution_address": "Av. Constitución, 3, Alcázar de San Juan", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Virgen de Altagracia", + "Hospital Virgen de Altagracia": { "collecting_institution_address": "Avda. D. Emiliano García Roldán, s/n, Manzanares,", "collecting_institution_email": "", "geo_loc_state": "Castilla-La Mancha", "geo_loc_region": "Ciudad Real", "geo_loc_city": "Manzanares", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Virgen de Altagracia", + "submitting_institution_address": "Avda. D. Emiliano García Roldán, s/n, Manzanares,", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital General de Valdepeñas", + "Hospital General de Valdepeñas": { "collecting_institution_address": "Av. de los Estudiantes, s/n, Valdepeñas", "collecting_institution_email": "", "geo_loc_state": "Castilla-La Mancha", "geo_loc_region": "Ciudad Real", "geo_loc_city": "Valdepeñas", - "geo_loc_country": "Spain" - }, - { - "collecting_institution": "Hospital General Universitario de Ciudad Real", - "collecting_institution_address": "C. Obispo Rafael Torija, s/n", - "collecting_institution_email": "", - "geo_loc_state": "Castilla-La Mancha", - "geo_loc_region": "Ciudad Real", - "geo_loc_city": "Ciudad Real", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital General de Valdepeñas", + "submitting_institution_address": "Av. de los Estudiantes, s/n, Valdepeñas", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Público Santa Bárbara", + "Hospital Público Santa Bárbara": { "collecting_institution_address": "C. Malagón s/n", "collecting_institution_email": "", "geo_loc_state": "Castilla-La Mancha", "geo_loc_region": "Ciudad Real", "geo_loc_city": "Puertollano", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Público Santa Bárbara", + "submitting_institution_address": "C. Malagón s/n", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Virgen de la Luz", + "Hospital Virgen de la Luz": { "collecting_institution_address": "Hermandad de Donantes de Sangre, 1", "collecting_institution_email": "", "geo_loc_state": "Castilla-La Mancha", "geo_loc_region": "Cuenca", "geo_loc_city": "Cuenca", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Virgen de la Luz", + "submitting_institution_address": "Hermandad de Donantes de Sangre, 1", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Universitario de Guadalajara", + "Hospital Universitario de Guadalajara": { "collecting_institution_address": "C. Donante de Sangre, S/N", "collecting_institution_email": "", "geo_loc_state": "Castilla-La Mancha", "geo_loc_region": "Guadalajara", "geo_loc_city": "Guadalajara", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario de Guadalajara", + "submitting_institution_address": "C. Donante de Sangre, S/N", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Virgen de la Salud", + "Hospital Virgen de la Salud": { "collecting_institution_address": "Calle Barber 30", "collecting_institution_email": "", "geo_loc_state": "Castilla-La Mancha", "geo_loc_region": "Toledo", "geo_loc_city": "Toledo", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Virgen de la Salud", + "submitting_institution_address": "Calle Barber 30", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital General Nuestra Sra. del Prado", + "Hospital General Nuestra Sra. del Prado": { "collecting_institution_address": "CTRA. MADRID, Av. Extremadura, KM 114", "collecting_institution_email": "", "geo_loc_state": "Castilla-La Mancha", "geo_loc_region": "Toledo", "geo_loc_city": "Talavera de la Reina", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital General Nuestra Sra. del Prado", + "submitting_institution_address": "CTRA. MADRID, Av. Extremadura, KM 114", + "submitting_institution_email": "" }, - { - "collecting_institution": "Consejería de Sanidad", + "Consejería de Sanidad": { "collecting_institution_address": "Avda. de Francia, 4.", "collecting_institution_email": "", "geo_loc_state": "Castilla-La Mancha", "geo_loc_region": "Toledo", "geo_loc_city": "Toledo", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Consejería de Sanidad", + "submitting_institution_address": "Avda. de Francia, 4.", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital General Universitario de Albacete", + "Hospital General Universitario de Albacete": { "collecting_institution_address": "Calle Hermanos Falcó 37", "collecting_institution_email": "", "geo_loc_state": "Castilla-La Mancha", "geo_loc_region": "Albacete", "geo_loc_city": "Albacete", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital General Universitario de Albacete", + "submitting_institution_address": "Calle Hermanos Falcó 37", + "submitting_institution_email": "" }, - { - "collecting_institution": "Consorcio LUCIA (SACYL,ITACYL UBU,UVa)", + "Consorcio LUCIA (SACYL,ITACYL UBU,UVa)": { "collecting_institution_address": "Paseo de Belen 19", "collecting_institution_email": "", "geo_loc_state": "Castilla y León", "geo_loc_region": "Valladolid", "geo_loc_city": "Valladolid", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Consorcio LUCIA (SACYL,ITACYL UBU,UVa)", + "submitting_institution_address": "Paseo de Belen 19", + "submitting_institution_email": "" }, - { - "collecting_institution": "Complejo Asistencial Universitario de Salamanca", + "Complejo Asistencial Universitario de Salamanca": { "collecting_institution_address": "P.º de San Vicente, 58", "collecting_institution_email": "", "geo_loc_state": "Castilla y León", "geo_loc_region": "Salamanca", "geo_loc_city": "Salamanca", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Complejo Asistencial Universitario de Salamanca", + "submitting_institution_address": "P.º de San Vicente, 58", + "submitting_institution_email": "" }, - { - "collecting_institution": "Gerencia de Salud de Area de Soria", + "Gerencia de Salud de Area de Soria": { "collecting_institution_address": "P.º el Espolón", "collecting_institution_email": "", "geo_loc_state": "Castilla y León", "geo_loc_region": "Soria", "geo_loc_city": "Soria", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Gerencia de Salud de Area de Soria", + "submitting_institution_address": "P.º el Espolón", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital General Río Carrión", + "Hospital General Río Carrión": { "collecting_institution_address": "Av. Donantes de Sangre, s/n", "collecting_institution_email": "", "geo_loc_state": "Castilla y León", "geo_loc_region": "Palencia", "geo_loc_city": "Palencia", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital General Río Carrión", + "submitting_institution_address": "Av. Donantes de Sangre, s/n", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Nuestra Señora de Sonsoles", + "Hospital Nuestra Señora de Sonsoles": { "collecting_institution_address": " Av. Juan Carlos I, s/n", "collecting_institution_email": "", "geo_loc_state": "Castilla y León", "geo_loc_region": "Avila", "geo_loc_city": "Avila", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Nuestra Señora de Sonsoles", + "submitting_institution_address": " Av. Juan Carlos I, s/n", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Universitario de Burgos", + "Hospital Universitario de Burgos": { "collecting_institution_address": "Av. Islas Baleares, 3", "collecting_institution_email": "", "geo_loc_state": "Castilla y León", "geo_loc_region": "Burgos", "geo_loc_city": "Burgos", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario de Burgos", + "submitting_institution_address": "Av. Islas Baleares, 3", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Universitari Vall d’Hebron", + "Hospital Universitari Vall d’Hebron": { "collecting_institution_address": " Passeig de la Vall d’Hebron, 119-129", "collecting_institution_email": "", "geo_loc_state": "Cataluña", "geo_loc_region": "Barcelona", "geo_loc_city": "Barcelona", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitari Vall d’Hebron", + "submitting_institution_address": " Passeig de la Vall d’Hebron, 119-129", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Universitari Germans Trias i Pujol", + "Hospital Universitari Germans Trias i Pujol": { "collecting_institution_address": " Crta del Canyet s/n", "collecting_institution_email": "", "geo_loc_state": "Cataluña", "geo_loc_region": "Barcelona", "geo_loc_city": "Badalona", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitari Germans Trias i Pujol", + "submitting_institution_address": " Crta del Canyet s/n", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Clínic de Barcelona", + "Hospital Clínic de Barcelona": { "collecting_institution_address": "C/Villarroel 170", "collecting_institution_email": "", "geo_loc_state": "Cataluña", "geo_loc_region": "Barcelona", "geo_loc_city": "Barcelona", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Clínic de Barcelona", + "submitting_institution_address": "C/Villarroel 170", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Universitari Bellvitge", + "Hospital Universitari Bellvitge": { "collecting_institution_address": "Carrer Feixa Llarga s/n ", "collecting_institution_email": "", "geo_loc_state": "Cataluña", "geo_loc_region": "Barcelona", "geo_loc_city": "L'Hospitalet de Llobregat", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitari Bellvitge", + "submitting_institution_address": "Carrer Feixa Llarga s/n ", + "submitting_institution_email": "" }, - { - "collecting_institution": "Lab Clínic ICS Camp de Tarragona-Terres de l'Ebre. Hospital Joan XXIII", + "Lab Clínic ICS Camp de Tarragona-Terres de l'Ebre. Hospital Joan XXIII": { "collecting_institution_address": "c/ Dr. Mallafrè Guasch, 4,", "collecting_institution_email": "", "geo_loc_state": "Cataluña", "geo_loc_region": "Tarragona", "geo_loc_city": "Tarragona", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Lab Clínic ICS Camp de Tarragona-Terres de l'Ebre. Hospital Joan XXIII", + "submitting_institution_address": "c/ Dr. Mallafrè Guasch, 4,", + "submitting_institution_email": "" }, - { - "collecting_institution": "LABORATORI DE REFERENCIA DE CATALUNYA", + "LABORATORI DE REFERENCIA DE CATALUNYA": { "collecting_institution_address": "Carrer de la Selva, 10", "collecting_institution_email": "", "geo_loc_state": "Cataluña", "geo_loc_region": "Barcelona", "geo_loc_city": "Barcelona", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "LABORATORI DE REFERENCIA DE CATALUNYA", + "submitting_institution_address": "Carrer de la Selva, 10", + "submitting_institution_email": "" }, - { - "collecting_institution": "Banc de Sang i Teixits Catalunya", + "Banc de Sang i Teixits Catalunya": { "collecting_institution_address": "Passeig del Taulat, 116", "collecting_institution_email": "", "geo_loc_state": "Cataluña", "geo_loc_region": "Barcelona", "geo_loc_city": "Barcelona", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Banc de Sang i Teixits Catalunya", + "submitting_institution_address": "Passeig del Taulat, 116", + "submitting_institution_email": "" }, - { - "collecting_institution": "Laboratorio Echevarne Sant Cugat del Vallès", + "Laboratorio Echevarne Sant Cugat del Vallès": { "collecting_institution_address": "Carrer de Martorell,20 Sant Cugat del Vallès", "collecting_institution_email": "", "geo_loc_state": "Cataluña", "geo_loc_region": "Barcelona", - "geo_loc_city": "Sant Cugat del Vallès", - "geo_loc_country": "Spain" + "geo_loc_city": "Sant Cugat del Valles", + "geo_loc_country": "Spain", + "submitting_institution": "Laboratorio Echevarne Sant Cugat del Vallès", + "submitting_institution_address": "Carrer de Martorell,20 Sant Cugat del Vallès", + "submitting_institution_email": "" }, - { - "collecting_institution": "Unitat de Genòmica i Medicina Personalitzada - Hospital Dr. Josep Trueta", + "Unitat de Genòmica i Medicina Personalitzada - Hospital Dr. Josep Trueta": { "collecting_institution_address": "Avinguda de França, S/N,", "collecting_institution_email": "", "geo_loc_state": "Cataluña", "geo_loc_region": "Girona", "geo_loc_city": "Girona", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Unitat de Genòmica i Medicina Personalitzada - Hospital Dr. Josep Trueta", + "submitting_institution_address": "Avinguda de França, S/N,", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Universitario San Jorge", + "Hospital Universitario San Jorge": { "collecting_institution_address": "Av. Martínez de Velasco, 36", "collecting_institution_email": "", - "geo_loc_state": "Aragón", + "geo_loc_state": "Aragon", "geo_loc_region": "Huesca", "geo_loc_city": "Huesca", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario San Jorge", + "submitting_institution_address": "Av. Martínez de Velasco, 36", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Universitario de Ceuta", + "Hospital Universitario de Ceuta": { "collecting_institution_address": "Colmenar s/n", "collecting_institution_email": "", "geo_loc_state": "Ceuta", "geo_loc_region": "Ceuta", "geo_loc_city": "Ceuta", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario de Ceuta", + "submitting_institution_address": "Colmenar s/n", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Comarcal de Melilla", + "Hospital Comarcal de Melilla": { "collecting_institution_address": "Remonta, 2", "collecting_institution_email": "", "geo_loc_state": "Melilla", "geo_loc_region": "Melilla", "geo_loc_city": "Melilla", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Comarcal de Melilla", + "submitting_institution_address": "Remonta, 2", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital de Mostoles", + "Hospital de Mostoles": { "collecting_institution_address": "C. Dr. Luis Montes, S/N", "collecting_institution_email": "", "geo_loc_state": "Madrid", "geo_loc_region": "Madrid", "geo_loc_city": "Mostoles", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital de Mostoles", + "submitting_institution_address": "C. Dr. Luis Montes, S/N", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Clínico San Carlos", + "Hospital Clínico San Carlos": { "collecting_institution_address": "Calle del Prof Martín Lagos", "collecting_institution_email": "", "geo_loc_state": "Madrid", "geo_loc_region": "Madrid", "geo_loc_city": "Madrid", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Clínico San Carlos", + "submitting_institution_address": "Calle del Prof Martín Lagos", + "submitting_institution_email": "" }, - { - "collecting_institution": "Centro Militar de Veterinaria de la Defensa", + "Centro Militar de Veterinaria de la Defensa": { "collecting_institution_address": "C. Darío Gazapo 3", "collecting_institution_email": "", "geo_loc_state": "Madrid", "geo_loc_region": "Madrid", "geo_loc_city": "Madrid", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Centro Militar de Veterinaria de la Defensa", + "submitting_institution_address": "C. Darío Gazapo 3", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Universitario Severo Ochoa", + "Hospital Universitario Severo Ochoa": { "collecting_institution_address": "Av. de Orellana, s/n, Leganés", "collecting_institution_email": "", "geo_loc_state": "Madrid", "geo_loc_region": "Madrid", - "geo_loc_city": "Leganés", - "geo_loc_country": "Spain" + "geo_loc_city": "Leganes", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Severo Ochoa", + "submitting_institution_address": "Av. de Orellana, s/n, Leganés", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Universitario de Getafe", + "Hospital Universitario de Getafe": { "collecting_institution_address": "Carr. Madrid - Toledo, Km 12,500, Getafe", "collecting_institution_email": "", "geo_loc_state": "Madrid", "geo_loc_region": "Madrid", "geo_loc_city": "Getafe", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario de Getafe", + "submitting_institution_address": "Carr. Madrid - Toledo, Km 12,500, Getafe", + "submitting_institution_email": "" }, - { - "collecting_institution": "Presidencia de Gobierno", + "Presidencia de Gobierno": { "collecting_institution_address": "", "collecting_institution_email": "", "geo_loc_state": "Madrid", "geo_loc_region": "Madrid", "geo_loc_city": "Madrid", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Presidencia de Gobierno", + "submitting_institution_address": "", + "submitting_institution_email": "" }, - { - "collecting_institution": "Ministerio de Sanidad, Servicios Sociales e Igualdad", + "Ministerio de Sanidad, Servicios Sociales e Igualdad": { "collecting_institution_address": "P.º del Prado, 18", "collecting_institution_email": "", "geo_loc_state": "Madrid", "geo_loc_region": "Madrid", "geo_loc_city": "Madrid", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Ministerio de Sanidad, Servicios Sociales e Igualdad", + "submitting_institution_address": "P.º del Prado, 18", + "submitting_institution_email": "" }, - { - "collecting_institution": "HU Virgen de la Arrixaca", + "HU Virgen de la Arrixaca": { "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n", "collecting_institution_email": "", "geo_loc_state": "Murcia", "geo_loc_region": "Murcia", "geo_loc_city": "Murcia", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "HU Virgen de la Arrixaca", + "submitting_institution_address": "Ctra. Madrid-Cartagena, s/n", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Universitario Reina Sofía", + "Hospital Universitario Reina Sofía": { "collecting_institution_address": "Av. Intendente Jorge Palacios, 1", "collecting_institution_email": "", "geo_loc_state": "Murcia", "geo_loc_region": "Murcia", "geo_loc_city": "Murcia", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Reina Sofía", + "submitting_institution_address": "Av. Intendente Jorge Palacios, 1", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital General Universitario Santa Lucía", + "Hospital General Universitario Santa Lucía": { "collecting_institution_address": "C. Minarete, s/n", "collecting_institution_email": "", "geo_loc_state": "Murcia", "geo_loc_region": "Murcia", "geo_loc_city": "Cartagena", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital General Universitario Santa Lucía", + "submitting_institution_address": "C. Minarete, s/n", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital General Universitario Los Arcos del Mar Menor", + "Hospital General Universitario Los Arcos del Mar Menor": { "collecting_institution_address": "Paraje Torre Octavio, 54, Pozo Aledo", "collecting_institution_email": "", "geo_loc_state": "Murcia", "geo_loc_region": "Murcia", "geo_loc_city": "Pozo Aledo", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital General Universitario Los Arcos del Mar Menor", + "submitting_institution_address": "Paraje Torre Octavio, 54, Pozo Aledo", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital General Universitario Morales Meseguer", + "Hospital General Universitario Morales Meseguer": { "collecting_institution_address": "Av. Marqués de Los Vélez, s/n", "collecting_institution_email": "", "geo_loc_state": "Murcia", "geo_loc_region": "Murcia", "geo_loc_city": "Murcia", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital General Universitario Morales Meseguer", + "submitting_institution_address": "Av. Marqués de Los Vélez, s/n", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Clínico Universitario Virgen de la Arrixaca", + "Hospital Clínico Universitario Virgen de la Arrixaca": { "collecting_institution_address": "Ctra. Madrid-Cartagena, s/n, El Palmar", "collecting_institution_email": "", "geo_loc_state": "Murcia", "geo_loc_region": "Murcia", "geo_loc_city": "Murcia", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Clínico Universitario Virgen de la Arrixaca", + "submitting_institution_address": "Ctra. Madrid-Cartagena, s/n, El Palmar", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Rafael Méndez de Lorca", + "Hospital Rafael Méndez de Lorca": { "collecting_institution_address": "Ctra.N-340, Lorca", "collecting_institution_email": "", "geo_loc_state": "Murcia", "geo_loc_region": "Murcia", "geo_loc_city": "Lorca", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Rafael Méndez de Lorca", + "submitting_institution_address": "Ctra.N-340, Lorca", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital de la Vega Lorenzo Guirao", + "Hospital de la Vega Lorenzo Guirao": { "collecting_institution_address": "Vereda de Morcillo, s/n, Cieza", "collecting_institution_email": "", "geo_loc_state": "Murcia", "geo_loc_region": "Murcia", "geo_loc_city": "Cieza", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital de la Vega Lorenzo Guirao", + "submitting_institution_address": "Vereda de Morcillo, s/n, Cieza", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Univeristario Donostia", + "Hospital Univeristario Donostia": { "collecting_institution_address": "Begiristain Doktorea Pasealekua, s/n", "collecting_institution_email": "", - "geo_loc_state": "País Vasco", + "geo_loc_state": "Pais Vasco", "geo_loc_region": "Guipúzcoa", "geo_loc_city": "Donostia", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Univeristario Donostia", + "submitting_institution_address": "Begiristain Doktorea Pasealekua, s/n", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Universitario de Badajoz", + "Hospital Universitario de Badajoz": { "collecting_institution_address": "Av. de Elvas, s/n", "collecting_institution_email": "", "geo_loc_state": "Extremadura", "geo_loc_region": "Badajoz", "geo_loc_city": "Badajoz", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario de Badajoz", + "submitting_institution_address": "Av. de Elvas, s/n", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital de Mérida", + "Hospital de Mérida": { "collecting_institution_address": "Av. Don Antonio Campos Hoyos, 26, Mérida", "collecting_institution_email": "", "geo_loc_state": "Extremadura", "geo_loc_region": "Badajoz", - "geo_loc_city": "Mérida", - "geo_loc_country": "Spain" + "geo_loc_city": "Merida", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital de Mérida", + "submitting_institution_address": "Av. Don Antonio Campos Hoyos, 26, Mérida", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital San Pedro de Alcantara", + "Hospital San Pedro de Alcantara": { "collecting_institution_address": "Av. Pablo Naranjo Porras, s/n", "collecting_institution_email": "", "geo_loc_state": "Extremadura", "geo_loc_region": "Caceres", "geo_loc_city": "Caceres", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital San Pedro de Alcantara", + "submitting_institution_address": "Av. Pablo Naranjo Porras, s/n", + "submitting_institution_email": "" }, - { - "collecting_institution": "Gerencia de Atención Primaria Pontevedra Sur", + "Gerencia de Atención Primaria Pontevedra Sur": { "collecting_institution_address": "Av. das Camelias, 109, Vigo", "collecting_institution_email": "", "geo_loc_state": "Galicia", "geo_loc_region": "Pontevedra", "geo_loc_city": "Vigo", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Gerencia de Atención Primaria Pontevedra Sur", + "submitting_institution_address": "Av. das Camelias, 109, Vigo", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Universitario Lucus Augusti", + "Hospital Universitario Lucus Augusti": { "collecting_institution_address": " Rúa Dr. Ulises Romero, 1", "collecting_institution_email": "", "geo_loc_state": "Galicia", "geo_loc_region": "Lugp", "geo_loc_city": "Lugo", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Lucus Augusti", + "submitting_institution_address": " Rúa Dr. Ulises Romero, 1", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Universitario de A Coruña", + "Hospital Universitario de A Coruña": { "collecting_institution_address": "As Xubias, 84", "collecting_institution_email": "", "geo_loc_state": "Galicia", "geo_loc_region": "A Coruña", "geo_loc_city": "A Coruña", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario de A Coruña", + "submitting_institution_address": "As Xubias, 84", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Clínico Universitario de Santiago", + "Hospital Clínico Universitario de Santiago": { "collecting_institution_address": "Rúa da Choupana, s/n, Santiago de Compostela", "collecting_institution_email": "", "geo_loc_state": "Galicia", "geo_loc_region": "A Coruña", "geo_loc_city": "Santiago de Compostela", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Clínico Universitario de Santiago", + "submitting_institution_address": "Rúa da Choupana, s/n, Santiago de Compostela", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Universitario de Navarra", + "Hospital Universitario de Navarra": { "collecting_institution_address": "C. de Irunlarrea, 3, Pamplona", "collecting_institution_email": "", "geo_loc_state": "Navarra", "geo_loc_region": "Navarra", "geo_loc_city": "Pamplona", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario de Navarra", + "submitting_institution_address": "C. de Irunlarrea, 3, Pamplona", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital General Universitario de Elche", + "Hospital General Universitario de Elche": { "collecting_institution_address": "Carrer Almazara, 11, Elche", "collecting_institution_email": "", "geo_loc_state": "Valenciana", "geo_loc_region": "Alicante", "geo_loc_city": "Elche", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital General Universitario de Elche", + "submitting_institution_address": "Carrer Almazara, 11, Elche", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital San Pedro", + "Hospital San Pedro": { "collecting_institution_address": "C. Piqueras, 98", "collecting_institution_email": "", "geo_loc_state": "La Rioja", "geo_loc_region": "La Rioja", "geo_loc_city": "Logroño", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital San Pedro", + "submitting_institution_address": "C. Piqueras, 98", + "submitting_institution_email": "" }, - { - "collecting_institution": "Hospital Universitario Txagorritxu", + "Hospital Universitario Txagorritxu": { "collecting_institution_address": " Jose Atxotegi Kalea, s/n", "collecting_institution_email": "", - "geo_loc_state": "País Vasco", + "geo_loc_state": "Pais Vasco", "geo_loc_region": "Alava", "geo_loc_city": "Gasteiz", - "geo_loc_country": "Spain" + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Txagorritxu", + "submitting_institution_address": " Jose Atxotegi Kalea, s/n", + "submitting_institution_email": "" } -] +} \ No newline at end of file From 287409fb7def1b1006d096a5c0e131ace94141c1 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 2 Mar 2023 17:28:39 +0100 Subject: [PATCH 1111/1454] Included a more flexible search for R1 and R2 files, using a new function called validate_R1_R2_delimiters --- relecov_tools/sftp_handle.py | 28 ++++++++++++++++++++++++++-- 1 file changed, 26 insertions(+), 2 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index dbd57de4..39d0a0fe 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -109,6 +109,12 @@ def __init__( self.sftp_passwd = relecov_tools.utils.prompt_password( msg="Enter your password" ) + self.allowed_R1_delimiters = config_json.get_configuration( + "allowed_R1_delimiters" + ) + self.allowed_R2_delimiters = config_json.get_configuration( + "allowed_R2_delimiters" + ) self.client = None def open_connection(self): @@ -238,6 +244,22 @@ def verify_md5_checksum(self, local_folder, file_list): ) return sftp_md5, required_retransmition + def validate_R1_R2_delimiters(self, f_name, orientation): + """Checks if file is R1 or R2 given a list of allowed delimiters""" + if orientation == "R1": + valid_delimiters = self.allowed_R1_delimiters + elif orientation == "R2": + valid_delimiters = self.allowed_R2_delimiters + else: + log.error("wrong direction parameter, aborting") + return False + matching = [True for x in valid_delimiters if x in f_name] + stderr.print(matching) + if len(matching) >= 1: + return True + else: + return False + def create_tmp_files_with_metadata_info( self, local_folder, file_list, md5_data, metadata_file ): @@ -260,14 +282,16 @@ def create_tmp_files_with_metadata_info( stderr.print("[red] Unable to copy Metadata file") return False data = copy.deepcopy(file_list) + # valid_R1_extensions = "" + # valid_R2_extensions = "" for s_name, values in file_list.items(): for _, f_name in values.items(): if not f_name.endswith(tuple(self.allowed_sample_ext)): stderr.print("[red] " + f_name + " has a not valid extension") - if "_R1_" in f_name: + if self.validate_R1_R2_delimiters(f_name, "R1"): data[s_name]["r1_fastq_filepath"] = md5_data[f_name][0] data[s_name]["fastq_r1_md5"] = md5_data[f_name][1] - elif "_R2_" in f_name: + elif self.validate_R1_R2_delimiters(f_name, "R2"): data[s_name]["r2_fastq_filepath"] = md5_data[f_name][0] data[s_name]["fastq_r2_md5"] = md5_data[f_name][1] else: From 90efeffbe79735b03bc8642e806654dd423f4acf Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 2 Mar 2023 17:31:11 +0100 Subject: [PATCH 1112/1454] Replaced '__all__' field option for each possible field in 'adding_fields'. Also included two new fields regarding R1 and R2 denominations in files and changed submitting_data info to be looked up along with the collecting_institution data --- relecov_tools/conf/configuration.json | 37 ++++++++++++++++++++++++--- 1 file changed, 34 insertions(+), 3 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 58793eca..34fa71a2 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -61,15 +61,26 @@ "laboratory_data": { "file": "laboratory_address.json", "map_field": "collecting_institution", - "adding_fields": "__all__" + "adding_fields": [ + "collecting_institution", + "collecting_institution_address", + "collecting_institution_email", + "geo_loc_state", + "geo_loc_region", + "geo_loc_city", + "geo_loc_country" + ] }, "geo_location_data": { "file": "geo_loc_cities.json", "map_field": "geo_loc_city", - "adding_fields": "__all__" + "adding_fields": [ + "geo_loc_latitude", + "geo_loc_longitude" + ] }, "submitting_data": { - "file": "submitter_address.json", + "file": "laboratory_address.json", "map_field": "submitting_institution", "adding_fields": [ "submitting_institution_address", @@ -170,6 +181,26 @@ "fastq.gz", "fasta" ], + "allowed_R1_delimiters": [ + "_R1_", + "_R1.", + ".R1.", + "Forward", + "forward", + "_1_", + "_1.", + ".1." + ], + "allowed_R2_delimiters": [ + "_R2_", + "_R2.", + ".R2.", + "Reverse", + "reverse", + "_2_", + "_2.", + ".2." + ], "GISAID_configuration": { "submitter": "GISAID_ID" }, From 72bbb598af61192b8c937669e69cab3bc17fa40b Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 2 Mar 2023 17:33:04 +0100 Subject: [PATCH 1113/1454] The changes in the configuration files allowed to reduce a lot of unnecessary code in process_json method. Also adapted adding_fields to the json files --- relecov_tools/read_lab_metadata.py | 59 ++++++++++++------------------ 1 file changed, 23 insertions(+), 36 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 71055493..567c5379 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -160,42 +160,23 @@ def process_from_json(self, m_data, json_fields): """Find the labels that are missing in the file to match the given schema.""" map_field = json_fields["map_field"] json_data = json_fields["j_data"] - if isinstance(json_data, dict): - for idx in range(len(m_data)): - try: - m_data[idx].update(json_data[m_data[idx][map_field]]) - except KeyError as error: - if str(error).lower() == "not provided": - log.error("Label was not provided, auto-completing columns") - else: - log.error( - f"Unknown map_field value for json data: \ - {str(map_field)}. Set as not provided" - ) - fields_to_add = { - x: "Not Provided" for x in json_fields["adding_fields"] - } - m_data[idx].update(fields_to_add) - elif isinstance(json_data, list): - # to avoid searching for data for each row, its stored temporarily. - tmp_data = {} - for idx in range(len(m_data)): - if m_data[idx][map_field] not in tmp_data: - for item in json_data: - if m_data[idx][map_field] == item[map_field]: - if json_fields["adding_fields"] == "__all__": - m_data[idx].update(item) - tmp_data[m_data[idx][map_field]] = item - else: - tmp_data[m_data[idx][map_field]] = {} - for field in json_fields["adding_fields"]: - m_data[idx][field] = item[field] - tmp_data[m_data[idx][map_field]][field] = item[ - field - ] - break + for idx in range(len(m_data)): + try: + m_data[idx].update(json_data[m_data[idx][map_field]]) + except KeyError as error: + if str(error).lower() == "not provided": + log.error("Label was not provided, auto-completing columns") else: - m_data[idx].update(tmp_data[m_data[idx][map_field]]) + log.error( + f"Unknown map_field value for json data: \ + {str(map_field)}. Set as not provided" + ) + stderr.error(f"[red] Unknown value for: {map_field} aborting") + sys.exit(1) + fields_to_add = { + x: "Not Provided" for x in json_fields["adding_fields"] + } + m_data[idx].update(fields_to_add) return m_data def adding_fields(self, metadata): @@ -217,7 +198,13 @@ def adding_fields(self, metadata): stderr.print("[blue] Processing sample data file") s_json = {} s_json["map_field"] = "collecting_lab_sample_id" - s_json["adding_field"] = "__all__" + s_json["adding_field"] = [ + "sequence_file_R1_fastq", + "sequence_file_R2_fastq" "sequence_file_R1_md5", + "sequence_file_R2_md5", + "r1_fastq_filepath", + "r2_fastq_filepath", + ] s_json["j_data"] = relecov_tools.utils.read_json_file(self.sample_list_file) metadata = self.process_from_json(metadata, s_json) stderr.print("[green] Processed sample data file.") From 55925df92131cb8e99a0be9a0dbdd814eb487604 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 3 Mar 2023 11:33:55 +0100 Subject: [PATCH 1114/1454] Fixed a missing comma and a wrong log.error message --- relecov_tools/read_lab_metadata.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 567c5379..db4457e7 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -169,9 +169,9 @@ def process_from_json(self, m_data, json_fields): else: log.error( f"Unknown map_field value for json data: \ - {str(map_field)}. Set as not provided" + {str(map_field)}. Aborting" ) - stderr.error(f"[red] Unknown value for: {map_field} aborting") + stderr.error(f"[red] Unknown value for: {map_field}. Aborting") sys.exit(1) fields_to_add = { x: "Not Provided" for x in json_fields["adding_fields"] @@ -200,7 +200,8 @@ def adding_fields(self, metadata): s_json["map_field"] = "collecting_lab_sample_id" s_json["adding_field"] = [ "sequence_file_R1_fastq", - "sequence_file_R2_fastq" "sequence_file_R1_md5", + "sequence_file_R2_fastq", + "sequence_file_R1_md5", "sequence_file_R2_md5", "r1_fastq_filepath", "r2_fastq_filepath", From 1c03bd641838490b796b29783584c20cc438423c Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 3 Mar 2023 11:41:17 +0100 Subject: [PATCH 1115/1454] Deleted submitter_address.json as its information is now included in laboratory_address.json --- relecov_tools/conf/submitter_address.json | 6 ------ 1 file changed, 6 deletions(-) delete mode 100644 relecov_tools/conf/submitter_address.json diff --git a/relecov_tools/conf/submitter_address.json b/relecov_tools/conf/submitter_address.json deleted file mode 100644 index 2d469de9..00000000 --- a/relecov_tools/conf/submitter_address.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "Instituto de Salud Carlos III": { - "submitting_institution_address": "Crta. Pozuelo Majadahonda S/N,", - "submitting_institution_email": "info@isciii.es" - } -} \ No newline at end of file From 76521e8383890835bc3277f65f304995ac602d00 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 3 Mar 2023 12:39:42 +0100 Subject: [PATCH 1116/1454] Grouped every field related to sftp_handle.py into sftp_handle key --- relecov_tools/conf/configuration.json | 62 ++++++++++++++------------- 1 file changed, 32 insertions(+), 30 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 34fa71a2..f30e7a94 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -170,37 +170,39 @@ "ISCIII": "ISCIII.json", "HUGTiP": "HUGTiP.json" }, - "sftp_connection": { - "sftp_server": "sftprelecov.isciii.es", - "sftp_port": "22" + "sftp_handle": { + "sftp_connection": { + "sftp_server": "sftprelecov.isciii.es", + "sftp_port": "22" + }, + "abort_if_md5_mismatch": "False", + "storage_local_folder": "/tmp/relecov", + "tmp_folder_for_metadata": "/tmp/relecov/tmp", + "allowed_sample_extensions": [ + "fastq.gz", + "fasta" + ], + "allowed_R1_delimiters": [ + "_R1_", + "_R1.", + ".R1.", + "Forward", + "forward", + "_1_", + "_1.", + ".1." + ], + "allowed_R2_delimiters": [ + "_R2_", + "_R2.", + ".R2.", + "Reverse", + "reverse", + "_2_", + "_2.", + ".2." + ] }, - "abort_if_md5_mismatch": "False", - "storage_local_folder": "/tmp/relecov", - "tmp_folder_for_metadata": "/tmp/relecov/tmp", - "allowed_sample_extensions": [ - "fastq.gz", - "fasta" - ], - "allowed_R1_delimiters": [ - "_R1_", - "_R1.", - ".R1.", - "Forward", - "forward", - "_1_", - "_1.", - ".1." - ], - "allowed_R2_delimiters": [ - "_R2_", - "_R2.", - ".R2.", - "Reverse", - "reverse", - "_2_", - "_2.", - ".2." - ], "GISAID_configuration": { "submitter": "GISAID_ID" }, From 3a210e0996ee24aa42a722640295790a265bcf54 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 3 Mar 2023 12:40:53 +0100 Subject: [PATCH 1117/1454] Adapted the code to the new changes in configuration.json --- relecov_tools/sftp_handle.py | 39 +++++++++++++++++++----------------- 1 file changed, 21 insertions(+), 18 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 39d0a0fe..b314bb22 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -38,8 +38,8 @@ def __init__( ): """Initializes the sftp object""" config_json = ConfigJson() - self.allowed_sample_ext = config_json.get_configuration( - "allowed_sample_extensions" + self.allowed_sample_ext = config_json.get_topic_data( + "sftp_handle", "allowed_sample_extensions" ) self.sftp_user = user self.sftp_passwd = passwd @@ -48,16 +48,18 @@ def __init__( self.sftp_server = config_json.get_topic_data( "sftp_connection", "sftp_server" ) - self.sftp_port = config_json.get_topic_data("sftp_connection", "sftp_port") - self.storage_local_folder = config_json.get_configuration( - "storage_local_folder" + self.sftp_port = config_json.get_topic_data("sftp_handle", "sftp_port") + self.storage_local_folder = config_json.get_topic_data( + "sftp_handle", "storage_local_folder" ) - self.metadata_tmp_folder = config_json.get_configuration( - "tmp_folder_for_metadata" + self.metadata_tmp_folder = config_json.get_topic_data( + "sftp_handle", "tmp_folder_for_metadata" ) self.abort_if_md5_mismatch = ( True - if config_json.get_configuration("abort_if_md5_mismatch") == "True" + if config_json.get_topic_data( + "sftp_handle", "abort_if_md5_mismatch" + ) == "True" else False ) else: @@ -76,14 +78,14 @@ def __init__( try: self.storage_local_folder = config["storage_local_folder"] except KeyError: - self.storage_local_folder = config_json.get_configuration( - "storage_local_folder" + self.storage_local_folder = config_json.get_topic_data( + "sftp_handle", "storage_local_folder" ) try: self.metadata_tmp_folder = config["tmp_metadata_folder"] except KeyError: - self.metadata_tmp_folder = config_json.get_configuration( - "tmp_folder_for_metadata" + self.metadata_tmp_folder = config_json.get_topic_data( + "sftp_handle", "tmp_folder_for_metadata" ) try: self.abort_if_md5_mismatch = ( @@ -92,8 +94,9 @@ def __init__( except KeyError: self.abort_if_md5_mismatch = ( True - if config_json.get_configuration("abort_if_md5_mismatch") - == "True" + if config_json.get_topic_data( + "sftp_handle", "abort_if_md5_mismatch" + ) == "True" else False ) self.sftp_user = config["sftp_user"] @@ -109,11 +112,11 @@ def __init__( self.sftp_passwd = relecov_tools.utils.prompt_password( msg="Enter your password" ) - self.allowed_R1_delimiters = config_json.get_configuration( - "allowed_R1_delimiters" + self.allowed_R1_delimiters = config_json.get_topic_data( + "sftp_handle", "allowed_R1_delimiters" ) - self.allowed_R2_delimiters = config_json.get_configuration( - "allowed_R2_delimiters" + self.allowed_R2_delimiters = config_json.get_topic_data( + "sftp_handle", "allowed_R2_delimiters" ) self.client = None From d2ce37750691a46a0544a3031b2ca42f40994b23 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 3 Mar 2023 12:45:49 +0100 Subject: [PATCH 1118/1454] linting. --- relecov_tools/sftp_handle.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index b314bb22..558128a3 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -57,9 +57,8 @@ def __init__( ) self.abort_if_md5_mismatch = ( True - if config_json.get_topic_data( - "sftp_handle", "abort_if_md5_mismatch" - ) == "True" + if config_json.get_topic_data("sftp_handle", "abort_if_md5_mismatch") + == "True" else False ) else: @@ -96,7 +95,8 @@ def __init__( True if config_json.get_topic_data( "sftp_handle", "abort_if_md5_mismatch" - ) == "True" + ) + == "True" else False ) self.sftp_user = config["sftp_user"] From 48bafd37eb23f80637825e0d59ba616ddebd753a Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 14 Mar 2023 09:20:05 +0100 Subject: [PATCH 1119/1454] Changed additional formating method --- relecov_tools/map_schema.py | 118 +++++++++++------------------------- 1 file changed, 35 insertions(+), 83 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index afbcc76e..7b272d77 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -40,18 +40,20 @@ def __init__( config_json.get_topic_data("json_schemas", "relecov_schema"), ) else: - if os.path.isfile(relecov_schema): - log.error("Relecov schema file %s does not exists", relecov_schema) + if not os.path.isfile(relecov_schema): + log.error("Relecov schema file %s does not exist", relecov_schema) stderr.print( - "[red] Relecov schema " + relecov_schema + "does not exists" + "[red] Relecov schema " + relecov_schema + " does not exist" ) exit(1) rel_schema_json = relecov_tools.utils.read_json_file(relecov_schema) try: Draft202012Validator.check_schema(rel_schema_json) except jsonschema.ValidationError: - log.error("Relecov schema does not fulfil Draft 202012 Validation ") - stderr.print("[red] Relecov schema does not fulfil Draft 202012 Validation") + log.error("Relecov schema does not fulfill Draft 202012 Validation ") + stderr.print( + "[red] Relecov schema does not fulfill Draft 202012 Validation" + ) sys.exit(1) self.relecov_schema = rel_schema_json @@ -91,7 +93,7 @@ def __init__( Draft202012Validator.check_schema(json_schema) except jsonschema.ValidationError: stderr.print( - "[red] Json schema does not fulfil Draft 202012 Validation" + "[red] Json schema does not fulfill Draft 202012 Validation" ) sys.exit(1) elif self.destination_schema == "ENA": @@ -120,7 +122,7 @@ def __init__( self.output_folder = output_folder def maping_schemas_based_on_geontology(self): - """Return a dictionnary with the properties of the mapped_to_schema as key and + """Return a dictionary with the properties of the mapped_to_schema as key and properties of Relecov Schema as value """ mapped_dict = OrderedDict() @@ -146,90 +148,36 @@ def mapping_json_data(self, mapping_schema_dict): map_sample_dict[item] = data[value] except KeyError as e: - log.warning("Property %s not set in the source data", e) + log.info("Property %s not set in the source data", e) mapped_data.append(map_sample_dict) return mapped_data def additional_formating(self, mapped_json_data): """Update data like MD5 to split in two fields, one for R1 file and - second for R2 + second for R2, and include fields with fixed values. """ + config_json = ConfigJson() + additional_data = config_json.get_topic_data( + "ENA_fields", "additional_formating" + ) + fixed_fields = config_json.get_topic_data("ENA_fields", "ena_fixed_fields") + not_provided_fields = config_json.get_configuration("ENA_fields")[ + "map_not_provided_fields" + ] if self.destination_schema == "ENA": for idx in range(len(self.json_data)): - mapped_json_data[idx]["collector_name"] = "unknown" - mapped_json_data[idx]["file_format"] = "FASTQ" - mapped_json_data[idx]["study_type"] = "Whole Genome Sequencing" - mapped_json_data[idx][ - "study_title" - ] = "RELECOV Spanish Network for genomics surveillance" - mapped_json_data[idx]["study_abstract"] = mapped_json_data[idx][ - "study_title" - ] - mapped_json_data[idx]["broker_name"] = "Instituto de Salud Carlos III" - mapped_json_data[idx]["host health state"] = "not provided" - mapped_json_data[idx]["center_name"] = self.json_data[idx][ - "collecting_institution" - ] - mapped_json_data[idx]["library_name"] = self.json_data[idx][ - "library_preparation_kit" - ] - mapped_json_data[idx]["sample_title"] = self.json_data[idx][ - "sequencing_sample_id" - ] - mapped_json_data[idx]["sample_name"] = self.json_data[idx][ - "sequencing_sample_id" - ] - mapped_json_data[idx]["host subject id"] = self.json_data[idx][ - "sequencing_sample_id" - ] - mapped_json_data[idx]["study_alias"] = self.json_data[idx][ - "schema_name" - ] - - mapped_json_data[idx]["sample_description"] = ( - self.json_data[idx]["anatomical_part"].split(" [", 1)[0] - + " " - + self.json_data[idx]["collection_method"].split(" [", 1)[0] - ) - mapped_json_data[idx]["isolate"] = self.json_data[idx][ - "isolate_sample_id" - ] - mapped_json_data[idx]["platform"] = self.json_data[idx][ - "sequencing_instrument_platform" - ].upper() - - mapped_json_data[idx]["authors"] = self.json_data[idx]["authors"] - mapped_json_data[idx]["design_description"] = ( - self.json_data[idx]["library_layout"].split(" [", 1)[0] - + " " - + self.json_data[idx]["library_preparation_kit"].split(" [", 1)[0] - + " " - + self.json_data[idx]["library_selection"].split(" [", 1)[0] - + " " - + self.json_data[idx]["library_source"].split(" [", 1)[0] - + " " - + self.json_data[idx]["library_strategy"].split(" [", 1)[0] - ) - mapped_json_data[idx]["insert_size"] = "0" - mapped_json_data[idx]["address"] = self.json_data[idx][ - "collecting_institution_address" - ] - "Adding all the 'not provided' fields that are not being captured" - config_json = ConfigJson() - fields = config_json.get_configuration("ENA_fields")[ - "map_not_provided_fields" - ] - mapped_json_data[idx]["r1_fastq_filepath"] = ( - self.json_data[idx]["r1_fastq_filepath"] - + self.json_data[idx]["sequence_file_R1_fastq"] - ) - mapped_json_data[idx]["r2_fastq_filepath"] = ( - self.json_data[idx]["r2_fastq_filepath"] - + self.json_data[idx]["sequence_file_R2_fastq"] - ) - for i, j in enumerate(fields): - mapped_json_data[idx][j] = "not provided" - + for key, value in fixed_fields.items(): + mapped_json_data[idx][key] = value + for key, _ in additional_data.items(): + formated_data = { + x: " ".join( + [self.json_data[idx][f].split(" [", 1)[0] for f in y] + ) + for x, y in additional_data.items() + } + mapped_json_data[idx][key] = formated_data[key] + for _, value in enumerate(not_provided_fields): + mapped_json_data[idx][value] = "Not Provided" return mapped_json_data def write_json_fo_file(self, mapped_json_data): @@ -241,6 +189,7 @@ def write_json_fo_file(self, mapped_json_data): f_sub_name + "_" + time + "_" + self.destination_schema + "_mapped.json" ) json_file = os.path.join(self.output_folder, file_name) + stderr.print("Writting mapped data to json file:", json_file) with open(json_file, "w", encoding="utf-8") as fh: fh.write( json.dumps( @@ -255,4 +204,7 @@ def map_to_data_to_new_schema(self): mapped_json_data = self.mapping_json_data(mapping_schema_dict) updated_json_data = self.additional_formating(mapped_json_data) self.write_json_fo_file(updated_json_data) + stderr.print( + f"[green]Mapping to {self.destination_schema} schema finished successfully" + ) return From 6f3b93133803e0754cd366c4c83ca17746728163 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 14 Mar 2023 09:31:34 +0100 Subject: [PATCH 1120/1454] Included ena_fixed_fields and changed logs --- relecov_tools/read_lab_metadata.py | 26 ++++++++++++++++++-------- 1 file changed, 18 insertions(+), 8 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index db4457e7..1f82369d 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -88,9 +88,12 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None def adding_fixed_fields(self, m_data): """Include fixed data that are always the same for each samples""" p_data = self.configuration.get_topic_data("lab_metadata", "fixed_fields") + ena_data = self.configuration.get_topic_data("ENA_fields", "ena_fixed_fields") for idx in range(len(m_data)): for key, value in p_data.items(): m_data[idx][key] = value + for key, value in ena_data.items(): + m_data[idx][key] = value m_data[idx]["schema_name"] = self.schema_name m_data[idx]["schema_version"] = self.schema_version return m_data @@ -132,7 +135,7 @@ def adding_post_processing(self, m_data): def adding_ontology_to_enum(self, m_data): """Read the schema to get the properties enum and, for those fields which have an enum property value, replace the value for the one - that is defined in the schema + that is defined in the schema. """ enum_dict = {} for prop, values in self.relecov_sch_json["properties"].items(): @@ -151,7 +154,7 @@ def adding_ontology_to_enum(self, m_data): if m_data[idx][key] in e_values: m_data[idx][key] = e_values[m_data[idx][key]] else: - log.error("No ontology could be added") + log.error(f"No ontology could be added in {str(key)}") continue return m_data @@ -164,14 +167,21 @@ def process_from_json(self, m_data, json_fields): try: m_data[idx].update(json_data[m_data[idx][map_field]]) except KeyError as error: - if str(error).lower() == "not provided": + if str(error.args[0]).lower() == "not provided": log.error("Label was not provided, auto-completing columns") + stderr.print( + f"Label {map_field} was not provided in sample {idx}, \ + auto-completing" + ) else: log.error( - f"Unknown map_field value for json data: \ + f"Unknown map_field value {error} for json data: \ {str(map_field)}. Aborting" ) - stderr.error(f"[red] Unknown value for: {map_field}. Aborting") + stderr.print( + f"[red] Unknown value {error} for: {map_field}\ + in sample {idx}. Aborting" + ) sys.exit(1) fields_to_add = { x: "Not Provided" for x in json_fields["adding_fields"] @@ -198,11 +208,11 @@ def adding_fields(self, metadata): stderr.print("[blue] Processing sample data file") s_json = {} s_json["map_field"] = "collecting_lab_sample_id" - s_json["adding_field"] = [ + s_json["adding_fields"] = [ + "fastq_r1_md5", + "fastq_r2_md5", "sequence_file_R1_fastq", "sequence_file_R2_fastq", - "sequence_file_R1_md5", - "sequence_file_R2_md5", "r1_fastq_filepath", "r2_fastq_filepath", ] From 499dd4bce0a78f4c968d26ace1162d62800bc4e3 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 14 Mar 2023 09:33:02 +0100 Subject: [PATCH 1121/1454] Added some fields from ENA and changed a few ontologies --- relecov_tools/schema/relecov_schema.json | 352 +++++++++++++++++++++-- 1 file changed, 321 insertions(+), 31 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 4835d608..c281625c 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -93,7 +93,7 @@ "examples": [ "" ], - "ontology": "NCIT:C53471", + "ontology": "GENEPIO:0001644", "type": "string", "description": "", "classification": "Database Identifiers", @@ -797,7 +797,7 @@ "Missing", "Restricted Access" ], - "ontology": "0", + "ontology": "GENEPIO:0001211", "type": "string", "description": "Source of the specimen, merge of anatomical_part, anatomical_material, body_product and collection method.", "examples": [ @@ -820,7 +820,7 @@ "Pleural cavity [UBERON:0002402]", "Trachea [UBERON:0003126]", "Rectum [UBERON:0001052]", - "Skin [UBERON:0001052]", + "Skin [UBERON:0001003]", "Stomach [UBERON:0000945]", "Upper respiratory tract [UBERON:0001557]", "Anterior Nares [UBERON:2001427]", @@ -851,8 +851,8 @@ }, "collection_device": { "enum": [ - "Air filter [GENEPIO:0100031]", - "Blood Collection Tube [GENEPIO:0100031]", + "Air filter [ENVO:00003968]", + "Blood Collection Tube [NCIT:C113122]", "Bronchoscope [NCIT:C17611]", "Collection Container [NCIT:C43446]", "Collection Cup [GENEPIO:0100026]", @@ -1273,7 +1273,7 @@ "Cluster/Outbreak investigation [GENEPIO:0100019]", "Multi-jurisdictional outbreak investigation [GENEPIO:0100020]", "Intra-jurisdictional outbreak investigation [GENEPIO:0100021]", - "Research [GENEPIO:0100022]", + "Research [GENEPIO:0100003]", "Viral passage experiment [GENEPIO:0100023]", "Protocol testing [GENEPIO:0100024]", "Not Applicable [GENEPIO:0001619]", @@ -1361,6 +1361,7 @@ "Nanopore COVID Midi: 2304 samples", "Nanopore COVID Mini: 576 samples", "Vela Diagnostics:ViroKey SQ FLEX Library Prep Reagents", + "Not Provided [GENEPIO:0001668]", "Other [NCIT:C17649]" ], "examples": [ @@ -1697,7 +1698,7 @@ "examples": [ "RANDOM PCR" ], - "ontology": "GENPIO_0001940", + "ontology": "GENEPIO_0001940", "type": "string", "description": "Library capture method.", "classification": "Sequencing", @@ -1706,31 +1707,31 @@ }, "library_strategy": { "enum": [ - "Bisultife-Seq strategy [GENPIO:0001975]", - "CTS strategy [GENPIO:0001978]", - "ChIP-Seq strategy [GENPIO:0001979]", - "DNase-Hypersensitivity strategy [GENPIO:0001980]", - "EST strategy [GENPIO:0001981]", - "FL-cDNA strategy [GENPIO:0001983]", - "MB-Seq strategy [GENPIO:0001984]", - "MNase-Seq strategy [GENPIO:0001985]", - "MRE-Seq strategy [GENPIO:0001986]", - "MeDIP-Seq strategy [GENPIO:0001987]", - "RNA-Seq strategy [GENPIO:0001990]", - "WCS strategy [GENPIO:0001991]", - "WGS strategy [GENPIO:0001992]", - "WXS strategy [GENPIO:0001993]", - "Amplicon [GENPIO:0001974]", - "Clone end strategy [GENPIO:0001976]", - "Clone strategy [GENPIO:0001977]", - "Finishing strategy [GENPIO:0001982]", - "Other library strategy [GENPIO:0001988]", - "Pool clone strategy [GENPIO:0001989]" + "Bisultife-Seq strategy [GENEPIO:0001975]", + "CTS strategy [GENEPIO:0001978]", + "ChIP-Seq strategy [GENEPIO:0001979]", + "DNase-Hypersensitivity strategy [GENEPIO:0001980]", + "EST strategy [GENEPIO:0001981]", + "FL-cDNA strategy [GENEPIO:0001983]", + "MB-Seq strategy [GENEPIO:0001984]", + "MNase-Seq strategy [GENEPIO:0001985]", + "MRE-Seq strategy [GENEPIO:0001986]", + "MeDIP-Seq strategy [GENEPIO:0001987]", + "RNA-Seq strategy [GENEPIO:0001990]", + "WCS strategy [GENEPIO:0001991]", + "WGS strategy [GENEPIO:0001992]", + "WXS strategy [GENEPIO:0001993]", + "Amplicon [GENEPIO:0001974]", + "Clone end strategy [GENEPIO:0001976]", + "Clone strategy [GENEPIO:0001977]", + "Finishing strategy [GENPEIO:0001982]", + "Other library strategy [GENEPIO:0001988]", + "Pool clone strategy [GENEPIO:0001989]" ], "examples": [ "WGS" ], - "ontology": "GENPIO_0001973", + "ontology": "GENEPIO_0001973", "type": "string", "description": "Overall sequencing strategy or approach.", "classification": "Sequencing", @@ -2133,7 +2134,7 @@ "2018102.consensus.fa" ], "classification": "Bioinformatic Analysis fields", - "label": "Consensus sequence name", + "label": "Consensus sequence filename", "fill_mode": "batch" }, "consensus_sequence_md5": { @@ -2720,7 +2721,7 @@ "label": "Experiment title", "fill_mode": "batch" }, - "ena_study_title": { + "study_title": { "examples": [ "e.g SARS-CoV-2 genomes from late April in Stockholm" ], @@ -2731,7 +2732,7 @@ "label": "Study title", "fill_mode": "batch" }, - "ena_broker_name": { + "broker_name": { "examples": [ "P17157_1007" ], @@ -2753,6 +2754,295 @@ "classification": "Public databases", "label": "First created date", "fill_mode": "batch" + }, + "collector_name": { + "examples": [ + "John Smith, unknown" + ], + "ontology": "GENEPIO:0001797", + "type": "string", + "description": "Name of the person who collected the specimen", + "clasification": "Sample collection and processing", + "label": "Sample collector name", + "table": "sample" + }, + "file_format": { + "examples": [ + "BAM,CRAM,FASTQ" + ], + "enum": [ + "BAM [format:2572]", + "CRAM [format:3462]", + "FASTQ [format:1930]" + ], + "ontology": "NMR:1001459", + "type": "string", + "description": "The run data file model.", + "clasification": "Submission ENA", + "label": "File format", + "table": [ + "experiments" + ] + }, + "host_health_state": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001388", + "type": "string", + "description": " Status of the host", + "clasification": "Host information", + "label": "Host health state", + "table": [ + "sample" + ] + }, + "schema_name": { + "examples": [ + "e.g Sweden" + ], + "ontology": "SIO_001066", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Study alias", + "table": [ + "study", + "experiments" + ] + }, + "study_abstract": { + "examples": [ + "Whole-genome sequences of SARS-CoV-2 from oro-pharyngeal swabs obtained from Belgian Covid-19 patients." + ], + "ontology": "OPMI:0000380", + "type": "string", + "description": " Briefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be inherited from a referenced publication.", + "clasification": "Submission ENA", + "label": "Study abstract", + "table": [ + "study" + ] + }, + "design_description": { + "examples": [ + "design_description_1" + ], + "ontology": "NCIT:C147139", + "type": "string", + "description": "", + "clasification": "", + "label": "Design description", + "table": [ + "experiments" + ] + }, + "definition for seropositive sample": { + "examples": [ + "" + ], + "ontology": "NCIT:C159692", + "type": "string", + "description": " The cut off value used by an investigatior in determining that a sample was seropositive.", + "clasification": "Sample collection and processing", + "label": "Definition for seropositive sample", + "table": [ + "sample" + ] + }, + "serotype (required for a seropositive sample)": { + "examples": [ + "h1n1" + ], + "ontology": "NCIT:C88894", + "type": "string", + "description": " erological variety of a species characterised by its antigenic properties. For influenza, ha subtype should be the letter h followed by a number between 1-16 unless novel subtype is identified and the na subtype should be the letter n followed by a number between 1-9 unless novel subtype is identified. If only one of the subtypes have been tested then use the format h5nx or hxn1.", + "clasification": "Sample collection and processing", + "label": "Serotype (required for a seropositive sample)", + "table": [ + "sample" + ] + }, + "host habitat": { + "examples": [ + "" + ], + "ontology": "ENVO:00002036", + "type": "string", + "description": "Natural habitat of the avian or mammalian host.", + "clasification": "Sample collection and processing", + "label": "Host habitat", + "table": [ + "sample" + ] + }, + "host description": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0000009", + "type": "string", + "description": "Other descriptive information relating to the host.", + "clasification": "Host information", + "label": "Host description", + "table": [ + "sample" + ] + }, + "gravidity": { + "examples": [ + "" + ], + "ontology": "OBI:0002456", + "type": "string", + "description": "Whether or not the subject is gravid. If so, report date due or date post-conception and specify which of these two dates is being reported.", + "clasification": "Host information", + "label": "Gravidity", + "table": [ + "sample" + ] + }, + "strain": { + "examples": [ + "" + ], + "ontology": "NCIT:C14419", + "type": "string", + "description": "Name of the strain from which the sample was obtained..", + "clasification": "Sample collection and processing", + "label": "Strain", + "table": [ + "sample" + ] + }, + "host disease outcome": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001390", + "type": "string", + "description": "Disease outcome in the host.", + "clasification": "Host information", + "label": "Host disease outcome", + "table": [ + "sample" + ] + }, + "type exposure": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001417", + "type": "string", + "description": " Date, Location e.g. type of gathering, Family cluster, etc.", + "clasification": "Host information", + "label": "Outbreak Exposure Event Location", + "table": [ + "sample" + ] + }, + "personal_protective_equipment": { + "examples": [ + "" + ], + "ontology": "NCIT:C173748", + "type": "string", + "description": "Use of personal protective equipment, such as gloves, gowns, during any type of exposure. Example: mask", + "clasification": "Host information", + "label": "Personal protective equipment", + "table": [ + "sample" + ] + }, + "subject exposure duration": { + "examples": [ + "e.g. Patient infected while traveling in …." + ], + "ontology": "NCIT:C83280", + "type": "string", + "description": "If the information is unknown or can not be shared, leave blank.", + "clasification": "Host information", + "label": "Additional Host Information" + }, + "hospitalisation": { + "examples": [], + "ontology": "NCIT:C25179", + "type": "string", + "description": " Was the subject confined to a hospital as a result of virus infection or problems occurring secondary to virus infection?", + "clasification": "Sample collection and processing", + "label": "Hospitalisation", + "table": "sample" + }, + "illness symptoms": { + "examples": [ + "cough, diarrhea, fever, headache, malaise, myalgia" + ], + "ontology": "GENEPIO:0001523", + "type": "string", + "description": "The symptoms that have been reported in relation to the illness. If multiple exposures are applicable, please state them separated by semicolon.", + "clasification": "Sample collection and processing", + "label": "Illness symptoms", + "table": "sample" + }, + "sample_description": { + "examples": [ + "Sample from Belgian Covid-19 patient. Sample was obtained at the Hospital AZ Rivierenland, in Antwerp, Belgium." + ], + "ontology": "sep:00196", + "type": "string", + "description": "Free text description of the sample.", + "clasification": "Sample collection and processing", + "label": "Sample Description", + "table": "sample" + }, + "library_construction_protocol": { + "examples": [ + "library_construction_protocol_1" + ], + "ontology": "NCIT:C41111", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Library Construction protocol", + "table": [ + "experiments" + ] + }, + "insert_size": { + "examples": [ + "350" + ], + "ontology": "GENEPIO_0000076", + "type": "string", + "description": "", + "clasification": "Sequencing", + "label": "Insert size" + }, + "experiment_alias": { + "examples": [ + "experiment_alias_7a" + ], + "ontology": "NCIT_C42790", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Experiment alias", + "table": [ + "experiments" + ] + }, + "run_alias": { + "examples": [ + "e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1" + ], + "ontology": "NCIT_C47911", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Run Alias", + "table": [ + "runs" + ] } } } From 7bf088ed5f6330ff35cb39cff88395d246b5b01e Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 14 Mar 2023 09:33:25 +0100 Subject: [PATCH 1122/1454] Added some fields and changed a few ontologies --- relecov_tools/schema/ena_schema.json | 104 +++++++++++++++++---------- 1 file changed, 68 insertions(+), 36 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 64fd9967..812962a6 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -104,7 +104,7 @@ ] }, "geographic location (country and/or sea)": { - "Enums": [ + "enum": [ "Afghanistan [GAZ:00006882]", "Albania [GAZ:00002953]", "Algeria [GAZ:00000563]", @@ -423,7 +423,7 @@ "label": "Geo Loc Longitude" }, "isolate": { - "ontology": "GENEPIO:0001123", + "ontology": "GENEPIO:0001644", "type": "string", "description": "Identifier of the specific isolate.", "examples": [ @@ -456,7 +456,7 @@ "clasification": "Sample collection and processing" }, "isolation source host-associated": { - "Enums": [ + "enum": [ "Blood [UBERON:0000178]", "Fluid [UBERON:0006314]", "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", @@ -482,7 +482,7 @@ "label": "Specimen source" }, "isolation source non-host-associated": { - "Enums": [ + "enum": [ "Air vent [ENVO:03501208]", "Banknote [ENVO:00003896]", "Bed rail [ENVO:03501209]", @@ -532,7 +532,7 @@ "label": "Environmental Material" }, "host common name": { - "Enums": [ + "enum": [ "Human [NCBITaxon:9606]", "Bat [NCBITaxon:9397]", "Cat [NCBITaxon:9685]", @@ -563,7 +563,7 @@ "table": "sample" }, "host scientific name": { - "Enums": [ + "enum": [ "Bos taurus [NCBITaxon:9913]", "Canis lupus familiaris [NCBITaxon:9615]", "Chiroptera [NCBITaxon:9397]", @@ -602,7 +602,7 @@ "examples": [ "e.g. #131" ], - "ontology": "GENEPIO:0001398", + "ontology": "GENEPIO:0000079", "type": "string", "description": "a unique identifier by which each subject can be referred to, de-identified.", "clasification": "Host information", @@ -765,7 +765,7 @@ ] }, "host sex": { - "Enums": [ + "enum": [ "Female [NCIT:C46110]", "Male [NCIT:C46109]", "Non-binary Gender [GSSO:000132]", @@ -800,7 +800,7 @@ "label": "Additional Host Information" }, "instrument_model": { - "Enums": [ + "enum": [ "Illumina sequencing instrument [GENEPIO:0100105]", "Illumina Genome Analyzer [GENEPIO:0100106]", "Illumina Genome Analyzer II [GENEPIO:0100107]", @@ -940,7 +940,7 @@ ] }, "scientific_name": { - "Enums": [ + "enum": [ "Coronaviridae [NCBITaxon:11118]", "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", "Not Applicable [GENEPIO:0001619]", @@ -1057,7 +1057,7 @@ "examples": [ "RANDOM PCR" ], - "ontology": "GENPIO_0001940", + "ontology": "GENEPIO_0001940", "type": "string", "description": "Library capture method.", "classification": "Sequencing", @@ -1079,31 +1079,31 @@ }, "library_strategy": { "enum": [ - "Bisultife-Seq strategy [GENPIO:0001975]", - "CTS strategy [GENPIO:0001978]", - "ChIP-Seq strategy [GENPIO:0001979]", - "DNase-Hypersensitivity strategy [GENPIO:0001980]", - "EST strategy [GENPIO:0001981]", - "FL-cDNA strategy [GENPIO:0001983]", - "MB-Seq strategy [GENPIO:0001984]", - "MNase-Seq strategy [GENPIO:0001985]", - "MRE-Seq strategy [GENPIO:0001986]", - "MeDIP-Seq strategy [GENPIO:0001987]", - "RNA-Seq strategy [GENPIO:0001990]", - "WCS strategy [GENPIO:0001991]", - "WGS strategy [GENPIO:0001992]", - "WXS strategy [GENPIO:0001993]", - "Amplicon [GENPIO:0001974]", - "Clone end strategy [GENPIO:0001976]", - "Clone strategy [GENPIO:0001977]", - "Finishing strategy [GENPIO:0001982]", - "Other library strategy [GENPIO:0001988]", - "Pool clone strategy [GENPIO:0001989]" + "Bisultife-Seq strategy [GENEPIO:0001975]", + "CTS strategy [GENEPIO:0001978]", + "ChIP-Seq strategy [GENEPIO:0001979]", + "DNase-Hypersensitivity strategy [GENEPIO:0001980]", + "EST strategy [GENEPIO:0001981]", + "FL-cDNA strategy [GENEPIO:0001983]", + "MB-Seq strategy [GENEPIO:0001984]", + "MNase-Seq strategy [GENEPIO:0001985]", + "MRE-Seq strategy [GENEPIO:0001986]", + "MeDIP-Seq strategy [GENEPIO:0001987]", + "RNA-Seq strategy [GENEPIO:0001990]", + "WCS strategy [GENEPIO:0001991]", + "WGS strategy [GENEPIO:0001992]", + "WXS strategy [GENEPIO:0001993]", + "Amplicon [GENEPIO:0001974]", + "Clone end strategy [GENEPIO:0001976]", + "Clone strategy [GENEPIO:0001977]", + "Finishing strategy [GENEPIO:0001982]", + "Other library strategy [GENEPIO:0001988]", + "Pool clone strategy [GENEPIO:0001989]" ], "examples": [ "WGS" ], - "ontology": "GENPIO_0001973", + "ontology": "GENEPIO_0001973", "type": "string", "description": "Overall sequencing strategy or approach.", "classification": "Sequencing", @@ -1127,7 +1127,7 @@ "examples": [ "e.g PAIRED" ], - "ontology": "GENEPIO_0001995", + "ontology": "GENEPIO:0001450", "type": "string", "description": "The submitter's name for this library.", "clasification": "Sequencing", @@ -1217,7 +1217,7 @@ "examples": [ "Whole-genome sequences of SARS-CoV-2 from oro-pharyngeal swabs obtained from Belgian Covid-19 patients." ], - "ontology": "NCIT:C93415", + "ontology": "OPMI:0000380", "type": "string", "description": " Briefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be inherited from a referenced publication.", "clasification": "Submission ENA", @@ -1226,7 +1226,7 @@ "study" ] }, - "sample_alias": { + "sample_name": { "examples": [ "s_20201007_026" ], @@ -1234,7 +1234,7 @@ "type": "string", "description": "", "clasification": "Submission ENA", - "label": "Sample alias", + "label": "Sample name", "table": [ "sample" ] @@ -1316,6 +1316,38 @@ "description": "", "clasification": "Submission ENA", "label": "Broker Name" + }, + "center_name": { + "examples": [ + "P17157_1007" + ], + "ontology": "GENEPIO:0001153", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Originating Laboratory" + }, + "authors": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001517", + "type": "string", + "description": "", + "classification": "Public databases", + "label": "Authors", + "fill_mode": "batch" + }, + "address": { + "examples": [ + "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" + ], + "ontology": "GENEPIO:0001158", + "type": "string", + "description": "The mailing address of the agency submitting the sample.", + "classification": "Sample collection and processing", + "label": "Originating Laboratory Address", + "fill_mode": "batch" } } } \ No newline at end of file From 5421e54fe329f7c5a2665dfd74bd4b8d42a93843 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 14 Mar 2023 09:33:42 +0100 Subject: [PATCH 1123/1454] Added some fields and changed a few ontologies --- relecov_tools/schema/gisaid_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/gisaid_schema.json b/relecov_tools/schema/gisaid_schema.json index 20c1ddcb..5e84e4e7 100644 --- a/relecov_tools/schema/gisaid_schema.json +++ b/relecov_tools/schema/gisaid_schema.json @@ -107,7 +107,7 @@ "label": "Host Age" }, "covv_specimen": { - "Enums": [ + "enum": [ "Blood [UBERON:0000178]", "Fluid [UBERON:0006314]", "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", @@ -139,7 +139,7 @@ "label": "Consensus sequence software name" }, "covv_gender": { - "Enums": [ + "enum": [ "Female [NCIT:C46110]", "Male [NCIT:C46109]", "Non-binary Gender [GSSO:000132]", From b0e980472a33732cd1e3ce1534801de4391047d5 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 14 Mar 2023 09:33:55 +0100 Subject: [PATCH 1124/1454] Added some fields and changed a few ontologies --- relecov_tools/schema/phage_schema.json | 93 +++++++++++++------------- 1 file changed, 47 insertions(+), 46 deletions(-) diff --git a/relecov_tools/schema/phage_schema.json b/relecov_tools/schema/phage_schema.json index b7ccc325..2524cf6c 100644 --- a/relecov_tools/schema/phage_schema.json +++ b/relecov_tools/schema/phage_schema.json @@ -127,7 +127,7 @@ "label": "Numer of variants with effect" }, "host_age_bin": { - "Enums": [ + "enum": [ "0 - 9 [GENEPIO:0100049]", "10 - 19 [GENEPIO:0100050]", "20 - 29 [GENEPIO:0100051]", @@ -153,7 +153,7 @@ ] }, "anatomical_material": { - "Enums": [ + "enum": [ "Blood [UBERON:0000178]", "Fluid [UBERON:0006314]", "Fluid (Cerebrospinal (CSF)) [UBERON:0001359]", @@ -208,7 +208,7 @@ ] }, "lab_host": { - "Enums": [ + "enum": [ "293/ACE2 Cell Line [GENEPIO:0100041]", "Caco2 Cell Line [BTO:0000195]", "Calu3 Cell Line [BTO:0002750]", @@ -241,7 +241,7 @@ "label": "Lab passage Host" }, "anatomical_part": { - "Enums": [ + "enum": [ "Anus [UBERON:0001245]", "Duodenum [UBERON:0002114]", "Eye [UBERON:0000970]", @@ -262,7 +262,7 @@ "Esophagus [UBERON:0001043]", "Ethmoid sinus [UBERON:0002453]", "Nasal Cavity [UBERON:0001707]", - "Middle Nasal Turbinate [UBERON:0005921]", + "Middle Nasal Turbinate [UBERON:0001762]", "Inferior Nasal Turbinate [UBERON:0005922]", "Nasopharynx (NP) [UBERON:0001728]", "Oropharynx (OP) [UBERON:0001729]", @@ -282,7 +282,7 @@ "label": "Anatomical Structure" }, "host_health_outcome": { - "Enums": [ + "enum": [ "Deceased [NCIT:C28554]", "Deteriorating [NCIT:C25254]", "Recovered [NCIT:C49498]", @@ -459,7 +459,7 @@ "label": "Commercial/Open-source/both" }, "prior_sars_cov_2_antiviral_treatment": { - "Enums": [ + "enum": [ "Prior antiviral treatment [GENEPIO:0100037]", "No prior antiviral treatment [GENEPIO:0100233]", "Not Applicable [GENEPIO:0001619]", @@ -476,7 +476,7 @@ ] }, "gene_name_2": { - "Enums": [ + "enum": [ "E gene (orf4) [GENEPIO:0100151]", "M gene (orf5) [GENEPIO:0100152]", "N gene (orf9) [GENEPIO:0100153]", @@ -526,7 +526,7 @@ "label": "Gene Name 2" }, "body_product": { - "Enums": [ + "enum": [ "Breast Milk [UBERON:0001913]", "Feces [UBERON:0001988]", "Mucus [UBERON:0000912]", @@ -576,9 +576,9 @@ "label": "Host ethnicity" }, "collection_device": { - "Enums": [ + "enum": [ "Air filter [ENVO:00003968]", - "Blood Collection Tube [OBI:0002859]", + "Blood Collection Tube [NCIT:C113122]", "Bronchoscope [OBI:0002826]", "Collection Container [OBI:0002088]", "Collection Cup [GENEPIO:0100026]", @@ -610,7 +610,7 @@ "label": "Collection Device" }, "purpose_of_sequencing": { - "Enums": [ + "enum": [ "Baseline surveillance (random sampling) [GENEPIO:0100005]", "Targeted surveillance (non-random sampling) [GENEPIO:0100006]", "Priority surveillance projects [GENEPIO:0100007]", @@ -681,7 +681,7 @@ "label": "Depth of coverage threshold" }, "specimen_processing": { - "Enums": [ + "enum": [ "Virus Passage [GENEPIO:0100039]", "RNA Re-Extraction (Post RT-PCR) [GENEPIO:0100040]", "Specimens Pooled [OBI:0600016]", @@ -809,7 +809,7 @@ "label": "Amplicon Version" }, "host_vaccination_status": { - "Enums": [ + "enum": [ "Fully Vaccinated [GENEPIO:0100100]", "Partially Vaccinated [GENEPIO:0100101]", "Not Vaccinated [GENEPIO:0100102]", @@ -887,7 +887,7 @@ "label": "If lineage identification Is Other, Specify" }, "location_of_exposure_geo_loc_name_country": { - "Enums": [ + "enum": [ "Afghanistan [GAZ:00006882]", "Albania [GAZ:00002953]", "Algeria [GAZ:00000563]", @@ -1248,7 +1248,7 @@ "label": "Diagnostic Pcr Ct Value 1" }, "collection_method": { - "Enums": [ + "enum": [ "Amniocentesis [NCIT:C52009]", "Aspiration [NCIT:C15631]", "Suprapubic Aspiration [GENEPIO:0100028]", @@ -1335,7 +1335,7 @@ "examples": [ "3/21/2020" ], - "ontology": "GENEPIO:0001179", + "ontology": "NCIT:C93644", "type": "string", "description": "The date on which the sample was received.", "format": "date", @@ -1353,7 +1353,7 @@ "label": "Quality control metrics " }, "host_common_name": { - "Enums": [ + "enum": [ "Human [NCBITaxon:9606]", "Bat [NCBITaxon:9397]", "Cat [NCBITaxon:9685]", @@ -1439,7 +1439,7 @@ "label": "Authors" }, "host_role": { - "Enums": [ + "enum": [ "Attendee [GENEPIO:0100249]", "Student [OMRSE:00000058]", "Patient [OMRSE:00000030]", @@ -1534,7 +1534,7 @@ "label": "GISAID Virus Name" }, "geo_loc_name_country": { - "Enums": [ + "enum": [ "Afghanistan [GAZ:00006882]", "Albania [GAZ:00002953]", "Algeria [GAZ:00000563]", @@ -1946,7 +1946,7 @@ "format": "date" }, "exposure_contact_level": { - "Enums": [ + "enum": [ "Direct (human-to-human contact) [TRANS:0000001]", "Indirect contact [GENEPIO:0100246]", "Close contact (face-to-face contact) [GENEPIO:0100247]", @@ -1984,7 +1984,7 @@ "label": "Sequencing Platforms " }, "prior_sars_cov_2_infection": { - "Enums": [ + "enum": [ "Prior infection [GENEPIO:0100234]", "No prior infection [GENEPIO:0100236]", "Not Applicable [GENEPIO:0001619]", @@ -2021,7 +2021,7 @@ "label": "Sample ID given by originating laboratory" }, "host_scientific_name": { - "Enums": [ + "enum": [ "Bos taurus [NCBITaxon:9913]", "Canis lupus familiaris [NCBITaxon:9615]", "Chiroptera [NCBITaxon:9397]", @@ -2054,7 +2054,7 @@ "label": "Host Scientific Name" }, "host_disease": { - "Enums": [ + "enum": [ "COVID-19 [MONDO:0100096]", "Not Applicable [GENEPIO:0001619]", "Not Collected [GENEPIO:0001620]", @@ -2169,7 +2169,7 @@ "format": "date" }, "exposure_event": { - "Enums": [ + "enum": [ "Mass Gathering [GENEPIO:0100237]", "Convention [GENEPIO:0100238]", "Convocation [GENEPIO:0100239]", @@ -2217,7 +2217,7 @@ ] }, "host_gender": { - "Enums": [ + "enum": [ "Female [NCIT:C46110]", "Male [NCIT:C46109]", "Non-binary Gender [GSSO:000132]", @@ -2275,7 +2275,7 @@ ] }, "exposure_setting": { - "Enums": [ + "enum": [ "Human Exposure [ECTO:3000005]", "Contact with Known COVID-19 Case [GENEPIO:0100184]", "Contact with Patient [GENEPIO:0100185]", @@ -2360,7 +2360,7 @@ ] }, "gene_name_1": { - "Enums": [ + "enum": [ "E gene (orf4) [GENEPIO:0100151]", "M gene (orf5) [GENEPIO:0100152]", "N gene (orf9) [GENEPIO:0100153]", @@ -2440,7 +2440,7 @@ "label": "reference genome accession" }, "host_residence_country": { - "Enums": [ + "enum": [ "Afghanistan [GAZ:00006882]", "Albania [GAZ:00002953]", "Algeria [GAZ:00000563]", @@ -2745,7 +2745,7 @@ "label": "Lineage/clade analysis software version" }, "complications": { - "Enums": [ + "enum": [ "Abnormal blood oxygen level [HP:0500165]", "Acute kidney injury [HP:0001919]", "Acute lung injury [MONDO:0015796]", @@ -2858,7 +2858,7 @@ "label": "umbrella bioproject accession" }, "biomaterial_extracted": { - "Enums": [ + "enum": [ "mRNA (cDNA) [OBI:0002754]", "RNA (Total) [OBI:0000895]", "RNA (Poly-A) [OBI:0000869]", @@ -2879,7 +2879,7 @@ "label": "Biomaterial Extracted" }, "host_age_unit": { - "Enums": [ + "enum": [ "months [UO:0000035]", "years [UO:0000036]", "Not Applicable [GENEPIO:0001619]", @@ -2906,7 +2906,7 @@ "label": "Geo Loc Latitude" }, "environmental_material": { - "Enums": [ + "enum": [ "Air vent [ENVO:03501208]", "Banknote [ENVO:00003896]", "Bed rail [ENVO:03501209]", @@ -2966,7 +2966,7 @@ "label": "Submitting Institution Email" }, "environmental_site": { - "Enums": [ + "enum": [ "Acute care facility [ENVO:03501135]", "Animal house [ENVO:00003040]", "Bathroom [ENVO:01000422]", @@ -3004,7 +3004,7 @@ "label": "Anthropogenic Geographic Feature" }, "pre_existing_conditions_and_risk_factors": { - "Enums": [ + "enum": [ "Age 60+ [VO:0004925]", "Anemia [HP:0001903]", "Anorexia [HP:0002039]", @@ -3119,7 +3119,7 @@ "format": "date" }, "variant_designation": { - "Enums": [ + "enum": [ "Variant of Interest (VOI) [GENEPIO:0100082]", "Variant of Concern (VOC) [GENEPIO:0100083]", "Variant Under Monitoring (VUM) [GENEPIO:0100279]" @@ -3164,7 +3164,7 @@ "label": "Variant Calling params" }, "sample_collected_in_quarantine": { - "Enums": [ + "enum": [ "Yes [NCIT:C49488]", "No [NCIT:C49487]", "Not Applicable [GENEPIO:0001619]", @@ -3191,7 +3191,7 @@ "label": "Originating Laboratory" }, "sequencing_instrument": { - "Enums": [ + "enum": [ "Illumina sequencing instrument [GENEPIO:0100105]", "Illumina Genome Analyzer [GENEPIO:0100106]", "Illumina Genome Analyzer II [GENEPIO:0100107]", @@ -3254,7 +3254,7 @@ "label": "Sequencing Instrument Model" }, "host_health_status_details": { - "Enums": [ + "enum": [ "Hospitalized [NCIT:C25179]", "Hospitalized (Non-ICU) [GENEPIO:0100045]", "Hospitalized (ICU) [GENEPIO:0100046]", @@ -3287,7 +3287,7 @@ "label": "Sample ID given by originating laboratory" }, "host_health_state": { - "Enums": [ + "enum": [ "Asymptomatic [NCIT:C3833]", "Deceased [NCIT:C28554]", "Healthy [NCIT:C115935]", @@ -3307,7 +3307,7 @@ ] }, "signs_and_symptoms": { - "Enums": [ + "enum": [ "Abnormal lung auscultation [HP:0030829]", "Ageusia (complete loss of taste) [HP:0041051]", "Parageusia (distorted sense of taste) [HP:0031249]", @@ -3449,12 +3449,13 @@ "ontology": "GENEPIO:0001461", "type": "string", "description": "The name of the consensus sequence file.", + "label": "Consensus sequence filename", "examples": [ "ncov123assembly.fasta" ] }, "purpose_of_sequencing_details": { - "Enums": [ + "enum": [ "Screened for S gene target failure (S dropout)", "Screened for mink variants", "Screened for B.1.1.7 variant", @@ -3508,7 +3509,7 @@ ] }, "organism": { - "Enums": [ + "enum": [ "Coronaviridae [NCBITaxon:11118]", "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", "Not Applicable [GENEPIO:0001619]", @@ -3517,7 +3518,7 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "GENEPIO:0001191", + "ontology": "NCIT:C43459", "type": "string", "description": "Taxonomic name of the organism.", "examples": [ @@ -3527,7 +3528,7 @@ "label": "Organism" }, "purpose_of_sampling": { - "Enums": [ + "enum": [ "Cluster/Outbreak Investigation [GENEPIO:0100001]", "Diagnostic Testing [GENEPIO:0100002]", "Research [GENEPIO:0100003]", @@ -3539,7 +3540,7 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "NCIT_C146997", + "ontology": "GENEPIO:0001198", "type": "string", "description": "The reason that the sample was collected.", "examples": [ From 2878b72e22506d7d325051fb9f27bd3c0eb3ca64 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 14 Mar 2023 09:35:15 +0100 Subject: [PATCH 1125/1454] Included ena_fixed_fields, additional_formating and changed a few values --- relecov_tools/conf/configuration.json | 36 ++++++++++++++++++++++++--- 1 file changed, 33 insertions(+), 3 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index f30e7a94..0df7c247 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -62,7 +62,6 @@ "file": "laboratory_address.json", "map_field": "collecting_institution", "adding_fields": [ - "collecting_institution", "collecting_institution_address", "collecting_institution_email", "geo_loc_state", @@ -352,7 +351,8 @@ "experiment_title": "Project for ENA submission RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "", - "study_id": "ERP137164" + "study_id": "ERP137164", + "ena_broker_name": "Instituto de Salud Carlos III" }, "tool": { "tool_name": "ena-upload-cli", @@ -438,6 +438,7 @@ "illness duration", "illness symptoms", "host disease outcome", + "host health state", "definition for seropositive sample", "library_construction_protocol", "serotype (required for a seropositive sample)", @@ -446,6 +447,35 @@ "host description", "gravidity", "host behaviour" - ] + ], + "ena_fixed_fields": { + "collector_name": "unknown", + "broker_name": "Instituto de Salud Carlos III", + "file_format": "FASTQ", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_abstract": "RELECOV Spanish Network for genomics surveillance", + "insert_size": "0" + }, + "additional_formating": { + "sample_description": [ + "anatomical_part", + "collection_method" + ], + "design_description": [ + "library_layout", + "library_preparation_kit", + "library_selection", + "library_source", + "library_strategy" + ], + "r1_fastq_filepath": [ + "r1_fastq_filepath", + "sequence_file_R1_fastq" + ], + "r2_fastq_filepath": [ + "r2_fastq_filepath", + "sequence_file_R2_fastq" + ] + } } } From e228cc24249da3da7b20883547a4cb6e40592d1f Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 14 Mar 2023 09:52:22 +0100 Subject: [PATCH 1126/1454] Removing duplicated process in adding_fixed_fields --- relecov_tools/read_lab_metadata.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 1f82369d..423cdfea 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -88,12 +88,9 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None def adding_fixed_fields(self, m_data): """Include fixed data that are always the same for each samples""" p_data = self.configuration.get_topic_data("lab_metadata", "fixed_fields") - ena_data = self.configuration.get_topic_data("ENA_fields", "ena_fixed_fields") for idx in range(len(m_data)): for key, value in p_data.items(): m_data[idx][key] = value - for key, value in ena_data.items(): - m_data[idx][key] = value m_data[idx]["schema_name"] = self.schema_name m_data[idx]["schema_version"] = self.schema_version return m_data From aa5e77c9f30f0a84cdb63803c0b13f7ee3287e13 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 14 Mar 2023 11:31:11 +0100 Subject: [PATCH 1127/1454] Removed redundant fields --- relecov_tools/schema/relecov_schema.json | 265 +---------------------- 1 file changed, 3 insertions(+), 262 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index c281625c..99653154 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2763,261 +2763,8 @@ "type": "string", "description": "Name of the person who collected the specimen", "clasification": "Sample collection and processing", - "label": "Sample collector name", - "table": "sample" + "label": "Sample collector name" }, - "file_format": { - "examples": [ - "BAM,CRAM,FASTQ" - ], - "enum": [ - "BAM [format:2572]", - "CRAM [format:3462]", - "FASTQ [format:1930]" - ], - "ontology": "NMR:1001459", - "type": "string", - "description": "The run data file model.", - "clasification": "Submission ENA", - "label": "File format", - "table": [ - "experiments" - ] - }, - "host_health_state": { - "examples": [ - "" - ], - "ontology": "GENEPIO:0001388", - "type": "string", - "description": " Status of the host", - "clasification": "Host information", - "label": "Host health state", - "table": [ - "sample" - ] - }, - "schema_name": { - "examples": [ - "e.g Sweden" - ], - "ontology": "SIO_001066", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Study alias", - "table": [ - "study", - "experiments" - ] - }, - "study_abstract": { - "examples": [ - "Whole-genome sequences of SARS-CoV-2 from oro-pharyngeal swabs obtained from Belgian Covid-19 patients." - ], - "ontology": "OPMI:0000380", - "type": "string", - "description": " Briefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be inherited from a referenced publication.", - "clasification": "Submission ENA", - "label": "Study abstract", - "table": [ - "study" - ] - }, - "design_description": { - "examples": [ - "design_description_1" - ], - "ontology": "NCIT:C147139", - "type": "string", - "description": "", - "clasification": "", - "label": "Design description", - "table": [ - "experiments" - ] - }, - "definition for seropositive sample": { - "examples": [ - "" - ], - "ontology": "NCIT:C159692", - "type": "string", - "description": " The cut off value used by an investigatior in determining that a sample was seropositive.", - "clasification": "Sample collection and processing", - "label": "Definition for seropositive sample", - "table": [ - "sample" - ] - }, - "serotype (required for a seropositive sample)": { - "examples": [ - "h1n1" - ], - "ontology": "NCIT:C88894", - "type": "string", - "description": " erological variety of a species characterised by its antigenic properties. For influenza, ha subtype should be the letter h followed by a number between 1-16 unless novel subtype is identified and the na subtype should be the letter n followed by a number between 1-9 unless novel subtype is identified. If only one of the subtypes have been tested then use the format h5nx or hxn1.", - "clasification": "Sample collection and processing", - "label": "Serotype (required for a seropositive sample)", - "table": [ - "sample" - ] - }, - "host habitat": { - "examples": [ - "" - ], - "ontology": "ENVO:00002036", - "type": "string", - "description": "Natural habitat of the avian or mammalian host.", - "clasification": "Sample collection and processing", - "label": "Host habitat", - "table": [ - "sample" - ] - }, - "host description": { - "examples": [ - "" - ], - "ontology": "GENEPIO:0000009", - "type": "string", - "description": "Other descriptive information relating to the host.", - "clasification": "Host information", - "label": "Host description", - "table": [ - "sample" - ] - }, - "gravidity": { - "examples": [ - "" - ], - "ontology": "OBI:0002456", - "type": "string", - "description": "Whether or not the subject is gravid. If so, report date due or date post-conception and specify which of these two dates is being reported.", - "clasification": "Host information", - "label": "Gravidity", - "table": [ - "sample" - ] - }, - "strain": { - "examples": [ - "" - ], - "ontology": "NCIT:C14419", - "type": "string", - "description": "Name of the strain from which the sample was obtained..", - "clasification": "Sample collection and processing", - "label": "Strain", - "table": [ - "sample" - ] - }, - "host disease outcome": { - "examples": [ - "" - ], - "ontology": "GENEPIO:0001390", - "type": "string", - "description": "Disease outcome in the host.", - "clasification": "Host information", - "label": "Host disease outcome", - "table": [ - "sample" - ] - }, - "type exposure": { - "examples": [ - "" - ], - "ontology": "GENEPIO:0001417", - "type": "string", - "description": " Date, Location e.g. type of gathering, Family cluster, etc.", - "clasification": "Host information", - "label": "Outbreak Exposure Event Location", - "table": [ - "sample" - ] - }, - "personal_protective_equipment": { - "examples": [ - "" - ], - "ontology": "NCIT:C173748", - "type": "string", - "description": "Use of personal protective equipment, such as gloves, gowns, during any type of exposure. Example: mask", - "clasification": "Host information", - "label": "Personal protective equipment", - "table": [ - "sample" - ] - }, - "subject exposure duration": { - "examples": [ - "e.g. Patient infected while traveling in …." - ], - "ontology": "NCIT:C83280", - "type": "string", - "description": "If the information is unknown or can not be shared, leave blank.", - "clasification": "Host information", - "label": "Additional Host Information" - }, - "hospitalisation": { - "examples": [], - "ontology": "NCIT:C25179", - "type": "string", - "description": " Was the subject confined to a hospital as a result of virus infection or problems occurring secondary to virus infection?", - "clasification": "Sample collection and processing", - "label": "Hospitalisation", - "table": "sample" - }, - "illness symptoms": { - "examples": [ - "cough, diarrhea, fever, headache, malaise, myalgia" - ], - "ontology": "GENEPIO:0001523", - "type": "string", - "description": "The symptoms that have been reported in relation to the illness. If multiple exposures are applicable, please state them separated by semicolon.", - "clasification": "Sample collection and processing", - "label": "Illness symptoms", - "table": "sample" - }, - "sample_description": { - "examples": [ - "Sample from Belgian Covid-19 patient. Sample was obtained at the Hospital AZ Rivierenland, in Antwerp, Belgium." - ], - "ontology": "sep:00196", - "type": "string", - "description": "Free text description of the sample.", - "clasification": "Sample collection and processing", - "label": "Sample Description", - "table": "sample" - }, - "library_construction_protocol": { - "examples": [ - "library_construction_protocol_1" - ], - "ontology": "NCIT:C41111", - "type": "string", - "description": "", - "clasification": "Sequencing", - "label": "Library Construction protocol", - "table": [ - "experiments" - ] - }, - "insert_size": { - "examples": [ - "350" - ], - "ontology": "GENEPIO_0000076", - "type": "string", - "description": "", - "clasification": "Sequencing", - "label": "Insert size" - }, "experiment_alias": { "examples": [ "experiment_alias_7a" @@ -3026,10 +2773,7 @@ "type": "string", "description": "", "clasification": "Submission ENA", - "label": "Experiment alias", - "table": [ - "experiments" - ] + "label": "Experiment alias" }, "run_alias": { "examples": [ @@ -3039,10 +2783,7 @@ "type": "string", "description": "", "clasification": "Submission ENA", - "label": "Run Alias", - "table": [ - "runs" - ] + "label": "Run Alias" } } } From 31eefdbbbc087f3f6a4be7ffeeb168e5c034df75 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 14 Mar 2023 11:32:00 +0100 Subject: [PATCH 1128/1454] fixed two ontology values --- relecov_tools/schema/ena_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 812962a6..e1672266 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -692,7 +692,7 @@ "examples": [ "" ], - "ontology": "NCIT:C14419", + "ontology": "GENEPIO:0001123", "type": "string", "description": "Name of the strain from which the sample was obtained..", "clasification": "Sample collection and processing", @@ -1068,7 +1068,7 @@ "examples": [ "library_construction_protocol_1" ], - "ontology": "NCIT:C41111", + "ontology": "GENEPIO:0001450", "type": "string", "description": "", "clasification": "Sequencing", From a4b9a3c13abe476e676634015635be5a60aa67c8 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 14 Mar 2023 11:32:57 +0100 Subject: [PATCH 1129/1454] moved collector_name to fixed_fields --- relecov_tools/conf/configuration.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 0df7c247..ccd0b428 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -4,7 +4,8 @@ "host_disease": "COVID-19", "tax_id": "2697049", "organism": "Severe acute respiratory syndrome coronavirus 2", - "study_type": "Whole Genome Sequencing" + "study_type": "Whole Genome Sequencing", + "collector_name": "Not Provided" }, "metadata_lab_heading": [ "Public Health sample id (SIVIES)", @@ -449,7 +450,6 @@ "host behaviour" ], "ena_fixed_fields": { - "collector_name": "unknown", "broker_name": "Instituto de Salud Carlos III", "file_format": "FASTQ", "study_title": "RELECOV Spanish Network for genomics surveillance", From dd19a0fe1668832e367527b9003e3f9d6225da61 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 14 Mar 2023 11:33:49 +0100 Subject: [PATCH 1130/1454] changed output file name and some logs --- relecov_tools/map_schema.py | 21 +++++++++++++-------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 7b272d77..d95b9ebb 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -126,14 +126,22 @@ def maping_schemas_based_on_geontology(self): properties of Relecov Schema as value """ mapped_dict = OrderedDict() + errors = {} for key, values in self.mapped_to_schema["properties"].items(): if values["ontology"] == "0": continue try: mapped_dict[key] = self.ontology[values["ontology"]] except KeyError as e: - log.error("Invalid ontology for %s", key) - stderr.print(f"[red] Ontology value {e} not in relecov schema") + errors[key] = str(e) + if len(errors) >= 1: + output_errs = "\n".join(f"{k}:{v}" for k, v in errors.items()) + log.error( + "Invalid ontology for: %s", str([x for x in errors.keys()]).strip("[]") + ) + stderr.print( + f"[red]Ontology values not found in relecov schema:\n", output_errs + ) return mapped_dict def mapping_json_data(self, mapping_schema_dict): @@ -183,10 +191,9 @@ def additional_formating(self, mapped_json_data): def write_json_fo_file(self, mapped_json_data): """Write metadata to json file""" os.makedirs(self.output_folder, exist_ok=True) - time = datetime.now().strftime("%Y_%m_%d_%H_%M") - f_sub_name = os.path.basename(self.json_file).split(".")[0] + time = datetime.now().strftime("%Y_%m_%d") file_name = ( - f_sub_name + "_" + time + "_" + self.destination_schema + "_mapped.json" + "mapped_metadata" + "_" + self.destination_schema + "_" + time + ".json" ) json_file = os.path.join(self.output_folder, file_name) stderr.print("Writting mapped data to json file:", json_file) @@ -204,7 +211,5 @@ def map_to_data_to_new_schema(self): mapped_json_data = self.mapping_json_data(mapping_schema_dict) updated_json_data = self.additional_formating(mapped_json_data) self.write_json_fo_file(updated_json_data) - stderr.print( - f"[green]Mapping to {self.destination_schema} schema finished successfully" - ) + stderr.print(f"[green]Finished mapping to {self.destination_schema} schema") return From 7a124bf4e147162aaeef6fcd8c1faaefe17c1493 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 14 Mar 2023 11:34:20 +0100 Subject: [PATCH 1131/1454] changed output file name --- relecov_tools/read_lab_metadata.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 423cdfea..9398e6c8 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -5,6 +5,7 @@ import os import sys import re +from datetime import datetime import relecov_tools.utils from relecov_tools.config_json import ConfigJson import relecov_tools.json_schema @@ -318,9 +319,7 @@ def create_metadata_json(self): extended_metadata = self.adding_fixed_fields(extended_metadata) completed_metadata = self.adding_ontology_to_enum(extended_metadata) file_name = ( - "processed_" - + os.path.splitext(os.path.basename(self.metadata_file))[0] - + ".json" + "processed_metadata_lab_" + datetime.now().strftime("%Y_%m_%d") + ".json" ) stderr.print("[blue] Writting output json file") os.makedirs(self.output_folder, exist_ok=True) From 2d7d6b04c2812e082de28fa3f76c1e32f6508d22 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 14 Mar 2023 11:46:38 +0100 Subject: [PATCH 1132/1454] linting --- relecov_tools/map_schema.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index d95b9ebb..6245c5aa 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -140,7 +140,7 @@ def maping_schemas_based_on_geontology(self): "Invalid ontology for: %s", str([x for x in errors.keys()]).strip("[]") ) stderr.print( - f"[red]Ontology values not found in relecov schema:\n", output_errs + f"[red]Ontology values not found in relecov schema:\n{output_errs}" ) return mapped_dict From 70a0dda9aa6a089d8c6f7d34463e24b534e13633 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 29 Mar 2023 09:57:47 +0200 Subject: [PATCH 1133/1454] Included --output_location as a new option for download process --- relecov_tools/__main__.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 08aa2429..c1ed9161 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -139,7 +139,13 @@ def relecov_tools_cli(verbose, log_file): @click.option( "-f", "--conf_file", - help="Configuration file (no params file)", + help="Configuration file (not params file)", +) +@click.option( + "-o", + "--output_location", + default=None, + help="Flag: Select location for downloaded files", ) @click.option( "-t", @@ -149,10 +155,10 @@ def relecov_tools_cli(verbose, log_file): default=None, help="Flag: Select which folders will be downloaded giving [paths] or via prompt", ) -def download(user, password, conf_file, user_relecov, password_relecov, target_folders): +def download(user, password, conf_file, user_relecov, password_relecov, output_location, target_folders): """Download files located in sftp server.""" sftp_connection = relecov_tools.sftp_handle.SftpHandle( - user, password, conf_file, user_relecov, password_relecov, target_folders + user, password, conf_file, user_relecov, password_relecov, output_location, target_folders ) sftp_connection.download() From 60868a3433e284fbe54f120615f36f5a15d9c74c Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 29 Mar 2023 09:58:24 +0200 Subject: [PATCH 1134/1454] Included the new --output_location parameter in the code --- relecov_tools/sftp_handle.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 558128a3..c0e4bd67 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -34,7 +34,8 @@ def __init__( conf_file=None, user_relecov=None, password_relecov=None, - target_folders=None, + output_location=None, + target_folders=None ): """Initializes the sftp object""" config_json = ConfigJson() @@ -46,7 +47,7 @@ def __init__( self.target_folders = target_folders if conf_file is None: self.sftp_server = config_json.get_topic_data( - "sftp_connection", "sftp_server" + "sftp_handle", "sftp_server" ) self.sftp_port = config_json.get_topic_data("sftp_handle", "sftp_port") self.storage_local_folder = config_json.get_topic_data( @@ -106,8 +107,10 @@ def __init__( log.error("Invalid configuration file %s", e) stderr.print("[red] Invalid configuration file {e} !") sys.exit(1) + if output_location is not None: + self.storage_local_folder = output_location if self.sftp_user is None: - self.sftp_user = relecov_tools.utils.prompt_text(msg="Enter the userid") + self.sftp_user = relecov_tools.utils.prompt_text(msg="Enter the user id") if self.sftp_passwd is None: self.sftp_passwd = relecov_tools.utils.prompt_password( msg="Enter your password" @@ -257,7 +260,6 @@ def validate_R1_R2_delimiters(self, f_name, orientation): log.error("wrong direction parameter, aborting") return False matching = [True for x in valid_delimiters if x in f_name] - stderr.print(matching) if len(matching) >= 1: return True else: @@ -285,8 +287,6 @@ def create_tmp_files_with_metadata_info( stderr.print("[red] Unable to copy Metadata file") return False data = copy.deepcopy(file_list) - # valid_R1_extensions = "" - # valid_R2_extensions = "" for s_name, values in file_list.items(): for _, f_name in values.items(): if not f_name.endswith(tuple(self.allowed_sample_ext)): @@ -449,7 +449,7 @@ def validate_fetched_files(self, fetched_folder): stderr.print(f"Files that mismatch: {str(mismatch_files)}") else: stderr.print( - "Showing some of the mismatches, check logs to see all of them: %s", + "Showing some of the mismatches, use --log-file to see all of them: %s", str(mismatch_files[0:9]), ) log.error(f"List of files that mismatch: {str(mismatch_files)}") @@ -545,7 +545,7 @@ def download(self): if len(corrupted) > 0 and self.abort_if_md5_mismatch: log.error("Stopping because of corrupted files %s", corrupted) stderr.print( - f"[red] Stop processing folder {folder} because of corrupted files {corrupted}" + f"[red] Stopped processing folder {folder} due to corrupted files {corrupted}" ) continue meta_file = self.find_metadata_file(result_data["local_folder"]) From c536bc2f0228887ca14847e59773453eaf93af0a Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 29 Mar 2023 09:59:42 +0200 Subject: [PATCH 1135/1454] Changed a few prints in the code for better readability --- relecov_tools/json_validation.py | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index b0b277ea..e5b9e837 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -36,12 +36,12 @@ def __init__( if json_data_file is None: json_data_file = relecov_tools.utils.prompt_path( - msg="Select the json file to validate" + msg="Select the json file to be validated" ) if out_folder is None: self.out_folder = relecov_tools.utils.prompt_path( - msg="Select the folder where to save excel with invalid data" + msg="Select the folder where excel file with invalid data will be saved" ) else: self.out_folder = out_folder @@ -121,7 +121,7 @@ def create_invalid_metadata(self, invalid_json, metadata, out_folder): stderr.print("[red] Some of the Samples are not validate") if metadata is None: metadata = relecov_tools.utils.prompt_path( - msg="Select the metadata file to select those samples not validated." + msg="Select the metadata file to select those not-validated samples." ) if not os.path.isfile(metadata): log.error("Metadata file %s does not exist", metadata) @@ -179,6 +179,3 @@ def validate(self): self.validate_schema() invalid_json = self.validate_instances() self.create_invalid_metadata(invalid_json, self.metadata, self.out_folder) - - # Enviar los errores por correo - # logging.handlers.SMTPHandler(mailhost=("smtp.gmail.com", 465), fromaddr=correo_isciii, toaddrs=correo_usuario, subject="Validation errors", credentials=(usurario,contraseña), secure=None, timeout=1.0) From 188f6c2e7c3685a45ce481b5bc87bc8a4a9542f0 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 29 Mar 2023 10:00:17 +0200 Subject: [PATCH 1136/1454] Changed some comments for better readability --- relecov_tools/read_lab_metadata.py | 18 +++++++----------- 1 file changed, 7 insertions(+), 11 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 9398e6c8..79f11d0f 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -87,7 +87,7 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None self.schema_version = self.relecov_sch_json["version"] def adding_fixed_fields(self, m_data): - """Include fixed data that are always the same for each samples""" + """Include fixed data that are always the same for every sample""" p_data = self.configuration.get_topic_data("lab_metadata", "fixed_fields") for idx in range(len(m_data)): for key, value in p_data.items(): @@ -97,9 +97,7 @@ def adding_fixed_fields(self, m_data): return m_data def adding_copy_from_other_field(self, m_data): - """Add in a new field the information that is already set in another - field. - """ + """Add a new field with information based in another field.""" p_data = self.configuration.get_topic_data( "lab_metadata", "required_copy_from_other_field" ) @@ -109,8 +107,7 @@ def adding_copy_from_other_field(self, m_data): return m_data def adding_post_processing(self, m_data): - """Add the fields that requires to set based on the existing value - in other field + """Add fields which values require post processing """ p_data = self.configuration.get_topic_data( "lab_metadata", "required_post_processing" @@ -169,7 +166,7 @@ def process_from_json(self, m_data, json_fields): log.error("Label was not provided, auto-completing columns") stderr.print( f"Label {map_field} was not provided in sample {idx}, \ - auto-completing" + auto-completing with Not Provided" ) else: log.error( @@ -188,8 +185,7 @@ def process_from_json(self, m_data, json_fields): return m_data def adding_fields(self, metadata): - """Add information that requires to handle json files to include in - the fields""" + """Add information located inside various json file as fields""" for key, values in self.json_req_files.items(): stderr.print(f"[blue] Processing {key}") @@ -232,10 +228,10 @@ def read_configuration_json_files(self): return c_files def read_metadata_file(self): - """Read the input metadata file from row 4, changes the metadata heading + """Reads the input metadata file from row 4, changes the metadata heading with their property name values defined in schema. Convert the date colunms value to the dd/mm/yyyy format. - Return list of dict with data, and errors + Return list of dicts with data and errors """ heading_row_number = 4 ws_metadata_lab = relecov_tools.utils.read_excel_file( From be8660258e45b7ce48d06f838846fd2c8c8b4dc2 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 29 Mar 2023 10:07:28 +0200 Subject: [PATCH 1137/1454] Black linting --- relecov_tools/__main__.py | 18 ++++++++++++++++-- relecov_tools/read_lab_metadata.py | 3 +-- relecov_tools/sftp_handle.py | 6 ++---- 3 files changed, 19 insertions(+), 8 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index c1ed9161..afb33045 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -155,10 +155,24 @@ def relecov_tools_cli(verbose, log_file): default=None, help="Flag: Select which folders will be downloaded giving [paths] or via prompt", ) -def download(user, password, conf_file, user_relecov, password_relecov, output_location, target_folders): +def download( + user, + password, + conf_file, + user_relecov, + password_relecov, + output_location, + target_folders, +): """Download files located in sftp server.""" sftp_connection = relecov_tools.sftp_handle.SftpHandle( - user, password, conf_file, user_relecov, password_relecov, output_location, target_folders + user, + password, + conf_file, + user_relecov, + password_relecov, + output_location, + target_folders, ) sftp_connection.download() diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 79f11d0f..8df52389 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -107,8 +107,7 @@ def adding_copy_from_other_field(self, m_data): return m_data def adding_post_processing(self, m_data): - """Add fields which values require post processing - """ + """Add fields which values require post processing""" p_data = self.configuration.get_topic_data( "lab_metadata", "required_post_processing" ) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index c0e4bd67..7e06ceee 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -35,7 +35,7 @@ def __init__( user_relecov=None, password_relecov=None, output_location=None, - target_folders=None + target_folders=None, ): """Initializes the sftp object""" config_json = ConfigJson() @@ -46,9 +46,7 @@ def __init__( self.sftp_passwd = passwd self.target_folders = target_folders if conf_file is None: - self.sftp_server = config_json.get_topic_data( - "sftp_handle", "sftp_server" - ) + self.sftp_server = config_json.get_topic_data("sftp_handle", "sftp_server") self.sftp_port = config_json.get_topic_data("sftp_handle", "sftp_port") self.storage_local_folder = config_json.get_topic_data( "sftp_handle", "storage_local_folder" From 10b6a8ac70806574eff7c4788ba8d31044b33600 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 31 Mar 2023 14:05:10 +0200 Subject: [PATCH 1138/1454] Changed help flag for --output_location --- relecov_tools/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index afb33045..8d4c09e4 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -145,7 +145,7 @@ def relecov_tools_cli(verbose, log_file): "-o", "--output_location", default=None, - help="Flag: Select location for downloaded files", + help="Flag: Select location for downloaded files, overrides config file location", ) @click.option( "-t", From 884388029a9677ee40b7aa570a7b0de0c989dab0 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 31 Mar 2023 14:06:49 +0200 Subject: [PATCH 1139/1454] Changed sftp_handle and metadata_lab_heading fields --- relecov_tools/conf/configuration.json | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index ccd0b428..2e8d84e1 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -31,7 +31,6 @@ "Host Age", "Host Gender", "Sequencing Date", - "Purpose of Sequencing", "Nucleic acid extraction protocol", "Commercial All-in-one library kit", "Library Preparation Kit", @@ -48,12 +47,10 @@ "Capture method", "Sequencing technique", "Library Layout", - "Read Length", "Gene Name 1", "Diagnostic Pcr Ct Value 1", "Gene Name 2", "Diagnostic Pcr Ct Value-2", - "Broker Name", "Authors", "Sequence file R1 fastq", "Sequence file R2 fastq" @@ -176,8 +173,7 @@ "sftp_port": "22" }, "abort_if_md5_mismatch": "False", - "storage_local_folder": "/tmp/relecov", - "tmp_folder_for_metadata": "/tmp/relecov/tmp", + "platform_storage_folder": "tmp/relecov", "allowed_sample_extensions": [ "fastq.gz", "fasta" From b73a47c24cb2778160ecc16edc3bf33e9cf4e812 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 31 Mar 2023 14:08:05 +0200 Subject: [PATCH 1140/1454] Reestructured the code in parse_file method --- relecov_tools/long_table_parse.py | 57 ++++++++++++++++++------------- 1 file changed, 33 insertions(+), 24 deletions(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index 6189a579..a57a630c 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -83,10 +83,9 @@ def parse_file(self): Validate the file by checking the header line """ - with open(self.file_path) as fh: + with open(self.file_path, encoding="utf-8-sig") as fh: lines = fh.readlines() - self.validate_file(lines[0].strip().split(",")) stderr.print("[green]Successful checking heading fields") stderr.print("[blue]Parsing the input file") heading_index = {} @@ -94,6 +93,24 @@ def parse_file(self): for heading in self.long_table_heading: heading_index[heading] = headings_from_csv.index(heading) + aux_dict = { + "Chromosome": "CHROM", + "Variant": {"pos": "POS", "alt": "ALT", "ref": "REF"}, + "Filter": "FILTER", + "VariantInSample": { + "dp": "DP", + "ref_dp": "REF_DP", + "alt_dp": "ALT_DP", + "af": "AF", + }, + "Effect": "EFFECT", + "VariantAnnotation": { + "hgvs_c": "HGVS_C", + "hgvs_p": "HGVS_P", + "hgvs_p_1_letter": "HGVS_P_1LETTER", + }, + } + samp_dict = {} for line in lines[1:]: line_s = line.strip().split(",") @@ -101,29 +118,14 @@ def parse_file(self): sample = line_s[heading_index["SAMPLE"]] if sample not in samp_dict: samp_dict[sample] = [] - variant_dict = {} - variant_dict["Chromosome"] = line_s[heading_index["CHROM"]] - variant_dict["Variant"] = { - "pos": line_s[heading_index["POS"]], - "alt": line_s[heading_index["ALT"]], - "ref": line_s[heading_index["REF"]], - } - - variant_dict["Filter"] = line_s[heading_index["FILTER"]] - - variant_dict["VariantInSample"] = { - "dp": line_s[heading_index["DP"]], - "ref_dp": line_s[heading_index["REF_DP"]], - "alt_dp": line_s[heading_index["ALT_DP"]], - "af": line_s[heading_index["AF"]], - } - - variant_dict["Effect"] = line_s[heading_index["EFFECT"]] - variant_dict["VariantAnnotation"] = { - "hgvs_c": line_s[heading_index["HGVS_C"]], - "hgvs_p": line_s[heading_index["HGVS_P"]], - "hgvs_p_1_letter": line_s[heading_index["HGVS_P_1LETTER"]], + variant_dict = { + key: ( + {key2: line_s[heading_index[val2]] for key2, val2 in value.items()} + if isinstance(value, dict) + else line_s[heading_index[value]] + ) + for key, value in aux_dict.items() } if re.search("&", line_s[heading_index["GENE"]]): @@ -148,6 +150,13 @@ def convert_to_json(self, samp_dict): result_regex = re.search( "variants_long_table_(.*).csv", os.path.basename(self.file_path) ) + if result_regex is None: + log.error("Analysis date not found in filename, aborting") + stderr.print( + f"[red]Error: filename must include analysis date in format YYYYMMDD" + ) + stderr.print(f"[red]e.g. variants_long_table_20220830.csv") + sys.exit(1) for key, values in samp_dict.items(): j_dict = {"sample_name": key, "analysis_date": result_regex.group(1)} j_dict["variants"] = values From 88318b3a6b764cdd5e9230f7030c6076b3e550de Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 31 Mar 2023 14:10:31 +0200 Subject: [PATCH 1141/1454] Changed variables to fit the changes in config file and reestructured some parts --- relecov_tools/sftp_handle.py | 75 +++++++++++++++++++++++------------- 1 file changed, 49 insertions(+), 26 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 7e06ceee..890fb4b5 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -51,9 +51,6 @@ def __init__( self.storage_local_folder = config_json.get_topic_data( "sftp_handle", "storage_local_folder" ) - self.metadata_tmp_folder = config_json.get_topic_data( - "sftp_handle", "tmp_folder_for_metadata" - ) self.abort_if_md5_mismatch = ( True if config_json.get_topic_data("sftp_handle", "abort_if_md5_mismatch") @@ -79,12 +76,6 @@ def __init__( self.storage_local_folder = config_json.get_topic_data( "sftp_handle", "storage_local_folder" ) - try: - self.metadata_tmp_folder = config["tmp_metadata_folder"] - except KeyError: - self.metadata_tmp_folder = config_json.get_topic_data( - "sftp_handle", "tmp_folder_for_metadata" - ) try: self.abort_if_md5_mismatch = ( True if config["abort_if_md5_mismatch"] == "True" else False @@ -263,13 +254,13 @@ def validate_R1_R2_delimiters(self, f_name, orientation): else: return False - def create_tmp_files_with_metadata_info( + def create_files_with_metadata_info( self, local_folder, file_list, md5_data, metadata_file ): """Copy metadata file from folder and create a file with the sample names """ - out_folder = self.metadata_tmp_folder + out_folder = self.storage_local_folder os.makedirs(out_folder, exist_ok=True) prefix_file_name = "_".join(local_folder.split("/")[-2:]) new_metadata_file = "metadata_lab_" + prefix_file_name + ".xlsx" @@ -296,6 +287,13 @@ def create_tmp_files_with_metadata_info( data[s_name]["r2_fastq_filepath"] = md5_data[f_name][0] data[s_name]["fastq_r2_md5"] = md5_data[f_name][1] else: + log.error( + "Sample %s does not have a valid R1 or R2 delimiter", f_name + ) + stderr.print( + f"[red]Orientation for sample {s_name} could not be ensured. \ + Not included in metadata" + ) pass with open(sample_data_path, "w", encoding="utf-8") as fh: fh.write(json.dumps(data, indent=4, sort_keys=True, ensure_ascii=False)) @@ -340,12 +338,33 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): meta_column_list = config_json.get_topic_data( "lab_metadata", "metadata_lab_heading" ) - index_fastq_r1 = meta_column_list.index("Sequence file R1 fastq") - index_fastq_r2 = meta_column_list.index("Sequence file R2 fastq") - for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): - if row[2] is not None: + header_row = [ + idx + 1 for idx, x in enumerate(ws_metadata_lab.values) if "CAMPO" in x + ][0] + metadata_header = [x.value for x in ws_metadata_lab[header_row]] + if meta_column_list != metadata_header[1:]: + diffs = [ + x + for x in (metadata_header[1:] + meta_column_list) + if x not in meta_column_list or x not in metadata_header + ] + log.error( + "Config field metadata_lab_heading is different from .xlsx header" + ) + stderr.print( + "[red]Header in metadata file is different from config file, aborting" + ) + stderr.print("[red]Differences: ", diffs) + sys.exit(1) + index_sampleID = metadata_header.index( + "Sample ID given by originating laboratory" + ) + index_fastq_r1 = metadata_header.index("Sequence file R1 fastq") + index_fastq_r2 = metadata_header.index("Sequence file R2 fastq") + for row in islice(ws_metadata_lab.values, header_row, ws_metadata_lab.max_row): + if row[index_sampleID] is not None: try: - s_name = str(row[2]) + s_name = str(row[index_sampleID]) except ValueError as e: stderr.print("[red] Unable to convert to string. ", e) if s_name not in sample_file_list: @@ -357,11 +376,14 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): index_fastq_r1 ] else: + # import pdb; pdb.set_trace() log.error( "Fastq_R1 not defined in Metadata file for sample %s", s_name ) - stderr.print("[red] No fastq R1 file for sample " + s_name) - return False + stderr.print( + "[red] No fastq R1 file for sample " + s_name + ". Aborting" + ) + sys.exit(1) if row[index_fastq_r2] is not None: sample_file_list[s_name]["sequence_file_R2_fastq"] = row[ index_fastq_r2 @@ -391,9 +413,9 @@ def validate_metadata_file(self, fetched_folder): stderr.print("[red] Too many metadata files on " + fetched_folder) return False target_meta_file = os.path.join(fetched_folder, meta_files[0]) - temp_folder = self.metadata_tmp_folder - os.makedirs(temp_folder, exist_ok=True) - local_meta_file = os.path.join(temp_folder, os.path.basename(target_meta_file)) + out_folder = self.storage_local_folder + os.makedirs(out_folder, exist_ok=True) + local_meta_file = os.path.join(out_folder, os.path.basename(target_meta_file)) try: self.client.get( target_meta_file, @@ -412,16 +434,16 @@ def validate_metadata_file(self, fetched_folder): def validate_fetched_files(self, fetched_folder): """Check if the files in the fetched folder are the ones defined in metadata file""" local_meta_file = self.validate_metadata_file(fetched_folder) - temp_folder = self.metadata_tmp_folder + out_folder = self.storage_local_folder if not local_meta_file: - log.error("Excel file for metadata not found %s", fetched_folder) + log.error("Excel file for metadata not found in %s", fetched_folder) stderr.print( "[red] Metadata file could not be obtained from " + fetched_folder ) return False allowed_extensions = self.allowed_sample_ext samples_files_list = self.get_sample_fastq_file_names( - temp_folder, local_meta_file + out_folder, local_meta_file ) samples_files_list = sorted( sum([list(fi.values()) for _, fi in samples_files_list.items()], []) @@ -433,6 +455,7 @@ def validate_fetched_files(self, fetched_folder): if samples_files_list == filtered_files_list: log.info("Files in %s match with metadata file", fetched_folder) stderr.print("Successfully validated files based on metadata") + os.remove(local_meta_file) return True else: log.error("Files in %s do not match metadata file", fetched_folder) @@ -451,7 +474,7 @@ def validate_fetched_files(self, fetched_folder): str(mismatch_files[0:9]), ) log.error(f"List of files that mismatch: {str(mismatch_files)}") - self.delete_local_folder(temp_folder) + self.delete_local_folder(out_folder) return False def delete_remote_files(self, fetched_folder, files): @@ -550,7 +573,7 @@ def download(self): sample_file_list = self.get_sample_fastq_file_names( result_data["local_folder"], meta_file ) - self.create_tmp_files_with_metadata_info( + self.create_files_with_metadata_info( result_data["local_folder"], sample_file_list, md5_files, meta_file ) # Collect data to send the request to relecov_platform From 20bf6a5af8a5c172779975309e3443fcbd773aad Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 31 Mar 2023 14:26:16 +0200 Subject: [PATCH 1142/1454] Reestructured the code in parse_file method. +linting --- relecov_tools/long_table_parse.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index a57a630c..e5190dd8 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -44,14 +44,14 @@ def __init__(self, file_path=None, output_directory=None): if not os.path.exists(self.file_path): log.error("Variant long table file %s does not exist ", self.file_path) stderr.print( - f"[red] Variant long table file {self.file_path} does not exist" + f"[red] Variant long table file {self.file_path} does not exist" ) sys.exit(1) if not self.file_path.endswith(".csv"): log.error("Variant long table file %s is not a csv file ", self.file_path) stderr.print( - f"[red] Variant long table file {self.file_path} must be a csv file" + f"[red] Variant long table file {self.file_path} must be a csv file" ) sys.exit(1) @@ -153,9 +153,9 @@ def convert_to_json(self, samp_dict): if result_regex is None: log.error("Analysis date not found in filename, aborting") stderr.print( - f"[red]Error: filename must include analysis date in format YYYYMMDD" + "[red]Error: filename must include analysis date in format YYYYMMDD" ) - stderr.print(f"[red]e.g. variants_long_table_20220830.csv") + stderr.print("[red]e.g. variants_long_table_20220830.csv") sys.exit(1) for key, values in samp_dict.items(): j_dict = {"sample_name": key, "analysis_date": result_regex.group(1)} From 49b0f86dd8bd032a4fc5c6c6d855d0fa6a256160 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 31 Mar 2023 19:01:48 +0200 Subject: [PATCH 1143/1454] changed parse_files code to retrieve aux_dict from config --- relecov_tools/long_table_parse.py | 19 ++----------------- 1 file changed, 2 insertions(+), 17 deletions(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index e5190dd8..cdf404ea 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -93,23 +93,8 @@ def parse_file(self): for heading in self.long_table_heading: heading_index[heading] = headings_from_csv.index(heading) - aux_dict = { - "Chromosome": "CHROM", - "Variant": {"pos": "POS", "alt": "ALT", "ref": "REF"}, - "Filter": "FILTER", - "VariantInSample": { - "dp": "DP", - "ref_dp": "REF_DP", - "alt_dp": "ALT_DP", - "af": "AF", - }, - "Effect": "EFFECT", - "VariantAnnotation": { - "hgvs_c": "HGVS_C", - "hgvs_p": "HGVS_P", - "hgvs_p_1_letter": "HGVS_P_1LETTER", - }, - } + config = ConfigJson() + aux_dict = config.get_configuration("long_table_parse_aux") samp_dict = {} for line in lines[1:]: From 06895e9d9ef3141a6132e7c9a3376b741bb15470 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 31 Mar 2023 19:02:27 +0200 Subject: [PATCH 1144/1454] Introduced long_table_parse_aux dict --- relecov_tools/conf/configuration.json | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 2e8d84e1..07cc3918 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -129,6 +129,27 @@ "CALLER", "LINEAGE" ], + "long_table_parse_aux": { + "Chromosome": "CHROM", + "Variant": { + "pos": "POS", + "alt": "ALT", + "ref": "REF" + }, + "Filter": "FILTER", + "VariantInSample": { + "dp": "DP", + "ref_dp": "REF_DP", + "alt_dp": "ALT_DP", + "af": "AF" + }, + "Effect": "EFFECT", + "VariantAnnotation": { + "hgvs_c": "HGVS_C", + "hgvs_p": "HGVS_P", + "hgvs_p_1_letter": "HGVS_P_1LETTER" + } + }, "gisaid_csv_headers": [ "submitter", "covv_virus_name", From 18cce2c370e486432d0194e83688ab9bcf2d35b5 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 31 Mar 2023 19:10:06 +0200 Subject: [PATCH 1145/1454] Renamed self.storage_local_folder for platform_storage_folder --- relecov_tools/sftp_handle.py | 31 ++++++++++++++++--------------- 1 file changed, 16 insertions(+), 15 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 890fb4b5..eb87d65d 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -48,8 +48,8 @@ def __init__( if conf_file is None: self.sftp_server = config_json.get_topic_data("sftp_handle", "sftp_server") self.sftp_port = config_json.get_topic_data("sftp_handle", "sftp_port") - self.storage_local_folder = config_json.get_topic_data( - "sftp_handle", "storage_local_folder" + self.platform_storage_folder = config_json.get_topic_data( + "sftp_handle", "platform_storage_folder" ) self.abort_if_md5_mismatch = ( True @@ -71,10 +71,10 @@ def __init__( self.sftp_port = config["sftp_port"] self.target_folders = config["target_folders"] try: - self.storage_local_folder = config["storage_local_folder"] + self.platform_storage_folder = config["platform_storage_folder"] except KeyError: - self.storage_local_folder = config_json.get_topic_data( - "sftp_handle", "storage_local_folder" + self.platform_storage_folder = config_json.get_topic_data( + "sftp_handle", "platform_storage_folder" ) try: self.abort_if_md5_mismatch = ( @@ -97,7 +97,7 @@ def __init__( stderr.print("[red] Invalid configuration file {e} !") sys.exit(1) if output_location is not None: - self.storage_local_folder = output_location + self.platform_storage_folder = output_location if self.sftp_user is None: self.sftp_user = relecov_tools.utils.prompt_text(msg="Enter the user id") if self.sftp_passwd is None: @@ -182,7 +182,7 @@ def get_files_from_sftp_folder(self, folder, files_list): log.info("Creating folder %s to download files", folder) result_data = {"unable_to_fetch": [], "fetched_files": []} date = datetime.today().strftime("%Y%m%d") - local_folder_path = os.path.join(self.storage_local_folder, folder, date) + local_folder_path = os.path.join(self.platform_storage_folder, folder, date) result_data["local_folder"] = local_folder_path os.makedirs(local_folder_path, exist_ok=True) log.info("created the folder to download files %s", local_folder_path) @@ -260,7 +260,7 @@ def create_files_with_metadata_info( """Copy metadata file from folder and create a file with the sample names """ - out_folder = self.storage_local_folder + out_folder = self.platform_storage_folder os.makedirs(out_folder, exist_ok=True) prefix_file_name = "_".join(local_folder.split("/")[-2:]) new_metadata_file = "metadata_lab_" + prefix_file_name + ".xlsx" @@ -305,7 +305,7 @@ def create_files_with_metadata_info( def create_main_folders(self, root_directory_list): """Create the main folder structure if not exists""" for folder in root_directory_list: - full_folder = os.path.join(self.storage_local_folder, folder) + full_folder = os.path.join(self.platform_storage_folder, folder) os.makedirs(full_folder, exist_ok=True) log.info("Created main folder for process %s", full_folder) return True @@ -413,9 +413,10 @@ def validate_metadata_file(self, fetched_folder): stderr.print("[red] Too many metadata files on " + fetched_folder) return False target_meta_file = os.path.join(fetched_folder, meta_files[0]) - out_folder = self.storage_local_folder - os.makedirs(out_folder, exist_ok=True) - local_meta_file = os.path.join(out_folder, os.path.basename(target_meta_file)) + os.makedirs(self.platform_storage_folder, exist_ok=True) + local_meta_file = os.path.join( + self.platform_storage_folder, os.path.basename(target_meta_file) + ) try: self.client.get( target_meta_file, @@ -434,7 +435,7 @@ def validate_metadata_file(self, fetched_folder): def validate_fetched_files(self, fetched_folder): """Check if the files in the fetched folder are the ones defined in metadata file""" local_meta_file = self.validate_metadata_file(fetched_folder) - out_folder = self.storage_local_folder + out_folder = self.platform_storage_folder if not local_meta_file: log.error("Excel file for metadata not found in %s", fetched_folder) stderr.print( @@ -503,11 +504,11 @@ def delete_local_folder(self, local_folder): def download(self): try: - os.makedirs(self.storage_local_folder, exist_ok=True) + os.makedirs(self.platform_storage_folder, exist_ok=True) except OSError as e: log.error("You do not have permissions to create folder %s", e) sys.exit(1) - os.chdir(self.storage_local_folder) + os.chdir(self.platform_storage_folder) if not self.open_connection(): log.error("Unable to establish connection towards sftp server") stderr.print("[red] Unable to establish sftp connection") From 9b564aaf5b69a12da445be32f7c426b5083d4be0 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 11 Apr 2023 17:59:04 +0200 Subject: [PATCH 1146/1454] Changed the print message of an error --- relecov_tools/rest_api.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/rest_api.py b/relecov_tools/rest_api.py index d1fb45ee..6ee1879e 100644 --- a/relecov_tools/rest_api.py +++ b/relecov_tools/rest_api.py @@ -68,7 +68,7 @@ def put_request(self, data, credentials, url): req.status_code, ) if req.status_code != 500: - stderr.print(f"[red] Unable to post data because {req.text}") + stderr.print(f"[red] Unable to put data because {req.text}") stderr.print(f"[red] Received error {req.status_code}") return {"ERROR": req.status_code} return {"Success": req.text} From 35a4f75b1ca5ea0a6af51950fa04ab001ed12a9e Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 11 Apr 2023 18:00:08 +0200 Subject: [PATCH 1147/1454] Removed a commented line with no purpose --- relecov_tools/sftp_handle.py | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index eb87d65d..cb8aede8 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -376,7 +376,6 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): index_fastq_r1 ] else: - # import pdb; pdb.set_trace() log.error( "Fastq_R1 not defined in Metadata file for sample %s", s_name ) From cf7e26f37ccd07a258a22b253e34a23253389ccf Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 11 Apr 2023 18:07:18 +0200 Subject: [PATCH 1148/1454] Fixed a missing field in map_iskylims_ function --- relecov_tools/feed_database.py | 24 ++++++++++-------------- 1 file changed, 10 insertions(+), 14 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 3c359902..2d1d7c33 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -95,7 +95,6 @@ def map_iskylims_sample_fields_values(self, sample_fields, s_project_fields): """Map the values to the properties send to databasee in json schema based on label """ - # collection_method = self.get_sample_type() sample_list = [] s_fields = list(sample_fields.keys()) for row in self.json_data: @@ -107,17 +106,17 @@ def map_iskylims_sample_fields_values(self, sample_fields, s_project_fields): value = found_ontology.group(1) if key in s_project_fields: s_dict[key] = value - elif key in s_fields: + if key in s_fields: s_dict[sample_fields[key]] = value - else: - # just for debug loginng write the fields that will not - # be inlcuded in iSkyLIMS request + if key not in s_project_fields and key not in s_fields: + # just for debugging, write the fields that will not + # be included in iSkyLIMS request log.info("not key %s in iSkyLIMS", key) - # include the fix value + # include the fixed value fixed_value = self.config_json.get_configuration("iskylims_fixed_values") for prop, val in fixed_value.items(): s_dict[prop] = val - # Adding tha specimen_source field for setting sampleType + # Adding tha specimen_source field to set sampleType s_dict["sampleType"] = row["specimen_source"] sample_list.append(s_dict) return sample_list @@ -154,15 +153,14 @@ def get_iskylims_fields_sample(self): if "ontology" in values: try: property = ontology_dict[values["ontology"]] - # sample_fields has a key the label in metadata and value - # the field name for sample + # sample_fields has a key, the label in metadata, and as value + # the field name for the sample sample_fields[property] = values["field_name"] except KeyError as e: stderr.print(f"[red]Error in map ontology {e}") else: - # for the ones that do no have ontologuy label is the sample field - # and the value is empty - # sample_fields[key] = "" + # for the ones that do not have ontology label in the sample field + # and have an empty value: sample_fields[key] = "" log.info("not ontology for item %s", values["field_name"]) # fetch label for sample Project s_project_url = self.database_settings["url_project_fields"] @@ -182,7 +180,6 @@ def get_iskylims_fields_sample(self): sys.exit(1) for field in s_project_fields_raw["DATA"]: s_project_fields.append(field["sampleProjectFieldName"]) - return [sample_fields, s_project_fields] def map_relecov_sample_data(self): @@ -222,7 +219,6 @@ def update_database(self, field_values, post_url): {"user": self.user, "pass": self.passwd}, self.database_settings[post_url], ) - if "ERROR" in result: if result["ERROR"] == "Server not available": # retry to connect to server From 175713028dadded06ad8655722a12bf6b20793a1 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 11 Apr 2023 18:08:38 +0200 Subject: [PATCH 1149/1454] Included read_length field and fixed a missing underscore --- relecov_tools/conf/configuration.json | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 07cc3918..28ab7f1c 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -316,7 +316,7 @@ "lineage_analysis_constellation_version": "constellation_version" }, "mapping_stats": { - "analysis_date": "analysis date", + "analysis_date": "analysis_date", "depth_of_coverage_value": "medianDPcoveragevirus", "number_of_variants_in_consensus": "Variantsinconsensusx10", "number_of_variants_with_effect": "MissenseVariants", @@ -326,7 +326,8 @@ "per_reads_virus": "%readsvirus", "per_unmapped": "%unmapedreads", "qc_filtered": "totalreads", - "reference_genome_accession": "Virussequence" + "reference_genome_accession": "Virussequence", + "read_length": "read_length" }, "mapping_variant_metrics": { "ns_per_100_kbp": "# Ns per 100kb consensus" @@ -344,9 +345,6 @@ "mapping_software_version": { "BOWTIE2_ALIGN": "bowtie2" }, - "mapping_software_version": { - "BOWTIE2_ALIGN": "bowtie2" - }, "preprocessing_software_version": { "FASTP": "fastp" }, From b178b8fc8cbcb167acd3c9dbfc30c7a76ae12fa6 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 11 Apr 2023 18:09:06 +0200 Subject: [PATCH 1150/1454] Changed a few comments --- relecov_tools/long_table_parse.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index cdf404ea..1a0d1e24 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -149,9 +149,7 @@ def convert_to_json(self, samp_dict): return j_list def save_to_file(self, j_list): - """Transform the parsed data into a jsonf file, naming as - "long_table_" + "current date" + ".json" - """ + """Transform the parsed data into a json file""" stderr.print("[blue]Saving parsed data to file") date_now = datetime.now().strftime("%Y_%m_%d_%H_%M_%S") file_name = "long_table_" + date_now + ".json" @@ -163,7 +161,7 @@ def save_to_file(self, j_list): def parsing_csv(self): """ - function called when using the relecov-tools long-table-parse function. + Function called when using the relecov-tools long-table-parse function. """ stderr.print("[blue]Starting reading the input file") parsed_data = self.parse_file() From 06d7794fe2c80c071edb49b9a93f28e77c27a003 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 13 Apr 2023 16:03:49 +0200 Subject: [PATCH 1151/1454] Included new fields into laboratory_address.json --- relecov_tools/conf/laboratory_address.json | 56 ++++++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 0f2ea6d3..079b75ce 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -10,6 +10,62 @@ "submitting_institution_address": "Crta. Pozuelo Majadahonda S/N,", "submitting_institution_email": "info@isciii.es" }, + "Complejo Hospitalario de Jaen":{ + "collecting_institution_address": "Avda. del Ejército Español nº10", + "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Jaen", + "geo_loc_city": "Jaen", + "geo_loc_country": "Spain", + "submitting_institution": "Complejo Hospitalario de Jaen", + "submitting_institution_address": "Avda. del Ejército Español nº10", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" + + }, + "Hospital de Poniente":{ + "collecting_institution_address": "Ctra Almerimar, 31", + "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Almeria", + "geo_loc_city": "El Ejido", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital de Poniente", + "submitting_institution_address": "Ctra Almerimar, 31", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" + }, + "Hospital Juan Ramon Jimenez":{ + "collecting_institution_address": "Ronda Norte, s/n", + "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Huelva", + "geo_loc_city": "Huelva", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Juan Ramon Jimenez", + "submitting_institution_address": "Ronda Norte, s/n", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" + }, + "Hospital Reina Sofia":{ + "collecting_institution_address": "Av. Menendez Pidal, s/n", + "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Cordoba", + "geo_loc_city": "Cordoba", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Reina Sofia", + "submitting_institution_address": "Av. Menendez Pidal, s/n", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" + }, + "Plataforma de Medicina Computacional, Fundación Progreso y Salud"{ + "collecting_institution_address": "Avda. Américo Vespucio, 15", + "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Sevilla", + "geo_loc_city": "Sevilla", + "geo_loc_country": "Spain", + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" + }, "Hospital Puerta del Mar": { "collecting_institution_address": "Av. Ana de Viya, 21", "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", From 4f763a4f9d9264c62dfdc15c793e4dd12426413a Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 13 Apr 2023 16:08:05 +0200 Subject: [PATCH 1152/1454] Included a new field --- relecov_tools/conf/geo_loc_cities.json | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/relecov_tools/conf/geo_loc_cities.json b/relecov_tools/conf/geo_loc_cities.json index 7678c393..5a4b1795 100644 --- a/relecov_tools/conf/geo_loc_cities.json +++ b/relecov_tools/conf/geo_loc_cities.json @@ -314,5 +314,9 @@ "Almeria": { "geo_loc_latitude": "36.72016", "geo_loc_longitude": "-4.42034" + }, + "El Ejido": { + "geo_loc_latitude": "36.772153", + "geo_loc_longitude": "-2.810602" } } From 8e93cc81a1471ba0841821934ce2d290407204ae Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 17 Apr 2023 09:54:58 +0200 Subject: [PATCH 1153/1454] Introduced new argument download_option in download function --- relecov_tools/__main__.py | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 8d4c09e4..605a1205 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -141,6 +141,16 @@ def relecov_tools_cli(verbose, log_file): "--conf_file", help="Configuration file (not params file)", ) +@click.option( + "-d", + "--download_option", + default=None, + multiple=False, + help="Select the download option: [download_only, download_clean, delete_only]. \ + download_only will only download the files \ + download_clean will remove files from sftp after download \ + delete_only will only delete the files", +) @click.option( "-o", "--output_location", @@ -153,7 +163,7 @@ def relecov_tools_cli(verbose, log_file): is_flag=False, flag_value="ALL", default=None, - help="Flag: Select which folders will be downloaded giving [paths] or via prompt", + help="Flag: Select which folders will be targeted giving [paths] or via prompt", ) def download( user, @@ -161,8 +171,9 @@ def download( conf_file, user_relecov, password_relecov, + download_option, output_location, - target_folders, + target_folders ): """Download files located in sftp server.""" sftp_connection = relecov_tools.sftp_handle.SftpHandle( @@ -171,11 +182,11 @@ def download( conf_file, user_relecov, password_relecov, + download_option, output_location, - target_folders, + target_folders ) - sftp_connection.download() - + sftp_connection.execute_process() # metadata @relecov_tools_cli.command(help_priority=3) From 746a47bc0bba7647f832ba8a9a3c058e166a51df Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 17 Apr 2023 09:55:28 +0200 Subject: [PATCH 1154/1454] Introduced allowed_download_options field in sftp_handle --- relecov_tools/conf/configuration.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 28ab7f1c..5b0e9565 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -218,6 +218,11 @@ "_2_", "_2.", ".2." + ], + "allowed_download_options": [ + "download_only", + "download_clean", + "delete_only" ] }, "GISAID_configuration": { From a871ccff70b6fe93a1883d3b2745cded6f825d03 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 17 Apr 2023 09:56:27 +0200 Subject: [PATCH 1155/1454] Included new functions to manage download/clean process --- relecov_tools/sftp_handle.py | 104 ++++++++++++++++++++++++----------- 1 file changed, 71 insertions(+), 33 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index cb8aede8..75b549bb 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -34,6 +34,7 @@ def __init__( conf_file=None, user_relecov=None, password_relecov=None, + download_option=None, output_location=None, target_folders=None, ): @@ -45,6 +46,15 @@ def __init__( self.sftp_user = user self.sftp_passwd = passwd self.target_folders = target_folders + self.allowed_download_options = config_json.get_topic_data( + "sftp_handle", "allowed_download_options" + ) + if download_option not in self.allowed_download_options: + self.download_option = relecov_tools.utils.prompt_selection( + "Options", self.allowed_download_options + ) + else: + self.download_option = download_option if conf_file is None: self.sftp_server = config_json.get_topic_data("sftp_handle", "sftp_server") self.sftp_port = config_json.get_topic_data("sftp_handle", "sftp_port") @@ -94,10 +104,15 @@ def __init__( self.pp = config["allowed_sample_extensions"] except KeyError as e: log.error("Invalid configuration file %s", e) - stderr.print("[red] Invalid configuration file {e} !") - sys.exit(1) + stderr.print(f"[red] Invalid configuration file {e} !") + sys.exit(1) if output_location is not None: - self.platform_storage_folder = output_location + if os.path.isdir(output_location): + self.platform_storage_folder = output_location + else: + log.error("Output location does not exist, aborting") + stderr.print("[red] Output location does not exist, aborting") + sys.exit(1) if self.sftp_user is None: self.sftp_user = relecov_tools.utils.prompt_text(msg="Enter the user id") if self.sftp_passwd is None: @@ -434,13 +449,9 @@ def validate_metadata_file(self, fetched_folder): def validate_fetched_files(self, fetched_folder): """Check if the files in the fetched folder are the ones defined in metadata file""" local_meta_file = self.validate_metadata_file(fetched_folder) - out_folder = self.platform_storage_folder if not local_meta_file: - log.error("Excel file for metadata not found in %s", fetched_folder) - stderr.print( - "[red] Metadata file could not be obtained from " + fetched_folder - ) return False + out_folder = self.platform_storage_folder allowed_extensions = self.allowed_sample_ext samples_files_list = self.get_sample_fastq_file_names( out_folder, local_meta_file @@ -469,11 +480,11 @@ def validate_fetched_files(self, fetched_folder): if len(mismatch_files) < 10: stderr.print(f"Files that mismatch: {str(mismatch_files)}") else: - stderr.print( + log.error( "Showing some of the mismatches, use --log-file to see all of them: %s", str(mismatch_files[0:9]), ) - log.error(f"List of files that mismatch: {str(mismatch_files)}") + log.info(f"Full list of files that mismatch: {str(mismatch_files)}") self.delete_local_folder(out_folder) return False @@ -483,8 +494,10 @@ def delete_remote_files(self, fetched_folder, files): for file in files: try: self.client.remove(os.path.join(fetched_folder, os.path.basename(file))) - log.info("%s Deleted from remote server", file) - except FileNotFoundError: + stderr.print("%s Deleted from remote server", file) + except Exception as e: + log.error("Could not delete file %s.", e) + stderr.print(f"Could not delete file {file}. Error: {e}") continue return @@ -501,25 +514,12 @@ def delete_local_folder(self, local_folder): shutil.rmtree(local_folder, ignore_errors=True) return True - def download(self): - try: - os.makedirs(self.platform_storage_folder, exist_ok=True) - except OSError as e: - log.error("You do not have permissions to create folder %s", e) - sys.exit(1) - os.chdir(self.platform_storage_folder) - if not self.open_connection(): - log.error("Unable to establish connection towards sftp server") - stderr.print("[red] Unable to establish sftp connection") - sys.exit(1) + def select_target_folders(self): root_directory_list = self.list_folders(".") - if not root_directory_list: - log.error("There are no folders under root directory") - sys.exit(1) if self.target_folders == "ALL": log.info("Showing folders from remote SFTP for user selection") target_folders = relecov_tools.utils.prompt_checkbox( - msg="Select the folders that will be downloaded", + msg="Select the folders that will be targeted", choices=sorted(root_directory_list), ) elif self.target_folders is None: @@ -531,23 +531,45 @@ def download(self): if not target_folders: log.error("There are no folders that match selection") sys.exit(1) - folders_to_download = {} + folders_to_process = {} # create_main_folders(root_directory_list) for folder in target_folders: list_files = self.get_file_list(folder) if len(list_files) > 0: - folders_to_download[folder] = list_files - if len(folders_to_download) == 0: - log.info("Exiting download.") - log.error("There are no files on sftp to dowload") + folders_to_process[folder] = list_files + else: + log.info("%s is empty") + continue + if len(folders_to_process) == 0: + log.info("Exiting process.") + log.error("There are no files in the selected folders") self.close_connection() sys.exit(0) + return folders_to_process + + def delete_targets(self, target_folders): + log.info("Initiating delete_only process") + folders_to_delete = target_folders + for folder, files in folders_to_delete.items(): + self.delete_remote_files(folder, files) + stderr.print(f"Delete process finished in {folder}") + def download(self, target_folders, option="download"): + log.info("Initiating download process") + try: + os.makedirs(self.platform_storage_folder, exist_ok=True) + except OSError as e: + log.error("You do not have permissions to create folder %s", e) + sys.exit(1) + os.chdir(self.platform_storage_folder) + folders_to_download = target_folders for folder, files in folders_to_download.items(): log.info("Processing folder %s", folder) stderr.print("Processing folder " + folder) # Validate that the files are the ones described in metadata. if not self.validate_fetched_files(folder): + log.error("Failed fetched files validation %s", folder) + stderr.print(f"[red]Invalid fetched files in {folder}, aborting") continue # get the files in each folder result_data = self.get_files_from_sftp_folder(folder, files) @@ -582,5 +604,21 @@ def download(self): ) for record in json_sample_data: pass - self.close_connection() + if option == "clean": + self.delete_targets(folder) return + + def execute_process(self): + if not self.open_connection(): + log.error("Unable to establish connection towards sftp server") + stderr.print("[red] Unable to establish sftp connection") + sys.exit(1) + target_folders = self.select_target_folders() + if self.download_option == "download_only": + self.download(target_folders, option="download") + if self.download_option == "download_clean": + self.download(target_folders, option="clean") + if self.download_option == "delete_only": + self.delete_targets(target_folders) + self.close_connection() + stderr.print("Finished execution") From 306e7146bde5ad19bc83541c343a21182c59b582 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 17 Apr 2023 10:08:19 +0200 Subject: [PATCH 1156/1454] Included new functions to manage download/clean process, linting --- relecov_tools/sftp_handle.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 75b549bb..bce940ca 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -105,7 +105,7 @@ def __init__( except KeyError as e: log.error("Invalid configuration file %s", e) stderr.print(f"[red] Invalid configuration file {e} !") - sys.exit(1) + sys.exit(1) if output_location is not None: if os.path.isdir(output_location): self.platform_storage_folder = output_location @@ -536,7 +536,7 @@ def select_target_folders(self): for folder in target_folders: list_files = self.get_file_list(folder) if len(list_files) > 0: - folders_to_process[folder] = list_files + folders_to_process[folder] = list_files else: log.info("%s is empty") continue @@ -546,7 +546,7 @@ def select_target_folders(self): self.close_connection() sys.exit(0) return folders_to_process - + def delete_targets(self, target_folders): log.info("Initiating delete_only process") folders_to_delete = target_folders @@ -604,10 +604,10 @@ def download(self, target_folders, option="download"): ) for record in json_sample_data: pass - if option == "clean": + if option == "clean": self.delete_targets(folder) return - + def execute_process(self): if not self.open_connection(): log.error("Unable to establish connection towards sftp server") From ec256c966abce5ab10246af8b0f6c60c28bfd198 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 17 Apr 2023 10:10:44 +0200 Subject: [PATCH 1157/1454] Included new functions to manage download/clean process, linting --- relecov_tools/__main__.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 605a1205..9bc23158 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -188,6 +188,7 @@ def download( ) sftp_connection.execute_process() + # metadata @relecov_tools_cli.command(help_priority=3) @click.option( From d17705a3d37f5f23795138e639a95e49ca8ab9a1 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 17 Apr 2023 10:14:37 +0200 Subject: [PATCH 1158/1454] Included new functions to manage download/clean process, linting2 --- relecov_tools/__main__.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 9bc23158..1a0d0736 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -173,7 +173,7 @@ def download( password_relecov, download_option, output_location, - target_folders + target_folders, ): """Download files located in sftp server.""" sftp_connection = relecov_tools.sftp_handle.SftpHandle( @@ -184,7 +184,7 @@ def download( password_relecov, download_option, output_location, - target_folders + target_folders, ) sftp_connection.execute_process() From 31185fd11cb1c6a1921b3674f8e56724ba624816 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 26 Apr 2023 12:54:55 +0200 Subject: [PATCH 1159/1454] included new fields in geo_loc_cities.json --- relecov_tools/conf/geo_loc_cities.json | 36 ++++++++++++++++---------- 1 file changed, 22 insertions(+), 14 deletions(-) diff --git a/relecov_tools/conf/geo_loc_cities.json b/relecov_tools/conf/geo_loc_cities.json index 5a4b1795..75ec4ca8 100644 --- a/relecov_tools/conf/geo_loc_cities.json +++ b/relecov_tools/conf/geo_loc_cities.json @@ -11,7 +11,7 @@ "geo_loc_latitude": "37.3900", "geo_loc_longitude": "-5.9900" }, - "Málaga": { + "Malaga": { "geo_loc_latitude": "36.7194", "geo_loc_longitude": "-4.4200" }, @@ -139,7 +139,7 @@ "geo_loc_latitude": "41.1187", "geo_loc_longitude": "1.2453" }, - "Cádiz": { + "Cadiz": { "geo_loc_latitude": "36.5350", "geo_loc_longitude": "-6.2975" }, @@ -215,10 +215,6 @@ "geo_loc_latitude": "41.7667", "geo_loc_longitude": "-2.4667" }, - "Caceres": { - "geo_loc_latitude": "39.4752671", - "geo_loc_longitude": "-6.3722951" - }, "Pontevedra": { "geo_loc_latitude": "42.4333", "geo_loc_longitude": "-8.6333" @@ -295,10 +291,6 @@ "geo_loc_latitude": "38.2669", "geo_loc_longitude": "-0.6983" }, - "Cadiz": { - "geo_loc_latitude": "36.52672", - "geo_loc_longitude": "-6.2891" - }, "Gasteiz": { "geo_loc_latitude": "42.85", "geo_loc_longitude": "-2.6667" @@ -307,10 +299,6 @@ "geo_loc_latitude": "36.51543", "geo_loc_longitude": "-4.88583" }, - "Malaga": { - "geo_loc_latitude": "36.72016", - "geo_loc_longitude": "-4.42034" - }, "Almeria": { "geo_loc_latitude": "36.72016", "geo_loc_longitude": "-4.42034" @@ -318,5 +306,25 @@ "El Ejido": { "geo_loc_latitude": "36.772153", "geo_loc_longitude": "-2.810602" + }, + "Antequera": { + "geo_loc_latitude": "37.030842", + "geo_loc_longitude": "-4.528663" + }, + "Huercal-Overa":{ + "geo_loc_latitude": "37.395605", + "geo_loc_longitude": "-1.942236" + }, + "Ronda":{ + "geo_loc_latitude": "36.745518", + "geo_loc_longitude": "-5.163095" + }, + "Velez-Malaga":{ + "geo_loc_latitude": "36.778904", + "geo_loc_longitude": "-4.100808" + }, + "Motril":{ + "geo_loc_latitude": "36.74611111", + "geo_loc_longitude": "-3.515" } } From 814d797a4d4d85e3b368f21b547c5a3903187306 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 26 Apr 2023 12:55:17 +0200 Subject: [PATCH 1160/1454] included new fields in laboratory_address.json --- relecov_tools/conf/laboratory_address.json | 153 ++++++++++++++++----- 1 file changed, 115 insertions(+), 38 deletions(-) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 079b75ce..94083a20 100644 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -10,6 +10,84 @@ "submitting_institution_address": "Crta. Pozuelo Majadahonda S/N,", "submitting_institution_email": "info@isciii.es" }, + "Hospital de Antequera":{ + "collecting_institution_address": "Avenida Poeta Muñoz Rojas, s/n", + "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Malaga", + "geo_loc_city": "Antequera", + "geo_loc_country": "Spain", + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" + }, + "Hospital La Inmaculada - Huércal Overa":{ + "collecting_institution_address": "Av. de la Dra. Ana Parra, s/n", + "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Almeria", + "geo_loc_city": "Huercal-Overa", + "geo_loc_country": "Spain", + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" + + }, + "Hospital de la Serranía":{ + "collecting_institution_address": "Calle San Pedro, Km 2", + "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Malaga", + "geo_loc_city": "Ronda", + "geo_loc_country": "Spain", + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" + }, + "Hospital La Axarquía":{ + "collecting_institution_address": "Av. del Sol, 43", + "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Malaga", + "geo_loc_city": "Velez-Malaga", + "geo_loc_country": "Spain", + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" + }, + "Hospital Santa Ana":{ + "collecting_institution_address": "Av. Enrique Martín Cuevas, s/n", + "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Granada", + "geo_loc_city": "Motril", + "geo_loc_country": "Spain", + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" + }, + "Hospital Regional Universitario de Malaga":{ + "collecting_institution_address": "Av. de Carlos Haya, 84", + "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Malaga", + "geo_loc_city": "Malaga", + "geo_loc_country": "Spain", + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" + }, + "Hospital Virgen de las Nieves":{ + "collecting_institution_address": "Av. de las Fuerzas Armadas, 2", + "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Granada", + "geo_loc_city": "Granada", + "geo_loc_country": "Spain", + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" + }, "Complejo Hospitalario de Jaen":{ "collecting_institution_address": "Avda. del Ejército Español nº10", "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", @@ -17,10 +95,9 @@ "geo_loc_region": "Jaen", "geo_loc_city": "Jaen", "geo_loc_country": "Spain", - "submitting_institution": "Complejo Hospitalario de Jaen", - "submitting_institution_address": "Avda. del Ejército Español nº10", + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" - }, "Hospital de Poniente":{ "collecting_institution_address": "Ctra Almerimar, 31", @@ -29,8 +106,8 @@ "geo_loc_region": "Almeria", "geo_loc_city": "El Ejido", "geo_loc_country": "Spain", - "submitting_institution": "Hospital de Poniente", - "submitting_institution_address": "Ctra Almerimar, 31", + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" }, "Hospital Juan Ramon Jimenez":{ @@ -40,8 +117,8 @@ "geo_loc_region": "Huelva", "geo_loc_city": "Huelva", "geo_loc_country": "Spain", - "submitting_institution": "Hospital Juan Ramon Jimenez", - "submitting_institution_address": "Ronda Norte, s/n", + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" }, "Hospital Reina Sofia":{ @@ -51,11 +128,11 @@ "geo_loc_region": "Cordoba", "geo_loc_city": "Cordoba", "geo_loc_country": "Spain", - "submitting_institution": "Hospital Reina Sofia", - "submitting_institution_address": "Av. Menendez Pidal, s/n", + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" }, - "Plataforma de Medicina Computacional, Fundación Progreso y Salud"{ + "Plataforma de Medicina Computacional, Fundación Progreso y Salud":{ "collecting_institution_address": "Avda. Américo Vespucio, 15", "collecting_institution_email": "joaquin.dopazo@juntadeandalucia.es", "geo_loc_state": "Andalucia", @@ -63,7 +140,7 @@ "geo_loc_city": "Sevilla", "geo_loc_country": "Spain", "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", - "submitting_institution_address": "Avda. Américo Vespucio, 15", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" }, "Hospital Puerta del Mar": { @@ -73,8 +150,8 @@ "geo_loc_region": "Cadiz", "geo_loc_city": "Cadiz", "geo_loc_country": "Spain", - "submitting_institution": "Hospital Puerta del Mar", - "submitting_institution_address": "Av. Ana de Viya, 21", + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" }, "Hospital Costa del Sol": { @@ -84,8 +161,8 @@ "geo_loc_region": "Malaga", "geo_loc_city": "Marbella", "geo_loc_country": "Spain", - "submitting_institution": "Hospital Costa del Sol", - "submitting_institution_address": "A-7, Km 187", + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" }, "Hospital Virgen de la Victoria": { @@ -95,8 +172,8 @@ "geo_loc_region": "Malaga", "geo_loc_city": "Malaga", "geo_loc_country": "Spain", - "submitting_institution": "Hospital Virgen de la Victoria", - "submitting_institution_address": "Campus de Teatinos, S/N", + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" }, "Complejo Hospitalario Torrecardenas": { @@ -106,8 +183,8 @@ "geo_loc_region": "Almeria", "geo_loc_city": "Almeria", "geo_loc_country": "Spain", - "submitting_institution": "Complejo Hospitalario Torrecardenas", - "submitting_institution_address": "C. Hermandad de Donantes de Sangre, s/n", + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" }, "Hospital Universitario San Cecilio": { @@ -117,9 +194,9 @@ "geo_loc_region": "Granada", "geo_loc_city": "Granada", "geo_loc_country": "Spain", - "submitting_institution": "Hospital Universitario San Cecilio", - "submitting_institution_address": "Av. del Conocimiento S/N", - "submitting_institution_email": "fegarcia@ugr.es" + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" }, "Microbiología HUC San Cecilio": { "collecting_institution_address": "Av. del Conocimiento S/N", @@ -128,9 +205,9 @@ "geo_loc_region": "Granada", "geo_loc_city": "Granada", "geo_loc_country": "Spain", - "submitting_institution": "Microbiología HUC San Cecilio", - "submitting_institution_address": "Av. del Conocimiento S/N", - "submitting_institution_email": "fegarcia@ugr.es" + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" }, "Microbiología. Hospital Universitario Virgen del Rocio": { "collecting_institution_address": "Avenida Manuel Siurot s/n", @@ -139,9 +216,9 @@ "geo_loc_region": "Sevilla", "geo_loc_city": "Sevilla", "geo_loc_country": "Spain", - "submitting_institution": "Microbiología. Hospital Universitario Virgen del Rocio", - "submitting_institution_address": "Avenida Manuel Siurot s/n", - "submitting_institution_email": "josea.lepe.sspa@juntadeandalucia.es" + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" }, "Hospital Universitario Virgen del Rocio": { "collecting_institution_address": "Avenida Manuel Siurot s/n", @@ -150,9 +227,9 @@ "geo_loc_region": "Sevilla", "geo_loc_city": "Sevilla", "geo_loc_country": "Spain", - "submitting_institution": "Hospital Universitario Virgen del Rocio", - "submitting_institution_address": "Avenida Manuel Siurot s/n", - "submitting_institution_email": "josea.lepe.sspa@juntadeandalucia.es" + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" }, "Hospital Clínico Universitario Lozano Blesa": { "collecting_institution_address": "S. Juan Bosco, 15", @@ -298,25 +375,25 @@ "submitting_institution_email": "" }, "Hospital General La Mancha Centro": { - "collecting_institution_address": "Av. Constitución, 3, Alcázar de San Juan", + "collecting_institution_address": "Av. Constitución, 3, Alcazar de San Juan", "collecting_institution_email": "", "geo_loc_state": "Castilla-La Mancha", "geo_loc_region": "Ciudad Real", - "geo_loc_city": "Alcázar de San Juan", + "geo_loc_city": "Alcazar de San Juan", "geo_loc_country": "Spain", "submitting_institution": "Hospital General La Mancha Centro", - "submitting_institution_address": "Av. Constitución, 3, Alcázar de San Juan", + "submitting_institution_address": "Av. Constitución, 3, Alcazar de San Juan", "submitting_institution_email": "" }, "Hospital Virgen de Altagracia": { - "collecting_institution_address": "Avda. D. Emiliano García Roldán, s/n, Manzanares,", + "collecting_institution_address": "Avda. D. Emiliano García Roldan, s/n, Manzanares,", "collecting_institution_email": "", "geo_loc_state": "Castilla-La Mancha", "geo_loc_region": "Ciudad Real", "geo_loc_city": "Manzanares", "geo_loc_country": "Spain", "submitting_institution": "Hospital Virgen de Altagracia", - "submitting_institution_address": "Avda. D. Emiliano García Roldán, s/n, Manzanares,", + "submitting_institution_address": "Avda. D. Emiliano García Roldan, s/n, Manzanares,", "submitting_institution_email": "" }, "Hospital General de Valdepeñas": { @@ -330,14 +407,14 @@ "submitting_institution_address": "Av. de los Estudiantes, s/n, Valdepeñas", "submitting_institution_email": "" }, - "Hospital Público Santa Bárbara": { + "Hospital Público Santa Barbara": { "collecting_institution_address": "C. Malagón s/n", "collecting_institution_email": "", "geo_loc_state": "Castilla-La Mancha", "geo_loc_region": "Ciudad Real", "geo_loc_city": "Puertollano", "geo_loc_country": "Spain", - "submitting_institution": "Hospital Público Santa Bárbara", + "submitting_institution": "Hospital Público Santa Barbara", "submitting_institution_address": "C. Malagón s/n", "submitting_institution_email": "" }, From 2eff7a5364f6778f5e3535285a24e355954c7c31 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 26 Apr 2023 12:57:58 +0200 Subject: [PATCH 1161/1454] changed local path setting to avoid deletion of existing folders --- relecov_tools/sftp_handle.py | 78 +++++++++++++++++------------------- 1 file changed, 36 insertions(+), 42 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index bce940ca..09c9b8ea 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -197,7 +197,10 @@ def get_files_from_sftp_folder(self, folder, files_list): log.info("Creating folder %s to download files", folder) result_data = {"unable_to_fetch": [], "fetched_files": []} date = datetime.today().strftime("%Y%m%d") - local_folder_path = os.path.join(self.platform_storage_folder, folder, date) + if self.platform_storage_folder == folder: + local_folder_path = os.path.join(self.platform_storage_folder, date) + else: + local_folder_path = os.path.join(self.platform_storage_folder, folder, date) result_data["local_folder"] = local_folder_path os.makedirs(local_folder_path, exist_ok=True) log.info("created the folder to download files %s", local_folder_path) @@ -224,6 +227,7 @@ def verify_md5_checksum(self, local_folder, file_list): successful_files = [] # fetch the md5 file if exists log.info("Searching for local md5 file") + stderr.print("[blue]Verifying file integrity in md5 hashes") sftp_md5 = relecov_tools.utils.get_md5_from_local_folder(local_folder) if len(sftp_md5) > 0: # check md5 checksum for eac file @@ -241,7 +245,6 @@ def verify_md5_checksum(self, local_folder, file_list): else: required_retransmition.append(f_name) log.error("%s requested file re-sending", f_name) - if len(set(file_list)) != len(sftp_md5) * 2: # create the md5 file from the ones not upload to server req_create_md5 = [ @@ -317,14 +320,6 @@ def create_files_with_metadata_info( ) return True - def create_main_folders(self, root_directory_list): - """Create the main folder structure if not exists""" - for folder in root_directory_list: - full_folder = os.path.join(self.platform_storage_folder, folder) - os.makedirs(full_folder, exist_ok=True) - log.info("Created main folder for process %s", full_folder) - return True - def find_metadata_file(self, local_folder): """Find excel extension file which contains metatada""" reg_for_xlsx = os.path.join(local_folder, "*.xlsx") @@ -372,7 +367,7 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): stderr.print("[red]Differences: ", diffs) sys.exit(1) index_sampleID = metadata_header.index( - "Sample ID given by originating laboratory" + "Sample ID given by the submitting laboratory" ) index_fastq_r1 = metadata_header.index("Sequence file R1 fastq") index_fastq_r2 = metadata_header.index("Sequence file R2 fastq") @@ -477,24 +472,24 @@ def validate_fetched_files(self, fetched_folder): ) set_list = set(filtered_files_list) mismatch_files = [fi for fi in samples_files_list if fi not in set_list] - if len(mismatch_files) < 10: - stderr.print(f"Files that mismatch: {str(mismatch_files)}") - else: - log.error( - "Showing some of the mismatches, use --log-file to see all of them: %s", - str(mismatch_files[0:9]), - ) - log.info(f"Full list of files that mismatch: {str(mismatch_files)}") - self.delete_local_folder(out_folder) + mismatch_rev = [fi for fi in set_list if fi not in samples_files_list] + log.error( + "Files in metadata that are not present in folder: %s", + str(mismatch_files), + ) + log.error( + "Files in folder that are not present in metadata %s", str(mismatch_rev) + ) return False def delete_remote_files(self, fetched_folder, files): """Delete files from remote server""" self.open_connection() + stderr.print(f"[blue]Deleting files in {fetched_folder}...") for file in files: try: self.client.remove(os.path.join(fetched_folder, os.path.basename(file))) - stderr.print("%s Deleted from remote server", file) + log.info("%s Deleted from remote server", file) except Exception as e: log.error("Could not delete file %s.", e) stderr.print(f"Could not delete file {file}. Error: {e}") @@ -532,28 +527,20 @@ def select_target_folders(self): log.error("There are no folders that match selection") sys.exit(1) folders_to_process = {} - # create_main_folders(root_directory_list) for folder in target_folders: list_files = self.get_file_list(folder) if len(list_files) > 0: folders_to_process[folder] = list_files else: - log.info("%s is empty") + log.info("%s is empty", folder) continue if len(folders_to_process) == 0: - log.info("Exiting process.") - log.error("There are no files in the selected folders") + log.info("Exiting process, folders were empty.") + log.error("There are no files in the selected folders.") self.close_connection() sys.exit(0) return folders_to_process - def delete_targets(self, target_folders): - log.info("Initiating delete_only process") - folders_to_delete = target_folders - for folder, files in folders_to_delete.items(): - self.delete_remote_files(folder, files) - stderr.print(f"Delete process finished in {folder}") - def download(self, target_folders, option="download"): log.info("Initiating download process") try: @@ -565,7 +552,7 @@ def download(self, target_folders, option="download"): folders_to_download = target_folders for folder, files in folders_to_download.items(): log.info("Processing folder %s", folder) - stderr.print("Processing folder " + folder) + stderr.print("[blue]Processing folder " + folder) # Validate that the files are the ones described in metadata. if not self.validate_fetched_files(folder): log.error("Failed fetched files validation %s", folder) @@ -573,6 +560,9 @@ def download(self, target_folders, option="download"): continue # get the files in each folder result_data = self.get_files_from_sftp_folder(folder, files) + log.info("Finished download for folder: %s", folder) + stderr.print(f"Finished download for folder {folder}") + md5_files, req_retransmition = self.verify_md5_checksum( result_data["local_folder"], result_data["fetched_files"] ) @@ -588,9 +578,12 @@ def download(self, target_folders, option="download"): if len(corrupted) > 0 and self.abort_if_md5_mismatch: log.error("Stopping because of corrupted files %s", corrupted) stderr.print( - f"[red] Stopped processing folder {folder} due to corrupted files {corrupted}" + f"[red] Stopped processing folder {folder} \ + due to corrupted files {corrupted}" ) continue + log.info("Finished md5 check for folder: %s", folder) + stderr.print(f"Successful md5 verification for folder {folder}") meta_file = self.find_metadata_file(result_data["local_folder"]) sample_file_list = self.get_sample_fastq_file_names( result_data["local_folder"], meta_file @@ -599,19 +592,17 @@ def download(self, target_folders, option="download"): result_data["local_folder"], sample_file_list, md5_files, meta_file ) # Collect data to send the request to relecov_platform - json_sample_data = self.create_json_with_downloaded_samples( - sample_file_list, folder - ) - for record in json_sample_data: - pass + self.create_json_with_downloaded_samples(sample_file_list, folder) + # If download_option is "download_clean", remove + # sftp folder content after download is finished if option == "clean": - self.delete_targets(folder) + self.delete_remote_files(folder, files) return def execute_process(self): if not self.open_connection(): log.error("Unable to establish connection towards sftp server") - stderr.print("[red] Unable to establish sftp connection") + stderr.print("[red]Unable to establish sftp connection") sys.exit(1) target_folders = self.select_target_folders() if self.download_option == "download_only": @@ -619,6 +610,9 @@ def execute_process(self): if self.download_option == "download_clean": self.download(target_folders, option="clean") if self.download_option == "delete_only": - self.delete_targets(target_folders) + log.info("Initiating delete_only process") + for folder, files in target_folders.items(): + self.delete_remote_files(folder, files) + stderr.print(f"Delete process finished in {folder}") self.close_connection() stderr.print("Finished execution") From fc93294c341677a0b56add4471057568ba145af2 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 26 Apr 2023 12:59:04 +0200 Subject: [PATCH 1162/1454] Changed a print message to ease debugging --- relecov_tools/read_lab_metadata.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 8df52389..c7b0e2c4 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -164,17 +164,17 @@ def process_from_json(self, m_data, json_fields): if str(error.args[0]).lower() == "not provided": log.error("Label was not provided, auto-completing columns") stderr.print( - f"Label {map_field} was not provided in sample {idx}, \ - auto-completing with Not Provided" + f"Label {map_field} was not provided in sample {idx}, " + + "auto-completing with Not Provided" ) else: log.error( - f"Unknown map_field value {error} for json data: \ - {str(map_field)}. Aborting" + f"Unknown map_field value {error} for json data: " + + f"{str(map_field)}. Aborting" ) stderr.print( - f"[red] Unknown value {error} for: {map_field}\ - in sample {idx}. Aborting" + f"[red] Unknown value {error} for: {map_field} " + + f"in sample {idx}. Aborting" ) sys.exit(1) fields_to_add = { @@ -200,7 +200,7 @@ def adding_fields(self, metadata): # Include Sample information data from sample json file stderr.print("[blue] Processing sample data file") s_json = {} - s_json["map_field"] = "collecting_lab_sample_id" + s_json["map_field"] = "submitting_lab_sample_id" s_json["adding_fields"] = [ "fastq_r1_md5", "fastq_r2_md5", From 3b866ac658aff95b8ce73f8dd9df607bb57d33ca Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 26 Apr 2023 13:00:10 +0200 Subject: [PATCH 1163/1454] Included new info into validation report message --- relecov_tools/json_validation.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index e5b9e837..9699a27e 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -73,6 +73,7 @@ def validate_instances(self): validated_json_data = [] invalid_json = [] errors = {} + error_keys = {} stderr.print("[blue] Start processing the json file") for item_row in self.json_data: # validate(instance=item_row, schema=json_schema) @@ -81,11 +82,11 @@ def validate_instances(self): else: # Count error types for error in validator.iter_errors(item_row): + error_keys[error.message] = error.absolute_path[0] if error.message in errors.keys(): errors[error.message] += 1 else: errors[error.message] = 1 - # log.error("Invalid sample data %s", error.message) # append row with errors invalid_json.append(item_row) @@ -98,7 +99,8 @@ def validate_instances(self): stderr.print( "[red]" + str(errors[error_type]) - + " samples failed validation:\n" + + " samples failed validation for " + + f"{error_keys[error_type]}:\n" + error_type ) stderr.print("[red] --------------------") From 263ef7cb9b4816c2d2ec0733a05c9e7a283ede1f Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 16 Aug 2023 11:02:14 +0200 Subject: [PATCH 1164/1454] Removed old ena_upload.py --- relecov_tools/ena_upload.py | 382 ------------------------------------ 1 file changed, 382 deletions(-) delete mode 100644 relecov_tools/ena_upload.py diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py deleted file mode 100644 index 5c3fceaa..00000000 --- a/relecov_tools/ena_upload.py +++ /dev/null @@ -1,382 +0,0 @@ -# from distutils.errors import LibError -import logging - -# from re import template - -# from pyparsing import col -import xml.etree.ElementTree as ET -import rich.console -import json - - -import pandas as pd - - -import sys -import os - -import ftplib -import relecov_tools.utils -from relecov_tools.config_json import ConfigJson - -from ena_upload.ena_upload import extract_targets - -# from ena_upload.ena_upload import submit_data -from ena_upload.ena_upload import run_construct -from ena_upload.ena_upload import construct_submission -from ena_upload.ena_upload import send_schemas -from ena_upload.ena_upload import process_receipt -from ena_upload.ena_upload import update_table - -# from ena_upload.ena_upload import make_update -# from ena_upload.ena_upload import process_receipt - -# from ena_upload.ena_upload import save_update -import site - -pd.options.mode.chained_assignment = None - -template_path = os.path.join(site.getsitepackages()[0], "ena_upload", "templates") -template_path = os.path.join(os.getcwd(), "relecov_tools/templates") - -log = logging.getLogger(__name__) -stderr = rich.console.Console( - stderr=True, - style="dim", - highlight=False, - force_terminal=relecov_tools.utils.rich_force_colors(), -) - - -class EnaUpload: - def __init__( - self, - user=None, - passwd=None, - center=None, - source_json=None, - dev=None, - customized_project=None, - action=None, - output_path=None, - ): - if user is None: - self.user = relecov_tools.utils.prompt_text( - msg="Enter your username defined in ENA" - ) - else: - self.user = user - if passwd is None: - self.passwd = relecov_tools.utils.prompt_password( - msg="Enter your password to ENA" - ) - else: - self.passwd = passwd - if center is None: - self.center = relecov_tools.utils.prompt_text(msg="Enter your center name") - else: - self.center = center - if source_json is None: - self.source_json_file = relecov_tools.utils.prompt_path( - msg="Select the ENA json file to upload" - ) - else: - self.source_json_file = source_json - if dev is None: - self.dev = relecov_tools.utils.prompt_yn_question( - msg="Do you want to test upload data?" - ) - else: - self.dev = dev - - if customized_project is None: - self.customized_project = None - else: - self.customized_project = customized_project - if action is None: - self.action = relecov_tools.utils.prompt_selection( - msg="Select the action to upload to ENA", - choices=["add", "modify", "cancel", "release"], - ) - else: - self.action = action.upper() - if output_path is None: - self.output_path = relecov_tools.utils.prompt_path( - msg="Select the folder to store the xml files" - ) - else: - self.output_path = output_path - - if not os.path.isfile(self.source_json_file): - log.error("json data file %s does not exist ", self.source_json_file) - stderr.print(f"[red]json data file {self.source_json_file} does not exist") - sys.exit(1) - with open(self.source_json_file, "r") as fh: - self.json_data = json.loads(fh.read()) - - def convert_input_json_to_ena(self): - """Split the input ena json, in samples and runs json""" - pass - - def create_dataframe(self, dataframe_name, fields_config, df_schemas): - df_list = [] - config_json = ConfigJson() - for index in range(len(dataframe_name)): - fields = config_json.get_configuration("ENA_fields")[fields_config[index]] - dataframe_name[index] = df_schemas[fields] - df_list.append(dataframe_name[index]) - - return df_list - - def rename_cols_df(self, dataframe_name, dataframe, col_name_og, col_name_final): - col_dict = {} - - for index in range(len(col_name_og)): - col_dict[col_name_og[index]] = col_name_final[index] - - dataframe_name = dataframe.rename(columns=col_dict) - - return dataframe_name - - def create_structure_to_ena(self): - """Convert json to dataframe required by ena-upload-cli package""" - - squema = self.source_json_file - fh_squema = open(squema) - squema_json = json.load(fh_squema) - fh_squema.close() - config_json = ConfigJson() - - df_schemas = pd.DataFrame(squema_json) - - dataframe_name_list = ["df_study", "df_samples", "df_run", "df_experiments"] - dataframe_fileds_config_list = [ - "df_study_fields", - "df_samples_fields", - "df_run_fields", - "df_experiment_fields", - ] - # Creating the dataframes df_Study, df_samples, df_run and df_experiment - df_list = self.create_dataframe( - dataframe_name_list, dataframe_fileds_config_list, df_schemas - ) - - df_study = df_list[0] - df_samples = df_list[1] - df_run = df_list[2] - df_experiments = df_list[3] - - # df_schema - """ - collecting_institution collection_date collector_name ... study_title study_type taxon_id -0 Hospital Clínic de Barcelona 2021-05-10 Inmaculada Casas ... RELECOV Spanish Network for genomics surveillance Surveillance 2697049 -1 Hospital Clínic de Barcelona 2021-05-07 Inmaculada Casas ... RELECOV Spanish Network for genomics surveillance Surveillance 2697049 - """ - # Parsing the dataframes specifically according to ENA requirements # - # df_study - df_study["alias"] = df_study["study_alias"] - df_study["title"] = df_study["study_title"] - df_study.insert(3, "status", self.action) - - """ - # df_study - alias title study_type status study_abstract -0 RELECOV RELECOV Spanish Network for genomics surveillance Surveillance ADD RELECOV Spanish Network for genomics surveillance -1 RELECOV RELECOV Spanish Network for genomics surveillance Surveillance ADD RELECOV Spanish Network for genomics surveillance - """ - - # df_samples - df_samples = self.rename_cols_df( - "df_samples", - df_samples, - config_json.get_configuration("ENA_fields")["rename_sample_list_og"], - config_json.get_configuration("ENA_fields")["rename_sample_list_final"], - ) - df_samples.insert(3, "status", self.action) - checklist = config_json.get_configuration("ENA_fields")["checklist"] - df_samples.insert(4, "ENA_CHECKLIST", checklist) - - """ - # df_samples - alias title taxon_id host health state ... scientific_name collector name collecting institution isolate -0 212164375 212164375 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212164375 -1 212163777 212163777 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212163777 -2 212153091 212153091 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212153091 - """ - # df_run - df_run.insert(1, "sequence_file_R1_fastq", "None") - df_run.insert(2, "sequence_file_R2_fastq", "None") - for i in range(len(df_schemas)): - df_run.loc[i, "sequence_file_R1_fastq"] = df_schemas.loc[ - i, "sequence_file_R1_fastq" - ] - - df_run.loc[i, "sequence_file_R2_fastq"] = df_schemas.loc[ - i, "sequence_file_R2_fastq" - ] - df_run.insert(3, "status", self.action) - - df_run = df_run.rename(columns={"sequence_file_R1_md5": "file_checksum"}) - - for i in range(len(df_run)): - df_run.loc[i, "alias"] = ( - str(df_run.loc[i, "sequence_file_R1_fastq"]) - + "_" - + str(df_run.loc[i, "sequence_file_R2_fastq"]) - ) - df_run.loc[i, "experiment_alias"] = ( - str(df_run.loc[i, "sequence_file_R1_fastq"]) - + "_" - + str(df_run.loc[i, "sequence_file_R2_fastq"]) - ) - - df_run.insert(5, "file_name", df_run["sequence_file_R1_fastq"]) - df_run2 = df_run.copy() - df_run2["file_name"] = df_run["sequence_file_R2_fastq"] - df_run2["file_checksum"] = df_run["sequence_file_R2_md5"] - df_run_final = pd.concat([df_run, df_run2]) - df_run_final.reset_index() - - """ - # df_run - experiment_alias sequence_file_R1_fastq sequence_file_R2_fastq ... file_type file_checksum fastq_r2_md5 -0 214821_S12 214821_S12_R1_001.fastq.gz 214821_S12_R2_001.fastq.gz ... fastq 372ca8b10a8eeb7a04107634baf340ab 7f5081eec1b64b171402b66f37fe640d -1 214821_S12 214822_S13_R1_001.fastq.gz 214822_S13_R2_001.fastq.gz ... fastq b268d7be80e80455bec0807b5961d23c a15be39feaf73eec9b2c026717878bba -2 214821_S12 214823_S1_R1_001.fastq.gz 214823_S1_R2_001.fastq.gz ... fastq c16bdbfc03c354496fcfb2c107e3cbf6 4d9b80b977a75bf7e2a4282ca910d94a - """ - # df_experiments - - df_experiments["instrument_model"] = df_experiments[ - "instrument_model" - ].str.lower() - df_experiments["sample_alias"] = df_samples["alias"] - df_experiments["title"] = df_study["study_abstract"] - df_experiments["study_alias"] = df_study["alias"] - df_experiments.insert(3, "status", self.action) - - for i in range(len(df_experiments)): - df_experiments.loc[i, "alias"] = ( - str(df_run.loc[i, "sequence_file_R1_fastq"]) - + "_" - + str(df_run.loc[i, "sequence_file_R2_fastq"]) - ) - - """ - # df_experiments example - experiment_alias title study_alias ... library_layout instrument_model alias -0 214821_S12 RELECOV Spanish Network for genomics surveillance RELECOV ... PAIRED Illumina MiSeq 214821_S12_R1_001.fastq.gz_214821_S12_R2_001.f... -1 214821_S12 RELECOV Spanish Network for genomics surveillance RELECOV ... PAIRED Illumina MiSeq 214822_S13_R1_001.fastq.gz_214822_S13_R2_001.f... -2 214821_S12 RELECOV Spanish Network for genomics surveillance RELECOV ... PAIRED Illumina MiSeq 214823_S1_R1_001.fastq.gz_214823_S1_R2_001.fas... - - """ - - ena_config = config_json.get_configuration("ENA_fields")["ENA_configuration"] - schema_dataframe = {} - schema_dataframe["sample"] = df_samples - schema_dataframe["run"] = df_run_final - schema_dataframe["experiment"] = df_experiments - schema_targets = extract_targets(self.action, schema_dataframe) - - if ena_config["study_id"] is not None: - schema_dataframe["study"] = df_study - - if ( - self.action == "ADD" - or self.action == "add" - or self.action == "MODIFY" - or self.action == "modify" - ): - file_paths = {} - file_paths_r2 = {} - for path in df_schemas["r1_fastq_filepath"]: - file_paths[os.path.basename(path)] = os.path.abspath(path) - - for path in df_schemas["r2_fastq_filepath"]: - file_paths_r2[os.path.basename(path)] = os.path.abspath(path) - - file_paths.update(file_paths_r2) - - # Submit data to webin ftp server. It should only upload fastq files in case the action is ADD. - # When the action is MODIFY rthe fastq are already submitted - - if self.action == "ADD" or self.action == "add": - session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) - - for filename, path in file_paths.items(): - print("Uploading path " + path + " and filename: " + filename) - - try: - file = open(path, "rb") # file to send - g = session.storbinary(f"STOR {filename}", file) - print(g) # send the file - file.close() # close file and FTP - except BaseException as err: - print(f"ERROR: {err}") - # print("ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000.") - - g2 = session.quit() - print(g2) - - """ - THE ENA_UPLOAD_CLI METHOD DOES NOT WORK (below) - chec = submit_data(file_paths, self.passwd, self.user) - print(chec) - When ADD/MODIFY: - requires source XMLs for 'run', 'experiment', 'sample', 'experiment' - schema_xmls record XMLs for all these schema and following 'submission' - """ - # - tool = config_json.get_configuration("ENA_fields")["tool"] - - schema_xmls = run_construct( - template_path, schema_targets, self.center, checklist, tool - ) - - submission_xml = construct_submission( - template_path, self.action, schema_xmls, self.center, checklist, tool - ) - schema_xmls["submission"] = submission_xml - - tree = ET.parse(schema_xmls["run"]) - root = tree.getroot() - - for files in root.iter("FILE"): - if "R2" in files.attrib["filename"]: - H = df_run_final.loc[ - df_run_final["sequence_file_R2_fastq"] - == files.attrib["filename"] - ].values[0][8] - files.set("checksum", H) - - tree.write(schema_xmls["run"]) - - if self.dev: - url = "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" - else: - url = "https://www.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" - - print(f"\nSubmitting XMLs to ENA server: {url}") - - receipt = send_schemas(schema_xmls, url, self.user, self.passwd).text - if not os.path.exists(self.output_path): - os.mkdir(self.output_path) - receipt_dir = os.path.join(self.output_path, "receipt.xml") - print(f"Printing receipt to {receipt_dir}") - - with open(f"{receipt_dir}", "w") as fw: - fw.write(receipt) - try: - schema_update = process_receipt(receipt.encode("utf-8"), self.action) - except ValueError: - log.error("There was an ERROR during submission:") - sys.exit(receipt) - - if self.action in ["ADD", "MODIFY"] or self.action in ["add", "modify"]: - schema_dataframe = update_table( - schema_dataframe, schema_targets, schema_update - ) - - def upload(self): - """Create the required files and upload to ENA""" - self.convert_input_json_to_ena() - self.create_structure_to_ena() From ebe4a8a1fec69647211025ff9582d20b7de43d05 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 16 Aug 2023 11:03:12 +0200 Subject: [PATCH 1165/1454] Included a new module to upload data to ena --- relecov_tools/upload_ena_protocol.py | 283 +++++++++++++++++++++++++++ 1 file changed, 283 insertions(+) create mode 100755 relecov_tools/upload_ena_protocol.py diff --git a/relecov_tools/upload_ena_protocol.py b/relecov_tools/upload_ena_protocol.py new file mode 100755 index 00000000..b400ed0f --- /dev/null +++ b/relecov_tools/upload_ena_protocol.py @@ -0,0 +1,283 @@ +# from distutils.errors import LibError +import logging + +# from re import template + +# from pyparsing import col +import xml.etree.ElementTree as ET +import rich.console +import json + + +import pandas as pd + + +import sys +import os + +import ftplib +import relecov_tools.utils +from relecov_tools.config_json import ConfigJson + +from ena_upload.ena_upload import extract_targets +from ena_upload.ena_upload import run_construct +from ena_upload.ena_upload import construct_submission +from ena_upload.ena_upload import send_schemas +from ena_upload.ena_upload import process_receipt +from ena_upload.ena_upload import update_table +from ena_upload.ena_upload import update_table_simple + +import site + +pd.options.mode.chained_assignment = None + +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + +class EnaUpload: + def __init__( + self, + user=None, + passwd=None, + center=None, + source_json=None, + template_path=None, + dev=None, + action=None, + accession=None, + output_path=None, + ): + if user is None: + self.user = relecov_tools.utils.prompt_text( + msg="Enter your username defined in ENA" + ) + else: + self.user = user + if passwd is None: + self.passwd = relecov_tools.utils.prompt_password( + msg="Enter your password to ENA" + ) + else: + self.passwd = passwd + if center is None: + self.center = relecov_tools.utils.prompt_text(msg="Enter your center name") + else: + self.center = center + if source_json is None: + self.source_json_file = relecov_tools.utils.prompt_path( + msg="Select the ENA json file to upload" + ) + else: + self.source_json_file = source_json + if template_path is None: + self.template_path = relecov_tools.utils.prompt_path( + msg="Select the folder containing ENA templates" + ) + #template_folder = "/home/user/git_repositories/relecov-tools/relecov_tools/templates" + else: + self.template_path = template_path + if not os.path.exists(self.template_path): + stderr.print("[red]Error: ENA template folder does not exist") + sys.exit(1) + if dev is None: + self.dev = relecov_tools.utils.prompt_yn_question( + msg="Do you want to test upload data?" + ) + else: + self.dev = dev + if accession == "empty": + self.accession = relecov_tools.utils.prompt_yn_question( + msg="Select the accession number for the submission" + ) + elif accession == "false": + self.accession = False + else: + self.accession = accession + if action is None: + self.action = relecov_tools.utils.prompt_selection( + msg="Select the action to upload to ENA", + choices=["ADD", "MODIFY", "CANCEL", "RELEASE"], + ) + elif action.upper() not in ["ADD", "MODIFY", "CANCEL", "RELEASE"]: + stderr.print(f"[red] Action '{action}' not supported") + sys.exit(1) + else: + self.action = action.upper() + if output_path is None: + self.output_path = relecov_tools.utils.prompt_path( + msg="Select the folder to store the xml files" + ) + else: + self.output_path = output_path + + config_json = ConfigJson() + self.config_json = config_json + + self.checklist = self.config_json.get_configuration("ENA_fields")["checklist"] + + if not os.path.isfile(self.source_json_file): + log.error("json data file %s does not exist ", self.source_json_file) + stderr.print(f"[red]json data file {self.source_json_file} does not exist") + sys.exit(1) + + with open(self.source_json_file, "r") as fh: + json_data = json.loads(fh.read()) + self.json_data = json_data + + if self.dev: + self.url = "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" + else: + self.url = "https://www.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" + + def table_formatting(self, schemas_dataframe, source): + """Some fields in the dataframe need special formatting""" + formated_df = schemas_dataframe[source] + formated_df.insert(3, "status", self.action) + formated_df.rename( + columns = {(str(source)+"_alias"):"alias", + (str(source)+"_title"):"title"}, + inplace = True + ) + if source == "sample": + formated_df.insert(4, "ENA_CHECKLIST", self.checklist) + """ + file_name and file_checksum are fields with a structure like this: + file_nameR1--file_nameR2 / file_checksumR1--file_checksumR2 + The run table needs a row for each strand, so these fields are splitted + """ + if source == "run": + formated_df["file_name"] = formated_df["file_name"].str.split("--") + formated_df = formated_df.explode("file_name").reset_index(drop=True) + formated_df["file_checksum"] = [ + x[1].split("--")[0] if x[0]%2 == 0 else x[1].split("--")[1] + for x in enumerate(formated_df["file_checksum"]) + ] + if source == "study": + formated_df = formated_df.drop_duplicates(subset=["alias"]) + stderr.print("study table:", formated_df) + + if isinstance(self.accession, str): + formated_df["accession"] = self.accession + + schemas_dataframe[source] = formated_df + return schemas_dataframe + + def dataframes_from_json(self, json_data): + """The xml is built using a dictionary of dataframes as a base structure""" + source_options = ["study", "sample", "run", "experiment"] + schemas_dataframe_raw = {} + + for source in source_options: + source_topic = "_".join(["df",source,"fields"]) + source_fields = self.config_json.get_topic_data("ENA_fields", source_topic) + source_dict = {field: [sample[field] for sample in json_data] + for field in source_fields} + schemas_dataframe_raw[source] = pd.DataFrame.from_dict(source_dict) + schemas_dataframe = self.table_formatting(schemas_dataframe_raw, source) + + return schemas_dataframe + + def save_tables(self, schemas_dataframe): + """Save the dataframes into csv files""" + stderr.print(f"Saving dataframes in {self.output_path}") + for source, table in schemas_dataframe.items(): + table_name = str(self.output_path+source+"_table.csv") + table.to_csv(table_name, sep=",") + + + def xml_submission(self, schemas_dataframe): + """The metadata is submitted in an xml format""" + + schema_targets = extract_targets(self.action, schemas_dataframe) + + tool = self.config_json.get_configuration("ENA_fields")["tool"] + + if self.action in ["ADD", "MODIFY"]: + schema_xmls = run_construct( + self.template_path, schema_targets, self.center, self.checklist, tool + ) + submission_xml = construct_submission( + self.template_path, self.action, schema_xmls, self.center, self.checklist, tool + ) + elif self.action in ['CANCEL', 'RELEASE']: + # when CANCEL/RELEASE, only the accessions are needed + # schema_xmls is only used to record the following 'submission' + schema_xmls = {} + submission_xml = construct_submission(self.template_path, self.action, + schema_targets, self.center, self.checklist, tool) + + schema_xmls["submission"] = submission_xml + + """Tree writes an xml file for the run fields""" + """tree = ET.parse(schema_xmls["run"]) + tree.write(schema_xmls["run"])""" + + print(f"\nSubmitting XMLs to ENA server: {self.url}") + receipt = send_schemas(schema_xmls, self.url, self.user, self.passwd).text + if not os.path.exists(self.output_path): + os.mkdir(self.output_path) + receipt_dir = os.path.join(self.output_path, "receipt.xml") + print(f"Printing receipt to {receipt_dir}") + + with open(f"{receipt_dir}", "w") as fw: + fw.write(receipt) + try: + schema_update = process_receipt(receipt.encode("utf-8"), self.action) + except ValueError: + log.error("There was an ERROR during submission:") + sys.exit(receipt) + + if str(self.action) in ["ADD", "MODIFY"]: + schemas_dataframe = update_table( + schemas_dataframe, schema_targets, schema_update + ) + else: + schemas_dataframe = update_table_simple(schemas_dataframe, + schema_targets, + self.action) + self.save_tables(schemas_dataframe) + return + + def fastq_submission(self, json_data): + """The fastq files are submitted apart from the metadata""" + stderr.print(f"Submitting fastq files") + json_dataframe = pd.DataFrame(json_data) + file_paths = {} + file_paths_r2 = {} + for path in json_dataframe["r1_fastq_filepath"]: + file_paths[os.path.basename(path)] = os.path.abspath(path) + + for path in json_dataframe["r2_fastq_filepath"]: + file_paths_r2[os.path.basename(path)] = os.path.abspath(path) + + file_paths.update(file_paths_r2) + + session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) + for filename, path in file_paths.items(): + print("Uploading path " + path + " and filename: " + filename) + try: + file = open(path, "rb") # file to send + g = session.storbinary(f"STOR {filename}", file) + print(g) # send the file + file.close() # close file and FTP + except BaseException as err: + print(f"ERROR: {err}") + # print("ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000.") + g2 = session.quit() + print(g2) + + return + + def upload(self): + """Create the required files and upload to ENA""" + schemas_dataframe = self.dataframes_from_json(self.json_data) + self.xml_submission(schemas_dataframe) + self.fastq_submission(self.json_data) + + stderr.print(f"[green] Finished execution") + return From 208ce456aa600e51070d6221922cefa03fff26f9 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 16 Aug 2023 11:05:29 +0200 Subject: [PATCH 1166/1454] upload-to-ena now executes the new module --- relecov_tools/__main__.py | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 1a0d0736..b7a99435 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -20,6 +20,7 @@ import relecov_tools.long_table_parse import relecov_tools.metadata_homogeneizer import relecov_tools.gisaid_upload +import relecov_tools.upload_ena_protocol log = logging.getLogger() @@ -262,20 +263,25 @@ def map(origin_schema, json_data, destination_schema, schema_file, output): @click.option("-p", "--password", help="password for the user to login") @click.option("-c", "--center", help="center name") @click.option("-e", "--ena_json", help="where the validated json is") -@click.option("-s", "--study", help="study/project name to include in xml files") +@click.option("-t", "--template_path", help="folder where the ENA templates are located") @click.option( "-a", "--action", - type=click.Choice(["add", "modify", "cancel", "release"], case_sensitive=False), + type=click.Choice(["ADD", "MODIFY", "CANCEL", "RELEASE"], case_sensitive=False), help="select one of the available options", ) @click.option("--dev", is_flag=True, default=False) +@click.option("-s", + "--accession", + is_flag=False, + flag_value="empty", + default="False", + help="Accession number given after submition, required for RELEASE action") @click.option("-o", "--output_path", help="output folder for the xml generated files") -def upload_to_ena(user, password, center, ena_json, dev, study, action, output_path): - """parsed data to create xml files to upload to ena""" - - upload_ena = relecov_tools.ena_upload.EnaUpload( - user, password, center, ena_json, dev, study, action, output_path +def upload_to_ena(user, password, center, ena_json, template_path, dev, action, accession, output_path): + """parse data to create xml files to upload to ena""" + upload_ena = relecov_tools.upload_ena_protocol.EnaUpload( + user, password, center, ena_json, template_path, dev, action, accession, output_path ) upload_ena.upload() From 1f017840e30c10349e9ee6ad2384a7599bfaa923 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 16 Aug 2023 11:13:00 +0200 Subject: [PATCH 1167/1454] Included additional formatting key and changed several ena fields --- relecov_tools/conf/configuration.json | 73 ++++++++++++++++++--------- 1 file changed, 50 insertions(+), 23 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 5b0e9565..8afb3bac 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -78,8 +78,9 @@ }, "submitting_data": { "file": "laboratory_address.json", - "map_field": "submitting_institution", + "map_field": "collecting_institution", "adding_fields": [ + "submitting_institution", "submitting_institution_address", "submitting_institution_email" ] @@ -371,60 +372,65 @@ "design_description": "Design Description", "experiment_title": "Project for ENA submission RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_type": "", + "study_type": "Whole Genome Sequencing", "study_id": "ERP137164", "ena_broker_name": "Instituto de Salud Carlos III" }, + "checklist": "ERC000033", + "templates_path": "", "tool": { "tool_name": "ena-upload-cli", "tool_version": "0.5.3" }, - "checklist": "ERC000033", "df_study_fields": [ - "study_type", - "study_abstract", "study_alias", - "study_title" + "study_title", + "study_type", + "study_abstract" ], - "df_samples_fields": [ - "sample_name", + "df_sample_fields": [ + "sample_alias", "sample_title", "collection date", "geographic location (country and/or sea)", + "sample_description", "host common name", "host scientific name", "host sex", "scientific_name", - "collector_name", + "collector name", "collecting institution", + "address", "isolate", "host subject id", "host health state", "authors", - "taxon_id", - "sample_description", - "address" + "taxon_id" ], "df_run_fields": [ - "r1_fastq_filepath", - "r2_fastq_filepath", + "run_alias", + "experiment_alias", + "file_name", "file_format", - "sequence_file_R1_md5", - "sequence_file_R2_md5", + "file_checksum", "collecting institution" ], "df_experiment_fields": [ + "experiment_alias", + "experiment_title", + "sample_alias", + "study_alias", + "design_description", "library_name", "library_strategy", "library_source", "library_selection", "library_layout", - "instrument_model", - "design_description", - "collecting institution", "library_construction_protocol", "insert_size", - "platform" + "platform", + "instrument_model", + "collecting institution" ], "rename_sample_list_og": [ "sample_name", @@ -450,7 +456,7 @@ "collector name", "collecting institution" ], - "map_not_provided_fields": [ + "common_missing_fields": [ "subject exposure", "subject exposure duration", "type exposure", @@ -472,12 +478,14 @@ "ena_fixed_fields": { "broker_name": "Instituto de Salud Carlos III", "file_format": "FASTQ", + "study_alias": "RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", - "study_abstract": "RELECOV Spanish Network for genomics surveillance", + "study_abstract": "RELECOV is a Spanish Network for genomics surveillance", "insert_size": "0" }, "additional_formating": { "sample_description": [ + "host_common_name", "anatomical_part", "collection_method" ], @@ -485,7 +493,6 @@ "library_layout", "library_preparation_kit", "library_selection", - "library_source", "library_strategy" ], "r1_fastq_filepath": [ @@ -495,6 +502,26 @@ "r2_fastq_filepath": [ "r2_fastq_filepath", "sequence_file_R2_fastq" + ], + "experiment_alias": [ + "isolate_sample_id", + "sample_collection_date" + ], + "run_alias": [ + "isolate_sample_id", + "sample_collection_date" + ], + "experiment_title": [ + "sequencing_instrument_model", + "isolate_sample_id" + ], + "file_name": [ + "sequence_file_R1_fastq", + "sequence_file_R2_fastq" + ], + "file_checksum": [ + "fastq_r1_md5", + "fastq_r2_md5" ] } } From c5775d520f6f4403ce61006996bca0843da921fd Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 16 Aug 2023 11:14:21 +0200 Subject: [PATCH 1168/1454] Introduced a new function to check for required fields and some error handling --- relecov_tools/map_schema.py | 71 +++++++++++++++++++++++++++++-------- 1 file changed, 57 insertions(+), 14 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 6245c5aa..25cf61c1 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -33,6 +33,7 @@ def __init__( output_folder=None, ): config_json = ConfigJson() + self.config_json = config_json if relecov_schema is None: relecov_schema = os.path.join( os.path.dirname(os.path.realpath(__file__)), @@ -127,17 +128,21 @@ def maping_schemas_based_on_geontology(self): """ mapped_dict = OrderedDict() errors = {} + not_provided_fields = self.config_json.get_configuration("ENA_fields")[ + "common_missing_fields" + ] for key, values in self.mapped_to_schema["properties"].items(): if values["ontology"] == "0": continue try: mapped_dict[key] = self.ontology[values["ontology"]] except KeyError as e: - errors[key] = str(e) + if key not in not_provided_fields: + errors[key] = str(e) if len(errors) >= 1: - output_errs = "\n".join(f"{k}:{v}" for k, v in errors.items()) + output_errs = "\n".join(f"{field}:{info}" for field, info in errors.items()) log.error( - "Invalid ontology for: %s", str([x for x in errors.keys()]).strip("[]") + "Invalid ontology for: %s", str([field for field in errors.keys()]).strip("[]") ) stderr.print( f"[red]Ontology values not found in relecov schema:\n{output_errs}" @@ -161,32 +166,69 @@ def mapping_json_data(self, mapping_schema_dict): return mapped_data def additional_formating(self, mapped_json_data): - """Update data like MD5 to split in two fields, one for R1 file and - second for R2, and include fields with fixed values. + """Update data that needs additional formating such as + word splitting and include fields with fixed values. """ - config_json = ConfigJson() - additional_data = config_json.get_topic_data( + additional_data = self.config_json.get_topic_data( "ENA_fields", "additional_formating" ) - fixed_fields = config_json.get_topic_data("ENA_fields", "ena_fixed_fields") - not_provided_fields = config_json.get_configuration("ENA_fields")[ - "map_not_provided_fields" + fixed_fields = self.config_json.get_topic_data("ENA_fields", "ena_fixed_fields") + not_provided_fields = self.config_json.get_configuration("ENA_fields")[ + "common_missing_fields" ] + if self.destination_schema == "ENA": for idx in range(len(self.json_data)): for key, value in fixed_fields.items(): mapped_json_data[idx][key] = value for key, _ in additional_data.items(): + """ + Some fields in ENA need special formatting such as sample_id+date + instead of directly merging them, -- is used as delimiter. + Also, the Not Provided fields are skipped in this process + """ formated_data = { - x: " ".join( - [self.json_data[idx][f].split(" [", 1)[0] for f in y] + x: "--".join( + [self.json_data[idx][f].split(" [", 1)[0] for f in y + if "Not Provided" not in self.json_data[idx][f].split(" [", 1)[0]] ) for x, y in additional_data.items() } + if "fastq_filepath" in key: + formated_data[key] = formated_data[key].replace("--","/") mapped_json_data[idx][key] = formated_data[key] for _, value in enumerate(not_provided_fields): - mapped_json_data[idx][value] = "Not Provided" - return mapped_json_data + if value in mapped_json_data[idx]: + continue + else: + mapped_json_data[idx][value] = "Not Provided" + + """This is a temporal solution for library_strategy. Once the values are also + mapped by the ontology (not only the fields) this should not be necessary""" + for sample in mapped_json_data: + sample["library_strategy"] = sample["library_strategy"].strip(" strategy") + + return mapped_json_data + + def check_required_fields(self, mapped_json_data, dest_schema): + """Checks which required fields are Not Provided""" + if dest_schema == "ENA": + required_fields = self.mapped_to_schema["required"] + + try: + not_provided_fields = { + sample["isolate"]:[field for field in required_fields if 'Not Provided' in sample[field]] + for sample in mapped_json_data} + except KeyError as e: + print(f"Field {e} could not be found in json data, aborting") + sys.exit(1) + notprov_report = "\n".join(f"Sample {key}: {str(val).strip('[]')}" + for key, val in not_provided_fields.items()) + stderr.print(f"[red]\nSome required fields were Not Provided:\n", notprov_report) + else: + return + return + def write_json_fo_file(self, mapped_json_data): """Write metadata to json file""" @@ -210,6 +252,7 @@ def map_to_data_to_new_schema(self): mapping_schema_dict = self.maping_schemas_based_on_geontology() mapped_json_data = self.mapping_json_data(mapping_schema_dict) updated_json_data = self.additional_formating(mapped_json_data) + validation = self.check_required_fields(mapped_json_data, self.destination_schema) self.write_json_fo_file(updated_json_data) stderr.print(f"[green]Finished mapping to {self.destination_schema} schema") return From 29181e6ebfad0508de2559f4003fb2dbe1de88f0 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 16 Aug 2023 11:15:58 +0200 Subject: [PATCH 1169/1454] Merged long_table_parse process into read_bioinfo_metadata process --- relecov_tools/read_bioinfo_metadata.py | 50 ++++++++++++++++++++------ 1 file changed, 39 insertions(+), 11 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 0affd7ca..22e2d537 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -11,6 +11,7 @@ import relecov_tools.utils from relecov_tools.config_json import ConfigJson +from relecov_tools.long_table_parse import LongTableParse # import relecov_tools.json_schema @@ -93,12 +94,14 @@ def include_data_from_mapping_stats(self, j_data): ) for row in j_data: + sample_name = row["submitting_lab_sample_id"] for field, value in mapping_fields.items(): try: - row[field] = map_data[row["sequencing_sample_id"]][value] + row[field] = map_data[row["submitting_lab_sample_id"]][value] except KeyError as e: log.error("Field %s not found in mapping stats", e) - stderr.print(f"[red]Field {e} not found in mapping stats") + stderr.print(f"[red]Field {e} not found in mapping stats for", + f"sample {sample_name}") sys.exit(1) return j_data @@ -108,10 +111,10 @@ def include_pangolin_data(self, j_data): "bioinfo_analysis", "mapping_pangolin" ) for row in j_data: - if "-" in row["sequencing_sample_id"]: - sample_name = row["sequencing_sample_id"].replace("-", "_") + if "-" in row["submitting_lab_sample_id"]: + sample_name = row["submitting_lab_sample_id"].replace("-", "_") else: - sample_name = row["sequencing_sample_id"] + sample_name = row["submitting_lab_sample_id"] f_name_regex = sample_name + ".pangolin.*.csv" f_path = os.path.join(self.input_folder, f_name_regex) @@ -165,10 +168,10 @@ def include_consensus_data(self, j_data): "bioinfo_analysis", "mapping_consensus" ) for row in j_data: - if "-" in row["sequencing_sample_id"]: - sample_name = row["sequencing_sample_id"].replace("-", "_") + if "-" in row["submitting_lab_sample_id"]: + sample_name = row["submitting_lab_sample_id"].replace("-", "_") else: - sample_name = row["sequencing_sample_id"] + sample_name = row["submitting_lab_sample_id"] f_name = sample_name + ".consensus.fa" f_path = os.path.join(self.input_folder, f_name) try: @@ -187,12 +190,33 @@ def include_consensus_data(self, j_data): row["consensus_sequence_filename"] = f_name row["consensus_sequence_md5"] = relecov_tools.utils.calculate_md5(f_path) base_calculation = int(row["read_length"]) * len(record_fasta) - if row["sequencing_sample_id"] != "": + if row["submitting_lab_sample_id"] != "": row["number_of_base_pairs_sequenced"] = str(base_calculation * 2) else: row["number_of_base_pairs_sequenced"] = str(base_calculation) return j_data + + def parse_long_table(self, long_table_path, output_folder): + file_match = os.path.join(long_table_path, "variants_long_table*.csv") + table_path = glob.glob(file_match) + if len(table_path) == 1: + table_path = glob.glob(file_match)[0] + else: + log.error("variants_long_table files found = %s", len(table_path)) + stderr.print(f"[red]Found {len(table_path)} variants_long_table files in ", + f"[red]{long_table_path}, aborting") + sys.exit(1) + if not os.path.isfile(table_path): + log.error("variants_long_table given file is not a file") + stderr.print("[red]Variants_long_table file, Aborting") + sys.exit(1) + long_table = LongTableParse(table_path, output_folder) + + long_table_parse = long_table.parsing_csv() + + return + def include_long_table_path(self, j_data): """Include the variant long table path by searchin the in input folder @@ -219,12 +243,14 @@ def include_variant_metrics(self, j_data): "bioinfo_analysis", "mapping_variant_metrics" ) for row in j_data: + sample_name = row["submitting_lab_sample_id"] for field, value in mapping_fields.items(): try: - row[field] = map_data[row["sequencing_sample_id"]][value] + row[field] = map_data[row["submitting_lab_sample_id"]][value] except KeyError as e: log.error("Field %s not found in mapping stats", e) - stderr.print(f"[red]Field {e} not found in mapping stats") + stderr.print(f"[red]Field {e} not found in mapping stats for", + f"sample {sample_name}") sys.exit(1) return j_data @@ -287,6 +313,8 @@ def create_bioinfo_file(self): j_data = self.include_pangolin_data(j_data) stderr.print("[blue]Adding consensus data") j_data = self.include_consensus_data(j_data) + stderr.print("[blue]Parsing variants_long_table info to json format...") + self.parse_long_table(self.input_folder, self.output_folder) stderr.print("[blue]Adding variant long table path") j_data = self.include_long_table_path(j_data) file_name = ( From 71416dec57544d2adc68596951623e32cde0d1d9 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 16 Aug 2023 11:16:48 +0200 Subject: [PATCH 1170/1454] Included a report for missing ontology values --- relecov_tools/read_lab_metadata.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index c7b0e2c4..ad6aea97 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -141,16 +141,21 @@ def adding_ontology_to_enum(self, m_data): enum_dict[prop][go_match.group(1)] = enum else: enum_dict[prop][enum] = enum - + ontology_errors = {} for idx in range(len(m_data)): for key, e_values in enum_dict.items(): if key in m_data[idx]: if m_data[idx][key] in e_values: m_data[idx][key] = e_values[m_data[idx][key]] else: - log.error(f"No ontology could be added in {str(key)}") + try: + ontology_errors[key] += 1 + except KeyError as e: + ontology_errors[key] = 1 continue - + if len(ontology_errors) >= 1: + stderr.print(f"[red] No ontology could be added in:", + "\n".join({f"{x} - {y} samples" for x,y in ontology_errors.items()})) return m_data def process_from_json(self, m_data, json_fields): @@ -284,7 +289,6 @@ def read_metadata_file(self): elif "sample id" in key.lower(): if isinstance(row[key], float) or isinstance(row[key], int): row[key] = str(int(row[key])) - else: if isinstance(row[key], float) or isinstance(row[key], int): row[key] = str(row[key]) From d304704dfa77000bd47e8ab1e8208a6cec53b406 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 16 Aug 2023 11:17:21 +0200 Subject: [PATCH 1171/1454] Introduced new fields and changed some ontology values --- relecov_tools/schema/ena_schema.json | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index e1672266..2d6ac920 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -751,7 +751,7 @@ "sample" ] }, - "personal_protective_equipment": { + "personal protective equipment": { "examples": [ "" ], @@ -980,6 +980,17 @@ "label": "Illness symptoms", "table": "sample" }, + "sample_alias": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001148", + "type": "string", + "description": "Unique Identifier for the sample", + "clasification": "Sample collection and processing", + "label": "Sample ID given by submitting laboratory", + "table": "sample" + }, "sample_description": { "examples": [ "Sample from Belgian Covid-19 patient. Sample was obtained at the Hospital AZ Rivierenland, in Antwerp, Belgium." From 20681771c63e0be577eba91f0bff7ad76089dca4 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 16 Aug 2023 11:18:06 +0200 Subject: [PATCH 1172/1454] Included ontology changes to match new ena-upload protocol --- relecov_tools/schema/relecov_schema.json | 53 ++++++++++++++++++++++-- 1 file changed, 50 insertions(+), 3 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 99653154..405a324f 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1831,6 +1831,29 @@ "label": "Filepath R2 fastq", "fill_mode": "batch" }, + "fastq_r1_md5": { + "examples": [ + "b5242d60471e5a5a97b35531dbbe8c30" + ], + "ontology": "MS_1000568", + "type": "string", + "description": "Checksum value to validate successful file transmission", + "classification": "Bioinformatics and QC metrics fields", + "label": "Fastq md5 r1", + "fill_mode": "sample", + "minLenght": "1" + }, + "fastq_r2_md5": { + "examples": [ + "b5242d60471e5a5a97b35531dbbe8c30" + ], + "ontology": "MS_1000569", + "type": "string", + "description": "Checksum value to validate successful file transmission", + "classification": "Bioinformatics and QC metrics fields", + "label": "Sequence fastq R2 md5", + "fill_mode": "sample" + }, "fast5_filename": { "examples": [ "batch1a_sequences.fast5" @@ -1853,6 +1876,19 @@ "label": "Filepath fast5", "fill_mode": "batch" }, + "processing_date": { + "examples": [ + "e.g 20220705" + ], + "ontology": "0", + "type": "string", + "format": "date", + "description": "The time the processing of the data started", + "classification": "Bioinformatics and QC metrics fields", + "label": "Analysis date", + "fill_mode": "batch", + "minLenght": "1" + }, "analysis_date": { "examples": [ "e.g 20220705" @@ -2447,9 +2483,6 @@ "fill_mode": "batch" }, "variant_name": { - "examples": [ - "Alpha" - ], "ontology": "", "type": "string", "description": "The variant classification of the lineage/clade i.e. alpha, beta, etc.", @@ -2732,6 +2765,20 @@ "label": "Study title", "fill_mode": "batch" }, + "ena_study_alias": { + "examples": [ + "e.g Sweden" + ], + "ontology": "SIO_001066", + "type": "string", + "description": "", + "clasification": "Submission ENA", + "label": "Study alias", + "table": [ + "study", + "experiments" + ] + }, "broker_name": { "examples": [ "P17157_1007" From 6a6d324630699d8d37bc4090ba5905780939dd8a Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 16 Aug 2023 11:37:32 +0200 Subject: [PATCH 1173/1454] New ena-upload protocol and processing changes, linting --- relecov_tools/__main__.py | 32 +++++++++---- relecov_tools/map_schema.py | 43 +++++++++++------ relecov_tools/read_bioinfo_metadata.py | 23 +++++---- relecov_tools/read_lab_metadata.py | 6 ++- relecov_tools/upload_ena_protocol.py | 65 ++++++++++++++++---------- 5 files changed, 110 insertions(+), 59 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index b7a99435..94810a34 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -263,7 +263,9 @@ def map(origin_schema, json_data, destination_schema, schema_file, output): @click.option("-p", "--password", help="password for the user to login") @click.option("-c", "--center", help="center name") @click.option("-e", "--ena_json", help="where the validated json is") -@click.option("-t", "--template_path", help="folder where the ENA templates are located") +@click.option( + "-t", "--template_path", help="folder where the ENA templates are located" +) @click.option( "-a", "--action", @@ -271,17 +273,29 @@ def map(origin_schema, json_data, destination_schema, schema_file, output): help="select one of the available options", ) @click.option("--dev", is_flag=True, default=False) -@click.option("-s", - "--accession", - is_flag=False, - flag_value="empty", - default="False", - help="Accession number given after submition, required for RELEASE action") +@click.option( + "-s", + "--accession", + is_flag=False, + flag_value="empty", + default="False", + help="Accession number given after submition, required for RELEASE action", +) @click.option("-o", "--output_path", help="output folder for the xml generated files") -def upload_to_ena(user, password, center, ena_json, template_path, dev, action, accession, output_path): +def upload_to_ena( + user, password, center, ena_json, template_path, dev, action, accession, output_path +): """parse data to create xml files to upload to ena""" upload_ena = relecov_tools.upload_ena_protocol.EnaUpload( - user, password, center, ena_json, template_path, dev, action, accession, output_path + user, + password, + center, + ena_json, + template_path, + dev, + action, + accession, + output_path, ) upload_ena.upload() diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 25cf61c1..daa4f562 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -142,7 +142,8 @@ def maping_schemas_based_on_geontology(self): if len(errors) >= 1: output_errs = "\n".join(f"{field}:{info}" for field, info in errors.items()) log.error( - "Invalid ontology for: %s", str([field for field in errors.keys()]).strip("[]") + "Invalid ontology for: %s", + str([field for field in errors.keys()]).strip("[]"), ) stderr.print( f"[red]Ontology values not found in relecov schema:\n{output_errs}" @@ -166,7 +167,7 @@ def mapping_json_data(self, mapping_schema_dict): return mapped_data def additional_formating(self, mapped_json_data): - """Update data that needs additional formating such as + """Update data that needs additional formating such as word splitting and include fields with fixed values. """ additional_data = self.config_json.get_topic_data( @@ -189,13 +190,17 @@ def additional_formating(self, mapped_json_data): """ formated_data = { x: "--".join( - [self.json_data[idx][f].split(" [", 1)[0] for f in y - if "Not Provided" not in self.json_data[idx][f].split(" [", 1)[0]] + [ + self.json_data[idx][f].split(" [", 1)[0] + for f in y + if "Not Provided" + not in self.json_data[idx][f].split(" [", 1)[0] + ] ) for x, y in additional_data.items() } if "fastq_filepath" in key: - formated_data[key] = formated_data[key].replace("--","/") + formated_data[key] = formated_data[key].replace("--", "/") mapped_json_data[idx][key] = formated_data[key] for _, value in enumerate(not_provided_fields): if value in mapped_json_data[idx]: @@ -208,8 +213,8 @@ def additional_formating(self, mapped_json_data): for sample in mapped_json_data: sample["library_strategy"] = sample["library_strategy"].strip(" strategy") - return mapped_json_data - + return mapped_json_data + def check_required_fields(self, mapped_json_data, dest_schema): """Checks which required fields are Not Provided""" if dest_schema == "ENA": @@ -217,19 +222,27 @@ def check_required_fields(self, mapped_json_data, dest_schema): try: not_provided_fields = { - sample["isolate"]:[field for field in required_fields if 'Not Provided' in sample[field]] - for sample in mapped_json_data} + sample["isolate"]: [ + field + for field in required_fields + if "Not Provided" in sample[field] + ] + for sample in mapped_json_data + } except KeyError as e: print(f"Field {e} could not be found in json data, aborting") sys.exit(1) - notprov_report = "\n".join(f"Sample {key}: {str(val).strip('[]')}" - for key, val in not_provided_fields.items()) - stderr.print(f"[red]\nSome required fields were Not Provided:\n", notprov_report) + notprov_report = "\n".join( + f"Sample {key}: {str(val).strip('[]')}" + for key, val in not_provided_fields.items() + ) + stderr.print( + f"[red]\nSome required fields were Not Provided:\n", notprov_report + ) else: return return - def write_json_fo_file(self, mapped_json_data): """Write metadata to json file""" os.makedirs(self.output_folder, exist_ok=True) @@ -252,7 +265,9 @@ def map_to_data_to_new_schema(self): mapping_schema_dict = self.maping_schemas_based_on_geontology() mapped_json_data = self.mapping_json_data(mapping_schema_dict) updated_json_data = self.additional_formating(mapped_json_data) - validation = self.check_required_fields(mapped_json_data, self.destination_schema) + validation = self.check_required_fields( + mapped_json_data, self.destination_schema + ) self.write_json_fo_file(updated_json_data) stderr.print(f"[green]Finished mapping to {self.destination_schema} schema") return diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 22e2d537..0b3551d3 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -100,8 +100,10 @@ def include_data_from_mapping_stats(self, j_data): row[field] = map_data[row["submitting_lab_sample_id"]][value] except KeyError as e: log.error("Field %s not found in mapping stats", e) - stderr.print(f"[red]Field {e} not found in mapping stats for", - f"sample {sample_name}") + stderr.print( + f"[red]Field {e} not found in mapping stats for", + f"sample {sample_name}", + ) sys.exit(1) return j_data @@ -196,7 +198,7 @@ def include_consensus_data(self, j_data): row["number_of_base_pairs_sequenced"] = str(base_calculation) return j_data - + def parse_long_table(self, long_table_path, output_folder): file_match = os.path.join(long_table_path, "variants_long_table*.csv") table_path = glob.glob(file_match) @@ -204,20 +206,21 @@ def parse_long_table(self, long_table_path, output_folder): table_path = glob.glob(file_match)[0] else: log.error("variants_long_table files found = %s", len(table_path)) - stderr.print(f"[red]Found {len(table_path)} variants_long_table files in ", - f"[red]{long_table_path}, aborting") + stderr.print( + f"[red]Found {len(table_path)} variants_long_table files in ", + f"[red]{long_table_path}, aborting", + ) sys.exit(1) if not os.path.isfile(table_path): log.error("variants_long_table given file is not a file") stderr.print("[red]Variants_long_table file, Aborting") sys.exit(1) long_table = LongTableParse(table_path, output_folder) - + long_table_parse = long_table.parsing_csv() return - def include_long_table_path(self, j_data): """Include the variant long table path by searchin the in input folder the file name that contains long_table.csv @@ -249,8 +252,10 @@ def include_variant_metrics(self, j_data): row[field] = map_data[row["submitting_lab_sample_id"]][value] except KeyError as e: log.error("Field %s not found in mapping stats", e) - stderr.print(f"[red]Field {e} not found in mapping stats for", - f"sample {sample_name}") + stderr.print( + f"[red]Field {e} not found in mapping stats for", + f"sample {sample_name}", + ) sys.exit(1) return j_data diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index ad6aea97..3a923a72 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -154,8 +154,10 @@ def adding_ontology_to_enum(self, m_data): ontology_errors[key] = 1 continue if len(ontology_errors) >= 1: - stderr.print(f"[red] No ontology could be added in:", - "\n".join({f"{x} - {y} samples" for x,y in ontology_errors.items()})) + stderr.print( + f"[red] No ontology could be added in:", + "\n".join({f"{x} - {y} samples" for x, y in ontology_errors.items()}), + ) return m_data def process_from_json(self, m_data, json_fields): diff --git a/relecov_tools/upload_ena_protocol.py b/relecov_tools/upload_ena_protocol.py index b400ed0f..44d84395 100755 --- a/relecov_tools/upload_ena_protocol.py +++ b/relecov_tools/upload_ena_protocol.py @@ -39,6 +39,7 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) + class EnaUpload: def __init__( self, @@ -78,7 +79,7 @@ def __init__( self.template_path = relecov_tools.utils.prompt_path( msg="Select the folder containing ENA templates" ) - #template_folder = "/home/user/git_repositories/relecov-tools/relecov_tools/templates" + # template_folder = "/home/user/git_repositories/relecov-tools/relecov_tools/templates" else: self.template_path = template_path if not os.path.exists(self.template_path): @@ -124,7 +125,7 @@ def __init__( log.error("json data file %s does not exist ", self.source_json_file) stderr.print(f"[red]json data file {self.source_json_file} does not exist") sys.exit(1) - + with open(self.source_json_file, "r") as fh: json_data = json.loads(fh.read()) self.json_data = json_data @@ -139,9 +140,11 @@ def table_formatting(self, schemas_dataframe, source): formated_df = schemas_dataframe[source] formated_df.insert(3, "status", self.action) formated_df.rename( - columns = {(str(source)+"_alias"):"alias", - (str(source)+"_title"):"title"}, - inplace = True + columns={ + (str(source) + "_alias"): "alias", + (str(source) + "_title"): "title", + }, + inplace=True, ) if source == "sample": formated_df.insert(4, "ENA_CHECKLIST", self.checklist) @@ -154,9 +157,9 @@ def table_formatting(self, schemas_dataframe, source): formated_df["file_name"] = formated_df["file_name"].str.split("--") formated_df = formated_df.explode("file_name").reset_index(drop=True) formated_df["file_checksum"] = [ - x[1].split("--")[0] if x[0]%2 == 0 else x[1].split("--")[1] + x[1].split("--")[0] if x[0] % 2 == 0 else x[1].split("--")[1] for x in enumerate(formated_df["file_checksum"]) - ] + ] if source == "study": formated_df = formated_df.drop_duplicates(subset=["alias"]) stderr.print("study table:", formated_df) @@ -173,23 +176,24 @@ def dataframes_from_json(self, json_data): schemas_dataframe_raw = {} for source in source_options: - source_topic = "_".join(["df",source,"fields"]) + source_topic = "_".join(["df", source, "fields"]) source_fields = self.config_json.get_topic_data("ENA_fields", source_topic) - source_dict = {field: [sample[field] for sample in json_data] - for field in source_fields} + source_dict = { + field: [sample[field] for sample in json_data] + for field in source_fields + } schemas_dataframe_raw[source] = pd.DataFrame.from_dict(source_dict) schemas_dataframe = self.table_formatting(schemas_dataframe_raw, source) return schemas_dataframe - + def save_tables(self, schemas_dataframe): """Save the dataframes into csv files""" stderr.print(f"Saving dataframes in {self.output_path}") for source, table in schemas_dataframe.items(): - table_name = str(self.output_path+source+"_table.csv") + table_name = str(self.output_path + source + "_table.csv") table.to_csv(table_name, sep=",") - def xml_submission(self, schemas_dataframe): """The metadata is submitted in an xml format""" @@ -202,14 +206,25 @@ def xml_submission(self, schemas_dataframe): self.template_path, schema_targets, self.center, self.checklist, tool ) submission_xml = construct_submission( - self.template_path, self.action, schema_xmls, self.center, self.checklist, tool + self.template_path, + self.action, + schema_xmls, + self.center, + self.checklist, + tool, + ) + elif self.action in ["CANCEL", "RELEASE"]: + # when CANCEL/RELEASE, only the accessions are needed + # schema_xmls is only used to record the following 'submission' + schema_xmls = {} + submission_xml = construct_submission( + self.template_path, + self.action, + schema_targets, + self.center, + self.checklist, + tool, ) - elif self.action in ['CANCEL', 'RELEASE']: - # when CANCEL/RELEASE, only the accessions are needed - # schema_xmls is only used to record the following 'submission' - schema_xmls = {} - submission_xml = construct_submission(self.template_path, self.action, - schema_targets, self.center, self.checklist, tool) schema_xmls["submission"] = submission_xml @@ -225,7 +240,7 @@ def xml_submission(self, schemas_dataframe): print(f"Printing receipt to {receipt_dir}") with open(f"{receipt_dir}", "w") as fw: - fw.write(receipt) + fw.write(receipt) try: schema_update = process_receipt(receipt.encode("utf-8"), self.action) except ValueError: @@ -237,12 +252,12 @@ def xml_submission(self, schemas_dataframe): schemas_dataframe, schema_targets, schema_update ) else: - schemas_dataframe = update_table_simple(schemas_dataframe, - schema_targets, - self.action) + schemas_dataframe = update_table_simple( + schemas_dataframe, schema_targets, self.action + ) self.save_tables(schemas_dataframe) return - + def fastq_submission(self, json_data): """The fastq files are submitted apart from the metadata""" stderr.print(f"Submitting fastq files") From 5c79d1dda3674b66f5f6a711e94a9dee6e34ea9e Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 16 Aug 2023 11:38:58 +0200 Subject: [PATCH 1174/1454] New ena-upload protocol and processing changes, linting2 --- relecov_tools/upload_ena_protocol.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/upload_ena_protocol.py b/relecov_tools/upload_ena_protocol.py index 44d84395..64c62172 100755 --- a/relecov_tools/upload_ena_protocol.py +++ b/relecov_tools/upload_ena_protocol.py @@ -260,7 +260,7 @@ def xml_submission(self, schemas_dataframe): def fastq_submission(self, json_data): """The fastq files are submitted apart from the metadata""" - stderr.print(f"Submitting fastq files") + stderr.print("Submitting fastq files") json_dataframe = pd.DataFrame(json_data) file_paths = {} file_paths_r2 = {} @@ -294,5 +294,5 @@ def upload(self): self.xml_submission(schemas_dataframe) self.fastq_submission(self.json_data) - stderr.print(f"[green] Finished execution") + stderr.print("[green] Finished execution") return From 33ef202573673a78e9f309b75b218a5025feaae7 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 16 Aug 2023 11:52:55 +0200 Subject: [PATCH 1175/1454] New ena-upload protocol and processing changes, linting3 --- relecov_tools/map_schema.py | 9 +++------ relecov_tools/read_bioinfo_metadata.py | 2 +- relecov_tools/read_lab_metadata.py | 4 ++-- relecov_tools/upload_ena_protocol.py | 14 -------------- 4 files changed, 6 insertions(+), 23 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index daa4f562..22e5bb40 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -13,7 +13,6 @@ # import jsonschema import relecov_tools.utils - log = logging.getLogger(__name__) stderr = rich.console.Console( stderr=True, @@ -207,7 +206,6 @@ def additional_formating(self, mapped_json_data): continue else: mapped_json_data[idx][value] = "Not Provided" - """This is a temporal solution for library_strategy. Once the values are also mapped by the ontology (not only the fields) this should not be necessary""" for sample in mapped_json_data: @@ -237,7 +235,8 @@ def check_required_fields(self, mapped_json_data, dest_schema): for key, val in not_provided_fields.items() ) stderr.print( - f"[red]\nSome required fields were Not Provided:\n", notprov_report + f"[red]\nSome required fields for {dest_schema} were Not Provided:\n", + notprov_report, ) else: return @@ -265,9 +264,7 @@ def map_to_data_to_new_schema(self): mapping_schema_dict = self.maping_schemas_based_on_geontology() mapped_json_data = self.mapping_json_data(mapping_schema_dict) updated_json_data = self.additional_formating(mapped_json_data) - validation = self.check_required_fields( - mapped_json_data, self.destination_schema - ) + self.check_required_fields(mapped_json_data, self.destination_schema) self.write_json_fo_file(updated_json_data) stderr.print(f"[green]Finished mapping to {self.destination_schema} schema") return diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 0b3551d3..eb2b670d 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -217,7 +217,7 @@ def parse_long_table(self, long_table_path, output_folder): sys.exit(1) long_table = LongTableParse(table_path, output_folder) - long_table_parse = long_table.parsing_csv() + long_table.parsing_csv() return diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 3a923a72..730d33c0 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -150,12 +150,12 @@ def adding_ontology_to_enum(self, m_data): else: try: ontology_errors[key] += 1 - except KeyError as e: + except KeyError: ontology_errors[key] = 1 continue if len(ontology_errors) >= 1: stderr.print( - f"[red] No ontology could be added in:", + "[red] No ontology could be added in:", "\n".join({f"{x} - {y} samples" for x, y in ontology_errors.items()}), ) return m_data diff --git a/relecov_tools/upload_ena_protocol.py b/relecov_tools/upload_ena_protocol.py index 64c62172..03a38626 100755 --- a/relecov_tools/upload_ena_protocol.py +++ b/relecov_tools/upload_ena_protocol.py @@ -1,20 +1,9 @@ -# from distutils.errors import LibError import logging - -# from re import template - -# from pyparsing import col -import xml.etree.ElementTree as ET import rich.console import json - - import pandas as pd - - import sys import os - import ftplib import relecov_tools.utils from relecov_tools.config_json import ConfigJson @@ -27,8 +16,6 @@ from ena_upload.ena_upload import update_table from ena_upload.ena_upload import update_table_simple -import site - pd.options.mode.chained_assignment = None log = logging.getLogger(__name__) @@ -39,7 +26,6 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) - class EnaUpload: def __init__( self, From 021b487c654ee632a8c5cc6c3a18e7419ecf25e8 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 16 Aug 2023 11:55:54 +0200 Subject: [PATCH 1176/1454] New ena-upload protocol and processing changes, linting4 --- relecov_tools/map_schema.py | 6 ++++-- relecov_tools/upload_ena_protocol.py | 1 + 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 22e5bb40..b64d7715 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -206,8 +206,10 @@ def additional_formating(self, mapped_json_data): continue else: mapped_json_data[idx][value] = "Not Provided" - """This is a temporal solution for library_strategy. Once the values are also - mapped by the ontology (not only the fields) this should not be necessary""" + """ + This is a temporal solution for library_strategy. Once the values are also + mapped by the ontology (not only the fields) this should not be necessary + """ for sample in mapped_json_data: sample["library_strategy"] = sample["library_strategy"].strip(" strategy") diff --git a/relecov_tools/upload_ena_protocol.py b/relecov_tools/upload_ena_protocol.py index 03a38626..9ec92fa3 100755 --- a/relecov_tools/upload_ena_protocol.py +++ b/relecov_tools/upload_ena_protocol.py @@ -26,6 +26,7 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) + class EnaUpload: def __init__( self, From 551bb58d09d6696e5524677aef1d58e264985c14 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 16 Aug 2023 15:44:37 +0200 Subject: [PATCH 1177/1454] New ena-upload protocol and processing changes, linting5 --- relecov_tools/__main__.py | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 94810a34..e75c9c3a 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -12,7 +12,6 @@ import relecov_tools.utils import relecov_tools.read_lab_metadata import relecov_tools.sftp_handle -import relecov_tools.ena_upload import relecov_tools.json_validation import relecov_tools.map_schema import relecov_tools.feed_database From 14957dda32719f8901837da925ee4588ff6bddd2 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 22 Aug 2023 13:31:16 +0200 Subject: [PATCH 1178/1454] Included required ENA fields in relecov schema --- relecov_tools/schema/relecov_schema.json | 42 ++++++++++++++++++++++++ 1 file changed, 42 insertions(+) mode change 100644 => 100755 relecov_tools/schema/relecov_schema.json diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json old mode 100644 new mode 100755 index 405a324f..2afa9e4c --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2802,6 +2802,48 @@ "label": "First created date", "fill_mode": "batch" }, + "host health state": { + "examples": [ + "" + ], + "ontology": "GENEPIO:0001388", + "type": "string", + "description": " Status of the host", + "clasification": "Host information", + "label": "Host health state", + "table": [ + "sample" + ] + }, + "ena_sample_description":{ + "examples": [ + "Sample from Belgian Covid-19 patient. Sample was obtained at the Hospital AZ Rivierenland, in Antwerp, Belgium." + ], + "ontology": "sep:00196", + "type": "string", + "description": "Free text description of the sample.", + "clasification": "Sample collection and processing", + "label": "Sample Description", + "table": "sample" + }, + "file_format": { + "examples": [ + "BAM,CRAM,FASTQ" + ], + "enum": [ + "BAM [format:2572]", + "CRAM [format:3462]", + "FASTQ [format:1930]" + ], + "ontology": "NMR:1001459", + "type": "string", + "description": "The run data file model.", + "clasification": "Submission ENA", + "label": "File format", + "table": [ + "experiments" + ] + }, "collector_name": { "examples": [ "John Smith, unknown" From 706729dd6089eeae049672ae445a5e534802c2d4 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 22 Aug 2023 13:33:03 +0200 Subject: [PATCH 1179/1454] Changed error reports of missing ontologies, now writes a file --- relecov_tools/map_schema.py | 25 +++++++++++++++++-------- 1 file changed, 17 insertions(+), 8 deletions(-) mode change 100644 => 100755 relecov_tools/map_schema.py diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py old mode 100644 new mode 100755 index b64d7715..56b3eff6 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -121,22 +121,29 @@ def __init__( self.ontology[values["ontology"]] = key self.output_folder = output_folder + if os.path.exists(os.path.join(output_folder,"mapping_errors.log")): + os.remove(os.path.join(output_folder,"mapping_errors.log")) + def maping_schemas_based_on_geontology(self): """Return a dictionary with the properties of the mapped_to_schema as key and properties of Relecov Schema as value """ mapped_dict = OrderedDict() errors = {} - not_provided_fields = self.config_json.get_configuration("ENA_fields")[ - "common_missing_fields" - ] + required_fields = self.mapped_to_schema["required"] + for key, values in self.mapped_to_schema["properties"].items(): if values["ontology"] == "0": continue try: mapped_dict[key] = self.ontology[values["ontology"]] except KeyError as e: - if key not in not_provided_fields: + if key in required_fields: + stderr.print( + f"[red]Required field {key} ontology is missing in relecov schema" + ) + sys.exit(1) + else: errors[key] = str(e) if len(errors) >= 1: output_errs = "\n".join(f"{field}:{info}" for field, info in errors.items()) @@ -144,9 +151,9 @@ def maping_schemas_based_on_geontology(self): "Invalid ontology for: %s", str([field for field in errors.keys()]).strip("[]"), ) - stderr.print( - f"[red]Ontology values not found in relecov schema:\n{output_errs}" - ) + stderr.print("[yellow]Some ontologies failed mapping.Check mapping_errors.log") + with open("mapping_errors.log", "w") as errs: + errs.write("Ontology mapping errors:\n"+output_errs+"\n") return mapped_dict def mapping_json_data(self, mapping_schema_dict): @@ -238,8 +245,10 @@ def check_required_fields(self, mapped_json_data, dest_schema): ) stderr.print( f"[red]\nSome required fields for {dest_schema} were Not Provided:\n", - notprov_report, + "Check mapping_errors.log for more details" ) + with open("mapping_errors.log", "a") as errs: + errs.write("Required fields missing:\n"+notprov_report) else: return return From b112a90c41478b5e22816f11aefa4aa4d894da51 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 22 Aug 2023 13:40:44 +0200 Subject: [PATCH 1180/1454] Changed map_schema error reports, now writes a file --- relecov_tools/map_schema.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 56b3eff6..31dfe184 100755 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -121,8 +121,8 @@ def __init__( self.ontology[values["ontology"]] = key self.output_folder = output_folder - if os.path.exists(os.path.join(output_folder,"mapping_errors.log")): - os.remove(os.path.join(output_folder,"mapping_errors.log")) + if os.path.exists(os.path.join(output_folder, "mapping_errors.log")): + os.remove(os.path.join(output_folder, "mapping_errors.log")) def maping_schemas_based_on_geontology(self): """Return a dictionary with the properties of the mapped_to_schema as key and @@ -141,7 +141,7 @@ def maping_schemas_based_on_geontology(self): if key in required_fields: stderr.print( f"[red]Required field {key} ontology is missing in relecov schema" - ) + ) sys.exit(1) else: errors[key] = str(e) @@ -151,9 +151,9 @@ def maping_schemas_based_on_geontology(self): "Invalid ontology for: %s", str([field for field in errors.keys()]).strip("[]"), ) - stderr.print("[yellow]Some ontologies failed mapping.Check mapping_errors.log") + stderr.print("\nSome ontologies failed mapping. Check mapping_errors.log") with open("mapping_errors.log", "w") as errs: - errs.write("Ontology mapping errors:\n"+output_errs+"\n") + errs.write("Ontology mapping errors:\n" + output_errs + "\n") return mapped_dict def mapping_json_data(self, mapping_schema_dict): @@ -245,10 +245,10 @@ def check_required_fields(self, mapped_json_data, dest_schema): ) stderr.print( f"[red]\nSome required fields for {dest_schema} were Not Provided:\n", - "Check mapping_errors.log for more details" + "Check mapping_errors.log for more details", ) with open("mapping_errors.log", "a") as errs: - errs.write("Required fields missing:\n"+notprov_report) + errs.write("Required fields missing:\n" + notprov_report) else: return return From fa712fd5cf99684b12257a90ca9d3c19389a219f Mon Sep 17 00:00:00 2001 From: Pablo Mata <76519482+Shettland@users.noreply.github.com> Date: Mon, 20 Nov 2023 16:12:28 +0100 Subject: [PATCH 1181/1454] Update README.md Updated the documentation of the modules from relecov-tools --- README.md | 92 +++++++++++++++++++++++++++++++++++++++++-------------- 1 file changed, 69 insertions(+), 23 deletions(-) diff --git a/README.md b/README.md index 200bfaad..ae99510c 100644 --- a/README.md +++ b/README.md @@ -58,14 +58,15 @@ Options: --help Show this message and exit. Commands: - download Download files located in sftp server. - read-metadata Create the json compliant to the relecov schema from... - validate Validate json file against schema. - map Convert data between phage plus schema to ENA,... - upload-to-ena parsed data to create xml files to upload to ena - upload-to-gisaid parsed data to create files to upload to gisaid - launch launch viralrecon in hpc - update-db feed database with metadata jsons + download Download files located in sftp server. + read-lab-metadata Create the json compliant to the relecov schema from... + read-bioinfo-metadata Create the json compliant to the relecov schema with Bioinfo Metadata. + validate Validate json file against schema. + map Convert data between phage plus schema to ENA,... + upload-to-ena parsed data to create xml files to upload to ena + upload-to-gisaid parsed data to create files to upload to gisaid + update-db feed database with metadata jsons + launch launch viralrecon in hpc ``` #### download The command `download` connects to a transfer protocol (currently sftp) and downloads all files in the different available folders in the passed credentials. In addition, it checks if the files in the current folder match the files in the metadata file and also checks if there are md5sum for each file. Else, it creates one before storing in the final repository. @@ -77,9 +78,15 @@ Usage: relecov-tools download [OPTIONS] Download files located in sftp server. Options: - -u, --user TEXT User name for login to sftp server - -p, --password TEXT password for the user to login - -f, --conf_file TEXT Configuration file in yaml format (no params file) + -u, --user User name for login to sftp server + -p, --password Password for the user to login + -d, --download_option Select the download option: [download_only, download_clean, delete_only]. + download_only will only download the files + download_clean will remove files from sftp after download + delete_only will only delete the files + -o, --output_location Flag: Select location for downloaded files, overrides config file location + -t, --target_folders Flag: Select which sftp folders will be targeted giving [paths] or via prompt + -f, --conf_file Configuration file in yaml format (no params file) --help Show this message and exit. ``` @@ -100,11 +107,11 @@ allowed_sample_extensions: - .fasta ``` -#### read-metadata -`read-metadata` command reads the excel file with laboratory metadata and processes it adding additional needed fields. +#### read-lab-metadata +`read-lab-metadata` command reads the excel file with laboratory metadata and processes it adding additional needed fields. ``` -$ relecov-tools read-metadata --help +$ relecov-tools read-lab-metadata --help Usage: relecov-tools read-metadata [OPTIONS] Create the json compliant to the relecov schema from the Metadata file. @@ -120,6 +127,21 @@ Usage: relecov-tools read-metadata [OPTIONS] An example for the metadata excel file can be found [here](./relecov_tools/example_data/METADATA_LAB_TEST.xlsx) +#### read-bioinfo-metadata +`read-bioinfo-metadata` Include the results from the Bioinformatics analysis (default: viralrecon) into the Json previously created with read-lab-metadata module. + +``` +$ relecov-tools read-bioinfo-metadata --help +Usage: relecov-tools read-bioinfo-metadata [OPTIONS] + + Create the json compliant to the relecov schema with Bioinfo Metadata. + + Options: + -j, --json_file Json file containing lab metadata + -i, --input_folder Path to folder containing analysis results + -o, --out_dir Path to save output file" +``` + #### validate `validate` commands validate the data in json format outputted by `read-metadata` command against a json schema, in this case the relecov [schema specification](./relecov_tools/schema/relecov_schema.json). @@ -166,24 +188,48 @@ Usage: relecov-tools upload-to-ena [OPTIONS] parsed data to create xml files to upload to ena Options: - -u, --user TEXT user name for login to ena - -p, --password TEXT password for the user to login - -e, --ena_json TEXT where the validated json is - -s, --study TEXT study/project name to include in xml files - -a, --action [add|modify|cancel|release] select one of the available options - --dev / --production + -u, --user user name for login to ena + -p, --password password for the user to login + -c, --center center name + -e, --ena_json where the validated json is + -t, --template_path path to folder containing ENA xml templates + -a, --action select one of the available options: [add|modify|cancel|release] + --dev Flag: Test submission + --upload_fastq Flag: Upload fastq files. Mandatory for "add" action + -m", --metadata_types List of metadata xml types to submit [study,experiment,run,sample] -o, --output_path TEXT output folder for the xml generated files --help Show this message and exit. ``` #### upload-to-gisaid -SOON +`upload-to-gisaid` uses the json mapped to gisaid schema to upload raw data and metadata to GISAID db -#### launch -SOON +``` +Usage: relecov-tools upload-to-gisaid [OPTIONS] + + parsed data to create xml files to upload to ena + + Options: + -u, --user user name for login + -p, --password password for the user to login + -c, --client_id client-ID provided by clisupport@gisaid.org + -t, --token path to athentication token + -e, --gisaid_json path to validated json mapped to GISAID + -i, --input_path path to fastas folder or multifasta file + -f, --frameshift frameshift notification: ["catch_all", "catch_none", "catch_novel"] + -x, --proxy_config introduce your proxy credentials as: username:password@proxy:port + --single Flag: input is a folder with several fasta files. + --gzip Flag: input fasta is gziped. +``` #### update-db + -u, --user user name for login + -p, --password password for the user to login + -t, --type Select the type of information to upload to database [sample,bioinfodata,variantdata] + -d, --databaseServer Name of the database server receiving the data [iskylims,relecov] + +#### launch SOON ### Python package mode From 691504582e97aff11e836620e936ae2a7e7cea32 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 19 Dec 2023 13:56:51 +0100 Subject: [PATCH 1182/1454] Included a filter for empty rows --- relecov_tools/utils.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index c6d112f7..dab67a03 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -45,7 +45,7 @@ def read_json_file(j_file): return data -def read_excel_file(f_name, sheet_name, heading_row, empty_value=True): +def read_excel_file(f_name, sheet_name, heading_row, leave_empty=True): """Read the input excel file and give the information in a list of dictionaries """ @@ -55,14 +55,16 @@ def read_excel_file(f_name, sheet_name, heading_row, empty_value=True): ws_data = [] for row in islice(ws_metadata_lab.values, heading_row, ws_metadata_lab.max_row): l_row = list(row) - data_row = {} # Ignore the empty rows + if all(cell is None for cell in l_row): + continue + data_row = {} for idx in range(0, len(heading)): if l_row[idx] is None: - if empty_value: + if leave_empty: data_row[heading[idx]] = "" else: - data_row[heading[idx]] = "Not Provided" + data_row[heading[idx]] = "Not Provided [GENEPIO:0001668]" else: data_row[heading[idx]] = l_row[idx] ws_data.append(data_row) From c61fae15813c777d7e03d041bf2dc58d684a055d Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 19 Dec 2023 13:58:07 +0100 Subject: [PATCH 1183/1454] Changed prints and some error handling --- relecov_tools/json_validation.py | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) mode change 100644 => 100755 relecov_tools/json_validation.py diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py old mode 100644 new mode 100755 index 9699a27e..fbb7fd3c --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -82,12 +82,14 @@ def validate_instances(self): else: # Count error types for error in validator.iter_errors(item_row): - error_keys[error.message] = error.absolute_path[0] - if error.message in errors.keys(): + try: + error_keys[error.message] = error.absolute_path[0] + except Exception as e: + error_keys[error.message] = error.message + if error.message in errors: errors[error.message] += 1 else: errors[error.message] = 1 - # log.error("Invalid sample data %s", error.message) # append row with errors invalid_json.append(item_row) @@ -136,7 +138,7 @@ def create_invalid_metadata(self, invalid_json, metadata, out_folder): sample_list = [] - stderr.print("[red] Start preparation of invalid samples") + stderr.print("Start preparation of invalid samples") for row in invalid_json: sample_list.append(str(row["collecting_lab_sample_id"])) @@ -153,7 +155,7 @@ def create_invalid_metadata(self, invalid_json, metadata, out_folder): if str(row[2].value) not in sample_list: row_to_del.append(row[0].row) - stderr.print("[red] Collected rows to create the excel file") + stderr.print("Collected rows to create the excel file") if len(row_to_del) > 0: row_to_del.sort(reverse=True) for idx in row_to_del: @@ -165,13 +167,13 @@ def create_invalid_metadata(self, invalid_json, metadata, out_folder): idx, e, ) - stderr.print("f[red] Unable to delete row {idx} becuase of {e}") + stderr.print(f"[red] Unable to delete row {idx} becuase of {e}") sys.exit(1) os.makedirs(out_folder, exist_ok=True) new_name = "invalid_" + os.path.basename(metadata) m_file = os.path.join(out_folder, new_name) - stderr.print("[red] Saving excel file with the invalid samples") + stderr.print("Saving excel file with the invalid samples") wb.save(m_file) return From 347b3252d5b4584478e8473bba72470452b96aff Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 19 Dec 2023 14:01:14 +0100 Subject: [PATCH 1184/1454] Cleaning unused code and changed some prints --- relecov_tools/sftp_handle.py | 17 ++--------------- 1 file changed, 2 insertions(+), 15 deletions(-) mode change 100644 => 100755 relecov_tools/sftp_handle.py diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py old mode 100644 new mode 100755 index 09c9b8ea..ee8d2eca --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -86,29 +86,15 @@ def __init__( self.platform_storage_folder = config_json.get_topic_data( "sftp_handle", "platform_storage_folder" ) - try: - self.abort_if_md5_mismatch = ( - True if config["abort_if_md5_mismatch"] == "True" else False - ) - except KeyError: - self.abort_if_md5_mismatch = ( - True - if config_json.get_topic_data( - "sftp_handle", "abort_if_md5_mismatch" - ) - == "True" - else False - ) self.sftp_user = config["sftp_user"] self.sftp_passwd = config["sftp_passwd"] - self.pp = config["allowed_sample_extensions"] except KeyError as e: log.error("Invalid configuration file %s", e) stderr.print(f"[red] Invalid configuration file {e} !") sys.exit(1) if output_location is not None: if os.path.isdir(output_location): - self.platform_storage_folder = output_location + self.platform_storage_folder = os.path.realpath(output_location) else: log.error("Output location does not exist, aborting") stderr.print("[red] Output location does not exist, aborting") @@ -206,6 +192,7 @@ def get_files_from_sftp_folder(self, folder, files_list): log.info("created the folder to download files %s", local_folder_path) self.open_connection() log.info("Trying to fetch files in remote server") + stderr.print(f"Fetching {len(files_list)} files from {folder}...") for file_list in files_list: try: self.client.get( From 99085dc3a629ada9ab8c258a654d1fc3dc000fbc Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 19 Dec 2023 14:02:57 +0100 Subject: [PATCH 1185/1454] Changed none for not_provided, included accession_fields for ena submission --- relecov_tools/conf/configuration.json | 69 +++++++-------------------- 1 file changed, 18 insertions(+), 51 deletions(-) mode change 100644 => 100755 relecov_tools/conf/configuration.json diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json old mode 100644 new mode 100755 index 8afb3bac..1485158a --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -279,20 +279,20 @@ ], "bioinfo_analysis": { "fixed_values": { - "assembly": "None", - "assembly_params": "None", + "assembly": "Not Provided [GENEPIO:0001668]", + "assembly_params": "Not Provided [GENEPIO:0001668]", "bioinformatics_protocol_software_name": "nf-core/viralrecon", "commercial_open_source_both": "Open Source", "consensus_params": "-p vcf -f", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", "dehosting_method_software_name": "KRAKEN2_KRAKEN2", "depth_of_coverage_threshold": ">10x", - "if_assembly_other": "None", - "if_bioinformatic_protocol_is_other_specify": "None", - "if_consensus_other": "None", - "if_lineage_identification_other": "None", - "if_mapping_other": "None", - "if_preprocessing_other": "None", + "if_assembly_other": "Not Provided [GENEPIO:0001668]", + "if_bioinformatic_protocol_is_other_specify": "Not Provided [GENEPIO:0001668]", + "if_consensus_other": "Not Provided [GENEPIO:0001668]", + "if_lineage_identification_other": "Not Provided [GENEPIO:0001668]", + "if_mapping_other": "Not Provided [GENEPIO:0001668]", + "if_preprocessing_other": "Not Provided [GENEPIO:0001668]", "lineage_analysis_software_name": "pangolin", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", @@ -301,6 +301,10 @@ "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", "variant_calling_software_name": "IVAR_VARIANTS" }, + "feed_empty_fields":{ + "lineage_analysis_date": "Not Provided [GENEPIO:0001668]", + "consensus_sequence_name": "Not Provided [GENEPIO:0001668]" + }, "required_file": { "variants_metrics": "summary_variants_metrics_mqc.csv", "versions": "software_versions.yml", @@ -432,49 +436,6 @@ "instrument_model", "collecting institution" ], - "rename_sample_list_og": [ - "sample_name", - "sample_title", - "geographic_location_(country_and/or_sea)", - "host_subject_id", - "collection_date", - "host_common_name", - "host sex", - "host_scientific_name", - "collector_name", - "collecting institution" - ], - "rename_sample_list_final": [ - "alias", - "title", - "geographic location (country and/or sea)", - "host subject id", - "collection date", - "host common name", - "host sex", - "host scientific name", - "collector name", - "collecting institution" - ], - "common_missing_fields": [ - "subject exposure", - "subject exposure duration", - "type exposure", - "personal protective equipment", - "hospitalisation", - "illness duration", - "illness symptoms", - "host disease outcome", - "host health state", - "definition for seropositive sample", - "library_construction_protocol", - "serotype (required for a seropositive sample)", - "strain", - "host habitat", - "host description", - "gravidity", - "host behaviour" - ], "ena_fixed_fields": { "broker_name": "Instituto de Salud Carlos III", "file_format": "FASTQ", @@ -483,6 +444,12 @@ "study_abstract": "RELECOV is a Spanish Network for genomics surveillance", "insert_size": "0" }, + "accession_fields": [ + "ena_study_accession", + "ena_sample_accession", + "ena_experiment_accession", + "ena_run_accession" + ], "additional_formating": { "sample_description": [ "host_common_name", From a497b7ea7e9593ff79cada4e326316e2d8800642 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 19 Dec 2023 14:05:40 +0100 Subject: [PATCH 1186/1454] changed madrid for comunidad de madrid --- relecov_tools/conf/laboratory_address.json | 75 +++++++++++++++++++--- 1 file changed, 65 insertions(+), 10 deletions(-) mode change 100644 => 100755 relecov_tools/conf/laboratory_address.json diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json old mode 100644 new mode 100755 index 94083a20..62f789ad --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -2,7 +2,7 @@ "Instituto de Salud Carlos III": { "collecting_institution_address": "Crta. Pozuelo Majadahonda S/N,", "collecting_institution_email": "info@isciii.es", - "geo_loc_state": "Madrid", + "geo_loc_state": "Comunidad de Madrid", "geo_loc_region": "Madrid", "geo_loc_city": "Madrid", "geo_loc_country": "Spain", @@ -685,7 +685,7 @@ "Hospital de Mostoles": { "collecting_institution_address": "C. Dr. Luis Montes, S/N", "collecting_institution_email": "", - "geo_loc_state": "Madrid", + "geo_loc_state": "Comunidad de Madrid", "geo_loc_region": "Madrid", "geo_loc_city": "Mostoles", "geo_loc_country": "Spain", @@ -696,7 +696,7 @@ "Hospital Clínico San Carlos": { "collecting_institution_address": "Calle del Prof Martín Lagos", "collecting_institution_email": "", - "geo_loc_state": "Madrid", + "geo_loc_state": "Comunidad de Madrid", "geo_loc_region": "Madrid", "geo_loc_city": "Madrid", "geo_loc_country": "Spain", @@ -707,7 +707,7 @@ "Centro Militar de Veterinaria de la Defensa": { "collecting_institution_address": "C. Darío Gazapo 3", "collecting_institution_email": "", - "geo_loc_state": "Madrid", + "geo_loc_state": "Comunidad de Madrid", "geo_loc_region": "Madrid", "geo_loc_city": "Madrid", "geo_loc_country": "Spain", @@ -718,7 +718,7 @@ "Hospital Universitario Severo Ochoa": { "collecting_institution_address": "Av. de Orellana, s/n, Leganés", "collecting_institution_email": "", - "geo_loc_state": "Madrid", + "geo_loc_state": "Comunidad de Madrid", "geo_loc_region": "Madrid", "geo_loc_city": "Leganes", "geo_loc_country": "Spain", @@ -729,7 +729,7 @@ "Hospital Universitario de Getafe": { "collecting_institution_address": "Carr. Madrid - Toledo, Km 12,500, Getafe", "collecting_institution_email": "", - "geo_loc_state": "Madrid", + "geo_loc_state": "Comunidad de Madrid", "geo_loc_region": "Madrid", "geo_loc_city": "Getafe", "geo_loc_country": "Spain", @@ -740,7 +740,7 @@ "Presidencia de Gobierno": { "collecting_institution_address": "", "collecting_institution_email": "", - "geo_loc_state": "Madrid", + "geo_loc_state": "Comunidad de Madrid", "geo_loc_region": "Madrid", "geo_loc_city": "Madrid", "geo_loc_country": "Spain", @@ -751,7 +751,7 @@ "Ministerio de Sanidad, Servicios Sociales e Igualdad": { "collecting_institution_address": "P.º del Prado, 18", "collecting_institution_email": "", - "geo_loc_state": "Madrid", + "geo_loc_state": "Comunidad de Madrid", "geo_loc_region": "Madrid", "geo_loc_city": "Madrid", "geo_loc_country": "Spain", @@ -949,7 +949,7 @@ "Hospital General Universitario de Elche": { "collecting_institution_address": "Carrer Almazara, 11, Elche", "collecting_institution_email": "", - "geo_loc_state": "Valenciana", + "geo_loc_state": "Comunitat Valenciana", "geo_loc_region": "Alicante", "geo_loc_city": "Elche", "geo_loc_country": "Spain", @@ -957,7 +957,7 @@ "submitting_institution_address": "Carrer Almazara, 11, Elche", "submitting_institution_email": "" }, - "Hospital San Pedro": { + "Hospital Universitario San Pedro": { "collecting_institution_address": "C. Piqueras, 98", "collecting_institution_email": "", "geo_loc_state": "La Rioja", @@ -978,5 +978,60 @@ "submitting_institution": "Hospital Universitario Txagorritxu", "submitting_institution_address": " Jose Atxotegi Kalea, s/n", "submitting_institution_email": "" + }, + "Hospital Universitari Arnau de Vilanova": { + "collecting_institution_address": "Av. Alcalde Rovira Roure, 80", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_region": "Lleida", + "geo_loc_city": "Lleida", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitari Arnau de Vilanova", + "submitting_institution_address": "Av. Alcalde Rovira Roure, 80", + "submitting_institution_email": "" + }, + "Hospital General Universitario de Castellon": { + "collecting_institution_address": "Avinguda de Benicassim, 128", + "collecting_institution_email": "", + "geo_loc_state": "Comunitat Valenciana", + "geo_loc_region": "Castellon", + "geo_loc_city": "Castellon de la Plana", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital General Universitario de Castellon", + "submitting_institution_address": "Avinguda de Benicassim, 128", + "submitting_institution_email": "" + }, + "Hospital Clínico de Valencia": { + "collecting_institution_address": "Av. de Blasco Ibañez, 17", + "collecting_institution_email": "", + "geo_loc_state": "Comunitat Valenciana", + "geo_loc_region": "Valencia", + "geo_loc_city": "Valencia", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital General Universitario de Castellon", + "submitting_institution_address": "Av. de Blasco Ibañez, 17", + "submitting_institution_email": "" + }, + "Hospital Universitario y Politecnico La Fe": { + "collecting_institution_address": "Avinguda de Fernando Abril Martorell, 106", + "collecting_institution_email": "", + "geo_loc_state": "Comunitat Valenciana", + "geo_loc_region": "Valencia", + "geo_loc_city": "Valencia", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario y Politecnico La Fe", + "submitting_institution_address": "Avinguda de Fernando Abril Martorell, 106", + "submitting_institution_email": "" + }, + "Hospital Universitario Doctor Peset": { + "collecting_institution_address": "Av. de Gaspar Aguilar, 90", + "collecting_institution_email": "", + "geo_loc_state": "Comunitat Valenciana", + "geo_loc_region": "Valencia", + "geo_loc_city": "Valencia", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital General Universitario de Castellon", + "submitting_institution_address": "Av. de Gaspar Aguilar, 90", + "submitting_institution_email": "" } } \ No newline at end of file From cf0c0f7214f445be161cb74985f57dc15410bb96 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 19 Dec 2023 14:06:48 +0100 Subject: [PATCH 1187/1454] Included ontology value for other --- relecov_tools/schema/relecov_schema.json | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 2afa9e4c..ce12a11f 100755 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1414,7 +1414,8 @@ "xGen SC2 Midnight1200 Amplicon Panel", "ViroKey SQ FLEX SARS-CoV-2 Primer Set", "NEBNext VarSkip Short SARS-CoV-2 primers", - "Other" + "Not Provided [GENEPIO:0001668]", + "Other [NCIT:C17649]" ], "examples": [ "ARTIC" @@ -1441,7 +1442,8 @@ "xGen SC2 Midnight1200 Amplicon Panel", "ViroKey SQ FLEX SARS-CoV-2 Primer Set", "NEBNext VarSkip Short SARS-CoV-2 primers", - "Other" + "Not Provided [GENEPIO:0001668]", + "Other [NCIT:C17649]" ], "examples": [ "ARTIC v4" @@ -1600,7 +1602,7 @@ "iSeq 100 i1 Reagent v2 (300-cycle) 4 pack", "iSeq 100 i1 Reagent v2 (300-cycle) 8 pack", "Not Provided [GENEPIO:0001668]", - "Other" + "Other [NCIT:C17649]" ], "examples": [ "iSeq 100 i1 Reagent v2 (300-cycle) 8 pack" @@ -1631,7 +1633,7 @@ "PacBio [GENEPIO:0001927]", "BGI", "MGI", - "Other" + "Other [NCIT:C17649]" ], "examples": [ "Illumina" @@ -1654,7 +1656,7 @@ "metatranscriptomic", "synthetic", "viral rna", - "other" + "other [NCIT:C17649]" ], "examples": [ "metagenomic" @@ -1693,7 +1695,7 @@ "Oligo-dT", "Inverse rRNA selection", "ChIP-Seq [GENEPIO:0001947]", - "Other" + "Other [NCIT:C17649]" ], "examples": [ "RANDOM PCR" From e22063e04675d1c802725b000613b386a68a17d5 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 19 Dec 2023 14:25:07 +0100 Subject: [PATCH 1188/1454] Changed click option for upload_ena_protocol module --- relecov_tools/__main__.py | 46 ++++++++++++++++++++------------------- 1 file changed, 24 insertions(+), 22 deletions(-) mode change 100644 => 100755 relecov_tools/__main__.py diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py old mode 100644 new mode 100755 index e75c9c3a..83a7db29 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -262,39 +262,41 @@ def map(origin_schema, json_data, destination_schema, schema_file, output): @click.option("-p", "--password", help="password for the user to login") @click.option("-c", "--center", help="center name") @click.option("-e", "--ena_json", help="where the validated json is") -@click.option( - "-t", "--template_path", help="folder where the ENA templates are located" -) +@click.option("-t", "--template_path", help="Path to ENA templates folder") @click.option( "-a", "--action", type=click.Choice(["ADD", "MODIFY", "CANCEL", "RELEASE"], case_sensitive=False), help="select one of the available options", ) -@click.option("--dev", is_flag=True, default=False) -@click.option( - "-s", - "--accession", - is_flag=False, - flag_value="empty", - default="False", - help="Accession number given after submition, required for RELEASE action", -) +@click.option("--dev", is_flag=True, default=False, help="Test submission") +@click.option("--upload_fastq", is_flag=True, default=False, help="Upload fastq files") +@click.option("-m", "--metadata_types", help="List of metadata xml types to submit") @click.option("-o", "--output_path", help="output folder for the xml generated files") def upload_to_ena( - user, password, center, ena_json, template_path, dev, action, accession, output_path + user, + password, + center, + ena_json, + template_path, + dev, + action, + metadata_types, + upload_fastq, + output_path ): """parse data to create xml files to upload to ena""" upload_ena = relecov_tools.upload_ena_protocol.EnaUpload( - user, - password, - center, - ena_json, - template_path, - dev, - action, - accession, - output_path, + user=user, + passwd=password, + center=center, + source_json=ena_json, + template_path=template_path, + dev=dev, + action=action, + metadata_types=metadata_types, + upload_fastq=upload_fastq, + output_path=output_path, ) upload_ena.upload() From f676ca5d367648cf75cdd181541d7c3b56129c37 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 19 Dec 2023 14:28:13 +0100 Subject: [PATCH 1189/1454] Small changes in error handling and prints --- relecov_tools/read_lab_metadata.py | 40 ++++++++++++++++-------------- 1 file changed, 21 insertions(+), 19 deletions(-) mode change 100644 => 100755 relecov_tools/read_lab_metadata.py diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py old mode 100644 new mode 100755 index 730d33c0..c29dee9e --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -76,7 +76,7 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None except KeyError: log.warning("Property %s does not have 'label' attribute", prop) stderr.print( - "[orange] Property " + prop + " does not have 'label' attribute" + "[orange]Property " + prop + " does not have 'label' attribute" ) continue @@ -155,7 +155,7 @@ def adding_ontology_to_enum(self, m_data): continue if len(ontology_errors) >= 1: stderr.print( - "[red] No ontology could be added in:", + "[red] No ontology could be added in:\n", "\n".join({f"{x} - {y} samples" for x, y in ontology_errors.items()}), ) return m_data @@ -168,10 +168,12 @@ def process_from_json(self, m_data, json_fields): try: m_data[idx].update(json_data[m_data[idx][map_field]]) except KeyError as error: - if str(error.args[0]).lower() == "not provided": + clean_error = re.sub('[\[].*?[\]]', '', str(error.args[0])) + if str(clean_error).lower().strip() == "not provided": log.error("Label was not provided, auto-completing columns") + sample_id = m_data[idx]["collecting_lab_sample_id"] stderr.print( - f"Label {map_field} was not provided in sample {idx}, " + f"Label {map_field} was not provided in sample {sample_id}, " + "auto-completing with Not Provided" ) else: @@ -185,7 +187,7 @@ def process_from_json(self, m_data, json_fields): ) sys.exit(1) fields_to_add = { - x: "Not Provided" for x in json_fields["adding_fields"] + x: "Not Provided [GENEPIO:0001668]" for x in json_fields["adding_fields"] } m_data[idx].update(fields_to_add) return m_data @@ -194,18 +196,18 @@ def adding_fields(self, metadata): """Add information located inside various json file as fields""" for key, values in self.json_req_files.items(): - stderr.print(f"[blue] Processing {key}") + stderr.print(f"[blue]Processing {key}") f_path = os.path.join( os.path.dirname(os.path.realpath(__file__)), "conf", values["file"] ) values["j_data"] = relecov_tools.utils.read_json_file(f_path) metadata = self.process_from_json(metadata, values) - stderr.print(f"[green] Processed {key}") + stderr.print(f"[green]Processed {key}") # As sample data file is comming in an input parameter, it cannot # be inside the configuration json file. # Include Sample information data from sample json file - stderr.print("[blue] Processing sample data file") + stderr.print("[blue]Processing sample data file") s_json = {} s_json["map_field"] = "submitting_lab_sample_id" s_json["adding_fields"] = [ @@ -218,7 +220,7 @@ def adding_fields(self, metadata): ] s_json["j_data"] = relecov_tools.utils.read_json_file(self.sample_list_file) metadata = self.process_from_json(metadata, s_json) - stderr.print("[green] Processed sample data file.") + stderr.print("[green]Processed sample data file.") return metadata def read_configuration_json_files(self): @@ -241,7 +243,7 @@ def read_metadata_file(self): """ heading_row_number = 4 ws_metadata_lab = relecov_tools.utils.read_excel_file( - self.metadata_file, "METADATA_LAB", heading_row_number, False + self.metadata_file, "METADATA_LAB", heading_row_number, leave_empty=False ) valid_metadata_rows = [] errors = {} @@ -256,7 +258,7 @@ def read_metadata_file(self): "Sample ID given for sequencing not found in row %s", row_number ) stderr.print( - f"[red] Sample ID given for sequencing not found in row {row_number}" + f"[red]Sample ID given for sequencing not found in row {row_number}" ) continue for key in row.keys(): @@ -266,7 +268,7 @@ def read_metadata_file(self): if "date" in key.lower(): if row[key] is None or str(row[key]).lower() == "not provided": log.info("Date was not provided") - row[key] = "Not Provided" + row[key] = "Not Provided [GENEPIO:0001668]" elif isinstance(row[key], int) or isinstance(row[key], float): log.info("Date given as an integer. Understood as a year") row[key] = str(int(row[key])) @@ -286,7 +288,7 @@ def read_metadata_file(self): "Invalid date format in sample %s", row_number ) stderr.print( - f"[red] Invalid date format in sample {sample_number}, {key}" + f"[red]Invalid date format in sample {sample_number}, {key}" ) elif "sample id" in key.lower(): if isinstance(row[key], float) or isinstance(row[key], int): @@ -298,23 +300,23 @@ def read_metadata_file(self): property_row[self.label_prop_dict[key]] = row[key] except KeyError as e: log.error("Error when mapping the label %s", e) - stderr.print(f"[red] Error when mapping the label {str(e)}") + stderr.print(f"[red]Error when mapping the label {str(e)}") continue valid_metadata_rows.append(property_row) return valid_metadata_rows, errors def create_metadata_json(self): - stderr.print("[blue] Reading Lab Metadata Excel File") + stderr.print("[blue]Reading Lab Metadata Excel File") valid_metadata_rows, errors = self.read_metadata_file() if len(errors) > 0: - stderr.print("[red] Stopped executing because errors were found") + stderr.print("[red]Stopped executing because errors were found") sys.exit(1) # Continue by adding extra information - stderr.print("[blue] Including additional information") + stderr.print("[blue]Including additional information") extended_metadata = self.adding_fields(valid_metadata_rows) - stderr.print("[blue] Including post processing information") + stderr.print("[blue]Including post processing information") extended_metadata = self.adding_post_processing(extended_metadata) extended_metadata = self.adding_copy_from_other_field(extended_metadata) extended_metadata = self.adding_fixed_fields(extended_metadata) @@ -322,7 +324,7 @@ def create_metadata_json(self): file_name = ( "processed_metadata_lab_" + datetime.now().strftime("%Y_%m_%d") + ".json" ) - stderr.print("[blue] Writting output json file") + stderr.print("[blue]Writting output json file") os.makedirs(self.output_folder, exist_ok=True) file_path = os.path.join(self.output_folder, file_name) relecov_tools.utils.write_json_fo_file(completed_metadata, file_path) From 8996c3d13ffe731f06db0a6ad470074e43dc699a Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 19 Dec 2023 14:29:28 +0100 Subject: [PATCH 1190/1454] Now report is output into a file, also detects not_provided fields --- relecov_tools/map_schema.py | 40 +++++++++++++++++-------------------- 1 file changed, 18 insertions(+), 22 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 31dfe184..80460b59 100755 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -140,18 +140,16 @@ def maping_schemas_based_on_geontology(self): except KeyError as e: if key in required_fields: stderr.print( - f"[red]Required field {key} ontology is missing in relecov schema" + f"[red]Required field {key} ontology missing in relecov schema" ) sys.exit(1) else: errors[key] = str(e) if len(errors) >= 1: output_errs = "\n".join(f"{field}:{info}" for field, info in errors.items()) - log.error( - "Invalid ontology for: %s", - str([field for field in errors.keys()]).strip("[]"), - ) - stderr.print("\nSome ontologies failed mapping. Check mapping_errors.log") + invalid_ontologies = str([field for field in errors.keys()]).strip("[]") + log.error("Invalid ontology for: "+invalid_ontologies) + stderr.print("[yellow]\nGot unmapped ontologies. Check mapping_errors.log") with open("mapping_errors.log", "w") as errs: errs.write("Ontology mapping errors:\n" + output_errs + "\n") return mapped_dict @@ -180,9 +178,6 @@ def additional_formating(self, mapped_json_data): "ENA_fields", "additional_formating" ) fixed_fields = self.config_json.get_topic_data("ENA_fields", "ena_fixed_fields") - not_provided_fields = self.config_json.get_configuration("ENA_fields")[ - "common_missing_fields" - ] if self.destination_schema == "ENA": for idx in range(len(self.json_data)): @@ -190,8 +185,8 @@ def additional_formating(self, mapped_json_data): mapped_json_data[idx][key] = value for key, _ in additional_data.items(): """ - Some fields in ENA need special formatting such as sample_id+date - instead of directly merging them, -- is used as delimiter. + Some fields in ENA need special formatting such as sample_id+date. + Instead of directly merging them, -- is used as delimiter. Also, the Not Provided fields are skipped in this process """ formated_data = { @@ -208,11 +203,6 @@ def additional_formating(self, mapped_json_data): if "fastq_filepath" in key: formated_data[key] = formated_data[key].replace("--", "/") mapped_json_data[idx][key] = formated_data[key] - for _, value in enumerate(not_provided_fields): - if value in mapped_json_data[idx]: - continue - else: - mapped_json_data[idx][value] = "Not Provided" """ This is a temporal solution for library_strategy. Once the values are also mapped by the ontology (not only the fields) this should not be necessary @@ -225,8 +215,12 @@ def additional_formating(self, mapped_json_data): def check_required_fields(self, mapped_json_data, dest_schema): """Checks which required fields are Not Provided""" if dest_schema == "ENA": + # The block below can probably go into an auxiliar function required_fields = self.mapped_to_schema["required"] - + for sample in mapped_json_data: + missing_required = [x for x in required_fields if x not in sample] + for field in missing_required: + sample[field] = "Not Provided" try: not_provided_fields = { sample["isolate"]: [ @@ -237,21 +231,23 @@ def check_required_fields(self, mapped_json_data, dest_schema): for sample in mapped_json_data } except KeyError as e: - print(f"Field {e} could not be found in json data, aborting") + print(f"Field {e} could not be found in json data. Aborting") + print() sys.exit(1) notprov_report = "\n".join( f"Sample {key}: {str(val).strip('[]')}" for key, val in not_provided_fields.items() ) stderr.print( - f"[red]\nSome required fields for {dest_schema} were Not Provided:\n", - "Check mapping_errors.log for more details", + f"[yellow]\nSome required fields for {dest_schema} were Not Provided:", + "[yellow]\nCheck mapping_errors.log for more details", ) with open("mapping_errors.log", "a") as errs: - errs.write("Required fields missing:\n" + notprov_report) + errs.write("Required fields Not Provided:\n" + notprov_report) else: + # Only ENA's schema is supported as yet return - return + return mapped_json_data def write_json_fo_file(self, mapped_json_data): """Write metadata to json file""" From eb42a87e9312c099251929db7f859690bd96d7cd Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 19 Dec 2023 14:31:42 +0100 Subject: [PATCH 1191/1454] Big changes to handle missing data in bioinfo results. Also some code reformatting --- relecov_tools/read_bioinfo_metadata.py | 201 +++++++++++++------------ 1 file changed, 103 insertions(+), 98 deletions(-) mode change 100644 => 100755 relecov_tools/read_bioinfo_metadata.py diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py old mode 100644 new mode 100755 index eb2b670d..435cd59b --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -68,14 +68,43 @@ def __init__( sys.exit(1) self.req_files[key] = f_path - def add_fixed_values(self, j_data): - """include the fixed data defined in configuration""" - f_values = self.configuration.get_topic_data("bioinfo_analysis", "fixed_values") + def add_fixed_values(self, j_data, fixed_values): + """include the fixed data defined in configuration or feed custom empty fields""" + f_values = self.configuration.get_topic_data("bioinfo_analysis", fixed_values) for row in j_data: for field, value in f_values.items(): row[field] = value return j_data + def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): + """Auxiliar function to iterate over variants and mapping tables to map metadata""" + errors=[] + field_errors={} + for row in j_data: + sample_name = row["submitting_lab_sample_id"] + if sample_name in map_data: + for field, value in mapping_fields.items(): + try: + row[field] = map_data[sample_name][value] + except KeyError as e: + field_errors[sample_name] = {field:e} + row[field] = "Not Provided [GENEPIO:0001668]" + continue + else: + errors.append(sample_name) + for field in mapping_fields.keys(): + row[field] = "Not Provided [GENEPIO:0001668]" + if errors: + lenerrs = len(errors) + log.error( + "{0} samples missing in {1}:\n{2}".format(lenerrs, table_name, errors) + ) + stderr.print(f"[red]{lenerrs} samples missing in {table_name}:\n{errors}") + if field_errors: + log.error("Fields not found in {0}:\n{1}".format(table_name, field_errors)) + stderr.print(f"[red]Missing values in {table_name}\n:{field_errors}") + return j_data + def include_data_from_mapping_stats(self, j_data): """By processing mapping stats file the following information is included in schema properties: depth_of_coverage_value, lineage_name, @@ -86,79 +115,66 @@ def include_data_from_mapping_stats(self, j_data): # position of the sample columns inside mapping file sample_position = 4 map_data = relecov_tools.utils.read_csv_file_return_dict( - self.req_files["mapping_stats"], "\t", sample_position + self.req_files["mapping_stats"], sep="\t", key_position=sample_position ) mapping_fields = self.configuration.get_topic_data( "bioinfo_analysis", "mapping_stats" ) - - for row in j_data: - sample_name = row["submitting_lab_sample_id"] - for field, value in mapping_fields.items(): - try: - row[field] = map_data[row["submitting_lab_sample_id"]][value] - except KeyError as e: - log.error("Field %s not found in mapping stats", e) - stderr.print( - f"[red]Field {e} not found in mapping stats for", - f"sample {sample_name}", - ) - sys.exit(1) - return j_data + j_data_with_mapping_stats = self.mapping_over_table( + j_data, map_data, mapping_fields, "mapping stats" + ) + return j_data_with_mapping_stats def include_pangolin_data(self, j_data): """Include pangolin data collecting form each file generated by pangolin""" mapping_fields = self.configuration.get_topic_data( "bioinfo_analysis", "mapping_pangolin" ) + missing_pango=[] for row in j_data: if "-" in row["submitting_lab_sample_id"]: sample_name = row["submitting_lab_sample_id"].replace("-", "_") else: sample_name = row["submitting_lab_sample_id"] - f_name_regex = sample_name + ".pangolin.*.csv" + f_name_regex = sample_name + ".pangolin*.csv" f_path = os.path.join(self.input_folder, f_name_regex) - pangolin_sample_file = glob.glob(f_path) - if pangolin_sample_file: - if len(pangolin_sample_file) == 1: - try: - result_regex = re.search( - "(.*)\.pangolin\.(.*)\.csv", pangolin_sample_file[0] - ) - row["lineage_analysis_date"] = result_regex.group(2) - row["lineage_analysis_date"] = datetime.strptime( - row["lineage_analysis_date"], "%Y%m%d" - ).strftime("%Y-%m-%d") - except Exception as e: - stderr.print( - f"[red] Pattern not found in file name. Error: {e}" - ) - try: - f_data = relecov_tools.utils.read_csv_file_return_dict( - result_regex.group(), "," - ) - except FileNotFoundError as e: - log.error("File %s not found ", e) - stderr.print(f"[red]File {e} not found") - # When file does not exist set all values to empty - for field, value in mapping_fields.items(): - row[field] = "" - continue - # sys.exit(1) - pang_key = list(f_data.keys())[0] - for field, value in mapping_fields.items(): - row[field] = f_data[pang_key][value] - else: - # We need to handle this when more than one analysis in the folder. How can we do this? Use the last one? + pango_files = glob.glob(f_path) + if pango_files: + if len(pango_files) > 1: stderr.print( - "[red] More than one pangolin file found for the same sample " + "[yellow]More than one pangolin file found for sample", + f"[yellow]{sample_name}. Selecting the most recent one", ) - sys.exit(1) + try: + pango_files = sorted( + pango_files, + key=lambda dt: datetime.strptime( + dt.split(".")[-2], "%Y%m%d" + ), + ) + row["lineage_analysis_date"] = pango_files[0].split(".")[-2] + except ValueError as e: + log.error("No date found in %s pangolin files", sample_name) + stderr.print(f"[red]No date found in sample {sample_name}", + f"[red]pangolin filenames: {pango_files}") + stderr.print("[Yellow] Using mapping analysis date instead") + # If no date in pangolin files, set date as analysis date + row["lineage_analysis_date"] = row["analysis_date"] + f_data = relecov_tools.utils.read_csv_file_return_dict( + pango_files[0], sep="," + ) + pang_key = list(f_data.keys())[0] + for field, value in mapping_fields.items(): + row[field] = f_data[pang_key][value] else: - stderr.print(f"[yellow] No pangolin file for sample: {sample_name}") - + missing_pango.append(sample_name) + for field in mapping_fields.keys(): + row[field] = "Not Provided [GENEPIO:0001668]" + if len(missing_pango) >= 1: + stderr.print(f"[yellow]{len(missing_pango)} samples missing pangolin.csv file:") + stderr.print(f"[yellow]{missing_pango}") return j_data def include_consensus_data(self, j_data): @@ -169,6 +185,7 @@ def include_consensus_data(self, j_data): mapping_fields = self.configuration.get_topic_data( "bioinfo_analysis", "mapping_consensus" ) + missing_consens = [] for row in j_data: if "-" in row["submitting_lab_sample_id"]: sample_name = row["submitting_lab_sample_id"].replace("-", "_") @@ -181,22 +198,30 @@ def include_consensus_data(self, j_data): f_path ) except FileNotFoundError as e: - log.error("File %s not found ", e) - stderr.print(f"[red]File {e} not found") + missing_consens.append(e.filename) for item in mapping_fields: - row[item] = "" + row[item] = "Not Provided [GENEPIO:0001668]" continue row["consensus_genome_length"] = str(len(record_fasta)) row["consensus_sequence_name"] = record_fasta.description row["consensus_sequence_filepath"] = self.input_folder row["consensus_sequence_filename"] = f_name row["consensus_sequence_md5"] = relecov_tools.utils.calculate_md5(f_path) - base_calculation = int(row["read_length"]) * len(record_fasta) - if row["submitting_lab_sample_id"] != "": - row["number_of_base_pairs_sequenced"] = str(base_calculation * 2) + if row["read_length"].isdigit(): + base_calculation = int(row["read_length"]) * len(record_fasta) + if row["submitting_lab_sample_id"] != "Not Provided [GENEPIO:0001668]": + row["number_of_base_pairs_sequenced"] = str(base_calculation * 2) + else: + row["number_of_base_pairs_sequenced"] = str(base_calculation) else: - row["number_of_base_pairs_sequenced"] = str(base_calculation) - + row["number_of_base_pairs_sequenced"] = "Not Provided [GENEPIO:0001668]" + conserrs = len(missing_consens) + if conserrs >= 1: + log.error( + "{0} Consensus files missing:\n{1}".format(conserrs, missing_consens) + ) + stderr.print(f"[yellow]{conserrs} samples missing consensus file:") + stderr.print(f"[yellow]\n{missing_consens}") return j_data def parse_long_table(self, long_table_path, output_folder): @@ -213,7 +238,7 @@ def parse_long_table(self, long_table_path, output_folder): sys.exit(1) if not os.path.isfile(table_path): log.error("variants_long_table given file is not a file") - stderr.print("[red]Variants_long_table file, Aborting") + stderr.print("[red]Variants_long_table file do not exist, Aborting") sys.exit(1) long_table = LongTableParse(table_path, output_folder) @@ -221,14 +246,12 @@ def parse_long_table(self, long_table_path, output_folder): return - def include_long_table_path(self, j_data): - """Include the variant long table path by searchin the in input folder - the file name that contains long_table.csv - """ - condition = os.path.join(self.input_folder, "*long_table.csv") + def include_custom_data(self, j_data): + """Include custom fields like variant-long-table path""" + condition = os.path.join(self.input_folder, "*variants_long_table*.csv") f_path = relecov_tools.utils.get_files_match_condition(condition) if len(f_path) == 0: - long_table_path = "" + long_table_path = "Not Provided [GENEPIO:0001668]" else: long_table_path = f_path[0] for row in j_data: @@ -240,37 +263,26 @@ def include_variant_metrics(self, j_data): metric file_exists """ map_data = relecov_tools.utils.read_csv_file_return_dict( - self.req_files["variants_metrics"], "," + self.req_files["variants_metrics"], sep="," ) mapping_fields = self.configuration.get_topic_data( "bioinfo_analysis", "mapping_variant_metrics" ) - for row in j_data: - sample_name = row["submitting_lab_sample_id"] - for field, value in mapping_fields.items(): - try: - row[field] = map_data[row["submitting_lab_sample_id"]][value] - except KeyError as e: - log.error("Field %s not found in mapping stats", e) - stderr.print( - f"[red]Field {e} not found in mapping stats for", - f"sample {sample_name}", - ) - sys.exit(1) - return j_data + j_data_with_variant_metrics = self.mapping_over_table( + j_data, map_data, mapping_fields, "variant metrics" + ) + return j_data_with_variant_metrics def include_software_versions(self, j_data): """Include versions from the yaml version file""" version_fields = self.configuration.get_topic_data( "bioinfo_analysis", "mapping_version" ) - try: versions = relecov_tools.utils.read_yml_file(self.req_files["versions"]) except YAMLError as e: log.error("Unable to process version file return error %s", e) - stderr.print("[red]Unable to process version file") - stderr.print(f" {e}") + stderr.print(f"[red]Unable to process version file {e}") sys.exit(1) for row in j_data: for field, version_data in version_fields.items(): @@ -288,15 +300,6 @@ def collect_info_from_lab_json(self): log.error("%s invalid json file", self.json_file) stderr.print(f"[red] {self.json_file} invalid json file") sys.exit(1) - # j_data = [] - # mapping_fields = self.configuration.get_topic_data( - # "bioinfo_analysis", "required_fields_from_lab_json" - # ) - # for row in json_lab_data: - # j_data_dict = {} - # for lab_field, bio_field in mapping_fields.items(): - # j_data_dict[bio_field] = row[lab_field] - # j_data.append(j_data_dict) return json_lab_data def create_bioinfo_file(self): @@ -307,7 +310,9 @@ def create_bioinfo_file(self): stderr.print("[blue]Reading lab metadata json") j_data = self.collect_info_from_lab_json() stderr.print("[blue]Adding fixed values") - j_data = self.add_fixed_values(j_data) + j_data = self.add_fixed_values(j_data,"fixed_values") + # Creating empty fields that are not managed in case of missing data + j_data = self.add_fixed_values(j_data,"feed_empty_fields") stderr.print("[blue]Adding data from mapping stats") j_data = self.include_data_from_mapping_stats(j_data) stderr.print("[blue]Adding software versions") @@ -321,7 +326,7 @@ def create_bioinfo_file(self): stderr.print("[blue]Parsing variants_long_table info to json format...") self.parse_long_table(self.input_folder, self.output_folder) stderr.print("[blue]Adding variant long table path") - j_data = self.include_long_table_path(j_data) + j_data = self.include_custom_data(j_data) file_name = ( "bioinfo_" + os.path.splitext(os.path.basename(self.json_file))[0] + ".json" ) From 831f4f79051566efcba03ca6d593e4103028b2e2 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 19 Dec 2023 14:33:55 +0100 Subject: [PATCH 1192/1454] Huge changes in how the submission is generated. Also handling of large number of samples --- relecov_tools/upload_ena_protocol.py | 197 +++++++++++++++++++-------- 1 file changed, 137 insertions(+), 60 deletions(-) diff --git a/relecov_tools/upload_ena_protocol.py b/relecov_tools/upload_ena_protocol.py index 9ec92fa3..6f5075c5 100755 --- a/relecov_tools/upload_ena_protocol.py +++ b/relecov_tools/upload_ena_protocol.py @@ -6,6 +6,7 @@ import os import ftplib import relecov_tools.utils +from datetime import datetime from relecov_tools.config_json import ConfigJson from ena_upload.ena_upload import extract_targets @@ -37,7 +38,8 @@ def __init__( template_path=None, dev=None, action=None, - accession=None, + metadata_types=None, + upload_fastq=None, output_path=None, ): if user is None: @@ -62,11 +64,15 @@ def __init__( ) else: self.source_json_file = source_json + if not os.path.exists(self.source_json_file): + log.error("json data file %s does not exist ", self.source_json_file) + stderr.print(f"[red]json data file {self.source_json_file} does not exist") + sys.exit(1) if template_path is None: self.template_path = relecov_tools.utils.prompt_path( msg="Select the folder containing ENA templates" ) - # template_folder = "/home/user/git_repositories/relecov-tools/relecov_tools/templates" + # e.g. template_folder = "/home/user/github_repositories/relecov-tools/relecov_tools/templates" else: self.template_path = template_path if not os.path.exists(self.template_path): @@ -78,14 +84,6 @@ def __init__( ) else: self.dev = dev - if accession == "empty": - self.accession = relecov_tools.utils.prompt_yn_question( - msg="Select the accession number for the submission" - ) - elif accession == "false": - self.accession = False - else: - self.accession = accession if action is None: self.action = relecov_tools.utils.prompt_selection( msg="Select the action to upload to ENA", @@ -96,35 +94,44 @@ def __init__( sys.exit(1) else: self.action = action.upper() + if output_path is None: self.output_path = relecov_tools.utils.prompt_path( msg="Select the folder to store the xml files" ) else: self.output_path = output_path + + self.upload_fastq_files = upload_fastq + + all_metadata_types = ["study","run","experiment","sample"] + if metadata_types is None: + # If not specified, all metadata xmls are generated and submitted + self.metadata_types = all_metadata_types + else: + self.metadata_types = metadata_types.split(",") + if not all(xml in all_metadata_types for xml in self.metadata_types): + wrong_types = [ + xml for xml in self.metadata_types if xml not in all_metadata_types + ] + log.error("Unsupported metadata xml types: "+str(wrong_types)) + stderr.print(f"[red]Unsupported metadata xml types: {wrong_types}") + sys.exit(1) config_json = ConfigJson() self.config_json = config_json - self.checklist = self.config_json.get_configuration("ENA_fields")["checklist"] - - if not os.path.isfile(self.source_json_file): - log.error("json data file %s does not exist ", self.source_json_file) - stderr.print(f"[red]json data file {self.source_json_file} does not exist") - sys.exit(1) - with open(self.source_json_file, "r") as fh: json_data = json.loads(fh.read()) self.json_data = json_data - if self.dev: self.url = "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" else: self.url = "https://www.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA" - def table_formatting(self, schemas_dataframe, source): + def table_formatting(self, schemas_dataframe_raw, source): """Some fields in the dataframe need special formatting""" - formated_df = schemas_dataframe[source] + formated_df = schemas_dataframe_raw[source] formated_df.insert(3, "status", self.action) formated_df.rename( columns={ @@ -133,6 +140,13 @@ def table_formatting(self, schemas_dataframe, source): }, inplace=True, ) + if self.action in ["CANCEL", "MODIFY", "RELEASE"]: + formated_df.rename( + columns={"ena_"+str(source) + "_accession": "accession"}, + inplace=True + ) + if source == "study": + formated_df = formated_df.drop_duplicates(subset=["alias"]) if source == "sample": formated_df.insert(4, "ENA_CHECKLIST", self.checklist) """ @@ -144,46 +158,74 @@ def table_formatting(self, schemas_dataframe, source): formated_df["file_name"] = formated_df["file_name"].str.split("--") formated_df = formated_df.explode("file_name").reset_index(drop=True) formated_df["file_checksum"] = [ - x[1].split("--")[0] if x[0] % 2 == 0 else x[1].split("--")[1] - for x in enumerate(formated_df["file_checksum"]) + x.split("--")[0] if index % 2 == 0 else x.split("--")[1] + for index, x in enumerate(formated_df["file_checksum"]) ] - if source == "study": - formated_df = formated_df.drop_duplicates(subset=["alias"]) - stderr.print("study table:", formated_df) - - if isinstance(self.accession, str): - formated_df["accession"] = self.accession - schemas_dataframe[source] = formated_df - return schemas_dataframe + return formated_df def dataframes_from_json(self, json_data): """The xml is built using a dictionary of dataframes as a base structure""" - source_options = ["study", "sample", "run", "experiment"] + source_options = self.metadata_types + schemas_dataframe = {} schemas_dataframe_raw = {} - + acces_fields = self.config_json.get_topic_data("ENA_fields", "accession_fields") + filtered_access_fields = [ + fd for fd in acces_fields if any(source in fd for source in source_options) + ] + all_missing_accessions = [] + if self.action in ["CANCEL", "MODIFY", "RELEASE"]: + for source in source_options: + missing_accessions = [ + samp["sample_name"] for samp in json_data for fd in + filtered_access_fields if (source in fd and fd not in samp.keys()) + ] + if missing_accessions: + log.error("Found samples in json without proper ena accessions") + stderr.print(f"[red]Found samples missing {source} accession ids:") + all_missing_accessions.extend(missing_accessions) + if all_missing_accessions: + stderr.print(f"Not committed samples:\n", all_missing_accessions) + for source in source_options: source_topic = "_".join(["df", source, "fields"]) source_fields = self.config_json.get_topic_data("ENA_fields", source_topic) + if self.action in ["CANCEL", "MODIFY", "RELEASE"]: + source_fields.append(str("ena_"+source+"_accession")) source_dict = { - field: [sample[field] for sample in json_data] - for field in source_fields + fld: [sample[fld] for sample in json_data if sample["sample_name"] + not in all_missing_accessions] for fld in source_fields } schemas_dataframe_raw[source] = pd.DataFrame.from_dict(source_dict) - schemas_dataframe = self.table_formatting(schemas_dataframe_raw, source) + schemas_dataframe[source] = self.table_formatting(schemas_dataframe_raw, source) return schemas_dataframe - def save_tables(self, schemas_dataframe): + def save_tables(self, schemas_dataframe, date): """Save the dataframes into csv files""" stderr.print(f"Saving dataframes in {self.output_path}") for source, table in schemas_dataframe.items(): - table_name = str(self.output_path + source + "_table.csv") + table_name = str(self.output_path + source + date + "_table.csv") table.to_csv(table_name, sep=",") - def xml_submission(self, schemas_dataframe): + def update_json(self, updated_schemas_df, json_data): + access_dict = {} + updated_json_data = json_data.copy() + for source, table in updated_schemas_df.items(): + access_list = [x for x in table["accession"]] + access_dict[source] = access_list + """run accessions are duplicated for R1/R2 so they need to be removed""" + if source == "run": + del access_dict[source][1::2] + for source, acclist in access_dict.items(): + accession_field_name = str("ena_"+source+"_accession") + for sample, accession in zip(updated_json_data, acclist): + sample[accession_field_name] = accession + return updated_json_data + + def xml_submission(self, json_data, schemas_dataframe, batch_index=None): """The metadata is submitted in an xml format""" - + import pdb; pdb.set_trace() schema_targets = extract_targets(self.action, schemas_dataframe) tool = self.config_json.get_configuration("ENA_fields")["tool"] @@ -212,19 +254,17 @@ def xml_submission(self, schemas_dataframe): self.checklist, tool, ) - schema_xmls["submission"] = submission_xml - """Tree writes an xml file for the run fields""" - """tree = ET.parse(schema_xmls["run"]) - tree.write(schema_xmls["run"])""" - - print(f"\nSubmitting XMLs to ENA server: {self.url}") + stderr.print(f"\nProcessing submission to ENA server: {self.url}") + import pdb; pdb.set_trace() receipt = send_schemas(schema_xmls, self.url, self.user, self.passwd).text if not os.path.exists(self.output_path): os.mkdir(self.output_path) - receipt_dir = os.path.join(self.output_path, "receipt.xml") - print(f"Printing receipt to {receipt_dir}") + date = str(datetime.now().strftime("%Y%m%d-%H%M%S")) + receipt_name = "receipt_"+date+".xml" + receipt_dir = os.path.join(self.output_path, receipt_name) + stderr.print(f"Printing receipt to {receipt_dir}") with open(f"{receipt_dir}", "w") as fw: fw.write(receipt) @@ -233,16 +273,26 @@ def xml_submission(self, schemas_dataframe): except ValueError: log.error("There was an ERROR during submission:") sys.exit(receipt) - if str(self.action) in ["ADD", "MODIFY"]: - schemas_dataframe = update_table( + updated_schemas_df = update_table( schemas_dataframe, schema_targets, schema_update ) else: - schemas_dataframe = update_table_simple( + updated_schemas_df = update_table_simple( schemas_dataframe, schema_targets, self.action ) - self.save_tables(schemas_dataframe) + + updated_json = self.update_json(updated_schemas_df, json_data) + if batch_index == None: + suffix = str("_"+date+".json") + else: + suffix = str("_"+date+"_batch"+str(batch_index)+".json") + updated_json_name = ( + os.path.splitext(os.path.basename(self.source_json_file))[0]+suffix + ) + relecov_tools.utils.write_json_fo_file(updated_json, updated_json_name) + + self.save_tables(updated_schemas_df, date) return def fastq_submission(self, json_data): @@ -261,25 +311,52 @@ def fastq_submission(self, json_data): session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) for filename, path in file_paths.items(): - print("Uploading path " + path + " and filename: " + filename) + stderr.print("Uploading path: " + path + " with filename: " + filename) try: file = open(path, "rb") # file to send g = session.storbinary(f"STOR {filename}", file) - print(g) # send the file + stderr.print(g) # send the file file.close() # close file and FTP except BaseException as err: - print(f"ERROR: {err}") + stderr.print(f"ERROR: {err}") # print("ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000.") g2 = session.quit() - print(g2) - + stderr.print(g2) + return + + def large_json_upload(self, json_data): + """ + Split large json into smaller jsons of maximum size 20 + due to limitations in submissions to ENA's API + """ + ena_api_limit = 20 + number_of_batchs = len(range(0, len(json_data), ena_api_limit)) + stderr.print(f"Splitting the json data in {number_of_batchs} batchs...") + for index, x in range(0, len(json_data), ena_api_limit): + batch_index = str(index+1) + stderr.print(f"[blue]Processing batch {batch_index}...") + self.standard_upload(json_data[x:x+ena_api_limit], batch_index) return - def upload(self): + def standard_upload(self, json_data, batch_index=None): """Create the required files and upload to ENA""" - schemas_dataframe = self.dataframes_from_json(self.json_data) - self.xml_submission(schemas_dataframe) - self.fastq_submission(self.json_data) + schemas_dataframe = self.dataframes_from_json(json_data) + stderr.print("[blue]Successfull creation of dataframes") + if self.upload_fastq_files: + self.fastq_submission(json_data) + stderr.print("Preparing xml files for submission...") + self.xml_submission(json_data, schemas_dataframe, batch_index) + return + def upload(self): + """Handle the data and upload it to ENA""" + if len(self.json_data) <= 50: + self.standard_upload(self.json_data) + else: + stderr.print("[yellow]Json is too large to be submitted. Splitting it...") + self.large_json_upload(self.json_data) stderr.print("[green] Finished execution") return + + + From fda41b0f9d08b7c9e8435423766989e2a70880df Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 19 Dec 2023 15:55:37 +0100 Subject: [PATCH 1193/1454] Big changes in upload_ena_protoccol and other modules, linting1 --- relecov_tools/__main__.py | 16 +++--- relecov_tools/map_schema.py | 2 +- relecov_tools/read_bioinfo_metadata.py | 32 ++++++------ relecov_tools/read_lab_metadata.py | 5 +- relecov_tools/upload_ena_protocol.py | 70 ++++++++++++++------------ 5 files changed, 69 insertions(+), 56 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 83a7db29..a576f9f8 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -274,16 +274,16 @@ def map(origin_schema, json_data, destination_schema, schema_file, output): @click.option("-m", "--metadata_types", help="List of metadata xml types to submit") @click.option("-o", "--output_path", help="output folder for the xml generated files") def upload_to_ena( - user, - password, - center, - ena_json, + user, + password, + center, + ena_json, template_path, - dev, - action, - metadata_types, + dev, + action, + metadata_types, upload_fastq, - output_path + output_path, ): """parse data to create xml files to upload to ena""" upload_ena = relecov_tools.upload_ena_protocol.EnaUpload( diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 80460b59..799e1f1e 100755 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -148,7 +148,7 @@ def maping_schemas_based_on_geontology(self): if len(errors) >= 1: output_errs = "\n".join(f"{field}:{info}" for field, info in errors.items()) invalid_ontologies = str([field for field in errors.keys()]).strip("[]") - log.error("Invalid ontology for: "+invalid_ontologies) + log.error("Invalid ontology for: " + invalid_ontologies) stderr.print("[yellow]\nGot unmapped ontologies. Check mapping_errors.log") with open("mapping_errors.log", "w") as errs: errs.write("Ontology mapping errors:\n" + output_errs + "\n") diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 435cd59b..7761620d 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -78,8 +78,8 @@ def add_fixed_values(self, j_data, fixed_values): def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): """Auxiliar function to iterate over variants and mapping tables to map metadata""" - errors=[] - field_errors={} + errors = [] + field_errors = {} for row in j_data: sample_name = row["submitting_lab_sample_id"] if sample_name in map_data: @@ -87,7 +87,7 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): try: row[field] = map_data[sample_name][value] except KeyError as e: - field_errors[sample_name] = {field:e} + field_errors[sample_name] = {field: e} row[field] = "Not Provided [GENEPIO:0001668]" continue else: @@ -98,7 +98,7 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): lenerrs = len(errors) log.error( "{0} samples missing in {1}:\n{2}".format(lenerrs, table_name, errors) - ) + ) stderr.print(f"[red]{lenerrs} samples missing in {table_name}:\n{errors}") if field_errors: log.error("Fields not found in {0}:\n{1}".format(table_name, field_errors)) @@ -131,7 +131,7 @@ def include_pangolin_data(self, j_data): mapping_fields = self.configuration.get_topic_data( "bioinfo_analysis", "mapping_pangolin" ) - missing_pango=[] + missing_pango = [] for row in j_data: if "-" in row["submitting_lab_sample_id"]: sample_name = row["submitting_lab_sample_id"].replace("-", "_") @@ -150,15 +150,15 @@ def include_pangolin_data(self, j_data): try: pango_files = sorted( pango_files, - key=lambda dt: datetime.strptime( - dt.split(".")[-2], "%Y%m%d" - ), + key=lambda dt: datetime.strptime(dt.split(".")[-2], "%Y%m%d"), ) row["lineage_analysis_date"] = pango_files[0].split(".")[-2] except ValueError as e: log.error("No date found in %s pangolin files", sample_name) - stderr.print(f"[red]No date found in sample {sample_name}", - f"[red]pangolin filenames: {pango_files}") + stderr.print( + f"[red]No date found in sample {sample_name}", + f"[red]pangolin filenames: {pango_files}", + ) stderr.print("[Yellow] Using mapping analysis date instead") # If no date in pangolin files, set date as analysis date row["lineage_analysis_date"] = row["analysis_date"] @@ -173,7 +173,9 @@ def include_pangolin_data(self, j_data): for field in mapping_fields.keys(): row[field] = "Not Provided [GENEPIO:0001668]" if len(missing_pango) >= 1: - stderr.print(f"[yellow]{len(missing_pango)} samples missing pangolin.csv file:") + stderr.print( + f"[yellow]{len(missing_pango)} samples missing pangolin.csv file:" + ) stderr.print(f"[yellow]{missing_pango}") return j_data @@ -218,8 +220,10 @@ def include_consensus_data(self, j_data): conserrs = len(missing_consens) if conserrs >= 1: log.error( - "{0} Consensus files missing:\n{1}".format(conserrs, missing_consens) + "{0} Consensus files missing:\n{1}".format( + conserrs, missing_consens ) + ) stderr.print(f"[yellow]{conserrs} samples missing consensus file:") stderr.print(f"[yellow]\n{missing_consens}") return j_data @@ -310,9 +314,9 @@ def create_bioinfo_file(self): stderr.print("[blue]Reading lab metadata json") j_data = self.collect_info_from_lab_json() stderr.print("[blue]Adding fixed values") - j_data = self.add_fixed_values(j_data,"fixed_values") + j_data = self.add_fixed_values(j_data, "fixed_values") # Creating empty fields that are not managed in case of missing data - j_data = self.add_fixed_values(j_data,"feed_empty_fields") + j_data = self.add_fixed_values(j_data, "feed_empty_fields") stderr.print("[blue]Adding data from mapping stats") j_data = self.include_data_from_mapping_stats(j_data) stderr.print("[blue]Adding software versions") diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index c29dee9e..4c21bc0e 100755 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -168,7 +168,7 @@ def process_from_json(self, m_data, json_fields): try: m_data[idx].update(json_data[m_data[idx][map_field]]) except KeyError as error: - clean_error = re.sub('[\[].*?[\]]', '', str(error.args[0])) + clean_error = re.sub("[\[].*?[\]]", "", str(error.args[0])) if str(clean_error).lower().strip() == "not provided": log.error("Label was not provided, auto-completing columns") sample_id = m_data[idx]["collecting_lab_sample_id"] @@ -187,7 +187,8 @@ def process_from_json(self, m_data, json_fields): ) sys.exit(1) fields_to_add = { - x: "Not Provided [GENEPIO:0001668]" for x in json_fields["adding_fields"] + x: "Not Provided [GENEPIO:0001668]" + for x in json_fields["adding_fields"] } m_data[idx].update(fields_to_add) return m_data diff --git a/relecov_tools/upload_ena_protocol.py b/relecov_tools/upload_ena_protocol.py index 6f5075c5..50f51140 100755 --- a/relecov_tools/upload_ena_protocol.py +++ b/relecov_tools/upload_ena_protocol.py @@ -101,10 +101,10 @@ def __init__( ) else: self.output_path = output_path - - self.upload_fastq_files = upload_fastq - all_metadata_types = ["study","run","experiment","sample"] + self.upload_fastq_files = upload_fastq + + all_metadata_types = ["study", "run", "experiment", "sample"] if metadata_types is None: # If not specified, all metadata xmls are generated and submitted self.metadata_types = all_metadata_types @@ -113,8 +113,8 @@ def __init__( if not all(xml in all_metadata_types for xml in self.metadata_types): wrong_types = [ xml for xml in self.metadata_types if xml not in all_metadata_types - ] - log.error("Unsupported metadata xml types: "+str(wrong_types)) + ] + log.error("Unsupported metadata xml types: " + str(wrong_types)) stderr.print(f"[red]Unsupported metadata xml types: {wrong_types}") sys.exit(1) @@ -142,9 +142,8 @@ def table_formatting(self, schemas_dataframe_raw, source): ) if self.action in ["CANCEL", "MODIFY", "RELEASE"]: formated_df.rename( - columns={"ena_"+str(source) + "_accession": "accession"}, - inplace=True - ) + columns={"ena_" + str(source) + "_accession": "accession"}, inplace=True + ) if source == "study": formated_df = formated_df.drop_duplicates(subset=["alias"]) if source == "sample": @@ -177,8 +176,10 @@ def dataframes_from_json(self, json_data): if self.action in ["CANCEL", "MODIFY", "RELEASE"]: for source in source_options: missing_accessions = [ - samp["sample_name"] for samp in json_data for fd in - filtered_access_fields if (source in fd and fd not in samp.keys()) + samp["sample_name"] + for samp in json_data + for fd in filtered_access_fields + if (source in fd and fd not in samp.keys()) ] if missing_accessions: log.error("Found samples in json without proper ena accessions") @@ -186,18 +187,24 @@ def dataframes_from_json(self, json_data): all_missing_accessions.extend(missing_accessions) if all_missing_accessions: stderr.print(f"Not committed samples:\n", all_missing_accessions) - + for source in source_options: source_topic = "_".join(["df", source, "fields"]) source_fields = self.config_json.get_topic_data("ENA_fields", source_topic) if self.action in ["CANCEL", "MODIFY", "RELEASE"]: - source_fields.append(str("ena_"+source+"_accession")) + source_fields.append(str("ena_" + source + "_accession")) source_dict = { - fld: [sample[fld] for sample in json_data if sample["sample_name"] - not in all_missing_accessions] for fld in source_fields + field: [ + sample[field] + for sample in json_data + if sample["sample_name"] not in all_missing_accessions + ] + for field in source_fields } schemas_dataframe_raw[source] = pd.DataFrame.from_dict(source_dict) - schemas_dataframe[source] = self.table_formatting(schemas_dataframe_raw, source) + schemas_dataframe[source] = self.table_formatting( + schemas_dataframe_raw, source + ) return schemas_dataframe @@ -218,14 +225,16 @@ def update_json(self, updated_schemas_df, json_data): if source == "run": del access_dict[source][1::2] for source, acclist in access_dict.items(): - accession_field_name = str("ena_"+source+"_accession") + accession_field_name = str("ena_" + source + "_accession") for sample, accession in zip(updated_json_data, acclist): sample[accession_field_name] = accession return updated_json_data def xml_submission(self, json_data, schemas_dataframe, batch_index=None): """The metadata is submitted in an xml format""" - import pdb; pdb.set_trace() + import pdb + + pdb.set_trace() schema_targets = extract_targets(self.action, schemas_dataframe) tool = self.config_json.get_configuration("ENA_fields")["tool"] @@ -257,12 +266,14 @@ def xml_submission(self, json_data, schemas_dataframe, batch_index=None): schema_xmls["submission"] = submission_xml stderr.print(f"\nProcessing submission to ENA server: {self.url}") - import pdb; pdb.set_trace() + import pdb + + pdb.set_trace() receipt = send_schemas(schema_xmls, self.url, self.user, self.passwd).text if not os.path.exists(self.output_path): os.mkdir(self.output_path) date = str(datetime.now().strftime("%Y%m%d-%H%M%S")) - receipt_name = "receipt_"+date+".xml" + receipt_name = "receipt_" + date + ".xml" receipt_dir = os.path.join(self.output_path, receipt_name) stderr.print(f"Printing receipt to {receipt_dir}") @@ -284,11 +295,11 @@ def xml_submission(self, json_data, schemas_dataframe, batch_index=None): updated_json = self.update_json(updated_schemas_df, json_data) if batch_index == None: - suffix = str("_"+date+".json") + suffix = str("_" + date + ".json") else: - suffix = str("_"+date+"_batch"+str(batch_index)+".json") + suffix = str("_" + date + "_batch" + str(batch_index) + ".json") updated_json_name = ( - os.path.splitext(os.path.basename(self.source_json_file))[0]+suffix + os.path.splitext(os.path.basename(self.source_json_file))[0] + suffix ) relecov_tools.utils.write_json_fo_file(updated_json, updated_json_name) @@ -323,19 +334,19 @@ def fastq_submission(self, json_data): g2 = session.quit() stderr.print(g2) return - + def large_json_upload(self, json_data): """ - Split large json into smaller jsons of maximum size 20 - due to limitations in submissions to ENA's API + Split large json into smaller jsons of maximum size 20 + due to limitations in submissions to ENA's API """ ena_api_limit = 20 number_of_batchs = len(range(0, len(json_data), ena_api_limit)) stderr.print(f"Splitting the json data in {number_of_batchs} batchs...") - for index, x in range(0, len(json_data), ena_api_limit): - batch_index = str(index+1) + for index, x in range(0, len(json_data), ena_api_limit): + batch_index = str(index + 1) stderr.print(f"[blue]Processing batch {batch_index}...") - self.standard_upload(json_data[x:x+ena_api_limit], batch_index) + self.standard_upload(json_data[x : x + ena_api_limit], batch_index) return def standard_upload(self, json_data, batch_index=None): @@ -357,6 +368,3 @@ def upload(self): self.large_json_upload(self.json_data) stderr.print("[green] Finished execution") return - - - From 9669582f8924072c211e1517cea72fbdc15a957e Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 19 Dec 2023 15:59:55 +0100 Subject: [PATCH 1194/1454] Big changes in upload_ena_protocol and other modules, linting2 --- relecov_tools/json_validation.py | 2 +- relecov_tools/read_bioinfo_metadata.py | 3 +-- relecov_tools/upload_ena_protocol.py | 4 ++-- 3 files changed, 4 insertions(+), 5 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index fbb7fd3c..80891f17 100755 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -84,7 +84,7 @@ def validate_instances(self): for error in validator.iter_errors(item_row): try: error_keys[error.message] = error.absolute_path[0] - except Exception as e: + except Exception: error_keys[error.message] = error.message if error.message in errors: errors[error.message] += 1 diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 7761620d..36ebd5dc 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -2,7 +2,6 @@ import os import sys -import re import logging import glob import rich.console @@ -153,7 +152,7 @@ def include_pangolin_data(self, j_data): key=lambda dt: datetime.strptime(dt.split(".")[-2], "%Y%m%d"), ) row["lineage_analysis_date"] = pango_files[0].split(".")[-2] - except ValueError as e: + except ValueError: log.error("No date found in %s pangolin files", sample_name) stderr.print( f"[red]No date found in sample {sample_name}", diff --git a/relecov_tools/upload_ena_protocol.py b/relecov_tools/upload_ena_protocol.py index 50f51140..f85efc21 100755 --- a/relecov_tools/upload_ena_protocol.py +++ b/relecov_tools/upload_ena_protocol.py @@ -186,7 +186,7 @@ def dataframes_from_json(self, json_data): stderr.print(f"[red]Found samples missing {source} accession ids:") all_missing_accessions.extend(missing_accessions) if all_missing_accessions: - stderr.print(f"Not committed samples:\n", all_missing_accessions) + stderr.print("Not committed samples:\n", all_missing_accessions) for source in source_options: source_topic = "_".join(["df", source, "fields"]) @@ -294,7 +294,7 @@ def xml_submission(self, json_data, schemas_dataframe, batch_index=None): ) updated_json = self.update_json(updated_schemas_df, json_data) - if batch_index == None: + if batch_index is None: suffix = str("_" + date + ".json") else: suffix = str("_" + date + "_batch" + str(batch_index) + ".json") From 467f99de0bf0fa8268571ffc85840573ae4a919f Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 22 Dec 2023 10:48:09 +0100 Subject: [PATCH 1195/1454] Big changes in upload_to_ena and others. Including new lab locations --- relecov_tools/conf/geo_loc_cities.json | 22 ++++- relecov_tools/conf/laboratory_address.json | 105 ++++++++++++++++++++- 2 files changed, 123 insertions(+), 4 deletions(-) mode change 100644 => 100755 relecov_tools/conf/geo_loc_cities.json diff --git a/relecov_tools/conf/geo_loc_cities.json b/relecov_tools/conf/geo_loc_cities.json old mode 100644 new mode 100755 index 75ec4ca8..f3f1c292 --- a/relecov_tools/conf/geo_loc_cities.json +++ b/relecov_tools/conf/geo_loc_cities.json @@ -326,5 +326,25 @@ "Motril":{ "geo_loc_latitude": "36.74611111", "geo_loc_longitude": "-3.515" + }, + "Mataro":{ + "geo_loc_latitude": "41.540444", + "geo_loc_longitude": "2.443782" + }, + "Calella":{ + "geo_loc_latitude": "41.612812", + "geo_loc_longitude": "2.653981" + }, + "Blanes":{ + "geo_loc_latitude": "41.675284", + "geo_loc_longitude": "2.789399" + }, + "Reus":{ + "geo_loc_latitude": "41.154857", + "geo_loc_longitude": "1.106481" + }, + "Tortosa":{ + "geo_loc_latitude": "40.814140", + "geo_loc_longitude": "0.522052" } -} +} \ No newline at end of file diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 62f789ad..5d75807d 100755 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -964,7 +964,7 @@ "geo_loc_region": "La Rioja", "geo_loc_city": "Logroño", "geo_loc_country": "Spain", - "submitting_institution": "Hospital San Pedro", + "submitting_institution": "Hospital Universitario San Pedro", "submitting_institution_address": "C. Piqueras, 98", "submitting_institution_email": "" }, @@ -1009,7 +1009,7 @@ "geo_loc_city": "Valencia", "geo_loc_country": "Spain", "submitting_institution": "Hospital General Universitario de Castellon", - "submitting_institution_address": "Av. de Blasco Ibañez, 17", + "submitting_institution_address": "Avinguda de Benicassim, 128", "submitting_institution_email": "" }, "Hospital Universitario y Politecnico La Fe": { @@ -1031,7 +1031,106 @@ "geo_loc_city": "Valencia", "geo_loc_country": "Spain", "submitting_institution": "Hospital General Universitario de Castellon", - "submitting_institution_address": "Av. de Gaspar Aguilar, 90", + "submitting_institution_address": "Avinguda de Benicassim, 128", + "submitting_institution_email": "" + }, + "Hospital de l'Esperansa": { + "collecting_institution_address": "Ptge. de Sant Josep la Muntanya, 12", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_region": "Barcelona", + "geo_loc_city": "Barcelona", + "geo_loc_country": "Spain", + "submitting_institution": "LABORATORI DE REFERENCIA DE CATALUNYA", + "submitting_institution_address": "Carrer de la Selva, 10", + "submitting_institution_email": "" + }, + "Centre Forum-Parc Salut Mar": { + "collecting_institution_address": "Carrer de Llull, 410", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_region": "Barcelona", + "geo_loc_city": "Barcelona", + "geo_loc_country": "Spain", + "submitting_institution": "LABORATORI DE REFERENCIA DE CATALUNYA", + "submitting_institution_address": "Carrer de la Selva, 10", + "submitting_institution_email": "" + }, + "Hospital Municipal de Badalona": { + "collecting_institution_address": "Via Augusta, 9-13", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_region": "Barcelona", + "geo_loc_city": "Badalona", + "geo_loc_country": "Spain", + "submitting_institution": "LABORATORI DE REFERENCIA DE CATALUNYA", + "submitting_institution_address": "Carrer de la Selva, 10", + "submitting_institution_email": "" + }, + "Hospital de Mataro": { + "collecting_institution_address": "Carrer de Cirera, 230", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_region": "Barcelona", + "geo_loc_city": "Mataro", + "geo_loc_country": "Spain", + "submitting_institution": "LABORATORI DE REFERENCIA DE CATALUNYA", + "submitting_institution_address": "Carrer de la Selva, 10", + "submitting_institution_email": "" + }, + "Parc Sanitari Pere Virgili": { + "collecting_institution_address": "Carrer d'Esteve Terradas, 30", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_region": "Barcelona", + "geo_loc_city": "Barcelona", + "geo_loc_country": "Spain", + "submitting_institution": "LABORATORI DE REFERENCIA DE CATALUNYA", + "submitting_institution_address": "Carrer de la Selva, 10", + "submitting_institution_email": "" + }, + "Hospital Comarcal Sant Jaume de Calella": { + "collecting_institution_address": "Carrer de Sant Jaume, 209-217", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_region": "Barcelona", + "geo_loc_city": "Calella", + "geo_loc_country": "Spain", + "submitting_institution": "LABORATORI DE REFERENCIA DE CATALUNYA", + "submitting_institution_address": "Carrer de la Selva, 10", + "submitting_institution_email": "" + }, + "Hospital Comarcal de la Selva": { + "collecting_institution_address": "Carrer Acces Cala Sant Francesc, 5", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_region": "Barcelona", + "geo_loc_city": "Blanes", + "geo_loc_country": "Spain", + "submitting_institution": "LABORATORI DE REFERENCIA DE CATALUNYA", + "submitting_institution_address": "Carrer de la Selva, 10", + "submitting_institution_email": "" + }, + "Hospital Universitari Sant Joan de Reus": { + "collecting_institution_address": "Avinguda del Doctor Josep Laporte, 2", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_region": "Tarragona", + "geo_loc_city": "Reus", + "geo_loc_country": "Spain", + "submitting_institution": "LABORATORI DE REFERENCIA DE CATALUNYA", + "submitting_institution_address": "Carrer de la Selva, 10", + "submitting_institution_email": "" + }, + "Clinica Terres de l'Ebre": { + "collecting_institution_address": "Plasa 1 d'octubre, 6-7", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_region": "Tarragona", + "geo_loc_city": "Tortosa", + "geo_loc_country": "Spain", + "submitting_institution": "LABORATORI DE REFERENCIA DE CATALUNYA", + "submitting_institution_address": "Carrer de la Selva, 10", "submitting_institution_email": "" } } \ No newline at end of file From 91069e1861991f09f43a6d5286884860016e6bdd Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 23 Jan 2024 16:26:49 +0100 Subject: [PATCH 1196/1454] Included big changes in md5 verification and error handling --- relecov_tools/sftp_handle.py | 757 ++++++++++++++++++++++------------- 1 file changed, 474 insertions(+), 283 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index ee8d2eca..4930c01a 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -3,13 +3,12 @@ from itertools import islice import copy import logging -import glob import json import rich.console import paramiko import sys import os -import shutil +import stat import yaml import openpyxl import relecov_tools.utils @@ -40,8 +39,8 @@ def __init__( ): """Initializes the sftp object""" config_json = ConfigJson() - self.allowed_sample_ext = config_json.get_topic_data( - "sftp_handle", "allowed_sample_extensions" + self.allowed_file_ext = config_json.get_topic_data( + "sftp_handle", "allowed_file_extensions" ) self.sftp_user = user self.sftp_passwd = passwd @@ -105,13 +104,15 @@ def __init__( self.sftp_passwd = relecov_tools.utils.prompt_password( msg="Enter your password" ) - self.allowed_R1_delimiters = config_json.get_topic_data( - "sftp_handle", "allowed_R1_delimiters" + self.metadata_lab_heading = config_json.get_topic_data( + "lab_metadata", "metadata_lab_heading" + ) + self.metadata_processing = config_json.get_topic_data( + "sftp_handle", "metadata_processing" ) - self.allowed_R2_delimiters = config_json.get_topic_data( - "sftp_handle", "allowed_R2_delimiters" + self.avoidable_characters = config_json.get_topic_data( + "sftp_handle", "skip_when_found" ) - self.client = None def open_connection(self): """Establishing sftp connection""" @@ -140,166 +141,202 @@ def close_connection(self): self.client.close() return True - def list_folders(self, folder_name): - """Creates a directories list from the given path""" + def list_remote_folders(self, folder_name, recursive=False): + """Creates a directories list from the given client remote path + + Args: + folder_name (str): folder name in remote path + recursive (bool, optional): finds all subdirectories too. Defaults to False. + + Returns: + directory_list(list(str)): Names of all folders within remote folder + """ log.info("Listing directories in %s", folder_name) directory_list = [] try: - content_list = self.client.listdir(folder_name) + content_list = self.client.listdir_attr(folder_name) except FileNotFoundError as e: log.error("Invalid folder at remote sftp %s", e) return False - for content in content_list: - try: - self.client.listdir(content) - except FileNotFoundError: - continue - directory_list.append(content) + def recursive_list(folder_name, client): + attribute_list = self.client.listdir_attr(folder_name) + for attribute in attribute_list: + if stat.S_ISDIR(attribute.st_mode): + abspath = os.path.join(folder_name, attribute.filename) + directory_list.append(abspath) + recursive_list(abspath, client) + else: + continue + return directory_list + if recursive: + directory_list = recursive_list(folder_name, self.client) + return directory_list + try: + directory_list = [ + item.filename for item in content_list if stat.S_ISDIR(item.st_mode) + ] + except AttributeError as e: + return False return directory_list def get_file_list(self, folder_name): - """Return a tuple with file name and directory path""" + """Return a tuple with file name and directory path from remote + + Args: + folder_name (str): name of folder in remote repository + + Returns: + file_list (list(str)): list of files in remote folder + """ log.info("Listing files in %s", folder_name) file_list = [] - content_list = self.client.listdir(folder_name) - for content in content_list: + content_list = self.client.listdir_attr(folder_name) + file_list = [ + os.path.join(folder_name, content.filename) + for content in content_list + if stat.S_ISREG(content.st_mode) + ] + return file_list + + def get_from_sftp(self, file, destination, exist_ok=False): + """Download a file from remote sftp + + Args: + file (str): path of the file in remote sftp + destination (str): local path of the file after download + exist_ok (bool): Skip download if file exists in local destination + + Returns: + bool: True if download was successful, False if it was not + """ + if os.path.exists(destination) and exist_ok: + return True + else: try: - sub_folder_files = self.client.listdir(folder_name + "/" + content) - for sub_folder_file in sub_folder_files: - file_list.append( - folder_name + "/" + content + "/" + sub_folder_file - ) - except FileNotFoundError: - file_list.append(folder_name + "/" + content) + self.client.get(file, destination) + return True + except FileNotFoundError as e: + log.error("Unable to fetch file %s ", e) + return False - return file_list + def create_local_folder(self, folder, date): + """Create folder to download files in local path using date - def get_files_from_sftp_folder(self, folder, files_list): - """Create the subfolder with the present date and fetch all files from - the sftp server + Args: + folder (str): name of remote folder to be downloaded + date (datetime.datetime): datetime in YYYYMMDD format + + Returns: + local_folder_path(str): path to the new created folder """ log.info("Creating folder %s to download files", folder) - result_data = {"unable_to_fetch": [], "fetched_files": []} - date = datetime.today().strftime("%Y%m%d") - if self.platform_storage_folder == folder: - local_folder_path = os.path.join(self.platform_storage_folder, date) + platform_storage_folder = self.platform_storage_folder + if platform_storage_folder == folder: + local_folder_path = os.path.join(platform_storage_folder, date) else: - local_folder_path = os.path.join(self.platform_storage_folder, folder, date) - result_data["local_folder"] = local_folder_path + local_folder_path = os.path.join(platform_storage_folder, folder, date) os.makedirs(local_folder_path, exist_ok=True) log.info("created the folder to download files %s", local_folder_path) - self.open_connection() + return local_folder_path + + def get_remote_folder_files(self, folder, local_folder, file_list): + """Create the subfolder with the present date and fetch all files from + the remote sftp server + + Args: + folder (str): name of remote folder to be downloaded + local_folder (str): name of local folder to store downloaded files + file_list (list(str)): list of files in remote folder to be downloaded + + Returns: + fetched_files(list(str)): list of successfully downloaded files + """ + fetched_files = list() log.info("Trying to fetch files in remote server") - stderr.print(f"Fetching {len(files_list)} files from {folder}...") - for file_list in files_list: - try: - self.client.get( - file_list, - os.path.join(local_folder_path, os.path.basename(file_list)), - ) - except FileNotFoundError as e: - log.error("Unable to fetch file %s ", e) - result_data["Unable_to_fetch"].append(file_list) - continue - result_data["fetched_files"].append(os.path.basename(file_list)) - return result_data + stderr.print(f"Fetching {len(file_list)} files from {folder}") + for file in file_list: + file_to_fetch = os.path.join(folder, os.path.basename(file)) + output_file = os.path.join(local_folder, os.path.basename(file)) + if self.get_from_sftp(file_to_fetch, output_file, exist_ok=True): + fetched_files.append(os.path.basename(file)) + else: + # Try to download again n times + for _ in range(3): + if self.get_from_sftp(file_to_fetch, output_file): + fetched_files.append(os.path.basename(file)) + break + else: + log.warning( + "Unable to fetch %s from %s after 3 tries", file, folder + ) - def verify_md5_checksum(self, local_folder, file_list): - """Get the md5 value from sftp match with the generated at local - folder + return fetched_files + + def find_remote_md5sum(self, folder, pattern="md5sum"): + """Search for a pattern in remote folder, by default is md5sum + + Args: + folder (str): folder path in remote repository + pattern (str, optional): Regex used to find file. Defaults to "md5sum". + + Returns: + md5_file(str): file basename if found. If not found returns False """ + all_files = self.get_file_list(folder) + md5_file = [file for file in all_files if pattern in file] + if len(md5_file) == 1: + return md5_file[0] + else: + return False + + def verify_md5_checksum(self, local_folder, fetched_files, fetched_md5): + """Check if the md5 value from sftp matches with the one generated locally""" required_retransmition = [] successful_files = [] # fetch the md5 file if exists log.info("Searching for local md5 file") stderr.print("[blue]Verifying file integrity in md5 hashes") - sftp_md5 = relecov_tools.utils.get_md5_from_local_folder(local_folder) - if len(sftp_md5) > 0: - # check md5 checksum for eac file - log.info("md5 file was not found in local, trying to fetch from SFTP") - for f_name, values in sftp_md5.items(): - f_path_name = os.path.join(local_folder, f_name) - # Checksum value is stored in the index 1 - if values[1] == relecov_tools.utils.calculate_md5(f_path_name): - log.info( - "Successful file download for %s in folder %s", - f_name, - local_folder, - ) - successful_files.append(f_name) - else: - required_retransmition.append(f_name) - log.error("%s requested file re-sending", f_name) - if len(set(file_list)) != len(sftp_md5) * 2: - # create the md5 file from the ones not upload to server - req_create_md5 = [ - v - for v in file_list - if (v not in successful_files and not v.endswith("*.md5")) - ] - sftp_md5.update( - relecov_tools.utils.create_md5_files(local_folder, req_create_md5) - ) - return sftp_md5, required_retransmition - - def validate_R1_R2_delimiters(self, f_name, orientation): - """Checks if file is R1 or R2 given a list of allowed delimiters""" - if orientation == "R1": - valid_delimiters = self.allowed_R1_delimiters - elif orientation == "R2": - valid_delimiters = self.allowed_R2_delimiters - else: - log.error("wrong direction parameter, aborting") - return False - matching = [True for x in valid_delimiters if x in f_name] - if len(matching) >= 1: - return True - else: - return False + avoid_chars = self.avoidable_characters + hash_dict = relecov_tools.utils.read_md5_checksum(fetched_md5, avoid_chars) + if not hash_dict: + return False, False + # check md5 checksum for each file + for f_name in hash_dict.keys(): + if f_name not in fetched_files: + # Skip those files in md5sum that were not downloaded by any reason + continue + f_path = os.path.join(local_folder, f_name) + if hash_dict[f_name] == relecov_tools.utils.calculate_md5(f_path): + successful_files.append(f_name) + log.info("Successful file download for %s", f_name) + else: + required_retransmition.append(f_name) + log.warning("%s requested file re-sending", f_name) + return successful_files, required_retransmition def create_files_with_metadata_info( - self, local_folder, file_list, md5_data, metadata_file + self, local_folder, samples_dict, md5_dict, metadata_file ): """Copy metadata file from folder and create a file with the sample names """ - out_folder = self.platform_storage_folder - os.makedirs(out_folder, exist_ok=True) prefix_file_name = "_".join(local_folder.split("/")[-2:]) new_metadata_file = "metadata_lab_" + prefix_file_name + ".xlsx" sample_data_file = "samples_data_" + prefix_file_name + ".json" - sample_data_path = os.path.join(out_folder, sample_data_file) - try: - shutil.copy( - os.path.join(local_folder, metadata_file), - os.path.join(out_folder, new_metadata_file), - ) - except OSError as e: - log.error("Unable to copy Metadata file %s", e) - stderr.print("[red] Unable to copy Metadata file") - return False - data = copy.deepcopy(file_list) - for s_name, values in file_list.items(): - for _, f_name in values.items(): - if not f_name.endswith(tuple(self.allowed_sample_ext)): - stderr.print("[red] " + f_name + " has a not valid extension") - if self.validate_R1_R2_delimiters(f_name, "R1"): - data[s_name]["r1_fastq_filepath"] = md5_data[f_name][0] - data[s_name]["fastq_r1_md5"] = md5_data[f_name][1] - elif self.validate_R1_R2_delimiters(f_name, "R2"): - data[s_name]["r2_fastq_filepath"] = md5_data[f_name][0] - data[s_name]["fastq_r2_md5"] = md5_data[f_name][1] - else: - log.error( - "Sample %s does not have a valid R1 or R2 delimiter", f_name - ) - stderr.print( - f"[red]Orientation for sample {s_name} could not be ensured. \ - Not included in metadata" - ) - pass + sample_data_path = os.path.join(local_folder, sample_data_file) + os.rename(metadata_file, os.path.join(local_folder, new_metadata_file)) + data = copy.deepcopy(samples_dict) + for sample, values in data.items(): + if not all(val for val in values): + del data[sample] + continue + values["r1_fastq_filepath"] = local_folder + values["fastq_r1_md5"] = md5_dict.get(values["sequence_file_R1_fastq"]) + if values.get("sequence_file_R2_fastq"): + values["r2_fastq_filepath"] = local_folder + values["fastq_r2_md5"] = md5_dict.get(values["sequence_file_R2_fastq"]) with open(sample_data_path, "w", encoding="utf-8") as fh: fh.write(json.dumps(data, indent=4, sort_keys=True, ensure_ascii=False)) log.info( @@ -307,37 +344,66 @@ def create_files_with_metadata_info( ) return True - def find_metadata_file(self, local_folder): - """Find excel extension file which contains metatada""" - reg_for_xlsx = os.path.join(local_folder, "*.xlsx") - ex_files = glob.glob(reg_for_xlsx) - if len(ex_files) == 0: - log.error("Excel file for metadata does not exist on %s", local_folder) - stderr.print("[red] Metadata file does not exist on " + local_folder) - return False - if len(ex_files) > 1: - log.error("Too many Excel files on folder %s", local_folder) - stderr.print("[red] Metadata file does not exist on " + local_folder) - return False - return ex_files[0] + def remove_duplicated_values(self, sample_file_dict): + """remove keys that share the same value due to duplication in sample_dict + + Args: + sample_file_dict (dict(str:dict(str:str))): dictionary with sample_name + and fastq-file paths. e.g. {sample1:{r1_fastq_filepath:sample1.fastq.gz}} + + Returns: + clean_sample_dict: sample_dictionary without duplications in values + """ + set_of_values = set() + duplicated_keys = set() + for sample, fastqs in sample_file_dict.items(): + # Dictionary keys are immutable, so you cannot use a regular set for a dict + hashable_fastqs = frozenset(fastqs.items()) + + if hashable_fastqs in set_of_values: + duplicated_keys.add(sample) + else: + set_of_values.add(hashable_fastqs) + non_duplicated_keys = { + k: v for k, v in sample_file_dict.items() if k not in duplicated_keys + } + clean_sample_dict = {key: sample_file_dict[key] for key in non_duplicated_keys} + if duplicated_keys: + log.warning("Found duplicated files in metadata") + stderr.print("[Orange]Found samples in metadata refering to the same file") + stderr.print("[Orange]These samples won't be processed: ", duplicated_keys) + + return clean_sample_dict def get_sample_fastq_file_names(self, local_folder, meta_f_path): - """ """ + """Read excel metadata template and create dictionary with files for each sample + + Args: + local_folder (str): folder where the excel file has been downloaded + meta_f_path (str): path to the downloaded excel file with metadata + + Returns: + clean_sample_dict(dict(str:{str:str})): Nested dictionary for each sample + {sample1: {"sequence_file_R1_fastq": "sample1_R1.fastq.gz", + "sequence_file_R2_fastq": "sample1_R2.fastq.gz"}, + sample2:{...} } + """ if not os.path.isfile(meta_f_path): - log.error("Metadata file does not exists on %s", local_folder) + log.error("Metadata file does not exist on %s", local_folder) stderr.print("[red] METADATA_LAB.xlsx do not exist in" + local_folder) return False wb_file = openpyxl.load_workbook(meta_f_path, data_only=True) - ws_metadata_lab = wb_file["METADATA_LAB"] - sample_file_list = {} + # TODO: Include METADATA_LAB and CAMPO as configuration.json parameters + ws_metadata_lab = wb_file[self.metadata_processing.get("excel_sheet")] + sample_file_dict = {} # find out the index for file names - config_json = ConfigJson() - meta_column_list = config_json.get_topic_data( - "lab_metadata", "metadata_lab_heading" - ) + meta_column_list = self.metadata_lab_heading + header_flag = self.metadata_processing.get("header_flag") header_row = [ - idx + 1 for idx, x in enumerate(ws_metadata_lab.values) if "CAMPO" in x + idx + 1 for idx, x in enumerate(ws_metadata_lab.values) if header_flag in x ][0] + for cell in ws_metadata_lab[header_row]: + cell.value = cell.value.strip() metadata_header = [x.value for x in ws_metadata_lab[header_row]] if meta_column_list != metadata_header[1:]: diffs = [ @@ -364,12 +430,12 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): s_name = str(row[index_sampleID]) except ValueError as e: stderr.print("[red] Unable to convert to string. ", e) - if s_name not in sample_file_list: - sample_file_list[s_name] = {} + if s_name not in sample_file_dict: + sample_file_dict[s_name] = {} else: print("Found duplicated sample ", s_name) if row[index_fastq_r1] is not None: - sample_file_list[s_name]["sequence_file_R1_fastq"] = row[ + sample_file_dict[s_name]["sequence_file_R1_fastq"] = row[ index_fastq_r1 ] else: @@ -379,125 +445,138 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): stderr.print( "[red] No fastq R1 file for sample " + s_name + ". Aborting" ) - sys.exit(1) + continue if row[index_fastq_r2] is not None: - sample_file_list[s_name]["sequence_file_R2_fastq"] = row[ + sample_file_dict[s_name]["sequence_file_R2_fastq"] = row[ index_fastq_r2 ] - return sample_file_list + # Remove duplicated files + clean_sample_dict = self.remove_duplicated_values(sample_file_dict) + return clean_sample_dict - def list_fetched_files(self, fetched_folder): - """Check if the metadata file exists""" - try: - log.info("List files in fetched folder %s", fetched_folder) - fetched_files_list = self.client.listdir(fetched_folder) - except FileNotFoundError as e: - log.error("Invalid folder at remote sftp %s", e) - return False - return fetched_files_list - - def validate_metadata_file(self, fetched_folder): - """Check if the metadata file exists""" - fetched_files_list = self.list_fetched_files(fetched_folder) - meta_files = [fi for fi in fetched_files_list if fi.endswith(".xlsx")] - if len(meta_files) == 0: - log.error("Excel file for metadata does not exist on %s", fetched_folder) - stderr.print("[red] Metadata file does not exist on " + fetched_folder) - return False + def validate_metadata_file(self, remote_folder, local_folder): + """Check if the metadata file exists + + Args: + remote_folder (_type_): _description_ + local_folder (_type_): _description_ + + Raises: + FileNotFoundError: If more than 1 metadata excel file or missing + + Returns: + local_meta_file: Path to downloaded metadata file. + """ + remote_files_list = self.get_file_list(remote_folder) + meta_files = [fi for fi in remote_files_list if fi.endswith(".xlsx")] + if not meta_files: + raise FileNotFoundError(f"Missing metadata file for {remote_folder}") if len(meta_files) > 1: - log.error("Too many Excel files on folder %s", fetched_folder) - stderr.print("[red] Too many metadata files on " + fetched_folder) - return False - target_meta_file = os.path.join(fetched_folder, meta_files[0]) + raise FileNotFoundError(f"[red]Too many metadata files in {remote_folder}") + target_meta_file = meta_files[0] os.makedirs(self.platform_storage_folder, exist_ok=True) - local_meta_file = os.path.join( - self.platform_storage_folder, os.path.basename(target_meta_file) - ) + local_meta_file = os.path.join(local_folder, os.path.basename(target_meta_file)) try: - self.client.get( - target_meta_file, - local_meta_file, - ) - except FileNotFoundError as e: - log.error("Unable to fetch metadata file %s ", e) - return False + self.get_from_sftp(target_meta_file, local_meta_file) + except (IOError, PermissionError) as e: + raise FileNotFoundError(f"[red]Unable to fetch metadata file {e}") log.info( "Obtained metadata file %s from %s", local_meta_file, - fetched_folder, + remote_folder, ) return local_meta_file - def validate_fetched_files(self, fetched_folder): - """Check if the files in the fetched folder are the ones defined in metadata file""" - local_meta_file = self.validate_metadata_file(fetched_folder) - if not local_meta_file: - return False - out_folder = self.platform_storage_folder - allowed_extensions = self.allowed_sample_ext - samples_files_list = self.get_sample_fastq_file_names( + def validate_remote_files(self, remote_folder, local_folder): + """Check if the files in the remote folder are the ones defined in metadata file + + Args: + remote_folder (str): Name of remote folder being validated + local_folder (str): Name of folder where files are being downloaded + + Raises: + FileNotFoundError: If there none of the files in remote folder are valid + + Returns: + sample_files_dict (dict): same structure as self.get_sample_fastq_file_names + local_meta_file (str): location of downloaded metadata excel file + """ + local_meta_file = self.validate_metadata_file(remote_folder, local_folder) + out_folder = os.path.dirname(local_meta_file) + allowed_extensions = self.allowed_file_ext + remote_files_list = [ + os.path.basename(file) for file in self.get_file_list(remote_folder) + ] + filtered_files_list = sorted( + [fi for fi in remote_files_list if fi.endswith(tuple(allowed_extensions))] + ) + sample_files_dict = self.get_sample_fastq_file_names( out_folder, local_meta_file ) - samples_files_list = sorted( - sum([list(fi.values()) for _, fi in samples_files_list.items()], []) + metafiles_list = sorted( + sum([list(fi.values()) for _, fi in sample_files_dict.items()], []) ) - fetched_files_list = self.list_fetched_files(fetched_folder) - filtered_files_list = sorted( - [fi for fi in fetched_files_list if fi.endswith(tuple(allowed_extensions))] - ) - if samples_files_list == filtered_files_list: - log.info("Files in %s match with metadata file", fetched_folder) + if all(file in filtered_files_list for file in metafiles_list): + log.info("Files in %s match with metadata file", remote_folder) stderr.print("Successfully validated files based on metadata") - os.remove(local_meta_file) - return True else: - log.error("Files in %s do not match metadata file", fetched_folder) + log.error("Some files in %s do not match metadata file", remote_folder) stderr.print( - "Files in " - + fetched_folder + "Some files in " + + remote_folder + " do not match the ones described in metadata" ) - set_list = set(filtered_files_list) - mismatch_files = [fi for fi in samples_files_list if fi not in set_list] - mismatch_rev = [fi for fi in set_list if fi not in samples_files_list] + set_list = set(metafiles_list) + mismatch_files = [fi for fi in filtered_files_list if fi not in set_list] + mismatch_rev = [fi for fi in set_list if fi not in filtered_files_list] log.error( - "Files in metadata that are not present in folder: %s", + "Files in folder that are not present in metadata %s", str(mismatch_files), ) log.error( - "Files in folder that are not present in metadata %s", str(mismatch_rev) + "Files in metadata that are not present in folder: %s", + str(mismatch_rev), ) - return False + # Try to check if the metadata filename lacks the proper extension + for sample, values in sample_files_dict.items(): + sample_files_dict[sample] = { + key: file + for key, value in values.items() + for file in filtered_files_list + if any(str(value) + ext in file for ext in allowed_extensions) + } + if not any(value for value in sample_files_dict.values()): + raise FileNotFoundError("No files from metadata found in %s", remote_folder) + return sample_files_dict, local_meta_file - def delete_remote_files(self, fetched_folder, files): - """Delete files from remote server""" - self.open_connection() - stderr.print(f"[blue]Deleting files in {fetched_folder}...") + def delete_remote_files(self, remote_folder, files): + """Delete files from remote folder + + Args: + remote_folder (str): path to folder in remote repository + files (list(str)): list of file basenames in remote repository + """ + stderr.print(f"[blue]Deleting files in {remote_folder}...") for file in files: try: - self.client.remove(os.path.join(fetched_folder, os.path.basename(file))) + self.client.remove(os.path.join(remote_folder, os.path.basename(file))) log.info("%s Deleted from remote server", file) - except Exception as e: - log.error("Could not delete file %s.", e) + except (IOError, PermissionError) as e: + log.error("Could not delete file %s.", str(e)) stderr.print(f"Could not delete file {file}. Error: {e}") continue return - def create_json_with_downloaded_samples(self, sample_file_list, folder): - """From the download information prepare a json file""" - sample_dict = {} - for sample in sample_file_list: - sample_dict[sample] = {"folder": folder} - return json.dumps(sample_dict, indent=4, sort_keys=True, ensure_ascii=False) - - def delete_local_folder(self, local_folder): - """Delete download folder because files does not complain requisites""" - log.info("Deleting local folder %s", local_folder) - shutil.rmtree(local_folder, ignore_errors=True) - return True - def select_target_folders(self): - root_directory_list = self.list_folders(".") + """Find the selected folders in remote if given, else select every folder + + Returns: + folders_to_process (dict(str:list)): Dictionary with folders and their files + """ + root_directory_list = self.list_remote_folders(".") + if not root_directory_list: + log.error("Error while listing folders in remote. Aborting") + sys.exit(1) if self.target_folders == "ALL": log.info("Showing folders from remote SFTP for user selection") target_folders = relecov_tools.utils.prompt_checkbox( @@ -511,16 +590,20 @@ def select_target_folders(self): tf for tf in root_directory_list if tf in self.target_folders ] if not target_folders: - log.error("There are no folders that match selection") + log.error("No remote folders matching selection %s", self.target_folders) + stderr.print("Found no remote folders matching selection") + stderr.print(f"List of remote folders: {str(root_directory_list)}") sys.exit(1) folders_to_process = {} - for folder in target_folders: - list_files = self.get_file_list(folder) - if len(list_files) > 0: - folders_to_process[folder] = list_files - else: - log.info("%s is empty", folder) - continue + for targeted_folder in target_folders: + full_folders = self.list_remote_folders(targeted_folder, recursive=True) + for folder in full_folders: + list_files = self.get_file_list(folder) + if list_files: + folders_to_process[folder] = list_files + else: + log.info("%s is empty", folder) + continue if len(folders_to_process) == 0: log.info("Exiting process, folders were empty.") log.error("There are no files in the selected folders.") @@ -528,65 +611,173 @@ def select_target_folders(self): sys.exit(0) return folders_to_process + def compress_and_update(self, fetched_files, files_to_compress, local_folder): + """compress the given list of files_to_compress and update files_list + + Args: + fetched_files (list(str)): list of all downloaded files + files_to_compress (list(str)): list of files that are uncompressed + + Returns: + fetched_files(list(str)): files list including the new compressed files + """ + compressed_files = list() + for file in files_to_compress: + f_path = os.path.join(local_folder, file) + try: + relecov_tools.utils.compress_file(f_path) + except FileNotFoundError: + log.error("Could not compress file %s", str(file)) + continue + # Remove file after compression is completed + compressed_files.append(file) + os.remove(f_path) + fetched_files = [ + (fi + ".gz" if fi in compressed_files else fi) for fi in fetched_files + ] + return fetched_files + + def process_filedict(self, valid_filedict, clean_fetchlist): + """Process the dictionary from validate_remote_files() to update filenames + and remove samples that failed any validation process. + + Args: + valid_filedict (dict{str:str}): same structure as validate_remote_files() + clean_fetchlist (list(str)): List of files that passed validation process + + Returns: + processed(dict{str:str}): Updated valid_filedict + """ + processed = {} + for sample, vals in valid_filedict.items(): + processed[sample] = { + r1r2_key: fetch + for r1r2_key, file in vals.items() + for fetch in clean_fetchlist + if file in fetch + } + all_fields_complete = all( + key in processed[sample].keys() for key in valid_filedict[sample].keys() + ) + if not all_fields_complete: + del processed[sample] + return processed + def download(self, target_folders, option="download"): + """Manages all the different functions to download files, verify their + integrity and create initial json with filepaths and md5 hashes + + Args: + target_folders (dict): dictionary + option (str, optional): Download option. Defaults to "download". + """ log.info("Initiating download process") + main_folder = self.platform_storage_folder try: - os.makedirs(self.platform_storage_folder, exist_ok=True) + os.makedirs(main_folder, exist_ok=True) except OSError as e: log.error("You do not have permissions to create folder %s", e) sys.exit(1) - os.chdir(self.platform_storage_folder) folders_to_download = target_folders - for folder, files in folders_to_download.items(): + date = datetime.today().strftime("%Y%m%d") + for folder in folders_to_download.keys(): log.info("Processing folder %s", folder) stderr.print("[blue]Processing folder " + folder) + # Check if the connection has been closed due to time limit + self.open_connection() # Validate that the files are the ones described in metadata. - if not self.validate_fetched_files(folder): - log.error("Failed fetched files validation %s", folder) - stderr.print(f"[red]Invalid fetched files in {folder}, aborting") + local_folder = self.create_local_folder(folder, date) + try: + valid_filedict, meta_file = self.validate_remote_files( + folder, local_folder + ) + except FileNotFoundError as failed_validation: + log.error(failed_validation) + stderr.print(f"[red]{failed_validation}") continue - # get the files in each folder - result_data = self.get_files_from_sftp_folder(folder, files) + # Get the files in each folder + files_to_download = [ + fi for vals in valid_filedict.values() for fi in vals.values() + ] + fetched_files = self.get_remote_folder_files( + folder, local_folder, files_to_download + ) log.info("Finished download for folder: %s", folder) stderr.print(f"Finished download for folder {folder}") - - md5_files, req_retransmition = self.verify_md5_checksum( - result_data["local_folder"], result_data["fetched_files"] - ) - # retrasmision of files in folder - if len(req_retransmition) > 0: - restransmition_data = self.get_files_from_sftp_folder( - folder, req_retransmition + remote_md5sum = self.find_remote_md5sum(folder) + if remote_md5sum: + # Get the md5checksum to validate integrity of files after download + fetched_md5 = os.path.join( + local_folder, os.path.basename(remote_md5sum) ) - md5_ret_files, corrupted = self.verify_md5_checksum( - result_data["local_folder"], restransmition_data["fetched_files"] + self.get_from_sftp(file=remote_md5sum, destination=fetched_md5) + fetched_files, req_retransmition = self.verify_md5_checksum( + local_folder, fetched_files, fetched_md5 ) - md5_files.update(md5_ret_files) - if len(corrupted) > 0 and self.abort_if_md5_mismatch: - log.error("Stopping because of corrupted files %s", corrupted) - stderr.print( - f"[red] Stopped processing folder {folder} \ - due to corrupted files {corrupted}" + # retrasmision of files in folder + if req_retransmition: + stderr.print(f"[Orange] Error during download, trying again...") + self.get_remote_folder_files( + folder, local_folder, req_retransmition ) - continue - log.info("Finished md5 check for folder: %s", folder) - stderr.print(f"Successful md5 verification for folder {folder}") - meta_file = self.find_metadata_file(result_data["local_folder"]) - sample_file_list = self.get_sample_fastq_file_names( - result_data["local_folder"], meta_file - ) + saved_files, corrupted = self.verify_md5_checksum( + local_folder, req_retransmition, fetched_md5 + ) + if saved_files: + fetched_files.extend(saved_files) + if corrupted: + log.warning("Found corrupted files: %s", str(corrupted)) + stderr.print(f"Found corrupted files: {str(corrupted)}") + c_paths = [os.path.join(local_folder, cor) for cor in corrupted] + [relecov_tools.utils.safe_remove(file) for file in c_paths] + if self.abort_if_md5_mismatch: + log.error("Aborting, corrupted files %s", str(corrupted)) + stderr.print( + f"[red] Stopped processing folder {folder} \ + due to corrupted files {corrupted}" + ) + relecov_tools.utils.delete_local_folder(local_folder) + continue + log.info("Finished md5 check for folder: %s", folder) + stderr.print(f"Successful md5 verification for folder {folder}") + else: + log.warning("No single md5sum file could be found in %s", folder) + stderr.print(f"[red]No single md5sum could be found in {folder}") + if not fetched_files: + log.warning("No files passed validation in folder %s", folder) + stderr.print(f"No files passed validation process for {folder}") + continue + clean_fetchlist = [ + fi for fi in fetched_files if fi.endswith(tuple(self.allowed_file_ext)) + ] + # Checking for uncompressed files + files_to_compress = [fi for fi in clean_fetchlist if not fi.endswith(".gz")] + if files_to_compress: + comp_files = str(len(files_to_compress)) + log.info("Found %s uncompressed files, compressing...", comp_files) + stderr.print(f"Found {comp_files} uncompressed files, compressing...") + clean_fetchlist = self.compress_and_update( + clean_fetchlist, files_to_compress, local_folder + ) + clean_pathlist = [os.path.join(local_folder, fi) for fi in clean_fetchlist] + md5_hashes = [ + relecov_tools.utils.calculate_md5(file) for file in clean_pathlist + ] + files_md5_dict = dict(zip(clean_fetchlist, md5_hashes)) + processed_filedict = self.process_filedict(valid_filedict, clean_fetchlist) self.create_files_with_metadata_info( - result_data["local_folder"], sample_file_list, md5_files, meta_file + local_folder, processed_filedict, files_md5_dict, meta_file ) - # Collect data to send the request to relecov_platform - self.create_json_with_downloaded_samples(sample_file_list, folder) # If download_option is "download_clean", remove # sftp folder content after download is finished if option == "clean": - self.delete_remote_files(folder, files) + self.delete_remote_files(folder, files_to_download) + stderr.print(f"[green]Finished processing {folder}") + self.close_connection() return def execute_process(self): + """Executes different processes depending on the download_option""" if not self.open_connection(): log.error("Unable to establish connection towards sftp server") stderr.print("[red]Unable to establish sftp connection") From 0b98f71894980c98e980240cfc3df9a4517a45a6 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 23 Jan 2024 16:28:54 +0100 Subject: [PATCH 1197/1454] Included read_md5_checksum and compress_file methods --- relecov_tools/utils.py | 92 ++++++++++++++++++++++++++++++------------ 1 file changed, 66 insertions(+), 26 deletions(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index dab67a03..4487a42e 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -10,6 +10,8 @@ import json import openpyxl import yaml +import gzip +import re from itertools import islice from Bio import SeqIO from rich.console import Console @@ -29,6 +31,14 @@ def file_exists(file_to_check): return False +def safe_remove(file_path): + try: + os.remove(file_path) + except OSError: + return False + return True + + def get_files_match_condition(condition): """find all path names that matches with the condition""" return glob.glob(condition) @@ -75,9 +85,8 @@ def read_excel_file(f_name, sheet_name, heading_row, leave_empty=True): def read_csv_file_return_dict(file_name, sep, key_position=None): """Read csv or tsv file, according to separator, and return a dictionary where the main key is the first column, if key position is None otherwise - the index value of the kwy position is used as key + the index value of the key position is used as key """ - try: with open(file_name, "r") as fh: lines = fh.readlines() @@ -126,7 +135,9 @@ def get_md5_from_local_folder(local_folder): reg_for_md5 = os.path.join(local_folder, "*.md5") # reg_for_non_md5 = os.path.join(local_folder, "*[!.md5]") md5_files = glob.glob(reg_for_md5) - if len(md5_files) > 0: + if not md5_files: + return False + else: for md5_file in md5_files: file_path_name, f_ext = os.path.splitext(md5_file) if not file_exists(file_path_name): @@ -134,11 +145,50 @@ def get_md5_from_local_folder(local_folder): continue file_name = os.path.basename(file_path_name) fh = open(md5_file, "r") - md5_results[file_name] = [local_folder, fh.read()] + md5_results[file_name] = fh.read() fh.close() return md5_results +def read_md5_checksum(file_name, avoid_chars=list()): + """Read MD5_checksum file and return a dict of {file: md5_hash} + + Args: + file_name (str): file containing "md5hash file" in tab separated format + avoid_chars (list(str), optional): Lines with any of these elements + will be skipped. Defaults to list(). + + Returns: + hash_dict(dict): dictionary of {file: md5_hash} + """ + try: + with open(file_name, "r") as file: + content = file.read() + except FileNotFoundError: + raise + clean_content = content.replace("*", "") + lines = clean_content.splitlines() + translation = str.maketrans("", "", "'\"") + if any("\t" in line for line in lines): + lines = [line.strip().translate(translation).split("\t") for line in lines] + else: + lines = [line.strip().translate(translation).split(" ") for line in lines] + clean_lines = [ + x for x in lines if not any(ch in string for ch in avoid_chars for string in x) + ] + # md5sum should always have 2 columns: hash - path + md5_lines = [line for line in clean_lines if len(line) == 2] + hash_dict = {re.split(r"[\\/]", line[1])[-1]: line[0].lower() for line in md5_lines} + return hash_dict + + +def delete_local_folder(folder): + """Delete download folder because files does not complain requisites""" + log.info("Deleting local folder %s", folder) + shutil.rmtree(folder, ignore_errors=True) + return True + + def calculate_md5(file_name): """Calculate the md5 value for the file name""" return hashlib.md5(open(file_name, "rb").read()).hexdigest() @@ -180,28 +230,18 @@ def write_json_fo_file(data, file_name): return True -def write_to_excel_file(data, f_name, sheet_name, post_process=None): - book = openpyxl.Workbook() - sheet = book.active - - for row in data: - sheet.append(row) - # adding one column with row number - if "insert_cols" in post_process: - sheet.insert_cols(post_process["insert_cols"]) - sheet["A1"] = "Campo" - counter = 1 - for i in range(len(data) - 1): - idx = "A" + str(counter + 1) - sheet[idx] = counter - counter += 1 - # adding 3 empty rows - if "insert_rows" in post_process: - for x in range(post_process["insert_rows"]): - sheet.insert_rows(1) - sheet.title = sheet_name - book.save(f_name) - return +def compress_file(file): + """compress a given file with gzip, adding .gz extension afterwards + + Args: + file (str): path to the given file + """ + try: + with open(file, "rb") as raw, gzip.open(f"{file}.gz", "wb") as comp: + comp.writelines(raw) + return True + except FileNotFoundError: + return False def rich_force_colors(): From 6be1b4bee8a136f0d3390de4691c35bab93525ee Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 23 Jan 2024 16:29:36 +0100 Subject: [PATCH 1198/1454] Changed fields to suit the ones in sftp_handle.py --- relecov_tools/conf/configuration.json | 42 +++++++++++---------------- 1 file changed, 17 insertions(+), 25 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 1485158a..920ef209 100755 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -194,36 +194,29 @@ "sftp_server": "sftprelecov.isciii.es", "sftp_port": "22" }, + "metadata_processing": { + "header_flag": "CAMPO", + "excel_sheet": "METADATA_LAB" + }, "abort_if_md5_mismatch": "False", - "platform_storage_folder": "tmp/relecov", - "allowed_sample_extensions": [ - "fastq.gz", - "fasta" - ], - "allowed_R1_delimiters": [ - "_R1_", - "_R1.", - ".R1.", - "Forward", - "forward", - "_1_", - "_1.", - ".1." - ], - "allowed_R2_delimiters": [ - "_R2_", - "_R2.", - ".R2.", - "Reverse", - "reverse", - "_2_", - "_2.", - ".2." + "platform_storage_folder": "/tmp/relecov", + "allowed_file_extensions": [ + ".fastq.gz", + ".fastq", + ".fq", + ".fq.gz", + ".fasta", + ".fasta.gz" ], "allowed_download_options": [ "download_only", "download_clean", "delete_only" + ], + "skip_when_found": [ + "#", + "Hash", + "Path" ] }, "GISAID_configuration": { @@ -369,7 +362,6 @@ "sequencing_sample_id": "sequencing_sample_id" } }, - "md5_file_name": "md5_check_file.csv", "ENA_fields": { "ENA_configuration": { "study_alias": "RELECOV", From 5f5fe7552570788908f0a0a0f4af5a245f5146a6 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 23 Jan 2024 16:45:09 +0100 Subject: [PATCH 1199/1454] Included big changes in md5 verification and error handling, linting --- relecov_tools/sftp_handle.py | 4 ++-- relecov_tools/utils.py | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) mode change 100644 => 100755 relecov_tools/utils.py diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 4930c01a..234a3eb7 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -177,7 +177,7 @@ def recursive_list(folder_name, client): directory_list = [ item.filename for item in content_list if stat.S_ISDIR(item.st_mode) ] - except AttributeError as e: + except AttributeError: return False return directory_list @@ -716,7 +716,7 @@ def download(self, target_folders, option="download"): ) # retrasmision of files in folder if req_retransmition: - stderr.print(f"[Orange] Error during download, trying again...") + stderr.print("[Yellow] Error during download, trying again...") self.get_remote_folder_files( folder, local_folder, req_retransmition ) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py old mode 100644 new mode 100755 index 4487a42e..5cd20039 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -12,6 +12,7 @@ import yaml import gzip import re +import shutil from itertools import islice from Bio import SeqIO from rich.console import Console From 1cc3dcbf43f3dee26bbdafb49bb929dc9375b825 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 29 Jan 2024 12:02:29 +0100 Subject: [PATCH 1200/1454] Small changes in utils.py --- relecov_tools/utils.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 5cd20039..f2461f72 100755 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -179,6 +179,9 @@ def read_md5_checksum(file_name, avoid_chars=list()): ] # md5sum should always have 2 columns: hash - path md5_lines = [line for line in clean_lines if len(line) == 2] + if not md5_lines: + return False + # split paths for both windows "\" and linux "/" using regex [\\/] hash_dict = {re.split(r"[\\/]", line[1])[-1]: line[0].lower() for line in md5_lines} return hash_dict From 688d983b5fa2c83cd6b0bac009c408fbc7b14840 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 29 Jan 2024 12:04:49 +0100 Subject: [PATCH 1201/1454] Included big changes in md5 verifivation and error handling, linting2 --- relecov_tools/gisaid_upload.py | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/relecov_tools/gisaid_upload.py b/relecov_tools/gisaid_upload.py index 597f8698..6e4fd346 100644 --- a/relecov_tools/gisaid_upload.py +++ b/relecov_tools/gisaid_upload.py @@ -103,9 +103,9 @@ def __init__( def complete_mand_fields(self, dataframe): """Complete mandatory empty fields with 'unknown'""" dataframe.loc[dataframe["covv_gender"] == "", "covv_gender"] = "unknown" - dataframe.loc[ - dataframe["covv_patient_age"] == "", "covv_patient_age" - ] = "unknown" + dataframe.loc[dataframe["covv_patient_age"] == "", "covv_patient_age"] = ( + "unknown" + ) authors = [authors_field for authors_field in dataframe["covv_authors"]] if "" in authors or "unknown" in authors: @@ -115,17 +115,17 @@ def complete_mand_fields(self, dataframe): ) sys.exit(1) - dataframe.loc[ - dataframe["covv_subm_lab_addr"] == "", "covv_subm_lab_addr" - ] = "unknown" + dataframe.loc[dataframe["covv_subm_lab_addr"] == "", "covv_subm_lab_addr"] = ( + "unknown" + ) dataframe.loc[dataframe["covv_subm_lab"] == "", "covv_subm_lab"] = "unknown" - dataframe.loc[ - dataframe["covv_orig_lab_addr"] == "", "covv_orig_lab_addr" - ] = "unknown" + dataframe.loc[dataframe["covv_orig_lab_addr"] == "", "covv_orig_lab_addr"] = ( + "unknown" + ) dataframe.loc[dataframe["covv_orig_lab"] == "", "covv_orig_lab"] = "unknown" - dataframe.loc[ - dataframe["covv_patient_status"] == "", "covv_patient_status" - ] = "unknown" + dataframe.loc[dataframe["covv_patient_status"] == "", "covv_patient_status"] = ( + "unknown" + ) dataframe.loc[dataframe["covv_type"] == "", "covv_type"] = "betacoronavirus" dataframe.loc[dataframe["covv_passage"] == "", "covv_passage"] = "Original" From aea08ba1855f88c23938b90a1ddf1d1c23319172 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 30 Jan 2024 12:12:11 +0100 Subject: [PATCH 1202/1454] Big changes in md5 verification, small hotfix for sftp_handle.py --- relecov_tools/sftp_handle.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 234a3eb7..f0b60ba8 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -420,7 +420,7 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): stderr.print("[red]Differences: ", diffs) sys.exit(1) index_sampleID = metadata_header.index( - "Sample ID given by the submitting laboratory" + "Sample ID given for sequencing" ) index_fastq_r1 = metadata_header.index("Sequence file R1 fastq") index_fastq_r2 = metadata_header.index("Sequence file R2 fastq") From e51aa5997c5cdba9df6641550d60c5cdd398a25f Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 31 Jan 2024 11:18:30 +0100 Subject: [PATCH 1203/1454] Big changes in md5 verification, small hotfix for sftp_handle.py, linting --- relecov_tools/sftp_handle.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index f0b60ba8..11f06eb7 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -419,9 +419,7 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): ) stderr.print("[red]Differences: ", diffs) sys.exit(1) - index_sampleID = metadata_header.index( - "Sample ID given for sequencing" - ) + index_sampleID = metadata_header.index("Sample ID given for sequencing") index_fastq_r1 = metadata_header.index("Sequence file R1 fastq") index_fastq_r2 = metadata_header.index("Sequence file R2 fastq") for row in islice(ws_metadata_lab.values, header_row, ws_metadata_lab.max_row): From 065373de388668ab371ac7e3122694cb14df60f2 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 15 Feb 2024 16:11:01 +0100 Subject: [PATCH 1204/1454] Included several changes to resolve conversations in #247 and fixed some bugs I found along the way --- relecov_tools/sftp_handle.py | 235 +++++++++++++++++++++++------------ 1 file changed, 156 insertions(+), 79 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 11f06eb7..580a5d46 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -25,6 +25,11 @@ ) +class MetadataError(Exception): + def __init__(self, message): + super().__init__(message) + + class SftpHandle: def __init__( self, @@ -100,6 +105,8 @@ def __init__( sys.exit(1) if self.sftp_user is None: self.sftp_user = relecov_tools.utils.prompt_text(msg="Enter the user id") + if isinstance(self.target_folders, str): + self.target_folders = self.target_folders.split(",") if self.sftp_passwd is None: self.sftp_passwd = relecov_tools.utils.prompt_password( msg="Enter your password" @@ -113,6 +120,9 @@ def __init__( self.avoidable_characters = config_json.get_topic_data( "sftp_handle", "skip_when_found" ) + self.samples_json_fields = config_json.get_topic_data( + "lab_metadata", "samples_json_fields" + ) def open_connection(self): """Establishing sftp connection""" @@ -138,7 +148,10 @@ def open_connection(self): def close_connection(self): """Closes SFTP connection""" log.info("Closing SFTP connection") - self.client.close() + try: + self.client.close() + except NameError: + return False return True def list_remote_folders(self, folder_name, recursive=False): @@ -155,13 +168,23 @@ def list_remote_folders(self, folder_name, recursive=False): directory_list = [] try: content_list = self.client.listdir_attr(folder_name) - except FileNotFoundError as e: + subfolders = any(stat.S_ISDIR(item.st_mode) for item in content_list) + except (FileNotFoundError, OSError) as e: log.error("Invalid folder at remote sftp %s", e) - return False + raise + if not subfolders: + return [folder_name] def recursive_list(folder_name, client): - attribute_list = self.client.listdir_attr(folder_name) + try: + attribute_list = self.client.listdir_attr(folder_name) + except (FileNotFoundError, OSError) as e: + log.error("Invalid folder at remote sftp %s", e) + raise for attribute in attribute_list: + # Messy workaround for corrupted folder + if "ion_torrent" in attribute.filename: + continue if stat.S_ISDIR(attribute.st_mode): abspath = os.path.join(folder_name, attribute.filename) directory_list.append(abspath) @@ -268,10 +291,7 @@ def get_remote_folder_files(self, folder, local_folder, file_list): fetched_files.append(os.path.basename(file)) break else: - log.warning( - "Unable to fetch %s from %s after 3 tries", file, folder - ) - + log.warning("Couldn't fetch %s from %s after 3 tries", file, folder) return fetched_files def find_remote_md5sum(self, folder, pattern="md5sum"): @@ -301,7 +321,8 @@ def verify_md5_checksum(self, local_folder, fetched_files, fetched_md5): avoid_chars = self.avoidable_characters hash_dict = relecov_tools.utils.read_md5_checksum(fetched_md5, avoid_chars) if not hash_dict: - return False, False + log.warning("md5sum file could not be read, md5 hashes won't be validated") + return fetched_files, False # check md5 checksum for each file for f_name in hash_dict.keys(): if f_name not in fetched_files: @@ -319,10 +340,18 @@ def verify_md5_checksum(self, local_folder, fetched_files, fetched_md5): def create_files_with_metadata_info( self, local_folder, samples_dict, md5_dict, metadata_file ): - """Copy metadata file from folder and create a file with the sample - names + """Copy metadata file from folder, extend samples_dict with md5hash for + each file. Then create a Json file with this dict + + Args: + local_folder (str): Path to folder with downloaded files and output + samples_dict (dict{str:str}): same structure as validate_remote_files() + md5_dict (dict(str:str)): Zipped dict of files_list and md5hash_list + metadata_file (str): Name of the downloaded metadata file to rename it """ - prefix_file_name = "_".join(local_folder.split("/")[-2:]) + samples_to_delete = [] + prefix_file_name = "_".join(local_folder.split("/")[-3:-1]) + # TODO: Move these prefixes to configuration.json new_metadata_file = "metadata_lab_" + prefix_file_name + ".xlsx" sample_data_file = "samples_data_" + prefix_file_name + ".json" sample_data_path = os.path.join(local_folder, sample_data_file) @@ -330,25 +359,29 @@ def create_files_with_metadata_info( data = copy.deepcopy(samples_dict) for sample, values in data.items(): if not all(val for val in values): - del data[sample] + log.warning("Sample %s incomplete. Not added to final Json", sample) + samples_to_delete.append(sample) continue + # TODO: Move these keys to configuration.json values["r1_fastq_filepath"] = local_folder values["fastq_r1_md5"] = md5_dict.get(values["sequence_file_R1_fastq"]) if values.get("sequence_file_R2_fastq"): values["r2_fastq_filepath"] = local_folder values["fastq_r2_md5"] = md5_dict.get(values["sequence_file_R2_fastq"]) + data = {key: val for key, val in data.items() if key not in samples_to_delete} with open(sample_data_path, "w", encoding="utf-8") as fh: fh.write(json.dumps(data, indent=4, sort_keys=True, ensure_ascii=False)) log.info( "Successfully created file with sample names list %s", sample_data_path ) - return True + return def remove_duplicated_values(self, sample_file_dict): """remove keys that share the same value due to duplication in sample_dict Args: sample_file_dict (dict(str:dict(str:str))): dictionary with sample_name + as keys and a dict for both R1 filename and/or R2 if paired-end reads and fastq-file paths. e.g. {sample1:{r1_fastq_filepath:sample1.fastq.gz}} Returns: @@ -393,7 +426,6 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): stderr.print("[red] METADATA_LAB.xlsx do not exist in" + local_folder) return False wb_file = openpyxl.load_workbook(meta_f_path, data_only=True) - # TODO: Include METADATA_LAB and CAMPO as configuration.json parameters ws_metadata_lab = wb_file[self.metadata_processing.get("excel_sheet")] sample_file_dict = {} # find out the index for file names @@ -405,7 +437,10 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): for cell in ws_metadata_lab[header_row]: cell.value = cell.value.strip() metadata_header = [x.value for x in ws_metadata_lab[header_row]] - if meta_column_list != metadata_header[1:]: + if ( + meta_column_list != metadata_header[1:] + and "Sequencing Institution" in metadata_header + ): diffs = [ x for x in (metadata_header[1:] + meta_column_list) @@ -418,8 +453,9 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): "[red]Header in metadata file is different from config file, aborting" ) stderr.print("[red]Differences: ", diffs) - sys.exit(1) + raise MetadataError(f"Metadata header different from config: {diffs}") index_sampleID = metadata_header.index("Sample ID given for sequencing") + index_layout = metadata_header.index("Library Layout") index_fastq_r1 = metadata_header.index("Sequence file R1 fastq") index_fastq_r2 = metadata_header.index("Sequence file R2 fastq") for row in islice(ws_metadata_lab.values, header_row, ws_metadata_lab.max_row): @@ -432,32 +468,43 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): sample_file_dict[s_name] = {} else: print("Found duplicated sample ", s_name) + if row[index_layout] == "paired" and row[index_fastq_r2] is None: + log.error( + "Sample %s is paired-end, but no R2 given", row[index_sampleID] + ) + continue + if row[index_layout] == "single" and row[index_fastq_r2] is not None: + log.error( + "Sample %s is single-end, but R1&R2 given", row[index_sampleID] + ) + continue if row[index_fastq_r1] is not None: + # TODO: move these keys to configuration.json sample_file_dict[s_name]["sequence_file_R1_fastq"] = row[ index_fastq_r1 ] else: - log.error( - "Fastq_R1 not defined in Metadata file for sample %s", s_name - ) + log.error("Fastq_R1 not defined in Metadata for sample %s", s_name) stderr.print( - "[red] No fastq R1 file for sample " + s_name + ". Aborting" + "[red]No fastq R1 file for sample " + s_name + ". Skipping" ) continue if row[index_fastq_r2] is not None: sample_file_dict[s_name]["sequence_file_R2_fastq"] = row[ index_fastq_r2 ] + # if not self.check_sample_files(sample_file_dict[s_name]): + # Remove duplicated files clean_sample_dict = self.remove_duplicated_values(sample_file_dict) return clean_sample_dict - def validate_metadata_file(self, remote_folder, local_folder): + def get_metadata_file(self, remote_folder, local_folder): """Check if the metadata file exists Args: - remote_folder (_type_): _description_ - local_folder (_type_): _description_ + remote_folder (str): path to the folder in remote repository + local_folder (str): path to the local folder Raises: FileNotFoundError: If more than 1 metadata excel file or missing @@ -470,14 +517,14 @@ def validate_metadata_file(self, remote_folder, local_folder): if not meta_files: raise FileNotFoundError(f"Missing metadata file for {remote_folder}") if len(meta_files) > 1: - raise FileNotFoundError(f"[red]Too many metadata files in {remote_folder}") + raise MetadataError(f"[red]Too many metadata files in {remote_folder}") target_meta_file = meta_files[0] os.makedirs(self.platform_storage_folder, exist_ok=True) local_meta_file = os.path.join(local_folder, os.path.basename(target_meta_file)) try: self.get_from_sftp(target_meta_file, local_meta_file) except (IOError, PermissionError) as e: - raise FileNotFoundError(f"[red]Unable to fetch metadata file {e}") + raise type(e)(f"[red]Unable to fetch metadata file {e.name}") log.info( "Obtained metadata file %s from %s", local_meta_file, @@ -493,13 +540,13 @@ def validate_remote_files(self, remote_folder, local_folder): local_folder (str): Name of folder where files are being downloaded Raises: - FileNotFoundError: If there none of the files in remote folder are valid + FileNotFoundError: If none of the files in remote folder are valid Returns: sample_files_dict (dict): same structure as self.get_sample_fastq_file_names local_meta_file (str): location of downloaded metadata excel file """ - local_meta_file = self.validate_metadata_file(remote_folder, local_folder) + local_meta_file = self.get_metadata_file(remote_folder, local_folder) out_folder = os.path.dirname(local_meta_file) allowed_extensions = self.allowed_file_ext remote_files_list = [ @@ -518,7 +565,7 @@ def validate_remote_files(self, remote_folder, local_folder): log.info("Files in %s match with metadata file", remote_folder) stderr.print("Successfully validated files based on metadata") else: - log.error("Some files in %s do not match metadata file", remote_folder) + log.warning("Some files in %s do not match metadata file", remote_folder) stderr.print( "Some files in " + remote_folder @@ -527,24 +574,31 @@ def validate_remote_files(self, remote_folder, local_folder): set_list = set(metafiles_list) mismatch_files = [fi for fi in filtered_files_list if fi not in set_list] mismatch_rev = [fi for fi in set_list if fi not in filtered_files_list] - log.error( - "Files in folder that are not present in metadata %s", - str(mismatch_files), + log.warning( + "Files in folder not present in metadata %s", str(mismatch_files) ) - log.error( - "Files in metadata that are not present in folder: %s", - str(mismatch_rev), + log.warning( + "Files in metadata not present in folder: %s", str(mismatch_rev) ) # Try to check if the metadata filename lacks the proper extension + log.info("Trying to match files without proper file extension") + sample_files_dict = self.process_filedict( + sample_files_dict, filtered_files_list + ) + """ext_dict = {} for sample, values in sample_files_dict.items(): - sample_files_dict[sample] = { - key: file - for key, value in values.items() + ext_dict[sample] = { + key: (file if str(val) in file else None) + for key, val in values.items() for file in filtered_files_list - if any(str(value) + ext in file for ext in allowed_extensions) } + # remove sample if it has missing files + if not all(x in filtered_files_list for x in ext_dict[sample].values()): + log.warning("Sample %s skipped: missing files in sftp", sample) + del ext_dict[sample]""" + """sample_files_dict = copy.deepcopy(ext_dict)""" if not any(value for value in sample_files_dict.values()): - raise FileNotFoundError("No files from metadata found in %s", remote_folder) + raise FileNotFoundError("No files from metadata found in ", remote_folder) return sample_files_dict, local_meta_file def delete_remote_files(self, remote_folder, files): @@ -571,7 +625,8 @@ def select_target_folders(self): Returns: folders_to_process (dict(str:list)): Dictionary with folders and their files """ - root_directory_list = self.list_remote_folders(".") + root_directory_list = self.list_remote_folders(".", recursive=True) + clean_root_list = [folder.replace("./", "") for folder in root_directory_list] if not root_directory_list: log.error("Error while listing folders in remote. Aborting") sys.exit(1) @@ -581,20 +636,22 @@ def select_target_folders(self): msg="Select the folders that will be targeted", choices=sorted(root_directory_list), ) - elif self.target_folders is None: - target_folders = root_directory_list + elif self.target_folders[0] is None and len(self.target_folders) == 1: + target_folders = clean_root_list else: - target_folders = [ - tf for tf in root_directory_list if tf in self.target_folders - ] + target_folders = [tf for tf in self.target_folders if tf in clean_root_list] if not target_folders: log.error("No remote folders matching selection %s", self.target_folders) stderr.print("Found no remote folders matching selection") - stderr.print(f"List of remote folders: {str(root_directory_list)}") + stderr.print(f"List of remote folders: {str(clean_root_list)}") sys.exit(1) folders_to_process = {} for targeted_folder in target_folders: - full_folders = self.list_remote_folders(targeted_folder, recursive=True) + try: + full_folders = self.list_remote_folders(targeted_folder, recursive=True) + except (FileNotFoundError, OSError) as e: + log.error(f"Error during sftp listing. {targeted_folder} skipped:", e) + continue for folder in full_folders: list_files = self.get_file_list(folder) if list_files: @@ -646,20 +703,24 @@ def process_filedict(self, valid_filedict, clean_fetchlist): Returns: processed(dict{str:str}): Updated valid_filedict """ - processed = {} + processed_dict = {} for sample, vals in valid_filedict.items(): - processed[sample] = { - r1r2_key: fetch - for r1r2_key, file in vals.items() - for fetch in clean_fetchlist - if file in fetch - } - all_fields_complete = all( - key in processed[sample].keys() for key in valid_filedict[sample].keys() - ) - if not all_fields_complete: - del processed[sample] - return processed + processed_dict[sample] = {} + for key, val in vals.items(): + processed_dict[sample][key] = None + for file in clean_fetchlist: + if val in file: + processed_dict[sample][key] = file + """processed_dict[sample] = { + key: (file if str(val) in file else None) + for key, val in vals.items() + for file in clean_fetchlist + }""" + # remove sample if it has missing files + if not all(x in clean_fetchlist for x in processed_dict[sample].values()): + log.warning("Sample %s skipped: missing files in sftp", sample) + del processed_dict[sample] + return processed_dict def download(self, target_folders, option="download"): """Manages all the different functions to download files, verify their @@ -679,19 +740,24 @@ def download(self, target_folders, option="download"): folders_to_download = target_folders date = datetime.today().strftime("%Y%m%d") for folder in folders_to_download.keys(): - log.info("Processing folder %s", folder) - stderr.print("[blue]Processing folder " + folder) + # Close previously open connection to avoid timeouts + try: + self.close_connection() + except paramiko.ssh_exception.NoValidConnectionsError: + pass # Check if the connection has been closed due to time limit self.open_connection() + log.info("Processing folder %s", folder) + stderr.print("[blue]Processing folder " + folder) # Validate that the files are the ones described in metadata. local_folder = self.create_local_folder(folder, date) try: valid_filedict, meta_file = self.validate_remote_files( folder, local_folder ) - except FileNotFoundError as failed_validation: + except (FileNotFoundError, MetadataError) as failed_validation: log.error(failed_validation) - stderr.print(f"[red]{failed_validation}") + stderr.print(f"[red]{failed_validation}, skipped") continue # Get the files in each folder files_to_download = [ @@ -700,6 +766,10 @@ def download(self, target_folders, option="download"): fetched_files = self.get_remote_folder_files( folder, local_folder, files_to_download ) + if not fetched_files: + log.warning("No files could be downloaded in folder %s", folder) + stderr.print(f"No files were downloaded process for {folder}") + continue log.info("Finished download for folder: %s", folder) stderr.print(f"Finished download for folder {folder}") remote_md5sum = self.find_remote_md5sum(folder) @@ -709,7 +779,7 @@ def download(self, target_folders, option="download"): local_folder, os.path.basename(remote_md5sum) ) self.get_from_sftp(file=remote_md5sum, destination=fetched_md5) - fetched_files, req_retransmition = self.verify_md5_checksum( + successful_files, req_retransmition = self.verify_md5_checksum( local_folder, fetched_files, fetched_md5 ) # retrasmision of files in folder @@ -722,12 +792,10 @@ def download(self, target_folders, option="download"): local_folder, req_retransmition, fetched_md5 ) if saved_files: - fetched_files.extend(saved_files) + successful_files.extend(saved_files) if corrupted: log.warning("Found corrupted files: %s", str(corrupted)) stderr.print(f"Found corrupted files: {str(corrupted)}") - c_paths = [os.path.join(local_folder, cor) for cor in corrupted] - [relecov_tools.utils.safe_remove(file) for file in c_paths] if self.abort_if_md5_mismatch: log.error("Aborting, corrupted files %s", str(corrupted)) stderr.print( @@ -736,15 +804,14 @@ def download(self, target_folders, option="download"): ) relecov_tools.utils.delete_local_folder(local_folder) continue + hash_dict = relecov_tools.utils.read_md5_checksum( + fetched_md5, self.avoidable_characters + ) log.info("Finished md5 check for folder: %s", folder) - stderr.print(f"Successful md5 verification for folder {folder}") + stderr.print(f"Finished md5 verification for folder {folder}") else: log.warning("No single md5sum file could be found in %s", folder) stderr.print(f"[red]No single md5sum could be found in {folder}") - if not fetched_files: - log.warning("No files passed validation in folder %s", folder) - stderr.print(f"No files passed validation process for {folder}") - continue clean_fetchlist = [ fi for fi in fetched_files if fi.endswith(tuple(self.allowed_file_ext)) ] @@ -758,10 +825,21 @@ def download(self, target_folders, option="download"): clean_fetchlist, files_to_compress, local_folder ) clean_pathlist = [os.path.join(local_folder, fi) for fi in clean_fetchlist] - md5_hashes = [ - relecov_tools.utils.calculate_md5(file) for file in clean_pathlist - ] - files_md5_dict = dict(zip(clean_fetchlist, md5_hashes)) + if remote_md5sum: + # Get hashes from provided md5sum, create them for those not provided + files_md5_dict = {} + for path in clean_pathlist: + f_name = os.path.basename(path) + if f_name in successful_files: + files_md5_dict[f_name] = hash_dict[f_name] + else: + log.info("Generating md5 hash for %s", f_name) + files_md5_dict[f_name] = relecov_tools.utils.calculate_md5(path) + else: + md5_hashes = [ + relecov_tools.utils.calculate_md5(path) for path in clean_pathlist + ] + files_md5_dict = dict(zip(clean_fetchlist, md5_hashes)) processed_filedict = self.process_filedict(valid_filedict, clean_fetchlist) self.create_files_with_metadata_info( local_folder, processed_filedict, files_md5_dict, meta_file @@ -771,7 +849,6 @@ def download(self, target_folders, option="download"): if option == "clean": self.delete_remote_files(folder, files_to_download) stderr.print(f"[green]Finished processing {folder}") - self.close_connection() return def execute_process(self): From da20a3d19a073f09c91460d06a97f8d5460a9cf9 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 15 Feb 2024 16:11:44 +0100 Subject: [PATCH 1205/1454] Included sequencing_institution and a sample_json_fields for sftp_handle module --- relecov_tools/conf/configuration.json | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 920ef209..33bd9cb6 100755 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -19,6 +19,7 @@ "GISAID id", "Originating Laboratory", "Submitting Institution", + "Sequencing Institution", "Sample Collection Date", "Sample Received Date", "Purpose of sampling", @@ -109,7 +110,15 @@ }, "required_copy_from_other_field": { "isolate_sample_id": "sequencing_sample_id" - } + }, + "samples_json_fields": [ + "fastq_r1_md5", + "fastq_r2_md5", + "sequence_file_R1_fastq", + "sequence_file_R2_fastq", + "r1_fastq_filepath", + "r2_fastq_filepath" + ] }, "long_table_heading": [ "SAMPLE", From 3a22ca734977c3b5e14adaf79e0ff50308dc23ec Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 16 Feb 2024 14:05:20 +0100 Subject: [PATCH 1206/1454] Removed commented code and unnecessary variable --- relecov_tools/sftp_handle.py | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 580a5d46..26775fd3 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -548,7 +548,6 @@ def validate_remote_files(self, remote_folder, local_folder): """ local_meta_file = self.get_metadata_file(remote_folder, local_folder) out_folder = os.path.dirname(local_meta_file) - allowed_extensions = self.allowed_file_ext remote_files_list = [ os.path.basename(file) for file in self.get_file_list(remote_folder) ] @@ -585,18 +584,6 @@ def validate_remote_files(self, remote_folder, local_folder): sample_files_dict = self.process_filedict( sample_files_dict, filtered_files_list ) - """ext_dict = {} - for sample, values in sample_files_dict.items(): - ext_dict[sample] = { - key: (file if str(val) in file else None) - for key, val in values.items() - for file in filtered_files_list - } - # remove sample if it has missing files - if not all(x in filtered_files_list for x in ext_dict[sample].values()): - log.warning("Sample %s skipped: missing files in sftp", sample) - del ext_dict[sample]""" - """sample_files_dict = copy.deepcopy(ext_dict)""" if not any(value for value in sample_files_dict.values()): raise FileNotFoundError("No files from metadata found in ", remote_folder) return sample_files_dict, local_meta_file @@ -711,11 +698,6 @@ def process_filedict(self, valid_filedict, clean_fetchlist): for file in clean_fetchlist: if val in file: processed_dict[sample][key] = file - """processed_dict[sample] = { - key: (file if str(val) in file else None) - for key, val in vals.items() - for file in clean_fetchlist - }""" # remove sample if it has missing files if not all(x in clean_fetchlist for x in processed_dict[sample].values()): log.warning("Sample %s skipped: missing files in sftp", sample) From 8207d6aab11a002d341e3381bdb212825b85521f Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 16 Feb 2024 14:06:14 +0100 Subject: [PATCH 1207/1454] Changed info to warning for files not found in md5sum --- relecov_tools/sftp_handle.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 26775fd3..c631547a 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -815,7 +815,7 @@ def download(self, target_folders, option="download"): if f_name in successful_files: files_md5_dict[f_name] = hash_dict[f_name] else: - log.info("Generating md5 hash for %s", f_name) + log.warning("File %s not found in md5sum. Creating it", f_name) files_md5_dict[f_name] = relecov_tools.utils.calculate_md5(path) else: md5_hashes = [ From b56aa159574440769c6515c7d9011a7bb196feae Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 16 Feb 2024 14:08:38 +0100 Subject: [PATCH 1208/1454] Big changes in sftp_handle. Brought back a variable that was necessary --- relecov_tools/sftp_handle.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index c631547a..90ba2894 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -548,6 +548,7 @@ def validate_remote_files(self, remote_folder, local_folder): """ local_meta_file = self.get_metadata_file(remote_folder, local_folder) out_folder = os.path.dirname(local_meta_file) + allowed_extensions = self.allowed_file_ext remote_files_list = [ os.path.basename(file) for file in self.get_file_list(remote_folder) ] From e02fd531e2e19e3f35185d4a064992b2c13bce68 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 19 Feb 2024 10:49:11 +0100 Subject: [PATCH 1209/1454] Typo fixing to anatomical_material_collection_method.json --- relecov_tools/conf/anatomical_material_collection_method.json | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 relecov_tools/conf/anatomical_material_collection_method.json diff --git a/relecov_tools/conf/anatomical_material_collection_method.json b/relecov_tools/conf/anatomical_material_collection_method.json old mode 100644 new mode 100755 From a9b2ceaf847be2858c126d186717071461251be4 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 19 Feb 2024 10:49:45 +0100 Subject: [PATCH 1210/1454] Included multiple laboratories and fixed some addresses --- relecov_tools/conf/laboratory_address.json | 419 +++++++++++++++++---- 1 file changed, 353 insertions(+), 66 deletions(-) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 5d75807d..ef5119df 100755 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -1,13 +1,13 @@ { - "Instituto de Salud Carlos III": { - "collecting_institution_address": "Crta. Pozuelo Majadahonda S/N,", + "Instituto de Salud Carlos III ": { + "collecting_institution_address": "Crta. Pozuelo Majadahonda S/N", "collecting_institution_email": "info@isciii.es", "geo_loc_state": "Comunidad de Madrid", "geo_loc_region": "Madrid", "geo_loc_city": "Madrid", "geo_loc_country": "Spain", "submitting_institution": "Instituto de Salud Carlos III", - "submitting_institution_address": "Crta. Pozuelo Majadahonda S/N,", + "submitting_institution_address": "Crta. Pozuelo Majadahonda S/N", "submitting_institution_email": "info@isciii.es" }, "Hospital de Antequera":{ @@ -254,7 +254,7 @@ "submitting_institution_email": "rbenito@salud.aragon.es" }, "Centro de Investigación Biomédica de Aragón": { - "collecting_institution_address": "Avenida San Juan Bosco 13", + "collecting_institution_address": "Avenida San Juan Bosco, 13", "collecting_institution_email": "mhpstrunk.iacs@aragon.es", "geo_loc_state": "Aragon", "geo_loc_region": "Zaragoza", @@ -265,14 +265,14 @@ "submitting_institution_email": "mhpstrunk.iacs@aragon.es" }, "Hospital Universitario Central de Asturias": { - "collecting_institution_address": " Av. Roma, s/n,", + "collecting_institution_address": "Av. Roma, s/n", "collecting_institution_email": "santiago.melon@sespa.es", "geo_loc_state": "Asturias", "geo_loc_region": "Asturias", - "geo_loc_city": "Asturias", + "geo_loc_city": "Oviedo", "geo_loc_country": "Spain", "submitting_institution": "Hospital Universitario Central de Asturias", - "submitting_institution_address": " Av. Roma, s/n,", + "submitting_institution_address": "Av. Roma, s/n", "submitting_institution_email": "santiago.melon@sespa.es" }, "Servicio de Microbiologia HU Son Espases": { @@ -286,14 +286,14 @@ "submitting_institution_address": " Ctra. Valldemossa 79", "submitting_institution_email": "antonio.oliver@ssib.es" }, - "Hospital Universitario Ntra. Sra de Candelaria": { + "Hospital Universitario Ntra. Sra de Candelaria (HUNSC)": { "collecting_institution_address": "Carretera del Rosario 145", "collecting_institution_email": "jalcflo@gobiernodecanarias.org", "geo_loc_state": "Islas Canarias", "geo_loc_region": "Santa Cruz de Tenerife", "geo_loc_city": "Santa Cruz de Tenerife", "geo_loc_country": "Spain", - "submitting_institution": "Hospital Universitario Ntra. Sra de Candelaria", + "submitting_institution": "Hospital Universitario Ntra. Sra de Candelaria (HUNSC)", "submitting_institution_address": "Carretera del Rosario 145", "submitting_institution_email": "jalcflo@gobiernodecanarias.org" }, @@ -309,14 +309,14 @@ "submitting_institution_email": "jlorenzo@iter.es" }, "Hospital Universitario de Canarias": { - "collecting_institution_address": "Carretera Ofra S/N, La Laguna", + "collecting_institution_address": "Carretera Ofra s/n, La Laguna", "collecting_institution_email": "", "geo_loc_state": "Islas Canarias", "geo_loc_region": "Santa Cruz de Tenerife", "geo_loc_city": "Santa Cruz de Tenerife", "geo_loc_country": "Spain", "submitting_institution": "Hospital Universitario de Canarias", - "submitting_institution_address": "Carretera Ofra S/N, La Laguna", + "submitting_institution_address": "Carretera Ofra s/n, La Laguna", "submitting_institution_email": "" }, "Hospital Universitario de Gran Canaria": { @@ -375,25 +375,25 @@ "submitting_institution_email": "" }, "Hospital General La Mancha Centro": { - "collecting_institution_address": "Av. Constitución, 3, Alcazar de San Juan", + "collecting_institution_address": "Av. Constitución, 3", "collecting_institution_email": "", "geo_loc_state": "Castilla-La Mancha", "geo_loc_region": "Ciudad Real", "geo_loc_city": "Alcazar de San Juan", "geo_loc_country": "Spain", "submitting_institution": "Hospital General La Mancha Centro", - "submitting_institution_address": "Av. Constitución, 3, Alcazar de San Juan", + "submitting_institution_address": "Av. Constitución, 3", "submitting_institution_email": "" }, "Hospital Virgen de Altagracia": { - "collecting_institution_address": "Avda. D. Emiliano García Roldan, s/n, Manzanares,", + "collecting_institution_address": "Avda. D. Emiliano García Roldan, s/n", "collecting_institution_email": "", "geo_loc_state": "Castilla-La Mancha", "geo_loc_region": "Ciudad Real", "geo_loc_city": "Manzanares", "geo_loc_country": "Spain", "submitting_institution": "Hospital Virgen de Altagracia", - "submitting_institution_address": "Avda. D. Emiliano García Roldan, s/n, Manzanares,", + "submitting_institution_address": "Avda. D. Emiliano García Roldan, s/n", "submitting_institution_email": "" }, "Hospital General de Valdepeñas": { @@ -550,48 +550,48 @@ "submitting_institution_address": "Av. Islas Baleares, 3", "submitting_institution_email": "" }, - "Hospital Universitari Vall d’Hebron": { - "collecting_institution_address": " Passeig de la Vall d’Hebron, 119-129", + "Hospital Universitari Vall d'Hebron": { + "collecting_institution_address": " Passeig de la Vall d'Hebron, 119-129", "collecting_institution_email": "", "geo_loc_state": "Cataluña", "geo_loc_region": "Barcelona", "geo_loc_city": "Barcelona", "geo_loc_country": "Spain", - "submitting_institution": "Hospital Universitari Vall d’Hebron", - "submitting_institution_address": " Passeig de la Vall d’Hebron, 119-129", + "submitting_institution": "Hospital Universitari Vall d'Hebron", + "submitting_institution_address": " Passeig de la Vall d'Hebron, 119-129", "submitting_institution_email": "" }, - "Hospital Universitari Germans Trias i Pujol": { + "Hospital Universitari Germans Trias i Pujol (HUGTiP)": { "collecting_institution_address": " Crta del Canyet s/n", "collecting_institution_email": "", "geo_loc_state": "Cataluña", "geo_loc_region": "Barcelona", "geo_loc_city": "Badalona", "geo_loc_country": "Spain", - "submitting_institution": "Hospital Universitari Germans Trias i Pujol", + "submitting_institution": "Hospital Universitari Germans Trias i Pujol (HUGTiP)", "submitting_institution_address": " Crta del Canyet s/n", "submitting_institution_email": "" }, - "Hospital Clínic de Barcelona": { + "Hospital Clínic de Barcelona (HCB)": { "collecting_institution_address": "C/Villarroel 170", "collecting_institution_email": "", "geo_loc_state": "Cataluña", "geo_loc_region": "Barcelona", "geo_loc_city": "Barcelona", "geo_loc_country": "Spain", - "submitting_institution": "Hospital Clínic de Barcelona", + "submitting_institution": "Hospital Clínic de Barcelona (HCB)", "submitting_institution_address": "C/Villarroel 170", "submitting_institution_email": "" }, - "Hospital Universitari Bellvitge": { - "collecting_institution_address": "Carrer Feixa Llarga s/n ", + "Hospital Universitari Bellvitge (HUB)": { + "collecting_institution_address": "Carrer Feixa Llarga s/n", "collecting_institution_email": "", "geo_loc_state": "Cataluña", "geo_loc_region": "Barcelona", "geo_loc_city": "L'Hospitalet de Llobregat", "geo_loc_country": "Spain", "submitting_institution": "Hospital Universitari Bellvitge", - "submitting_institution_address": "Carrer Feixa Llarga s/n ", + "submitting_institution_address": "Carrer Feixa Llarga s/n", "submitting_institution_email": "" }, "Lab Clínic ICS Camp de Tarragona-Terres de l'Ebre. Hospital Joan XXIII": { @@ -716,14 +716,14 @@ "submitting_institution_email": "" }, "Hospital Universitario Severo Ochoa": { - "collecting_institution_address": "Av. de Orellana, s/n, Leganés", + "collecting_institution_address": "Av. de Orellana, s/n", "collecting_institution_email": "", "geo_loc_state": "Comunidad de Madrid", "geo_loc_region": "Madrid", - "geo_loc_city": "Leganes", + "geo_loc_city": "Leganés", "geo_loc_country": "Spain", "submitting_institution": "Hospital Universitario Severo Ochoa", - "submitting_institution_address": "Av. de Orellana, s/n, Leganés", + "submitting_institution_address": "Av. de Orellana, s/n", "submitting_institution_email": "" }, "Hospital Universitario de Getafe": { @@ -826,14 +826,14 @@ "submitting_institution_email": "" }, "Hospital Rafael Méndez de Lorca": { - "collecting_institution_address": "Ctra.N-340, Lorca", + "collecting_institution_address": "Ctra. N-340, Lorca", "collecting_institution_email": "", "geo_loc_state": "Murcia", "geo_loc_region": "Murcia", "geo_loc_city": "Lorca", "geo_loc_country": "Spain", "submitting_institution": "Hospital Rafael Méndez de Lorca", - "submitting_institution_address": "Ctra.N-340, Lorca", + "submitting_institution_address": "Ctra. N-340, Lorca", "submitting_institution_email": "" }, "Hospital de la Vega Lorenzo Guirao": { @@ -847,7 +847,7 @@ "submitting_institution_address": "Vereda de Morcillo, s/n, Cieza", "submitting_institution_email": "" }, - "Hospital Univeristario Donostia": { + "Hospital Universitario Donostia": { "collecting_institution_address": "Begiristain Doktorea Pasealekua, s/n", "collecting_institution_email": "", "geo_loc_state": "Pais Vasco", @@ -870,14 +870,14 @@ "submitting_institution_email": "" }, "Hospital de Mérida": { - "collecting_institution_address": "Av. Don Antonio Campos Hoyos, 26, Mérida", + "collecting_institution_address": "Av. Don Antonio Campos Hoyos, 26", "collecting_institution_email": "", "geo_loc_state": "Extremadura", "geo_loc_region": "Badajoz", "geo_loc_city": "Merida", "geo_loc_country": "Spain", "submitting_institution": "Hospital de Mérida", - "submitting_institution_address": "Av. Don Antonio Campos Hoyos, 26, Mérida", + "submitting_institution_address": "Av. Don Antonio Campos Hoyos, 26", "submitting_institution_email": "" }, "Hospital San Pedro de Alcantara": { @@ -925,14 +925,14 @@ "submitting_institution_email": "" }, "Hospital Clínico Universitario de Santiago": { - "collecting_institution_address": "Rúa da Choupana, s/n, Santiago de Compostela", + "collecting_institution_address": "Rúa da Choupana, s/n", "collecting_institution_email": "", "geo_loc_state": "Galicia", "geo_loc_region": "A Coruña", "geo_loc_city": "Santiago de Compostela", "geo_loc_country": "Spain", "submitting_institution": "Hospital Clínico Universitario de Santiago", - "submitting_institution_address": "Rúa da Choupana, s/n, Santiago de Compostela", + "submitting_institution_address": "Rúa da Choupana, s/n", "submitting_institution_email": "" }, "Hospital Universitario de Navarra": { @@ -946,16 +946,16 @@ "submitting_institution_address": "C. de Irunlarrea, 3, Pamplona", "submitting_institution_email": "" }, - "Hospital General Universitario de Elche": { + "Hospital General Universitario de Elx": { "collecting_institution_address": "Carrer Almazara, 11, Elche", "collecting_institution_email": "", "geo_loc_state": "Comunitat Valenciana", "geo_loc_region": "Alicante", "geo_loc_city": "Elche", "geo_loc_country": "Spain", - "submitting_institution": "Hospital General Universitario de Elche", - "submitting_institution_address": "Carrer Almazara, 11, Elche", - "submitting_institution_email": "" + "submitting_institution": "FISABIO-Epidemiología Molecular", + "submitting_institution_address": "Av. Roma, s/n", + "submitting_institution_email": "santiago.melon@sespa.es" }, "Hospital Universitario San Pedro": { "collecting_institution_address": "C. Piqueras, 98", @@ -990,49 +990,38 @@ "submitting_institution_address": "Av. Alcalde Rovira Roure, 80", "submitting_institution_email": "" }, - "Hospital General Universitario de Castellon": { - "collecting_institution_address": "Avinguda de Benicassim, 128", - "collecting_institution_email": "", - "geo_loc_state": "Comunitat Valenciana", - "geo_loc_region": "Castellon", - "geo_loc_city": "Castellon de la Plana", - "geo_loc_country": "Spain", - "submitting_institution": "Hospital General Universitario de Castellon", - "submitting_institution_address": "Avinguda de Benicassim, 128", - "submitting_institution_email": "" - }, - "Hospital Clínico de Valencia": { + "Hospital Clínico Universitario de Valencia": { "collecting_institution_address": "Av. de Blasco Ibañez, 17", "collecting_institution_email": "", "geo_loc_state": "Comunitat Valenciana", "geo_loc_region": "Valencia", "geo_loc_city": "Valencia", "geo_loc_country": "Spain", - "submitting_institution": "Hospital General Universitario de Castellon", - "submitting_institution_address": "Avinguda de Benicassim, 128", - "submitting_institution_email": "" + "submitting_institution": "FISABIO-Epidemiología Molecular", + "submitting_institution_address": "Av. Roma, s/n", + "submitting_institution_email": "santiago.melon@sespa.es" }, - "Hospital Universitario y Politecnico La Fe": { + "Hospital Universitario y Politécnico La Fe de Valencia": { "collecting_institution_address": "Avinguda de Fernando Abril Martorell, 106", "collecting_institution_email": "", "geo_loc_state": "Comunitat Valenciana", "geo_loc_region": "Valencia", "geo_loc_city": "Valencia", "geo_loc_country": "Spain", - "submitting_institution": "Hospital Universitario y Politecnico La Fe", - "submitting_institution_address": "Avinguda de Fernando Abril Martorell, 106", - "submitting_institution_email": "" + "submitting_institution": "FISABIO-Epidemiología Molecular", + "submitting_institution_address": "Av. Roma, s/n", + "submitting_institution_email": "santiago.melon@sespa.es" }, - "Hospital Universitario Doctor Peset": { + "Hospital Doctor Peset de Valencia": { "collecting_institution_address": "Av. de Gaspar Aguilar, 90", "collecting_institution_email": "", "geo_loc_state": "Comunitat Valenciana", "geo_loc_region": "Valencia", "geo_loc_city": "Valencia", "geo_loc_country": "Spain", - "submitting_institution": "Hospital General Universitario de Castellon", - "submitting_institution_address": "Avinguda de Benicassim, 128", - "submitting_institution_email": "" + "submitting_institution": "FISABIO-Epidemiología Molecular", + "submitting_institution_address": "Av. Roma, s/n", + "submitting_institution_email": "santiago.melon@sespa.es" }, "Hospital de l'Esperansa": { "collecting_institution_address": "Ptge. de Sant Josep la Muntanya, 12", @@ -1072,7 +1061,7 @@ "collecting_institution_email": "", "geo_loc_state": "Cataluña", "geo_loc_region": "Barcelona", - "geo_loc_city": "Mataro", + "geo_loc_city": "Mataró", "geo_loc_country": "Spain", "submitting_institution": "LABORATORI DE REFERENCIA DE CATALUNYA", "submitting_institution_address": "Carrer de la Selva, 10", @@ -1089,7 +1078,7 @@ "submitting_institution_address": "Carrer de la Selva, 10", "submitting_institution_email": "" }, - "Hospital Comarcal Sant Jaume de Calella": { + "Hospital Comarcal St. Jaume de Calella": { "collecting_institution_address": "Carrer de Sant Jaume, 209-217", "collecting_institution_email": "", "geo_loc_state": "Cataluña", @@ -1132,5 +1121,303 @@ "submitting_institution": "LABORATORI DE REFERENCIA DE CATALUNYA", "submitting_institution_address": "Carrer de la Selva, 10", "submitting_institution_email": "" + }, + "Hospital de Jarrio": { + "collecting_institution_address": "Lugar Jarrio, s/n", + "collecting_institution_email": "", + "geo_loc_state": "Asturias", + "geo_loc_region": "Asturias", + "geo_loc_city": "Jarrio", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Central de Asturias", + "submitting_institution_address": "Av. Roma, s/n", + "submitting_institution_email": "santiago.melon@sespa.es" + }, + "Hospital Carmen y Severo Ochoa": { + "collecting_institution_address": "Lugar Sienra, 11", + "collecting_institution_email": "", + "geo_loc_state": "Asturias", + "geo_loc_region": "Asturias", + "geo_loc_city": "Cangas del Narcea", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Central de Asturias", + "submitting_institution_address": "Av. Roma, s/n", + "submitting_institution_email": "santiago.melon@sespa.es" + }, + "Hospital Universitario San Agustín": { + "collecting_institution_address": "Calle Cabruñana, 19", + "collecting_institution_email": "", + "geo_loc_state": "Asturias", + "geo_loc_region": "Asturias", + "geo_loc_city": "Avilés", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Central de Asturias", + "submitting_institution_address": "Av. Roma, s/n", + "submitting_institution_email": "santiago.melon@sespa.es" + }, + "Hospital Monte Naranco": { + "collecting_institution_address": "Avenida Doctores Fernández Vega, 107", + "collecting_institution_email": "", + "geo_loc_state": "Asturias", + "geo_loc_region": "Asturias", + "geo_loc_city": "Oviedo", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Central de Asturias", + "submitting_institution_address": "Av. Roma, s/n", + "submitting_institution_email": "santiago.melon@sespa.es" + }, + "Hospital Universitario de Cabueñes": { + "collecting_institution_address": "Calle Prados, 395", + "collecting_institution_email": "", + "geo_loc_state": "Asturias", + "geo_loc_region": "Asturias", + "geo_loc_city": "Gijón", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Central de Asturias", + "submitting_institution_address": "Av. Roma, s/n", + "submitting_institution_email": "santiago.melon@sespa.es" + }, + "Hospital de Jove": { + "collecting_institution_address": "Avenida Eduardo Castro, s/n", + "collecting_institution_email": "", + "geo_loc_state": "Asturias", + "geo_loc_region": "Asturias", + "geo_loc_city": "Gijón", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Central de Asturias", + "submitting_institution_address": "Av. Roma, s/n", + "submitting_institution_email": "santiago.melon@sespa.es" + }, + "Hospital del Oriente de Asturias F. Grande Covián": { + "collecting_institution_address": "Barrio Castañera, 42", + "collecting_institution_email": "", + "geo_loc_state": "Asturias", + "geo_loc_region": "Asturias", + "geo_loc_city": "Arriondas", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Central de Asturias", + "submitting_institution_address": "Av. Roma, s/n", + "submitting_institution_email": "santiago.melon@sespa.es" + }, + "Hospital Vital Alvarez Buylla": { + "collecting_institution_address": "Calle Vistalegre, 2", + "collecting_institution_email": "", + "geo_loc_state": "Asturias", + "geo_loc_region": "Asturias", + "geo_loc_city": "Mieres", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Central de Asturias", + "submitting_institution_address": "Av. Roma, s/n", + "submitting_institution_email": "santiago.melon@sespa.es" + }, + "Hospital Valle del Nalón": { + "collecting_institution_address": "Polígono de Riaño, s/n", + "collecting_institution_email": "", + "geo_loc_state": "Asturias", + "geo_loc_region": "Asturias", + "geo_loc_city": "Langreo", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Central de Asturias", + "submitting_institution_address": "Av. Roma, s/n", + "submitting_institution_email": "santiago.melon@sespa.es" + }, + "FISABIO-Epidemiología Molecular": { + "collecting_institution_address": "Av. de Catalunya, 21", + "collecting_institution_email": "", + "geo_loc_state": "Comunitat Valenciana", + "geo_loc_region": "Valencia", + "geo_loc_city": "Valencia", + "geo_loc_country": "Spain", + "submitting_institution": "FISABIO-Epidemiología Molecular", + "submitting_institution_address": "Av. de Catalunya, 21", + "submitting_institution_email": "santiago.melon@sespa.es" + }, + "Hospital General Universitario de Alicante": { + "collecting_institution_address": "Calle Pintor Baeza, 11", + "collecting_institution_email": "", + "geo_loc_state": "Comunitat Valenciana", + "geo_loc_region": "Valencia", + "geo_loc_city": "Alicante", + "geo_loc_country": "Spain", + "submitting_institution": "FISABIO-Epidemiología Molecular", + "submitting_institution_address": "Av. Roma, s/n", + "submitting_institution_email": "santiago.melon@sespa.es" + }, + "Consorcio Hospital General Universitario de Valencia": { + "collecting_institution_address": "Av. de les Tres Creus, 2", + "collecting_institution_email": "", + "geo_loc_state": "Comunitat Valenciana", + "geo_loc_region": "Valencia", + "geo_loc_city": "Valencia", + "geo_loc_country": "Spain", + "submitting_institution": "FISABIO-Epidemiología Molecular", + "submitting_institution_address": "Av. Roma, s/n", + "submitting_institution_email": "santiago.melon@sespa.es" + }, + "Hospital General Universitario de Castellón": { + "collecting_institution_address": "Avinguda de Benicàssim, 128", + "collecting_institution_email": "", + "geo_loc_state": "Comunitat Valenciana", + "geo_loc_region": "Valencia", + "geo_loc_city": "Castellón de la Plana", + "geo_loc_country": "Spain", + "submitting_institution": "FISABIO-Epidemiología Molecular", + "submitting_institution_address": "Av. Roma, s/n", + "submitting_institution_email": "santiago.melon@sespa.es" + }, + "CAP La Salut EAP Badalona": { + "collecting_institution_address": " Passatge dels Encants, s/n", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_region": "Barcelona", + "geo_loc_city": "Badalona", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitari Germans Trias i Pujol (HUGTiP)", + "submitting_institution_address": " Crta del Canyet s/n", + "submitting_institution_email": "" + }, + "CAP Mataró-6 (Gatassa)": { + "collecting_institution_address": "Camí del Mig, 36", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_region": "Barcelona", + "geo_loc_city": "Mataró", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitari Germans Trias i Pujol (HUGTiP)", + "submitting_institution_address": " Crta del Canyet s/n", + "submitting_institution_email": "" + }, + "CAP Can Mariner Santa Coloma-1": { + "collecting_institution_address": "Carrer de Sant Carles, 79", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_region": "Tarragona", + "geo_loc_city": "Santa Coloma de Gramenet", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitari Germans Trias i Pujol (HUGTiP)", + "submitting_institution_address": " Crta del Canyet s/n", + "submitting_institution_email": "" + }, + "CAP Montmeló (Montornès)": { + "collecting_institution_address": "Carrer de Can Parera, 7", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_region": "Tarragona", + "geo_loc_city": "Montornès del Vallès", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitari Germans Trias i Pujol (HUGTiP)", + "submitting_institution_address": " Crta del Canyet s/n", + "submitting_institution_email": "" + }, + "Hospital García Orcoyen": { + "collecting_institution_address": "Calle Sta. Soria, 22", + "collecting_institution_email": "", + "geo_loc_state": "Navarra", + "geo_loc_region": "Navarra", + "geo_loc_city": "Estella", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario de Navarra", + "submitting_institution_address": "C. de Irunlarrea, 3, Pamplona", + "submitting_institution_email": "" + }, + "Hospital Reina Sofía_Tudela": { + "collecting_institution_address": "Carretera de Tarazona, Km. 4", + "collecting_institution_email": "", + "geo_loc_state": "Navarra", + "geo_loc_region": "Navarra", + "geo_loc_city": "Tudela", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario de Navarra", + "submitting_institution_address": "C. de Irunlarrea, 3, Pamplona", + "submitting_institution_email": "" + }, + "Clínica Universidad de Navarra": { + "collecting_institution_address": "Av. de Pío XII, 36", + "collecting_institution_email": "", + "geo_loc_state": "Navarra", + "geo_loc_region": "Navarra", + "geo_loc_city": "Pamplona", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario de Navarra", + "submitting_institution_address": "C. de Irunlarrea, 3, Pamplona", + "submitting_institution_email": "" + }, + "CATLAB": { + "collecting_institution_address": "Vial St Jordi, s/n", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_region": "Barcelona", + "geo_loc_city": "Viladecavalls", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitari Germans Trias i Pujol (HUGTiP)", + "submitting_institution_address": " Crta del Canyet s/n", + "submitting_institution_email": "" + }, + "Fundació Althaia-Manresa": { + "collecting_institution_address": "Carrer del Dr. Joan Soler, 1-3", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_region": "Barcelona", + "geo_loc_city": "Manresa", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitari Germans Trias i Pujol (HUGTiP)", + "submitting_institution_address": " Crta del Canyet s/n", + "submitting_institution_email": "" + }, + "H U RAMÓN Y CAJAL": { + "collecting_institution_address": "Ctra. Colmenar Viejo, km.9, 100", + "collecting_institution_email": "", + "geo_loc_state": "Comunidad de Madrid", + "geo_loc_region": "Madrid", + "geo_loc_city": "Madrid", + "geo_loc_country": "Spain", + "submitting_institution": "H U RAMÓN Y CAJAL", + "submitting_institution_address": "Ctra. Colmenar Viejo, km.9, 100", + "submitting_institution_email": "" + }, + "Hospital Universitario Cruces": { + "collecting_institution_address": "Plaza Cruces, s/n", + "collecting_institution_email": "", + "geo_loc_state": "Pais Vasco", + "geo_loc_region": "Vizcaya", + "geo_loc_city": "Baracaldo", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Cruces", + "submitting_institution_address": "Plaza Cruces, s/n", + "submitting_institution_email": "" + }, + "Hospital de Urduliz-Alfredo Espinosa": { + "collecting_institution_address": "Goieta Kalea, 32", + "collecting_institution_email": "", + "geo_loc_state": "Pais Vasco", + "geo_loc_region": "Vizcaya", + "geo_loc_city": "Urdúliz", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Cruces", + "submitting_institution_address": "Plaza Cruces, s/n", + "submitting_institution_email": "" + }, + "Hospital San Eloy": { + "collecting_institution_address": "Av. A. Miranda, 5002", + "collecting_institution_email": "", + "geo_loc_state": "Pais Vasco", + "geo_loc_region": "Vizcaya", + "geo_loc_city": "Barakaldo", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Cruces", + "submitting_institution_address": "Plaza Cruces, s/n", + "submitting_institution_email": "" + }, + "Hospital de Gorliz": { + "collecting_institution_address": "Urezarantza ibiltokia, 1", + "collecting_institution_email": "", + "geo_loc_state": "Pais Vasco", + "geo_loc_region": "Vizcaya", + "geo_loc_city": "Gorliz", + "geo_loc_country": "Spain", + "submitting_institution": "Hospital Universitario Cruces", + "submitting_institution_address": "Plaza Cruces, s/n", + "submitting_institution_email": "" } -} \ No newline at end of file + +} From acfbdd4b2a52e60f6b127c04080b315de7f5ca81 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 19 Feb 2024 10:50:13 +0100 Subject: [PATCH 1211/1454] Included multiple locations and updated some names --- relecov_tools/conf/geo_loc_cities.json | 81 ++++++++++++++++++++++++-- 1 file changed, 75 insertions(+), 6 deletions(-) diff --git a/relecov_tools/conf/geo_loc_cities.json b/relecov_tools/conf/geo_loc_cities.json index f3f1c292..535a7b28 100755 --- a/relecov_tools/conf/geo_loc_cities.json +++ b/relecov_tools/conf/geo_loc_cities.json @@ -103,7 +103,7 @@ "geo_loc_latitude": "38.9956", "geo_loc_longitude": "-1.8558" }, - "Castellon de la Plana": { + "Castellón de la Plana": { "geo_loc_latitude": "39.9831", "geo_loc_longitude": "-0.0331" }, @@ -251,11 +251,11 @@ "geo_loc_latitude": "41.4667", "geo_loc_longitude": "2.0833" }, - "Mostoles": { + "Móstoles": { "geo_loc_latitude": "40.3223", "geo_loc_longitude": "-3.865" }, - "Leganes": { + "Leganés": { "geo_loc_latitude": "40.3281", "geo_loc_longitude": "-3.7644" }, @@ -324,10 +324,10 @@ "geo_loc_longitude": "-4.100808" }, "Motril":{ - "geo_loc_latitude": "36.74611111", + "geo_loc_latitude": "36.746111", "geo_loc_longitude": "-3.515" }, - "Mataro":{ + "Mataró":{ "geo_loc_latitude": "41.540444", "geo_loc_longitude": "2.443782" }, @@ -346,5 +346,74 @@ "Tortosa":{ "geo_loc_latitude": "40.814140", "geo_loc_longitude": "0.522052" + }, + "Oviedo":{ + "geo_loc_latitude": "43.36316", + "geo_loc_longitude": "-5.85352" + }, + "Jarrio":{ + "geo_loc_latitude": "43.54444", + "geo_loc_longitude": "-6.74722" + }, + "Avilés":{ + "geo_loc_latitude": "43.551944", + "geo_loc_longitude": "-5.936111" + }, + "Gijón":{ + "geo_loc_latitude": "43.5345709", + "geo_loc_longitude": "-5.6675865" + }, + "Cangas del Narcea":{ + "geo_loc_latitude": "43.165833", + "geo_loc_longitude": "-6.541666" + }, + "Arriondas":{ + "geo_loc_latitude": "43.381388", + "geo_loc_longitude": "-5.184444" + }, + "Mieres":{ + "geo_loc_latitude": "43.226388", + "geo_loc_longitude": "-5.781388" + }, + "Langreo":{ + "geo_loc_latitude": "43.165833", + "geo_loc_longitude": "-6.541666" + }, + "Santa Coloma de Gramenet":{ + "geo_loc_latitude": "41.448215", + "geo_loc_longitude": "2.211027" + }, + "Montornès del Vallès":{ + "geo_loc_latitude": "41.546434", + "geo_loc_longitude": "2.268351" + }, + "Tudela":{ + "geo_loc_latitude": "42.060165", + "geo_loc_longitude": "-1.608065" + }, + "Estella":{ + "geo_loc_latitude": "42.672969", + "geo_loc_longitude": "-2.032974" + }, + "Viladecavalls":{ + "geo_loc_latitude": "41.552843", + "geo_loc_longitude": "1.952722" + }, + "Manresa":{ + "geo_loc_latitude": "41.727944", + "geo_loc_longitude": "1.823089" + }, + "Barakaldo":{ + "geo_loc_latitude": "43.282025", + "geo_loc_longitude": "-2.984338" + }, + "Gorliz":{ + "geo_loc_latitude": "43.416987", + "geo_loc_longitude": "-2.9448381" + }, + "Urdúliz":{ + "geo_loc_latitude": "43.375278", + "geo_loc_longitude": "-2.960000" } -} \ No newline at end of file + +} From 52b2022ca9e2614c0761637ad5990299218b6335 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 19 Feb 2024 10:50:38 +0100 Subject: [PATCH 1212/1454] Changed some enums and included Sequencing_institution --- relecov_tools/schema/relecov_schema.json | 63 +++++++++++++++--------- 1 file changed, 39 insertions(+), 24 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index ce12a11f..804a74db 100755 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2,10 +2,11 @@ "schema": "https://json-schema.org/draft/2020-12/schema", "id": "https://github.com/BU-ISCIII/relecov-tools/blob/develop/relecov_tools/schema/relecov_schema.json", "title": "RELECOV schema", - "description":"Json schema including the ", + "description":"Json schema that specifies the structure, content, and validation rules for RELECOV metadata", "version": "1.0.0", "required": [ "collecting_lab_sample_id", + "sequencing_sample_id", "collecting_institution", "submitting_institution", "sample_collection_date", @@ -15,7 +16,9 @@ "isolate_sample_id", "host_scientific_name", "sequencing_instrument_model", - "sequencing_instrument_platform" + "sequencing_instrument_platform", + "enrichment_panel", + "enrichment_panel_version" ], "type": "object", "properties": { @@ -113,6 +116,15 @@ "fill_mode": "sample", "minLenght": "1" }, + "sequencing_institution": { + "ontology": "GENEPIO:0100416", + "type": "string", + "description": "The name of the agency that generated the sequence", + "classification": "Sequencing", + "label": "Sequencing Institution", + "fill_mode": "sample", + "minLenght": "1" + }, "submitting_lab_sample_id": { "examples": [ "" @@ -470,7 +482,6 @@ "Zimbabwe [GAZ:00001106]", "Not Applicable [GENEPIO:0001619]", "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], @@ -656,7 +667,7 @@ "Oropharynx Vacuum Aspiration", "Lower respiratory tract Biopsy", "Bronchus Biopsy", - "Lung Biopsy", + "Lung biopsy", "Bronchiole Biopsy", "Alveolar sac Biopsy", "Pleural sac Biopsy", @@ -777,7 +788,7 @@ "Ethmoid sinus Wash", "Nasal Cavity Wash", "Middle Nasal Turbinate Wash", - "Nasopharynx Wash", + "Nasopharynx Wash", "Oropharynx Wash", "Feces", "Mucus", @@ -795,7 +806,8 @@ "Not Collected", "Not Provided", "Missing", - "Restricted Access" + "Restricted Access", + "Not Provided [GENEPIO:0001668]" ], "ontology": "GENEPIO:0001211", "type": "string", @@ -964,7 +976,7 @@ "N95 Mask [OBI:0002790]", "Nurse Call Button [ENVO:03501215]", "Paper [ENVO:03501256]", - "Particulate Matter [ENVO:01000060]", + "Particulate matter [ENVO:01000060]", "Plastic [ENVO:01000404]", "PPE Gown [GENEPIO:0100025]", "Sewage [ENVO:00002018]", @@ -1036,9 +1048,10 @@ "enum": [ "Coronaviridae [NCBITaxon:11118]", "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", + "Respiratory syncytial virus [NCBITaxon:12814]", + "Influenza virus (organism) [SNOMED:725894000]", "Not Applicable [GENEPIO:0001619]", "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], @@ -1115,8 +1128,6 @@ "Sus scrofa domesticus [NCBITaxon:9825]", "Viverridae [NCBITaxon:9673]", "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], @@ -1234,8 +1245,6 @@ "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", "MGI DNBSEQ-G50 [GENEPIO:0100150]", "Not Applicable [GENEPIO:0001619]", - "Not Collected [GENEPIO:0001620]", - "Not Provided [GENEPIO:0001668]", "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], @@ -1325,7 +1334,7 @@ "Illumina COVIDSeq Test [CIDO:0020172]", "ABL DeepChek® Assay WG SC2 V1", "Not Provided [GENEPIO:0001668]", - "Other" + "Other [NCIT:C17649]" ], "examples": [ "Illumina COVIDSeq Test" @@ -1381,7 +1390,8 @@ "Custom probes [OMIT:0016112]", "Custom amplicon [OMIT:0016112]", "No enrichment [NCIT:C154307]", - "Other [NCIT:C17649]" + "Other [NCIT:C17649]", + "Not Provided [GENEPIO:0001668]" ], "examples": [ "AMPLICON" @@ -1409,12 +1419,11 @@ "ARTIC", "Illumina respiratory Virus Oligo Panel", "Illumina AmpliSeq Community panel", - "Illumina AmpliSeq SARS-CoV-2 Research Panel for Illumina", + "Illumina AmpliSeq SARS-CoV-2 Research Panel for Illumina", "Ion AmpliSeq SARS-CoV-2 Research Panel", "xGen SC2 Midnight1200 Amplicon Panel", "ViroKey SQ FLEX SARS-CoV-2 Primer Set", "NEBNext VarSkip Short SARS-CoV-2 primers", - "Not Provided [GENEPIO:0001668]", "Other [NCIT:C17649]" ], "examples": [ @@ -1434,6 +1443,11 @@ "ARTIC v3", "ARTIC v4", "ARTIC v4.1", + "ARTIC v5", + "ARTIC v5.1", + "ARTIC v5.2", + "ARTIC v5.3", + "ARTIC v5.3.2", "Illumina AmpliSeq Community panel", "Illumina AmpliSeq SARS-CoV-2 Research Panel for Illumina", "Illumina Respiratory Virus Oligos Panel V1", @@ -1442,7 +1456,6 @@ "xGen SC2 Midnight1200 Amplicon Panel", "ViroKey SQ FLEX SARS-CoV-2 Primer Set", "NEBNext VarSkip Short SARS-CoV-2 primers", - "Not Provided [GENEPIO:0001668]", "Other [NCIT:C17649]" ], "examples": [ @@ -1514,7 +1527,7 @@ "TG HiSeq Rapid SBS Kit v2 (50 Cycle)", "HiSeq SR Cluster Kit v4 cBot", "TG HiSeq SR Cluster Kit v4 - cBot", - "TG HiSeq PE Cluster Kit v4 – cBot", + "TG HiSeq PE Cluster Kit v4 - cBot", "HiSeq X Ten Reagent Kit v2.5", "HiSeq X Ten Reagent Kit v2.5 - 10 pack", "HiSeq X Five Reagent Kit v2.5", @@ -1574,9 +1587,9 @@ "NovaSeq 6000 S2 Reagent Kit (300 cycles)", "NovaSeq 6000 S4 Reagent Kit (200 cycles)", "NovaSeq 6000 S4 Reagent Kit (300 cycles)", - "NovaSeq 6000 S4 Reagent Kit (300 Cycles) – 10 pack", - "NovaSeq 6000 S4 Reagent Kit (300 Cycles) – 20 pack", - "NovaSeq 6000 S4 Reagent Kit (300 Cycles) – 40 pack", + "NovaSeq 6000 S4 Reagent Kit (300 Cycles) - 10 pack", + "NovaSeq 6000 S4 Reagent Kit (300 Cycles) - 20 pack", + "NovaSeq 6000 S4 Reagent Kit (300 Cycles) - 40 pack", "NovaSeq Library Tubes Accessory Pack (24 tubes)", "NovaSeq XP 4-Lane Kit v1.5", "NovaSeq XP 2-Lane Kit v1.5", @@ -1597,7 +1610,7 @@ "TG TruSeq SBS Kit v3 - HS (200-cycles)", "TruSeq SBS Kit v5-GA", "TruSeq SR Cluster Kit v3-cBot-HS", - "TG TruSeq SR Cluster Kit v1–cBot - HS", + "TG TruSeq SR Cluster Kit v1-cBot - HS", "iSeq 100 i1 Reagent v2 (300-cycle)", "iSeq 100 i1 Reagent v2 (300-cycle) 4 pack", "iSeq 100 i1 Reagent v2 (300-cycle) 8 pack", @@ -1656,7 +1669,8 @@ "metatranscriptomic", "synthetic", "viral rna", - "other [NCIT:C17649]" + "other [NCIT:C17649]", + "Not Provided [GENEPIO:0001668]" ], "examples": [ "metagenomic" @@ -1695,7 +1709,8 @@ "Oligo-dT", "Inverse rRNA selection", "ChIP-Seq [GENEPIO:0001947]", - "Other [NCIT:C17649]" + "Other [NCIT:C17649]", + "Not Provided [GENEPIO:0001668]" ], "examples": [ "RANDOM PCR" From 24c73ae4d4b824d67f7bae634b836fd9d633c37b Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 27 Feb 2024 16:01:12 +0100 Subject: [PATCH 1213/1454] added yml containing bioinfo results pattern --- .../conf/bioinfo_search_patterns.yml | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 relecov_tools/conf/bioinfo_search_patterns.yml diff --git a/relecov_tools/conf/bioinfo_search_patterns.yml b/relecov_tools/conf/bioinfo_search_patterns.yml new file mode 100644 index 00000000..2b11a715 --- /dev/null +++ b/relecov_tools/conf/bioinfo_search_patterns.yml @@ -0,0 +1,31 @@ +viralrecon: + version_info: + fn: software_versions.yml + required: true + mapping_stats: + fn: "mapping_illumina_stats.tab" + content: "analysis_date medianDPcoveragevirus Variantsinconsensusx10 MissenseVariants Coverage>10x(%) %Ns10x %readshost %readsvirus %unmapedreads totalreads Virussequence read_length" + required: true + num_lines: 1 + pangolin: + fn: ".pangolin.csv" + content: "scorpio_call lineage version pangolin_version scorpio_version constellation_version" + num_lines: 1 + vairants_long_table: + fn: "variants_long_table.csv" + content: "SAMPLE,CHROM,POS,REF,ALT,FILTER,DP,REF_DP,ALT_DP,AF,GENE,EFFECT,HGVS_C,HGVS_P,HGVS_P_1LETTER,CALLER,LINEAGE" + num_lines: 1 + required: true + consensus: + fn: ".consensus.fa" + content: + - "consensus_sequence_name" + - "consensus_genome_length" + - "consensus_sequence_filename" + - "consensus_sequence_filepath" + - "consensus_sequence_md5" + - "number_of_base_pairs_sequenced" + summary_mqc: + fn: "summary_variants_metrics_mqc.csv" + content: "# Ns per 100kb consensu" + required: true From ef3c16149824fb08cb01c56303b33806c7931e4e Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 27 Feb 2024 16:45:11 +0100 Subject: [PATCH 1214/1454] enable to parse yaml config file for bioinfo metadata --- .../conf/bioinfo_search_patterns.yml | 3 ++- relecov_tools/read_bioinfo_metadata.py | 23 ++++++++++++++++++- relecov_tools/utils.py | 9 ++++++++ 3 files changed, 33 insertions(+), 2 deletions(-) diff --git a/relecov_tools/conf/bioinfo_search_patterns.yml b/relecov_tools/conf/bioinfo_search_patterns.yml index 2b11a715..13bb37b3 100644 --- a/relecov_tools/conf/bioinfo_search_patterns.yml +++ b/relecov_tools/conf/bioinfo_search_patterns.yml @@ -1,6 +1,6 @@ viralrecon: version_info: - fn: software_versions.yml + fn: "software_versions.yml" required: true mapping_stats: fn: "mapping_illumina_stats.tab" @@ -18,6 +18,7 @@ viralrecon: required: true consensus: fn: ".consensus.fa" + required: false content: - "consensus_sequence_name" - "consensus_genome_length" diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 36ebd5dc..21ace1ba 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -1,5 +1,4 @@ #!/usr/bin/env python - import os import sys import logging @@ -29,6 +28,8 @@ def __init__( json_file=None, input_folder=None, output_folder=None, + software='viralrecon', # default? + yaml_file=None, ): if json_file is None: json_file = relecov_tools.utils.prompt_path( @@ -53,6 +54,26 @@ def __init__( else: self.output_folder = output_folder + # TODO: Available software list can be retrieved from conf/bioinfo_search_patterns.yml + # TODO: Add error if software is not in the list (sys exit) + if software is None: + software = relecov_tools.utils.prompt_path( + msg="Select the software, pipeline or tool use in the bioinformatic analysis (available: 'viralrecon'): " + ) + self.software_name = software + + if yaml_file is None: + stderr.print( + "[grey] [INFO]: Applying default YAML bioinformatics configuration file." + ) + yaml_file = os.path.join(os.path.dirname(__file__), "conf", "bioinfo_search_patterns.yml") + else: + if not os.path.isfile(yaml_file): + log.error("yaml file %s does not exist ", yaml_file) + stderr.print(f"[red] file {yaml_file} does not exist") + sys.exit(1) + self.yaml_data = relecov_tools.utils.get_yaml_topic(yaml_file, self.software_name) + config_json = ConfigJson() self.configuration = config_json required_files = self.configuration.get_topic_data( diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index f2461f72..dcc8689a 100755 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -129,6 +129,15 @@ def read_yml_file(file_name): except yaml.YAMLError: raise +def get_yaml_topic(file_name, topic): + """Parse dict to retrieve scope properties""" + try: + yaml_file = read_yml_file(file_name) + return yaml_file.get(topic, {}) + except AttributeError: + raise TypeError("file_name must be a dictionary-like object") + except Exception as e: + raise RuntimeError(f"An error occurred: {str(e)}") def get_md5_from_local_folder(local_folder): """Fetch the md5 values for each file in the file list""" From 56d603912e6d8fc216107c0df422e82c36ad3e67 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 29 Feb 2024 16:59:45 +0100 Subject: [PATCH 1215/1454] add automated scanning of files in a directory --- relecov_tools/read_bioinfo_metadata.py | 32 ++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 21ace1ba..63fbc65e 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -1,10 +1,12 @@ #!/usr/bin/env python +# TODO: Add new dependencies to pkg import os import sys import logging import glob import rich.console from datetime import datetime +from tqdm import tqdm from yaml import YAMLError import relecov_tools.utils @@ -88,6 +90,33 @@ def __init__( sys.exit(1) self.req_files[key] = f_path + def get_software_required_files(self): + """Load required softwaew specific files and patterns from YAML.""" + self.required_file_name = {} + self.required_file_content = {} + + for key, value in self.yaml_data.items(): + if 'required' in value and value['required']: + self.required_file_name[key] = value.get('fn','') + self.required_file_content[key] = value.get('content','') + + def scann_directory(self): + """Scann bioinfo analysis directory and search for files""" + total_files = sum(len(files) for _, _, files in os.walk(self.input_folder)) + self.get_software_required_files() + required_files_found = {key: [] for key in self.required_file_name} + + with tqdm(total=total_files, desc=f'\tScanning...') as pbar: + for target_file, file_pattern in self.required_file_name.items(): + for root, _, files in os.walk(self.input_folder, topdown=True): + for file_name in files: + # FIXME: might be better regex than endswith + if file_name.endswith(file_pattern): + file_path = os.path.join(root, file_name) + required_files_found[target_file].append(file_path) + pbar.update(1) # FIXME: is not correctly processing each file + return(required_files_found) + def add_fixed_values(self, j_data, fixed_values): """include the fixed data defined in configuration or feed custom empty fields""" f_values = self.configuration.get_topic_data("bioinfo_analysis", fixed_values) @@ -331,6 +360,9 @@ def create_bioinfo_file(self): metadata json, mapping_stats, and more information from the files inside input directory """ + stderr.print(f"[blue]Sanning for {self.software_name} files..") + self.scann_directory() + stderr.print("[blue]Reading lab metadata json") j_data = self.collect_info_from_lab_json() stderr.print("[blue]Adding fixed values") From 64636d0195c5387bbbda4e0575c38b4721948c28 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 29 Feb 2024 17:19:07 +0100 Subject: [PATCH 1216/1454] add validation steps on required files --- relecov_tools/read_bioinfo_metadata.py | 37 +++++++++++++++++++++++--- 1 file changed, 34 insertions(+), 3 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 63fbc65e..4404865f 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -23,7 +23,8 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) - +# TODO: add required fields to j_data (read_lab + read_bioinf) +# TODO: Scan should work in multiple samples. Files found must detect N samples output files. class BioinfoMetadata: def __init__( self, @@ -117,6 +118,35 @@ def scann_directory(self): pbar.update(1) # FIXME: is not correctly processing each file return(required_files_found) + # TODO: This verification step might be executed for each sample since there are sample-specific files. + def validate_software_mandatory_files(self, files): + """Verify that all required files are present""" + missing = [] + if len(files) == 0: + log.error("No mandatory files for %s found in folder: %s", + self.software_name, + self.input_folder + ) + stderr.print( + f"[red]\tValidation Failed: No mandatory files found in folder: {self.input_folder}. " + ) + sys.exit(1) + for key, values in files.items(): + if len(values)==0: + missing.append(key) + if len(missing) > 0: + stderr.print( + f"[red]\tValidation Failed: Missing files for {self.software_name}:" + ) + for i in missing: + stderr.print( + f"\t- {self.required_file_name[i]}" + ) + sys.exit(1) + stderr.print( + f"[green]\tValidation Approved" + ) + def add_fixed_values(self, j_data, fixed_values): """include the fixed data defined in configuration or feed custom empty fields""" f_values = self.configuration.get_topic_data("bioinfo_analysis", fixed_values) @@ -361,8 +391,9 @@ def create_bioinfo_file(self): inside input directory """ stderr.print(f"[blue]Sanning for {self.software_name} files..") - self.scann_directory() - + scanned_files_mapping = self.scann_directory() + stderr.print(f"[blue]Verifying {self.software_name} required files..") + self.validate_software_mandatory_files(scanned_files_mapping) stderr.print("[blue]Reading lab metadata json") j_data = self.collect_info_from_lab_json() stderr.print("[blue]Adding fixed values") From 3e05aa78139673007a526329c4ee8207916bdb84 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 4 Mar 2024 18:36:16 +0100 Subject: [PATCH 1217/1454] organize bioinfo config settings according to software --- relecov_tools/__main__.py | 5 +- relecov_tools/conf/bioinfo_config.json | 94 ++++++++++++++++++++++++++ relecov_tools/conf/configuration.json | 92 ------------------------- relecov_tools/read_bioinfo_metadata.py | 25 ++++--- 4 files changed, 113 insertions(+), 103 deletions(-) create mode 100644 relecov_tools/conf/bioinfo_config.json diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index a576f9f8..cb89ab25 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -418,12 +418,13 @@ def update_db(user, password, json, type, databaseServer): ) @click.option("-i", "--input_folder", type=click.Path(), help="Path to input files") @click.option("-o", "--out_dir", type=click.Path(), help="Path to save output file") -def read_bioinfo_metadata(json_file, input_folder, out_dir): +@click.option("-s", "--software_name", help="Name of the software/pipeline used.") +def read_bioinfo_metadata(json_file, input_folder, out_dir, software_name): """ Create the json compliant from the Bioinfo Metadata. """ new_bioinfo_metadata = relecov_tools.read_bioinfo_metadata.BioinfoMetadata( - json_file, input_folder, out_dir + json_file, input_folder, out_dir, software_name, ) new_bioinfo_metadata.create_bioinfo_file() diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json new file mode 100644 index 00000000..2d478970 --- /dev/null +++ b/relecov_tools/conf/bioinfo_config.json @@ -0,0 +1,94 @@ +{ + "viralrecon": { + "fixed_values": { + "assembly": "Not Provided [GENEPIO:0001668]", + "assembly_params": "Not Provided [GENEPIO:0001668]", + "bioinformatics_protocol_software_name": "nf-core/viralrecon", + "commercial_open_source_both": "Open Source", + "consensus_params": "-p vcf -f", + "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", + "dehosting_method_software_name": "KRAKEN2_KRAKEN2", + "depth_of_coverage_threshold": ">10x", + "if_assembly_other": "Not Provided [GENEPIO:0001668]", + "if_bioinformatic_protocol_is_other_specify": "Not Provided [GENEPIO:0001668]", + "if_consensus_other": "Not Provided [GENEPIO:0001668]", + "if_lineage_identification_other": "Not Provided [GENEPIO:0001668]", + "if_mapping_other": "Not Provided [GENEPIO:0001668]", + "if_preprocessing_other": "Not Provided [GENEPIO:0001668]", + "lineage_analysis_software_name": "pangolin", + "mapping_params": "--seed 1", + "mapping_software_name": "BOWTIE2_ALIGN", + "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", + "preprocessing_software_name": "FASTP", + "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", + "variant_calling_software_name": "IVAR_VARIANTS" + }, + "feed_empty_fields":{ + "lineage_analysis_date": "Not Provided [GENEPIO:0001668]", + "consensus_sequence_name": "Not Provided [GENEPIO:0001668]" + }, + "required_file": { + "variants_metrics": "summary_variants_metrics_mqc.csv", + "versions": "software_versions.yml", + "mapping_stats": "mapping_illumina_stats.tab" + }, + "mapping_consensus": [ + "consensus_genome_length", + "consensus_sequence_filename", + "consensus_sequence_filepath", + "consensus_sequence_md5", + "number_of_base_pairs_sequenced" + ], + "mapping_pangolin": { + "variant_name": "scorpio_call", + "lineage_name": "lineage", + "lineage_algorithm_software_version": "version", + "lineage_analysis_software_version": "pangolin_version", + "lineage_analysis_scorpio_version": "scorpio_version", + "lineage_analysis_constellation_version": "constellation_version" + }, + "mapping_stats": { + "analysis_date": "analysis_date", + "depth_of_coverage_value": "medianDPcoveragevirus", + "number_of_variants_in_consensus": "Variantsinconsensusx10", + "number_of_variants_with_effect": "MissenseVariants", + "per_genome_greater_10x": "Coverage>10x(%)", + "per_Ns": "%Ns10x", + "per_reads_host": "%readshost", + "per_reads_virus": "%readsvirus", + "per_unmapped": "%unmapedreads", + "qc_filtered": "totalreads", + "reference_genome_accession": "Virussequence", + "read_length": "read_length" + }, + "mapping_variant_metrics": { + "ns_per_100_kbp": "# Ns per 100kb consensus" + }, + "mapping_version": { + "bioinformatics_protocol_software_version": { + "Workflow": "nf-core/viralrecon" + }, + "consensus_sequence_software_version": { + "BCFTOOLS_CONSENSUS": "bcftools" + }, + "dehosting_method_software_version": { + "KRAKEN2_KRAKEN2": "kraken2" + }, + "mapping_software_version": { + "BOWTIE2_ALIGN": "bowtie2" + }, + "preprocessing_software_version": { + "FASTP": "fastp" + }, + "variant_calling_software_version": { + "IVAR_VARIANTS": "ivar" + } + }, + "required_fields_from_lab_json": { + "read_length": "number_of_base_pairs_sequenced", + "schema_name": "schema_name", + "schema_version": "schema_version", + "sequencing_sample_id": "sequencing_sample_id" + } + } +} \ No newline at end of file diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 33bd9cb6..18ccb7b9 100755 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -279,98 +279,6 @@ "sequencing_sample_id", "submitting_lab_sample_id" ], - "bioinfo_analysis": { - "fixed_values": { - "assembly": "Not Provided [GENEPIO:0001668]", - "assembly_params": "Not Provided [GENEPIO:0001668]", - "bioinformatics_protocol_software_name": "nf-core/viralrecon", - "commercial_open_source_both": "Open Source", - "consensus_params": "-p vcf -f", - "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", - "dehosting_method_software_name": "KRAKEN2_KRAKEN2", - "depth_of_coverage_threshold": ">10x", - "if_assembly_other": "Not Provided [GENEPIO:0001668]", - "if_bioinformatic_protocol_is_other_specify": "Not Provided [GENEPIO:0001668]", - "if_consensus_other": "Not Provided [GENEPIO:0001668]", - "if_lineage_identification_other": "Not Provided [GENEPIO:0001668]", - "if_mapping_other": "Not Provided [GENEPIO:0001668]", - "if_preprocessing_other": "Not Provided [GENEPIO:0001668]", - "lineage_analysis_software_name": "pangolin", - "mapping_params": "--seed 1", - "mapping_software_name": "BOWTIE2_ALIGN", - "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", - "preprocessing_software_name": "FASTP", - "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", - "variant_calling_software_name": "IVAR_VARIANTS" - }, - "feed_empty_fields":{ - "lineage_analysis_date": "Not Provided [GENEPIO:0001668]", - "consensus_sequence_name": "Not Provided [GENEPIO:0001668]" - }, - "required_file": { - "variants_metrics": "summary_variants_metrics_mqc.csv", - "versions": "software_versions.yml", - "mapping_stats": "mapping_illumina_stats.tab" - }, - "mapping_consensus": [ - "consensus_genome_length", - "consensus_sequence_filename", - "consensus_sequence_filepath", - "consensus_sequence_md5", - "number_of_base_pairs_sequenced" - ], - "mapping_pangolin": { - "variant_name": "scorpio_call", - "lineage_name": "lineage", - "lineage_algorithm_software_version": "version", - "lineage_analysis_software_version": "pangolin_version", - "lineage_analysis_scorpio_version": "scorpio_version", - "lineage_analysis_constellation_version": "constellation_version" - }, - "mapping_stats": { - "analysis_date": "analysis_date", - "depth_of_coverage_value": "medianDPcoveragevirus", - "number_of_variants_in_consensus": "Variantsinconsensusx10", - "number_of_variants_with_effect": "MissenseVariants", - "per_genome_greater_10x": "Coverage>10x(%)", - "per_Ns": "%Ns10x", - "per_reads_host": "%readshost", - "per_reads_virus": "%readsvirus", - "per_unmapped": "%unmapedreads", - "qc_filtered": "totalreads", - "reference_genome_accession": "Virussequence", - "read_length": "read_length" - }, - "mapping_variant_metrics": { - "ns_per_100_kbp": "# Ns per 100kb consensus" - }, - "mapping_version": { - "bioinformatics_protocol_software_version": { - "Workflow": "nf-core/viralrecon" - }, - "consensus_sequence_software_version": { - "BCFTOOLS_CONSENSUS": "bcftools" - }, - "dehosting_method_software_version": { - "KRAKEN2_KRAKEN2": "kraken2" - }, - "mapping_software_version": { - "BOWTIE2_ALIGN": "bowtie2" - }, - "preprocessing_software_version": { - "FASTP": "fastp" - }, - "variant_calling_software_version": { - "IVAR_VARIANTS": "ivar" - } - }, - "required_fields_from_lab_json": { - "read_length": "number_of_base_pairs_sequenced", - "schema_name": "schema_name", - "schema_version": "schema_version", - "sequencing_sample_id": "sequencing_sample_id" - } - }, "ENA_fields": { "ENA_configuration": { "study_alias": "RELECOV", diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 36ebd5dc..405ca571 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -1,5 +1,4 @@ #!/usr/bin/env python - import os import sys import logging @@ -29,6 +28,7 @@ def __init__( json_file=None, input_folder=None, output_folder=None, + software='viralrecon', ): if json_file is None: json_file = relecov_tools.utils.prompt_path( @@ -53,10 +53,17 @@ def __init__( else: self.output_folder = output_folder - config_json = ConfigJson() + if software is None: + software = relecov_tools.utils.prompt_path( + msg="Select the software, pipeline or tool use in the bioinformatic analysis (available: 'viralrecon'): " + ) + self.software_name = software + + json_file = os.path.join(os.path.dirname(__file__), "conf", "bioinfo_config.json") + config_json = ConfigJson(json_file) self.configuration = config_json required_files = self.configuration.get_topic_data( - "bioinfo_analysis", "required_file" + self.software_name, "required_file" ) self.req_files = {} for key, file in required_files.items(): @@ -69,7 +76,7 @@ def __init__( def add_fixed_values(self, j_data, fixed_values): """include the fixed data defined in configuration or feed custom empty fields""" - f_values = self.configuration.get_topic_data("bioinfo_analysis", fixed_values) + f_values = self.configuration.get_topic_data(self.software_name, fixed_values) for row in j_data: for field, value in f_values.items(): row[field] = value @@ -118,7 +125,7 @@ def include_data_from_mapping_stats(self, j_data): ) mapping_fields = self.configuration.get_topic_data( - "bioinfo_analysis", "mapping_stats" + self.software_name, "mapping_stats" ) j_data_with_mapping_stats = self.mapping_over_table( j_data, map_data, mapping_fields, "mapping stats" @@ -128,7 +135,7 @@ def include_data_from_mapping_stats(self, j_data): def include_pangolin_data(self, j_data): """Include pangolin data collecting form each file generated by pangolin""" mapping_fields = self.configuration.get_topic_data( - "bioinfo_analysis", "mapping_pangolin" + self.software_name, "mapping_pangolin" ) missing_pango = [] for row in j_data: @@ -184,7 +191,7 @@ def include_consensus_data(self, j_data): """ mapping_fields = self.configuration.get_topic_data( - "bioinfo_analysis", "mapping_consensus" + self.software_name, "mapping_consensus" ) missing_consens = [] for row in j_data: @@ -269,7 +276,7 @@ def include_variant_metrics(self, j_data): self.req_files["variants_metrics"], sep="," ) mapping_fields = self.configuration.get_topic_data( - "bioinfo_analysis", "mapping_variant_metrics" + self.software_name, "mapping_variant_metrics" ) j_data_with_variant_metrics = self.mapping_over_table( j_data, map_data, mapping_fields, "variant metrics" @@ -279,7 +286,7 @@ def include_variant_metrics(self, j_data): def include_software_versions(self, j_data): """Include versions from the yaml version file""" version_fields = self.configuration.get_topic_data( - "bioinfo_analysis", "mapping_version" + self.software_name, "mapping_version" ) try: versions = relecov_tools.utils.read_yml_file(self.req_files["versions"]) From 122108329534757e2998ebdcbe628f6ea590ec7c Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 11 Mar 2024 13:44:42 +0100 Subject: [PATCH 1218/1454] Added methods for scanning bioinfo results files regardless they sub-dir level and updated previous method to parse the new bioinfo config file --- relecov_tools/conf/bioinfo_config.json | 151 ++++++++++++++++--------- relecov_tools/long_table_parse.py | 16 ++- relecov_tools/read_bioinfo_metadata.py | 138 +++++++++++++++------- 3 files changed, 201 insertions(+), 104 deletions(-) diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index 2d478970..823ae59f 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -1,9 +1,104 @@ -{ +{ "viralrecon": { + "version_info": { + "fn": "software_versions.yml", + "required": true + }, + "mapping_stats": { + "fn": "mapping_illumina_stats.tab", + "ff": "tsv", + "sample_column": 1, + "num_lines": 1, + "required": true, + "content": { + "analysis_date": "analysis_date", + "depth_of_coverage_value": "medianDPcoveragevirus", + "number_of_variants_in_consensus": "Variantsinconsensusx10", + "number_of_variants_with_effect": "MissenseVariants", + "per_genome_greater_10x": "Coverage>10x(%)", + "per_Ns": "%Ns10x", + "per_reads_host": "%readshost", + "per_reads_virus": "%readsvirus", + "per_unmapped": "%unmapedreads", + "qc_filtered": "totalreads", + "reference_genome_accession": "Virussequence", + "read_length": "read_length" + } + }, + "mapping_pangolin": { + "fn": ".pangolin.csv", + "ff": "tsv", + "sample_column": 1, + "num_lines": 1, + "required": false, + "content": { + "variant_name": "scorpio_call", + "lineage_name": "lineage", + "lineage_algorithm_software_version": "version", + "lineage_analysis_software_version": "pangolin_version", + "lineage_analysis_scorpio_version": "scorpio_version", + "lineage_analysis_constellation_version": "constellation_version" + } + }, + "variants_long_table": { + "fn": "variants_long_table.csv", + "ff": "csv", + "num_lines": 1, + "required": true, + "content": { + "sample" : "SAMPLE", + "chromosome": "CHROM", + "pos": "POS", + "alt": "ALT", + "ref": "REF", + "Filter": "FILTER", + "dp": "DP", + "ref_dp": "REF_DP", + "alt_dp": "ALT_DP", + "af": "AF", + "effect": "EFFECT", + "hgvs_c": "HGVS_C", + "hgvs_p": "HGVS_P", + "hgvs_p_1_letter": "HGVS_P_1LETTER", + "caller" : "CALLER", + "lineage" : "LINEAGE", + "gene" : "GENE" + } + }, + "mapping_consensus": { + "fn": ".consensus.fa", + "ff": "fasta", + "required": false, + "content": { + "consensus_sequence_name" : "Not Provided [GENEPIO:0001668]", + "consensus_genome_length" : "Not Provided [GENEPIO:0001668]", + "consensus_sequence_filename" : "Not Provided [GENEPIO:0001668]", + "consensus_sequence_filepath" : "Not Provided [GENEPIO:0001668]", + "consensus_sequence_md5" : "Not Provided [GENEPIO:0001668]", + "number_of_base_pairs_sequenced" : "Not Provided [GENEPIO:0001668]" + } + }, + "summary_mqc": { + "fn": "summary_variants_metrics_mqc.csv", + "ff": "csv", + "num_lines": 1, + "required": true, + "content": { + "ns_per_100_kbp": "# Ns per 100kb consensus" + } + }, + "workflow_summary": { + "fn": "multiqc_report.html", + "ff": "html", + "required": true, + "content": { + "bioinformatics_protocol_software_name": "nf-core/viralrecon Workflow Summary", + "variant_calling_software_name": "IVAR_VARIANTS" + } + }, "fixed_values": { "assembly": "Not Provided [GENEPIO:0001668]", "assembly_params": "Not Provided [GENEPIO:0001668]", - "bioinformatics_protocol_software_name": "nf-core/viralrecon", "commercial_open_source_both": "Open Source", "consensus_params": "-p vcf -f", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", @@ -18,52 +113,12 @@ "lineage_analysis_software_name": "pangolin", "mapping_params": "--seed 1", "mapping_software_name": "BOWTIE2_ALIGN", - "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", + "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", "preprocessing_software_name": "FASTP", - "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", - "variant_calling_software_name": "IVAR_VARIANTS" - }, - "feed_empty_fields":{ + "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m10", "lineage_analysis_date": "Not Provided [GENEPIO:0001668]", "consensus_sequence_name": "Not Provided [GENEPIO:0001668]" }, - "required_file": { - "variants_metrics": "summary_variants_metrics_mqc.csv", - "versions": "software_versions.yml", - "mapping_stats": "mapping_illumina_stats.tab" - }, - "mapping_consensus": [ - "consensus_genome_length", - "consensus_sequence_filename", - "consensus_sequence_filepath", - "consensus_sequence_md5", - "number_of_base_pairs_sequenced" - ], - "mapping_pangolin": { - "variant_name": "scorpio_call", - "lineage_name": "lineage", - "lineage_algorithm_software_version": "version", - "lineage_analysis_software_version": "pangolin_version", - "lineage_analysis_scorpio_version": "scorpio_version", - "lineage_analysis_constellation_version": "constellation_version" - }, - "mapping_stats": { - "analysis_date": "analysis_date", - "depth_of_coverage_value": "medianDPcoveragevirus", - "number_of_variants_in_consensus": "Variantsinconsensusx10", - "number_of_variants_with_effect": "MissenseVariants", - "per_genome_greater_10x": "Coverage>10x(%)", - "per_Ns": "%Ns10x", - "per_reads_host": "%readshost", - "per_reads_virus": "%readsvirus", - "per_unmapped": "%unmapedreads", - "qc_filtered": "totalreads", - "reference_genome_accession": "Virussequence", - "read_length": "read_length" - }, - "mapping_variant_metrics": { - "ns_per_100_kbp": "# Ns per 100kb consensus" - }, "mapping_version": { "bioinformatics_protocol_software_version": { "Workflow": "nf-core/viralrecon" @@ -83,12 +138,6 @@ "variant_calling_software_version": { "IVAR_VARIANTS": "ivar" } - }, - "required_fields_from_lab_json": { - "read_length": "number_of_base_pairs_sequenced", - "schema_name": "schema_name", - "schema_version": "schema_version", - "sequencing_sample_id": "sequencing_sample_id" } } -} \ No newline at end of file +} diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index 1a0d1e24..fd3a8a3a 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -63,9 +63,11 @@ def __init__(self, file_path=None, output_directory=None): self.output_directory = output_directory Path(self.output_directory).mkdir(parents=True, exist_ok=True) - config_json = ConfigJson() - self.long_table_heading = config_json.get_configuration("long_table_heading") - + json_file = os.path.join(os.path.dirname(__file__), "conf", "bioinfo_config.json") + config_json = ConfigJson(json_file) + #self.long_table_heading = config_json.get_configuration("long_table_heading") + self.software_config = config_json.get_configuration('viralrecon') + self.long_table_heading = self.software_config["variants_long_table"]["content"] def validate_file(self, heading): """Check if long table file has all mandatory fields defined in configuration file @@ -90,12 +92,9 @@ def parse_file(self): stderr.print("[blue]Parsing the input file") heading_index = {} headings_from_csv = lines[0].strip().split(",") - for heading in self.long_table_heading: + for heading in self.long_table_heading.values(): heading_index[heading] = headings_from_csv.index(heading) - config = ConfigJson() - aux_dict = config.get_configuration("long_table_parse_aux") - samp_dict = {} for line in lines[1:]: line_s = line.strip().split(",") @@ -110,7 +109,7 @@ def parse_file(self): if isinstance(value, dict) else line_s[heading_index[value]] ) - for key, value in aux_dict.items() + for key, value in self.long_table_heading.items() } if re.search("&", line_s[heading_index["GENE"]]): @@ -125,7 +124,6 @@ def parse_file(self): else: variant_dict["Gene"] = line_s[heading_index["GENE"]] samp_dict[sample].append(variant_dict) - stderr.print("[green]Successful parsing data") return samp_dict diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 405ca571..a917f577 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -5,6 +5,7 @@ import glob import rich.console from datetime import datetime +from tqdm import tqdm from yaml import YAMLError import relecov_tools.utils @@ -21,7 +22,7 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) - +# TODO: Create 2 master function that validates file presence/content and transfrom from csv,tsv,... to json. class BioinfoMetadata: def __init__( self, @@ -62,21 +63,68 @@ def __init__( json_file = os.path.join(os.path.dirname(__file__), "conf", "bioinfo_config.json") config_json = ConfigJson(json_file) self.configuration = config_json - required_files = self.configuration.get_topic_data( - self.software_name, "required_file" - ) - self.req_files = {} - for key, file in required_files.items(): - f_path = os.path.join(self.input_folder, file) - if not os.path.isfile(f_path): - log.error("File %s does not exist", file) - stderr.print(f"[red]File {file} does not exist") - sys.exit(1) - self.req_files[key] = f_path + def get_software_required_files(self): + """Load required softwaew specific files and patterns""" + self.software_config = self.configuration.get_configuration(self.software_name) + self.required_file_name = {} + self.required_file_content = {} + + for key, value in self.software_config.items(): + if 'required' in value and value['required']: + self.required_file_name[key] = value.get('fn','') + self.required_file_content[key] = value.get('content','') + stderr.print(self.required_file_name) + + def scann_directory(self): + """Scann bioinfo analysis directory and search for files""" + total_files = sum(len(files) for _, _, files in os.walk(self.input_folder)) + self.get_software_required_files() + required_files_found = {key: '' for key in self.required_file_name} + + with tqdm(total=total_files, desc=f'\tScanning...') as pbar: + for key, value in self.required_file_name.items(): + for root, _, files in os.walk(self.input_folder, topdown=True): + for file_name in files: + # FIXME: might be better regex than endswith + if value.endswith(file_name): + file_path = os.path.join(root, file_name) + required_files_found[key]= file_path + pbar.update(1) # FIXME: is not correctly processing each file + return required_files_found + +# def validate_software_mandatory_files(self, files): +# """Verify that all required files are present""" +# missing = [] +# if len(files) == 0: +# log.error("No mandatory files for %s found in folder: %s", +# self.software_name, +# self.input_folder +# ) +# stderr.print( +# f"[red]\tValidation Failed: No mandatory files found in #folder: {self.input_folder}. " +# ) +# sys.exit(1) +# for key, values in files.items(): +# if len(values)==0: +# missing.append(key) +# if len(missing) > 0: +# stderr.print( +# f"[red]\tValidation Failed: Missing files for {self.#software_name}:" +# ) +# for i in missing: +# stderr.print( +# f"\t- {self.required_file_name[i]}" +# ) +# sys.exit(1) +# stderr.print( +# f"[green]\tValidation Approved" +# ) + + # TODO: we can make a rule in bioinfo_config.json where all software-properties must have a field callded "fixed_values". This way the second argument wont't be necessary def add_fixed_values(self, j_data, fixed_values): """include the fixed data defined in configuration or feed custom empty fields""" - f_values = self.configuration.get_topic_data(self.software_name, fixed_values) + f_values = self.software_config["fixed_values"] for row in j_data: for field, value in f_values.items(): row[field] = value @@ -111,7 +159,11 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): stderr.print(f"[red]Missing values in {table_name}\n:{field_errors}") return j_data - def include_data_from_mapping_stats(self, j_data): + #def include_data(self, j_data, topic): + # topic_json = self.configuration.get_topic_data(topic) + + # FIXME: All maping items says not provided in the output json. Origin above def. Wait. It might be due to unmatched samples name. Create a lab metadata with identical sample names. + def include_data_from_mapping_stats(self, j_data, files_dict): """By processing mapping stats file the following information is included in schema properties: depth_of_coverage_value, lineage_name, number_of_variants_in_consensus, number_of_variants_with_effect, @@ -121,12 +173,10 @@ def include_data_from_mapping_stats(self, j_data): # position of the sample columns inside mapping file sample_position = 4 map_data = relecov_tools.utils.read_csv_file_return_dict( - self.req_files["mapping_stats"], sep="\t", key_position=sample_position + files_dict["mapping_stats"], sep="\t", key_position=sample_position ) - mapping_fields = self.configuration.get_topic_data( - self.software_name, "mapping_stats" - ) + mapping_fields = self.software_config["mapping_stats"]["content"] j_data_with_mapping_stats = self.mapping_over_table( j_data, map_data, mapping_fields, "mapping stats" ) @@ -134,9 +184,7 @@ def include_data_from_mapping_stats(self, j_data): def include_pangolin_data(self, j_data): """Include pangolin data collecting form each file generated by pangolin""" - mapping_fields = self.configuration.get_topic_data( - self.software_name, "mapping_pangolin" - ) + mapping_fields = self.software_config["mapping_pangolin"]["content"] missing_pango = [] for row in j_data: if "-" in row["submitting_lab_sample_id"]: @@ -189,10 +237,7 @@ def include_consensus_data(self, j_data): """Include genome length, name, file name, path and md5 by preprocessing each file of consensus.fa """ - - mapping_fields = self.configuration.get_topic_data( - self.software_name, "mapping_consensus" - ) + mapping_fields = self.software_config["mapping_consensus"]["content"] missing_consens = [] for row in j_data: if "-" in row["submitting_lab_sample_id"]: @@ -223,15 +268,16 @@ def include_consensus_data(self, j_data): row["number_of_base_pairs_sequenced"] = str(base_calculation) else: row["number_of_base_pairs_sequenced"] = "Not Provided [GENEPIO:0001668]" - conserrs = len(missing_consens) - if conserrs >= 1: - log.error( - "{0} Consensus files missing:\n{1}".format( - conserrs, missing_consens - ) + # TODO: WAIT TO FIXED IN POST ADAPTATION PR + conserrs = len(missing_consens) + if conserrs >= 1: + log.error( + "{0} Consensus files missing:\n{1}".format( + conserrs, missing_consens ) - stderr.print(f"[yellow]{conserrs} samples missing consensus file:") - stderr.print(f"[yellow]\n{missing_consens}") + ) + stderr.print(f"[yellow]{conserrs} samples missing consensus file:") + stderr.print(f"[yellow]\n{missing_consens}") return j_data def parse_long_table(self, long_table_path, output_folder): @@ -268,28 +314,27 @@ def include_custom_data(self, j_data): row["long_table_path"] = long_table_path return j_data - def include_variant_metrics(self, j_data): + # TODO: Rename this module to include_custom_mqc data and exend its application. + def include_variant_metrics(self, j_data, files_dict): """Include the # Ns per 100kb consensus from the summary variant metric file_exists """ map_data = relecov_tools.utils.read_csv_file_return_dict( - self.req_files["variants_metrics"], sep="," - ) - mapping_fields = self.configuration.get_topic_data( - self.software_name, "mapping_variant_metrics" + files_dict["summary_mqc"], sep="," ) + mapping_fields = self.software_config["summary_mqc"]["content"] j_data_with_variant_metrics = self.mapping_over_table( j_data, map_data, mapping_fields, "variant metrics" ) return j_data_with_variant_metrics + # TODO: fpath should be imported from req_file found. def include_software_versions(self, j_data): """Include versions from the yaml version file""" - version_fields = self.configuration.get_topic_data( - self.software_name, "mapping_version" - ) + version_fields = self.software_config["mapping_version"] + f_path = os.path.join(self.input_folder, self.required_file_name["version_info"]) try: - versions = relecov_tools.utils.read_yml_file(self.req_files["versions"]) + versions = relecov_tools.utils.read_yml_file(f_path) except YAMLError as e: log.error("Unable to process version file return error %s", e) stderr.print(f"[red]Unable to process version file {e}") @@ -317,6 +362,11 @@ def create_bioinfo_file(self): metadata json, mapping_stats, and more information from the files inside input directory """ + self.get_software_required_files() + stderr.print(f"[blue]Sanning for {self.software_name} files..") + req_files = self.scann_directory() + #stderr.print(f"[blue]Verifying {self.software_name} required #files..") + #self.validate_software_mandatory_files(req_files) stderr.print("[blue]Reading lab metadata json") j_data = self.collect_info_from_lab_json() stderr.print("[blue]Adding fixed values") @@ -324,11 +374,11 @@ def create_bioinfo_file(self): # Creating empty fields that are not managed in case of missing data j_data = self.add_fixed_values(j_data, "feed_empty_fields") stderr.print("[blue]Adding data from mapping stats") - j_data = self.include_data_from_mapping_stats(j_data) + j_data = self.include_data_from_mapping_stats(j_data, req_files) stderr.print("[blue]Adding software versions") j_data = self.include_software_versions(j_data) stderr.print("[blue]Adding summary variant metrics") - j_data = self.include_variant_metrics(j_data) + j_data = self.include_variant_metrics(j_data, req_files) stderr.print("[blue]Adding pangolin information") j_data = self.include_pangolin_data(j_data) stderr.print("[blue]Adding consensus data") From 408dd6d55b15d39f617e54bba30b5092b768cda9 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 12 Mar 2024 12:55:29 +0100 Subject: [PATCH 1219/1454] update scanning folder method to detect both required and non-required files --- relecov_tools/read_bioinfo_metadata.py | 111 +++++++++++++++---------- 1 file changed, 66 insertions(+), 45 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index a67b8868..65e3a002 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -65,10 +65,10 @@ def __init__( json_file = os.path.join(os.path.dirname(__file__), "conf", "bioinfo_config.json") config_json = ConfigJson(json_file) self.configuration = config_json + self.software_config = self.configuration.get_configuration(self.software_name) def get_software_required_files(self): - """Load required softwaew specific files and patterns""" - self.software_config = self.configuration.get_configuration(self.software_name) + """Load required software specific files and patterns""" self.required_file_name = {} self.required_file_content = {} @@ -76,24 +76,46 @@ def get_software_required_files(self): if 'required' in value and value['required']: self.required_file_name[key] = value.get('fn','') self.required_file_content[key] = value.get('content','') - stderr.print(self.required_file_name) def scann_directory(self): """Scann bioinfo analysis directory and search for files""" total_files = sum(len(files) for _, _, files in os.walk(self.input_folder)) - self.get_software_required_files() - required_files_found = {key: '' for key in self.required_file_name} - - with tqdm(total=total_files, desc=f'\tScanning...') as pbar: - for key, value in self.required_file_name.items(): + files_found = {} + with tqdm(total=total_files, desc='\tScanning...') as pbar: + for topic_key, topic_details in self.software_config.items(): + if not 'fn' in topic_details: #try/except fn + continue for root, _, files in os.walk(self.input_folder, topdown=True): - for file_name in files: - # FIXME: might be better regex than endswith - if value.endswith(file_name): - file_path = os.path.join(root, file_name) - required_files_found[key]= file_path - pbar.update(1) # FIXME: is not correctly processing each file - return required_files_found + matching_files = [os.path.join(root, file_name) for file_name in files if file_name.endswith(topic_details['fn'])] + if len(matching_files) == 1: + # Only one file match found, add it as a string + files_found[topic_key] = matching_files[0] + elif len(matching_files) > 1: + # Multiple file matches found, add them as a list + files_found[topic_key] = matching_files + for _ in matching_files: + pbar.update(1) + if len(files_found) < 1: + log.error( + "No files found in %s.", self.output_folder + ) + stderr.print(f"[red] No files found in {self.output_folder}.") + sys.exit(1) + else: + return files_found + + def map_filesfound_to_bioinfo_json(self, dict): + """Integrate files found (outidr) and software config JSON data into a single mapped structure.""" + integrated_json = self.software_config + for key, value in dict.items(): + if key in integrated_json: + if isinstance(integrated_json[key], list): + # If the existing value is a list, extend it with the new file paths + integrated_json[key]['file_paths'].extend(value) + else: + # If the existing value is not a list, create a new list with the file paths + integrated_json[key]['file_paths'] = value + return integrated_json # def validate_software_mandatory_files(self, files): # """Verify that all required files are present""" @@ -364,37 +386,36 @@ def create_bioinfo_file(self): metadata json, mapping_stats, and more information from the files inside input directory """ - self.get_software_required_files() stderr.print(f"[blue]Sanning for {self.software_name} files..") - req_files = self.scann_directory() + files_dict = self.scann_directory() #stderr.print(f"[blue]Verifying {self.software_name} required #files..") #self.validate_software_mandatory_files(req_files) - stderr.print("[blue]Reading lab metadata json") - j_data = self.collect_info_from_lab_json() - stderr.print("[blue]Adding fixed values") - j_data = self.add_fixed_values(j_data, "fixed_values") - # Creating empty fields that are not managed in case of missing data - j_data = self.add_fixed_values(j_data, "feed_empty_fields") - stderr.print("[blue]Adding data from mapping stats") - j_data = self.include_data_from_mapping_stats(j_data, req_files) - stderr.print("[blue]Adding software versions") - j_data = self.include_software_versions(j_data) - stderr.print("[blue]Adding summary variant metrics") - j_data = self.include_variant_metrics(j_data, req_files) - stderr.print("[blue]Adding pangolin information") - j_data = self.include_pangolin_data(j_data) - stderr.print("[blue]Adding consensus data") - j_data = self.include_consensus_data(j_data) - stderr.print("[blue]Parsing variants_long_table info to json format...") - self.parse_long_table(self.input_folder, self.output_folder) - stderr.print("[blue]Adding variant long table path") - j_data = self.include_custom_data(j_data) - file_name = ( - "bioinfo_" + os.path.splitext(os.path.basename(self.json_file))[0] + ".json" - ) - stderr.print("[blue]Writting output json file") - os.makedirs(self.output_folder, exist_ok=True) - file_path = os.path.join(self.output_folder, file_name) - relecov_tools.utils.write_json_fo_file(j_data, file_path) - stderr.print("[green]Sucessful creation of bioinfo analyis file") + #stderr.print("[blue]Reading lab metadata json") + #j_data = self.collect_info_from_lab_json() + #stderr.print("[blue]Adding fixed values") + #j_data = self.add_fixed_values(j_data, "fixed_values") + ## Creating empty fields that are not managed in case #of missing data + #j_data = self.add_fixed_values(j_data, #"feed_empty_fields") + #stderr.print("[blue]Adding data from mapping stats") + #j_data = self.include_data_from_mapping_stats(j_data, #req_files) + #stderr.print("[blue]Adding software versions") + #j_data = self.include_software_versions(j_data) + #stderr.print("[blue]Adding summary variant metrics") + #j_data = self.include_variant_metrics(j_data, #req_files) + #stderr.print("[blue]Adding pangolin information") + #j_data = self.include_pangolin_data(j_data) + #stderr.print("[blue]Adding consensus data") + #j_data = self.include_consensus_data(j_data) + #stderr.print("[blue]Parsing variants_long_table info #to json format...") + #self.parse_long_table(self.input_folder, self.#output_folder) + #stderr.print("[blue]Adding variant long table path") + #j_data = self.include_custom_data(j_data) + #file_name = ( + # "bioinfo_" + os.path.splitext(os.path.basename#(self.json_file))[0] + ".json" + #) + #stderr.print("[blue]Writting output json file") + #os.makedirs(self.output_folder, exist_ok=True) + #file_path = os.path.join(self.output_folder, #file_name) + #relecov_tools.utils.write_json_fo_file(j_data, #file_path) + #stderr.print("[green]Sucessful creation of bioinfo #analyis file") return True From 9c238f2e4e4d48cdf61940bb49189d3fff2cb528 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 13 Mar 2024 12:52:17 +0100 Subject: [PATCH 1220/1454] rm version scope and rename property field names in bioinfo config --- relecov_tools/conf/bioinfo_config.json | 31 ++++++++++++++------------ 1 file changed, 17 insertions(+), 14 deletions(-) diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index 823ae59f..3bb53e43 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -1,14 +1,11 @@ { "viralrecon": { - "version_info": { - "fn": "software_versions.yml", - "required": true - }, "mapping_stats": { "fn": "mapping_illumina_stats.tab", - "ff": "tsv", - "sample_column": 1, - "num_lines": 1, + "ff": "\t", + "file_per_sample": false, + "sample_col_idx": 5, + "header_row_dix": 1, "required": true, "content": { "analysis_date": "analysis_date", @@ -27,9 +24,9 @@ }, "mapping_pangolin": { "fn": ".pangolin.csv", - "ff": "tsv", - "sample_column": 1, - "num_lines": 1, + "ff": ",", + "file_per_sample": true, + "header_row_dix": 1, "required": false, "content": { "variant_name": "scorpio_call", @@ -42,8 +39,10 @@ }, "variants_long_table": { "fn": "variants_long_table.csv", - "ff": "csv", - "num_lines": 1, + "ff": ",", + "file_per_sample": false, + "sample_col_idx": 1, + "header_row_dix": 1, "required": true, "content": { "sample" : "SAMPLE", @@ -68,6 +67,7 @@ "mapping_consensus": { "fn": ".consensus.fa", "ff": "fasta", + "file_per_sample": true, "required": false, "content": { "consensus_sequence_name" : "Not Provided [GENEPIO:0001668]", @@ -80,8 +80,10 @@ }, "summary_mqc": { "fn": "summary_variants_metrics_mqc.csv", - "ff": "csv", - "num_lines": 1, + "ff": ",", + "file_per_sample": false, + "sample_col_idx": 1, + "header_row_dix": 1, "required": true, "content": { "ns_per_100_kbp": "# Ns per 100kb consensus" @@ -90,6 +92,7 @@ "workflow_summary": { "fn": "multiqc_report.html", "ff": "html", + "file_per_sample": false, "required": true, "content": { "bioinformatics_protocol_software_name": "nf-core/viralrecon Workflow Summary", From 01f33a58df11e374329042c32d1b3da7305ccd37 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 14 Mar 2024 09:35:09 +0100 Subject: [PATCH 1221/1454] dummy changes - rename method, add todos and update comments --- relecov_tools/read_bioinfo_metadata.py | 35 +++++++++++++++----------- 1 file changed, 21 insertions(+), 14 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 65e3a002..9e0327cf 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -22,7 +22,8 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) -# TODO: Create 2 master function that validates file presence/content and transfrom from csv,tsv,... to json. +# TODO: Create 2 master function that validates file presence/content and transfrom from csv,tsv,... to json. +# TODO: Cosider eval py + func property in json to be able to discriminate between collated files and sample-specific files. class BioinfoMetadata: def __init__( self, @@ -55,18 +56,17 @@ def __init__( self.output_folder = output_folder # TODO: Available software list can be retrieved from conf/bioinfo_search_patterns.yml - # TODO: Add error if software is not in the list (sys exit) + # TODO: Add error if software is not in the list (sys exit). Add output to global log. if software is None: software = relecov_tools.utils.prompt_path( msg="Select the software, pipeline or tool use in the bioinformatic analysis (available: 'viralrecon'): " ) self.software_name = software - json_file = os.path.join(os.path.dirname(__file__), "conf", "bioinfo_config.json") - config_json = ConfigJson(json_file) - self.configuration = config_json - self.software_config = self.configuration.get_configuration(self.software_name) + config = ConfigJson(json_file) + self.software_config = config.get_configuration(self.software_name) + # FIXME: This must be refacored. not used so far. def get_software_required_files(self): """Load required software specific files and patterns""" self.required_file_name = {} @@ -76,7 +76,8 @@ def get_software_required_files(self): if 'required' in value and value['required']: self.required_file_name[key] = value.get('fn','') self.required_file_content[key] = value.get('content','') - + + # TODO: Add report of files found/not-found to global log def scann_directory(self): """Scann bioinfo analysis directory and search for files""" total_files = sum(len(files) for _, _, files in os.walk(self.input_folder)) @@ -88,10 +89,10 @@ def scann_directory(self): for root, _, files in os.walk(self.input_folder, topdown=True): matching_files = [os.path.join(root, file_name) for file_name in files if file_name.endswith(topic_details['fn'])] if len(matching_files) == 1: - # Only one file match found, add it as a string + # Only one file match found, add it as a string (collated files) files_found[topic_key] = matching_files[0] elif len(matching_files) > 1: - # Multiple file matches found, add them as a list + # Multiple file matches found, add them as a list (per sample files) files_found[topic_key] = matching_files for _ in matching_files: pbar.update(1) @@ -102,9 +103,10 @@ def scann_directory(self): stderr.print(f"[red] No files found in {self.output_folder}.") sys.exit(1) else: + stderr.print("\tRetrieving files found ...") return files_found - def map_filesfound_to_bioinfo_json(self, dict): + def inject_filesfound_to_bioinfo_json(self, dict): """Integrate files found (outidr) and software config JSON data into a single mapped structure.""" integrated_json = self.software_config for key, value in dict.items(): @@ -116,6 +118,7 @@ def map_filesfound_to_bioinfo_json(self, dict): # If the existing value is not a list, create a new list with the file paths integrated_json[key]['file_paths'] = value return integrated_json + # def validate_software_mandatory_files(self, files): # """Verify that all required files are present""" @@ -263,6 +266,7 @@ def include_consensus_data(self, j_data): """ mapping_fields = self.software_config["mapping_consensus"]["content"] missing_consens = [] + # FIXME: Replace sequencing_sample_id for row in j_data: if "-" in row["submitting_lab_sample_id"]: sample_name = row["submitting_lab_sample_id"].replace("-", "_") @@ -386,12 +390,15 @@ def create_bioinfo_file(self): metadata json, mapping_stats, and more information from the files inside input directory """ - stderr.print(f"[blue]Sanning for {self.software_name} files..") - files_dict = self.scann_directory() + stderr.print(f"[blue]Sanning input directory...") + files_found = self.scann_directory() + stderr.print(f"[blue] Adding discovered files in {self.input_folder} to their corresponding JSON properties defined in {self.json_file}...") + bioinfo_json_extended = self.inject_filesfound_to_bioinfo_json(files_found) + # TODO: Add here req-file parsin sysexit. Easy mode: if file_path not in item, sys.exit #stderr.print(f"[blue]Verifying {self.software_name} required #files..") #self.validate_software_mandatory_files(req_files) - #stderr.print("[blue]Reading lab metadata json") - #j_data = self.collect_info_from_lab_json() + stderr.print("[blue]Reading lab metadata json") + j_data = self.collect_info_from_lab_json() #stderr.print("[blue]Adding fixed values") #j_data = self.add_fixed_values(j_data, "fixed_values") ## Creating empty fields that are not managed in case #of missing data From aaf9902a53cefcfb61b0bfdae83d793c3afe39cf Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 14 Mar 2024 10:46:47 +0100 Subject: [PATCH 1222/1454] add validation required files method --- relecov_tools/read_bioinfo_metadata.py | 59 ++++++++++++-------------- 1 file changed, 27 insertions(+), 32 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 9e0327cf..331537b9 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -118,35 +118,31 @@ def inject_filesfound_to_bioinfo_json(self, dict): # If the existing value is not a list, create a new list with the file paths integrated_json[key]['file_paths'] = value return integrated_json - -# def validate_software_mandatory_files(self, files): -# """Verify that all required files are present""" -# missing = [] -# if len(files) == 0: -# log.error("No mandatory files for %s found in folder: %s", -# self.software_name, -# self.input_folder -# ) -# stderr.print( -# f"[red]\tValidation Failed: No mandatory files found in #folder: {self.input_folder}. " -# ) -# sys.exit(1) -# for key, values in files.items(): -# if len(values)==0: -# missing.append(key) -# if len(missing) > 0: -# stderr.print( -# f"[red]\tValidation Failed: Missing files for {self.#software_name}:" -# ) -# for i in missing: -# stderr.print( -# f"\t- {self.required_file_name[i]}" -# ) -# sys.exit(1) -# stderr.print( -# f"[green]\tValidation Approved" -# ) + + # TODO: Add validation to master log file. + # TODO: Add checking file format based on config. + # TODO: ¿Add content validation?. This might be better to be implemented when geting metadata from input files. + def validate_software_mandatory_files(self, json): + missing_required = [] + for key in json.keys(): + if json[key].get('required') is True: + try: + json[key]['file_paths'] + except KeyError: + missing_required.append(key) + else: + continue + if len(missing_required) >= 1: + log.error("\tMissing required files:") + stderr.print("[red]\tMissing required files:") + for i in missing_required: + log.error("[red]\t\t- %s", i) + stderr.print(f"\t\t- {i}") + sys.exit(1) + else: + stderr.print("[green]\tValidation passed :)") + return # TODO: we can make a rule in bioinfo_config.json where all software-properties must have a field callded "fixed_values". This way the second argument wont't be necessary def add_fixed_values(self, j_data, fixed_values): @@ -392,11 +388,10 @@ def create_bioinfo_file(self): """ stderr.print(f"[blue]Sanning input directory...") files_found = self.scann_directory() - stderr.print(f"[blue] Adding discovered files in {self.input_folder} to their corresponding JSON properties defined in {self.json_file}...") + stderr.print(f"[blue]Extending bioinfo config json with files found...") bioinfo_json_extended = self.inject_filesfound_to_bioinfo_json(files_found) - # TODO: Add here req-file parsin sysexit. Easy mode: if file_path not in item, sys.exit - #stderr.print(f"[blue]Verifying {self.software_name} required #files..") - #self.validate_software_mandatory_files(req_files) + stderr.print(f"[blue]Validating required files...") + self.validate_software_mandatory_files(bioinfo_json_extended) stderr.print("[blue]Reading lab metadata json") j_data = self.collect_info_from_lab_json() #stderr.print("[blue]Adding fixed values") From 255dbe1a2a8bd7067a3d44c3f506a22020400a2d Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 14 Mar 2024 11:41:13 +0100 Subject: [PATCH 1223/1454] rename variables for better understanding --- relecov_tools/read_bioinfo_metadata.py | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 331537b9..2090c11e 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -106,18 +106,18 @@ def scann_directory(self): stderr.print("\tRetrieving files found ...") return files_found - def inject_filesfound_to_bioinfo_json(self, dict): - """Integrate files found (outidr) and software config JSON data into a single mapped structure.""" - integrated_json = self.software_config - for key, value in dict.items(): - if key in integrated_json: - if isinstance(integrated_json[key], list): + def extend_software_config(self, files_dict): + """Inject files found (input dir) into software config JSON""" + extended_json = self.software_config + for key, value in files_dict.items(): + if key in extended_json: + if isinstance(extended_json[key], list): # If the existing value is a list, extend it with the new file paths - integrated_json[key]['file_paths'].extend(value) + extended_json[key]['file_paths'].extend(value) else: # If the existing value is not a list, create a new list with the file paths - integrated_json[key]['file_paths'] = value - return integrated_json + extended_json[key]['file_paths'] = value + return extended_json # TODO: Add validation to master log file. @@ -389,9 +389,9 @@ def create_bioinfo_file(self): stderr.print(f"[blue]Sanning input directory...") files_found = self.scann_directory() stderr.print(f"[blue]Extending bioinfo config json with files found...") - bioinfo_json_extended = self.inject_filesfound_to_bioinfo_json(files_found) + software_config_extended = self.extend_software_config(files_found) stderr.print(f"[blue]Validating required files...") - self.validate_software_mandatory_files(bioinfo_json_extended) + self.validate_software_mandatory_files(software_config_extended) stderr.print("[blue]Reading lab metadata json") j_data = self.collect_info_from_lab_json() #stderr.print("[blue]Adding fixed values") From 2164f45c8878a9d4e06f966f73bd5b78d2f68b40 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 5 Mar 2024 17:26:29 +0100 Subject: [PATCH 1224/1454] Optimized imports and included some more like pandas or warnings --- relecov_tools/sftp_handle.py | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 90ba2894..4711290d 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -1,17 +1,23 @@ #!/usr/bin/env python -from datetime import datetime -from itertools import islice import copy import logging import json -import rich.console -import paramiko import sys import os import stat import yaml -import openpyxl +import warnings +import rich.console +import paramiko import relecov_tools.utils +from datetime import datetime +from itertools import islice +from collections import OrderedDict +from secrets import token_hex +from csv import writer as csv_writer, Error as CsvError +from openpyxl import load_workbook as openpyxl_load_workbook +from pandas import read_excel, ExcelWriter, concat +from pandas.errors import ParserError, EmptyDataError from relecov_tools.config_json import ConfigJson # from relecov_tools.rest_api import RestApi From 22c75ae00ce9f387cd917c30463e38e9502e1241 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 5 Mar 2024 17:31:55 +0100 Subject: [PATCH 1225/1454] Introduced big process to merge subfolders in remote sftp before download begins --- relecov_tools/sftp_handle.py | 288 +++++++++++++++++++++++++++++++++++ 1 file changed, 288 insertions(+) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 4711290d..a3d7ad7d 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -613,6 +613,294 @@ def delete_remote_files(self, remote_folder, files): continue return + def move_processing_fastqs(self, folders_with_metadata): + """Gather all the files from any subfolder into a processing folder + + Args: + folders_with_metadata (dict(str:list)): Dictionary updated from merge_md5sums() + + Returns: + folders_with_metadata (dict(str:list)): Same dict updated with files successfully moved + """ + log.info("Moving remote files to each temporal processing folder") + stderr.print(f"[blue]Moving remote files to each temporal processing folder") + for folder, files in folders_with_metadata.items(): + self.current_folder = folder.split("/")[0] + successful_files = [] + for file in files: + if not file.endswith(tuple(self.allowed_file_ext)): + continue + file_dest = os.path.join(folder, os.path.basename(file)) + try: + # Paramiko.SSHClient.sftp_open does not have a method to copy files + self.client.rename(file, file_dest) + successful_files.append(file_dest) + except OSError: + if file in folders_with_metadata[folder]: + error_text = "File named %s already in %s. Skipped" + log.warning(error_text % (file, self.current_folder)) + self.include_warning(error_text % (file, self.current_folder)) + else: + error_text = "Error while moving file %s" + log.error(error_text % file) + self.include_error(error_text % file) + folders_with_metadata[folder] = successful_files + return folders_with_metadata + + def merge_md5sums(self, folders_with_metadata): + """Download the md5sums for each folder, merge them into a single one, + upload them to the remote processing folder. + + Args: + folders_with_metadata (dict(str:list)): Dictionary with remote folders + and their files. All subfolder filenames are merged into a single key. + + Raises: + FileNotFoundError: If no md5sum file is found in the folder + + Returns: + folders_with_metadata: Same dict updated with the merged md5sum file + """ + output_location = self.platform_storage_folder + log.info("Merging md5sum files from remote folders...") + stderr.print("[blue]Merging md5sum files from remote folders...") + + # TODO: Include this function in relecov_tools.utils + def md5_merger(md5_filelist, avoid_chars=None): + md5dict_list = [] + for md5sum in md5_filelist: + hash_dict = relecov_tools.utils.read_md5_checksum(md5sum, avoid_chars) + if hash_dict: + md5dict_list.append(hash_dict) + # Sort hashes and files back to the original order. + merged_md5 = { + md5: file for mdict in md5dict_list for file, md5 in mdict.items() + } + return merged_md5 + + def md5_handler(md5sumlist, output_location): + downloaded_md5files = [] + for md5sum in md5sumlist: + md5_name = "_".join([token_hex(nbytes=12), "md5_temp.md5"]) + fetched_md5 = os.path.join(output_location, md5_name) + if self.get_from_sftp(file=md5sum, destination=fetched_md5): + downloaded_md5files.append(fetched_md5) + merged_md5 = md5_merger(downloaded_md5files, self.avoidable_characters) + if merged_md5: + merged_name = "_".join([folder.split("/")[0], "md5sum.md5"]) + merged_md5_path = os.path.join(output_location, merged_name) + with open(merged_md5_path, "w") as md5out: + write_md5 = csv_writer(md5out, delimiter="\t") + write_md5.writerows(merged_md5.items()) + md5_dest = os.path.join(folder, os.path.basename(merged_md5_path)) + self.client.put(localpath=merged_md5_path, remotepath=md5_dest) + # Remove local files once merged and uploaded + [os.remove(md5_file) for md5_file in downloaded_md5files] + return md5_dest + else: + error_text = "No md5sum could be processed in remote folder" + raise FileNotFoundError(error_text) + + for folder in folders_with_metadata.keys(): + self.current_folder = folder.split("/")[0] + md5flag = "md5sum" + md5sumlist = [fi for fi in folders_with_metadata[folder] if md5flag in fi] + if not md5sumlist: + error_text = "No md5sum could be found in remote folder" + log.warning(error_text) + stderr.print(f"[yellow]{error_text}") + self.include_warning(error_text) + continue + folders_with_metadata[folder] = [ + fi for fi in folders_with_metadata[folder] if fi not in md5sumlist + ] + try: + uploaded_md5 = md5_handler(md5sumlist, output_location) + except (FileNotFoundError, OSError, PermissionError, CsvError) as e: + error_text = "Could not merge md5files for %s. Reason: %s" + log.warning(error_text % (self.current_folder, str(e))) + stderr.print(f"[yellow]{error_text % (self.current_folder, str(e))}") + self.include_warning(error_text % (self.current_folder, str(e))) + continue + if uploaded_md5: + folders_with_metadata[folder].append(uploaded_md5) + + return folders_with_metadata + + def merge_metadata(self, metadata_sheet=None, *metadata_tables): + """Merge a variable number of metadata dataframes to the first one. Merge them + only into a certain sheet from a multi-sheet excel file if sheetname is given. + + Args: + metadata_sheet (str): Name of the sheet containing metadata in excel file + *metadata_tables (list(pandas.DataFrame)): Dataframes to be merged + + Returns: + merged_df (pandas.DataFrame): A merged dataframe from the given tables + """ + meta_sheet = metadata_sheet + for idx, table in enumerate(metadata_tables): + if idx == 0: + merged_df = table + continue + if meta_sheet: + merged_df[meta_sheet] = concat( + [merged_df[meta_sheet], table[meta_sheet]], ignore_index=True + ) + else: + merged_df = concat([merged_df, table], ignore_index=True) + return merged_df + + def excel_to_df(self, excel_file, metadata_sheet, header_flag): + """Read an excel file, return a dict with a dataframe for each sheet in it. + Process the given sheet with metadata, removing all rows until header is found + + Args: + excel_file (str): Path to the local excel file with metadata + metadata_sheet (str): Name of the sheet containing metadata in excel file + header_flag (str): Name of one of the columns from the metadata header + + Raises: + MetadataError: If no header could be found matching header flag + + Returns: + excel_df (dict(str:pandas.DataFrame)): Dict {name_of_excel_sheet:DataFrame} + containing all sheets in the excel file as pandas dataframes. + """ + # Get every sheet from the first excel file + excel_df = read_excel(excel_file, sheet_name=None) # index_col=None + meta_df = excel_df[metadata_sheet] + if header_flag in meta_df.columns: + return excel_df + header_row = None + for idx in range(len(meta_df)): + if any(meta_df.loc[idx, x] == header_flag for x in meta_df.columns): + header_row = idx + if not header_row: + error_text = "Header could not be found for excel file %s" + raise MetadataError(str(error_text % excel_file)) + meta_df.columns = meta_df.iloc[header_row] + excel_df[metadata_sheet] = meta_df.drop(meta_df.index[: (header_row + 1)]) + excel_df[metadata_sheet] = excel_df[metadata_sheet].reset_index(drop=True) + return excel_df + + def merge_subfolders(self, target_folders): + """For each first-level folder in the sftp, merge all the subfolders within + it in a single one called '*_tmp_processing' by moving all the fastq files from + them. Merge the metadata excel and md5 files from each subfolder too. + + Args: + target_folders (dict(str:list)): Dictionary with folders and their files + + Returns: + clean_target_folders (dict(str:list)): Dict with '*_tmp_processing' folders + and their content. All subfolder filenames are merged into a single key. + """ + """clean_folders = { + fd:v for fd,v in target_folders.items() if "tmp_processing" not in fd + }""" + clean_folders = target_folders + metadata_ws = self.metadata_processing.get("excel_sheet") + header_flag = self.metadata_processing.get("header_flag") + output_location = self.platform_storage_folder + date_and_time = datetime.today().strftime("%Y%m%d%-H%M%S") + + def upload_merged_df(merged_excel_path, last_main_folder, merged_df): + self.client.mkdir(last_main_folder) + pd_writer = ExcelWriter(merged_excel_path, engine="xlsxwriter") + for sheet in merged_df.keys(): + format_sheet = merged_df[sheet].astype(str)[merged_df[sheet].notnull()] + format_sheet.to_excel(pd_writer, sheet_name=sheet, index=False) + pd_writer.close() + dest = os.path.join(last_main_folder, os.path.basename(merged_excel_path)) + self.client.put(merged_excel_path, dest) + return + + folders_with_metadata = {} + merged_df = None + log.info("Setting %s remote folders...", str(len(clean_folders.keys()))) + stderr.print(f"[blue]Setting {len(clean_folders.keys())} remote folders...") + for folder in sorted(clean_folders.keys()): + self.current_folder = folder + + try: + downloaded_metadata = self.get_metadata_file(folder, output_location) + except (FileNotFoundError, OSError, PermissionError, MetadataError) as err: + error_text = "Remote folder %s skipped. Reason: %s" + log.error(error_text % (folder, err)) + self.include_error(error_text % (folder, err)) + continue + try: + self.read_metadata_file(downloaded_metadata, return_data=False) + except MetadataError as header_error: + error_text = " Folder skipped: %s" + os.remove(downloaded_metadata) + log.error(str(folder, str(error_text % str(header_error)))) + self.include_error(error_text % header_error) + continue + # Create a temporal name to avoid duplicated filenames + meta_filename = "_".join([folder.split("/")[-1], "metadata_temp.xlsx"]) + local_meta = os.path.join(output_location, meta_filename) + os.rename(downloaded_metadata, local_meta) + + # Taking the main folder for each lab as reference to merge + main_folder = folder.split("/")[0] + temporal_foldername = "_".join([date_and_time, "tmp_processing"]) + temp_folder = os.path.join(main_folder, temporal_foldername) + # Get every file except the excel ones as they are going to be merged + filelist = [fi for fi in target_folders[folder] if not fi.endswith(".xlsx")] + if not folders_with_metadata.get(temp_folder): + log_text = "Trying to merge metadata from %s in %s" + log.info(log_text % (main_folder, temp_folder)) + stderr.print(f"[blue]{log_text % (main_folder, temp_folder)}") + if merged_df: + # Write the previous merged metadata df before overriding it + try: + upload_merged_df(merged_excel_path, last_main_folder, merged_df) + folders_with_metadata[last_main_folder].append(excel_name) + except OSError: + error_text = "Error uploading merged metadata back to sftp" + log.error(error_text) + self.include_error(error_text) + del folders_with_metadata[last_main_folder] + try: + merged_df = self.excel_to_df(local_meta, metadata_ws, header_flag) + except (ParserError, EmptyDataError, MetadataError, KeyError) as e: + meta_name = os.path.basename(downloaded_metadata) + error_text = "%s skipped. Error while processing excel %s: %s" + log.error(error_text % (main_folder, meta_name, str(e))) + self.include_error(error_text % (main_folder, meta_name, str(e))) + continue + folders_with_metadata[temp_folder] = [] + folders_with_metadata[temp_folder].extend(filelist) + # rename metadata file to avoid filename duplications + excel_name = "_".join([folder.split("/")[0], "merged_metadata.xlsx"]) + merged_excel_path = os.path.join(output_location, excel_name) + os.rename(local_meta, merged_excel_path) + # Keep a track of the main_folder for next iteration + last_main_folder = temp_folder + else: + # If temp_folder has subfolders in it, merge everything + folders_with_metadata[temp_folder].extend(filelist) + new_df = self.excel_to_df(local_meta, metadata_ws, header_flag) + merged_df = self.merge_metadata(metadata_ws, merged_df, new_df) + # End of loop + + # Write last dataframe to file once loop is finished + if folders_with_metadata.get(last_main_folder): + if excel_name not in folders_with_metadata[last_main_folder]: + upload_merged_df(merged_excel_path, last_main_folder, merged_df) + folders_with_metadata[last_main_folder].append(excel_name) + + # Merge md5files and upload them to tmp_processing folder + merged_md5_folders = self.merge_md5sums(folders_with_metadata) + # Move all the files from each subfolder into its tmp_processing folder + clean_target_folders = self.move_processing_fastqs(merged_md5_folders) + log_text = "Remote folders merged into %s folders. Proceed with processing" + log.info(log_text % len(clean_target_folders.keys())) + stderr.print(f"[green]{log_text % len(clean_target_folders.keys())}") + return clean_target_folders + def select_target_folders(self): """Find the selected folders in remote if given, else select every folder From 56f71e4ec1e2ccc00d069a696225f9242f579c0a Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 5 Mar 2024 17:33:00 +0100 Subject: [PATCH 1226/1454] Introduced several functions to create a custom log summary of all the processes --- relecov_tools/sftp_handle.py | 44 ++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index a3d7ad7d..c05ffce4 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -1128,6 +1128,50 @@ def download(self, target_folders, option="download"): stderr.print(f"[green]Finished processing {folder}") return + def include_error(self, entry, sample=None): + self.update_summary(log_type="error", entry=entry, sample=sample) + return + + def include_warning(self, entry, sample=None): + self.update_summary(log_type="warning", entry=entry, sample=sample) + return + + def update_summary(self, log_type, entry, sample=None): + feed_dict = OrderedDict({"valid": False, "errors": [], "warnings": []}) + current_folder = str(self.current_folder).replace("./", "").split("/")[0] + entry = str(entry) + sample = str(sample) + if current_folder not in self.logs.keys(): + self.logs[current_folder] = feed_dict + self.logs[current_folder]["samples"] = OrderedDict() + if sample == "None": + if log_type == "error": + self.logs[current_folder]["errors"].append(entry) + elif log_type == "warning": + self.logs[current_folder]["warnings"].append(entry) + else: + if sample not in self.logs[current_folder]["samples"].keys(): + self.logs[current_folder]["samples"][sample] = feed_dict + if log_type == "error": + self.logs[current_folder]["samples"][sample]["errors"].append(entry) + elif log_type == "warning": + self.logs[current_folder]["samples"][sample]["warnings"].append(entry) + return + + def create_error_summary(self): + for folder in self.logs.keys(): + if not self.logs[folder]["errors"]: + self.logs[folder]["valid"] = True + for sample in self.logs[folder]["samples"].keys(): + if not self.logs[folder]["samples"][sample]["errors"]: + self.logs[folder]["samples"][sample]["valid"] = True + filename = "_".join([datetime.today().strftime("%Y%m%d"), "log_summary.json"]) + summary_path = os.path.join(self.platform_storage_folder, filename) + with open(summary_path, "w", encoding="utf-8") as f: + f.write(json.dumps(self.logs, indent=4, sort_keys=True, ensure_ascii=False)) + stderr.print(f"Process summary printed in {summary_path}") + return + def execute_process(self): """Executes different processes depending on the download_option""" if not self.open_connection(): From bdfc25c7794a682fdf5d5631db72cdbf8624b5e3 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 5 Mar 2024 17:37:36 +0100 Subject: [PATCH 1227/1454] Created a separate method to read excel metadata file, also included warnings & errors to log summary --- relecov_tools/sftp_handle.py | 127 ++++++++++++++++++++--------------- 1 file changed, 74 insertions(+), 53 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index c05ffce4..70414468 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -408,34 +408,32 @@ def remove_duplicated_values(self, sample_file_dict): } clean_sample_dict = {key: sample_file_dict[key] for key in non_duplicated_keys} if duplicated_keys: - log.warning("Found duplicated files in metadata") - stderr.print("[Orange]Found samples in metadata refering to the same file") + error_text = "Samples in metadata refering to the same file. " + log.warning(error_text + str(duplicated_keys)) + stderr.print(f"[Orange]{error_text}") stderr.print("[Orange]These samples won't be processed: ", duplicated_keys) + [self.include_error(error_text, sample) for sample in duplicated_keys] return clean_sample_dict - def get_sample_fastq_file_names(self, local_folder, meta_f_path): - """Read excel metadata template and create dictionary with files for each sample + def read_metadata_file(self, meta_f_path, return_data=True): + """Read excel file, check if the header matches with the one defined in config Args: - local_folder (str): folder where the excel file has been downloaded - meta_f_path (str): path to the downloaded excel file with metadata + meta_f_path (str): Path to the excel_file + + Raises: + MetadataError: If the header in the excel is different from config Returns: - clean_sample_dict(dict(str:{str:str})): Nested dictionary for each sample - {sample1: {"sequence_file_R1_fastq": "sample1_R1.fastq.gz", - "sequence_file_R2_fastq": "sample1_R2.fastq.gz"}, - sample2:{...} } + ws_metadata_lab: openpyxl's workbook metadata sheet of the excel file + metadata_header: column names of the header + header_row: row where the header is located in the sheet """ - if not os.path.isfile(meta_f_path): - log.error("Metadata file does not exist on %s", local_folder) - stderr.print("[red] METADATA_LAB.xlsx do not exist in" + local_folder) - return False - wb_file = openpyxl.load_workbook(meta_f_path, data_only=True) + warnings.simplefilter(action="ignore", category=UserWarning) + wb_file = openpyxl_load_workbook(meta_f_path, data_only=True) ws_metadata_lab = wb_file[self.metadata_processing.get("excel_sheet")] - sample_file_dict = {} # find out the index for file names - meta_column_list = self.metadata_lab_heading header_flag = self.metadata_processing.get("header_flag") header_row = [ idx + 1 for idx, x in enumerate(ws_metadata_lab.values) if header_flag in x @@ -443,13 +441,11 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): for cell in ws_metadata_lab[header_row]: cell.value = cell.value.strip() metadata_header = [x.value for x in ws_metadata_lab[header_row]] - if ( - meta_column_list != metadata_header[1:] - and "Sequencing Institution" in metadata_header - ): + meta_column_list = self.metadata_lab_heading + if meta_column_list != metadata_header[1:]: diffs = [ x - for x in (metadata_header[1:] + meta_column_list) + for x in set(metadata_header[1:] + meta_column_list) if x not in meta_column_list or x not in metadata_header ] log.error( @@ -460,47 +456,72 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): ) stderr.print("[red]Differences: ", diffs) raise MetadataError(f"Metadata header different from config: {diffs}") - index_sampleID = metadata_header.index("Sample ID given for sequencing") - index_layout = metadata_header.index("Library Layout") - index_fastq_r1 = metadata_header.index("Sequence file R1 fastq") - index_fastq_r2 = metadata_header.index("Sequence file R2 fastq") - for row in islice(ws_metadata_lab.values, header_row, ws_metadata_lab.max_row): + if return_data: + return ws_metadata_lab, metadata_header, header_row + else: + return True + + def get_sample_fastq_file_names(self, local_folder, meta_f_path): + """Read excel metadata template and create dictionary with files for each sample + + Args: + local_folder (str): folder where the excel file has been downloaded + meta_f_path (str): path to the downloaded excel file with metadata + + Returns: + clean_sample_dict(dict(str:{str:str})): Nested dictionary for each sample + {sample1: {"sequence_file_R1_fastq": "sample1_R1.fastq.gz", + "sequence_file_R2_fastq": "sample1_R2.fastq.gz"}, + sample2:{...} } + """ + if not os.path.isfile(meta_f_path): + log.error("Metadata file does not exist on %s", local_folder) + stderr.print("[red] METADATA_LAB.xlsx do not exist in" + local_folder) + return False + sample_file_dict = {} + metadata_ws, meta_header, header_row = self.read_metadata_file(meta_f_path) + index_sampleID = meta_header.index("Sample ID given for sequencing") + index_layout = meta_header.index("Library Layout") + index_fastq_r1 = meta_header.index("Sequence file R1 fastq") + index_fastq_r2 = meta_header.index("Sequence file R2 fastq") + for row in islice(metadata_ws.values, header_row, metadata_ws.max_row): if row[index_sampleID] is not None: + row_complete = True try: s_name = str(row[index_sampleID]) except ValueError as e: - stderr.print("[red] Unable to convert to string. ", e) + stderr.print("[red]Unable to convert to string. ", e) + continue if s_name not in sample_file_dict: sample_file_dict[s_name] = {} else: print("Found duplicated sample ", s_name) + s_name = "_".join([s_name, str(token_hex(nbytes=8))]) if row[index_layout] == "paired" and row[index_fastq_r2] is None: - log.error( - "Sample %s is paired-end, but no R2 given", row[index_sampleID] - ) - continue + error_text = "Sample %s is paired-end, but no R2 given" + log.error(str(error_text % str(row[index_sampleID]))) + self.include_error(error_text % str(row[index_sampleID]), s_name) + row_complete = False if row[index_layout] == "single" and row[index_fastq_r2] is not None: - log.error( - "Sample %s is single-end, but R1&R2 given", row[index_sampleID] - ) - continue - if row[index_fastq_r1] is not None: - # TODO: move these keys to configuration.json - sample_file_dict[s_name]["sequence_file_R1_fastq"] = row[ - index_fastq_r1 - ] - else: - log.error("Fastq_R1 not defined in Metadata for sample %s", s_name) - stderr.print( - "[red]No fastq R1 file for sample " + s_name + ". Skipping" - ) - continue - if row[index_fastq_r2] is not None: - sample_file_dict[s_name]["sequence_file_R2_fastq"] = row[ - index_fastq_r2 - ] - # if not self.check_sample_files(sample_file_dict[s_name]): - + error_text = "Sample %s is single-end, but R1&R2 given" + log.error(str(error_text % str(row[index_sampleID]))) + self.include_error(error_text % str(row[index_sampleID]), s_name) + row_complete = False + if row_complete: + if row[index_fastq_r1] is not None: + # TODO: move these keys to configuration.json + sample_file_dict[s_name]["sequence_file_R1_fastq"] = row[ + index_fastq_r1 + ] + if row[index_fastq_r2] is not None: + sample_file_dict[s_name]["sequence_file_R2_fastq"] = row[ + index_fastq_r2 + ] + else: + error_text = "Fastq_R1 not defined in Metadata for sample %s" + log.error(str(error_text % s_name)) + stderr.print(f"[red]{str(error_text % s_name)}") + self.include_error(str(error_text % s_name), s_name) # Remove duplicated files clean_sample_dict = self.remove_duplicated_values(sample_file_dict) return clean_sample_dict From 66ad5139d11afc8d14792903b7a889229532281d Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 5 Mar 2024 17:39:53 +0100 Subject: [PATCH 1228/1454] Better handling of corrupted files, moving them to a corrupt folder and deleting from metadata --- relecov_tools/sftp_handle.py | 60 ++++++++++++++++++++++++------------ 1 file changed, 41 insertions(+), 19 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 70414468..32056e50 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -1077,39 +1077,56 @@ def download(self, target_folders, option="download"): local_folder, os.path.basename(remote_md5sum) ) self.get_from_sftp(file=remote_md5sum, destination=fetched_md5) - successful_files, req_retransmition = self.verify_md5_checksum( + successful_files, corrupted = self.verify_md5_checksum( local_folder, fetched_files, fetched_md5 ) - # retrasmision of files in folder - if req_retransmition: - stderr.print("[Yellow] Error during download, trying again...") - self.get_remote_folder_files( - folder, local_folder, req_retransmition - ) + # try to download the files again to discard errors during download + if corrupted: + stderr.print("[gold1]Found md5 mismatches, downloading again...") + self.get_remote_folder_files(folder, local_folder, corrupted) saved_files, corrupted = self.verify_md5_checksum( - local_folder, req_retransmition, fetched_md5 + local_folder, corrupted, fetched_md5 ) if saved_files: successful_files.extend(saved_files) if corrupted: - log.warning("Found corrupted files: %s", str(corrupted)) - stderr.print(f"Found corrupted files: {str(corrupted)}") + corr_fold = os.path.join(local_folder, "corrupted") + os.mkdir(corr_fold) + error_text = "Found corrupted files: %s. Moved to: %s" + log.warning(error_text % (str(corrupted), corr_fold)) + stderr.print(f"[red]{error_text % (str(corrupted), corr_fold)}") + self.include_warning(error_text % (str(corrupted), "/corrupt/")) + [self.include_error("md5 mismatch", corr) for corr in corrupted] + for corr_file in corrupted: + path = os.path.join(local_folder, corr_file) + try: + os.rename(path, os.path.join(corr_fold, corr_file)) + except (FileNotFoundError, PermissionError, OSError) as e: + error_text = ( + "Could not move corrupted file %s to %s: %s" + ) + log.error(error_text % (path, corr_fold, e)) + stderr.print( + f"[red]{error_text % (path, corr_fold, e)}" + ) if self.abort_if_md5_mismatch: - log.error("Aborting, corrupted files %s", str(corrupted)) - stderr.print( - f"[red] Stopped processing folder {folder} \ - due to corrupted files {corrupted}" - ) + error_text = "Stop processing %s due to corrupted files." + log.error(error_text % folder) + stderr.print(f"[red]{error_text % folder}") + self.include_error(error_text % "folder") relecov_tools.utils.delete_local_folder(local_folder) continue hash_dict = relecov_tools.utils.read_md5_checksum( fetched_md5, self.avoidable_characters ) log.info("Finished md5 check for folder: %s", folder) - stderr.print(f"Finished md5 verification for folder {folder}") + stderr.print(f"[blue]Finished md5 verification for folder {folder}") else: - log.warning("No single md5sum file could be found in %s", folder) - stderr.print(f"[red]No single md5sum could be found in {folder}") + error_text = "No single md5sum file could be found in %s" % folder + log.warning(error_text) + stderr.print(f"[red]{error_text}") + self.include_error(error_text) + clean_fetchlist = [ fi for fi in fetched_files if fi.endswith(tuple(self.allowed_file_ext)) ] @@ -1130,8 +1147,13 @@ def download(self, target_folders, option="download"): f_name = os.path.basename(path) if f_name in successful_files: files_md5_dict[f_name] = hash_dict[f_name] + elif f_name in corrupted: + clean_fetchlist.remove(f_name) else: - log.warning("File %s not found in md5sum. Creating it", f_name) + if not str(f_name).rstrip(".gz") in files_to_compress: + error_text = "File %s not found in md5sum. Creating hash" + log.warning(error_text % f_name) + self.include_warning(str(error_text % f_name), f_name) files_md5_dict[f_name] = relecov_tools.utils.calculate_md5(path) else: md5_hashes = [ From 70a10346658ec20935289de291a657a1b9c9888a Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 5 Mar 2024 17:40:49 +0100 Subject: [PATCH 1229/1454] Small change in recursive listing, client was not necessary --- relecov_tools/sftp_handle.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 32056e50..8c9d39e6 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -181,7 +181,7 @@ def list_remote_folders(self, folder_name, recursive=False): if not subfolders: return [folder_name] - def recursive_list(folder_name, client): + def recursive_list(folder_name): try: attribute_list = self.client.listdir_attr(folder_name) except (FileNotFoundError, OSError) as e: @@ -194,13 +194,13 @@ def recursive_list(folder_name, client): if stat.S_ISDIR(attribute.st_mode): abspath = os.path.join(folder_name, attribute.filename) directory_list.append(abspath) - recursive_list(abspath, client) + recursive_list(abspath) else: continue return directory_list if recursive: - directory_list = recursive_list(folder_name, self.client) + directory_list = recursive_list(folder_name) return directory_list try: directory_list = [ From 9735470b8f8450ce6be0744a410e781ec1d9ecf1 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 5 Mar 2024 17:42:34 +0100 Subject: [PATCH 1230/1454] Included many calls to the brand new log_summary method in order to generate custom log summary --- relecov_tools/sftp_handle.py | 74 ++++++++++++++++++++++-------------- 1 file changed, 46 insertions(+), 28 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 8c9d39e6..70c132ad 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -113,6 +113,7 @@ def __init__( self.sftp_user = relecov_tools.utils.prompt_text(msg="Enter the user id") if isinstance(self.target_folders, str): self.target_folders = self.target_folders.split(",") + self.logs = {} if self.sftp_passwd is None: self.sftp_passwd = relecov_tools.utils.prompt_password( msg="Enter your password" @@ -282,6 +283,7 @@ def get_remote_folder_files(self, folder, local_folder, file_list): Returns: fetched_files(list(str)): list of successfully downloaded files """ + fetched_files = list() log.info("Trying to fetch files in remote server") stderr.print(f"Fetching {len(file_list)} files from {folder}") @@ -327,7 +329,9 @@ def verify_md5_checksum(self, local_folder, fetched_files, fetched_md5): avoid_chars = self.avoidable_characters hash_dict = relecov_tools.utils.read_md5_checksum(fetched_md5, avoid_chars) if not hash_dict: - log.warning("md5sum file could not be read, md5 hashes won't be validated") + error_text = "md5sum file could not be read, md5 hashes won't be validated" + log.warning(error_text) + self.include_warning(error_text) return fetched_files, False # check md5 checksum for each file for f_name in hash_dict.keys(): @@ -362,10 +366,13 @@ def create_files_with_metadata_info( sample_data_file = "samples_data_" + prefix_file_name + ".json" sample_data_path = os.path.join(local_folder, sample_data_file) os.rename(metadata_file, os.path.join(local_folder, new_metadata_file)) + error_text = "Sample %s incomplete. Not added to final Json" + data = copy.deepcopy(samples_dict) for sample, values in data.items(): if not all(val for val in values): - log.warning("Sample %s incomplete. Not added to final Json", sample) + log.error(str(error_text % sample)) + self.include_error(str(error_text % sample), sample) samples_to_delete.append(sample) continue # TODO: Move these keys to configuration.json @@ -374,12 +381,11 @@ def create_files_with_metadata_info( if values.get("sequence_file_R2_fastq"): values["r2_fastq_filepath"] = local_folder values["fastq_r2_md5"] = md5_dict.get(values["sequence_file_R2_fastq"]) - data = {key: val for key, val in data.items() if key not in samples_to_delete} + if samples_to_delete: + data = {k: v for k, v in data.items() if k not in samples_to_delete} with open(sample_data_path, "w", encoding="utf-8") as fh: fh.write(json.dumps(data, indent=4, sort_keys=True, ensure_ascii=False)) - log.info( - "Successfully created file with sample names list %s", sample_data_path - ) + log.info("Successfully created json file with samples %s", sample_data_path) return def remove_duplicated_values(self, sample_file_dict): @@ -592,28 +598,27 @@ def validate_remote_files(self, remote_folder, local_folder): log.info("Files in %s match with metadata file", remote_folder) stderr.print("Successfully validated files based on metadata") else: - log.warning("Some files in %s do not match metadata file", remote_folder) - stderr.print( - "Some files in " - + remote_folder - + " do not match the ones described in metadata" - ) + log_text = "Some files in %s do not match the ones described in metadata" + log.warning(log_text % remote_folder) + stderr.print(f"[gold1]{log_text % remote_folder}") set_list = set(metafiles_list) mismatch_files = [fi for fi in filtered_files_list if fi not in set_list] mismatch_rev = [fi for fi in set_list if fi not in filtered_files_list] - log.warning( - "Files in folder not present in metadata %s", str(mismatch_files) - ) - log.warning( - "Files in metadata not present in folder: %s", str(mismatch_rev) - ) + error_text1 = "Files in folder missing in metadata %s" + log.warning(error_text1 % str(mismatch_files)) + self.include_warning(error_text1 % str(mismatch_files)) + error_text2 = "Files in metadata missing in folder %s" + log.warning(error_text2 % str(mismatch_rev)) + self.include_warning(error_text2 % str(mismatch_rev)) # Try to check if the metadata filename lacks the proper extension log.info("Trying to match files without proper file extension") sample_files_dict = self.process_filedict( sample_files_dict, filtered_files_list ) if not any(value for value in sample_files_dict.values()): - raise FileNotFoundError("No files from metadata found in ", remote_folder) + raise FileNotFoundError( + "No files from metadata found in %s" % remote_folder + ) return sample_files_dict, local_meta_file def delete_remote_files(self, remote_folder, files): @@ -933,11 +938,11 @@ def select_target_folders(self): if not root_directory_list: log.error("Error while listing folders in remote. Aborting") sys.exit(1) - if self.target_folders == "ALL": + if self.target_folders[0] == "ALL": log.info("Showing folders from remote SFTP for user selection") target_folders = relecov_tools.utils.prompt_checkbox( msg="Select the folders that will be targeted", - choices=sorted(root_directory_list), + choices=sorted(clean_root_list), ) elif self.target_folders[0] is None and len(self.target_folders) == 1: target_folders = clean_root_list @@ -985,7 +990,9 @@ def compress_and_update(self, fetched_files, files_to_compress, local_folder): try: relecov_tools.utils.compress_file(f_path) except FileNotFoundError: - log.error("Could not compress file %s", str(file)) + error_text = "Could not compress file %s, file not found" % str(file) + log.error(error_text) + self.include_error(error_text, f_path) continue # Remove file after compression is completed compressed_files.append(file) @@ -1016,7 +1023,9 @@ def process_filedict(self, valid_filedict, clean_fetchlist): processed_dict[sample][key] = file # remove sample if it has missing files if not all(x in clean_fetchlist for x in processed_dict[sample].values()): - log.warning("Sample %s skipped: missing files in sftp", sample) + error_text = "Sample %s skipped: missing files in sftp" % sample + log.error(error_text) + self.include_error(error_text, sample) del processed_dict[sample] return processed_dict @@ -1038,6 +1047,7 @@ def download(self, target_folders, option="download"): folders_to_download = target_folders date = datetime.today().strftime("%Y%m%d") for folder in folders_to_download.keys(): + self.current_folder = folder.split("/")[0] # Close previously open connection to avoid timeouts try: self.close_connection() @@ -1048,14 +1058,16 @@ def download(self, target_folders, option="download"): log.info("Processing folder %s", folder) stderr.print("[blue]Processing folder " + folder) # Validate that the files are the ones described in metadata. + local_folder = self.create_local_folder(folder, date) try: valid_filedict, meta_file = self.validate_remote_files( folder, local_folder ) - except (FileNotFoundError, MetadataError) as failed_validation: - log.error(failed_validation) - stderr.print(f"[red]{failed_validation}, skipped") + except (FileNotFoundError, IOError, PermissionError, MetadataError) as fail: + log.error(fail) + stderr.print(f"[red]{fail}, skipped") + self.include_error(fail) continue # Get the files in each folder files_to_download = [ @@ -1065,8 +1077,10 @@ def download(self, target_folders, option="download"): folder, local_folder, files_to_download ) if not fetched_files: - log.warning("No files could be downloaded in folder %s", folder) - stderr.print(f"No files were downloaded process for {folder}") + error_text = "No files could be downloaded in folder %s" % str(folder) + log.warning(error_text) + stderr.print(f"{error_text}") + self.include_error(error_text) continue log.info("Finished download for folder: %s", folder) stderr.print(f"Finished download for folder {folder}") @@ -1222,6 +1236,7 @@ def execute_process(self): stderr.print("[red]Unable to establish sftp connection") sys.exit(1) target_folders = self.select_target_folders() + target_folders = self.merge_subfolders(target_folders) if self.download_option == "download_only": self.download(target_folders, option="download") if self.download_option == "download_clean": @@ -1232,4 +1247,7 @@ def execute_process(self): self.delete_remote_files(folder, files) stderr.print(f"Delete process finished in {folder}") self.close_connection() + if self.logs: + log.info("Printing process summary to %s", self.platform_storage_folder) + self.create_error_summary() stderr.print("Finished execution") From 358e9241d468fce3cd36b7cd89c29515976ba951 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 5 Mar 2024 17:43:39 +0100 Subject: [PATCH 1231/1454] Included handling for comma separated md5sum files --- relecov_tools/utils.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index f2461f72..b813069f 100755 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -172,6 +172,8 @@ def read_md5_checksum(file_name, avoid_chars=list()): translation = str.maketrans("", "", "'\"") if any("\t" in line for line in lines): lines = [line.strip().translate(translation).split("\t") for line in lines] + elif any("," in line for line in lines): + lines = [line.strip().translate(translation).split(",") for line in lines] else: lines = [line.strip().translate(translation).split(" ") for line in lines] clean_lines = [ From 7177108a7de39d1e178e9f01844b86178f682b02 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 5 Mar 2024 17:44:07 +0100 Subject: [PATCH 1232/1454] Included new requirements like precise openpyxl version and xlsxwriter --- requirements.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 1e1b0a9d..868f2cbe 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,6 +7,7 @@ rich>=10.0.0 requests==2.27.1 paramiko>=2.10.1 pyyaml -openpyxl +openpyxl>=3.1.2 ena-upload-cli bio==1.4.0 +xlsxwriter From 9888f0ec18fd6cbceb4fee6b065f025e135fff54 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 11 Mar 2024 08:56:43 +0100 Subject: [PATCH 1233/1454] Included sftp merge and log summary in download module, linting --- relecov_tools/sftp_handle.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 70c132ad..35de5672 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -843,7 +843,7 @@ def upload_merged_df(merged_excel_path, last_main_folder, merged_df): return folders_with_metadata = {} - merged_df = None + merged_df = merged_excel_path = last_main_folder = excel_name = None log.info("Setting %s remote folders...", str(len(clean_folders.keys()))) stderr.print(f"[blue]Setting {len(clean_folders.keys())} remote folders...") for folder in sorted(clean_folders.keys()): From 54a7611058a6021aa48add91da67dd9f48e46889 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 11 Mar 2024 08:57:39 +0100 Subject: [PATCH 1234/1454] Included sftp merge and log summary in download module, linting2 --- relecov_tools/sftp_handle.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 35de5672..5e43b18a 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -649,7 +649,7 @@ def move_processing_fastqs(self, folders_with_metadata): folders_with_metadata (dict(str:list)): Same dict updated with files successfully moved """ log.info("Moving remote files to each temporal processing folder") - stderr.print(f"[blue]Moving remote files to each temporal processing folder") + stderr.print("[blue]Moving remote files to each temporal processing folder") for folder, files in folders_with_metadata.items(): self.current_folder = folder.split("/")[0] successful_files = [] From 328a77681604588e1e884e99bdb16e42aa072044 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 12 Mar 2024 16:13:48 +0100 Subject: [PATCH 1235/1454] Fixed error for new duplicated handling --- relecov_tools/sftp_handle.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 5e43b18a..5ab9595f 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -501,8 +501,10 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): if s_name not in sample_file_dict: sample_file_dict[s_name] = {} else: - print("Found duplicated sample ", s_name) + stderr.print("Found duplicated sample name: ", s_name) s_name = "_".join([s_name, str(token_hex(nbytes=8))]) + stderr.print("Duplicated sample renamed to ", s_name) + sample_file_dict[s_name] = {} if row[index_layout] == "paired" and row[index_fastq_r2] is None: error_text = "Sample %s is paired-end, but no R2 given" log.error(str(error_text % str(row[index_sampleID]))) From d8ff0c158475c77713a46fbafd3ca08bfb910fcb Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 12 Mar 2024 16:17:57 +0100 Subject: [PATCH 1236/1454] Distinguish if files are missing from sftp or due to filtering process --- relecov_tools/sftp_handle.py | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 5ab9595f..0f3e4150 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -615,7 +615,7 @@ def validate_remote_files(self, remote_folder, local_folder): # Try to check if the metadata filename lacks the proper extension log.info("Trying to match files without proper file extension") sample_files_dict = self.process_filedict( - sample_files_dict, filtered_files_list + sample_files_dict, filtered_files_list, processed=True ) if not any(value for value in sample_files_dict.values()): raise FileNotFoundError( @@ -1004,17 +1004,22 @@ def compress_and_update(self, fetched_files, files_to_compress, local_folder): ] return fetched_files - def process_filedict(self, valid_filedict, clean_fetchlist): + def process_filedict(self, valid_filedict, clean_fetchlist, processed=False): """Process the dictionary from validate_remote_files() to update filenames and remove samples that failed any validation process. Args: valid_filedict (dict{str:str}): same structure as validate_remote_files() clean_fetchlist (list(str)): List of files that passed validation process + processed (bool): Indicates if filedict has been processed previously Returns: processed(dict{str:str}): Updated valid_filedict """ + if processed: + error_text = "Sample %s skipped: missing files in sftp" + else: + error_text = "Sample %s skipped: missing files after processing" processed_dict = {} for sample, vals in valid_filedict.items(): processed_dict[sample] = {} @@ -1025,9 +1030,8 @@ def process_filedict(self, valid_filedict, clean_fetchlist): processed_dict[sample][key] = file # remove sample if it has missing files if not all(x in clean_fetchlist for x in processed_dict[sample].values()): - error_text = "Sample %s skipped: missing files in sftp" % sample - log.error(error_text) - self.include_error(error_text, sample) + log.error(str(error_text % sample)) + self.include_error(str(error_text % sample), sample) del processed_dict[sample] return processed_dict From af45883bdf3c0a0dc9c4a48ea29b613d6c8d4961 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 12 Mar 2024 16:19:15 +0100 Subject: [PATCH 1237/1454] Correct handling of None values, also moved remote folder validation to auxiliar method --- relecov_tools/sftp_handle.py | 39 ++++++++++++++++++++++++------------ 1 file changed, 26 insertions(+), 13 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 0f3e4150..448e4a01 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -832,32 +832,33 @@ def merge_subfolders(self, target_folders): header_flag = self.metadata_processing.get("header_flag") output_location = self.platform_storage_folder date_and_time = datetime.today().strftime("%Y%m%d%-H%M%S") + exts = self.allowed_file_ext def upload_merged_df(merged_excel_path, last_main_folder, merged_df): self.client.mkdir(last_main_folder) pd_writer = ExcelWriter(merged_excel_path, engine="xlsxwriter") for sheet in merged_df.keys(): - format_sheet = merged_df[sheet].astype(str)[merged_df[sheet].notnull()] + format_sheet = merged_df[sheet].astype(str) + format_sheet.replace('nan', None, inplace=True) format_sheet.to_excel(pd_writer, sheet_name=sheet, index=False) pd_writer.close() dest = os.path.join(last_main_folder, os.path.basename(merged_excel_path)) self.client.put(merged_excel_path, dest) return - folders_with_metadata = {} - merged_df = merged_excel_path = last_main_folder = excel_name = None - log.info("Setting %s remote folders...", str(len(clean_folders.keys()))) - stderr.print(f"[blue]Setting {len(clean_folders.keys())} remote folders...") - for folder in sorted(clean_folders.keys()): - self.current_folder = folder - + def pre_validate_folder(folder, folder_files): + if not any(file.endswith(tuple(exts)) for file in folder_files): + error_text = "Remote folder %s skipped. No sequencing files found." + log.error(error_text % folder) + self.include_error(error_text % folder) + return try: downloaded_metadata = self.get_metadata_file(folder, output_location) except (FileNotFoundError, OSError, PermissionError, MetadataError) as err: error_text = "Remote folder %s skipped. Reason: %s" log.error(error_text % (folder, err)) self.include_error(error_text % (folder, err)) - continue + return try: self.read_metadata_file(downloaded_metadata, return_data=False) except MetadataError as header_error: @@ -865,14 +866,26 @@ def upload_merged_df(merged_excel_path, last_main_folder, merged_df): os.remove(downloaded_metadata) log.error(str(folder, str(error_text % str(header_error)))) self.include_error(error_text % header_error) + return + return downloaded_metadata + + folders_with_metadata = {} + merged_df = merged_excel_path = last_main_folder = excel_name = None + log.info("Setting %s remote folders...", str(len(clean_folders.keys()))) + stderr.print(f"[blue]Setting {len(clean_folders.keys())} remote folders...") + for folder in sorted(clean_folders.keys()): + self.current_folder = folder + downloaded_metadata = pre_validate_folder(folder, clean_folders[folder]) + if not downloaded_metadata: continue # Create a temporal name to avoid duplicated filenames meta_filename = "_".join([folder.split("/")[-1], "metadata_temp.xlsx"]) local_meta = os.path.join(output_location, meta_filename) os.rename(downloaded_metadata, local_meta) - # Taking the main folder for each lab as reference to merge + # Taking the main folder for each lab as reference for merge and logs main_folder = folder.split("/")[0] + self.current_folder = main_folder temporal_foldername = "_".join([date_and_time, "tmp_processing"]) temp_folder = os.path.join(main_folder, temporal_foldername) # Get every file except the excel ones as they are going to be merged @@ -887,9 +900,9 @@ def upload_merged_df(merged_excel_path, last_main_folder, merged_df): upload_merged_df(merged_excel_path, last_main_folder, merged_df) folders_with_metadata[last_main_folder].append(excel_name) except OSError: - error_text = "Error uploading merged metadata back to sftp" - log.error(error_text) - self.include_error(error_text) + error_text = "Error uploading merged metadata back to sftp: %s" + log.error(error_text % last_main_folder) + self.include_error(error_text % last_main_folder) del folders_with_metadata[last_main_folder] try: merged_df = self.excel_to_df(local_meta, metadata_ws, header_flag) From 10acf065479e71623a41801278b9e53ceea7fda1 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 12 Mar 2024 16:19:57 +0100 Subject: [PATCH 1238/1454] Updated log_summary method to distinguish from subfolders in case its needed --- relecov_tools/sftp_handle.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 448e4a01..4aa1488f 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -1214,9 +1214,8 @@ def include_warning(self, entry, sample=None): def update_summary(self, log_type, entry, sample=None): feed_dict = OrderedDict({"valid": False, "errors": [], "warnings": []}) - current_folder = str(self.current_folder).replace("./", "").split("/")[0] - entry = str(entry) - sample = str(sample) + current_folder = str(self.current_folder).replace("./", "") + entry, sample = tuple(str(entry), str(sample)) if current_folder not in self.logs.keys(): self.logs[current_folder] = feed_dict self.logs[current_folder]["samples"] = OrderedDict() @@ -1241,7 +1240,7 @@ def create_error_summary(self): for sample in self.logs[folder]["samples"].keys(): if not self.logs[folder]["samples"][sample]["errors"]: self.logs[folder]["samples"][sample]["valid"] = True - filename = "_".join([datetime.today().strftime("%Y%m%d"), "log_summary.json"]) + filename = datetime.today().strftime("%Y%m%d%-H%M%S") + "_log_summary.json" summary_path = os.path.join(self.platform_storage_folder, filename) with open(summary_path, "w", encoding="utf-8") as f: f.write(json.dumps(self.logs, indent=4, sort_keys=True, ensure_ascii=False)) From d045026beed2a6408dcc3cd55f60b04131a23cf8 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 12 Mar 2024 16:22:48 +0100 Subject: [PATCH 1239/1454] Correct handling of None values, linting --- relecov_tools/sftp_handle.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 4aa1488f..0490bf1d 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -839,7 +839,7 @@ def upload_merged_df(merged_excel_path, last_main_folder, merged_df): pd_writer = ExcelWriter(merged_excel_path, engine="xlsxwriter") for sheet in merged_df.keys(): format_sheet = merged_df[sheet].astype(str) - format_sheet.replace('nan', None, inplace=True) + format_sheet.replace("nan", None, inplace=True) format_sheet.to_excel(pd_writer, sheet_name=sheet, index=False) pd_writer.close() dest = os.path.join(last_main_folder, os.path.basename(merged_excel_path)) From b4383c6b4582f4350b3b6fef9b4479617e937103 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 12 Mar 2024 16:29:57 +0100 Subject: [PATCH 1240/1454] Updated log_summary method, linting --- relecov_tools/sftp_handle.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 0490bf1d..41596c9e 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -1215,7 +1215,7 @@ def include_warning(self, entry, sample=None): def update_summary(self, log_type, entry, sample=None): feed_dict = OrderedDict({"valid": False, "errors": [], "warnings": []}) current_folder = str(self.current_folder).replace("./", "") - entry, sample = tuple(str(entry), str(sample)) + entry, sample = (str(entry), str(sample)) if current_folder not in self.logs.keys(): self.logs[current_folder] = feed_dict self.logs[current_folder]["samples"] = OrderedDict() From a18dfcec1cb744dda64c95a6982fbd53b903e16a Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 14 Mar 2024 13:35:08 +0100 Subject: [PATCH 1241/1454] Way better handling of samples pointing to the same file --- relecov_tools/sftp_handle.py | 33 +++++++++++++++++---------------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 41596c9e..24cbd393 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -399,26 +399,27 @@ def remove_duplicated_values(self, sample_file_dict): Returns: clean_sample_dict: sample_dictionary without duplications in values """ - set_of_values = set() - duplicated_keys = set() - for sample, fastqs in sample_file_dict.items(): - # Dictionary keys are immutable, so you cannot use a regular set for a dict - hashable_fastqs = frozenset(fastqs.items()) - - if hashable_fastqs in set_of_values: - duplicated_keys.add(sample) - else: - set_of_values.add(hashable_fastqs) + inverted_dict = {} + for sample, fastq_dict in sample_file_dict.items(): + # Dictionary values are not hashable, so you need to create a tuple of them + samp_fastqs = tuple(fastq_dict.values()) + # Setting values as keys to find those samples refering to the same file + for fastq in samp_fastqs: + inverted_dict[fastq] = inverted_dict.get(fastq, []) + [sample] + duplicated_dict = {k: v for k, v in inverted_dict.items() if len(v) > 1} + dup_samples_list = [samp for dups in duplicated_dict.values() for samp in dups] non_duplicated_keys = { - k: v for k, v in sample_file_dict.items() if k not in duplicated_keys + k: v for k, v in sample_file_dict.items() if k not in dup_samples_list } clean_sample_dict = {key: sample_file_dict[key] for key in non_duplicated_keys} - if duplicated_keys: - error_text = "Samples in metadata refering to the same file. " - log.warning(error_text + str(duplicated_keys)) + if dup_samples_list: + error_text = "Multiple samples in metadata pointing to the same file: %s" + log.warning(error_text % duplicated_dict) + self.include_warning(error_text % duplicated_dict) stderr.print(f"[Orange]{error_text}") - stderr.print("[Orange]These samples won't be processed: ", duplicated_keys) - [self.include_error(error_text, sample) for sample in duplicated_keys] + stderr.print("[Orange]These samples won't be processed: ", dup_samples_list) + for fastq, samples in duplicated_dict.items(): + [self.include_error(str(error_text % fastq), samp) for samp in samples] return clean_sample_dict From 2001215e4ceaacdea3e43bf5b65d30a1060398c3 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 14 Mar 2024 13:37:39 +0100 Subject: [PATCH 1242/1454] Enhanced logs and error handling for corrupted or missing md5 files --- relecov_tools/sftp_handle.py | 43 ++++++++++++++++++++++++------------ 1 file changed, 29 insertions(+), 14 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 24cbd393..83aac2a9 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -616,7 +616,7 @@ def validate_remote_files(self, remote_folder, local_folder): # Try to check if the metadata filename lacks the proper extension log.info("Trying to match files without proper file extension") sample_files_dict = self.process_filedict( - sample_files_dict, filtered_files_list, processed=True + sample_files_dict, filtered_files_list ) if not any(value for value in sample_files_dict.values()): raise FileNotFoundError( @@ -1003,22 +1003,26 @@ def compress_and_update(self, fetched_files, files_to_compress, local_folder): compressed_files = list() for file in files_to_compress: f_path = os.path.join(local_folder, file) - try: - relecov_tools.utils.compress_file(f_path) - except FileNotFoundError: + compressed = relecov_tools.utils.compress_file(f_path) + if not compressed: error_text = "Could not compress file %s, file not found" % str(file) log.error(error_text) self.include_error(error_text, f_path) continue # Remove file after compression is completed compressed_files.append(file) - os.remove(f_path) + try: + os.remove(f_path) + except (FileNotFoundError, PermissionError) as e: + log.warning(f"Could not delete file: {e}") fetched_files = [ (fi + ".gz" if fi in compressed_files else fi) for fi in fetched_files ] return fetched_files - def process_filedict(self, valid_filedict, clean_fetchlist, processed=False): + def process_filedict( + self, valid_filedict, clean_fetchlist, corrupted=[], md5miss=[] + ): """Process the dictionary from validate_remote_files() to update filenames and remove samples that failed any validation process. @@ -1030,22 +1034,26 @@ def process_filedict(self, valid_filedict, clean_fetchlist, processed=False): Returns: processed(dict{str:str}): Updated valid_filedict """ - if processed: - error_text = "Sample %s skipped: missing files in sftp" - else: - error_text = "Sample %s skipped: missing files after processing" processed_dict = {} + error_text = "md5 mismatch for %s" + warning_text = "File %s not found in md5sum. Creating hash" for sample, vals in valid_filedict.items(): processed_dict[sample] = {} for key, val in vals.items(): processed_dict[sample][key] = None + if val in corrupted: + self.include_error(error_text % val, sample) + if val in md5miss: + self.include_warning(warning_text % val, sample) for file in clean_fetchlist: if val in file: processed_dict[sample][key] = file # remove sample if it has missing files if not all(x in clean_fetchlist for x in processed_dict[sample].values()): + if not corrupted: + error_text = "Sample %s skipped: missing files in sftp" + self.include_error(str(error_text % sample), sample) log.error(str(error_text % sample)) - self.include_error(str(error_text % sample), sample) del processed_dict[sample] return processed_dict @@ -1130,7 +1138,6 @@ def download(self, target_folders, option="download"): log.warning(error_text % (str(corrupted), corr_fold)) stderr.print(f"[red]{error_text % (str(corrupted), corr_fold)}") self.include_warning(error_text % (str(corrupted), "/corrupt/")) - [self.include_error("md5 mismatch", corr) for corr in corrupted] for corr_file in corrupted: path = os.path.join(local_folder, corr_file) try: @@ -1164,6 +1171,8 @@ def download(self, target_folders, option="download"): clean_fetchlist = [ fi for fi in fetched_files if fi.endswith(tuple(self.allowed_file_ext)) ] + + clean_fetchlist = [fi for fi in clean_fetchlist if fi not in corrupted] # Checking for uncompressed files files_to_compress = [fi for fi in clean_fetchlist if not fi.endswith(".gz")] if files_to_compress: @@ -1176,6 +1185,7 @@ def download(self, target_folders, option="download"): clean_pathlist = [os.path.join(local_folder, fi) for fi in clean_fetchlist] if remote_md5sum: # Get hashes from provided md5sum, create them for those not provided + not_md5sum = [] files_md5_dict = {} for path in clean_pathlist: f_name = os.path.basename(path) @@ -1187,14 +1197,19 @@ def download(self, target_folders, option="download"): if not str(f_name).rstrip(".gz") in files_to_compress: error_text = "File %s not found in md5sum. Creating hash" log.warning(error_text % f_name) - self.include_warning(str(error_text % f_name), f_name) + not_md5sum.append(f_name) + else: + log.info("File %s was compressed, creating md5hash", f_name) files_md5_dict[f_name] = relecov_tools.utils.calculate_md5(path) else: md5_hashes = [ relecov_tools.utils.calculate_md5(path) for path in clean_pathlist ] files_md5_dict = dict(zip(clean_fetchlist, md5_hashes)) - processed_filedict = self.process_filedict(valid_filedict, clean_fetchlist) + + processed_filedict = self.process_filedict( + valid_filedict, clean_fetchlist, corrupted=corrupted, md5miss=not_md5sum + ) self.create_files_with_metadata_info( local_folder, processed_filedict, files_md5_dict, meta_file ) From 76c46cb42d11929424338b2dfad49ccd72659ac1 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 14 Mar 2024 13:38:52 +0100 Subject: [PATCH 1243/1454] Adding description to internal methods and fixing dup variable --- relecov_tools/sftp_handle.py | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 83aac2a9..def1f4f3 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -696,6 +696,7 @@ def merge_md5sums(self, folders_with_metadata): # TODO: Include this function in relecov_tools.utils def md5_merger(md5_filelist, avoid_chars=None): + """Merge all md5 files from a given list into a single multi-line md5sum""" md5dict_list = [] for md5sum in md5_filelist: hash_dict = relecov_tools.utils.read_md5_checksum(md5sum, avoid_chars) @@ -708,6 +709,8 @@ def md5_merger(md5_filelist, avoid_chars=None): return merged_md5 def md5_handler(md5sumlist, output_location): + """Download all the remote md5sum files in a list, merge them + into a single md5checksum and upload it back to sftp""" downloaded_md5files = [] for md5sum in md5sumlist: md5_name = "_".join([token_hex(nbytes=12), "md5_temp.md5"]) @@ -825,10 +828,6 @@ def merge_subfolders(self, target_folders): clean_target_folders (dict(str:list)): Dict with '*_tmp_processing' folders and their content. All subfolder filenames are merged into a single key. """ - """clean_folders = { - fd:v for fd,v in target_folders.items() if "tmp_processing" not in fd - }""" - clean_folders = target_folders metadata_ws = self.metadata_processing.get("excel_sheet") header_flag = self.metadata_processing.get("header_flag") output_location = self.platform_storage_folder @@ -836,6 +835,7 @@ def merge_subfolders(self, target_folders): exts = self.allowed_file_ext def upload_merged_df(merged_excel_path, last_main_folder, merged_df): + """Upload metadata dataframe merged from all subfolders back to sftp""" self.client.mkdir(last_main_folder) pd_writer = ExcelWriter(merged_excel_path, engine="xlsxwriter") for sheet in merged_df.keys(): @@ -848,6 +848,7 @@ def upload_merged_df(merged_excel_path, last_main_folder, merged_df): return def pre_validate_folder(folder, folder_files): + """Check if remote folder has sequencing files and a valid metadata file""" if not any(file.endswith(tuple(exts)) for file in folder_files): error_text = "Remote folder %s skipped. No sequencing files found." log.error(error_text % folder) @@ -872,11 +873,11 @@ def pre_validate_folder(folder, folder_files): folders_with_metadata = {} merged_df = merged_excel_path = last_main_folder = excel_name = None - log.info("Setting %s remote folders...", str(len(clean_folders.keys()))) - stderr.print(f"[blue]Setting {len(clean_folders.keys())} remote folders...") - for folder in sorted(clean_folders.keys()): + log.info("Setting %s remote folders...", str(len(target_folders.keys()))) + stderr.print(f"[blue]Setting {len(target_folders.keys())} remote folders...") + for folder in sorted(target_folders.keys()): self.current_folder = folder - downloaded_metadata = pre_validate_folder(folder, clean_folders[folder]) + downloaded_metadata = pre_validate_folder(folder, target_folders[folder]) if not downloaded_metadata: continue # Create a temporal name to avoid duplicated filenames From f36784d31145b16a352094b47ceadea317fe34b5 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 14 Mar 2024 13:39:43 +0100 Subject: [PATCH 1244/1454] Small changes to fix bugs in target_folders and log_summary --- relecov_tools/sftp_handle.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index def1f4f3..8f198468 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -560,7 +560,7 @@ def get_metadata_file(self, remote_folder, local_folder): try: self.get_from_sftp(target_meta_file, local_meta_file) except (IOError, PermissionError) as e: - raise type(e)(f"[red]Unable to fetch metadata file {e.name}") + raise type(e)(f"[red]Unable to fetch metadata file {e}") log.info( "Obtained metadata file %s from %s", local_meta_file, @@ -800,7 +800,7 @@ def excel_to_df(self, excel_file, metadata_sheet, header_flag): containing all sheets in the excel file as pandas dataframes. """ # Get every sheet from the first excel file - excel_df = read_excel(excel_file, sheet_name=None) # index_col=None + excel_df = read_excel(excel_file, dtype=str, sheet_name=None) meta_df = excel_df[metadata_sheet] if header_flag in meta_df.columns: return excel_df @@ -955,14 +955,14 @@ def select_target_folders(self): if not root_directory_list: log.error("Error while listing folders in remote. Aborting") sys.exit(1) - if self.target_folders[0] == "ALL": + if self.target_folders is None: + target_folders = clean_root_list + elif self.target_folders[0] == "ALL": log.info("Showing folders from remote SFTP for user selection") target_folders = relecov_tools.utils.prompt_checkbox( msg="Select the folders that will be targeted", choices=sorted(clean_root_list), ) - elif self.target_folders[0] is None and len(self.target_folders) == 1: - target_folders = clean_root_list else: target_folders = [tf for tf in self.target_folders if tf in clean_root_list] if not target_folders: @@ -1234,7 +1234,7 @@ def update_summary(self, log_type, entry, sample=None): current_folder = str(self.current_folder).replace("./", "") entry, sample = (str(entry), str(sample)) if current_folder not in self.logs.keys(): - self.logs[current_folder] = feed_dict + self.logs[current_folder] = feed_dict.copy() self.logs[current_folder]["samples"] = OrderedDict() if sample == "None": if log_type == "error": @@ -1243,7 +1243,7 @@ def update_summary(self, log_type, entry, sample=None): self.logs[current_folder]["warnings"].append(entry) else: if sample not in self.logs[current_folder]["samples"].keys(): - self.logs[current_folder]["samples"][sample] = feed_dict + self.logs[current_folder]["samples"][sample] = feed_dict.copy() if log_type == "error": self.logs[current_folder]["samples"][sample]["errors"].append(entry) elif log_type == "warning": From 03e3ada6333ad93d714ba0e9b77f944fbb1fe72f Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 14 Mar 2024 17:02:01 +0100 Subject: [PATCH 1245/1454] Fixed duplicated validation of metadata header --- relecov_tools/sftp_handle.py | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 8f198468..c371cc09 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -442,9 +442,13 @@ def read_metadata_file(self, meta_f_path, return_data=True): ws_metadata_lab = wb_file[self.metadata_processing.get("excel_sheet")] # find out the index for file names header_flag = self.metadata_processing.get("header_flag") - header_row = [ - idx + 1 for idx, x in enumerate(ws_metadata_lab.values) if header_flag in x - ][0] + try: + header_row = [ + i + 1 for i, x in enumerate(ws_metadata_lab.values) if header_flag in x + ][0] + except IndexError: + error_text = "Header could not be found for excel file %s" + raise MetadataError(str(error_text % os.path.basename(meta_f_path))) for cell in ws_metadata_lab[header_row]: cell.value = cell.value.strip() metadata_header = [x.value for x in ws_metadata_lab[header_row]] @@ -808,9 +812,6 @@ def excel_to_df(self, excel_file, metadata_sheet, header_flag): for idx in range(len(meta_df)): if any(meta_df.loc[idx, x] == header_flag for x in meta_df.columns): header_row = idx - if not header_row: - error_text = "Header could not be found for excel file %s" - raise MetadataError(str(error_text % excel_file)) meta_df.columns = meta_df.iloc[header_row] excel_df[metadata_sheet] = meta_df.drop(meta_df.index[: (header_row + 1)]) excel_df[metadata_sheet] = excel_df[metadata_sheet].reset_index(drop=True) From 09c00c1ddd11f7489de7757841aff506ef4b7e1d Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 14 Mar 2024 17:02:28 +0100 Subject: [PATCH 1246/1454] Removed duplicated variable from merge_metadata() --- relecov_tools/sftp_handle.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index c371cc09..157f924f 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -763,18 +763,17 @@ def md5_handler(md5sumlist, output_location): return folders_with_metadata - def merge_metadata(self, metadata_sheet=None, *metadata_tables): + def merge_metadata(self, meta_sheet=None, *metadata_tables): """Merge a variable number of metadata dataframes to the first one. Merge them only into a certain sheet from a multi-sheet excel file if sheetname is given. Args: - metadata_sheet (str): Name of the sheet containing metadata in excel file + meta_sheet (str): Name of the sheet containing metadata in excel file *metadata_tables (list(pandas.DataFrame)): Dataframes to be merged Returns: merged_df (pandas.DataFrame): A merged dataframe from the given tables """ - meta_sheet = metadata_sheet for idx, table in enumerate(metadata_tables): if idx == 0: merged_df = table From f3a5f99c281903ef45d4400b7e29c994ebbac55c Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 15 Mar 2024 12:08:32 +0100 Subject: [PATCH 1247/1454] added file format handlers and new method to add bioinfo metadata --- relecov_tools/read_bioinfo_metadata.py | 64 +++++++++++++++++++++++++- 1 file changed, 63 insertions(+), 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 2090c11e..41a7f376 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -144,6 +144,65 @@ def validate_software_mandatory_files(self, json): stderr.print("[green]\tValidation passed :)") return + # TODO: also version's files shoudld be paresed independiently. + # TODO: Before arriving here we need to validate properties fiels on collated and persample files(~mandatory fields). + def add_bioinfo_results_metadata(self, files_dict, j_data): + """Add bioinfo results metadata to processed read lab metadata (j_data)""" + # TODO: add manatory fields: one for collated and one for sample-specific files + mandatory_fields = ['fn', 'ff', 'required', 'content', 'file_paths'] + for key in files_dict.keys(): + try: + files_dict[key].get('file_paths') + except KeyError: + continue + # TODO: in progress + # Parses sample-specific files (i.e: SAMPLE1.consensus.fa) + if isinstance(files_dict[key].get('file_paths'), list): + stderr.print("") + #self.map_metadata_persample_files() + # Parses collated files (i.e: mapping_illumina_stats.tab) + elif isinstance(files_dict[key].get('file_paths'), str): + j_data_mapped = self.map_metadata_collated_files( + files_dict[key], + j_data + ) + return + + def map_metadata_collated_files(self, bioinfo_dict, j_data): + """Handles different file formats in collated files, reads their content, and maps it to j_data""" + # We will be able to add here as many handlers as we need + file_extension_handlers = { + "\t": self.handle_csv_file, + ",": self.handle_csv_file, + #"html": self.handle_multiqc_html_file, + } + file_format = bioinfo_dict['ff'] + if file_format in file_extension_handlers: + handler_function = file_extension_handlers[file_format] + j_data_mapped = handler_function(bioinfo_dict, j_data) + return j_data_mapped + else: + stderr.print(f"[red]Unrecognized defined file format {bioinfo_dict['ff'] in {bioinfo_dict['fn']}}") + return None + + def handle_csv_file(self, bioinfo_dict, j_data): + """handle csv/tsv file and map it with read lab metadata (j_data)""" + map_data = relecov_tools.utils.read_csv_file_return_dict( + file_name = bioinfo_dict['file_paths'], + sep = bioinfo_dict['ff'], + key_position = (bioinfo_dict['sample_col_idx']-1) + ) + j_data_mapped = self.mapping_over_table( + j_data, + map_data, + bioinfo_dict['content'], + bioinfo_dict['file_paths'] + ) + return j_data_mapped + + #def handle_multiqc_html_file(self, bioinfo_dict, j_data): + # """Reads multiqc_report html""" + # TODO: we can make a rule in bioinfo_config.json where all software-properties must have a field callded "fixed_values". This way the second argument wont't be necessary def add_fixed_values(self, j_data, fixed_values): """include the fixed data defined in configuration or feed custom empty fields""" @@ -394,8 +453,11 @@ def create_bioinfo_file(self): self.validate_software_mandatory_files(software_config_extended) stderr.print("[blue]Reading lab metadata json") j_data = self.collect_info_from_lab_json() + stderr.print(f"[blue]Adding metadata from {self.input_folder} into read lab metadata...") + j_data = self.add_bioinfo_results_metadata(software_config_extended, j_data) #stderr.print("[blue]Adding fixed values") - #j_data = self.add_fixed_values(j_data, "fixed_values") + #j_data = self.add_fixed_values(j_data, #"fixed_values") + #stderr.print(j_data) ## Creating empty fields that are not managed in case #of missing data #j_data = self.add_fixed_values(j_data, #"feed_empty_fields") #stderr.print("[blue]Adding data from mapping stats") From 4a944cace43e0e4d97fbf1c490b04f91247874eb Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 22 Mar 2024 12:30:34 +0100 Subject: [PATCH 1248/1454] add method to handle program versions info in multiqc_report.html --- relecov_tools/conf/bioinfo_config.json | 27 +++----------- relecov_tools/read_bioinfo_metadata.py | 49 ++++++++++++++++++++++++-- requirements.txt | 2 ++ 3 files changed, 54 insertions(+), 24 deletions(-) diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index 3bb53e43..2c2569e6 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -95,8 +95,11 @@ "file_per_sample": false, "required": true, "content": { - "bioinformatics_protocol_software_name": "nf-core/viralrecon Workflow Summary", - "variant_calling_software_name": "IVAR_VARIANTS" + "bioinformatics_protocol_software_version": "nf-core/viralrecon", + "consensus_sequence_software_version": "bcftools", + "dehosting_method_software_version": "kraken2", + "mapping_software_version":"bowtie2", + "preprocessing_software_version":"fastp", "variant_calling_software_version":"ivar" } }, "fixed_values": { @@ -121,26 +124,6 @@ "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m10", "lineage_analysis_date": "Not Provided [GENEPIO:0001668]", "consensus_sequence_name": "Not Provided [GENEPIO:0001668]" - }, - "mapping_version": { - "bioinformatics_protocol_software_version": { - "Workflow": "nf-core/viralrecon" - }, - "consensus_sequence_software_version": { - "BCFTOOLS_CONSENSUS": "bcftools" - }, - "dehosting_method_software_version": { - "KRAKEN2_KRAKEN2": "kraken2" - }, - "mapping_software_version": { - "BOWTIE2_ALIGN": "bowtie2" - }, - "preprocessing_software_version": { - "FASTP": "fastp" - }, - "variant_calling_software_version": { - "IVAR_VARIANTS": "ivar" - } } } } diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 41a7f376..80711cb3 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -7,6 +7,7 @@ from datetime import datetime from tqdm import tqdm from yaml import YAMLError +from bs4 import BeautifulSoup import relecov_tools.utils from relecov_tools.config_json import ConfigJson @@ -149,7 +150,7 @@ def validate_software_mandatory_files(self, json): def add_bioinfo_results_metadata(self, files_dict, j_data): """Add bioinfo results metadata to processed read lab metadata (j_data)""" # TODO: add manatory fields: one for collated and one for sample-specific files - mandatory_fields = ['fn', 'ff', 'required', 'content', 'file_paths'] + # mandatory_fields = ['fn', 'ff', 'required', 'content', 'file_paths'] for key in files_dict.keys(): try: files_dict[key].get('file_paths') @@ -174,7 +175,7 @@ def map_metadata_collated_files(self, bioinfo_dict, j_data): file_extension_handlers = { "\t": self.handle_csv_file, ",": self.handle_csv_file, - #"html": self.handle_multiqc_html_file, + "html": self.handle_multiqc_html_file, } file_format = bioinfo_dict['ff'] if file_format in file_extension_handlers: @@ -185,6 +186,50 @@ def map_metadata_collated_files(self, bioinfo_dict, j_data): stderr.print(f"[red]Unrecognized defined file format {bioinfo_dict['ff'] in {bioinfo_dict['fn']}}") return None + def handle_multiqc_html_file(self, html_dict_scope, j_data): + """Reads html file, finds table containing programs info, and map it to j_data""" + program_versions = {} + with open(html_dict_scope['file_paths'], 'r') as html_file: + html_content = html_file.read() + # Load HTML + soup = BeautifulSoup(html_content, features="lxml") + # Get version's div id + div_id = "mqc-module-section-software_versions" + versions_div = soup.find('div', id=div_id) + # Get version's metadata data + if versions_div: + table = versions_div.find('table', class_='table') + if table: + rows = table.find_all('tr') + for row in rows[1:]: #skipping header + columns = row.find_all('td') + if len(columns) == 3: + program_name = columns[1].text.strip() + version = columns[2].text.strip() + program_versions[program_name] = version + else: + stderr.print(f"[red] HTML entry error in {columns}. HTML table expected format should be \n Process Name\n\n Software \n.") + else: + stderr.print(f"[red] Missing table containing software versions in {html_dict_scope['file_paths']}.") + sys.exit(1) + else: + log.error(f"Required div section 'mqc-module-section-software_versions' not found in file {html_dict_scope['file_paths']}.") + stderr.print(f"[red] No div section 'mqc-module-section-software_versions' was found in {html_dict_scope['file_paths']}.") + sys.exit(1) + + # Adding mqc sofware versions to j_data + field_errors = {} + for row in j_data: + sample_name = row["submitting_lab_sample_id"] + for field, values in html_dict_scope['content'].items(): + try: + row[field] = program_versions[values] + except KeyError as e: + field_errors[sample_name] = {field: e} + row[field] = "Not Provided [GENEPIO:0001668]" + continue + return j_data + def handle_csv_file(self, bioinfo_dict, j_data): """handle csv/tsv file and map it with read lab metadata (j_data)""" map_data = relecov_tools.utils.read_csv_file_return_dict( diff --git a/requirements.txt b/requirements.txt index 1e1b0a9d..75cf3770 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,3 +10,5 @@ pyyaml openpyxl ena-upload-cli bio==1.4.0 +bs4==0.0.2 +tqdm From 04f0010d8f799c1e2d72d1996a92b9b408265625 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 22 Mar 2024 12:35:24 +0100 Subject: [PATCH 1249/1454] forgot to remove old method to parse sw versions --- relecov_tools/read_bioinfo_metadata.py | 19 ------------------- 1 file changed, 19 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 80711cb3..4ae64fd0 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -456,23 +456,6 @@ def include_variant_metrics(self, j_data, files_dict): ) return j_data_with_variant_metrics - # TODO: fpath should be imported from req_file found. - def include_software_versions(self, j_data): - """Include versions from the yaml version file""" - version_fields = self.software_config["mapping_version"] - f_path = os.path.join(self.input_folder, self.required_file_name["version_info"]) - try: - versions = relecov_tools.utils.read_yml_file(f_path) - except YAMLError as e: - log.error("Unable to process version file return error %s", e) - stderr.print(f"[red]Unable to process version file {e}") - sys.exit(1) - for row in j_data: - for field, version_data in version_fields.items(): - for key, value in version_data.items(): - row[field] = versions[key][value] - return j_data - def collect_info_from_lab_json(self): """Create the list of dictionaries from the data that is on json lab metadata file. Return j_data that is used to add the rest of the fields @@ -507,8 +490,6 @@ def create_bioinfo_file(self): #j_data = self.add_fixed_values(j_data, #"feed_empty_fields") #stderr.print("[blue]Adding data from mapping stats") #j_data = self.include_data_from_mapping_stats(j_data, #req_files) - #stderr.print("[blue]Adding software versions") - #j_data = self.include_software_versions(j_data) #stderr.print("[blue]Adding summary variant metrics") #j_data = self.include_variant_metrics(j_data, #req_files) #stderr.print("[blue]Adding pangolin information") From 49ea8bd6db17df73f640633018138682c51c542b Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 22 Mar 2024 13:07:35 +0100 Subject: [PATCH 1250/1454] update fixed values module and minor code changes --- relecov_tools/conf/bioinfo_config.json | 2 +- relecov_tools/read_bioinfo_metadata.py | 36 +++++++++++++++----------- 2 files changed, 22 insertions(+), 16 deletions(-) diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index 2c2569e6..8679d38d 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -99,7 +99,7 @@ "consensus_sequence_software_version": "bcftools", "dehosting_method_software_version": "kraken2", "mapping_software_version":"bowtie2", - "preprocessing_software_version":"fastp", "variant_calling_software_version":"ivar" + "preprocessing_software_version":"fastp","variant_calling_software_version":"ivar" } }, "fixed_values": { diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 4ae64fd0..a55dadc7 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -78,14 +78,14 @@ def get_software_required_files(self): self.required_file_name[key] = value.get('fn','') self.required_file_content[key] = value.get('content','') - # TODO: Add report of files found/not-found to global log + # TODO: Add report of files found/not-found to master log def scann_directory(self): - """Scann bioinfo analysis directory and search for files""" + """Scann bioinfo analysis directory and search for files present in bioinfo json config""" total_files = sum(len(files) for _, _, files in os.walk(self.input_folder)) files_found = {} with tqdm(total=total_files, desc='\tScanning...') as pbar: for topic_key, topic_details in self.software_config.items(): - if not 'fn' in topic_details: #try/except fn + if 'fn' not in topic_details: #try/except fn continue for root, _, files in os.walk(self.input_folder, topdown=True): matching_files = [os.path.join(root, file_name) for file_name in files if file_name.endswith(topic_details['fn'])] @@ -164,11 +164,12 @@ def add_bioinfo_results_metadata(self, files_dict, j_data): # Parses collated files (i.e: mapping_illumina_stats.tab) elif isinstance(files_dict[key].get('file_paths'), str): j_data_mapped = self.map_metadata_collated_files( - files_dict[key], - j_data + files_dict[key], + j_data ) - return + return j_data_mapped + # TODO: recover file format parsing errors def map_metadata_collated_files(self, bioinfo_dict, j_data): """Handles different file formats in collated files, reads their content, and maps it to j_data""" # We will be able to add here as many handlers as we need @@ -185,7 +186,7 @@ def map_metadata_collated_files(self, bioinfo_dict, j_data): else: stderr.print(f"[red]Unrecognized defined file format {bioinfo_dict['ff'] in {bioinfo_dict['fn']}}") return None - + def handle_multiqc_html_file(self, html_dict_scope, j_data): """Reads html file, finds table containing programs info, and map it to j_data""" program_versions = {} @@ -456,6 +457,14 @@ def include_variant_metrics(self, j_data, files_dict): ) return j_data_with_variant_metrics + def add_fixed_values(self, j_data): + """include the fixed data defined in configuration or feed custom empty fields""" + f_values = self.software_config["fixed_values"] + for row in j_data: + for field, value in f_values.items(): + row[field] = value + return j_data + def collect_info_from_lab_json(self): """Create the list of dictionaries from the data that is on json lab metadata file. Return j_data that is used to add the rest of the fields @@ -473,21 +482,16 @@ def create_bioinfo_file(self): metadata json, mapping_stats, and more information from the files inside input directory """ - stderr.print(f"[blue]Sanning input directory...") + stderr.print("[blue]Sanning input directory...") files_found = self.scann_directory() - stderr.print(f"[blue]Extending bioinfo config json with files found...") + stderr.print("[blue]Extending bioinfo config json with files found...") software_config_extended = self.extend_software_config(files_found) - stderr.print(f"[blue]Validating required files...") + stderr.print("[blue]Validating required files...") self.validate_software_mandatory_files(software_config_extended) stderr.print("[blue]Reading lab metadata json") j_data = self.collect_info_from_lab_json() stderr.print(f"[blue]Adding metadata from {self.input_folder} into read lab metadata...") j_data = self.add_bioinfo_results_metadata(software_config_extended, j_data) - #stderr.print("[blue]Adding fixed values") - #j_data = self.add_fixed_values(j_data, #"fixed_values") - #stderr.print(j_data) - ## Creating empty fields that are not managed in case #of missing data - #j_data = self.add_fixed_values(j_data, #"feed_empty_fields") #stderr.print("[blue]Adding data from mapping stats") #j_data = self.include_data_from_mapping_stats(j_data, #req_files) #stderr.print("[blue]Adding summary variant metrics") @@ -500,6 +504,8 @@ def create_bioinfo_file(self): #self.parse_long_table(self.input_folder, self.#output_folder) #stderr.print("[blue]Adding variant long table path") #j_data = self.include_custom_data(j_data) + stderr.print("[blue]Adding fixed values") + j_data = self.add_fixed_values(j_data) #file_name = ( # "bioinfo_" + os.path.splitext(os.path.basename#(self.json_file))[0] + ".json" #) From 7bc6d93ffeea1c719c43e6dd355f243cdb412298 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 22 Mar 2024 13:48:43 +0100 Subject: [PATCH 1251/1454] remove old unused methods that are now already embebed into map_metadat_collated_files --- relecov_tools/read_bioinfo_metadata.py | 89 -------------------------- 1 file changed, 89 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index a55dadc7..ba95ac41 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -230,33 +230,6 @@ def handle_multiqc_html_file(self, html_dict_scope, j_data): row[field] = "Not Provided [GENEPIO:0001668]" continue return j_data - - def handle_csv_file(self, bioinfo_dict, j_data): - """handle csv/tsv file and map it with read lab metadata (j_data)""" - map_data = relecov_tools.utils.read_csv_file_return_dict( - file_name = bioinfo_dict['file_paths'], - sep = bioinfo_dict['ff'], - key_position = (bioinfo_dict['sample_col_idx']-1) - ) - j_data_mapped = self.mapping_over_table( - j_data, - map_data, - bioinfo_dict['content'], - bioinfo_dict['file_paths'] - ) - return j_data_mapped - - #def handle_multiqc_html_file(self, bioinfo_dict, j_data): - # """Reads multiqc_report html""" - - # TODO: we can make a rule in bioinfo_config.json where all software-properties must have a field callded "fixed_values". This way the second argument wont't be necessary - def add_fixed_values(self, j_data, fixed_values): - """include the fixed data defined in configuration or feed custom empty fields""" - f_values = self.software_config["fixed_values"] - for row in j_data: - for field, value in f_values.items(): - row[field] = value - return j_data def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): """Auxiliar function to iterate over variants and mapping tables to map metadata""" @@ -290,26 +263,6 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): #def include_data(self, j_data, topic): # topic_json = self.configuration.get_topic_data(topic) - # FIXME: All maping items says not provided in the output json. Origin above def. Wait. It might be due to unmatched samples name. Create a lab metadata with identical sample names. - def include_data_from_mapping_stats(self, j_data, files_dict): - """By processing mapping stats file the following information is - included in schema properties: depth_of_coverage_value, lineage_name, - number_of_variants_in_consensus, number_of_variants_with_effect, - per_genome_greater_10x. per_Ns. per_reads_host, per_reads_virus. - per_unmapped, qc_filtered, reference_genome_accession - """ - # position of the sample columns inside mapping file - sample_position = 4 - map_data = relecov_tools.utils.read_csv_file_return_dict( - files_dict["mapping_stats"], sep="\t", key_position=sample_position - ) - - mapping_fields = self.software_config["mapping_stats"]["content"] - j_data_with_mapping_stats = self.mapping_over_table( - j_data, map_data, mapping_fields, "mapping stats" - ) - return j_data_with_mapping_stats - def include_pangolin_data(self, j_data): """Include pangolin data collecting form each file generated by pangolin""" mapping_fields = self.software_config["mapping_pangolin"]["content"] @@ -409,28 +362,6 @@ def include_consensus_data(self, j_data): stderr.print(f"[yellow]\n{missing_consens}") return j_data - def parse_long_table(self, long_table_path, output_folder): - file_match = os.path.join(long_table_path, "variants_long_table*.csv") - table_path = glob.glob(file_match) - if len(table_path) == 1: - table_path = glob.glob(file_match)[0] - else: - log.error("variants_long_table files found = %s", len(table_path)) - stderr.print( - f"[red]Found {len(table_path)} variants_long_table files in ", - f"[red]{long_table_path}, aborting", - ) - sys.exit(1) - if not os.path.isfile(table_path): - log.error("variants_long_table given file is not a file") - stderr.print("[red]Variants_long_table file do not exist, Aborting") - sys.exit(1) - long_table = LongTableParse(table_path, output_folder) - - long_table.parsing_csv() - - return - def include_custom_data(self, j_data): """Include custom fields like variant-long-table path""" condition = os.path.join(self.input_folder, "*variants_long_table*.csv") @@ -443,20 +374,6 @@ def include_custom_data(self, j_data): row["long_table_path"] = long_table_path return j_data - # TODO: Rename this module to include_custom_mqc data and exend its application. - def include_variant_metrics(self, j_data, files_dict): - """Include the # Ns per 100kb consensus from the summary variant - metric file_exists - """ - map_data = relecov_tools.utils.read_csv_file_return_dict( - files_dict["summary_mqc"], sep="," - ) - mapping_fields = self.software_config["summary_mqc"]["content"] - j_data_with_variant_metrics = self.mapping_over_table( - j_data, map_data, mapping_fields, "variant metrics" - ) - return j_data_with_variant_metrics - def add_fixed_values(self, j_data): """include the fixed data defined in configuration or feed custom empty fields""" f_values = self.software_config["fixed_values"] @@ -492,16 +409,10 @@ def create_bioinfo_file(self): j_data = self.collect_info_from_lab_json() stderr.print(f"[blue]Adding metadata from {self.input_folder} into read lab metadata...") j_data = self.add_bioinfo_results_metadata(software_config_extended, j_data) - #stderr.print("[blue]Adding data from mapping stats") - #j_data = self.include_data_from_mapping_stats(j_data, #req_files) - #stderr.print("[blue]Adding summary variant metrics") - #j_data = self.include_variant_metrics(j_data, #req_files) #stderr.print("[blue]Adding pangolin information") #j_data = self.include_pangolin_data(j_data) #stderr.print("[blue]Adding consensus data") #j_data = self.include_consensus_data(j_data) - #stderr.print("[blue]Parsing variants_long_table info #to json format...") - #self.parse_long_table(self.input_folder, self.#output_folder) #stderr.print("[blue]Adding variant long table path") #j_data = self.include_custom_data(j_data) stderr.print("[blue]Adding fixed values") From 952b5d8efd1349079b83a260af61c2c0c6957177 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 22 Mar 2024 16:01:07 +0100 Subject: [PATCH 1252/1454] renaming variables for better understanding --- relecov_tools/read_bioinfo_metadata.py | 55 +++++++++++++++++--------- 1 file changed, 36 insertions(+), 19 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index ba95ac41..f4f266fa 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -147,30 +147,32 @@ def validate_software_mandatory_files(self, json): # TODO: also version's files shoudld be paresed independiently. # TODO: Before arriving here we need to validate properties fiels on collated and persample files(~mandatory fields). - def add_bioinfo_results_metadata(self, files_dict, j_data): - """Add bioinfo results metadata to processed read lab metadata (j_data)""" + def add_bioinfo_results_metadata(self, bioinfo_dict, j_data): + """Iterates over each property in the bioinfo_dict""" # TODO: add manatory fields: one for collated and one for sample-specific files # mandatory_fields = ['fn', 'ff', 'required', 'content', 'file_paths'] - for key in files_dict.keys(): + for key in bioinfo_dict.keys(): try: - files_dict[key].get('file_paths') + bioinfo_dict[key].get('file_paths') except KeyError: continue - # TODO: in progress # Parses sample-specific files (i.e: SAMPLE1.consensus.fa) - if isinstance(files_dict[key].get('file_paths'), list): + if isinstance(bioinfo_dict[key].get('file_paths'), list): stderr.print("") - #self.map_metadata_persample_files() + j_data_mapped = self.map_metadata_persample_files( + bioinfo_dict[key], + j_data + ) # Parses collated files (i.e: mapping_illumina_stats.tab) - elif isinstance(files_dict[key].get('file_paths'), str): + elif isinstance(bioinfo_dict[key].get('file_paths'), str): j_data_mapped = self.map_metadata_collated_files( - files_dict[key], + bioinfo_dict[key], j_data ) return j_data_mapped # TODO: recover file format parsing errors - def map_metadata_collated_files(self, bioinfo_dict, j_data): + def map_metadata_collated_files(self, bioinfo_dict_scope, j_data): """Handles different file formats in collated files, reads their content, and maps it to j_data""" # We will be able to add here as many handlers as we need file_extension_handlers = { @@ -178,19 +180,34 @@ def map_metadata_collated_files(self, bioinfo_dict, j_data): ",": self.handle_csv_file, "html": self.handle_multiqc_html_file, } - file_format = bioinfo_dict['ff'] + file_format = bioinfo_dict_scope['ff'] if file_format in file_extension_handlers: handler_function = file_extension_handlers[file_format] - j_data_mapped = handler_function(bioinfo_dict, j_data) + j_data_mapped = handler_function(bioinfo_dict_scope, j_data) return j_data_mapped else: - stderr.print(f"[red]Unrecognized defined file format {bioinfo_dict['ff'] in {bioinfo_dict['fn']}}") + stderr.print(f"[red]Unrecognized defined file format {bioinfo_dict_scope['ff'] in {bioinfo_dict_scope['fn']}}") return None - def handle_multiqc_html_file(self, html_dict_scope, j_data): + def handle_csv_file(self, bioinfo_dict_scope, j_data): + """handle csv/tsv file and map it with read lab metadata (j_data)""" + map_data = relecov_tools.utils.read_csv_file_return_dict( + file_name = bioinfo_dict_scope['file_paths'], + sep = bioinfo_dict_scope['ff'], + key_position = (bioinfo_dict_scope['sample_col_idx']-1) + ) + j_data_mapped = self.mapping_over_table( + j_data, + map_data, + bioinfo_dict_scope['content'], + bioinfo_dict_scope['file_paths'] + ) + return j_data_mapped + + def handle_multiqc_html_file(self, bioinfo_dict_scope, j_data): """Reads html file, finds table containing programs info, and map it to j_data""" program_versions = {} - with open(html_dict_scope['file_paths'], 'r') as html_file: + with open(bioinfo_dict_scope['file_paths'], 'r') as html_file: html_content = html_file.read() # Load HTML soup = BeautifulSoup(html_content, features="lxml") @@ -211,18 +228,18 @@ def handle_multiqc_html_file(self, html_dict_scope, j_data): else: stderr.print(f"[red] HTML entry error in {columns}. HTML table expected format should be \n Process Name\n\n Software \n.") else: - stderr.print(f"[red] Missing table containing software versions in {html_dict_scope['file_paths']}.") + stderr.print(f"[red] Missing table containing software versions in {bioinfo_dict_scope['file_paths']}.") sys.exit(1) else: - log.error(f"Required div section 'mqc-module-section-software_versions' not found in file {html_dict_scope['file_paths']}.") - stderr.print(f"[red] No div section 'mqc-module-section-software_versions' was found in {html_dict_scope['file_paths']}.") + log.error(f"Required div section 'mqc-module-section-software_versions' not found in file {bioinfo_dict_scope['file_paths']}.") + stderr.print(f"[red] No div section 'mqc-module-section-software_versions' was found in {bioinfo_dict_scope['file_paths']}.") sys.exit(1) # Adding mqc sofware versions to j_data field_errors = {} for row in j_data: sample_name = row["submitting_lab_sample_id"] - for field, values in html_dict_scope['content'].items(): + for field, values in bioinfo_dict_scope['content'].items(): try: row[field] = program_versions[values] except KeyError as e: From ecc68a51d960451faeb7ab58c6dc2b9138e13dd8 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 22 Mar 2024 17:25:29 +0100 Subject: [PATCH 1253/1454] added workaround to generalize parsing of sample-specific files --- relecov_tools/read_bioinfo_metadata.py | 29 +++++++++++++++----------- 1 file changed, 17 insertions(+), 12 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index f4f266fa..24af6cdf 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -170,7 +170,20 @@ def add_bioinfo_results_metadata(self, bioinfo_dict, j_data): j_data ) return j_data_mapped - + + def map_metadata_persample_files(self, bioinfo_dict_scope, j_data): + """""" + file_name = bioinfo_dict_scope['fn'] + file_format = bioinfo_dict_scope['ff'] + if file_format == ',' and 'pangolin' in file_name: + j_data_mapped = self.include_pangolin_data(j_data) + elif file_format == 'fasta' and 'consensus' in file_name: + j_data_mapped = self.handle_consensus_fasta(bioinfo_dict_scope, j_data) + else: + stderr.warning(f"[red]No available methods to parse file format '{file_format}' and file name '{file_name}'.") + return + return j_data_mapped + # TODO: recover file format parsing errors def map_metadata_collated_files(self, bioinfo_dict_scope, j_data): """Handles different file formats in collated files, reads their content, and maps it to j_data""" @@ -277,9 +290,6 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): stderr.print(f"[red]Missing values in {table_name}\n:{field_errors}") return j_data - #def include_data(self, j_data, topic): - # topic_json = self.configuration.get_topic_data(topic) - def include_pangolin_data(self, j_data): """Include pangolin data collecting form each file generated by pangolin""" mapping_fields = self.software_config["mapping_pangolin"]["content"] @@ -331,11 +341,10 @@ def include_pangolin_data(self, j_data): stderr.print(f"[yellow]{missing_pango}") return j_data - def include_consensus_data(self, j_data): + def handle_consensus_fasta(self, bioinfo_dict_scope, j_data): """Include genome length, name, file name, path and md5 by preprocessing - each file of consensus.fa - """ - mapping_fields = self.software_config["mapping_consensus"]["content"] + each file of consensus.fa""" + mapping_fields = bioinfo_dict_scope["content"] missing_consens = [] # FIXME: Replace sequencing_sample_id for row in j_data: @@ -426,10 +435,6 @@ def create_bioinfo_file(self): j_data = self.collect_info_from_lab_json() stderr.print(f"[blue]Adding metadata from {self.input_folder} into read lab metadata...") j_data = self.add_bioinfo_results_metadata(software_config_extended, j_data) - #stderr.print("[blue]Adding pangolin information") - #j_data = self.include_pangolin_data(j_data) - #stderr.print("[blue]Adding consensus data") - #j_data = self.include_consensus_data(j_data) #stderr.print("[blue]Adding variant long table path") #j_data = self.include_custom_data(j_data) stderr.print("[blue]Adding fixed values") From adc09348846dd5a61ce58f8426a9b054894f236a Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 25 Mar 2024 09:03:27 +0100 Subject: [PATCH 1254/1454] fix typo in config and remove todo --- relecov_tools/conf/bioinfo_config.json | 8 ++++---- relecov_tools/read_bioinfo_metadata.py | 1 - 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index 8679d38d..5ab16e5b 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -5,7 +5,7 @@ "ff": "\t", "file_per_sample": false, "sample_col_idx": 5, - "header_row_dix": 1, + "header_row_idx": 1, "required": true, "content": { "analysis_date": "analysis_date", @@ -26,7 +26,7 @@ "fn": ".pangolin.csv", "ff": ",", "file_per_sample": true, - "header_row_dix": 1, + "header_row_idx": 1, "required": false, "content": { "variant_name": "scorpio_call", @@ -42,7 +42,7 @@ "ff": ",", "file_per_sample": false, "sample_col_idx": 1, - "header_row_dix": 1, + "header_row_idx": 1, "required": true, "content": { "sample" : "SAMPLE", @@ -83,7 +83,7 @@ "ff": ",", "file_per_sample": false, "sample_col_idx": 1, - "header_row_dix": 1, + "header_row_idx": 1, "required": true, "content": { "ns_per_100_kbp": "# Ns per 100kb consensus" diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 24af6cdf..67423a5f 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -145,7 +145,6 @@ def validate_software_mandatory_files(self, json): stderr.print("[green]\tValidation passed :)") return - # TODO: also version's files shoudld be paresed independiently. # TODO: Before arriving here we need to validate properties fiels on collated and persample files(~mandatory fields). def add_bioinfo_results_metadata(self, bioinfo_dict, j_data): """Iterates over each property in the bioinfo_dict""" From 3b9adba17ca86a1fdc677ef30a4b919822fed2f5 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 25 Mar 2024 10:10:12 +0100 Subject: [PATCH 1255/1454] fix assignment of variable in scope consensus --- relecov_tools/conf/bioinfo_config.json | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index 5ab16e5b..984339b0 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -122,8 +122,7 @@ "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", "preprocessing_software_name": "FASTP", "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m10", - "lineage_analysis_date": "Not Provided [GENEPIO:0001668]", - "consensus_sequence_name": "Not Provided [GENEPIO:0001668]" + "lineage_analysis_date": "Not Provided [GENEPIO:0001668]" } } } From 2244890586f78e2b021949c7b08c7aa08b167c57 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 25 Mar 2024 14:25:29 +0100 Subject: [PATCH 1256/1454] fix remaining old methods after code refactoring --- relecov_tools/read_bioinfo_metadata.py | 33 ++++++++++++++++---------- 1 file changed, 20 insertions(+), 13 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 67423a5f..bc5d8225 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -174,8 +174,10 @@ def map_metadata_persample_files(self, bioinfo_dict_scope, j_data): """""" file_name = bioinfo_dict_scope['fn'] file_format = bioinfo_dict_scope['ff'] + file_paths = bioinfo_dict_scope['file_paths'] if file_format == ',' and 'pangolin' in file_name: - j_data_mapped = self.include_pangolin_data(j_data) + pango_path = os.path.dirname(file_paths[0]) + j_data_mapped = self.include_pangolin_data(pango_path, j_data) elif file_format == 'fasta' and 'consensus' in file_name: j_data_mapped = self.handle_consensus_fasta(bioinfo_dict_scope, j_data) else: @@ -289,19 +291,22 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): stderr.print(f"[red]Missing values in {table_name}\n:{field_errors}") return j_data - def include_pangolin_data(self, j_data): + # TODO: haven't improved yet + def include_pangolin_data(self, dir_path, j_data): """Include pangolin data collecting form each file generated by pangolin""" mapping_fields = self.software_config["mapping_pangolin"]["content"] missing_pango = [] for row in j_data: + # Get read lab sample id if "-" in row["submitting_lab_sample_id"]: sample_name = row["submitting_lab_sample_id"].replace("-", "_") else: sample_name = row["submitting_lab_sample_id"] - + # Get the name of pangolin csv file/s f_name_regex = sample_name + ".pangolin*.csv" - f_path = os.path.join(self.input_folder, f_name_regex) + f_path = os.path.join(dir_path, f_name_regex) pango_files = glob.glob(f_path) + # Parse pangolin files if pango_files: if len(pango_files) > 1: stderr.print( @@ -345,6 +350,7 @@ def handle_consensus_fasta(self, bioinfo_dict_scope, j_data): each file of consensus.fa""" mapping_fields = bioinfo_dict_scope["content"] missing_consens = [] + consensus_dir_path = os.path.dirname(bioinfo_dict_scope['file_paths'][0]) # FIXME: Replace sequencing_sample_id for row in j_data: if "-" in row["submitting_lab_sample_id"]: @@ -352,7 +358,7 @@ def handle_consensus_fasta(self, bioinfo_dict_scope, j_data): else: sample_name = row["submitting_lab_sample_id"] f_name = sample_name + ".consensus.fa" - f_path = os.path.join(self.input_folder, f_name) + f_path = os.path.join(consensus_dir_path, f_name) try: record_fasta = relecov_tools.utils.read_fasta_return_SeqIO_instance( f_path @@ -434,16 +440,17 @@ def create_bioinfo_file(self): j_data = self.collect_info_from_lab_json() stderr.print(f"[blue]Adding metadata from {self.input_folder} into read lab metadata...") j_data = self.add_bioinfo_results_metadata(software_config_extended, j_data) + #TODO: This should be refactor according to new file-handling implementation #stderr.print("[blue]Adding variant long table path") #j_data = self.include_custom_data(j_data) stderr.print("[blue]Adding fixed values") j_data = self.add_fixed_values(j_data) - #file_name = ( - # "bioinfo_" + os.path.splitext(os.path.basename#(self.json_file))[0] + ".json" - #) - #stderr.print("[blue]Writting output json file") - #os.makedirs(self.output_folder, exist_ok=True) - #file_path = os.path.join(self.output_folder, #file_name) - #relecov_tools.utils.write_json_fo_file(j_data, #file_path) - #stderr.print("[green]Sucessful creation of bioinfo #analyis file") + file_name = ( + "bioinfo_" + os.path.splitext(os.path.basename(self.json_file))[0] + ".json" + ) + stderr.print("[blue]Writting output json file") + os.makedirs(self.output_folder, exist_ok=True) + file_path = os.path.join(self.output_folder, file_name) + relecov_tools.utils.write_json_fo_file(j_data, file_path) + stderr.print("[green]Sucessful creation of bioinfo #analyis file") return True From cf8f495cd4f146e8b847ebbad59057d1204b4f2e Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 25 Mar 2024 16:10:21 +0100 Subject: [PATCH 1257/1454] remove tqdm dependency --- relecov_tools/read_bioinfo_metadata.py | 34 ++++++++++++-------------- requirements.txt | 1 - 2 files changed, 16 insertions(+), 19 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index bc5d8225..9e2fc5c5 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -5,7 +5,6 @@ import glob import rich.console from datetime import datetime -from tqdm import tqdm from yaml import YAMLError from bs4 import BeautifulSoup @@ -83,28 +82,27 @@ def scann_directory(self): """Scann bioinfo analysis directory and search for files present in bioinfo json config""" total_files = sum(len(files) for _, _, files in os.walk(self.input_folder)) files_found = {} - with tqdm(total=total_files, desc='\tScanning...') as pbar: - for topic_key, topic_details in self.software_config.items(): - if 'fn' not in topic_details: #try/except fn - continue - for root, _, files in os.walk(self.input_folder, topdown=True): - matching_files = [os.path.join(root, file_name) for file_name in files if file_name.endswith(topic_details['fn'])] - if len(matching_files) == 1: - # Only one file match found, add it as a string (collated files) - files_found[topic_key] = matching_files[0] - elif len(matching_files) > 1: - # Multiple file matches found, add them as a list (per sample files) - files_found[topic_key] = matching_files - for _ in matching_files: - pbar.update(1) + + for topic_key, topic_details in self.software_config.items(): + if 'fn' not in topic_details: #try/except fn + continue + for root, _, files in os.walk(self.input_folder, topdown=True): + matching_files = [os.path.join(root, file_name) for file_name in files if file_name.endswith(topic_details['fn'])] + if len(matching_files) == 1: + # Only one file match found, add it as a string (collated files) + files_found[topic_key] = matching_files[0] + elif len(matching_files) > 1: + # Multiple file matches found, add them as a list (per sample files) + files_found[topic_key] = matching_files + if len(files_found) < 1: log.error( - "No files found in %s.", self.output_folder + "No files found in %s.", self.input_folder ) - stderr.print(f"[red] No files found in {self.output_folder}.") + stderr.print(f"[red]\tNo files found in {self.input_folder}.") sys.exit(1) else: - stderr.print("\tRetrieving files found ...") + stderr.print(f"\t[green]\tScannig process succeed (total {total_files} found).") return files_found def extend_software_config(self, files_dict): diff --git a/requirements.txt b/requirements.txt index 75cf3770..d0fe58a6 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,4 +11,3 @@ openpyxl ena-upload-cli bio==1.4.0 bs4==0.0.2 -tqdm From fd33f3a78503d66d3811f515cfad346e250cb48e Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 25 Mar 2024 16:41:53 +0100 Subject: [PATCH 1258/1454] clean unused method for required files and update method's name and description --- relecov_tools/read_bioinfo_metadata.py | 25 ++++++++----------------- 1 file changed, 8 insertions(+), 17 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 9e2fc5c5..aa29efb8 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -66,17 +66,6 @@ def __init__( config = ConfigJson(json_file) self.software_config = config.get_configuration(self.software_name) - # FIXME: This must be refacored. not used so far. - def get_software_required_files(self): - """Load required software specific files and patterns""" - self.required_file_name = {} - self.required_file_content = {} - - for key, value in self.software_config.items(): - if 'required' in value and value['required']: - self.required_file_name[key] = value.get('fn','') - self.required_file_content[key] = value.get('content','') - # TODO: Add report of files found/not-found to master log def scann_directory(self): """Scann bioinfo analysis directory and search for files present in bioinfo json config""" @@ -105,8 +94,10 @@ def scann_directory(self): stderr.print(f"\t[green]\tScannig process succeed (total {total_files} found).") return files_found - def extend_software_config(self, files_dict): - """Inject files found (input dir) into software config JSON""" + def add_filepaths_to_software_config(self, files_dict): + """ + Adds file paths to the software configuration JSON by creating the 'file_paths' property with files found during the scanning process. + """ extended_json = self.software_config for key, value in files_dict.items(): if key in extended_json: @@ -118,7 +109,6 @@ def extend_software_config(self, files_dict): extended_json[key]['file_paths'] = value return extended_json - # TODO: Add validation to master log file. # TODO: Add checking file format based on config. # TODO: ¿Add content validation?. This might be better to be implemented when geting metadata from input files. @@ -429,9 +419,10 @@ def create_bioinfo_file(self): inside input directory """ stderr.print("[blue]Sanning input directory...") - files_found = self.scann_directory() - stderr.print("[blue]Extending bioinfo config json with files found...") - software_config_extended = self.extend_software_config(files_found) + files_found_dict = self.scann_directory() + stderr.print("[blue]Adding files found to bioinfo config json...") + stderr.print(files_found_dict) + software_config_extended = self.add_filepaths_to_software_config(files_found_dict) stderr.print("[blue]Validating required files...") self.validate_software_mandatory_files(software_config_extended) stderr.print("[blue]Reading lab metadata json") From 3c925506defe87105ede501f92a7b6af6e49d785 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 25 Mar 2024 17:19:12 +0100 Subject: [PATCH 1259/1454] add method to vaildate software name --- relecov_tools/read_bioinfo_metadata.py | 28 ++++++++++++++++++-------- 1 file changed, 20 insertions(+), 8 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index aa29efb8..e5808c59 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -54,17 +54,30 @@ def __init__( ) else: self.output_folder = output_folder - - # TODO: Available software list can be retrieved from conf/bioinfo_search_patterns.yml - # TODO: Add error if software is not in the list (sys exit). Add output to global log. + + json_file = os.path.join(os.path.dirname(__file__), "conf", "bioinfo_config.json") + config = ConfigJson(json_file) if software is None: software = relecov_tools.utils.prompt_path( - msg="Select the software, pipeline or tool use in the bioinformatic analysis (available: 'viralrecon'): " + msg="Select the software, pipeline or tool use in the bioinformatic analysis: " ) self.software_name = software - json_file = os.path.join(os.path.dirname(__file__), "conf", "bioinfo_config.json") - config = ConfigJson(json_file) - self.software_config = config.get_configuration(self.software_name) + + available_software = self.get_available_software(json_file) + if self.software_name in available_software: + self.software_config = config.get_configuration(self.software_name) + else: + log.error( + "No configuration available for %s. Currently, the only available software options are: %s", self.software_name, ", ".join(available_software) + ) + stderr.print(f"[red]No configuration available for {self.software_name}. Currently, the only available software options are:: {', '.join(available_software)}") + sys.exit(1) + + def get_available_software(self, json): + """Get list of available software in configuration""" + config = relecov_tools.utils.read_json_file(json) + available_software = list(config.keys()) + return available_software # TODO: Add report of files found/not-found to master log def scann_directory(self): @@ -421,7 +434,6 @@ def create_bioinfo_file(self): stderr.print("[blue]Sanning input directory...") files_found_dict = self.scann_directory() stderr.print("[blue]Adding files found to bioinfo config json...") - stderr.print(files_found_dict) software_config_extended = self.add_filepaths_to_software_config(files_found_dict) stderr.print("[blue]Validating required files...") self.validate_software_mandatory_files(software_config_extended) From a30e38ef432ab0e7a8e2aa5bafcebd5405a31ef7 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 26 Mar 2024 13:34:35 +0100 Subject: [PATCH 1260/1454] rename input variables to avoid variable naming collision --- relecov_tools/read_bioinfo_metadata.py | 32 +++++++++++++------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index e5808c59..3abc31e0 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -27,20 +27,20 @@ class BioinfoMetadata: def __init__( self, - json_file=None, + readlabmeta_json_file=None, input_folder=None, output_folder=None, software='viralrecon', ): - if json_file is None: - json_file = relecov_tools.utils.prompt_path( + if readlabmeta_json_file is None: + readlabmeta_json_file = relecov_tools.utils.prompt_path( msg="Select the json file that was created by the read-lab-metadata" ) - if not os.path.isfile(json_file): - log.error("json file %s does not exist ", json_file) - stderr.print(f"[red] file {json_file} does not exist") + if not os.path.isfile(readlabmeta_json_file): + log.error("json file %s does not exist ", readlabmeta_json_file) + stderr.print(f"[red] file {readlabmeta_json_file} does not exist") sys.exit(1) - self.json_file = json_file + self.readlabmeta_json_file = readlabmeta_json_file if input_folder is None: self.input_folder = relecov_tools.utils.prompt_path( @@ -55,17 +55,17 @@ def __init__( else: self.output_folder = output_folder - json_file = os.path.join(os.path.dirname(__file__), "conf", "bioinfo_config.json") - config = ConfigJson(json_file) + bioinfo_json_file = os.path.join(os.path.dirname(__file__), "conf", "bioinfo_config.json") if software is None: software = relecov_tools.utils.prompt_path( msg="Select the software, pipeline or tool use in the bioinformatic analysis: " ) self.software_name = software - available_software = self.get_available_software(json_file) + available_software = self.get_available_software(bioinfo_json_file) + bioinfo_config = ConfigJson(bioinfo_json_file) if self.software_name in available_software: - self.software_config = config.get_configuration(self.software_name) + self.software_config = bioinfo_config.get_configuration(self.software_name) else: log.error( "No configuration available for %s. Currently, the only available software options are: %s", self.software_name, ", ".join(available_software) @@ -419,10 +419,10 @@ def collect_info_from_lab_json(self): metadata file. Return j_data that is used to add the rest of the fields """ try: - json_lab_data = relecov_tools.utils.read_json_file(self.json_file) + json_lab_data = relecov_tools.utils.read_json_file(self.readlabmeta_json_file) except ValueError: - log.error("%s invalid json file", self.json_file) - stderr.print(f"[red] {self.json_file} invalid json file") + log.error("%s invalid json file", self.readlabmeta_json_file) + stderr.print(f"[red] {self.readlabmeta_json_file} invalid json file") sys.exit(1) return json_lab_data @@ -447,11 +447,11 @@ def create_bioinfo_file(self): stderr.print("[blue]Adding fixed values") j_data = self.add_fixed_values(j_data) file_name = ( - "bioinfo_" + os.path.splitext(os.path.basename(self.json_file))[0] + ".json" + "bioinfo_" + os.path.splitext(os.path.basename(self.readlabmeta_json_file))[0] + ".json" ) stderr.print("[blue]Writting output json file") os.makedirs(self.output_folder, exist_ok=True) file_path = os.path.join(self.output_folder, file_name) relecov_tools.utils.write_json_fo_file(j_data, file_path) - stderr.print("[green]Sucessful creation of bioinfo #analyis file") + stderr.print("[green]Sucessful creation of bioinfo analyis file") return True From 03e86391b07af608adb1a4cf5ad1f76f0ce0ebe5 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 26 Mar 2024 16:41:15 +0100 Subject: [PATCH 1261/1454] added method to report process log and update methods: scann, add file paths and validate required files --- relecov_tools/read_bioinfo_metadata.py | 96 +++++++++++++++++--------- 1 file changed, 65 insertions(+), 31 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 3abc31e0..95abc978 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -55,15 +55,15 @@ def __init__( else: self.output_folder = output_folder - bioinfo_json_file = os.path.join(os.path.dirname(__file__), "conf", "bioinfo_config.json") + self.bioinfo_json_file = os.path.join(os.path.dirname(__file__), "conf", "bioinfo_config.json") if software is None: software = relecov_tools.utils.prompt_path( msg="Select the software, pipeline or tool use in the bioinformatic analysis: " ) self.software_name = software - available_software = self.get_available_software(bioinfo_json_file) - bioinfo_config = ConfigJson(bioinfo_json_file) + available_software = self.get_available_software(self.bioinfo_json_file) + bioinfo_config = ConfigJson(self.bioinfo_json_file) if self.software_name in available_software: self.software_config = bioinfo_config.get_configuration(self.software_name) else: @@ -72,16 +72,27 @@ def __init__( ) stderr.print(f"[red]No configuration available for {self.software_name}. Currently, the only available software options are:: {', '.join(available_software)}") sys.exit(1) + self.log_report = {'error': {}, 'valid': {}, 'warning': {}} def get_available_software(self, json): """Get list of available software in configuration""" config = relecov_tools.utils.read_json_file(json) available_software = list(config.keys()) return available_software + + def update_log_report(self, method_name, status, message): + if status == 'valid': + self.log_report['valid'].setdefault(method_name, []).append(message) + elif status == 'error': + self.log_report['error'].setdefault(method_name, []).append(message) + elif status == 'warning': + self.log_report['warning'].setdefault(method_name, []).append(message) + else: + raise ValueError("Invalid status provided.") - # TODO: Add report of files found/not-found to master log + # TODO: Add log report def scann_directory(self): - """Scann bioinfo analysis directory and search for files present in bioinfo json config""" + """Scanns bioinfo analysis directory and identifies files according to the file name patterns defined in the software configuration json.""" total_files = sum(len(files) for _, _, files in os.walk(self.input_folder)) files_found = {} @@ -90,63 +101,87 @@ def scann_directory(self): continue for root, _, files in os.walk(self.input_folder, topdown=True): matching_files = [os.path.join(root, file_name) for file_name in files if file_name.endswith(topic_details['fn'])] - if len(matching_files) == 1: - # Only one file match found, add it as a string (collated files) - files_found[topic_key] = matching_files[0] - elif len(matching_files) > 1: - # Multiple file matches found, add them as a list (per sample files) + if len(matching_files) >= 1: files_found[topic_key] = matching_files - if len(files_found) < 1: + self.update_log_report( + self.scann_directory.__name__, + 'error', + f"No files found in {self.input_folder}" + ) log.error( - "No files found in %s.", self.input_folder + "\tNo files found in %s according to %s file name patterns..", + self.input_folder, + os.path.basename(self.bioinfo_json_file) ) - stderr.print(f"[red]\tNo files found in {self.input_folder}.") + stderr.print(f"\t[red]No files found in {self.input_folder} according to {os.path.basename(self.bioinfo_json_file)} file name patterns.") sys.exit(1) else: - stderr.print(f"\t[green]\tScannig process succeed (total {total_files} found).") + self.update_log_report( + self.scann_directory.__name__, + 'valid', + "Scannig process succeed" + ) + stderr.print(f"\t[green]Scannig process succeed (total scanned files: {total_files}).") return files_found def add_filepaths_to_software_config(self, files_dict): """ Adds file paths to the software configuration JSON by creating the 'file_paths' property with files found during the scanning process. """ - extended_json = self.software_config + cc = 0 + extended_software_config = self.software_config for key, value in files_dict.items(): - if key in extended_json: - if isinstance(extended_json[key], list): - # If the existing value is a list, extend it with the new file paths - extended_json[key]['file_paths'].extend(value) - else: - # If the existing value is not a list, create a new list with the file paths - extended_json[key]['file_paths'] = value - return extended_json + if key in extended_software_config: + if len(value) != 0 or value: + extended_software_config[key]['file_paths'] = value + cc+=1 + if cc == 0: + self.update_log_report( + self.add_filepaths_to_software_config.__name__, + 'error', + "No files path added to configuration json" + ) + else: + self.update_log_report( + self.add_filepaths_to_software_config.__name__, + 'valid', + "Files path added to configuration json" + ) + stderr.print("\t[green]Files path added to their scope in bioinfo configuration file.") + return extended_software_config - # TODO: Add validation to master log file. - # TODO: Add checking file format based on config. - # TODO: ¿Add content validation?. This might be better to be implemented when geting metadata from input files. def validate_software_mandatory_files(self, json): missing_required = [] for key in json.keys(): if json[key].get('required') is True: try: json[key]['file_paths'] + self.update_log_report( + self.validate_software_mandatory_files.__name__, + 'valid', + f"Found '{json[key]['fn']}'" + ) except KeyError: missing_required.append(key) + self.update_log_report( + self.validate_software_mandatory_files.__name__, + 'error', + f"Missing '{json[key]['fn']}'" + ) else: continue if len(missing_required) >= 1: log.error("\tMissing required files:") stderr.print("[red]\tMissing required files:") for i in missing_required: - log.error("[red]\t\t- %s", i) - stderr.print(f"\t\t- {i}") + log.error("\t\t- %s", i) + stderr.print(f"[red]\t\t- {i} (file name expected pattern '{json[i]['fn']}')") sys.exit(1) else: - stderr.print("[green]\tValidation passed :)") + stderr.print("[green]\tValidation passed.") return - # TODO: Before arriving here we need to validate properties fiels on collated and persample files(~mandatory fields). def add_bioinfo_results_metadata(self, bioinfo_dict, j_data): """Iterates over each property in the bioinfo_dict""" # TODO: add manatory fields: one for collated and one for sample-specific files @@ -158,7 +193,6 @@ def add_bioinfo_results_metadata(self, bioinfo_dict, j_data): continue # Parses sample-specific files (i.e: SAMPLE1.consensus.fa) if isinstance(bioinfo_dict[key].get('file_paths'), list): - stderr.print("") j_data_mapped = self.map_metadata_persample_files( bioinfo_dict[key], j_data From e63c905e481de4f7a00ca46e523ec606267e8637 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 27 Mar 2024 16:23:11 +0100 Subject: [PATCH 1262/1454] improve method add_bioinfo_results_metadata and add it feature to update process log --- relecov_tools/read_bioinfo_metadata.py | 42 ++++++++++++++++++++------ 1 file changed, 33 insertions(+), 9 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 95abc978..197400cf 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -183,26 +183,50 @@ def validate_software_mandatory_files(self, json): return def add_bioinfo_results_metadata(self, bioinfo_dict, j_data): - """Iterates over each property in the bioinfo_dict""" - # TODO: add manatory fields: one for collated and one for sample-specific files - # mandatory_fields = ['fn', 'ff', 'required', 'content', 'file_paths'] + """ + Adds metadata from bioinformatics results to the JSON data. + + This method iterates over each property in the provided bioinfo_dict, which contains information about file paths (discovered during the scanning process), along with their specific file configuration. + + If the property specifies files per sample, it maps metadata for each sample-specific file. + If the property specifies collated files. + """ for key in bioinfo_dict.keys(): try: - bioinfo_dict[key].get('file_paths') + bioinfo_dict[key]['file_paths'] except KeyError: + self.update_log_report( + self.add_bioinfo_results_metadata.__name__, + 'warning', + f"No file path found for '{self.software_name}.{key}'" + ) continue # Parses sample-specific files (i.e: SAMPLE1.consensus.fa) - if isinstance(bioinfo_dict[key].get('file_paths'), list): + if bioinfo_dict[key].get('file_per_sample') is True: j_data_mapped = self.map_metadata_persample_files( bioinfo_dict[key], j_data ) # Parses collated files (i.e: mapping_illumina_stats.tab) - elif isinstance(bioinfo_dict[key].get('file_paths'), str): - j_data_mapped = self.map_metadata_collated_files( - bioinfo_dict[key], - j_data + elif bioinfo_dict[key].get('file_per_sample') is False: + if len(bioinfo_dict[key].get('file_paths')) == 1: + bioinfo_dict[key]['file_paths'] = bioinfo_dict[key]['file_paths'][0] + j_data_mapped = self.map_metadata_collated_files( + bioinfo_dict[key], + j_data + ) + else: + stderr.print(f"\t[yellow]Ignoring {key}. See log_report.") + self.update_log_report( + self.add_bioinfo_results_metadata.__name__, + 'warning', + f"Collated files can't have more han one matching file. Please check {self.bioinfo_json_file} section: : '{self.software_name}.{key}'" ) + else: + if key != 'fixed_values': + # TODO: update log file + stderr.print(f"\t[yellow]Value 'file_per_sample' is missing in {self.bioinfo_json_file} section: '{self.software_name}.{key}'. This field is required to properly handle file configuration.") + continue return j_data_mapped def map_metadata_persample_files(self, bioinfo_dict_scope, j_data): From 9c1dc56173639d29a5e84b8f7c990da4e7143b9d Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 27 Mar 2024 16:42:41 +0100 Subject: [PATCH 1263/1454] fix stderr.print identation and minor update of method description --- relecov_tools/read_bioinfo_metadata.py | 36 +++++++++++++------------- 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 197400cf..db4d4c81 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -175,8 +175,8 @@ def validate_software_mandatory_files(self, json): log.error("\tMissing required files:") stderr.print("[red]\tMissing required files:") for i in missing_required: - log.error("\t\t- %s", i) - stderr.print(f"[red]\t\t- {i} (file name expected pattern '{json[i]['fn']}')") + log.error("\t- %s", i) + stderr.print(f"[red]\t- {i} (file name expected pattern '{json[i]['fn']}')") sys.exit(1) else: stderr.print("[green]\tValidation passed.") @@ -230,7 +230,7 @@ def add_bioinfo_results_metadata(self, bioinfo_dict, j_data): return j_data_mapped def map_metadata_persample_files(self, bioinfo_dict_scope, j_data): - """""" + """The method processes metadata associated with per sample files and integrates it into the JSON data.""" file_name = bioinfo_dict_scope['fn'] file_format = bioinfo_dict_scope['ff'] file_paths = bioinfo_dict_scope['file_paths'] @@ -308,7 +308,7 @@ def handle_multiqc_html_file(self, bioinfo_dict_scope, j_data): stderr.print(f"[red] No div section 'mqc-module-section-software_versions' was found in {bioinfo_dict_scope['file_paths']}.") sys.exit(1) - # Adding mqc sofware versions to j_data + # mapping mqc sofware versions to j_data field_errors = {} for row in j_data: sample_name = row["submitting_lab_sample_id"] @@ -322,7 +322,7 @@ def handle_multiqc_html_file(self, bioinfo_dict_scope, j_data): return j_data def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): - """Auxiliar function to iterate over variants and mapping tables to map metadata""" + """Auxiliar function to iterate over table's content and map it to metadata (j_data)""" errors = [] field_errors = {} for row in j_data: @@ -342,12 +342,12 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): if errors: lenerrs = len(errors) log.error( - "{0} samples missing in {1}:\n{2}".format(lenerrs, table_name, errors) + "\t{0} samples missing in {1}:\n\t{2}".format(lenerrs, table_name, errors) ) - stderr.print(f"[red]{lenerrs} samples missing in {table_name}:\n{errors}") + stderr.print(f"\t[red]{lenerrs} samples missing in {table_name}:\n\t{errors}") if field_errors: - log.error("Fields not found in {0}:\n{1}".format(table_name, field_errors)) - stderr.print(f"[red]Missing values in {table_name}\n:{field_errors}") + log.error("\tFields not found in {0}:\n\t{1}".format(table_name, field_errors)) + stderr.print(f"\t[red]Missing values in {table_name}:\n\t{field_errors}") return j_data # TODO: haven't improved yet @@ -379,12 +379,12 @@ def include_pangolin_data(self, dir_path, j_data): ) row["lineage_analysis_date"] = pango_files[0].split(".")[-2] except ValueError: - log.error("No date found in %s pangolin files", sample_name) + log.error("\tNo date found in %s pangolin files", sample_name) stderr.print( - f"[red]No date found in sample {sample_name}", - f"[red]pangolin filenames: {pango_files}", + f"\t[red]No date found in sample {sample_name}. Pangolin filenames:", + f"\n\t[red]{pango_files}", ) - stderr.print("[Yellow] Using mapping analysis date instead") + stderr.print("\t[yellow]Using mapping analysis date instead") # If no date in pangolin files, set date as analysis date row["lineage_analysis_date"] = row["analysis_date"] f_data = relecov_tools.utils.read_csv_file_return_dict( @@ -399,9 +399,9 @@ def include_pangolin_data(self, dir_path, j_data): row[field] = "Not Provided [GENEPIO:0001668]" if len(missing_pango) >= 1: stderr.print( - f"[yellow]{len(missing_pango)} samples missing pangolin.csv file:" + f"\t[yellow]{len(missing_pango)} samples missing pangolin.csv file:" ) - stderr.print(f"[yellow]{missing_pango}") + stderr.print(f"\t[yellow]{missing_pango}") return j_data def handle_consensus_fasta(self, bioinfo_dict_scope, j_data): @@ -444,12 +444,12 @@ def handle_consensus_fasta(self, bioinfo_dict_scope, j_data): conserrs = len(missing_consens) if conserrs >= 1: log.error( - "{0} Consensus files missing:\n{1}".format( + "\t{0} Consensus files missing:\n\t{1}".format( conserrs, missing_consens ) ) - stderr.print(f"[yellow]{conserrs} samples missing consensus file:") - stderr.print(f"[yellow]\n{missing_consens}") + stderr.print(f"\t[yellow]{conserrs} samples missing consensus file:") + stderr.print(f"\n\t[yellow]{missing_consens}") return j_data def include_custom_data(self, j_data): From b6fa530dba7eeaf3eea00b7ab2f08fabca790c9c Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 1 Apr 2024 16:10:58 +0200 Subject: [PATCH 1264/1454] allow regex in scann_directory --- relecov_tools/conf/bioinfo_config.json | 2 +- relecov_tools/read_bioinfo_metadata.py | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index 984339b0..58d66c2e 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -23,7 +23,7 @@ } }, "mapping_pangolin": { - "fn": ".pangolin.csv", + "fn": ".pangolin(?:.*?)?\\.csv$", "ff": ",", "file_per_sample": true, "header_row_idx": 1, diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index db4d4c81..e647457d 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -90,7 +90,6 @@ def update_log_report(self, method_name, status, message): else: raise ValueError("Invalid status provided.") - # TODO: Add log report def scann_directory(self): """Scanns bioinfo analysis directory and identifies files according to the file name patterns defined in the software configuration json.""" total_files = sum(len(files) for _, _, files in os.walk(self.input_folder)) @@ -100,7 +99,7 @@ def scann_directory(self): if 'fn' not in topic_details: #try/except fn continue for root, _, files in os.walk(self.input_folder, topdown=True): - matching_files = [os.path.join(root, file_name) for file_name in files if file_name.endswith(topic_details['fn'])] + matching_files = [os.path.join(root, file_name) for file_name in files if re.search(topic_details['fn'], file_name)] if len(matching_files) >= 1: files_found[topic_key] = matching_files if len(files_found) < 1: From 17b91c06cc3797b2e779ef3be355be7eb43c2c3c Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 2 Apr 2024 12:00:55 +0200 Subject: [PATCH 1265/1454] add function to select the most recent file of a sample given a list of files --- relecov_tools/read_bioinfo_metadata.py | 38 ++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index e647457d..f86a6273 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -276,6 +276,44 @@ def handle_csv_file(self, bioinfo_dict_scope, j_data): ) return j_data_mapped + def select_most_recent_files_per_sample(self, paths_list): + """Selects the most recent file for each sample among potentially duplicated files. + Input: + - paths_list: a list of sample's file paths. + """ + filename_groups = {} + # Count occurrences of each filename and group files by sample names + for file in paths_list: + file_name = os.path.basename(file).split('.')[0] + if file_name in filename_groups : + filename_groups [file_name].append(file) + else: + filename_groups [file_name] = [file] + + # Filter out sample names with only one file + duplicated_files = [(sample_name, file_paths) for sample_name, file_paths in filename_groups.items() if len(file_paths) > 1] + + # Iterate over duplicated files to select the most recent one for each sample + for sample_name, file_paths in duplicated_files: + stderr.print(f"More than one pangolin file found for sample {sample_name}. Selecting the most recent one.") + + # Sort files by modification time (most recent first) + sorted_files = sorted(file_paths, key=lambda file_path: os.path.getmtime (file_path), reverse=True) + + # Select the most recent file + selected_file = sorted_files[0] + stderr.print(f"Selected file for sample {sample_name}: {selected_file}") + + # Remove other files for the same sample from the filtered_files dictionary + filename_groups[sample_name] = [selected_file] + + # Update filename_groups with filtered files + filename_groups = [(sample_name, file_path) for sample_name, file_paths in filename_groups.items() for file_path in file_paths] + + # Reformat variable to retrieve a list of file paths + file_path_list = [sample_file_path for _, sample_file_path in filename_groups] + return file_path_list + def handle_multiqc_html_file(self, bioinfo_dict_scope, j_data): """Reads html file, finds table containing programs info, and map it to j_data""" program_versions = {} From 6243562eb67726a74395741c8366fbcd2862617a Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 3 Apr 2024 13:40:40 +0200 Subject: [PATCH 1266/1454] add new strategy to: first, handle files; and second, mapping bioinfo-data over lab metadata --- relecov_tools/conf/bioinfo_config.json | 12 ++- relecov_tools/read_bioinfo_metadata.py | 129 +++++++++++++------------ 2 files changed, 73 insertions(+), 68 deletions(-) diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index 58d66c2e..89d55fa3 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -2,11 +2,12 @@ "viralrecon": { "mapping_stats": { "fn": "mapping_illumina_stats.tab", - "ff": "\t", + "ff": "tsv", "file_per_sample": false, "sample_col_idx": 5, "header_row_idx": 1, "required": true, + "function": null, "content": { "analysis_date": "analysis_date", "depth_of_coverage_value": "medianDPcoveragevirus", @@ -24,7 +25,7 @@ }, "mapping_pangolin": { "fn": ".pangolin(?:.*?)?\\.csv$", - "ff": ",", + "ff": "csv", "file_per_sample": true, "header_row_idx": 1, "required": false, @@ -39,11 +40,12 @@ }, "variants_long_table": { "fn": "variants_long_table.csv", - "ff": ",", + "ff": "csv", "file_per_sample": false, "sample_col_idx": 1, "header_row_idx": 1, "required": true, + "function": null, "content": { "sample" : "SAMPLE", "chromosome": "CHROM", @@ -80,11 +82,12 @@ }, "summary_mqc": { "fn": "summary_variants_metrics_mqc.csv", - "ff": ",", + "ff": "csv", "file_per_sample": false, "sample_col_idx": 1, "header_row_idx": 1, "required": true, + "function": null, "content": { "ns_per_100_kbp": "# Ns per 100kb consensus" } @@ -94,6 +97,7 @@ "ff": "html", "file_per_sample": false, "required": true, + "function": null, "content": { "bioinformatics_protocol_software_version": "nf-core/viralrecon", "consensus_sequence_software_version": "bcftools", diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index f86a6273..c411b0b5 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -180,7 +180,8 @@ def validate_software_mandatory_files(self, json): else: stderr.print("[green]\tValidation passed.") return - + + # TODO: ADD LOG REPORT def add_bioinfo_results_metadata(self, bioinfo_dict, j_data): """ Adds metadata from bioinformatics results to the JSON data. @@ -189,8 +190,13 @@ def add_bioinfo_results_metadata(self, bioinfo_dict, j_data): If the property specifies files per sample, it maps metadata for each sample-specific file. If the property specifies collated files. - """ + """ for key in bioinfo_dict.keys(): + # This skip files that will be parsed with other methods + if key == 'workflow_summary' or key == "fixed_values": + continue + + # Verify files found are present in key[file_paths]. try: bioinfo_dict[key]['file_paths'] except KeyError: @@ -200,81 +206,76 @@ def add_bioinfo_results_metadata(self, bioinfo_dict, j_data): f"No file path found for '{self.software_name}.{key}'" ) continue - # Parses sample-specific files (i.e: SAMPLE1.consensus.fa) - if bioinfo_dict[key].get('file_per_sample') is True: - j_data_mapped = self.map_metadata_persample_files( - bioinfo_dict[key], - j_data + + # Handling files + data_to_map = self.handling_files(bioinfo_dict[key]) + + # Adding data to j_data + if data_to_map: + j_data_mapped = self.mapping_over_table( + j_data, + data_to_map, + bioinfo_dict[key]['content'], + bioinfo_dict[key]['file_paths'] ) - # Parses collated files (i.e: mapping_illumina_stats.tab) - elif bioinfo_dict[key].get('file_per_sample') is False: - if len(bioinfo_dict[key].get('file_paths')) == 1: - bioinfo_dict[key]['file_paths'] = bioinfo_dict[key]['file_paths'][0] - j_data_mapped = self.map_metadata_collated_files( - bioinfo_dict[key], - j_data - ) - else: - stderr.print(f"\t[yellow]Ignoring {key}. See log_report.") - self.update_log_report( - self.add_bioinfo_results_metadata.__name__, - 'warning', - f"Collated files can't have more han one matching file. Please check {self.bioinfo_json_file} section: : '{self.software_name}.{key}'" - ) else: - if key != 'fixed_values': - # TODO: update log file - stderr.print(f"\t[yellow]Value 'file_per_sample' is missing in {self.bioinfo_json_file} section: '{self.software_name}.{key}'. This field is required to properly handle file configuration.") - continue + continue return j_data_mapped - def map_metadata_persample_files(self, bioinfo_dict_scope, j_data): - """The method processes metadata associated with per sample files and integrates it into the JSON data.""" + # TODO: Add log report(recover file format parsing errors) + def handling_files(self, bioinfo_dict_scope): + """Handles different file formats (sourced from ./metadata_homogenizer.py) + """ file_name = bioinfo_dict_scope['fn'] - file_format = bioinfo_dict_scope['ff'] - file_paths = bioinfo_dict_scope['file_paths'] - if file_format == ',' and 'pangolin' in file_name: - pango_path = os.path.dirname(file_paths[0]) - j_data_mapped = self.include_pangolin_data(pango_path, j_data) - elif file_format == 'fasta' and 'consensus' in file_name: - j_data_mapped = self.handle_consensus_fasta(bioinfo_dict_scope, j_data) - else: - stderr.warning(f"[red]No available methods to parse file format '{file_format}' and file name '{file_name}'.") - return - return j_data_mapped + file_extension = os.path.splitext(file_name)[1] + + # Parsing key position + try: + bioinfo_dict_scope['sample_col_idx'] + sample_idx_possition = bioinfo_dict_scope['sample_col_idx']-1 + except KeyError: + sample_idx_possition = None - # TODO: recover file format parsing errors - def map_metadata_collated_files(self, bioinfo_dict_scope, j_data): - """Handles different file formats in collated files, reads their content, and maps it to j_data""" - # We will be able to add here as many handlers as we need - file_extension_handlers = { - "\t": self.handle_csv_file, - ",": self.handle_csv_file, - "html": self.handle_multiqc_html_file, - } - file_format = bioinfo_dict_scope['ff'] - if file_format in file_extension_handlers: - handler_function = file_extension_handlers[file_format] - j_data_mapped = handler_function(bioinfo_dict_scope, j_data) - return j_data_mapped + # Parsing files + func_name = bioinfo_dict_scope["function"] + if func_name is None: + if file_name.endswith('.csv'): + data = relecov_tools.utils.read_csv_file_return_dict( + file_name=bioinfo_dict_scope['file_paths'][0], + sep=",", + key_position=sample_idx_possition + ) + return data + elif file_name.endswith('.tsv') or file_name.endswith('.tab'): + data = relecov_tools.utils.read_csv_file_return_dict( + file_name=bioinfo_dict_scope['file_paths'][0], + sep="\t", + key_position=sample_idx_possition + ) + else: + stderr.print(f"[red]Unrecognized defined file name extension {file_extension} in {bioinfo_dict_scope['fn']}") + sys.exit() else: - stderr.print(f"[red]Unrecognized defined file format {bioinfo_dict_scope['ff'] in {bioinfo_dict_scope['fn']}}") - return None - - def handle_csv_file(self, bioinfo_dict_scope, j_data): + try: + # TODO: ADD stdout to identify which data is being added. + # Attempt to get the method by name + method_to_call = getattr(self, func_name) + data = method_to_call(bioinfo_dict_scope['file_paths']) + except AttributeError as e: + if "not found" in str(e): + stderr.print(f"[red]Function '{func_name}' not found in class.") + return None + return data + + + def handle_csv_file(self, bioinfo_dict_scope): """handle csv/tsv file and map it with read lab metadata (j_data)""" map_data = relecov_tools.utils.read_csv_file_return_dict( file_name = bioinfo_dict_scope['file_paths'], sep = bioinfo_dict_scope['ff'], key_position = (bioinfo_dict_scope['sample_col_idx']-1) ) - j_data_mapped = self.mapping_over_table( - j_data, - map_data, - bioinfo_dict_scope['content'], - bioinfo_dict_scope['file_paths'] - ) - return j_data_mapped + return map_data def select_most_recent_files_per_sample(self, paths_list): """Selects the most recent file for each sample among potentially duplicated files. From 70a814825e58a18beb19e390e7d62ea16f8c8ede Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 3 Apr 2024 14:03:28 +0200 Subject: [PATCH 1267/1454] refactor methods pangolin, consensus, and software version to adhere to new data handling/mapping strategy. --- relecov_tools/conf/bioinfo_config.json | 17 ++- relecov_tools/read_bioinfo_metadata.py | 182 +++++++++++-------------- relecov_tools/utils.py | 16 +++ 3 files changed, 105 insertions(+), 110 deletions(-) diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index 89d55fa3..79e61d10 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -29,13 +29,15 @@ "file_per_sample": true, "header_row_idx": 1, "required": false, + "function": "handle_pangolin_data", "content": { "variant_name": "scorpio_call", "lineage_name": "lineage", "lineage_algorithm_software_version": "version", "lineage_analysis_software_version": "pangolin_version", "lineage_analysis_scorpio_version": "scorpio_version", - "lineage_analysis_constellation_version": "constellation_version" + "lineage_analysis_constellation_version": "constellation_version", + "lineage_analysis_date":"Not Provided [GENEPIO:0001668]" } }, "variants_long_table": { @@ -71,13 +73,14 @@ "ff": "fasta", "file_per_sample": true, "required": false, + "function": "handle_consensus_fasta", "content": { - "consensus_sequence_name" : "Not Provided [GENEPIO:0001668]", - "consensus_genome_length" : "Not Provided [GENEPIO:0001668]", - "consensus_sequence_filename" : "Not Provided [GENEPIO:0001668]", - "consensus_sequence_filepath" : "Not Provided [GENEPIO:0001668]", - "consensus_sequence_md5" : "Not Provided [GENEPIO:0001668]", - "number_of_base_pairs_sequenced" : "Not Provided [GENEPIO:0001668]" + "consensus_sequence_name" : "sequence_name", + "consensus_genome_length" : "genome_length", + "consensus_sequence_filename" : "sequence_filename", + "consensus_sequence_filepath" : "sequence_filepath", + "consensus_sequence_md5" : "sequence_md5", + "number_of_base_pairs_sequenced" : "number_of_base_pairs_sequenced" } }, "summary_mqc": { diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index c411b0b5..9a49a044 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -315,17 +315,18 @@ def select_most_recent_files_per_sample(self, paths_list): file_path_list = [sample_file_path for _, sample_file_path in filename_groups] return file_path_list - def handle_multiqc_html_file(self, bioinfo_dict_scope, j_data): + # TODO: add log report + def get_multiqc_software_versions(self, bioinfo_dict_scope, j_data): """Reads html file, finds table containing programs info, and map it to j_data""" + # Handle multiqc_report.html + f_path = bioinfo_dict_scope['file_paths'][0] program_versions = {} - with open(bioinfo_dict_scope['file_paths'], 'r') as html_file: + + with open(f_path, 'r') as html_file: html_content = html_file.read() - # Load HTML soup = BeautifulSoup(html_content, features="lxml") - # Get version's div id div_id = "mqc-module-section-software_versions" versions_div = soup.find('div', id=div_id) - # Get version's metadata data if versions_div: table = versions_div.find('table', class_='table') if table: @@ -346,7 +347,7 @@ def handle_multiqc_html_file(self, bioinfo_dict_scope, j_data): stderr.print(f"[red] No div section 'mqc-module-section-software_versions' was found in {bioinfo_dict_scope['file_paths']}.") sys.exit(1) - # mapping mqc sofware versions to j_data + # Mapping multiqc sofware versions to j_data field_errors = {} for row in j_data: sample_name = row["submitting_lab_sample_id"] @@ -364,8 +365,8 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): errors = [] field_errors = {} for row in j_data: - sample_name = row["submitting_lab_sample_id"] - if sample_name in map_data: + sample_name = row["submitting_lab_sample_id"].replace("-", "_") + if sample_name in map_data.keys(): for field, value in mapping_fields.items(): try: row[field] = map_data[sample_name][value] @@ -379,116 +380,89 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): row[field] = "Not Provided [GENEPIO:0001668]" if errors: lenerrs = len(errors) + # work around when map_data comes from several per-sample tables instead of single table + if len(table_name) > 1: + table_name = (os.path.dirname(table_name[0])) log.error( - "\t{0} samples missing in {1}:\n\t{2}".format(lenerrs, table_name, errors) - ) - stderr.print(f"\t[red]{lenerrs} samples missing in {table_name}:\n\t{errors}") + "\t{0} samples missing in {1}:\n\t{2}".format(lenerrs, table_name, errors) + ) + stderr.print(f"\t[red]{lenerrs} samples missing in {table_name}:\n\t{errors}") if field_errors: log.error("\tFields not found in {0}:\n\t{1}".format(table_name, field_errors)) stderr.print(f"\t[red]Missing values in {table_name}:\n\t{field_errors}") return j_data - # TODO: haven't improved yet - def include_pangolin_data(self, dir_path, j_data): - """Include pangolin data collecting form each file generated by pangolin""" - mapping_fields = self.software_config["mapping_pangolin"]["content"] - missing_pango = [] - for row in j_data: - # Get read lab sample id - if "-" in row["submitting_lab_sample_id"]: - sample_name = row["submitting_lab_sample_id"].replace("-", "_") - else: - sample_name = row["submitting_lab_sample_id"] - # Get the name of pangolin csv file/s - f_name_regex = sample_name + ".pangolin*.csv" - f_path = os.path.join(dir_path, f_name_regex) - pango_files = glob.glob(f_path) - # Parse pangolin files - if pango_files: - if len(pango_files) > 1: - stderr.print( - "[yellow]More than one pangolin file found for sample", - f"[yellow]{sample_name}. Selecting the most recent one", - ) + def handle_pangolin_data(self, files_list):#, j_data): + """Parse pangolin data (csv) into JSON and map it to each sample in the provided j_data. + """ + # Handling pangolin data + pango_data_processed = {} + try: + files_list_processed = self.select_most_recent_files_per_sample(files_list) + for pango_file in files_list_processed: try: - pango_files = sorted( - pango_files, - key=lambda dt: datetime.strptime(dt.split(".")[-2], "%Y%m%d"), + pango_data = relecov_tools.utils.read_csv_file_return_dict( + pango_file, sep="," ) - row["lineage_analysis_date"] = pango_files[0].split(".")[-2] - except ValueError: - log.error("\tNo date found in %s pangolin files", sample_name) - stderr.print( - f"\t[red]No date found in sample {sample_name}. Pangolin filenames:", - f"\n\t[red]{pango_files}", + # Add custom content in pangolin + pango_data_key = next(iter(pango_data)) + pango_data[pango_data_key]['lineage_analysis_date'] = relecov_tools.utils.get_file_date( + pango_file ) - stderr.print("\t[yellow]Using mapping analysis date instead") - # If no date in pangolin files, set date as analysis date - row["lineage_analysis_date"] = row["analysis_date"] - f_data = relecov_tools.utils.read_csv_file_return_dict( - pango_files[0], sep="," - ) - pang_key = list(f_data.keys())[0] - for field, value in mapping_fields.items(): - row[field] = f_data[pang_key][value] - else: - missing_pango.append(sample_name) - for field in mapping_fields.keys(): - row[field] = "Not Provided [GENEPIO:0001668]" - if len(missing_pango) >= 1: - stderr.print( - f"\t[yellow]{len(missing_pango)} samples missing pangolin.csv file:" - ) - stderr.print(f"\t[yellow]{missing_pango}") - return j_data - def handle_consensus_fasta(self, bioinfo_dict_scope, j_data): - """Include genome length, name, file name, path and md5 by preprocessing - each file of consensus.fa""" - mapping_fields = bioinfo_dict_scope["content"] + # Rename key in f_data + pango_data_updated = {key.split()[0]: value for key, value in pango_data.items()} + pango_data_processed.update(pango_data_updated) + except (FileNotFoundError, IndexError) as e: + stderr.print(f"[red]Error processing file {pango_file}: {e}") + continue + except Exception as e: + stderr.print(f"[red]Error occurred while processing files: {e}") + sys.exit() + return pango_data_processed + + # FIXME: only in item is saved in consensus_data_processed. but at least two are ok. + def handle_consensus_fasta(self, files_list): + """Handling consensus fasta data (*.consensus.fa)""" + consensus_data_processed = {} missing_consens = [] - consensus_dir_path = os.path.dirname(bioinfo_dict_scope['file_paths'][0]) - # FIXME: Replace sequencing_sample_id - for row in j_data: - if "-" in row["submitting_lab_sample_id"]: - sample_name = row["submitting_lab_sample_id"].replace("-", "_") - else: - sample_name = row["submitting_lab_sample_id"] - f_name = sample_name + ".consensus.fa" - f_path = os.path.join(consensus_dir_path, f_name) + for consensus_file in files_list: try: record_fasta = relecov_tools.utils.read_fasta_return_SeqIO_instance( - f_path + consensus_file ) except FileNotFoundError as e: missing_consens.append(e.filename) - for item in mapping_fields: - row[item] = "Not Provided [GENEPIO:0001668]" continue - row["consensus_genome_length"] = str(len(record_fasta)) - row["consensus_sequence_name"] = record_fasta.description - row["consensus_sequence_filepath"] = self.input_folder - row["consensus_sequence_filename"] = f_name - row["consensus_sequence_md5"] = relecov_tools.utils.calculate_md5(f_path) - if row["read_length"].isdigit(): - base_calculation = int(row["read_length"]) * len(record_fasta) - if row["submitting_lab_sample_id"] != "Not Provided [GENEPIO:0001668]": - row["number_of_base_pairs_sequenced"] = str(base_calculation * 2) - else: - row["number_of_base_pairs_sequenced"] = str(base_calculation) - else: - row["number_of_base_pairs_sequenced"] = "Not Provided [GENEPIO:0001668]" - # TODO: WAIT TO FIXED IN POST ADAPTATION PR - conserrs = len(missing_consens) - if conserrs >= 1: - log.error( - "\t{0} Consensus files missing:\n\t{1}".format( - conserrs, missing_consens + sample_key = re.sub(self.software_config['mapping_consensus']['fn'], '', os.path.basename(consensus_file)) + + # Initialize dictionary for the consensus file if it doesn't exist + consensus_dict = {sample_key:{} } + if sample_key not in consensus_dict: + consensus_dict[sample_key] = {} + + consensus_dict[sample_key]['sequence_name'] = record_fasta.description + consensus_dict[sample_key]['genome_length'] = str(len(record_fasta)) + consensus_dict[sample_key]['sequence_filepath'] = os.path.dirname(consensus_file) + consensus_dict[sample_key]['sequence_filename'] = sample_key + self.software_config['mapping_consensus']['fn'] + consensus_dict[sample_key]['sequence_md5'] = relecov_tools.utils.calculate_md5(consensus_file) + consensus_data_processed.update(consensus_dict) + + + # TODO: Not sure this is correct. If not, recover previous version: https://github.com/BU-ISCIII/relecov-tools/blob/09c00c1ddd11f7489de7757841aff506ef4b7e1d/relecov_tools/read_bioinfo_metadata.py#L211-L218 + consensus_dict[sample_key]['number_of_base_pairs_sequenced'] = len(record_fasta.seq) + + # Report missing consensus + conserrs = len(missing_consens) + if conserrs >= 1: + log.error( + "\t{0} Consensus files missing:\n\t{1}".format( + conserrs, missing_consens + ) ) - ) - stderr.print(f"\t[yellow]{conserrs} samples missing consensus file:") - stderr.print(f"\n\t[yellow]{missing_consens}") - return j_data + stderr.print(f"\t[yellow]{conserrs} samples missing consensus file:") + stderr.print(f"\n\t[yellow]{missing_consens}") + return consensus_data_processed def include_custom_data(self, j_data): """Include custom fields like variant-long-table path""" @@ -537,9 +511,11 @@ def create_bioinfo_file(self): j_data = self.collect_info_from_lab_json() stderr.print(f"[blue]Adding metadata from {self.input_folder} into read lab metadata...") j_data = self.add_bioinfo_results_metadata(software_config_extended, j_data) - #TODO: This should be refactor according to new file-handling implementation - #stderr.print("[blue]Adding variant long table path") - #j_data = self.include_custom_data(j_data) + stderr.print("[blue]Adding software versions to read lab metadata...") + j_data = self.get_multiqc_software_versions(software_config_extended['workflow_summary'], j_data) + # FIXME: this isn't refactored and requires to be reimplemented from older version of this module + ##stderr.print("[blue]Adding variant long table path") + ##j_data = self.include_custom_data(j_data) stderr.print("[blue]Adding fixed values") j_data = self.add_fixed_values(j_data) file_name = ( diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index f2461f72..8789a23e 100755 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -16,6 +16,7 @@ from itertools import islice from Bio import SeqIO from rich.console import Console +from datetime import datetime log = logging.getLogger(__name__) @@ -306,3 +307,18 @@ def prompt_skip_folder_creation(): def prompt_checkbox(msg, choices): selected_options = questionary.checkbox(msg, choices=choices).unsafe_ask() return selected_options + +def get_file_date(file_path): + """Get the modification date of a file.""" + try: + # Get the modification time of the file + mtime = os.path.getmtime(file_path) + # Convert the modification time to a datetime object + file_date = datetime.fromtimestamp(mtime) + # Format date + formatted_date = file_date.strftime("%Y/%m/%d") + return formatted_date + except FileNotFoundError: + # Handle file not found error + print(f"File not found: {file_path}") + return None From d4add27af768b02c22f636439028040470293fb6 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 4 Apr 2024 10:04:18 +0200 Subject: [PATCH 1268/1454] fix method handle_consensus_fasta --- relecov_tools/read_bioinfo_metadata.py | 48 +++++++++++--------------- 1 file changed, 21 insertions(+), 27 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 9a49a044..a1eb0c3b 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -421,7 +421,6 @@ def handle_pangolin_data(self, files_list):#, j_data): sys.exit() return pango_data_processed - # FIXME: only in item is saved in consensus_data_processed. but at least two are ok. def handle_consensus_fasta(self, files_list): """Handling consensus fasta data (*.consensus.fa)""" consensus_data_processed = {} @@ -436,33 +435,28 @@ def handle_consensus_fasta(self, files_list): continue sample_key = re.sub(self.software_config['mapping_consensus']['fn'], '', os.path.basename(consensus_file)) - # Initialize dictionary for the consensus file if it doesn't exist - consensus_dict = {sample_key:{} } - if sample_key not in consensus_dict: - consensus_dict[sample_key] = {} - - consensus_dict[sample_key]['sequence_name'] = record_fasta.description - consensus_dict[sample_key]['genome_length'] = str(len(record_fasta)) - consensus_dict[sample_key]['sequence_filepath'] = os.path.dirname(consensus_file) - consensus_dict[sample_key]['sequence_filename'] = sample_key + self.software_config['mapping_consensus']['fn'] - consensus_dict[sample_key]['sequence_md5'] = relecov_tools.utils.calculate_md5(consensus_file) - consensus_data_processed.update(consensus_dict) - - - # TODO: Not sure this is correct. If not, recover previous version: https://github.com/BU-ISCIII/relecov-tools/blob/09c00c1ddd11f7489de7757841aff506ef4b7e1d/relecov_tools/read_bioinfo_metadata.py#L211-L218 - consensus_dict[sample_key]['number_of_base_pairs_sequenced'] = len(record_fasta.seq) - - # Report missing consensus - conserrs = len(missing_consens) - if conserrs >= 1: - log.error( - "\t{0} Consensus files missing:\n\t{1}".format( - conserrs, missing_consens - ) + # Update consensus data for the sample key + consensus_data_processed[sample_key] = { + 'sequence_name': record_fasta.description, + 'genome_length': str(len(record_fasta)), + 'sequence_filepath': os.path.dirname(consensus_file), + 'sequence_filename': sample_key, + 'sequence_md5': relecov_tools.utils.calculate_md5(consensus_file), + # TODO: Not sure this is correct. If not, recover previous version: https://github.com/BU-ISCIII/relecov-tools/blob/09c00c1ddd11f7489de7757841aff506ef4b7e1d/relecov_tools/read_bioinfo_metadata.py#L211-L218 + 'number_of_base_pairs_sequenced': len(record_fasta.seq) + } + + # Report missing consensus + conserrs = len(missing_consens) + if conserrs >= 1: + log.error( + "\t{0} Consensus files missing:\n\t{1}".format( + conserrs, missing_consens ) - stderr.print(f"\t[yellow]{conserrs} samples missing consensus file:") - stderr.print(f"\n\t[yellow]{missing_consens}") - return consensus_data_processed + ) + stderr.print(f"\t[yellow]{conserrs} samples missing consensus file:") + stderr.print(f"\n\t[yellow]{missing_consens}") + return consensus_data_processed def include_custom_data(self, j_data): """Include custom fields like variant-long-table path""" From 7c4377b0714280feb3275be8dd8b6b1c31bb07be Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 4 Apr 2024 10:30:01 +0200 Subject: [PATCH 1269/1454] exported method select-most-recent-file from read-bioinfo-metadata to utils --- relecov_tools/read_bioinfo_metadata.py | 42 ++------------------------ relecov_tools/utils.py | 37 +++++++++++++++++++++++ 2 files changed, 39 insertions(+), 40 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index a1eb0c3b..0ca19bc7 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -277,44 +277,6 @@ def handle_csv_file(self, bioinfo_dict_scope): ) return map_data - def select_most_recent_files_per_sample(self, paths_list): - """Selects the most recent file for each sample among potentially duplicated files. - Input: - - paths_list: a list of sample's file paths. - """ - filename_groups = {} - # Count occurrences of each filename and group files by sample names - for file in paths_list: - file_name = os.path.basename(file).split('.')[0] - if file_name in filename_groups : - filename_groups [file_name].append(file) - else: - filename_groups [file_name] = [file] - - # Filter out sample names with only one file - duplicated_files = [(sample_name, file_paths) for sample_name, file_paths in filename_groups.items() if len(file_paths) > 1] - - # Iterate over duplicated files to select the most recent one for each sample - for sample_name, file_paths in duplicated_files: - stderr.print(f"More than one pangolin file found for sample {sample_name}. Selecting the most recent one.") - - # Sort files by modification time (most recent first) - sorted_files = sorted(file_paths, key=lambda file_path: os.path.getmtime (file_path), reverse=True) - - # Select the most recent file - selected_file = sorted_files[0] - stderr.print(f"Selected file for sample {sample_name}: {selected_file}") - - # Remove other files for the same sample from the filtered_files dictionary - filename_groups[sample_name] = [selected_file] - - # Update filename_groups with filtered files - filename_groups = [(sample_name, file_path) for sample_name, file_paths in filename_groups.items() for file_path in file_paths] - - # Reformat variable to retrieve a list of file paths - file_path_list = [sample_file_path for _, sample_file_path in filename_groups] - return file_path_list - # TODO: add log report def get_multiqc_software_versions(self, bioinfo_dict_scope, j_data): """Reads html file, finds table containing programs info, and map it to j_data""" @@ -392,13 +354,13 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): stderr.print(f"\t[red]Missing values in {table_name}:\n\t{field_errors}") return j_data - def handle_pangolin_data(self, files_list):#, j_data): + def handle_pangolin_data(self, files_list): """Parse pangolin data (csv) into JSON and map it to each sample in the provided j_data. """ # Handling pangolin data pango_data_processed = {} try: - files_list_processed = self.select_most_recent_files_per_sample(files_list) + files_list_processed = relecov_tools.utils.select_most_recent_files_per_sample(files_list) for pango_file in files_list_processed: try: pango_data = relecov_tools.utils.read_csv_file_return_dict( diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 8789a23e..4149eea3 100755 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -322,3 +322,40 @@ def get_file_date(file_path): # Handle file not found error print(f"File not found: {file_path}") return None + +def select_most_recent_files_per_sample(paths_list): + """Selects the most recent file for each sample among potentially duplicated files. + Input: + - paths_list: a list of sample's file paths. + Output: + - List of file paths containig the most recent/up-to-date file for each sample. + """ + filename_groups = {} + # Count occurrences of each filename and group files by sample names + for file in paths_list: + file_name = os.path.basename(file).split('.')[0] + if file_name in filename_groups : + filename_groups[file_name].append(file) + else: + filename_groups[file_name] = [file] + + # Filter out sample names with only one file + duplicated_files = [(sample_name, file_paths) for sample_name, file_paths in filename_groups.items() if len(file_paths) > 1] + + # Iterate over duplicated files to select the most recent one for each sample + for sample_name, file_paths in duplicated_files: + stderr.print(f"More than one pangolin file found for sample {sample_name}. Selecting the most recent one.") + # Sort files by modification time (most recent first) + sorted_files = sorted(file_paths, key=lambda file_path: os.path.getmtime (file_path), reverse=True) + # Select the most recent file + selected_file = sorted_files[0] + stderr.print(f"Selected file for sample {sample_name}: {selected_file}") + # Remove other files for the same sample from the filtered_files dictionary + filename_groups[sample_name] = [selected_file] + + # Update filename_groups with filtered files + filename_groups = [(sample_name, file_path) for sample_name, file_paths in filename_groups.items() for file_path in file_paths] + + # Reformat variable to retrieve a list of file paths + file_path_list = [sample_file_path for _, sample_file_path in filename_groups] + return file_path_list From 204c1884bb8896d93ae704907adc1e34c46e607e Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 4 Apr 2024 10:52:06 +0200 Subject: [PATCH 1270/1454] add todos and missing imported library --- relecov_tools/read_bioinfo_metadata.py | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 0ca19bc7..2f67dead 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -4,6 +4,7 @@ import logging import glob import rich.console +import re from datetime import datetime from yaml import YAMLError from bs4 import BeautifulSoup @@ -22,8 +23,12 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) -# TODO: Create 2 master function that validates file presence/content and transfrom from csv,tsv,... to json. -# TODO: Cosider eval py + func property in json to be able to discriminate between collated files and sample-specific files. +# FIXME: longtable parsing old method needs to be recovered. New implementation has errors while parsing it. +# TODO: Add method to validate bioinfo_config.json file requirements. +# TODO: Cosider eval py + func property in json to be able to discriminate between collated files and sample-specific files. +# TODO: replace submitting_lab_id by sequencing_sample_id +# TODO: manage bioinfo config and files_found paths in separate variables. +# TODO: improve method's description (specifically 'handling_files') class BioinfoMetadata: def __init__( self, @@ -223,6 +228,7 @@ def add_bioinfo_results_metadata(self, bioinfo_dict, j_data): return j_data_mapped # TODO: Add log report(recover file format parsing errors) + # TODO: add better stdout/err to show which method is being called. def handling_files(self, bioinfo_dict_scope): """Handles different file formats (sourced from ./metadata_homogenizer.py) """ @@ -322,6 +328,7 @@ def get_multiqc_software_versions(self, bioinfo_dict_scope, j_data): continue return j_data + # TODO: update log report def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): """Auxiliar function to iterate over table's content and map it to metadata (j_data)""" errors = [] @@ -354,6 +361,7 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): stderr.print(f"\t[red]Missing values in {table_name}:\n\t{field_errors}") return j_data + # TODO: add log report def handle_pangolin_data(self, files_list): """Parse pangolin data (csv) into JSON and map it to each sample in the provided j_data. """ @@ -383,6 +391,7 @@ def handle_pangolin_data(self, files_list): sys.exit() return pango_data_processed + # TODO: add log report def handle_consensus_fasta(self, files_list): """Handling consensus fasta data (*.consensus.fa)""" consensus_data_processed = {} @@ -420,6 +429,7 @@ def handle_consensus_fasta(self, files_list): stderr.print(f"\n\t[yellow]{missing_consens}") return consensus_data_processed + # TODO: add log report def include_custom_data(self, j_data): """Include custom fields like variant-long-table path""" condition = os.path.join(self.input_folder, "*variants_long_table*.csv") @@ -432,6 +442,7 @@ def include_custom_data(self, j_data): row["long_table_path"] = long_table_path return j_data + # TODO: this is too harcoded. Find a way to add file's path of required files when calling handlers functions. def add_fixed_values(self, j_data): """include the fixed data defined in configuration or feed custom empty fields""" f_values = self.software_config["fixed_values"] From 79c49a0497aee451723f2429691d83ecbca5b39d Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 4 Apr 2024 12:17:51 +0200 Subject: [PATCH 1271/1454] recover independent management of software-config and files-found variables --- relecov_tools/read_bioinfo_metadata.py | 97 ++++++++++---------------- 1 file changed, 37 insertions(+), 60 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 2f67dead..d881aea6 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -27,7 +27,6 @@ # TODO: Add method to validate bioinfo_config.json file requirements. # TODO: Cosider eval py + func property in json to be able to discriminate between collated files and sample-specific files. # TODO: replace submitting_lab_id by sequencing_sample_id -# TODO: manage bioinfo config and files_found paths in separate variables. # TODO: improve method's description (specifically 'handling_files') class BioinfoMetadata: def __init__( @@ -129,65 +128,40 @@ def scann_directory(self): stderr.print(f"\t[green]Scannig process succeed (total scanned files: {total_files}).") return files_found - def add_filepaths_to_software_config(self, files_dict): - """ - Adds file paths to the software configuration JSON by creating the 'file_paths' property with files found during the scanning process. - """ - cc = 0 - extended_software_config = self.software_config - for key, value in files_dict.items(): - if key in extended_software_config: - if len(value) != 0 or value: - extended_software_config[key]['file_paths'] = value - cc+=1 - if cc == 0: - self.update_log_report( - self.add_filepaths_to_software_config.__name__, - 'error', - "No files path added to configuration json" - ) - else: - self.update_log_report( - self.add_filepaths_to_software_config.__name__, - 'valid', - "Files path added to configuration json" - ) - stderr.print("\t[green]Files path added to their scope in bioinfo configuration file.") - return extended_software_config - - def validate_software_mandatory_files(self, json): + def validate_software_mandatory_files(self, files_dict): missing_required = [] - for key in json.keys(): - if json[key].get('required') is True: + for key in self.software_config: + if self.software_config[key].get('required') is True: try: - json[key]['file_paths'] + files_dict[key] self.update_log_report( self.validate_software_mandatory_files.__name__, 'valid', - f"Found '{json[key]['fn']}'" + f"Found {self.software_name}.{key}" ) except KeyError: missing_required.append(key) self.update_log_report( self.validate_software_mandatory_files.__name__, 'error', - f"Missing '{json[key]['fn']}'" + f"Missing '{files_dict[key]['fn']}'" ) else: continue + if len(missing_required) >= 1: log.error("\tMissing required files:") stderr.print("[red]\tMissing required files:") for i in missing_required: log.error("\t- %s", i) - stderr.print(f"[red]\t- {i} (file name expected pattern '{json[i]['fn']}')") + stderr.print(f"[red]\t- {i} (file name expected pattern '{files_dict[i]['fn']}')") sys.exit(1) else: stderr.print("[green]\tValidation passed.") return # TODO: ADD LOG REPORT - def add_bioinfo_results_metadata(self, bioinfo_dict, j_data): + def add_bioinfo_results_metadata(self, files_dict, j_data): """ Adds metadata from bioinformatics results to the JSON data. @@ -196,14 +170,19 @@ def add_bioinfo_results_metadata(self, bioinfo_dict, j_data): If the property specifies files per sample, it maps metadata for each sample-specific file. If the property specifies collated files. """ - for key in bioinfo_dict.keys(): + for key in self.software_config.keys(): # This skip files that will be parsed with other methods if key == 'workflow_summary' or key == "fixed_values": continue # Verify files found are present in key[file_paths]. try: - bioinfo_dict[key]['file_paths'] + files_dict[key] + self.update_log_report( + self.add_bioinfo_results_metadata.__name__, + 'valid', + f"Start processing '{self.software_name}.{key}'" + ) except KeyError: self.update_log_report( self.add_bioinfo_results_metadata.__name__, @@ -213,15 +192,15 @@ def add_bioinfo_results_metadata(self, bioinfo_dict, j_data): continue # Handling files - data_to_map = self.handling_files(bioinfo_dict[key]) + data_to_map = self.handling_files(files_dict[key], key) # Adding data to j_data if data_to_map: j_data_mapped = self.mapping_over_table( j_data, data_to_map, - bioinfo_dict[key]['content'], - bioinfo_dict[key]['file_paths'] + self.software_config[key]['content'], + files_dict[key] ) else: continue @@ -229,44 +208,44 @@ def add_bioinfo_results_metadata(self, bioinfo_dict, j_data): # TODO: Add log report(recover file format parsing errors) # TODO: add better stdout/err to show which method is being called. - def handling_files(self, bioinfo_dict_scope): + def handling_files(self, file_list, file_key): """Handles different file formats (sourced from ./metadata_homogenizer.py) """ - file_name = bioinfo_dict_scope['fn'] + file_name = self.software_config[file_key].get('fn') file_extension = os.path.splitext(file_name)[1] # Parsing key position try: - bioinfo_dict_scope['sample_col_idx'] - sample_idx_possition = bioinfo_dict_scope['sample_col_idx']-1 + self.software_config[file_key]['sample_col_idx'] + sample_idx_possition = self.software_config[file_key]['sample_col_idx']-1 except KeyError: sample_idx_possition = None # Parsing files - func_name = bioinfo_dict_scope["function"] + func_name = self.software_config[file_key]["function"] if func_name is None: if file_name.endswith('.csv'): data = relecov_tools.utils.read_csv_file_return_dict( - file_name=bioinfo_dict_scope['file_paths'][0], + file_name=file_list[0], sep=",", key_position=sample_idx_possition ) return data elif file_name.endswith('.tsv') or file_name.endswith('.tab'): data = relecov_tools.utils.read_csv_file_return_dict( - file_name=bioinfo_dict_scope['file_paths'][0], + file_name=file_list[0], sep="\t", key_position=sample_idx_possition ) else: - stderr.print(f"[red]Unrecognized defined file name extension {file_extension} in {bioinfo_dict_scope['fn']}") + stderr.print(f"[red]Unrecognized defined file name extension {file_extension} in {file_name}") sys.exit() else: try: # TODO: ADD stdout to identify which data is being added. # Attempt to get the method by name method_to_call = getattr(self, func_name) - data = method_to_call(bioinfo_dict_scope['file_paths']) + data = method_to_call(file_list) except AttributeError as e: if "not found" in str(e): stderr.print(f"[red]Function '{func_name}' not found in class.") @@ -284,10 +263,10 @@ def handle_csv_file(self, bioinfo_dict_scope): return map_data # TODO: add log report - def get_multiqc_software_versions(self, bioinfo_dict_scope, j_data): + def get_multiqc_software_versions(self, file_list, j_data): """Reads html file, finds table containing programs info, and map it to j_data""" # Handle multiqc_report.html - f_path = bioinfo_dict_scope['file_paths'][0] + f_path = file_list[0] program_versions = {} with open(f_path, 'r') as html_file: @@ -308,18 +287,18 @@ def get_multiqc_software_versions(self, bioinfo_dict_scope, j_data): else: stderr.print(f"[red] HTML entry error in {columns}. HTML table expected format should be \n Process Name\n\n Software \n.") else: - stderr.print(f"[red] Missing table containing software versions in {bioinfo_dict_scope['file_paths']}.") + stderr.print(f"[red] Missing table containing software versions in file {f_path}.") sys.exit(1) else: - log.error(f"Required div section 'mqc-module-section-software_versions' not found in file {bioinfo_dict_scope['file_paths']}.") - stderr.print(f"[red] No div section 'mqc-module-section-software_versions' was found in {bioinfo_dict_scope['file_paths']}.") + log.error(f"Required div section 'mqc-module-section-software_versions' not found in file {f_path}.") + stderr.print(f"[red] No div section 'mqc-module-section-software_versions' was found in {f_path}.") sys.exit(1) # Mapping multiqc sofware versions to j_data field_errors = {} for row in j_data: sample_name = row["submitting_lab_sample_id"] - for field, values in bioinfo_dict_scope['content'].items(): + for field, values in self.software_config['workflow_summary'].get('content').items(): try: row[field] = program_versions[values] except KeyError as e: @@ -470,16 +449,14 @@ def create_bioinfo_file(self): """ stderr.print("[blue]Sanning input directory...") files_found_dict = self.scann_directory() - stderr.print("[blue]Adding files found to bioinfo config json...") - software_config_extended = self.add_filepaths_to_software_config(files_found_dict) stderr.print("[blue]Validating required files...") - self.validate_software_mandatory_files(software_config_extended) + self.validate_software_mandatory_files(files_found_dict) stderr.print("[blue]Reading lab metadata json") j_data = self.collect_info_from_lab_json() stderr.print(f"[blue]Adding metadata from {self.input_folder} into read lab metadata...") - j_data = self.add_bioinfo_results_metadata(software_config_extended, j_data) + j_data = self.add_bioinfo_results_metadata(files_found_dict, j_data) stderr.print("[blue]Adding software versions to read lab metadata...") - j_data = self.get_multiqc_software_versions(software_config_extended['workflow_summary'], j_data) + j_data = self.get_multiqc_software_versions(files_found_dict['workflow_summary'], j_data) # FIXME: this isn't refactored and requires to be reimplemented from older version of this module ##stderr.print("[blue]Adding variant long table path") ##j_data = self.include_custom_data(j_data) From 3e3eac18de19de74e9e6b0dbd7cd060e79d4902e Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 4 Apr 2024 12:36:54 +0200 Subject: [PATCH 1272/1454] remove method and config items that are not necessary anymore --- relecov_tools/conf/bioinfo_config.json | 12 ------------ relecov_tools/read_bioinfo_metadata.py | 21 +++------------------ 2 files changed, 3 insertions(+), 30 deletions(-) diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index 79e61d10..f559f545 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -2,8 +2,6 @@ "viralrecon": { "mapping_stats": { "fn": "mapping_illumina_stats.tab", - "ff": "tsv", - "file_per_sample": false, "sample_col_idx": 5, "header_row_idx": 1, "required": true, @@ -25,8 +23,6 @@ }, "mapping_pangolin": { "fn": ".pangolin(?:.*?)?\\.csv$", - "ff": "csv", - "file_per_sample": true, "header_row_idx": 1, "required": false, "function": "handle_pangolin_data", @@ -42,8 +38,6 @@ }, "variants_long_table": { "fn": "variants_long_table.csv", - "ff": "csv", - "file_per_sample": false, "sample_col_idx": 1, "header_row_idx": 1, "required": true, @@ -70,8 +64,6 @@ }, "mapping_consensus": { "fn": ".consensus.fa", - "ff": "fasta", - "file_per_sample": true, "required": false, "function": "handle_consensus_fasta", "content": { @@ -85,8 +77,6 @@ }, "summary_mqc": { "fn": "summary_variants_metrics_mqc.csv", - "ff": "csv", - "file_per_sample": false, "sample_col_idx": 1, "header_row_idx": 1, "required": true, @@ -97,8 +87,6 @@ }, "workflow_summary": { "fn": "multiqc_report.html", - "ff": "html", - "file_per_sample": false, "required": true, "function": null, "content": { diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index d881aea6..425050d7 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -13,8 +13,6 @@ from relecov_tools.config_json import ConfigJson from relecov_tools.long_table_parse import LongTableParse -# import relecov_tools.json_schema - log = logging.getLogger(__name__) stderr = rich.console.Console( stderr=True, @@ -163,19 +161,15 @@ def validate_software_mandatory_files(self, files_dict): # TODO: ADD LOG REPORT def add_bioinfo_results_metadata(self, files_dict, j_data): """ - Adds metadata from bioinformatics results to the JSON data. - - This method iterates over each property in the provided bioinfo_dict, which contains information about file paths (discovered during the scanning process), along with their specific file configuration. - - If the property specifies files per sample, it maps metadata for each sample-specific file. - If the property specifies collated files. + Adds metadata from bioinformatics results to j_data. + 1. Handles metadata in bioinformatic files found + 2. Mapping handled bioinfo metadata into j_data. """ for key in self.software_config.keys(): # This skip files that will be parsed with other methods if key == 'workflow_summary' or key == "fixed_values": continue - # Verify files found are present in key[file_paths]. try: files_dict[key] self.update_log_report( @@ -253,15 +247,6 @@ def handling_files(self, file_list, file_key): return data - def handle_csv_file(self, bioinfo_dict_scope): - """handle csv/tsv file and map it with read lab metadata (j_data)""" - map_data = relecov_tools.utils.read_csv_file_return_dict( - file_name = bioinfo_dict_scope['file_paths'], - sep = bioinfo_dict_scope['ff'], - key_position = (bioinfo_dict_scope['sample_col_idx']-1) - ) - return map_data - # TODO: add log report def get_multiqc_software_versions(self, file_list, j_data): """Reads html file, finds table containing programs info, and map it to j_data""" From c6e14997332d5556b2ed3c4f428e737d8d5f46f2 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 2 Apr 2024 11:40:17 +0200 Subject: [PATCH 1273/1454] Body_product for blood set to not applicable --- relecov_tools/conf/anatomical_material_collection_method.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/anatomical_material_collection_method.json b/relecov_tools/conf/anatomical_material_collection_method.json index bdd273ad..05e5c0cf 100755 --- a/relecov_tools/conf/anatomical_material_collection_method.json +++ b/relecov_tools/conf/anatomical_material_collection_method.json @@ -974,7 +974,7 @@ "Blood": { "anatomical_part": "Not Applicable", "collection_method": "Not Applicable", - "body_product": "Blood", + "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, "Cerebrospinal Fluid": { From a23aa7b89180159ff354031546e361bf14a954d5 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 1 Apr 2024 14:41:48 +0200 Subject: [PATCH 1274/1454] Changed collecting id for sequencing sample id --- relecov_tools/json_validation.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 80891f17..3f289464 100755 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -98,11 +98,17 @@ def validate_instances(self): stderr.print("[blue] VALIDATION SUMMARY") stderr.print("[blue] --------------------") for error_type in errors.keys(): + num_of_errors = str(errors[error_type]) + field_with_error = error_keys[error_type] + log.error( + "%s samples failed validation for %s:\n%s", + num_of_errors, field_with_error, error_type + ) stderr.print( "[red]" - + str(errors[error_type]) + + num_of_errors + " samples failed validation for " - + f"{error_keys[error_type]}:\n" + + f"{field_with_error}:\n" + error_type ) stderr.print("[red] --------------------") @@ -141,7 +147,7 @@ def create_invalid_metadata(self, invalid_json, metadata, out_folder): stderr.print("Start preparation of invalid samples") for row in invalid_json: - sample_list.append(str(row["collecting_lab_sample_id"])) + sample_list.append(str(row["sequencing_sample_id"])) wb = openpyxl.load_workbook(metadata) ws_sheet = wb["METADATA_LAB"] From e72a1b3616a11ff0584346aa3ef71e47c6236731 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 1 Apr 2024 14:36:00 +0200 Subject: [PATCH 1275/1454] Added missing gisaid field in relecov schema --- relecov_tools/schema/relecov_schema.json | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 804a74db..ae7cd7e1 100755 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2694,6 +2694,15 @@ "label": "GISAID Virus Name", "fill_mode": "sample" }, + "gisaid_covv_type": { + "examples": ["betacoronavirus"], + "ontology": "NCIT:C25284", + "type": "string", + "description": "default must remain 'betacoronavirus'", + "clasification": "Database Identifiers", + "label": "GISAID covv type", + "fill_mode": "sample" + }, "ena_analysis_accession": { "examples": [ "" From 1ffa213c4629d6dd10c1ec2e68ef2931239b58e6 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 1 Apr 2024 14:40:25 +0200 Subject: [PATCH 1276/1454] Error fix in postprocessing, included gisaid handling --- relecov_tools/map_schema.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 799e1f1e..326534b2 100755 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -192,10 +192,10 @@ def additional_formating(self, mapped_json_data): formated_data = { x: "--".join( [ - self.json_data[idx][f].split(" [", 1)[0] + self.json_data[idx].get(f, "").split(" [", 1)[0] for f in y if "Not Provided" - not in self.json_data[idx][f].split(" [", 1)[0] + not in self.json_data[idx].get(f, "").split(" [", 1)[0] ] ) for x, y in additional_data.items() @@ -203,11 +203,16 @@ def additional_formating(self, mapped_json_data): if "fastq_filepath" in key: formated_data[key] = formated_data[key].replace("--", "/") mapped_json_data[idx][key] = formated_data[key] + elif self.destination_schema == "GISAID": + for idx in range(len(self.json_data)): + mapped_json_data[idx]["covv_type"] = "betacoronavirus" """ This is a temporal solution for library_strategy. Once the values are also mapped by the ontology (not only the fields) this should not be necessary """ for sample in mapped_json_data: + if not sample.get("library_strategy"): + continue sample["library_strategy"] = sample["library_strategy"].strip(" strategy") return mapped_json_data From 8feb07428503145f67fc936420037a6f0b3784cd Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 4 Apr 2024 09:32:27 +0200 Subject: [PATCH 1277/1454] Included scripts and datasets for testing --- .../data/map_validate/metadata_lab_test.xlsx | Bin 0 -> 34210 bytes .../processed_metadata_lab_test.json | 517 ++++++++++++++++++ .../read_lab_metadata/metadata_lab_test.xlsx | Bin 0 -> 34210 bytes .../read_lab_metadata/samples_data_test.json | 79 +++ tests/data/sftp_handle/configuration.json | 496 +++++++++++++++++ .../sftp_handle/datatest1/SAMPLE1_R1.fastq.gz | Bin 0 -> 210 bytes .../sftp_handle/datatest1/SAMPLE1_R2.fastq.gz | Bin 0 -> 208 bytes .../sftp_handle/datatest1/SAMPLE3_R1.fastq.gz | Bin 0 -> 237 bytes .../sftp_handle/datatest1/SAMPLE3_R2.fastq.gz | Bin 0 -> 237 bytes .../sftp_handle/datatest1/SAMPLE4_R1.fastq.gz | Bin 0 -> 180 bytes .../sftp_handle/datatest1/SAMPLE4_R2.fastq.gz | Bin 0 -> 175 bytes .../sftp_handle/datatest1/SAMPLE5_R1.fastq.gz | Bin 0 -> 214 bytes .../sftp_handle/datatest1/SAMPLE5_R2.fastq.gz | Bin 0 -> 214 bytes .../sftp_handle/datatest1/SAMPLE6_R1.fastq.gz | Bin 0 -> 202 bytes .../sftp_handle/datatest1/SAMPLE6_R2.fastq.gz | Bin 0 -> 198 bytes .../sftp_handle/datatest1/Singlesamp.fastq.gz | Bin 0 -> 238 bytes tests/data/sftp_handle/datatest1/md5sum.txt | 12 + .../datatest1/metadata_validation_test.xlsx | Bin 0 -> 94049 bytes .../datatest2/SAMPLE20_TEST2_R1.fastq.gz | Bin 0 -> 416 bytes .../datatest2/SAMPLE20_TEST2_R2.fastq.gz | Bin 0 -> 401 bytes .../datatest2/SAMPLE21_TEST2_R1.fastq.gz | Bin 0 -> 219 bytes .../datatest2/SAMPLE21_TEST2_R2.fastq.gz | Bin 0 -> 220 bytes .../datatest2/SAMPLE22_TEST2_R1.fastq.gz | Bin 0 -> 193 bytes .../datatest2/SAMPLE22_TEST2_R2.fastq.gz | Bin 0 -> 198 bytes .../datatest2/SAMPLE23_TEST2_R1.fastq | 8 + .../datatest2/SAMPLE23_TEST2_R2.fastq | 8 + .../datatest2/SAMPLE24_TEST2_R1.fastq.gz | Bin 0 -> 204 bytes .../datatest2/SAMPLE24_TEST2_R2.fastq.gz | Bin 0 -> 212 bytes .../datatest2/SAMPLE25_TEST2_R1.fastq.gz | Bin 0 -> 234 bytes tests/data/sftp_handle/datatest2/md5sum.csv | 18 + .../test2_metadata_template_v2.0.1.xlsx | Bin 0 -> 94749 bytes .../empty_test/SAMPLE20_TEST2_R1.fastq.gz | Bin 0 -> 416 bytes .../empty_test/SAMPLE20_TEST2_R2.fastq.gz | Bin 0 -> 401 bytes .../empty_test/SAMPLE21_TEST2_R1.fastq.gz | Bin 0 -> 44 bytes .../empty_test/SAMPLE21_TEST2_R2.fastq.gz | Bin 0 -> 44 bytes tests/test_read_lab_metadata.py | 33 ++ tests/test_sftp_handle.py | 88 +++ 37 files changed, 1259 insertions(+) create mode 100755 tests/data/map_validate/metadata_lab_test.xlsx create mode 100755 tests/data/map_validate/processed_metadata_lab_test.json create mode 100755 tests/data/read_lab_metadata/metadata_lab_test.xlsx create mode 100755 tests/data/read_lab_metadata/samples_data_test.json create mode 100755 tests/data/sftp_handle/configuration.json create mode 100644 tests/data/sftp_handle/datatest1/SAMPLE1_R1.fastq.gz create mode 100644 tests/data/sftp_handle/datatest1/SAMPLE1_R2.fastq.gz create mode 100644 tests/data/sftp_handle/datatest1/SAMPLE3_R1.fastq.gz create mode 100644 tests/data/sftp_handle/datatest1/SAMPLE3_R2.fastq.gz create mode 100644 tests/data/sftp_handle/datatest1/SAMPLE4_R1.fastq.gz create mode 100644 tests/data/sftp_handle/datatest1/SAMPLE4_R2.fastq.gz create mode 100644 tests/data/sftp_handle/datatest1/SAMPLE5_R1.fastq.gz create mode 100644 tests/data/sftp_handle/datatest1/SAMPLE5_R2.fastq.gz create mode 100644 tests/data/sftp_handle/datatest1/SAMPLE6_R1.fastq.gz create mode 100644 tests/data/sftp_handle/datatest1/SAMPLE6_R2.fastq.gz create mode 100644 tests/data/sftp_handle/datatest1/Singlesamp.fastq.gz create mode 100755 tests/data/sftp_handle/datatest1/md5sum.txt create mode 100755 tests/data/sftp_handle/datatest1/metadata_validation_test.xlsx create mode 100644 tests/data/sftp_handle/datatest2/SAMPLE20_TEST2_R1.fastq.gz create mode 100644 tests/data/sftp_handle/datatest2/SAMPLE20_TEST2_R2.fastq.gz create mode 100644 tests/data/sftp_handle/datatest2/SAMPLE21_TEST2_R1.fastq.gz create mode 100644 tests/data/sftp_handle/datatest2/SAMPLE21_TEST2_R2.fastq.gz create mode 100644 tests/data/sftp_handle/datatest2/SAMPLE22_TEST2_R1.fastq.gz create mode 100644 tests/data/sftp_handle/datatest2/SAMPLE22_TEST2_R2.fastq.gz create mode 100644 tests/data/sftp_handle/datatest2/SAMPLE23_TEST2_R1.fastq create mode 100644 tests/data/sftp_handle/datatest2/SAMPLE23_TEST2_R2.fastq create mode 100644 tests/data/sftp_handle/datatest2/SAMPLE24_TEST2_R1.fastq.gz create mode 100644 tests/data/sftp_handle/datatest2/SAMPLE24_TEST2_R2.fastq.gz create mode 100644 tests/data/sftp_handle/datatest2/SAMPLE25_TEST2_R1.fastq.gz create mode 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"r1_fastq_filepath": "tests/20240320", + "r2_fastq_filepath": "tests/20240320", + "sequence_file_R1_fastq": "SAMPLE21_TEST2_R1.fastq.gz", + "sequence_file_R2_fastq": "SAMPLE21_TEST2_R2.fastq.gz" + }, + "35184262": { + "fastq_r1_md5": "99ab59db60c96551ecd9067000cdbb2a", + "fastq_r2_md5": "c58920e0893dd51c25ab4ea0a1aee5c5", + "r1_fastq_filepath": "tests/20240320", + "r2_fastq_filepath": "tests/20240320", + "sequence_file_R1_fastq": "SAMPLE22_TEST2_R1.fastq.gz", + "sequence_file_R2_fastq": "SAMPLE22_TEST2_R2.fastq.gz" + }, + "37145959EXT": { + "fastq_r1_md5": "dc340063a9f08257157ef4ead6c5b34c", + "fastq_r2_md5": "9a6eaf7e8f93963510cf756ba90ce524", + "r1_fastq_filepath": "tests/20240320", + "r2_fastq_filepath": "tests/20240320", + "sequence_file_R1_fastq": "SAMPLE23_TEST2_R1.fastq.gz", + "sequence_file_R2_fastq": "SAMPLE23_TEST2_R2.fastq.gz" + }, + "39156982": { + "fastq_r1_md5": "81b05b2b94880749efc19af6ffeac7a6", + "fastq_r2_md5": "b2dcec994291f6b507ec06afe646069d", + "r1_fastq_filepath": "tests/20240320", + "r2_fastq_filepath": "tests/20240320", + "sequence_file_R1_fastq": "SAMPLE24_TEST2_R1.fastq.gz", + "sequence_file_R2_fastq": "SAMPLE24_TEST2_R2.fastq.gz" + }, + "SINGLEID": { + "fastq_r1_md5": "112d5d2ff3845236576732f7c7dc8b06", + "r1_fastq_filepath": "tests/20240320", + "sequence_file_R1_fastq": "Singlesamp.fastq.gz" + }, + "id1000": { + "fastq_r1_md5": "c1551cdf3d5e9849b80a082051907a72", + "fastq_r2_md5": "449407f85d7ed4388b7d8a51e28d97a8", + "r1_fastq_filepath": "tests/20240320", + "r2_fastq_filepath": "tests/20240320", + "sequence_file_R1_fastq": "SAMPLE1_R1.fastq.gz", + "sequence_file_R2_fastq": "SAMPLE1_R2.fastq.gz" + }, + "id4000_BAD": { + "fastq_r1_md5": "5d838ce4a93bcf12d3031a5f9ffd4acf", + "fastq_r2_md5": "0a9b0a590b4773e5e4c90c391979a685", + "r1_fastq_filepath": "tests/20240320", + "r2_fastq_filepath": "tests/20240320", + "sequence_file_R1_fastq": "SAMPLE4_R1.fastq.gz", + "sequence_file_R2_fastq": "SAMPLE4_R2.fastq.gz" + }, + "id5000GOOD": { + "fastq_r1_md5": "d04d32f14ca56f968d07f61d68598639", + "fastq_r2_md5": "66a057995ac925e3203ff1afdd5770ec", + "r1_fastq_filepath": "tests/20240320", + "r2_fastq_filepath": "tests/20240320", + "sequence_file_R1_fastq": "SAMPLE5_R1.fastq.gz", + "sequence_file_R2_fastq": "SAMPLE5_R2.fastq.gz" + }, + "id6000GOOD": { + "fastq_r1_md5": "0d55b49614d1c38582b69ccded1b22c4", + "fastq_r2_md5": "50afab6751cce654b973bb336cf3b3eb", + "r1_fastq_filepath": "tests/20240320", + "r2_fastq_filepath": "tests/20240320", + "sequence_file_R1_fastq": "SAMPLE6_R1.fastq.gz", + "sequence_file_R2_fastq": "SAMPLE6_R2.fastq.gz" + } +} \ No newline at end of file diff --git a/tests/data/sftp_handle/configuration.json b/tests/data/sftp_handle/configuration.json new file mode 100755 index 00000000..33bd9cb6 --- /dev/null +++ b/tests/data/sftp_handle/configuration.json @@ -0,0 +1,496 @@ +{ + "lab_metadata": { + "fixed_fields": { + "host_disease": "COVID-19", + "tax_id": "2697049", + "organism": "Severe acute respiratory syndrome coronavirus 2", + "study_type": "Whole Genome Sequencing", + "collector_name": "Not Provided" + }, + "metadata_lab_heading": [ + "Public Health sample id (SIVIES)", + "Sample ID given by originating laboratory", + "Sample ID given by the submitting laboratory", + "Sample ID given in the microbiology lab", + "Sample ID given if multiple rna-extraction or passages", + "Sample ID given for sequencing", + "ENA Sample ID", + "GISAID Virus Name", + "GISAID id", + "Originating Laboratory", + "Submitting Institution", + "Sequencing Institution", + "Sample Collection Date", + "Sample Received Date", + "Purpose of sampling", + "Biological Sample Storage Condition", + "Specimen source", + "Environmental Material", + "Environmental System", + "Collection Device", + "Host", + "Host Age", + "Host Gender", + "Sequencing Date", + "Nucleic acid extraction protocol", + "Commercial All-in-one library kit", + "Library Preparation Kit", + "Enrichment Protocol", + "If Enrichment Protocol Is Other, Specify", + "Enrichment panel/assay", + "If Enrichment panel/assay Is Other, Specify", + "Enrichment panel/assay version", + "Number Of Samples In Run", + "Runid", + "Sequencing Instrument Model", + "Flowcell Kit", + "Source material", + "Capture method", + "Sequencing technique", + "Library Layout", + "Gene Name 1", + "Diagnostic Pcr Ct Value 1", + "Gene Name 2", + "Diagnostic Pcr Ct Value-2", + "Authors", + "Sequence file R1 fastq", + "Sequence file R2 fastq" + ], + "lab_metadata_req_json": { + "laboratory_data": { + "file": "laboratory_address.json", + "map_field": "collecting_institution", + "adding_fields": [ + "collecting_institution_address", + "collecting_institution_email", + "geo_loc_state", + "geo_loc_region", + "geo_loc_city", + "geo_loc_country" + ] + }, + "geo_location_data": { + "file": "geo_loc_cities.json", + "map_field": "geo_loc_city", + "adding_fields": [ + "geo_loc_latitude", + "geo_loc_longitude" + ] + }, + "submitting_data": { + "file": "laboratory_address.json", + "map_field": "collecting_institution", + "adding_fields": [ + "submitting_institution", + "submitting_institution_address", + "submitting_institution_email" + ] + }, + "specimen_source_splitting": { + "file": "anatomical_material_collection_method.json", + "map_field": "specimen_source", + "adding_fields": [ + "anatomical_material", + "anatomical_part", + "body_product", + "collection_method" + ] + } + }, + "required_post_processing": { + "host_common_name": { + "Human": "host_scientific_name::Homo sapiens" + }, + "sequencing_instrument_model": { + "Illumina": "sequencing_instrument_platform::Illumina", + "PacBio": "sequencing_instrument_platform::PacBio", + "Ion Torrent": "sequencing_instrument_platform::Ion Torrent", + "Oxford Nanopore": "sequencing_instrument_platform::Oxford Nanopore" + } + }, + "required_copy_from_other_field": { + "isolate_sample_id": "sequencing_sample_id" + }, + "samples_json_fields": [ + "fastq_r1_md5", + "fastq_r2_md5", + "sequence_file_R1_fastq", + "sequence_file_R2_fastq", + "r1_fastq_filepath", + "r2_fastq_filepath" + ] + }, + "long_table_heading": [ + "SAMPLE", + "CHROM", + "POS", + "REF", + "ALT", + "FILTER", + "DP", + "REF_DP", + "ALT_DP", + "AF", + "GENE", + "EFFECT", + "HGVS_C", + "HGVS_P", + "HGVS_P_1LETTER", + "CALLER", + "LINEAGE" + ], + "long_table_parse_aux": { + "Chromosome": "CHROM", + "Variant": { + "pos": "POS", + "alt": "ALT", + "ref": "REF" + }, + "Filter": "FILTER", + "VariantInSample": { + "dp": "DP", + "ref_dp": "REF_DP", + "alt_dp": "ALT_DP", + "af": "AF" + }, + "Effect": "EFFECT", + "VariantAnnotation": { + "hgvs_c": "HGVS_C", + "hgvs_p": "HGVS_P", + "hgvs_p_1_letter": "HGVS_P_1LETTER" + } + }, + "gisaid_csv_headers": [ + "submitter", + "covv_virus_name", + "covv_type", + "covv_passage", + "covv_collection_date", + "covv_location", + "covv_add_location", + "covv_host", + "covv_add_host_info", + "covv_sampling_strategy", + "covv_gender", + "covv_patient_age", + "covv_patient_status", + "covv_specimen", + "covv_outbreak", + "covv_last_vaccinated", + "covv_treatment", + "covv_seq_technology", + "covv_assembly_method", + "covv_coverage", + "covv_orig_lab", + "covv_orig_lab_addr", + "covv_provider_sample_id", + "covv_subm_lab", + "covv_subm_lab_addr", + "covv_subm_sample_id", + "covv_authors" + ], + "json_schemas": { + "relecov_schema": "relecov_schema.json", + "ena_schema": "ena_schema.json", + "gisaid_schema": "gisaid_schema.json" + }, + "institution_mapping_file": { + "ISCIII": "ISCIII.json", + "HUGTiP": "HUGTiP.json" + }, + "sftp_handle": { + "sftp_connection": { + "sftp_server": "sftprelecov.isciii.es", + "sftp_port": "22" + }, + "metadata_processing": { + "header_flag": "CAMPO", + "excel_sheet": "METADATA_LAB" + }, + "abort_if_md5_mismatch": "False", + "platform_storage_folder": "/tmp/relecov", + "allowed_file_extensions": [ + ".fastq.gz", + ".fastq", + ".fq", + ".fq.gz", + ".fasta", + ".fasta.gz" + ], + "allowed_download_options": [ + "download_only", + "download_clean", + "delete_only" + ], + "skip_when_found": [ + "#", + "Hash", + "Path" + ] + }, + "GISAID_configuration": { + "submitter": "GISAID_ID" + }, + "external_url": { + "iskylims": { + "server": "http://relecov-iskylims.isciiides.es", + "url": "/wetlab/api/", + "store_samples": "createSampleData", + "url_project_fields": "sampleProjectFields", + "url_sample_fields": "sampleFields", + "param_sample_project": "project", + "project_name": "relecov", + "token": "" + }, + "relecov": { + "server": "http://relecov-platform.isciiides.es", + "url": "/api/", + "store_samples": "createSampleData", + "bioinfodata": "createBioinfoData", + "variantdata": "createVariantData", + "sftp_info": "sftpInfo", + "token": "" + } + }, + "iskylims_fixed_values": { + "patientCore": "", + "sampleProject": "Relecov", + "onlyRecorded": "Yes", + "sampleLocation": "Not defined" + }, + "relecov_sample_metadata": [ + "authors", + "collecting_institution", + "collecting_lab_sample_id", + "ena_broker_name", + "ena_sample_accession", + "gisaid_accession_id", + "gisaid_virus_name", + "microbiology_lab_sample_id", + "r1_fastq_filepath", + "r2_fastq_filepath", + "schema_name", + "schema_version", + "sequencing_date", + "sequence_file_R1_md5", + "sequence_file_R2_md5", + "sequence_file_R1_fastq", + "sequence_file_R2_fastq", + "sequencing_sample_id", + "submitting_lab_sample_id" + ], + "bioinfo_analysis": { + "fixed_values": { + "assembly": "Not Provided [GENEPIO:0001668]", + "assembly_params": "Not Provided [GENEPIO:0001668]", + "bioinformatics_protocol_software_name": "nf-core/viralrecon", + "commercial_open_source_both": "Open Source", + "consensus_params": "-p vcf -f", + "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", + "dehosting_method_software_name": "KRAKEN2_KRAKEN2", + "depth_of_coverage_threshold": ">10x", + "if_assembly_other": "Not Provided [GENEPIO:0001668]", + "if_bioinformatic_protocol_is_other_specify": "Not Provided [GENEPIO:0001668]", + "if_consensus_other": "Not Provided [GENEPIO:0001668]", + "if_lineage_identification_other": "Not Provided [GENEPIO:0001668]", + "if_mapping_other": "Not Provided [GENEPIO:0001668]", + "if_preprocessing_other": "Not Provided [GENEPIO:0001668]", + "lineage_analysis_software_name": "pangolin", + "mapping_params": "--seed 1", + "mapping_software_name": "BOWTIE2_ALIGN", + "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", + "preprocessing_software_name": "FASTP", + "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", + "variant_calling_software_name": "IVAR_VARIANTS" + }, + "feed_empty_fields":{ + "lineage_analysis_date": "Not Provided [GENEPIO:0001668]", + "consensus_sequence_name": "Not Provided [GENEPIO:0001668]" + }, + "required_file": { + "variants_metrics": "summary_variants_metrics_mqc.csv", + "versions": "software_versions.yml", + "mapping_stats": "mapping_illumina_stats.tab" + }, + "mapping_consensus": [ + "consensus_genome_length", + "consensus_sequence_filename", + "consensus_sequence_filepath", + "consensus_sequence_md5", + "number_of_base_pairs_sequenced" + ], + "mapping_pangolin": { + "variant_name": "scorpio_call", + "lineage_name": "lineage", + "lineage_algorithm_software_version": "version", + "lineage_analysis_software_version": "pangolin_version", + "lineage_analysis_scorpio_version": "scorpio_version", + "lineage_analysis_constellation_version": "constellation_version" + }, + "mapping_stats": { + "analysis_date": "analysis_date", + "depth_of_coverage_value": "medianDPcoveragevirus", + "number_of_variants_in_consensus": "Variantsinconsensusx10", + "number_of_variants_with_effect": "MissenseVariants", + "per_genome_greater_10x": "Coverage>10x(%)", + "per_Ns": "%Ns10x", + "per_reads_host": "%readshost", + "per_reads_virus": "%readsvirus", + "per_unmapped": "%unmapedreads", + "qc_filtered": "totalreads", + "reference_genome_accession": "Virussequence", + "read_length": "read_length" + }, + "mapping_variant_metrics": { + "ns_per_100_kbp": "# Ns per 100kb consensus" + }, + "mapping_version": { + "bioinformatics_protocol_software_version": { + "Workflow": "nf-core/viralrecon" + }, + "consensus_sequence_software_version": { + "BCFTOOLS_CONSENSUS": "bcftools" + }, + "dehosting_method_software_version": { + "KRAKEN2_KRAKEN2": "kraken2" + }, + "mapping_software_version": { + "BOWTIE2_ALIGN": "bowtie2" + }, + "preprocessing_software_version": { + "FASTP": "fastp" + }, + "variant_calling_software_version": { + "IVAR_VARIANTS": "ivar" + } + }, + "required_fields_from_lab_json": { + "read_length": "number_of_base_pairs_sequenced", + "schema_name": "schema_name", + "schema_version": "schema_version", + "sequencing_sample_id": "sequencing_sample_id" + } + }, + "ENA_fields": { + "ENA_configuration": { + "study_alias": "RELECOV", + "design_description": "Design Description", + "experiment_title": "Project for ENA submission RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "Whole Genome Sequencing", + "study_id": "ERP137164", + "ena_broker_name": "Instituto de Salud Carlos III" + }, + "checklist": "ERC000033", + "templates_path": "", + "tool": { + "tool_name": "ena-upload-cli", + "tool_version": "0.5.3" + }, + "df_study_fields": [ + "study_alias", + "study_title", + "study_type", + "study_abstract" + ], + "df_sample_fields": [ + "sample_alias", + "sample_title", + "collection date", + "geographic location (country and/or sea)", + "sample_description", + "host common name", + "host scientific name", + "host sex", + "scientific_name", + "collector name", + "collecting institution", + "address", + "isolate", + "host subject id", + "host health state", + "authors", + "taxon_id" + ], + "df_run_fields": [ + "run_alias", + "experiment_alias", + "file_name", + "file_format", + "file_checksum", + "collecting institution" + ], + "df_experiment_fields": [ + "experiment_alias", + "experiment_title", + "sample_alias", + "study_alias", + "design_description", + "library_name", + "library_strategy", + "library_source", + "library_selection", + "library_layout", + "library_construction_protocol", + "insert_size", + "platform", + "instrument_model", + "collecting institution" + ], + "ena_fixed_fields": { + "broker_name": "Instituto de Salud Carlos III", + "file_format": "FASTQ", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_abstract": "RELECOV is a Spanish Network for genomics surveillance", + "insert_size": "0" + }, + "accession_fields": [ + "ena_study_accession", + "ena_sample_accession", + "ena_experiment_accession", + "ena_run_accession" + ], + "additional_formating": { + "sample_description": [ + "host_common_name", + "anatomical_part", + "collection_method" + ], + "design_description": [ + "library_layout", + 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zydEZpoU|oU`Fu_yh?BS2Fv_-RsL+TLCx(ge7&t5=8sah3hYXJBus|pT9HS67Vv<#3 vAgj^T5xT?7o#ndM9jhJZ$`PE(fzpDrD8-NJ>gQSci){G^(sqgC Date: Thu, 4 Apr 2024 09:33:14 +0200 Subject: [PATCH 1278/1454] Created actions tests for download, read-lab, map and validation modules --- .github/workflows/test_modules.yml | 108 +++++++++++++++++++++++++++++ 1 file changed, 108 insertions(+) create mode 100755 .github/workflows/test_modules.yml diff --git a/.github/workflows/test_modules.yml b/.github/workflows/test_modules.yml new file mode 100755 index 00000000..a21bbcac --- /dev/null +++ b/.github/workflows/test_modules.yml @@ -0,0 +1,108 @@ +name: Python Package using Conda + +on: + push: + branches: [main, develop] + pull_request: + branches: [main, develop] + +env: + TEST_USER: ${{ secrets.TEST_USER }} + TEST_PASSWORD: ${{ secrets.TEST_PASSWORD }} + TEST_PORT: ${{ secrets.TEST_PORT }} + CONF_FILE: ${{ github.workspace }}/relecov_tools/conf/configuration.json + +jobs: + test_sftp_handle: + runs-on: ubuntu-latest + strategy: + max-parallel: 1 + matrix: + download_options: ["download_only", "download_clean", "delete_only"] + target_folders: ["", "-t COD-test-1"] + + steps: + - name: Set up Python 3.9.16 + uses: actions/setup-python@v3 + with: + python-version: '3.9.16' + + - name: Checkout code + uses: actions/checkout@v3 + with: + path: . + + - name: Install package and dependencies + run: | + pip install -r requirements.txt + pip install . + + - name: Run sftp_handle tests + run: | + python3 tests/test_sftp_handle.py --download_option ${{ matrix.download_options }} ${{ matrix.target_folders }} + env: + OUTPUT_LOCATION: ${{ github.workspace }}/tests/ + + test_map: + runs-on: ubuntu-latest + strategy: + max-parallel: 2 + matrix: + map_args: ["-d 'ENA' -f relecov_tools/schema/ena_schema.json", "-d 'GISAID' -f relecov_tools/schema/gisaid_schema.json"] + steps: + - name: Set up Python 3.9.16 + uses: actions/setup-python@v3 + with: + python-version: '3.9.16' + - name: Checkout code + uses: actions/checkout@v3 + with: + path: . + - name: Install package and dependencies + run: | + pip install -r requirements.txt + pip install . + - name: Run each module tests + run: | + relecov-tools map -j tests/data/map_validate/processed_metadata_lab_test.json -p relecov_tools/schema/relecov_schema.json ${{ matrix.map_args }} -o . + env: + OUTPUT_LOCATION: ${{ github.workspace }}/tests/ + - name: Upload output file + uses: actions/upload-artifact@v2 + with: + name: test-output + path: output.txt + + test_all_modules: + runs-on: ubuntu-latest + strategy: + max-parallel: 3 + matrix: + modules: ["read-lab-metadata", "read-bioinfo-metadata", "validate"] + steps: + - name: Set up Python 3.9.16 + uses: actions/setup-python@v3 + with: + python-version: '3.9.16' + - name: Checkout code + uses: actions/checkout@v3 + with: + path: . + - name: Install package and dependencies + run: | + pip install -r requirements.txt + pip install . + - name: Run each module tests + run: | + if [ "${{ matrix.modules }}" == "read-lab-metadata" ]; then + relecov-tools read-lab-metadata -m tests/data/read_lab_metadata/metadata_lab_test.xlsx -s tests/data/read_lab_metadata/samples_data_test.json -o $OUTPUT_LOCATION + elif [ "${{ matrix.modules }}" == "validate" ]; then + relecov-tools validate -j tests/data/map_validate/processed_metadata_lab_test.json -s relecov_tools/schema/relecov_schema.json -m tests/data/map_validate/metadata_lab_test.xlsx -o $OUTPUT_LOCATION + fi + env: + OUTPUT_LOCATION: ${{ github.workspace }}/tests/ + - name: Upload output file + uses: actions/upload-artifact@v2 + with: + name: test-output + path: output.txt \ No newline at end of file From c71f7ce0674a4caa3513d87abad0067df00782ca Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 4 Apr 2024 10:37:39 +0200 Subject: [PATCH 1279/1454] Fixed json_validation for testing. Linting --- relecov_tools/json_validation.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 3f289464..94ccec00 100755 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -102,7 +102,9 @@ def validate_instances(self): field_with_error = error_keys[error_type] log.error( "%s samples failed validation for %s:\n%s", - num_of_errors, field_with_error, error_type + num_of_errors, + field_with_error, + error_type, ) stderr.print( "[red]" From 2b97e79d00f5c04240d978c51b9bfedc5cca2a8f Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 4 Apr 2024 11:08:18 +0200 Subject: [PATCH 1280/1454] Removed unnecessary script to test read-lab-metadata --- tests/test_read_lab_metadata.py | 33 --------------------------------- 1 file changed, 33 deletions(-) delete mode 100755 tests/test_read_lab_metadata.py diff --git a/tests/test_read_lab_metadata.py b/tests/test_read_lab_metadata.py deleted file mode 100755 index a38888d6..00000000 --- a/tests/test_read_lab_metadata.py +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env python -import json -import glob -import argparse -from relecov_tools.read_lab_metadata import RelecovMetadata - - -def main(): - parser = argparse.ArgumentParser() - parser.add_argument( - "-m", - "--metadata_file", - type=str, - help="Metadata file", - ) - parser.add_argument("-s", "--sample_list_file", type=str, help="Samples data file") - args = parser.parse_args() - metadata_file = args.metadata_file - sample_list_file = args.sample_list_file - exec_read_lab = RelecovMetadata( - metadata_file=metadata_file, - sample_list_file=sample_list_file, - output_folder="tests/output/", - ) - exec_read_lab.create_metadata_json() - assert_results() - - -def assert_results(): - processed_metadata = glob.glob("tests/output/processed_metadata_lab*.json") - processed_metadata_content = json.loads(processed_metadata[0]) - orig_processed_content = json.loads("tests/data/processed_metadata.json") - assert processed_metadata_content == orig_processed_content From f45aa7569f8895491fad0ef4a1ccef4e01edc409 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 5 Apr 2024 09:02:11 +0200 Subject: [PATCH 1281/1454] Changed calling method for env variables --- tests/test_sftp_handle.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/test_sftp_handle.py b/tests/test_sftp_handle.py index 552df5ee..1e09a70c 100755 --- a/tests/test_sftp_handle.py +++ b/tests/test_sftp_handle.py @@ -17,10 +17,10 @@ def main(): args = parser.parse_args() val_dict = { - "user": os.getenv("TEST_USER"), - "password": os.getenv("TEST_PASSWORD"), + "user": os.environ["TEST_USER"], + "password": os.environ["TEST_PASSWORD"], "download_option": args.download_option, - "output_location": os.getenv("OUTPUT_LOCATION"), + "output_location": os.environ["OUTPUT_LOCATION"], "target_folders": args.target_folders, } prepare_remote_test(**val_dict) @@ -40,7 +40,7 @@ def prepare_remote_test(**kwargs): target_folders=kwargs["target_folders"], ) print("Openning connection to sftp") - sftp_connection.sftp_port = os.getenv("TEST_PORT") + sftp_connection.sftp_port = os.environ["TEST_PORT"] if not sftp_connection.open_connection(): print("Could not open connection to remote sftp") sys.exit(1) From 430327162d9c3dab13537275300fdb5fed07f291 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 5 Apr 2024 09:10:16 +0200 Subject: [PATCH 1282/1454] Moved global test_modules env variables to sftp_handle job --- .github/workflows/test_modules.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test_modules.yml b/.github/workflows/test_modules.yml index a21bbcac..bad81c38 100755 --- a/.github/workflows/test_modules.yml +++ b/.github/workflows/test_modules.yml @@ -7,9 +7,6 @@ on: branches: [main, develop] env: - TEST_USER: ${{ secrets.TEST_USER }} - TEST_PASSWORD: ${{ secrets.TEST_PASSWORD }} - TEST_PORT: ${{ secrets.TEST_PORT }} CONF_FILE: ${{ github.workspace }}/relecov_tools/conf/configuration.json jobs: @@ -41,6 +38,9 @@ jobs: run: | python3 tests/test_sftp_handle.py --download_option ${{ matrix.download_options }} ${{ matrix.target_folders }} env: + TEST_USER: ${{ secrets.TEST_USER }} + TEST_PASSWORD: ${{ secrets.TEST_PASSWORD }} + TEST_PORT: ${{ secrets.TEST_PORT }} OUTPUT_LOCATION: ${{ github.workspace }}/tests/ test_map: From 4db8f78fb8315ee445c7b27e068f7ce2936d4f0d Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 5 Apr 2024 09:40:55 +0200 Subject: [PATCH 1283/1454] Tests are now performed in every branch --- .github/workflows/test_modules.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test_modules.yml b/.github/workflows/test_modules.yml index bad81c38..c7506ab1 100755 --- a/.github/workflows/test_modules.yml +++ b/.github/workflows/test_modules.yml @@ -2,9 +2,9 @@ name: Python Package using Conda on: push: - branches: [main, develop] + branches: "**" pull_request: - branches: [main, develop] + branches: "**" env: CONF_FILE: ${{ github.workspace }}/relecov_tools/conf/configuration.json From 5b7be27d65a3f59726b69f5f4a99fb27e2301dee Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 5 Apr 2024 10:45:07 +0200 Subject: [PATCH 1284/1454] Changed PR tests to pull_request_target --- .github/workflows/test_modules.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_modules.yml b/.github/workflows/test_modules.yml index c7506ab1..9145c693 100755 --- a/.github/workflows/test_modules.yml +++ b/.github/workflows/test_modules.yml @@ -3,7 +3,7 @@ name: Python Package using Conda on: push: branches: "**" - pull_request: + pull_request_target: branches: "**" env: From ea87a75098bd55f1a90104e5fbabbc41cd67be4a Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 5 Apr 2024 12:49:11 +0200 Subject: [PATCH 1285/1454] Included a test for security checking --- .github/workflows/test_modules.yml | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test_modules.yml b/.github/workflows/test_modules.yml index 9145c693..dd30bf94 100755 --- a/.github/workflows/test_modules.yml +++ b/.github/workflows/test_modules.yml @@ -7,9 +7,24 @@ on: branches: "**" env: - CONF_FILE: ${{ github.workspace }}/relecov_tools/conf/configuration.json + GITHUB_TOKEN: ${{ secrets.TOKEN_ACTIONS }} jobs: + security_check: + - name: Get User Permission + id: checkAccess + uses: actions-cool/check-user-permission@v2 + with: + require: write + username: ${{ github.triggering_actor }} + - name: Check User Permission + if: steps.checkAccess.outputs.require-result == 'false' + run: | + echo "${{ github.triggering_actor }} does not have permissions on this repo." + echo "Current permission level is ${{ steps.checkAccess.outputs.user-permission }}" + echo "Job originally triggered by ${{ github.actor }}" + exit 1 + test_sftp_handle: runs-on: ubuntu-latest strategy: From fe368e33857f8774724a8d4aaede36e38440d8bf Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 5 Apr 2024 12:54:31 +0200 Subject: [PATCH 1286/1454] Included type of pull request to run workflows --- .github/workflows/test_modules.yml | 30 +++++++++++++++++------------- 1 file changed, 17 insertions(+), 13 deletions(-) diff --git a/.github/workflows/test_modules.yml b/.github/workflows/test_modules.yml index dd30bf94..571ce7a1 100755 --- a/.github/workflows/test_modules.yml +++ b/.github/workflows/test_modules.yml @@ -4,6 +4,8 @@ on: push: branches: "**" pull_request_target: + types: + - opened branches: "**" env: @@ -11,19 +13,21 @@ env: jobs: security_check: - - name: Get User Permission - id: checkAccess - uses: actions-cool/check-user-permission@v2 - with: - require: write - username: ${{ github.triggering_actor }} - - name: Check User Permission - if: steps.checkAccess.outputs.require-result == 'false' - run: | - echo "${{ github.triggering_actor }} does not have permissions on this repo." - echo "Current permission level is ${{ steps.checkAccess.outputs.user-permission }}" - echo "Job originally triggered by ${{ github.actor }}" - exit 1 + runs-on: ubuntu-latest + steps: + - name: Get User Permission + id: checkAccess + uses: actions-cool/check-user-permission@v2 + with: + require: write + username: ${{ github.triggering_actor }} + - name: Check User Permission + if: steps.checkAccess.outputs.require-result == 'false' + run: | + echo "${{ github.triggering_actor }} does not have permissions on this repo." + echo "Current permission level is ${{ steps.checkAccess.outputs.user-permission }}" + echo "Job originally triggered by ${{ github.actor }}" + exit 1 test_sftp_handle: runs-on: ubuntu-latest From db8f57becde2dcd58f61fd9e1895b9699541735d Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 5 Apr 2024 16:03:07 +0200 Subject: [PATCH 1287/1454] add new methods to show progress log report --- relecov_tools/read_bioinfo_metadata.py | 383 ++++++++++++++++++------- relecov_tools/utils.py | 26 +- requirements.txt | 1 + 3 files changed, 312 insertions(+), 98 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 425050d7..1a8e0952 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -26,6 +26,7 @@ # TODO: Cosider eval py + func property in json to be able to discriminate between collated files and sample-specific files. # TODO: replace submitting_lab_id by sequencing_sample_id # TODO: improve method's description (specifically 'handling_files') +# TODO: fix/improve stdout missing values / fields not found in mapping-over-table class BioinfoMetadata: def __init__( self, @@ -34,14 +35,24 @@ def __init__( output_folder=None, software='viralrecon', ): + self.log_report = {'error': {}, 'valid': {}, 'warning': {}} if readlabmeta_json_file is None: readlabmeta_json_file = relecov_tools.utils.prompt_path( msg="Select the json file that was created by the read-lab-metadata" ) if not os.path.isfile(readlabmeta_json_file): - log.error("json file %s does not exist ", readlabmeta_json_file) - stderr.print(f"[red] file {readlabmeta_json_file} does not exist") - sys.exit(1) + self.update_log_report( + self.__init__.__name__, + 'error', + f"file {readlabmeta_json_file} does not exist" + ) + sys.exit( + relecov_tools.utils.print_log_report( + self.log_report, + None, + ["error"] + ) + ) self.readlabmeta_json_file = readlabmeta_json_file if input_folder is None: @@ -69,12 +80,18 @@ def __init__( if self.software_name in available_software: self.software_config = bioinfo_config.get_configuration(self.software_name) else: - log.error( - "No configuration available for %s. Currently, the only available software options are: %s", self.software_name, ", ".join(available_software) + self.update_log_report( + self.__init__.__name__, + 'error', + f"No configuration available for '{self.software_name}'. Currently, the only available software options are:: {', '.join(available_software)}" + ) + sys.exit( + relecov_tools.utils.print_log_report( + self.log_report, + None, + ["error"] + ) ) - stderr.print(f"[red]No configuration available for {self.software_name}. Currently, the only available software options are:: {', '.join(available_software)}") - sys.exit(1) - self.log_report = {'error': {}, 'valid': {}, 'warning': {}} def get_available_software(self, json): """Get list of available software in configuration""" @@ -94,92 +111,103 @@ def update_log_report(self, method_name, status, message): def scann_directory(self): """Scanns bioinfo analysis directory and identifies files according to the file name patterns defined in the software configuration json.""" + method_name=f"{self.scann_directory.__name__}" total_files = sum(len(files) for _, _, files in os.walk(self.input_folder)) files_found = {} - for topic_key, topic_details in self.software_config.items(): - if 'fn' not in topic_details: #try/except fn + for topic_key, topic_scope in self.software_config.items(): + if 'fn' not in topic_scope: #try/except fn + self.update_log_report( + method_name, + 'warning', + f"No 'fn' (file pattern) found in '{self.software_name}.{topic_key}'." + ) continue for root, _, files in os.walk(self.input_folder, topdown=True): - matching_files = [os.path.join(root, file_name) for file_name in files if re.search(topic_details['fn'], file_name)] + matching_files = [os.path.join(root, file_name) for file_name in files if re.search(topic_scope['fn'], file_name)] if len(matching_files) >= 1: files_found[topic_key] = matching_files + if len(files_found) < 1: self.update_log_report( - self.scann_directory.__name__, + method_name, 'error', - f"No files found in {self.input_folder}" + f"No files found in '{self.input_folder}' according to '{os.path.basename(self.bioinfo_json_file)}' file name patterns." ) - log.error( - "\tNo files found in %s according to %s file name patterns..", - self.input_folder, - os.path.basename(self.bioinfo_json_file) + sys.exit( + relecov_tools.utils.print_log_report( + self.log_report, + method_name, + ["error"] + ) ) - stderr.print(f"\t[red]No files found in {self.input_folder} according to {os.path.basename(self.bioinfo_json_file)} file name patterns.") - sys.exit(1) else: self.update_log_report( self.scann_directory.__name__, 'valid', - "Scannig process succeed" + f"Scannig process succeed. Scanned {total_files} files." ) - stderr.print(f"\t[green]Scannig process succeed (total scanned files: {total_files}).") + relecov_tools.utils.print_log_report( + self.log_report, + method_name, + ['valid','warning'] + ) + return files_found def validate_software_mandatory_files(self, files_dict): + method_name=f"self.validate_software_mandatory_files.__name__" missing_required = [] for key in self.software_config: if self.software_config[key].get('required') is True: try: files_dict[key] - self.update_log_report( - self.validate_software_mandatory_files.__name__, - 'valid', - f"Found {self.software_name}.{key}" - ) except KeyError: missing_required.append(key) - self.update_log_report( - self.validate_software_mandatory_files.__name__, - 'error', - f"Missing '{files_dict[key]['fn']}'" - ) + continue else: continue if len(missing_required) >= 1: - log.error("\tMissing required files:") - stderr.print("[red]\tMissing required files:") - for i in missing_required: - log.error("\t- %s", i) - stderr.print(f"[red]\t- {i} (file name expected pattern '{files_dict[i]['fn']}')") - sys.exit(1) + self.update_log_report( + method_name, + 'error', + f"Missing mandatory files in {self.software_name}.{key}:{', '.join(missing_required)}" + ) + sys.exit( + relecov_tools.utils.print_log_report( + self.log_report, + method_name, + ["error"] + ) + ) else: - stderr.print("[green]\tValidation passed.") + self.update_log_report( + method_name, + 'valid', + "Successfull validation of mandatory files." + ) return - # TODO: ADD LOG REPORT def add_bioinfo_results_metadata(self, files_dict, j_data): """ Adds metadata from bioinformatics results to j_data. 1. Handles metadata in bioinformatic files found 2. Mapping handled bioinfo metadata into j_data. - """ + """ + method_name=f"{self.add_bioinfo_results_metadata.__name__}" for key in self.software_config.keys(): + self.current_config_key = key # This skip files that will be parsed with other methods if key == 'workflow_summary' or key == "fixed_values": continue try: files_dict[key] - self.update_log_report( - self.add_bioinfo_results_metadata.__name__, - 'valid', - f"Start processing '{self.software_name}.{key}'" - ) + stderr.print(f"[blue]Start processing {self.software_name}.{key}") except KeyError: self.update_log_report( - self.add_bioinfo_results_metadata.__name__, + method_name, 'warning', f"No file path found for '{self.software_name}.{key}'" ) @@ -188,23 +216,32 @@ def add_bioinfo_results_metadata(self, files_dict, j_data): # Handling files data_to_map = self.handling_files(files_dict[key], key) - # Adding data to j_data + # Mapping data to j_data if data_to_map: j_data_mapped = self.mapping_over_table( - j_data, - data_to_map, - self.software_config[key]['content'], - files_dict[key] + j_data=j_data, + map_data=data_to_map, + mapping_fields=self.software_config[key]['content'], + table_name=files_dict[key] ) else: + self.update_log_report( + method_name, + 'warning', + f"No metadata generated while processing '{self.software_name}.{key}'" + ) continue + relecov_tools.utils.print_log_report( + self.log_report, + method_name, + ['valid','waring'] + ) return j_data_mapped - # TODO: Add log report(recover file format parsing errors) - # TODO: add better stdout/err to show which method is being called. def handling_files(self, file_list, file_key): """Handles different file formats (sourced from ./metadata_homogenizer.py) """ + method_name=f"{self.add_bioinfo_results_metadata.__name__}:{self.handling_files.__name__}" file_name = self.software_config[file_key].get('fn') file_extension = os.path.splitext(file_name)[1] @@ -214,6 +251,11 @@ def handling_files(self, file_list, file_key): sample_idx_possition = self.software_config[file_key]['sample_col_idx']-1 except KeyError: sample_idx_possition = None + self.update_log_report( + method_name, + 'warning', + f"No sample-index-column defined in '{self.software_name}.{file_key}'. Using default instead." + ) # Parsing files func_name = self.software_config[file_key]["function"] @@ -232,24 +274,41 @@ def handling_files(self, file_list, file_key): key_position=sample_idx_possition ) else: - stderr.print(f"[red]Unrecognized defined file name extension {file_extension} in {file_name}") - sys.exit() + self.update_log_report( + method_name, + 'error', + f"Unrecognized defined file name extension '{file_extension}' in '{file_name}'." + ) + sys.exit( + relecov_tools.utils.print_log_report( + self.log_report, + None, + ["error"] + ) + ) else: try: - # TODO: ADD stdout to identify which data is being added. # Attempt to get the method by name method_to_call = getattr(self, func_name) data = method_to_call(file_list) except AttributeError as e: - if "not found" in str(e): - stderr.print(f"[red]Function '{func_name}' not found in class.") - return None + self.update_log_report( + self.add_bioinfo_results_metadata.__name__, + 'error', + f"Error occurred while parsing '{func_name}': {e}." + ) + sys.exit( + relecov_tools.utils.print_log_report( + self.log_report, + None, + sections=["error"] + ) + ) return data - - # TODO: add log report def get_multiqc_software_versions(self, file_list, j_data): """Reads html file, finds table containing programs info, and map it to j_data""" + method_name=f"{self.get_multiqc_software_versions.__name__}" # Handle multiqc_report.html f_path = file_list[0] program_versions = {} @@ -270,15 +329,45 @@ def get_multiqc_software_versions(self, file_list, j_data): version = columns[2].text.strip() program_versions[program_name] = version else: - stderr.print(f"[red] HTML entry error in {columns}. HTML table expected format should be \n Process Name\n\n Software \n.") + self.update_log_report( + method_name, + 'error', + f"HTML entry error in {columns}. HTML table expected format should be \n Process Name\n\n Software \n." + ) + sys.exit( + relecov_tools.utils.print_log_report( + self.log_report, + method_name, + ["error"] + ) + ) else: - stderr.print(f"[red] Missing table containing software versions in file {f_path}.") - sys.exit(1) + self.update_log_report( + method_name, + 'error', + f"Unable to locate the table containing software versions in file {f_path} under div section {div_id}." + ) + sys.exit( + relecov_tools.utils.print_log_report( + self.log_report, + method_name, + ["error"] + ) + ) else: - log.error(f"Required div section 'mqc-module-section-software_versions' not found in file {f_path}.") - stderr.print(f"[red] No div section 'mqc-module-section-software_versions' was found in {f_path}.") - sys.exit(1) - + self.update_log_report( + self.get_multiqc_software_versions.__name__, + 'error', + f"Failed to locate the required '{div_id}' div section in the '{f_path}' file." + ) + sys.exit( + relecov_tools.utils.print_log_report( + self.log_report, + method_name, + ["error"] + ) + ) + # Mapping multiqc sofware versions to j_data field_errors = {} for row in j_data: @@ -290,19 +379,41 @@ def get_multiqc_software_versions(self, file_list, j_data): field_errors[sample_name] = {field: e} row[field] = "Not Provided [GENEPIO:0001668]" continue + + # update progress log + if len(field_errors) > 0: + self.update_log_report( + method_name, + 'warning', + f"Encountered field errors while mapping data: {field_errors}" + ) + else: + self.update_log_report( + method_name, + 'valid', + "Successfully mapped data." + ) + relecov_tools.utils.print_log_report( + self.log_report, + method_name, + ['valid', 'warning'] + ) return j_data # TODO: update log report def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): """Auxiliar function to iterate over table's content and map it to metadata (j_data)""" + method_name=f"{self.mapping_over_table.__name__}:{self.software_name}.{self.current_config_key}" errors = [] field_errors = {} + field_vaild = {} for row in j_data: sample_name = row["submitting_lab_sample_id"].replace("-", "_") if sample_name in map_data.keys(): for field, value in mapping_fields.items(): try: row[field] = map_data[sample_name][value] + field_vaild[sample_name] = {field:value} except KeyError as e: field_errors[sample_name] = {field: e} row[field] = "Not Provided [GENEPIO:0001668]" @@ -313,22 +424,46 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): row[field] = "Not Provided [GENEPIO:0001668]" if errors: lenerrs = len(errors) - # work around when map_data comes from several per-sample tables instead of single table + # work around when map_data comes from several per-sample tables/files instead of single table (from list to str) if len(table_name) > 1: table_name = (os.path.dirname(table_name[0])) - log.error( - "\t{0} samples missing in {1}:\n\t{2}".format(lenerrs, table_name, errors) - ) - stderr.print(f"\t[red]{lenerrs} samples missing in {table_name}:\n\t{errors}") - if field_errors: - log.error("\tFields not found in {0}:\n\t{1}".format(table_name, field_errors)) - stderr.print(f"\t[red]Missing values in {table_name}:\n\t{field_errors}") + else: + table_name = table_name[0] + self.update_log_report( + method_name, + 'warning', + f"{lenerrs} samples missing in '{table_name}': {', '.join(errors)}." + ) + else: + self.update_log_report( + method_name, + 'valid', + "Successfully mapped data." + ) + + if len(field_errors) > 0: + self.update_log_report( + method_name, + 'warning', + f"Missing fields in {table_name}:\n\t{field_errors}" + ) + else: + self.update_log_report( + method_name, + 'valid', + f"Successfully mapped fields in {', '.join(field_vaild.keys())} - {table_name}." + ) + relecov_tools.utils.print_log_report( + self.log_report, + method_name, + ["warning","valid"] + ) return j_data - # TODO: add log report def handle_pangolin_data(self, files_list): """Parse pangolin data (csv) into JSON and map it to each sample in the provided j_data. """ + method_name=f"{self.add_bioinfo_results_metadata.__name__}:{self.handle_pangolin_data.__name__}" # Handling pangolin data pango_data_processed = {} try: @@ -347,17 +482,42 @@ def handle_pangolin_data(self, files_list): # Rename key in f_data pango_data_updated = {key.split()[0]: value for key, value in pango_data.items()} pango_data_processed.update(pango_data_updated) + self.update_log_report( + method_name, + 'valid', + f"Successfully handled data in {pango_file}." + ) except (FileNotFoundError, IndexError) as e: - stderr.print(f"[red]Error processing file {pango_file}: {e}") - continue + self.update_log_report( + method_name, + 'error', + f"Error processing file {pango_file}: {e}" + ) + sys.exit( + relecov_tools.utils.print_log_report( + self.log_report, + method_name, + ["error"] + ) + ) except Exception as e: - stderr.print(f"[red]Error occurred while processing files: {e}") - sys.exit() + self.update_log_report( + method_name, + 'error' + f"Error occurred while processing files: {e}" + ) + sys.exit( + relecov_tools.utils.print_log_report( + self.log_report, + method_name, + ["error"] + ) + ) return pango_data_processed - # TODO: add log report def handle_consensus_fasta(self, files_list): """Handling consensus fasta data (*.consensus.fa)""" + method_name=f"{self.add_bioinfo_results_metadata.__name__}:{self.handle_consensus_fasta.__name__}" consensus_data_processed = {} missing_consens = [] for consensus_file in files_list: @@ -384,13 +544,11 @@ def handle_consensus_fasta(self, files_list): # Report missing consensus conserrs = len(missing_consens) if conserrs >= 1: - log.error( - "\t{0} Consensus files missing:\n\t{1}".format( - conserrs, missing_consens - ) + self.update_log_report( + method_name, + 'warning', + f"{conserrs} samples missing in consensus file: {missing_consens}" ) - stderr.print(f"\t[yellow]{conserrs} samples missing consensus file:") - stderr.print(f"\n\t[yellow]{missing_consens}") return consensus_data_processed # TODO: add log report @@ -409,10 +567,29 @@ def include_custom_data(self, j_data): # TODO: this is too harcoded. Find a way to add file's path of required files when calling handlers functions. def add_fixed_values(self, j_data): """include the fixed data defined in configuration or feed custom empty fields""" - f_values = self.software_config["fixed_values"] - for row in j_data: - for field, value in f_values.items(): - row[field] = value + try: + f_values = self.software_config["fixed_values"] + for row in j_data: + for field, value in f_values.items(): + row[field] = value + self.update_log_report( + self.add_fixed_values.__name__, + 'valid', + "Fields added successfully." + ) + except KeyError as e: + self.update_log_report( + self.add_fixed_values.__name__, + 'warning', + f"Error found while adding fixed values: {e}" + ) + pass + relecov_tools.utils.print_log_report( + self.log_report, + self.add_fixed_values.__name__, + ["warning", "valid"] + + ) return j_data def collect_info_from_lab_json(self): @@ -422,9 +599,18 @@ def collect_info_from_lab_json(self): try: json_lab_data = relecov_tools.utils.read_json_file(self.readlabmeta_json_file) except ValueError: - log.error("%s invalid json file", self.readlabmeta_json_file) - stderr.print(f"[red] {self.readlabmeta_json_file} invalid json file") - sys.exit(1) + self.update_log_report( + self.collect_info_from_lab_json.__name__, + 'error', + f"Invalid lab-metadata json file: self.{self.readlabmeta_json_file}" + ) + sys.exit( + relecov_tools.utils.print_log_report( + self.log_report, + None, + ["error"] + ) + ) return json_lab_data def create_bioinfo_file(self): @@ -447,8 +633,13 @@ def create_bioinfo_file(self): ##j_data = self.include_custom_data(j_data) stderr.print("[blue]Adding fixed values") j_data = self.add_fixed_values(j_data) + # Show log report: + #relecov_tools.utils.print_log_report(self.log_report) + # Generate readlab + bioinfolab processed metadata. file_name = ( - "bioinfo_" + os.path.splitext(os.path.basename(self.readlabmeta_json_file))[0] + ".json" + "bioinfo_" + + os.path.splitext(os.path.basename(self.readlabmeta_json_file))[0] + + ".json" ) stderr.print("[blue]Writting output json file") os.makedirs(self.output_folder, exist_ok=True) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 4149eea3..4b3b8963 100755 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -17,6 +17,7 @@ from Bio import SeqIO from rich.console import Console from datetime import datetime +from tabulate import tabulate log = logging.getLogger(__name__) @@ -344,12 +345,12 @@ def select_most_recent_files_per_sample(paths_list): # Iterate over duplicated files to select the most recent one for each sample for sample_name, file_paths in duplicated_files: - stderr.print(f"More than one pangolin file found for sample {sample_name}. Selecting the most recent one.") + stderr.print(f"\tMore than one file found for sample {sample_name}. Selecting the most recent one.") # Sort files by modification time (most recent first) sorted_files = sorted(file_paths, key=lambda file_path: os.path.getmtime (file_path), reverse=True) # Select the most recent file selected_file = sorted_files[0] - stderr.print(f"Selected file for sample {sample_name}: {selected_file}") + stderr.print(f"\tSelected file for sample {sample_name}: {selected_file}") # Remove other files for the same sample from the filtered_files dictionary filename_groups[sample_name] = [selected_file] @@ -359,3 +360,24 @@ def select_most_recent_files_per_sample(paths_list): # Reformat variable to retrieve a list of file paths file_path_list = [sample_file_path for _, sample_file_path in filename_groups] return file_path_list + +def print_log_report(log_report, categories=None, sections=["warning", "valid", "error"]): + color_codes = { + "error": "\033[91m", # Red + "warning": "\033[93m", # Orange + "valid": "\033[92m", # Green + "reset": "\033[0m" # Reset color + } + + table_data = [] + for section_name, section_data in log_report.items(): + if section_name in sections: + for category, items in section_data.items(): + if categories is None or category in categories: + colored_category = f"{color_codes[section_name]}{category}{color_codes['reset']}" + for item in items: + colored_message = f"{color_codes[section_name]}{item}{color_codes['reset']}" + table_data.append([section_name, colored_category, colored_message]) + + print(tabulate(table_data, headers=["Log type", "Category", "Message"], tablefmt="fancy_grid")) + diff --git a/requirements.txt b/requirements.txt index d0fe58a6..c74cc031 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,3 +11,4 @@ openpyxl ena-upload-cli bio==1.4.0 bs4==0.0.2 +tabulate From 0da2f6601e841d0e897c3d702594c321bb27e703 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 5 Apr 2024 16:38:52 +0200 Subject: [PATCH 1288/1454] update methods description, rdelete accomplished todos and add small fixes --- relecov_tools/read_bioinfo_metadata.py | 59 +++++++++++++++++++------- 1 file changed, 43 insertions(+), 16 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 1a8e0952..b5169c0a 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -33,7 +33,7 @@ def __init__( readlabmeta_json_file=None, input_folder=None, output_folder=None, - software='viralrecon', + software=None, ): self.log_report = {'error': {}, 'valid': {}, 'warning': {}} if readlabmeta_json_file is None: @@ -100,6 +100,7 @@ def get_available_software(self, json): return available_software def update_log_report(self, method_name, status, message): + """Update progress log report""" if status == 'valid': self.log_report['valid'].setdefault(method_name, []).append(message) elif status == 'error': @@ -156,7 +157,8 @@ def scann_directory(self): return files_found def validate_software_mandatory_files(self, files_dict): - method_name=f"self.validate_software_mandatory_files.__name__" + """"Validates the presence of all mandatory files as defined in the software configuration JSON.""" + method_name=f"{self.validate_software_mandatory_files.__name__}" missing_required = [] for key in self.software_config: if self.software_config[key].get('required') is True: @@ -192,11 +194,12 @@ def validate_software_mandatory_files(self, files_dict): def add_bioinfo_results_metadata(self, files_dict, j_data): """ Adds metadata from bioinformatics results to j_data. - 1. Handles metadata in bioinformatic files found + 1. Handles metadata in bioinformatic files found. 2. Mapping handled bioinfo metadata into j_data. """ method_name=f"{self.add_bioinfo_results_metadata.__name__}" for key in self.software_config.keys(): + # Update bioinfo cofiguration key/scope self.current_config_key = key # This skip files that will be parsed with other methods if key == 'workflow_summary' or key == "fixed_values": @@ -214,7 +217,7 @@ def add_bioinfo_results_metadata(self, files_dict, j_data): continue # Handling files - data_to_map = self.handling_files(files_dict[key], key) + data_to_map = self.handling_files(files_dict[key]) # Mapping data to j_data if data_to_map: @@ -238,27 +241,51 @@ def add_bioinfo_results_metadata(self, files_dict, j_data): ) return j_data_mapped - def handling_files(self, file_list, file_key): - """Handles different file formats (sourced from ./metadata_homogenizer.py) + def handling_files(self, file_list): + """ + (inspired from ./metadata_homogenizer.py) + Handles different file formats to extract data regardless of their structure. The goal is to extract the data contained in files specified in ${file_list}, using either 'standard' handlers defined in this class or pipeline-specific file handlers. + + A file handler method must generate a data structure as follow: + + { + 'SAMPLE1': { + 'field1': 'value1' + 'field2': 'value2' + 'field3': 'value3' + }, + SAMPLE2': { + 'field1': 'value1' + 'field2': 'value2' + 'field3': 'value3' + }, + ... + } + + Input: + file_list (list): A list of file path/s to be processed. + + Returns: + dict: A single dictionary containing extracted data for each sample. """ method_name=f"{self.add_bioinfo_results_metadata.__name__}:{self.handling_files.__name__}" - file_name = self.software_config[file_key].get('fn') + file_name = self.software_config[self.current_config_key].get('fn') file_extension = os.path.splitext(file_name)[1] # Parsing key position try: - self.software_config[file_key]['sample_col_idx'] - sample_idx_possition = self.software_config[file_key]['sample_col_idx']-1 + self.software_config[self.current_config_key]['sample_col_idx'] + sample_idx_possition = self.software_config[self.current_config_key]['sample_col_idx']-1 except KeyError: sample_idx_possition = None self.update_log_report( method_name, 'warning', - f"No sample-index-column defined in '{self.software_name}.{file_key}'. Using default instead." + f"No sample-index-column defined in '{self.software_name}.{self.current_config_key}'. Using default instead." ) # Parsing files - func_name = self.software_config[file_key]["function"] + func_name = self.software_config[self.current_config_key]["function"] if func_name is None: if file_name.endswith('.csv'): data = relecov_tools.utils.read_csv_file_return_dict( @@ -307,7 +334,7 @@ def handling_files(self, file_list, file_key): return data def get_multiqc_software_versions(self, file_list, j_data): - """Reads html file, finds table containing programs info, and map it to j_data""" + """Reads multiqc html file, finds table containing software version info, and map it to j_data""" method_name=f"{self.get_multiqc_software_versions.__name__}" # Handle multiqc_report.html f_path = file_list[0] @@ -400,9 +427,9 @@ def get_multiqc_software_versions(self, file_list, j_data): ) return j_data - # TODO: update log report def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): - """Auxiliar function to iterate over table's content and map it to metadata (j_data)""" + """ + Function that maps structure data containing fields per sample into j_data. """ method_name=f"{self.mapping_over_table.__name__}:{self.software_name}.{self.current_config_key}" errors = [] field_errors = {} @@ -461,7 +488,7 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): return j_data def handle_pangolin_data(self, files_list): - """Parse pangolin data (csv) into JSON and map it to each sample in the provided j_data. + """File handler to parse pangolin data (csv) into JSON structured format. """ method_name=f"{self.add_bioinfo_results_metadata.__name__}:{self.handle_pangolin_data.__name__}" # Handling pangolin data @@ -516,7 +543,7 @@ def handle_pangolin_data(self, files_list): return pango_data_processed def handle_consensus_fasta(self, files_list): - """Handling consensus fasta data (*.consensus.fa)""" + """File handler to parse consensus fasta data (*.consensus.fa) into JSON structured format""" method_name=f"{self.add_bioinfo_results_metadata.__name__}:{self.handle_consensus_fasta.__name__}" consensus_data_processed = {} missing_consens = [] From 1e78a24314f96b4011b70338f78add73e3c0e8cc Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 5 Apr 2024 17:13:38 +0200 Subject: [PATCH 1289/1454] recover method from older version to parse viralrecon long table --- relecov_tools/read_bioinfo_metadata.py | 30 +++++++++++++++++++++----- 1 file changed, 25 insertions(+), 5 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index b5169c0a..450a4e0e 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -23,10 +23,7 @@ # FIXME: longtable parsing old method needs to be recovered. New implementation has errors while parsing it. # TODO: Add method to validate bioinfo_config.json file requirements. -# TODO: Cosider eval py + func property in json to be able to discriminate between collated files and sample-specific files. # TODO: replace submitting_lab_id by sequencing_sample_id -# TODO: improve method's description (specifically 'handling_files') -# TODO: fix/improve stdout missing values / fields not found in mapping-over-table class BioinfoMetadata: def __init__( self, @@ -578,6 +575,28 @@ def handle_consensus_fasta(self, files_list): ) return consensus_data_processed + def parse_long_table(self, long_table_path, output_folder): + file_match = os.path.join(long_table_path, "variants_long_table*.csv") + table_path = glob.glob(file_match) + if len(table_path) == 1: + table_path = glob.glob(file_match)[0] + else: + log.error("variants_long_table files found = %s", len(table_path)) + stderr.print( + f"[red]Found {len(table_path)} variants_long_table files in ", + f"[red]{long_table_path}, aborting", + ) + sys.exit(1) + if not os.path.isfile(table_path): + log.error("variants_long_table given file is not a file") + stderr.print("[red]Variants_long_table file do not exist, Aborting") + sys.exit(1) + long_table = LongTableParse(table_path, output_folder) + + long_table.parsing_csv() + return None + + # TODO: add log report def include_custom_data(self, j_data): """Include custom fields like variant-long-table path""" @@ -660,8 +679,9 @@ def create_bioinfo_file(self): ##j_data = self.include_custom_data(j_data) stderr.print("[blue]Adding fixed values") j_data = self.add_fixed_values(j_data) - # Show log report: - #relecov_tools.utils.print_log_report(self.log_report) + stderr.print("[blue]Parsing variants_long_table info to json format...") + self.parse_long_table(self.input_folder, self.output_folder) + # Generate readlab + bioinfolab processed metadata. file_name = ( "bioinfo_" From 97d5e6a2ae6c19325333aebc2033f5621754b858 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 5 Apr 2024 18:03:49 +0200 Subject: [PATCH 1290/1454] adaptation of method parse_long_table to refactored module --- relecov_tools/conf/bioinfo_config.json | 4 +- relecov_tools/long_table_parse.py | 2 +- relecov_tools/read_bioinfo_metadata.py | 54 +++++++++++++++----------- 3 files changed, 34 insertions(+), 26 deletions(-) diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index f559f545..80a052b4 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -37,11 +37,11 @@ } }, "variants_long_table": { - "fn": "variants_long_table.csv", + "fn": "variants_long_table(?:_\\d{8})?\\.csv$", "sample_col_idx": 1, "header_row_idx": 1, "required": true, - "function": null, + "function": "parse_long_table", "content": { "sample" : "SAMPLE", "chromosome": "CHROM", diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index fd3a8a3a..f1d97a08 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -29,7 +29,7 @@ class LongTableParse: - parse_a_list_of_dictionaries() : returns generated_JSON - saving_file(generated_JSON) - parsing_csv() : It manages all this proccess: - - calling first to parse_a_list_of_dictionaries() and then calling to saving_file() + - calling first to parse_a_list_of_dictionaries() and then calling to saving_file() """ diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 450a4e0e..61649693 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -21,9 +21,9 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) -# FIXME: longtable parsing old method needs to be recovered. New implementation has errors while parsing it. # TODO: Add method to validate bioinfo_config.json file requirements. # TODO: replace submitting_lab_id by sequencing_sample_id +# TODO: mv pipeline-specific methods to future assets/pipeline_utils/ class BioinfoMetadata: def __init__( self, @@ -228,7 +228,7 @@ def add_bioinfo_results_metadata(self, files_dict, j_data): self.update_log_report( method_name, 'warning', - f"No metadata generated while processing '{self.software_name}.{key}'" + f"No metadata to perform standard mapping while processing '{self.software_name}.{key}'" ) continue relecov_tools.utils.print_log_report( @@ -575,25 +575,36 @@ def handle_consensus_fasta(self, files_list): ) return consensus_data_processed - def parse_long_table(self, long_table_path, output_folder): - file_match = os.path.join(long_table_path, "variants_long_table*.csv") - table_path = glob.glob(file_match) - if len(table_path) == 1: - table_path = glob.glob(file_match)[0] - else: - log.error("variants_long_table files found = %s", len(table_path)) - stderr.print( - f"[red]Found {len(table_path)} variants_long_table files in ", - f"[red]{long_table_path}, aborting", - ) - sys.exit(1) - if not os.path.isfile(table_path): - log.error("variants_long_table given file is not a file") - stderr.print("[red]Variants_long_table file do not exist, Aborting") - sys.exit(1) - long_table = LongTableParse(table_path, output_folder) + def parse_long_table(self, files_list): + method_name = f"{self.parse_long_table.__name__}" + # Hanfling long table data + + if len(files_list) == 1: + files_list_processed = files_list[0] + if not os.path.isfile(files_list_processed): + self.update_log_report( + method_name, + 'error', + f"{files_list_processed} given file is not a file" + ) + sys.exit( + relecov_tools.utils.print_log_report( + self.log_report, method_name, ['error'] + ) + ) + long_table = LongTableParse(files_list_processed, self.output_folder, self.log_report) + long_table.parsing_csv() + elif len(files_list) >1: + self.update_log_report( + method_name, + 'warning', + f"Found {len(files_list)} variants_long_table files. This version is unable to process more than one variants long table each time." + ) - long_table.parsing_csv() + relecov_tools.utils.print_log_report( + self.log_report, method_name, ['valid', 'warning'] + ) + # This needs to return none to avoid being parsed by method mapping-over-table return None @@ -679,9 +690,6 @@ def create_bioinfo_file(self): ##j_data = self.include_custom_data(j_data) stderr.print("[blue]Adding fixed values") j_data = self.add_fixed_values(j_data) - stderr.print("[blue]Parsing variants_long_table info to json format...") - self.parse_long_table(self.input_folder, self.output_folder) - # Generate readlab + bioinfolab processed metadata. file_name = ( "bioinfo_" From ddd5522105bb1c6c6617ce56b7e307b781f1fddc Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 5 Apr 2024 19:10:18 +0200 Subject: [PATCH 1291/1454] 1-relocate module that adds custom long-table data. 2-Now j_data is environmental. 3-Dummy changes. --- relecov_tools/long_table_parse.py | 40 +++++++++++++++------ relecov_tools/read_bioinfo_metadata.py | 50 ++++++++++++-------------- relecov_tools/utils.py | 1 + 3 files changed, 54 insertions(+), 37 deletions(-) diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index f1d97a08..9df5f3aa 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -33,7 +33,7 @@ class LongTableParse: """ - def __init__(self, file_path=None, output_directory=None): + def __init__(self, file_path=None, output_directory=None, j_data=None): if file_path is None: self.file_path = relecov_tools.utils.prompt_path( msg="Select the csv file which contains variant long table information" @@ -68,6 +68,13 @@ def __init__(self, file_path=None, output_directory=None): #self.long_table_heading = config_json.get_configuration("long_table_heading") self.software_config = config_json.get_configuration('viralrecon') self.long_table_heading = self.software_config["variants_long_table"]["content"] + + if not j_data: + stderr.print("[red]\tError: No read lab metadata file found. Long-table-parsing aborted.") + sys.exit(1) + else: + self.j_data = j_data + def validate_file(self, heading): """Check if long table file has all mandatory fields defined in configuration file @@ -88,8 +95,7 @@ def parse_file(self): with open(self.file_path, encoding="utf-8-sig") as fh: lines = fh.readlines() - stderr.print("[green]Successful checking heading fields") - stderr.print("[blue]Parsing the input file") + stderr.print("[green]\tSuccessful checking heading fields") heading_index = {} headings_from_csv = lines[0].strip().split(",") for heading in self.long_table_heading.values(): @@ -124,7 +130,7 @@ def parse_file(self): else: variant_dict["Gene"] = line_s[heading_index["GENE"]] samp_dict[sample].append(variant_dict) - stderr.print("[green]Successful parsing data") + stderr.print("[green]\tSuccessful parsing data") return samp_dict def convert_to_json(self, samp_dict): @@ -148,21 +154,35 @@ def convert_to_json(self, samp_dict): def save_to_file(self, j_list): """Transform the parsed data into a json file""" - stderr.print("[blue]Saving parsed data to file") date_now = datetime.now().strftime("%Y_%m_%d_%H_%M_%S") file_name = "long_table_" + date_now + ".json" file_path = os.path.join(self.output_directory, file_name) - with open(file_path, "w") as fh: - fh.write(json.dumps(j_list, indent=4)) - return + try: + with open(file_path, "w") as fh: + fh.write(json.dumps(j_list, indent=4)) + stderr.print("[green]\tParsed data successfully saved to file:", file_path) + except Exception as e: + stderr.print("[red]\tError saving parsed data to file:", str(e)) + + def add_custom_longtable_data(self, j_data): + """Auxiliary function to add custom fields likevariant-long-table into j_data""" + if len(self.file_path) == 0: + long_table_path = "Not Provided [GENEPIO:0001668]" + else: + long_table_path = self.file_path + for row in j_data: + row["long_table_path"] = str(long_table_path) + return j_data def parsing_csv(self): """ Function called when using the relecov-tools long-table-parse function. """ - stderr.print("[blue]Starting reading the input file") + # Parsing longtable file parsed_data = self.parse_file() j_list = self.convert_to_json(parsed_data) + # Saving long table data into a file self.save_to_file(j_list) - stderr.print("[green]Process completed") + stderr.print("[green]\tProcess completed") + return diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 61649693..8e2ae4d6 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -32,7 +32,10 @@ def __init__( output_folder=None, software=None, ): + # Init process log self.log_report = {'error': {}, 'valid': {}, 'warning': {}} + + # Parse read-lab-meta-data if readlabmeta_json_file is None: readlabmeta_json_file = relecov_tools.utils.prompt_path( msg="Select the json file that was created by the read-lab-metadata" @@ -52,6 +55,11 @@ def __init__( ) self.readlabmeta_json_file = readlabmeta_json_file + # Initialize j_data object + stderr.print("[blue]Reading lab metadata json") + self.j_data = self.collect_info_from_lab_json() + + # Parse input/output folder if input_folder is None: self.input_folder = relecov_tools.utils.prompt_path( msg="Select the input folder" @@ -65,13 +73,13 @@ def __init__( else: self.output_folder = output_folder + # Parse bioinfo configuration self.bioinfo_json_file = os.path.join(os.path.dirname(__file__), "conf", "bioinfo_config.json") if software is None: software = relecov_tools.utils.prompt_path( msg="Select the software, pipeline or tool use in the bioinformatic analysis: " ) self.software_name = software - available_software = self.get_available_software(self.bioinfo_json_file) bioinfo_config = ConfigJson(self.bioinfo_json_file) if self.software_name in available_software: @@ -186,6 +194,11 @@ def validate_software_mandatory_files(self, files_dict): 'valid', "Successfull validation of mandatory files." ) + relecov_tools.utils.print_log_report( + self.log_report, + method_name, + ['valid','waring'] + ) return def add_bioinfo_results_metadata(self, files_dict, j_data): @@ -228,7 +241,7 @@ def add_bioinfo_results_metadata(self, files_dict, j_data): self.update_log_report( method_name, 'warning', - f"No metadata to perform standard mapping while processing '{self.software_name}.{key}'" + f"No metadata found to perform standard mapping when processing '{self.software_name}.{key}'" ) continue relecov_tools.utils.print_log_report( @@ -592,35 +605,20 @@ def parse_long_table(self, files_list): self.log_report, method_name, ['error'] ) ) - long_table = LongTableParse(files_list_processed, self.output_folder, self.log_report) + long_table = LongTableParse(files_list_processed, self.output_folder, self.j_data) + # Parsing long table data and saving it long_table.parsing_csv() + # Adding custom long_table data to j_data + self.j_data = long_table.add_custom_longtable_data(self.j_data) elif len(files_list) >1: self.update_log_report( method_name, 'warning', f"Found {len(files_list)} variants_long_table files. This version is unable to process more than one variants long table each time." ) - - relecov_tools.utils.print_log_report( - self.log_report, method_name, ['valid', 'warning'] - ) # This needs to return none to avoid being parsed by method mapping-over-table return None - - # TODO: add log report - def include_custom_data(self, j_data): - """Include custom fields like variant-long-table path""" - condition = os.path.join(self.input_folder, "*variants_long_table*.csv") - f_path = relecov_tools.utils.get_files_match_condition(condition) - if len(f_path) == 0: - long_table_path = "Not Provided [GENEPIO:0001668]" - else: - long_table_path = f_path[0] - for row in j_data: - row["long_table_path"] = long_table_path - return j_data - # TODO: this is too harcoded. Find a way to add file's path of required files when calling handlers functions. def add_fixed_values(self, j_data): """include the fixed data defined in configuration or feed custom empty fields""" @@ -679,17 +677,15 @@ def create_bioinfo_file(self): files_found_dict = self.scann_directory() stderr.print("[blue]Validating required files...") self.validate_software_mandatory_files(files_found_dict) - stderr.print("[blue]Reading lab metadata json") - j_data = self.collect_info_from_lab_json() stderr.print(f"[blue]Adding metadata from {self.input_folder} into read lab metadata...") - j_data = self.add_bioinfo_results_metadata(files_found_dict, j_data) + self.j_data = self.add_bioinfo_results_metadata(files_found_dict, self.j_data) stderr.print("[blue]Adding software versions to read lab metadata...") - j_data = self.get_multiqc_software_versions(files_found_dict['workflow_summary'], j_data) + self.j_data = self.get_multiqc_software_versions(files_found_dict['workflow_summary'], self.j_data) # FIXME: this isn't refactored and requires to be reimplemented from older version of this module ##stderr.print("[blue]Adding variant long table path") ##j_data = self.include_custom_data(j_data) stderr.print("[blue]Adding fixed values") - j_data = self.add_fixed_values(j_data) + self.j_data = self.add_fixed_values(self.j_data) # Generate readlab + bioinfolab processed metadata. file_name = ( "bioinfo_" @@ -699,6 +695,6 @@ def create_bioinfo_file(self): stderr.print("[blue]Writting output json file") os.makedirs(self.output_folder, exist_ok=True) file_path = os.path.join(self.output_folder, file_name) - relecov_tools.utils.write_json_fo_file(j_data, file_path) + relecov_tools.utils.write_json_fo_file(self.j_data, file_path) stderr.print("[green]Sucessful creation of bioinfo analyis file") return True diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 4b3b8963..e648ba53 100755 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -334,6 +334,7 @@ def select_most_recent_files_per_sample(paths_list): filename_groups = {} # Count occurrences of each filename and group files by sample names for file in paths_list: + # TODO: So far, it uses split method to identify this pattern: [sample1.pangolin.csv, sample1.pangolin_20240310.csv]. It should be improve to parse files based on a different character matching field. file_name = os.path.basename(file).split('.')[0] if file_name in filename_groups : filename_groups[file_name].append(file) From 8581669198167a67fd327ea7ff52c7846e00de7d Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 5 Apr 2024 20:11:40 +0200 Subject: [PATCH 1292/1454] mv report logs methods to the new class BioinfoReportLog --- relecov_tools/read_bioinfo_metadata.py | 252 +++++++++---------------- 1 file changed, 90 insertions(+), 162 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 8e2ae4d6..e5f08f8c 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -2,7 +2,6 @@ import os import sys import logging -import glob import rich.console import re from datetime import datetime @@ -21,10 +20,41 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) +class BioinfoReportLog: + def __init__(self, log_report=None): + if not log_report: + self.report = {'error': {}, 'valid': {}, 'warning': {}} + else: + self.report = log_report + + def update_log_report(self, method_name, status, message): + """Update progress log report""" + if status == 'valid': + self.report['valid'].setdefault(method_name, []).append(message) + return self.report + elif status == 'error': + self.report['error'].setdefault(method_name, []).append(message) + return self.report + elif status == 'warning': + self.report['warning'].setdefault(method_name, []).append(message) + return self.report + else: + raise ValueError("Invalid status provided.") + + def print_log_report(self, name, sections): + """Calls log report printer.""" + relecov_tools.utils.print_log_report( + self.report, + name, + sections + ) + + # TODO: Add method to validate bioinfo_config.json file requirements. # TODO: replace submitting_lab_id by sequencing_sample_id # TODO: mv pipeline-specific methods to future assets/pipeline_utils/ -class BioinfoMetadata: +# fixme: INCOMING IMPLEMENTATION ---> REPORT LOG IS NOW A CLASS. +class BioinfoMetadata(BioinfoReportLog): def __init__( self, readlabmeta_json_file=None, @@ -33,7 +63,8 @@ def __init__( software=None, ): # Init process log - self.log_report = {'error': {}, 'valid': {}, 'warning': {}} + super().__init__() + self.log_report = BioinfoReportLog() # Parse read-lab-meta-data if readlabmeta_json_file is None: @@ -41,17 +72,13 @@ def __init__( msg="Select the json file that was created by the read-lab-metadata" ) if not os.path.isfile(readlabmeta_json_file): - self.update_log_report( + self.log_report.update_log_report( self.__init__.__name__, 'error', f"file {readlabmeta_json_file} does not exist" ) sys.exit( - relecov_tools.utils.print_log_report( - self.log_report, - None, - ["error"] - ) + self.log_report.print_log_report(self.__init__.__name__, ['error']) ) self.readlabmeta_json_file = readlabmeta_json_file @@ -85,17 +112,13 @@ def __init__( if self.software_name in available_software: self.software_config = bioinfo_config.get_configuration(self.software_name) else: - self.update_log_report( + self.log_report.update_log_report( self.__init__.__name__, 'error', f"No configuration available for '{self.software_name}'. Currently, the only available software options are:: {', '.join(available_software)}" ) sys.exit( - relecov_tools.utils.print_log_report( - self.log_report, - None, - ["error"] - ) + self.log_report.print_log_report(self.__init__.__name__, ['error']) ) def get_available_software(self, json): @@ -103,17 +126,6 @@ def get_available_software(self, json): config = relecov_tools.utils.read_json_file(json) available_software = list(config.keys()) return available_software - - def update_log_report(self, method_name, status, message): - """Update progress log report""" - if status == 'valid': - self.log_report['valid'].setdefault(method_name, []).append(message) - elif status == 'error': - self.log_report['error'].setdefault(method_name, []).append(message) - elif status == 'warning': - self.log_report['warning'].setdefault(method_name, []).append(message) - else: - raise ValueError("Invalid status provided.") def scann_directory(self): """Scanns bioinfo analysis directory and identifies files according to the file name patterns defined in the software configuration json.""" @@ -123,7 +135,7 @@ def scann_directory(self): for topic_key, topic_scope in self.software_config.items(): if 'fn' not in topic_scope: #try/except fn - self.update_log_report( + self.log_report.update_log_report( method_name, 'warning', f"No 'fn' (file pattern) found in '{self.software_name}.{topic_key}'." @@ -135,30 +147,21 @@ def scann_directory(self): files_found[topic_key] = matching_files if len(files_found) < 1: - self.update_log_report( + self.log_report.update_log_report( method_name, 'error', f"No files found in '{self.input_folder}' according to '{os.path.basename(self.bioinfo_json_file)}' file name patterns." ) sys.exit( - relecov_tools.utils.print_log_report( - self.log_report, - method_name, - ["error"] - ) + self.log_report.print_log_report(method_name, ["error"]) ) else: - self.update_log_report( + self.log_report.update_log_report( self.scann_directory.__name__, 'valid', f"Scannig process succeed. Scanned {total_files} files." ) - relecov_tools.utils.print_log_report( - self.log_report, - method_name, - ['valid','warning'] - ) - + self.log_report.print_log_report(method_name, ['valid','warning']) return files_found def validate_software_mandatory_files(self, files_dict): @@ -176,29 +179,20 @@ def validate_software_mandatory_files(self, files_dict): continue if len(missing_required) >= 1: - self.update_log_report( + self.log_report.update_log_report( method_name, 'error', f"Missing mandatory files in {self.software_name}.{key}:{', '.join(missing_required)}" ) - sys.exit( - relecov_tools.utils.print_log_report( - self.log_report, - method_name, - ["error"] - ) - ) + sys.exit(self.log_report.print_log_report(method_name,["error"])) else: - self.update_log_report( + self.log_report.update_log_report( method_name, 'valid', "Successfull validation of mandatory files." ) - relecov_tools.utils.print_log_report( - self.log_report, - method_name, - ['valid','waring'] - ) + + self.log_report.print_log_report(method_name, ['valid', 'waring']) return def add_bioinfo_results_metadata(self, files_dict, j_data): @@ -219,7 +213,7 @@ def add_bioinfo_results_metadata(self, files_dict, j_data): files_dict[key] stderr.print(f"[blue]Start processing {self.software_name}.{key}") except KeyError: - self.update_log_report( + self.log_report.update_log_report( method_name, 'warning', f"No file path found for '{self.software_name}.{key}'" @@ -238,17 +232,13 @@ def add_bioinfo_results_metadata(self, files_dict, j_data): table_name=files_dict[key] ) else: - self.update_log_report( + self.log_report.update_log_report( method_name, 'warning', f"No metadata found to perform standard mapping when processing '{self.software_name}.{key}'" ) continue - relecov_tools.utils.print_log_report( - self.log_report, - method_name, - ['valid','waring'] - ) + self.log_report.print_log_report(method_name, ['valid','waring']) return j_data_mapped def handling_files(self, file_list): @@ -288,7 +278,7 @@ def handling_files(self, file_list): sample_idx_possition = self.software_config[self.current_config_key]['sample_col_idx']-1 except KeyError: sample_idx_possition = None - self.update_log_report( + self.log_report.update_log_report( method_name, 'warning', f"No sample-index-column defined in '{self.software_name}.{self.current_config_key}'. Using default instead." @@ -311,36 +301,24 @@ def handling_files(self, file_list): key_position=sample_idx_possition ) else: - self.update_log_report( + self.log_report.update_log_report( method_name, 'error', f"Unrecognized defined file name extension '{file_extension}' in '{file_name}'." ) - sys.exit( - relecov_tools.utils.print_log_report( - self.log_report, - None, - ["error"] - ) - ) + sys.exit(self.log_report.print_log_report(method_name,["error"])) else: try: # Attempt to get the method by name method_to_call = getattr(self, func_name) data = method_to_call(file_list) except AttributeError as e: - self.update_log_report( + self.log_report.update_log_report( self.add_bioinfo_results_metadata.__name__, 'error', f"Error occurred while parsing '{func_name}': {e}." ) - sys.exit( - relecov_tools.utils.print_log_report( - self.log_report, - None, - sections=["error"] - ) - ) + sys.exit(self.log_report.print_log_report(method_name,["error"])) return data def get_multiqc_software_versions(self, file_list, j_data): @@ -366,44 +344,26 @@ def get_multiqc_software_versions(self, file_list, j_data): version = columns[2].text.strip() program_versions[program_name] = version else: - self.update_log_report( + self.log_report.update_log_report( method_name, 'error', f"HTML entry error in {columns}. HTML table expected format should be \n Process Name\n\n Software \n." ) - sys.exit( - relecov_tools.utils.print_log_report( - self.log_report, - method_name, - ["error"] - ) - ) + sys.exit(self.log_report.print_log_report(method_name,["error"])) else: - self.update_log_report( + self.log_report.update_log_report( method_name, 'error', f"Unable to locate the table containing software versions in file {f_path} under div section {div_id}." ) - sys.exit( - relecov_tools.utils.print_log_report( - self.log_report, - method_name, - ["error"] - ) - ) + sys.exit(self.log_report.print_log_report(method_name,["error"])) else: - self.update_log_report( + self.log_report.update_log_report( self.get_multiqc_software_versions.__name__, 'error', f"Failed to locate the required '{div_id}' div section in the '{f_path}' file." ) - sys.exit( - relecov_tools.utils.print_log_report( - self.log_report, - method_name, - ["error"] - ) - ) + sys.exit(self.log_report.print_log_report(method_name,["error"])) # Mapping multiqc sofware versions to j_data field_errors = {} @@ -419,27 +379,24 @@ def get_multiqc_software_versions(self, file_list, j_data): # update progress log if len(field_errors) > 0: - self.update_log_report( + self.log_report.update_log_report( method_name, 'warning', f"Encountered field errors while mapping data: {field_errors}" ) else: - self.update_log_report( + self.log_report.update_log_report( method_name, 'valid', "Successfully mapped data." ) - relecov_tools.utils.print_log_report( - self.log_report, - method_name, - ['valid', 'warning'] - ) + self.log_report.print_log_report(method_name,["valid","warning"]) return j_data def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): """ - Function that maps structure data containing fields per sample into j_data. """ + Function that maps structure data containing fields per sample into j_data. + """ method_name=f"{self.mapping_over_table.__name__}:{self.software_name}.{self.current_config_key}" errors = [] field_errors = {} @@ -466,35 +423,31 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): table_name = (os.path.dirname(table_name[0])) else: table_name = table_name[0] - self.update_log_report( + self.log_report.update_log_report( method_name, 'warning', f"{lenerrs} samples missing in '{table_name}': {', '.join(errors)}." ) else: - self.update_log_report( + self.log_report.update_log_report( method_name, 'valid', "Successfully mapped data." ) if len(field_errors) > 0: - self.update_log_report( + self.log_report.update_log_report( method_name, 'warning', f"Missing fields in {table_name}:\n\t{field_errors}" ) else: - self.update_log_report( + self.log_report.update_log_report( method_name, 'valid', f"Successfully mapped fields in {', '.join(field_vaild.keys())} - {table_name}." ) - relecov_tools.utils.print_log_report( - self.log_report, - method_name, - ["warning","valid"] - ) + self.log_report.print_log_report(method_name,["warning","valid"]) return j_data def handle_pangolin_data(self, files_list): @@ -519,37 +472,25 @@ def handle_pangolin_data(self, files_list): # Rename key in f_data pango_data_updated = {key.split()[0]: value for key, value in pango_data.items()} pango_data_processed.update(pango_data_updated) - self.update_log_report( + self.log_report.update_log_report( method_name, 'valid', f"Successfully handled data in {pango_file}." ) except (FileNotFoundError, IndexError) as e: - self.update_log_report( + self.log_report.update_log_report( method_name, 'error', f"Error processing file {pango_file}: {e}" ) - sys.exit( - relecov_tools.utils.print_log_report( - self.log_report, - method_name, - ["error"] - ) - ) + sys.exit(self.log_report.print_log_report(method_name,["error"])) except Exception as e: - self.update_log_report( + self.log_report.update_log_report( method_name, 'error' f"Error occurred while processing files: {e}" ) - sys.exit( - relecov_tools.utils.print_log_report( - self.log_report, - method_name, - ["error"] - ) - ) + sys.exit(self.log_report.print_log_report(method_name,["error"])) return pango_data_processed def handle_consensus_fasta(self, files_list): @@ -581,7 +522,7 @@ def handle_consensus_fasta(self, files_list): # Report missing consensus conserrs = len(missing_consens) if conserrs >= 1: - self.update_log_report( + self.log_report.update_log_report( method_name, 'warning', f"{conserrs} samples missing in consensus file: {missing_consens}" @@ -595,23 +536,19 @@ def parse_long_table(self, files_list): if len(files_list) == 1: files_list_processed = files_list[0] if not os.path.isfile(files_list_processed): - self.update_log_report( + self.log_report.update_log_report( method_name, 'error', f"{files_list_processed} given file is not a file" ) - sys.exit( - relecov_tools.utils.print_log_report( - self.log_report, method_name, ['error'] - ) - ) + sys.exit(self.log_report.print_log_report(method_name,["error"])) long_table = LongTableParse(files_list_processed, self.output_folder, self.j_data) # Parsing long table data and saving it long_table.parsing_csv() # Adding custom long_table data to j_data self.j_data = long_table.add_custom_longtable_data(self.j_data) elif len(files_list) >1: - self.update_log_report( + self.log_report.update_log_report( method_name, 'warning', f"Found {len(files_list)} variants_long_table files. This version is unable to process more than one variants long table each time." @@ -622,50 +559,41 @@ def parse_long_table(self, files_list): # TODO: this is too harcoded. Find a way to add file's path of required files when calling handlers functions. def add_fixed_values(self, j_data): """include the fixed data defined in configuration or feed custom empty fields""" + method_name=f"{self.add_fixed_values.__name__}" try: f_values = self.software_config["fixed_values"] for row in j_data: for field, value in f_values.items(): row[field] = value - self.update_log_report( - self.add_fixed_values.__name__, + self.log_report.update_log_report( + method_name, 'valid', "Fields added successfully." ) except KeyError as e: - self.update_log_report( - self.add_fixed_values.__name__, + self.log_report.update_log_report( + method_name, 'warning', f"Error found while adding fixed values: {e}" ) pass - relecov_tools.utils.print_log_report( - self.log_report, - self.add_fixed_values.__name__, - ["warning", "valid"] - - ) + self.log_report.print_log_report(method_name,["valid","waring"]) return j_data def collect_info_from_lab_json(self): """Create the list of dictionaries from the data that is on json lab metadata file. Return j_data that is used to add the rest of the fields """ + method_name=f"{self.collect_info_from_lab_json.__name__}" try: json_lab_data = relecov_tools.utils.read_json_file(self.readlabmeta_json_file) except ValueError: - self.update_log_report( + self.log_report.update_log_report( self.collect_info_from_lab_json.__name__, 'error', f"Invalid lab-metadata json file: self.{self.readlabmeta_json_file}" ) - sys.exit( - relecov_tools.utils.print_log_report( - self.log_report, - None, - ["error"] - ) - ) + sys.exit(self.log_report.print_log_report(method_name,["error"])) return json_lab_data def create_bioinfo_file(self): From 36820084464b4de91b18719ea24ce5b37419adcc Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Sat, 6 Apr 2024 20:08:25 +0200 Subject: [PATCH 1293/1454] pipeline-specific methods are now invoked from assets/pipeline_utils --- .../assets/pipeline_utils/viralrecon.py | 129 ++++++++++++++++++ relecov_tools/long_table_parse.py | 41 +++--- relecov_tools/read_bioinfo_metadata.py | 121 ++-------------- 3 files changed, 162 insertions(+), 129 deletions(-) create mode 100644 relecov_tools/assets/pipeline_utils/viralrecon.py diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py new file mode 100644 index 00000000..a57582a6 --- /dev/null +++ b/relecov_tools/assets/pipeline_utils/viralrecon.py @@ -0,0 +1,129 @@ +#!/usr/bin/env python +import os +import sys +import re +import logging + +import relecov_tools.utils +from relecov_tools.read_bioinfo_metadata import BioinfoReportLog +from relecov_tools.read_bioinfo_metadata import BioinfoMetadata +from relecov_tools.long_table_parse import LongTableParse + +log = logging.getLogger(__name__) + +def handle_pangolin_data(files_list): + """File handler to parse pangolin data (csv) into JSON structured format. + """ + method_name = f"{handle_pangolin_data.__name__}" + method_log_report = BioinfoReportLog() + + # Handling pangolin data + pango_data_processed = {} + try: + files_list_processed = relecov_tools.utils.select_most_recent_files_per_sample(files_list) + for pango_file in files_list_processed: + try: + pango_data = relecov_tools.utils.read_csv_file_return_dict( + pango_file, sep="," + ) + # Add custom content in pangolin + pango_data_key = next(iter(pango_data)) + pango_data[pango_data_key]['lineage_analysis_date'] = relecov_tools.utils.get_file_date( + pango_file + ) + + # Rename key in f_data + pango_data_updated = {key.split()[0]: value for key, value in pango_data.items()} + pango_data_processed.update(pango_data_updated) + method_log_report.update_log_report( + method_name, + 'valid', + f"Successfully handled data in {pango_file}." + ) + except (FileNotFoundError, IndexError) as e: + method_log_report.update_log_report( + method_name, + 'error', + f"Error processing file {pango_file}: {e}" + ) + sys.exit( + method_log_report.print_log_report(method_name, ['error']) + ) + except Exception as e: + method_log_report.update_log_report( + method_name, + 'error', + f"Error occurred while processing files: {e}" + ) + sys.exit( + method_log_report.print_log_report(method_name, ['error']) + ) + return pango_data_processed + +def parse_long_table(files_list): + method_name = f"{parse_long_table.__name__}" + method_log_report = BioinfoReportLog() + + # Hanfling long table data + if len(files_list) == 1: + files_list_processed = files_list[0] + if not os.path.isfile(files_list_processed): + method_log_report.update_log_report( + method_name, + 'error', + f"{files_list_processed} given file is not a file" + ) + sys.exit(method_log_report.print_log_report(method_name,["error"])) + long_table = LongTableParse(files_list_processed) + # Parsing long table data and saving it + long_table.parsing_csv() + # FIXME: cannot write over j_data when this function is invoked from a differnt file. + # Adding custom long_table data to j_data + # self.j_data = long_table.add_custom_longtable_data(self.j_data) + elif len(files_list) > 1: + method_log_report.update_log_report( + method_name, + 'warning', + f"Found {len(files_list)} variants_long_table files. This version is unable to process more than one variants long table each time." + ) + # This needs to return none to avoid being parsed by method mapping-over-table + return None + +def handle_consensus_fasta(files_list): + """File handler to parse consensus fasta data (*.consensus.fa) into JSON structured format""" + method_name = f"{handle_consensus_fasta.__name__}" + method_log_report = BioinfoReportLog() + + consensus_data_processed = {} + missing_consens = [] + for consensus_file in files_list: + try: + record_fasta = relecov_tools.utils.read_fasta_return_SeqIO_instance( + consensus_file + ) + except FileNotFoundError as e: + missing_consens.append(e.filename) + continue + sample_key = os.path.splitext(os.path.basename(consensus_file))[0] + + # Update consensus data for the sample key + consensus_data_processed[sample_key] = { + 'sequence_name': record_fasta.description, + 'genome_length': str(len(record_fasta)), + 'sequence_filepath': os.path.dirname(consensus_file), + 'sequence_filename': sample_key, + 'sequence_md5': relecov_tools.utils.calculate_md5(consensus_file), + # TODO: Not sure this is correct. If not, recover previous version: https://github.com/BU-ISCIII/relecov-tools/blob/09c00c1ddd11f7489de7757841aff506ef4b7e1d/relecov_tools/read_bioinfo_metadata.py#L211-L218 + 'number_of_base_pairs_sequenced': len(record_fasta.seq) + } + + # Report missing consensus + conserrs = len(missing_consens) + if conserrs >= 1: + method_log_report.update_log_report( + method_name, + 'warning', + f"{conserrs} samples missing in consensus file: {missing_consens}" + ) + method_log_report.print_log_report(method_name, ['valid','warning']) + return consensus_data_processed diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index 9df5f3aa..262f6e98 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -10,6 +10,7 @@ import relecov_tools from relecov_tools.config_json import ConfigJson +import relecov_tools.utils # from relecov_tools.rest_api import RestApi @@ -56,9 +57,15 @@ def __init__(self, file_path=None, output_directory=None, j_data=None): sys.exit(1) if output_directory is None: - self.output_directory = relecov_tools.utils.prompt_path( - msg="Select the output folder" + use_default = relecov_tools.utils.prompt_yn_question( + "Use default path?: " ) + if use_default: + self.output_directory = os.getcwd() + else: + self.output_directory = relecov_tools.utils.prompt_path( + msg="Select the output folder:" + ) else: self.output_directory = output_directory Path(self.output_directory).mkdir(parents=True, exist_ok=True) @@ -69,11 +76,12 @@ def __init__(self, file_path=None, output_directory=None, j_data=None): self.software_config = config_json.get_configuration('viralrecon') self.long_table_heading = self.software_config["variants_long_table"]["content"] - if not j_data: - stderr.print("[red]\tError: No read lab metadata file found. Long-table-parsing aborted.") - sys.exit(1) - else: - self.j_data = j_data + # FIXME: See fixme details in function parse_long_table relecov_tools.assets.pipeline_utils.viralrecon. + #if not j_data: + # stderr.print("[red]\tError: No read lab metadata file found. #Long-table-parsing aborted.") + # sys.exit(1) + #else: + # self.j_data = j_data def validate_file(self, heading): """Check if long table file has all mandatory fields defined in @@ -165,15 +173,16 @@ def save_to_file(self, j_list): except Exception as e: stderr.print("[red]\tError saving parsed data to file:", str(e)) - def add_custom_longtable_data(self, j_data): - """Auxiliary function to add custom fields likevariant-long-table into j_data""" - if len(self.file_path) == 0: - long_table_path = "Not Provided [GENEPIO:0001668]" - else: - long_table_path = self.file_path - for row in j_data: - row["long_table_path"] = str(long_table_path) - return j_data + # FIXME: See fixme details in function parse_long_table relecov_tools.assets.pipeline_utils.viralrecon. + #def add_custom_longtable_data(self, j_data): + # """Auxiliary function to add custom fields likevariant-long-table #into j_data""" + # if len(self.file_path) == 0: + # long_table_path = "Not Provided [GENEPIO:0001668]" + # else: + # long_table_path = self.file_path + # for row in j_data: + # row["long_table_path"] = str(long_table_path) + # return j_data def parsing_csv(self): """ diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index e5f08f8c..68d01c9a 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -10,7 +10,6 @@ import relecov_tools.utils from relecov_tools.config_json import ConfigJson -from relecov_tools.long_table_parse import LongTableParse log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -52,8 +51,6 @@ def print_log_report(self, name, sections): # TODO: Add method to validate bioinfo_config.json file requirements. # TODO: replace submitting_lab_id by sequencing_sample_id -# TODO: mv pipeline-specific methods to future assets/pipeline_utils/ -# fixme: INCOMING IMPLEMENTATION ---> REPORT LOG IS NOW A CLASS. class BioinfoMetadata(BioinfoReportLog): def __init__( self, @@ -309,10 +306,14 @@ def handling_files(self, file_list): sys.exit(self.log_report.print_log_report(method_name,["error"])) else: try: - # Attempt to get the method by name - method_to_call = getattr(self, func_name) - data = method_to_call(file_list) - except AttributeError as e: + # Dynamically import the function from the specified module + utils_name = f"relecov_tools.assets.pipeline_utils.{self.software_name}" + import_statement = f"from {utils_name} import {func_name}" + exec(import_statement) + + # Get method name and execute it. + data = eval(func_name + "(file_list)") + except Exception as e: self.log_report.update_log_report( self.add_bioinfo_results_metadata.__name__, 'error', @@ -450,112 +451,6 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): self.log_report.print_log_report(method_name,["warning","valid"]) return j_data - def handle_pangolin_data(self, files_list): - """File handler to parse pangolin data (csv) into JSON structured format. - """ - method_name=f"{self.add_bioinfo_results_metadata.__name__}:{self.handle_pangolin_data.__name__}" - # Handling pangolin data - pango_data_processed = {} - try: - files_list_processed = relecov_tools.utils.select_most_recent_files_per_sample(files_list) - for pango_file in files_list_processed: - try: - pango_data = relecov_tools.utils.read_csv_file_return_dict( - pango_file, sep="," - ) - # Add custom content in pangolin - pango_data_key = next(iter(pango_data)) - pango_data[pango_data_key]['lineage_analysis_date'] = relecov_tools.utils.get_file_date( - pango_file - ) - - # Rename key in f_data - pango_data_updated = {key.split()[0]: value for key, value in pango_data.items()} - pango_data_processed.update(pango_data_updated) - self.log_report.update_log_report( - method_name, - 'valid', - f"Successfully handled data in {pango_file}." - ) - except (FileNotFoundError, IndexError) as e: - self.log_report.update_log_report( - method_name, - 'error', - f"Error processing file {pango_file}: {e}" - ) - sys.exit(self.log_report.print_log_report(method_name,["error"])) - except Exception as e: - self.log_report.update_log_report( - method_name, - 'error' - f"Error occurred while processing files: {e}" - ) - sys.exit(self.log_report.print_log_report(method_name,["error"])) - return pango_data_processed - - def handle_consensus_fasta(self, files_list): - """File handler to parse consensus fasta data (*.consensus.fa) into JSON structured format""" - method_name=f"{self.add_bioinfo_results_metadata.__name__}:{self.handle_consensus_fasta.__name__}" - consensus_data_processed = {} - missing_consens = [] - for consensus_file in files_list: - try: - record_fasta = relecov_tools.utils.read_fasta_return_SeqIO_instance( - consensus_file - ) - except FileNotFoundError as e: - missing_consens.append(e.filename) - continue - sample_key = re.sub(self.software_config['mapping_consensus']['fn'], '', os.path.basename(consensus_file)) - - # Update consensus data for the sample key - consensus_data_processed[sample_key] = { - 'sequence_name': record_fasta.description, - 'genome_length': str(len(record_fasta)), - 'sequence_filepath': os.path.dirname(consensus_file), - 'sequence_filename': sample_key, - 'sequence_md5': relecov_tools.utils.calculate_md5(consensus_file), - # TODO: Not sure this is correct. If not, recover previous version: https://github.com/BU-ISCIII/relecov-tools/blob/09c00c1ddd11f7489de7757841aff506ef4b7e1d/relecov_tools/read_bioinfo_metadata.py#L211-L218 - 'number_of_base_pairs_sequenced': len(record_fasta.seq) - } - - # Report missing consensus - conserrs = len(missing_consens) - if conserrs >= 1: - self.log_report.update_log_report( - method_name, - 'warning', - f"{conserrs} samples missing in consensus file: {missing_consens}" - ) - return consensus_data_processed - - def parse_long_table(self, files_list): - method_name = f"{self.parse_long_table.__name__}" - # Hanfling long table data - - if len(files_list) == 1: - files_list_processed = files_list[0] - if not os.path.isfile(files_list_processed): - self.log_report.update_log_report( - method_name, - 'error', - f"{files_list_processed} given file is not a file" - ) - sys.exit(self.log_report.print_log_report(method_name,["error"])) - long_table = LongTableParse(files_list_processed, self.output_folder, self.j_data) - # Parsing long table data and saving it - long_table.parsing_csv() - # Adding custom long_table data to j_data - self.j_data = long_table.add_custom_longtable_data(self.j_data) - elif len(files_list) >1: - self.log_report.update_log_report( - method_name, - 'warning', - f"Found {len(files_list)} variants_long_table files. This version is unable to process more than one variants long table each time." - ) - # This needs to return none to avoid being parsed by method mapping-over-table - return None - # TODO: this is too harcoded. Find a way to add file's path of required files when calling handlers functions. def add_fixed_values(self, j_data): """include the fixed data defined in configuration or feed custom empty fields""" From d84358b4447504788f5f1608726f1b3e310fe7dd Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Sat, 6 Apr 2024 20:15:19 +0200 Subject: [PATCH 1294/1454] improve description and remove already accomplished todo tasks --- relecov_tools/read_bioinfo_metadata.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 68d01c9a..71dea5c7 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -258,6 +258,7 @@ def handling_files(self, file_list): }, ... } + Note: ensure that 'field1','field2','field3' corresponds with the values especifies in the 'content' section of each software configuration scope (see: conf/bioinfo_config.json). Input: file_list (list): A list of file path/s to be processed. @@ -451,7 +452,6 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): self.log_report.print_log_report(method_name,["warning","valid"]) return j_data - # TODO: this is too harcoded. Find a way to add file's path of required files when calling handlers functions. def add_fixed_values(self, j_data): """include the fixed data defined in configuration or feed custom empty fields""" method_name=f"{self.add_fixed_values.__name__}" @@ -504,9 +504,6 @@ def create_bioinfo_file(self): self.j_data = self.add_bioinfo_results_metadata(files_found_dict, self.j_data) stderr.print("[blue]Adding software versions to read lab metadata...") self.j_data = self.get_multiqc_software_versions(files_found_dict['workflow_summary'], self.j_data) - # FIXME: this isn't refactored and requires to be reimplemented from older version of this module - ##stderr.print("[blue]Adding variant long table path") - ##j_data = self.include_custom_data(j_data) stderr.print("[blue]Adding fixed values") self.j_data = self.add_fixed_values(self.j_data) # Generate readlab + bioinfolab processed metadata. From 2ba03f74114672d3808d51a8abb6b2bc58e6c891 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Sun, 7 Apr 2024 17:03:55 +0200 Subject: [PATCH 1295/1454] fix flake8 linting --- .../assets/pipeline_utils/viralrecon.py | 21 +-- relecov_tools/long_table_parse.py | 36 ++--- relecov_tools/read_bioinfo_metadata.py | 137 ++++++++---------- relecov_tools/utils.py | 14 +- 4 files changed, 97 insertions(+), 111 deletions(-) diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py index a57582a6..103cdd8a 100644 --- a/relecov_tools/assets/pipeline_utils/viralrecon.py +++ b/relecov_tools/assets/pipeline_utils/viralrecon.py @@ -1,16 +1,15 @@ #!/usr/bin/env python import os import sys -import re import logging import relecov_tools.utils from relecov_tools.read_bioinfo_metadata import BioinfoReportLog -from relecov_tools.read_bioinfo_metadata import BioinfoMetadata from relecov_tools.long_table_parse import LongTableParse log = logging.getLogger(__name__) + def handle_pangolin_data(files_list): """File handler to parse pangolin data (csv) into JSON structured format. """ @@ -37,13 +36,13 @@ def handle_pangolin_data(files_list): pango_data_processed.update(pango_data_updated) method_log_report.update_log_report( method_name, - 'valid', + 'valid', f"Successfully handled data in {pango_file}." ) except (FileNotFoundError, IndexError) as e: method_log_report.update_log_report( method_name, - 'error', + 'error', f"Error processing file {pango_file}: {e}" ) sys.exit( @@ -60,6 +59,7 @@ def handle_pangolin_data(files_list): ) return pango_data_processed + def parse_long_table(files_list): method_name = f"{parse_long_table.__name__}" method_log_report = BioinfoReportLog() @@ -73,7 +73,7 @@ def parse_long_table(files_list): 'error', f"{files_list_processed} given file is not a file" ) - sys.exit(method_log_report.print_log_report(method_name,["error"])) + sys.exit(method_log_report.print_log_report(method_name, ["error"])) long_table = LongTableParse(files_list_processed) # Parsing long table data and saving it long_table.parsing_csv() @@ -82,13 +82,14 @@ def parse_long_table(files_list): # self.j_data = long_table.add_custom_longtable_data(self.j_data) elif len(files_list) > 1: method_log_report.update_log_report( - method_name, + method_name, 'warning', f"Found {len(files_list)} variants_long_table files. This version is unable to process more than one variants long table each time." ) - # This needs to return none to avoid being parsed by method mapping-over-table + # This needs to return none to avoid being parsed by method mapping-over-table return None + def handle_consensus_fasta(files_list): """File handler to parse consensus fasta data (*.consensus.fa) into JSON structured format""" method_name = f"{handle_consensus_fasta.__name__}" @@ -115,15 +116,15 @@ def handle_consensus_fasta(files_list): 'sequence_md5': relecov_tools.utils.calculate_md5(consensus_file), # TODO: Not sure this is correct. If not, recover previous version: https://github.com/BU-ISCIII/relecov-tools/blob/09c00c1ddd11f7489de7757841aff506ef4b7e1d/relecov_tools/read_bioinfo_metadata.py#L211-L218 'number_of_base_pairs_sequenced': len(record_fasta.seq) - } + } # Report missing consensus conserrs = len(missing_consens) if conserrs >= 1: method_log_report.update_log_report( method_name, - 'warning', + 'warning', f"{conserrs} samples missing in consensus file: {missing_consens}" ) - method_log_report.print_log_report(method_name, ['valid','warning']) + method_log_report.print_log_report(method_name, ['valid', 'warning']) return consensus_data_processed diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index 262f6e98..3e216576 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -72,16 +72,16 @@ def __init__(self, file_path=None, output_directory=None, j_data=None): json_file = os.path.join(os.path.dirname(__file__), "conf", "bioinfo_config.json") config_json = ConfigJson(json_file) - #self.long_table_heading = config_json.get_configuration("long_table_heading") + # self.long_table_heading = config_json.get_configuration("long_table_heading") self.software_config = config_json.get_configuration('viralrecon') self.long_table_heading = self.software_config["variants_long_table"]["content"] - # FIXME: See fixme details in function parse_long_table relecov_tools.assets.pipeline_utils.viralrecon. - #if not j_data: - # stderr.print("[red]\tError: No read lab metadata file found. #Long-table-parsing aborted.") - # sys.exit(1) - #else: - # self.j_data = j_data + # FIXME: See fixme details in function parse_long_table relecov_tools.assets.pipeline_utils.viralrecon. + # if not j_data: + # stderr.print("[red]\tError: No read lab metadata file found. #Long-table-parsing aborted.") + # sys.exit(1) + # else: + # self.j_data = j_data def validate_file(self, heading): """Check if long table file has all mandatory fields defined in @@ -172,17 +172,17 @@ def save_to_file(self, j_list): stderr.print("[green]\tParsed data successfully saved to file:", file_path) except Exception as e: stderr.print("[red]\tError saving parsed data to file:", str(e)) - - # FIXME: See fixme details in function parse_long_table relecov_tools.assets.pipeline_utils.viralrecon. - #def add_custom_longtable_data(self, j_data): - # """Auxiliary function to add custom fields likevariant-long-table #into j_data""" - # if len(self.file_path) == 0: - # long_table_path = "Not Provided [GENEPIO:0001668]" - # else: - # long_table_path = self.file_path - # for row in j_data: - # row["long_table_path"] = str(long_table_path) - # return j_data + + # FIXME: See fixme details in function parse_long_table relecov_tools.assets.pipeline_utils.viralrecon. + # def add_custom_longtable_data(self, j_data): + # """Auxiliary function to add custom fields likevariant-long-table #into j_data""" + # if len(self.file_path) == 0: + # long_table_path = "Not Provided [GENEPIO:0001668]" + # else: + # long_table_path = self.file_path + # for row in j_data: + # row["long_table_path"] = str(long_table_path) + # return j_data def parsing_csv(self): """ diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 71dea5c7..0a75a378 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -4,8 +4,6 @@ import logging import rich.console import re -from datetime import datetime -from yaml import YAMLError from bs4 import BeautifulSoup import relecov_tools.utils @@ -19,13 +17,14 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) + class BioinfoReportLog: def __init__(self, log_report=None): if not log_report: self.report = {'error': {}, 'valid': {}, 'warning': {}} else: self.report = log_report - + def update_log_report(self, method_name, status, message): """Update progress log report""" if status == 'valid': @@ -39,7 +38,7 @@ def update_log_report(self, method_name, status, message): return self.report else: raise ValueError("Invalid status provided.") - + def print_log_report(self, name, sections): """Calls log report printer.""" relecov_tools.utils.print_log_report( @@ -48,7 +47,7 @@ def print_log_report(self, name, sections): sections ) - + # TODO: Add method to validate bioinfo_config.json file requirements. # TODO: replace submitting_lab_id by sequencing_sample_id class BioinfoMetadata(BioinfoReportLog): @@ -60,10 +59,10 @@ def __init__( software=None, ): # Init process log - super().__init__() + super().__init__() self.log_report = BioinfoReportLog() - - # Parse read-lab-meta-data + + # Parse read-lab-meta-data if readlabmeta_json_file is None: readlabmeta_json_file = relecov_tools.utils.prompt_path( msg="Select the json file that was created by the read-lab-metadata" @@ -96,7 +95,7 @@ def __init__( ) else: self.output_folder = output_folder - + # Parse bioinfo configuration self.bioinfo_json_file = os.path.join(os.path.dirname(__file__), "conf", "bioinfo_config.json") if software is None: @@ -117,7 +116,7 @@ def __init__( sys.exit( self.log_report.print_log_report(self.__init__.__name__, ['error']) ) - + def get_available_software(self, json): """Get list of available software in configuration""" config = relecov_tools.utils.read_json_file(json) @@ -126,15 +125,15 @@ def get_available_software(self, json): def scann_directory(self): """Scanns bioinfo analysis directory and identifies files according to the file name patterns defined in the software configuration json.""" - method_name=f"{self.scann_directory.__name__}" + method_name = f"{self.scann_directory.__name__}" total_files = sum(len(files) for _, _, files in os.walk(self.input_folder)) files_found = {} - for topic_key, topic_scope in self.software_config.items(): - if 'fn' not in topic_scope: #try/except fn + for topic_key, topic_scope in self.software_config.items(): + if 'fn' not in topic_scope: # try/except fn self.log_report.update_log_report( method_name, - 'warning', + 'warning', f"No 'fn' (file pattern) found in '{self.software_name}.{topic_key}'." ) continue @@ -142,11 +141,10 @@ def scann_directory(self): matching_files = [os.path.join(root, file_name) for file_name in files if re.search(topic_scope['fn'], file_name)] if len(matching_files) >= 1: files_found[topic_key] = matching_files - if len(files_found) < 1: self.log_report.update_log_report( method_name, - 'error', + 'error', f"No files found in '{self.input_folder}' according to '{os.path.basename(self.bioinfo_json_file)}' file name patterns." ) sys.exit( @@ -155,15 +153,15 @@ def scann_directory(self): else: self.log_report.update_log_report( self.scann_directory.__name__, - 'valid', + 'valid', f"Scannig process succeed. Scanned {total_files} files." ) - self.log_report.print_log_report(method_name, ['valid','warning']) + self.log_report.print_log_report(method_name, ['valid', 'warning']) return files_found def validate_software_mandatory_files(self, files_dict): """"Validates the presence of all mandatory files as defined in the software configuration JSON.""" - method_name=f"{self.validate_software_mandatory_files.__name__}" + method_name = f"{self.validate_software_mandatory_files.__name__}" missing_required = [] for key in self.software_config: if self.software_config[key].get('required') is True: @@ -174,68 +172,63 @@ def validate_software_mandatory_files(self, files_dict): continue else: continue - if len(missing_required) >= 1: self.log_report.update_log_report( method_name, - 'error', + 'error', f"Missing mandatory files in {self.software_name}.{key}:{', '.join(missing_required)}" ) - sys.exit(self.log_report.print_log_report(method_name,["error"])) + sys.exit(self.log_report.print_log_report(method_name, ["error"])) else: self.log_report.update_log_report( method_name, - 'valid', + 'valid', "Successfull validation of mandatory files." ) - self.log_report.print_log_report(method_name, ['valid', 'waring']) return - + def add_bioinfo_results_metadata(self, files_dict, j_data): """ Adds metadata from bioinformatics results to j_data. 1. Handles metadata in bioinformatic files found. - 2. Mapping handled bioinfo metadata into j_data. + 2. Mapping handled bioinfo metadata into j_data. """ - method_name=f"{self.add_bioinfo_results_metadata.__name__}" + method_name = f"{self.add_bioinfo_results_metadata.__name__}" for key in self.software_config.keys(): # Update bioinfo cofiguration key/scope self.current_config_key = key # This skip files that will be parsed with other methods if key == 'workflow_summary' or key == "fixed_values": continue - try: files_dict[key] stderr.print(f"[blue]Start processing {self.software_name}.{key}") except KeyError: self.log_report.update_log_report( method_name, - 'warning', + 'warning', f"No file path found for '{self.software_name}.{key}'" ) continue - # Handling files data_to_map = self.handling_files(files_dict[key]) - # Mapping data to j_data if data_to_map: j_data_mapped = self.mapping_over_table( - j_data=j_data, - map_data=data_to_map, + j_data=j_data, + map_data=data_to_map, mapping_fields=self.software_config[key]['content'], table_name=files_dict[key] ) else: self.log_report.update_log_report( method_name, - 'warning', + 'warning', f"No metadata found to perform standard mapping when processing '{self.software_name}.{key}'" ) continue - self.log_report.print_log_report(method_name, ['valid','waring']) + self.log_report.print_log_report(method_name, ['valid', 'waring']) return j_data_mapped def handling_files(self, file_list): @@ -244,7 +237,6 @@ def handling_files(self, file_list): Handles different file formats to extract data regardless of their structure. The goal is to extract the data contained in files specified in ${file_list}, using either 'standard' handlers defined in this class or pipeline-specific file handlers. A file handler method must generate a data structure as follow: - { 'SAMPLE1': { 'field1': 'value1' @@ -258,7 +250,7 @@ def handling_files(self, file_list): }, ... } - Note: ensure that 'field1','field2','field3' corresponds with the values especifies in the 'content' section of each software configuration scope (see: conf/bioinfo_config.json). + Note: ensure that 'field1','field2','field3' corresponds with the values especifies in the 'content' section of each software configuration scope (see: conf/bioinfo_config.json). Input: file_list (list): A list of file path/s to be processed. @@ -266,24 +258,22 @@ def handling_files(self, file_list): Returns: dict: A single dictionary containing extracted data for each sample. """ - method_name=f"{self.add_bioinfo_results_metadata.__name__}:{self.handling_files.__name__}" + method_name = f"{self.add_bioinfo_results_metadata.__name__}:{self.handling_files.__name__}" file_name = self.software_config[self.current_config_key].get('fn') file_extension = os.path.splitext(file_name)[1] - # Parsing key position try: self.software_config[self.current_config_key]['sample_col_idx'] - sample_idx_possition = self.software_config[self.current_config_key]['sample_col_idx']-1 + sample_idx_possition = self.software_config[self.current_config_key]['sample_col_idx'] - 1 except KeyError: sample_idx_possition = None self.log_report.update_log_report( method_name, - 'warning', + 'warning', f"No sample-index-column defined in '{self.software_name}.{self.current_config_key}'. Using default instead." ) - # Parsing files - func_name = self.software_config[self.current_config_key]["function"] + func_name = self.software_config[self.current_config_key]["function"] if func_name is None: if file_name.endswith('.csv'): data = relecov_tools.utils.read_csv_file_return_dict( @@ -301,10 +291,10 @@ def handling_files(self, file_list): else: self.log_report.update_log_report( method_name, - 'error', + 'error', f"Unrecognized defined file name extension '{file_extension}' in '{file_name}'." ) - sys.exit(self.log_report.print_log_report(method_name,["error"])) + sys.exit(self.log_report.print_log_report(method_name, ["error"])) else: try: # Dynamically import the function from the specified module @@ -317,15 +307,15 @@ def handling_files(self, file_list): except Exception as e: self.log_report.update_log_report( self.add_bioinfo_results_metadata.__name__, - 'error', + 'error', f"Error occurred while parsing '{func_name}': {e}." ) - sys.exit(self.log_report.print_log_report(method_name,["error"])) + sys.exit(self.log_report.print_log_report(method_name, ["error"])) return data def get_multiqc_software_versions(self, file_list, j_data): """Reads multiqc html file, finds table containing software version info, and map it to j_data""" - method_name=f"{self.get_multiqc_software_versions.__name__}" + method_name = f"{self.get_multiqc_software_versions.__name__}" # Handle multiqc_report.html f_path = file_list[0] program_versions = {} @@ -339,7 +329,7 @@ def get_multiqc_software_versions(self, file_list, j_data): table = versions_div.find('table', class_='table') if table: rows = table.find_all('tr') - for row in rows[1:]: #skipping header + for row in rows[1:]: # skipping header columns = row.find_all('td') if len(columns) == 3: program_name = columns[1].text.strip() @@ -348,24 +338,24 @@ def get_multiqc_software_versions(self, file_list, j_data): else: self.log_report.update_log_report( method_name, - 'error', + 'error', f"HTML entry error in {columns}. HTML table expected format should be \n Process Name\n\n Software \n." ) - sys.exit(self.log_report.print_log_report(method_name,["error"])) + sys.exit(self.log_report.print_log_report(method_name, ["error"])) else: self.log_report.update_log_report( method_name, - 'error', + 'error', f"Unable to locate the table containing software versions in file {f_path} under div section {div_id}." ) - sys.exit(self.log_report.print_log_report(method_name,["error"])) + sys.exit(self.log_report.print_log_report(method_name, ["error"])) else: self.log_report.update_log_report( self.get_multiqc_software_versions.__name__, - 'error', + 'error', f"Failed to locate the required '{div_id}' div section in the '{f_path}' file." ) - sys.exit(self.log_report.print_log_report(method_name,["error"])) + sys.exit(self.log_report.print_log_report(method_name, ["error"])) # Mapping multiqc sofware versions to j_data field_errors = {} @@ -376,30 +366,30 @@ def get_multiqc_software_versions(self, file_list, j_data): row[field] = program_versions[values] except KeyError as e: field_errors[sample_name] = {field: e} - row[field] = "Not Provided [GENEPIO:0001668]" + row[field] = "Not Provided [GENEPIO:0001668]" continue # update progress log if len(field_errors) > 0: self.log_report.update_log_report( method_name, - 'warning', + 'warning', f"Encountered field errors while mapping data: {field_errors}" ) else: self.log_report.update_log_report( method_name, - 'valid', + 'valid', "Successfully mapped data." ) - self.log_report.print_log_report(method_name,["valid","warning"]) + self.log_report.print_log_report(method_name, ["valid", "warning"]) return j_data def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): """ Function that maps structure data containing fields per sample into j_data. """ - method_name=f"{self.mapping_over_table.__name__}:{self.software_name}.{self.current_config_key}" + method_name = f"{self.mapping_over_table.__name__}:{self.software_name}.{self.current_config_key}" errors = [] field_errors = {} field_vaild = {} @@ -409,7 +399,7 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): for field, value in mapping_fields.items(): try: row[field] = map_data[sample_name][value] - field_vaild[sample_name] = {field:value} + field_vaild[sample_name] = {field: value} except KeyError as e: field_errors[sample_name] = {field: e} row[field] = "Not Provided [GENEPIO:0001668]" @@ -427,34 +417,33 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): table_name = table_name[0] self.log_report.update_log_report( method_name, - 'warning', + 'warning', f"{lenerrs} samples missing in '{table_name}': {', '.join(errors)}." ) else: self.log_report.update_log_report( method_name, - 'valid', + 'valid', "Successfully mapped data." ) - if len(field_errors) > 0: self.log_report.update_log_report( method_name, - 'warning', + 'warning', f"Missing fields in {table_name}:\n\t{field_errors}" ) else: self.log_report.update_log_report( method_name, - 'valid', + 'valid', f"Successfully mapped fields in {', '.join(field_vaild.keys())} - {table_name}." ) - self.log_report.print_log_report(method_name,["warning","valid"]) + self.log_report.print_log_report(method_name, ["valid", "warning"]) return j_data def add_fixed_values(self, j_data): """include the fixed data defined in configuration or feed custom empty fields""" - method_name=f"{self.add_fixed_values.__name__}" + method_name = f"{self.add_fixed_values.__name__}" try: f_values = self.software_config["fixed_values"] for row in j_data: @@ -472,14 +461,14 @@ def add_fixed_values(self, j_data): f"Error found while adding fixed values: {e}" ) pass - self.log_report.print_log_report(method_name,["valid","waring"]) + self.log_report.print_log_report(method_name, ["valid", "waring"]) return j_data def collect_info_from_lab_json(self): """Create the list of dictionaries from the data that is on json lab metadata file. Return j_data that is used to add the rest of the fields """ - method_name=f"{self.collect_info_from_lab_json.__name__}" + method_name = f"{self.collect_info_from_lab_json.__name__}" try: json_lab_data = relecov_tools.utils.read_json_file(self.readlabmeta_json_file) except ValueError: @@ -488,7 +477,7 @@ def collect_info_from_lab_json(self): 'error', f"Invalid lab-metadata json file: self.{self.readlabmeta_json_file}" ) - sys.exit(self.log_report.print_log_report(method_name,["error"])) + sys.exit(self.log_report.print_log_report(method_name, ["error"])) return json_lab_data def create_bioinfo_file(self): @@ -503,13 +492,13 @@ def create_bioinfo_file(self): stderr.print(f"[blue]Adding metadata from {self.input_folder} into read lab metadata...") self.j_data = self.add_bioinfo_results_metadata(files_found_dict, self.j_data) stderr.print("[blue]Adding software versions to read lab metadata...") - self.j_data = self.get_multiqc_software_versions(files_found_dict['workflow_summary'], self.j_data) + self.j_data = self.get_multiqc_software_versions(files_found_dict['workflow_summary'], self.j_data) stderr.print("[blue]Adding fixed values") self.j_data = self.add_fixed_values(self.j_data) # Generate readlab + bioinfolab processed metadata. file_name = ( - "bioinfo_" - + os.path.splitext(os.path.basename(self.readlabmeta_json_file))[0] + "bioinfo_" + + os.path.splitext(os.path.basename(self.readlabmeta_json_file))[0] + ".json" ) stderr.print("[blue]Writting output json file") diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 338d6e6d..31cb9c4b 100755 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -311,6 +311,7 @@ def prompt_checkbox(msg, choices): selected_options = questionary.checkbox(msg, choices=choices).unsafe_ask() return selected_options + def get_file_date(file_path): """Get the modification date of a file.""" try: @@ -326,6 +327,7 @@ def get_file_date(file_path): print(f"File not found: {file_path}") return None + def select_most_recent_files_per_sample(paths_list): """Selects the most recent file for each sample among potentially duplicated files. Input: @@ -336,34 +338,31 @@ def select_most_recent_files_per_sample(paths_list): filename_groups = {} # Count occurrences of each filename and group files by sample names for file in paths_list: - # TODO: So far, it uses split method to identify this pattern: [sample1.pangolin.csv, sample1.pangolin_20240310.csv]. It should be improve to parse files based on a different character matching field. + # TODO: So far, it uses split method to identify this pattern: [sample1.pangolin.csv, sample1.pangolin_20240310.csv]. It should be improve to parse files based on a different character matching field. file_name = os.path.basename(file).split('.')[0] if file_name in filename_groups : filename_groups[file_name].append(file) else: filename_groups[file_name] = [file] - # Filter out sample names with only one file duplicated_files = [(sample_name, file_paths) for sample_name, file_paths in filename_groups.items() if len(file_paths) > 1] - # Iterate over duplicated files to select the most recent one for each sample for sample_name, file_paths in duplicated_files: stderr.print(f"\tMore than one file found for sample {sample_name}. Selecting the most recent one.") # Sort files by modification time (most recent first) - sorted_files = sorted(file_paths, key=lambda file_path: os.path.getmtime (file_path), reverse=True) + sorted_files = sorted(file_paths, key=lambda file_path: os.path.getmtime(file_path), reverse=True) # Select the most recent file selected_file = sorted_files[0] stderr.print(f"\tSelected file for sample {sample_name}: {selected_file}") # Remove other files for the same sample from the filtered_files dictionary filename_groups[sample_name] = [selected_file] - # Update filename_groups with filtered files filename_groups = [(sample_name, file_path) for sample_name, file_paths in filename_groups.items() for file_path in file_paths] - # Reformat variable to retrieve a list of file paths file_path_list = [sample_file_path for _, sample_file_path in filename_groups] return file_path_list + def print_log_report(log_report, categories=None, sections=["warning", "valid", "error"]): color_codes = { "error": "\033[91m", # Red @@ -371,7 +370,6 @@ def print_log_report(log_report, categories=None, sections=["warning", "valid", "valid": "\033[92m", # Green "reset": "\033[0m" # Reset color } - table_data = [] for section_name, section_data in log_report.items(): if section_name in sections: @@ -381,6 +379,4 @@ def print_log_report(log_report, categories=None, sections=["warning", "valid", for item in items: colored_message = f"{color_codes[section_name]}{item}{color_codes['reset']}" table_data.append([section_name, colored_category, colored_message]) - print(tabulate(table_data, headers=["Log type", "Category", "Message"], tablefmt="fancy_grid")) - From ddfc9b54a20a28362c70a957ed5916c3fd64ea30 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Sun, 7 Apr 2024 17:06:53 +0200 Subject: [PATCH 1296/1454] fix black linting --- relecov_tools/__main__.py | 5 +- .../assets/pipeline_utils/viralrecon.py | 61 +++--- relecov_tools/long_table_parse.py | 10 +- relecov_tools/read_bioinfo_metadata.py | 204 +++++++++--------- relecov_tools/utils.py | 58 +++-- 5 files changed, 178 insertions(+), 160 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index cb89ab25..754618e8 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -424,7 +424,10 @@ def read_bioinfo_metadata(json_file, input_folder, out_dir, software_name): Create the json compliant from the Bioinfo Metadata. """ new_bioinfo_metadata = relecov_tools.read_bioinfo_metadata.BioinfoMetadata( - json_file, input_folder, out_dir, software_name, + json_file, + input_folder, + out_dir, + software_name, ) new_bioinfo_metadata.create_bioinfo_file() diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py index 103cdd8a..d33fc1e4 100644 --- a/relecov_tools/assets/pipeline_utils/viralrecon.py +++ b/relecov_tools/assets/pipeline_utils/viralrecon.py @@ -11,15 +11,16 @@ def handle_pangolin_data(files_list): - """File handler to parse pangolin data (csv) into JSON structured format. - """ + """File handler to parse pangolin data (csv) into JSON structured format.""" method_name = f"{handle_pangolin_data.__name__}" method_log_report = BioinfoReportLog() # Handling pangolin data pango_data_processed = {} try: - files_list_processed = relecov_tools.utils.select_most_recent_files_per_sample(files_list) + files_list_processed = relecov_tools.utils.select_most_recent_files_per_sample( + files_list + ) for pango_file in files_list_processed: try: pango_data = relecov_tools.utils.read_csv_file_return_dict( @@ -27,36 +28,28 @@ def handle_pangolin_data(files_list): ) # Add custom content in pangolin pango_data_key = next(iter(pango_data)) - pango_data[pango_data_key]['lineage_analysis_date'] = relecov_tools.utils.get_file_date( - pango_file + pango_data[pango_data_key]["lineage_analysis_date"] = ( + relecov_tools.utils.get_file_date(pango_file) ) # Rename key in f_data - pango_data_updated = {key.split()[0]: value for key, value in pango_data.items()} + pango_data_updated = { + key.split()[0]: value for key, value in pango_data.items() + } pango_data_processed.update(pango_data_updated) method_log_report.update_log_report( - method_name, - 'valid', - f"Successfully handled data in {pango_file}." + method_name, "valid", f"Successfully handled data in {pango_file}." ) except (FileNotFoundError, IndexError) as e: method_log_report.update_log_report( - method_name, - 'error', - f"Error processing file {pango_file}: {e}" - ) - sys.exit( - method_log_report.print_log_report(method_name, ['error']) + method_name, "error", f"Error processing file {pango_file}: {e}" ) + sys.exit(method_log_report.print_log_report(method_name, ["error"])) except Exception as e: method_log_report.update_log_report( - method_name, - 'error', - f"Error occurred while processing files: {e}" - ) - sys.exit( - method_log_report.print_log_report(method_name, ['error']) + method_name, "error", f"Error occurred while processing files: {e}" ) + sys.exit(method_log_report.print_log_report(method_name, ["error"])) return pango_data_processed @@ -69,9 +62,7 @@ def parse_long_table(files_list): files_list_processed = files_list[0] if not os.path.isfile(files_list_processed): method_log_report.update_log_report( - method_name, - 'error', - f"{files_list_processed} given file is not a file" + method_name, "error", f"{files_list_processed} given file is not a file" ) sys.exit(method_log_report.print_log_report(method_name, ["error"])) long_table = LongTableParse(files_list_processed) @@ -83,8 +74,8 @@ def parse_long_table(files_list): elif len(files_list) > 1: method_log_report.update_log_report( method_name, - 'warning', - f"Found {len(files_list)} variants_long_table files. This version is unable to process more than one variants long table each time." + "warning", + f"Found {len(files_list)} variants_long_table files. This version is unable to process more than one variants long table each time.", ) # This needs to return none to avoid being parsed by method mapping-over-table return None @@ -109,13 +100,13 @@ def handle_consensus_fasta(files_list): # Update consensus data for the sample key consensus_data_processed[sample_key] = { - 'sequence_name': record_fasta.description, - 'genome_length': str(len(record_fasta)), - 'sequence_filepath': os.path.dirname(consensus_file), - 'sequence_filename': sample_key, - 'sequence_md5': relecov_tools.utils.calculate_md5(consensus_file), + "sequence_name": record_fasta.description, + "genome_length": str(len(record_fasta)), + "sequence_filepath": os.path.dirname(consensus_file), + "sequence_filename": sample_key, + "sequence_md5": relecov_tools.utils.calculate_md5(consensus_file), # TODO: Not sure this is correct. If not, recover previous version: https://github.com/BU-ISCIII/relecov-tools/blob/09c00c1ddd11f7489de7757841aff506ef4b7e1d/relecov_tools/read_bioinfo_metadata.py#L211-L218 - 'number_of_base_pairs_sequenced': len(record_fasta.seq) + "number_of_base_pairs_sequenced": len(record_fasta.seq), } # Report missing consensus @@ -123,8 +114,8 @@ def handle_consensus_fasta(files_list): if conserrs >= 1: method_log_report.update_log_report( method_name, - 'warning', - f"{conserrs} samples missing in consensus file: {missing_consens}" + "warning", + f"{conserrs} samples missing in consensus file: {missing_consens}", ) - method_log_report.print_log_report(method_name, ['valid', 'warning']) + method_log_report.print_log_report(method_name, ["valid", "warning"]) return consensus_data_processed diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index 3e216576..1f6e6b95 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -57,9 +57,7 @@ def __init__(self, file_path=None, output_directory=None, j_data=None): sys.exit(1) if output_directory is None: - use_default = relecov_tools.utils.prompt_yn_question( - "Use default path?: " - ) + use_default = relecov_tools.utils.prompt_yn_question("Use default path?: ") if use_default: self.output_directory = os.getcwd() else: @@ -70,10 +68,12 @@ def __init__(self, file_path=None, output_directory=None, j_data=None): self.output_directory = output_directory Path(self.output_directory).mkdir(parents=True, exist_ok=True) - json_file = os.path.join(os.path.dirname(__file__), "conf", "bioinfo_config.json") + json_file = os.path.join( + os.path.dirname(__file__), "conf", "bioinfo_config.json" + ) config_json = ConfigJson(json_file) # self.long_table_heading = config_json.get_configuration("long_table_heading") - self.software_config = config_json.get_configuration('viralrecon') + self.software_config = config_json.get_configuration("viralrecon") self.long_table_heading = self.software_config["variants_long_table"]["content"] # FIXME: See fixme details in function parse_long_table relecov_tools.assets.pipeline_utils.viralrecon. diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 0a75a378..7b508533 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -21,31 +21,27 @@ class BioinfoReportLog: def __init__(self, log_report=None): if not log_report: - self.report = {'error': {}, 'valid': {}, 'warning': {}} + self.report = {"error": {}, "valid": {}, "warning": {}} else: self.report = log_report def update_log_report(self, method_name, status, message): """Update progress log report""" - if status == 'valid': - self.report['valid'].setdefault(method_name, []).append(message) + if status == "valid": + self.report["valid"].setdefault(method_name, []).append(message) return self.report - elif status == 'error': - self.report['error'].setdefault(method_name, []).append(message) + elif status == "error": + self.report["error"].setdefault(method_name, []).append(message) return self.report - elif status == 'warning': - self.report['warning'].setdefault(method_name, []).append(message) + elif status == "warning": + self.report["warning"].setdefault(method_name, []).append(message) return self.report else: raise ValueError("Invalid status provided.") def print_log_report(self, name, sections): """Calls log report printer.""" - relecov_tools.utils.print_log_report( - self.report, - name, - sections - ) + relecov_tools.utils.print_log_report(self.report, name, sections) # TODO: Add method to validate bioinfo_config.json file requirements. @@ -70,11 +66,11 @@ def __init__( if not os.path.isfile(readlabmeta_json_file): self.log_report.update_log_report( self.__init__.__name__, - 'error', - f"file {readlabmeta_json_file} does not exist" + "error", + f"file {readlabmeta_json_file} does not exist", ) sys.exit( - self.log_report.print_log_report(self.__init__.__name__, ['error']) + self.log_report.print_log_report(self.__init__.__name__, ["error"]) ) self.readlabmeta_json_file = readlabmeta_json_file @@ -97,7 +93,9 @@ def __init__( self.output_folder = output_folder # Parse bioinfo configuration - self.bioinfo_json_file = os.path.join(os.path.dirname(__file__), "conf", "bioinfo_config.json") + self.bioinfo_json_file = os.path.join( + os.path.dirname(__file__), "conf", "bioinfo_config.json" + ) if software is None: software = relecov_tools.utils.prompt_path( msg="Select the software, pipeline or tool use in the bioinformatic analysis: " @@ -110,11 +108,11 @@ def __init__( else: self.log_report.update_log_report( self.__init__.__name__, - 'error', - f"No configuration available for '{self.software_name}'. Currently, the only available software options are:: {', '.join(available_software)}" + "error", + f"No configuration available for '{self.software_name}'. Currently, the only available software options are:: {', '.join(available_software)}", ) sys.exit( - self.log_report.print_log_report(self.__init__.__name__, ['error']) + self.log_report.print_log_report(self.__init__.__name__, ["error"]) ) def get_available_software(self, json): @@ -130,41 +128,43 @@ def scann_directory(self): files_found = {} for topic_key, topic_scope in self.software_config.items(): - if 'fn' not in topic_scope: # try/except fn + if "fn" not in topic_scope: # try/except fn self.log_report.update_log_report( method_name, - 'warning', - f"No 'fn' (file pattern) found in '{self.software_name}.{topic_key}'." + "warning", + f"No 'fn' (file pattern) found in '{self.software_name}.{topic_key}'.", ) continue for root, _, files in os.walk(self.input_folder, topdown=True): - matching_files = [os.path.join(root, file_name) for file_name in files if re.search(topic_scope['fn'], file_name)] + matching_files = [ + os.path.join(root, file_name) + for file_name in files + if re.search(topic_scope["fn"], file_name) + ] if len(matching_files) >= 1: files_found[topic_key] = matching_files if len(files_found) < 1: self.log_report.update_log_report( method_name, - 'error', - f"No files found in '{self.input_folder}' according to '{os.path.basename(self.bioinfo_json_file)}' file name patterns." - ) - sys.exit( - self.log_report.print_log_report(method_name, ["error"]) + "error", + f"No files found in '{self.input_folder}' according to '{os.path.basename(self.bioinfo_json_file)}' file name patterns.", ) + sys.exit(self.log_report.print_log_report(method_name, ["error"])) else: self.log_report.update_log_report( self.scann_directory.__name__, - 'valid', - f"Scannig process succeed. Scanned {total_files} files." + "valid", + f"Scannig process succeed. Scanned {total_files} files.", ) - self.log_report.print_log_report(method_name, ['valid', 'warning']) + self.log_report.print_log_report(method_name, ["valid", "warning"]) return files_found def validate_software_mandatory_files(self, files_dict): - """"Validates the presence of all mandatory files as defined in the software configuration JSON.""" + """ "Validates the presence of all mandatory files as defined in the software configuration JSON.""" method_name = f"{self.validate_software_mandatory_files.__name__}" missing_required = [] for key in self.software_config: - if self.software_config[key].get('required') is True: + if self.software_config[key].get("required") is True: try: files_dict[key] except KeyError: @@ -175,17 +175,15 @@ def validate_software_mandatory_files(self, files_dict): if len(missing_required) >= 1: self.log_report.update_log_report( method_name, - 'error', - f"Missing mandatory files in {self.software_name}.{key}:{', '.join(missing_required)}" + "error", + f"Missing mandatory files in {self.software_name}.{key}:{', '.join(missing_required)}", ) sys.exit(self.log_report.print_log_report(method_name, ["error"])) else: self.log_report.update_log_report( - method_name, - 'valid', - "Successfull validation of mandatory files." + method_name, "valid", "Successfull validation of mandatory files." ) - self.log_report.print_log_report(method_name, ['valid', 'waring']) + self.log_report.print_log_report(method_name, ["valid", "waring"]) return def add_bioinfo_results_metadata(self, files_dict, j_data): @@ -199,7 +197,7 @@ def add_bioinfo_results_metadata(self, files_dict, j_data): # Update bioinfo cofiguration key/scope self.current_config_key = key # This skip files that will be parsed with other methods - if key == 'workflow_summary' or key == "fixed_values": + if key == "workflow_summary" or key == "fixed_values": continue try: files_dict[key] @@ -207,8 +205,8 @@ def add_bioinfo_results_metadata(self, files_dict, j_data): except KeyError: self.log_report.update_log_report( method_name, - 'warning', - f"No file path found for '{self.software_name}.{key}'" + "warning", + f"No file path found for '{self.software_name}.{key}'", ) continue # Handling files @@ -218,17 +216,17 @@ def add_bioinfo_results_metadata(self, files_dict, j_data): j_data_mapped = self.mapping_over_table( j_data=j_data, map_data=data_to_map, - mapping_fields=self.software_config[key]['content'], - table_name=files_dict[key] + mapping_fields=self.software_config[key]["content"], + table_name=files_dict[key], ) else: self.log_report.update_log_report( method_name, - 'warning', - f"No metadata found to perform standard mapping when processing '{self.software_name}.{key}'" + "warning", + f"No metadata found to perform standard mapping when processing '{self.software_name}.{key}'", ) continue - self.log_report.print_log_report(method_name, ['valid', 'waring']) + self.log_report.print_log_report(method_name, ["valid", "waring"]) return j_data_mapped def handling_files(self, file_list): @@ -259,40 +257,38 @@ def handling_files(self, file_list): dict: A single dictionary containing extracted data for each sample. """ method_name = f"{self.add_bioinfo_results_metadata.__name__}:{self.handling_files.__name__}" - file_name = self.software_config[self.current_config_key].get('fn') + file_name = self.software_config[self.current_config_key].get("fn") file_extension = os.path.splitext(file_name)[1] # Parsing key position try: - self.software_config[self.current_config_key]['sample_col_idx'] - sample_idx_possition = self.software_config[self.current_config_key]['sample_col_idx'] - 1 + self.software_config[self.current_config_key]["sample_col_idx"] + sample_idx_possition = ( + self.software_config[self.current_config_key]["sample_col_idx"] - 1 + ) except KeyError: sample_idx_possition = None self.log_report.update_log_report( method_name, - 'warning', - f"No sample-index-column defined in '{self.software_name}.{self.current_config_key}'. Using default instead." + "warning", + f"No sample-index-column defined in '{self.software_name}.{self.current_config_key}'. Using default instead.", ) # Parsing files func_name = self.software_config[self.current_config_key]["function"] if func_name is None: - if file_name.endswith('.csv'): + if file_name.endswith(".csv"): data = relecov_tools.utils.read_csv_file_return_dict( - file_name=file_list[0], - sep=",", - key_position=sample_idx_possition + file_name=file_list[0], sep=",", key_position=sample_idx_possition ) return data - elif file_name.endswith('.tsv') or file_name.endswith('.tab'): + elif file_name.endswith(".tsv") or file_name.endswith(".tab"): data = relecov_tools.utils.read_csv_file_return_dict( - file_name=file_list[0], - sep="\t", - key_position=sample_idx_possition + file_name=file_list[0], sep="\t", key_position=sample_idx_possition ) else: self.log_report.update_log_report( method_name, - 'error', - f"Unrecognized defined file name extension '{file_extension}' in '{file_name}'." + "error", + f"Unrecognized defined file name extension '{file_extension}' in '{file_name}'.", ) sys.exit(self.log_report.print_log_report(method_name, ["error"])) else: @@ -307,8 +303,8 @@ def handling_files(self, file_list): except Exception as e: self.log_report.update_log_report( self.add_bioinfo_results_metadata.__name__, - 'error', - f"Error occurred while parsing '{func_name}': {e}." + "error", + f"Error occurred while parsing '{func_name}': {e}.", ) sys.exit(self.log_report.print_log_report(method_name, ["error"])) return data @@ -320,17 +316,17 @@ def get_multiqc_software_versions(self, file_list, j_data): f_path = file_list[0] program_versions = {} - with open(f_path, 'r') as html_file: + with open(f_path, "r") as html_file: html_content = html_file.read() soup = BeautifulSoup(html_content, features="lxml") div_id = "mqc-module-section-software_versions" - versions_div = soup.find('div', id=div_id) + versions_div = soup.find("div", id=div_id) if versions_div: - table = versions_div.find('table', class_='table') + table = versions_div.find("table", class_="table") if table: - rows = table.find_all('tr') + rows = table.find_all("tr") for row in rows[1:]: # skipping header - columns = row.find_all('td') + columns = row.find_all("td") if len(columns) == 3: program_name = columns[1].text.strip() version = columns[2].text.strip() @@ -338,22 +334,24 @@ def get_multiqc_software_versions(self, file_list, j_data): else: self.log_report.update_log_report( method_name, - 'error', - f"HTML entry error in {columns}. HTML table expected format should be \n Process Name\n\n Software \n." + "error", + f"HTML entry error in {columns}. HTML table expected format should be \n Process Name\n\n Software \n.", + ) + sys.exit( + self.log_report.print_log_report(method_name, ["error"]) ) - sys.exit(self.log_report.print_log_report(method_name, ["error"])) else: self.log_report.update_log_report( method_name, - 'error', - f"Unable to locate the table containing software versions in file {f_path} under div section {div_id}." + "error", + f"Unable to locate the table containing software versions in file {f_path} under div section {div_id}.", ) sys.exit(self.log_report.print_log_report(method_name, ["error"])) else: self.log_report.update_log_report( self.get_multiqc_software_versions.__name__, - 'error', - f"Failed to locate the required '{div_id}' div section in the '{f_path}' file." + "error", + f"Failed to locate the required '{div_id}' div section in the '{f_path}' file.", ) sys.exit(self.log_report.print_log_report(method_name, ["error"])) @@ -361,7 +359,9 @@ def get_multiqc_software_versions(self, file_list, j_data): field_errors = {} for row in j_data: sample_name = row["submitting_lab_sample_id"] - for field, values in self.software_config['workflow_summary'].get('content').items(): + for field, values in ( + self.software_config["workflow_summary"].get("content").items() + ): try: row[field] = program_versions[values] except KeyError as e: @@ -373,14 +373,12 @@ def get_multiqc_software_versions(self, file_list, j_data): if len(field_errors) > 0: self.log_report.update_log_report( method_name, - 'warning', - f"Encountered field errors while mapping data: {field_errors}" + "warning", + f"Encountered field errors while mapping data: {field_errors}", ) else: self.log_report.update_log_report( - method_name, - 'valid', - "Successfully mapped data." + method_name, "valid", "Successfully mapped data." ) self.log_report.print_log_report(method_name, ["valid", "warning"]) return j_data @@ -412,31 +410,29 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): lenerrs = len(errors) # work around when map_data comes from several per-sample tables/files instead of single table (from list to str) if len(table_name) > 1: - table_name = (os.path.dirname(table_name[0])) + table_name = os.path.dirname(table_name[0]) else: table_name = table_name[0] self.log_report.update_log_report( method_name, - 'warning', - f"{lenerrs} samples missing in '{table_name}': {', '.join(errors)}." + "warning", + f"{lenerrs} samples missing in '{table_name}': {', '.join(errors)}.", ) else: self.log_report.update_log_report( - method_name, - 'valid', - "Successfully mapped data." + method_name, "valid", "Successfully mapped data." ) if len(field_errors) > 0: self.log_report.update_log_report( method_name, - 'warning', - f"Missing fields in {table_name}:\n\t{field_errors}" + "warning", + f"Missing fields in {table_name}:\n\t{field_errors}", ) else: self.log_report.update_log_report( method_name, - 'valid', - f"Successfully mapped fields in {', '.join(field_vaild.keys())} - {table_name}." + "valid", + f"Successfully mapped fields in {', '.join(field_vaild.keys())} - {table_name}.", ) self.log_report.print_log_report(method_name, ["valid", "warning"]) return j_data @@ -450,15 +446,11 @@ def add_fixed_values(self, j_data): for field, value in f_values.items(): row[field] = value self.log_report.update_log_report( - method_name, - 'valid', - "Fields added successfully." + method_name, "valid", "Fields added successfully." ) except KeyError as e: self.log_report.update_log_report( - method_name, - 'warning', - f"Error found while adding fixed values: {e}" + method_name, "warning", f"Error found while adding fixed values: {e}" ) pass self.log_report.print_log_report(method_name, ["valid", "waring"]) @@ -470,12 +462,14 @@ def collect_info_from_lab_json(self): """ method_name = f"{self.collect_info_from_lab_json.__name__}" try: - json_lab_data = relecov_tools.utils.read_json_file(self.readlabmeta_json_file) + json_lab_data = relecov_tools.utils.read_json_file( + self.readlabmeta_json_file + ) except ValueError: self.log_report.update_log_report( self.collect_info_from_lab_json.__name__, - 'error', - f"Invalid lab-metadata json file: self.{self.readlabmeta_json_file}" + "error", + f"Invalid lab-metadata json file: self.{self.readlabmeta_json_file}", ) sys.exit(self.log_report.print_log_report(method_name, ["error"])) return json_lab_data @@ -489,10 +483,14 @@ def create_bioinfo_file(self): files_found_dict = self.scann_directory() stderr.print("[blue]Validating required files...") self.validate_software_mandatory_files(files_found_dict) - stderr.print(f"[blue]Adding metadata from {self.input_folder} into read lab metadata...") + stderr.print( + f"[blue]Adding metadata from {self.input_folder} into read lab metadata..." + ) self.j_data = self.add_bioinfo_results_metadata(files_found_dict, self.j_data) stderr.print("[blue]Adding software versions to read lab metadata...") - self.j_data = self.get_multiqc_software_versions(files_found_dict['workflow_summary'], self.j_data) + self.j_data = self.get_multiqc_software_versions( + files_found_dict["workflow_summary"], self.j_data + ) stderr.print("[blue]Adding fixed values") self.j_data = self.add_fixed_values(self.j_data) # Generate readlab + bioinfolab processed metadata. diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 31cb9c4b..c1edcc83 100755 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -330,53 +330,79 @@ def get_file_date(file_path): def select_most_recent_files_per_sample(paths_list): """Selects the most recent file for each sample among potentially duplicated files. - Input: - - paths_list: a list of sample's file paths. - Output: - - List of file paths containig the most recent/up-to-date file for each sample. + Input: + - paths_list: a list of sample's file paths. + Output: + - List of file paths containig the most recent/up-to-date file for each sample. """ filename_groups = {} # Count occurrences of each filename and group files by sample names for file in paths_list: # TODO: So far, it uses split method to identify this pattern: [sample1.pangolin.csv, sample1.pangolin_20240310.csv]. It should be improve to parse files based on a different character matching field. - file_name = os.path.basename(file).split('.')[0] - if file_name in filename_groups : + file_name = os.path.basename(file).split(".")[0] + if file_name in filename_groups: filename_groups[file_name].append(file) else: filename_groups[file_name] = [file] # Filter out sample names with only one file - duplicated_files = [(sample_name, file_paths) for sample_name, file_paths in filename_groups.items() if len(file_paths) > 1] + duplicated_files = [ + (sample_name, file_paths) + for sample_name, file_paths in filename_groups.items() + if len(file_paths) > 1 + ] # Iterate over duplicated files to select the most recent one for each sample for sample_name, file_paths in duplicated_files: - stderr.print(f"\tMore than one file found for sample {sample_name}. Selecting the most recent one.") + stderr.print( + f"\tMore than one file found for sample {sample_name}. Selecting the most recent one." + ) # Sort files by modification time (most recent first) - sorted_files = sorted(file_paths, key=lambda file_path: os.path.getmtime(file_path), reverse=True) + sorted_files = sorted( + file_paths, key=lambda file_path: os.path.getmtime(file_path), reverse=True + ) # Select the most recent file selected_file = sorted_files[0] stderr.print(f"\tSelected file for sample {sample_name}: {selected_file}") # Remove other files for the same sample from the filtered_files dictionary filename_groups[sample_name] = [selected_file] # Update filename_groups with filtered files - filename_groups = [(sample_name, file_path) for sample_name, file_paths in filename_groups.items() for file_path in file_paths] + filename_groups = [ + (sample_name, file_path) + for sample_name, file_paths in filename_groups.items() + for file_path in file_paths + ] # Reformat variable to retrieve a list of file paths file_path_list = [sample_file_path for _, sample_file_path in filename_groups] return file_path_list -def print_log_report(log_report, categories=None, sections=["warning", "valid", "error"]): +def print_log_report( + log_report, categories=None, sections=["warning", "valid", "error"] +): color_codes = { "error": "\033[91m", # Red "warning": "\033[93m", # Orange "valid": "\033[92m", # Green - "reset": "\033[0m" # Reset color + "reset": "\033[0m", # Reset color } table_data = [] for section_name, section_data in log_report.items(): if section_name in sections: for category, items in section_data.items(): if categories is None or category in categories: - colored_category = f"{color_codes[section_name]}{category}{color_codes['reset']}" + colored_category = ( + f"{color_codes[section_name]}{category}{color_codes['reset']}" + ) for item in items: - colored_message = f"{color_codes[section_name]}{item}{color_codes['reset']}" - table_data.append([section_name, colored_category, colored_message]) - print(tabulate(table_data, headers=["Log type", "Category", "Message"], tablefmt="fancy_grid")) + colored_message = ( + f"{color_codes[section_name]}{item}{color_codes['reset']}" + ) + table_data.append( + [section_name, colored_category, colored_message] + ) + print( + tabulate( + table_data, + headers=["Log type", "Category", "Message"], + tablefmt="fancy_grid", + ) + ) From 4696d68f36db353f6407ad566da3a2714346dd6e Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Sun, 7 Apr 2024 17:43:45 +0200 Subject: [PATCH 1297/1454] arranged methods and added new coments --- relecov_tools/read_bioinfo_metadata.py | 111 +++++++++++++------------ 1 file changed, 57 insertions(+), 54 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 7b508533..93386e13 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -46,6 +46,7 @@ def print_log_report(self, name, sections): # TODO: Add method to validate bioinfo_config.json file requirements. # TODO: replace submitting_lab_id by sequencing_sample_id +# FIXME: Method include custom data. class BioinfoMetadata(BioinfoReportLog): def __init__( self, @@ -309,6 +310,60 @@ def handling_files(self, file_list): sys.exit(self.log_report.print_log_report(method_name, ["error"])) return data + def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): + """ + Function that maps structure data containing fields per sample into j_data. + """ + method_name = f"{self.mapping_over_table.__name__}:{self.software_name}.{self.current_config_key}" + errors = [] + field_errors = {} + field_vaild = {} + for row in j_data: + sample_name = row["submitting_lab_sample_id"].replace("-", "_") + if sample_name in map_data.keys(): + for field, value in mapping_fields.items(): + try: + row[field] = map_data[sample_name][value] + field_vaild[sample_name] = {field: value} + except KeyError as e: + field_errors[sample_name] = {field: e} + row[field] = "Not Provided [GENEPIO:0001668]" + continue + else: + errors.append(sample_name) + for field in mapping_fields.keys(): + row[field] = "Not Provided [GENEPIO:0001668]" + if errors: + lenerrs = len(errors) + # work around when map_data comes from several per-sample tables/files instead of single table (from list to str) + if len(table_name) > 1: + table_name = os.path.dirname(table_name[0]) + else: + table_name = table_name[0] + self.log_report.update_log_report( + method_name, + "warning", + f"{lenerrs} samples missing in '{table_name}': {', '.join(errors)}.", + ) + else: + self.log_report.update_log_report( + method_name, "valid", "Successfully mapped data." + ) + if len(field_errors) > 0: + self.log_report.update_log_report( + method_name, + "warning", + f"Missing fields in {table_name}:\n\t{field_errors}", + ) + else: + self.log_report.update_log_report( + method_name, + "valid", + f"Successfully mapped fields in {', '.join(field_vaild.keys())} - {table_name}.", + ) + self.log_report.print_log_report(method_name, ["valid", "warning"]) + return j_data + def get_multiqc_software_versions(self, file_list, j_data): """Reads multiqc html file, finds table containing software version info, and map it to j_data""" method_name = f"{self.get_multiqc_software_versions.__name__}" @@ -383,60 +438,6 @@ def get_multiqc_software_versions(self, file_list, j_data): self.log_report.print_log_report(method_name, ["valid", "warning"]) return j_data - def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): - """ - Function that maps structure data containing fields per sample into j_data. - """ - method_name = f"{self.mapping_over_table.__name__}:{self.software_name}.{self.current_config_key}" - errors = [] - field_errors = {} - field_vaild = {} - for row in j_data: - sample_name = row["submitting_lab_sample_id"].replace("-", "_") - if sample_name in map_data.keys(): - for field, value in mapping_fields.items(): - try: - row[field] = map_data[sample_name][value] - field_vaild[sample_name] = {field: value} - except KeyError as e: - field_errors[sample_name] = {field: e} - row[field] = "Not Provided [GENEPIO:0001668]" - continue - else: - errors.append(sample_name) - for field in mapping_fields.keys(): - row[field] = "Not Provided [GENEPIO:0001668]" - if errors: - lenerrs = len(errors) - # work around when map_data comes from several per-sample tables/files instead of single table (from list to str) - if len(table_name) > 1: - table_name = os.path.dirname(table_name[0]) - else: - table_name = table_name[0] - self.log_report.update_log_report( - method_name, - "warning", - f"{lenerrs} samples missing in '{table_name}': {', '.join(errors)}.", - ) - else: - self.log_report.update_log_report( - method_name, "valid", "Successfully mapped data." - ) - if len(field_errors) > 0: - self.log_report.update_log_report( - method_name, - "warning", - f"Missing fields in {table_name}:\n\t{field_errors}", - ) - else: - self.log_report.update_log_report( - method_name, - "valid", - f"Successfully mapped fields in {', '.join(field_vaild.keys())} - {table_name}.", - ) - self.log_report.print_log_report(method_name, ["valid", "warning"]) - return j_data - def add_fixed_values(self, j_data): """include the fixed data defined in configuration or feed custom empty fields""" method_name = f"{self.add_fixed_values.__name__}" @@ -479,6 +480,7 @@ def create_bioinfo_file(self): metadata json, mapping_stats, and more information from the files inside input directory """ + # Find and validate bioinfo files stderr.print("[blue]Sanning input directory...") files_found_dict = self.scann_directory() stderr.print("[blue]Validating required files...") @@ -486,6 +488,7 @@ def create_bioinfo_file(self): stderr.print( f"[blue]Adding metadata from {self.input_folder} into read lab metadata..." ) + # Add bioinfo metadata to j_data self.j_data = self.add_bioinfo_results_metadata(files_found_dict, self.j_data) stderr.print("[blue]Adding software versions to read lab metadata...") self.j_data = self.get_multiqc_software_versions( From d8b7229c69c9245e917f48e2fd1be8d806339584 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Sun, 7 Apr 2024 17:44:53 +0200 Subject: [PATCH 1298/1454] send remaining pipeline-specific file to assets --- relecov_tools/__main__.py | 3 +- .../assets/pipeline_utils/viralrecon.py | 191 ++++++++++++++++- relecov_tools/long_table_parse.py | 197 ------------------ 3 files changed, 192 insertions(+), 199 deletions(-) delete mode 100644 relecov_tools/long_table_parse.py diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 754618e8..75ded811 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -10,6 +10,7 @@ import rich.traceback import relecov_tools.utils +import relecov_tools.assets.pipeline_utils.viralrecon import relecov_tools.read_lab_metadata import relecov_tools.sftp_handle import relecov_tools.json_validation @@ -443,7 +444,7 @@ def read_bioinfo_metadata(json_file, input_folder, out_dir, software_name): ) @click.option("-o", "--output", type=click.Path(), help="Path to save json output") def long_table_parse(longtable_file, output): - new_json_parse = relecov_tools.long_table_parse.LongTableParse( + new_json_parse = relecov_tools.assets.pipeline_utils.viralrecon.LongTableParse( longtable_file, output ) """Create Json file from long table""" diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py index d33fc1e4..e9257fd0 100644 --- a/relecov_tools/assets/pipeline_utils/viralrecon.py +++ b/relecov_tools/assets/pipeline_utils/viralrecon.py @@ -1,15 +1,204 @@ #!/usr/bin/env python +import json import os import sys +import re import logging +import rich +import os.path + +from pathlib import Path +from datetime import datetime import relecov_tools.utils +from relecov_tools.config_json import ConfigJson from relecov_tools.read_bioinfo_metadata import BioinfoReportLog -from relecov_tools.long_table_parse import LongTableParse log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + + +# INIT Class +class LongTableParse: + """ + - parse_a_list_of_dictionaries() : returns generated_JSON + - saving_file(generated_JSON) + - parsing_csv() : It manages all this proccess: + - calling first to parse_a_list_of_dictionaries() and then calling to saving_file() + + """ + + def __init__(self, file_path=None, output_directory=None, j_data=None): + if file_path is None: + self.file_path = relecov_tools.utils.prompt_path( + msg="Select the csv file which contains variant long table information" + ) + else: + self.file_path = file_path + + if not os.path.exists(self.file_path): + log.error("Variant long table file %s does not exist ", self.file_path) + stderr.print( + f"[red] Variant long table file {self.file_path} does not exist" + ) + sys.exit(1) + + if not self.file_path.endswith(".csv"): + log.error("Variant long table file %s is not a csv file ", self.file_path) + stderr.print( + f"[red] Variant long table file {self.file_path} must be a csv file" + ) + sys.exit(1) + + if output_directory is None: + use_default = relecov_tools.utils.prompt_yn_question("Use default path?: ") + if use_default: + self.output_directory = os.getcwd() + else: + self.output_directory = relecov_tools.utils.prompt_path( + msg="Select the output folder:" + ) + else: + self.output_directory = output_directory + Path(self.output_directory).mkdir(parents=True, exist_ok=True) + + json_file = os.path.join( + os.path.dirname(__file__), "..", "..", "conf", "bioinfo_config.json" + ) + config_json = ConfigJson(json_file) + self.software_config = config_json.get_configuration("viralrecon") + self.long_table_heading = self.software_config["variants_long_table"]["content"] + + # FIXME: See fixme details in function parse_long_table relecov_tools.assets.pipeline_utils.viralrecon. + # if not j_data: + # stderr.print("[red]\tError: No read lab metadata file found. #Long-table-parsing aborted.") + # sys.exit(1) + # else: + # self.j_data = j_data + + def validate_file(self, heading): + """Check if long table file has all mandatory fields defined in + configuration file + """ + for field in self.long_table_heading: + if field not in heading: + log.error("Incorrect format file. %s is missing", field) + stderr.print(f"[red]Incorrect Format. {field} is missing in file") + sys.exit(1) + return True + + def parse_file(self): + """This function generates a json file from the csv file entered by + the user (long_table.csv). + Validate the file by checking the header line + """ + + with open(self.file_path, encoding="utf-8-sig") as fh: + lines = fh.readlines() + + stderr.print("[green]\tSuccessful checking heading fields") + heading_index = {} + headings_from_csv = lines[0].strip().split(",") + for heading in self.long_table_heading.values(): + heading_index[heading] = headings_from_csv.index(heading) + + samp_dict = {} + for line in lines[1:]: + line_s = line.strip().split(",") + + sample = line_s[heading_index["SAMPLE"]] + if sample not in samp_dict: + samp_dict[sample] = [] + + variant_dict = { + key: ( + {key2: line_s[heading_index[val2]] for key2, val2 in value.items()} + if isinstance(value, dict) + else line_s[heading_index[value]] + ) + for key, value in self.long_table_heading.items() + } + + if re.search("&", line_s[heading_index["GENE"]]): + # Example + # 215184,NC_045512.2,27886,AAACGAACATGAAATT,A,PASS,1789,1756,1552,0.87,ORF7b&ORF8,gene_fusion,n.27887_27901delAACGAACATGAAATT,.,.,ivar,B.1.1.318 + # This only occurs (for now) as gene fusion, so we just duplicate lines with same values + genes = re.split("&", line_s[heading_index["GENE"]]) + for gene in genes: + variant_dict_copy = variant_dict.copy() + variant_dict_copy["Gene"] = gene + samp_dict[sample].append(variant_dict_copy) + else: + variant_dict["Gene"] = line_s[heading_index["GENE"]] + samp_dict[sample].append(variant_dict) + stderr.print("[green]\tSuccessful parsing data") + return samp_dict + + def convert_to_json(self, samp_dict): + j_list = [] + # Grab date from filename + result_regex = re.search( + "variants_long_table_(.*).csv", os.path.basename(self.file_path) + ) + if result_regex is None: + log.error("Analysis date not found in filename, aborting") + stderr.print( + "[red]Error: filename must include analysis date in format YYYYMMDD" + ) + stderr.print("[red]e.g. variants_long_table_20220830.csv") + sys.exit(1) + for key, values in samp_dict.items(): + j_dict = {"sample_name": key, "analysis_date": result_regex.group(1)} + j_dict["variants"] = values + j_list.append(j_dict) + return j_list + + def save_to_file(self, j_list): + """Transform the parsed data into a json file""" + date_now = datetime.now().strftime("%Y_%m_%d_%H_%M_%S") + file_name = "long_table_" + date_now + ".json" + file_path = os.path.join(self.output_directory, file_name) + + try: + with open(file_path, "w") as fh: + fh.write(json.dumps(j_list, indent=4)) + stderr.print("[green]\tParsed data successfully saved to file:", file_path) + except Exception as e: + stderr.print("[red]\tError saving parsed data to file:", str(e)) + + # FIXME: See fixme details in function parse_long_table relecov_tools.assets.pipeline_utils.viralrecon. + # def add_custom_longtable_data(self, j_data): + # """Auxiliary function to add custom fields likevariant-long-table #into j_data""" + # if len(self.file_path) == 0: + # long_table_path = "Not Provided [GENEPIO:0001668]" + # else: + # long_table_path = self.file_path + # for row in j_data: + # row["long_table_path"] = str(long_table_path) + # return j_data + + def parsing_csv(self): + """ + Function called when using the relecov-tools long-table-parse function. + """ + # Parsing longtable file + parsed_data = self.parse_file() + j_list = self.convert_to_json(parsed_data) + # Saving long table data into a file + self.save_to_file(j_list) + stderr.print("[green]\tProcess completed") + return + + +# END of Class +# START util functions def handle_pangolin_data(files_list): """File handler to parse pangolin data (csv) into JSON structured format.""" method_name = f"{handle_pangolin_data.__name__}" diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py deleted file mode 100644 index 1f6e6b95..00000000 --- a/relecov_tools/long_table_parse.py +++ /dev/null @@ -1,197 +0,0 @@ -import json -import re -import logging -import sys -import rich -import os.path - -from pathlib import Path -from datetime import datetime - -import relecov_tools -from relecov_tools.config_json import ConfigJson -import relecov_tools.utils - - -# from relecov_tools.rest_api import RestApi - -log = logging.getLogger(__name__) -stderr = rich.console.Console( - stderr=True, - style="dim", - highlight=False, - force_terminal=relecov_tools.utils.rich_force_colors(), -) -# - - -class LongTableParse: - """ - - parse_a_list_of_dictionaries() : returns generated_JSON - - saving_file(generated_JSON) - - parsing_csv() : It manages all this proccess: - - calling first to parse_a_list_of_dictionaries() and then calling to saving_file() - - """ - - def __init__(self, file_path=None, output_directory=None, j_data=None): - if file_path is None: - self.file_path = relecov_tools.utils.prompt_path( - msg="Select the csv file which contains variant long table information" - ) - else: - self.file_path = file_path - - if not os.path.exists(self.file_path): - log.error("Variant long table file %s does not exist ", self.file_path) - stderr.print( - f"[red] Variant long table file {self.file_path} does not exist" - ) - sys.exit(1) - - if not self.file_path.endswith(".csv"): - log.error("Variant long table file %s is not a csv file ", self.file_path) - stderr.print( - f"[red] Variant long table file {self.file_path} must be a csv file" - ) - sys.exit(1) - - if output_directory is None: - use_default = relecov_tools.utils.prompt_yn_question("Use default path?: ") - if use_default: - self.output_directory = os.getcwd() - else: - self.output_directory = relecov_tools.utils.prompt_path( - msg="Select the output folder:" - ) - else: - self.output_directory = output_directory - Path(self.output_directory).mkdir(parents=True, exist_ok=True) - - json_file = os.path.join( - os.path.dirname(__file__), "conf", "bioinfo_config.json" - ) - config_json = ConfigJson(json_file) - # self.long_table_heading = config_json.get_configuration("long_table_heading") - self.software_config = config_json.get_configuration("viralrecon") - self.long_table_heading = self.software_config["variants_long_table"]["content"] - - # FIXME: See fixme details in function parse_long_table relecov_tools.assets.pipeline_utils.viralrecon. - # if not j_data: - # stderr.print("[red]\tError: No read lab metadata file found. #Long-table-parsing aborted.") - # sys.exit(1) - # else: - # self.j_data = j_data - - def validate_file(self, heading): - """Check if long table file has all mandatory fields defined in - configuration file - """ - for field in self.long_table_heading: - if field not in heading: - log.error("Incorrect format file. %s is missing", field) - stderr.print(f"[red]Incorrect Format. {field} is missing in file") - sys.exit(1) - return True - - def parse_file(self): - """This function generates a json file from the csv file entered by - the user (long_table.csv). - Validate the file by checking the header line - """ - - with open(self.file_path, encoding="utf-8-sig") as fh: - lines = fh.readlines() - - stderr.print("[green]\tSuccessful checking heading fields") - heading_index = {} - headings_from_csv = lines[0].strip().split(",") - for heading in self.long_table_heading.values(): - heading_index[heading] = headings_from_csv.index(heading) - - samp_dict = {} - for line in lines[1:]: - line_s = line.strip().split(",") - - sample = line_s[heading_index["SAMPLE"]] - if sample not in samp_dict: - samp_dict[sample] = [] - - variant_dict = { - key: ( - {key2: line_s[heading_index[val2]] for key2, val2 in value.items()} - if isinstance(value, dict) - else line_s[heading_index[value]] - ) - for key, value in self.long_table_heading.items() - } - - if re.search("&", line_s[heading_index["GENE"]]): - # Example - # 215184,NC_045512.2,27886,AAACGAACATGAAATT,A,PASS,1789,1756,1552,0.87,ORF7b&ORF8,gene_fusion,n.27887_27901delAACGAACATGAAATT,.,.,ivar,B.1.1.318 - # This only occurs (for now) as gene fusion, so we just duplicate lines with same values - genes = re.split("&", line_s[heading_index["GENE"]]) - for gene in genes: - variant_dict_copy = variant_dict.copy() - variant_dict_copy["Gene"] = gene - samp_dict[sample].append(variant_dict_copy) - else: - variant_dict["Gene"] = line_s[heading_index["GENE"]] - samp_dict[sample].append(variant_dict) - stderr.print("[green]\tSuccessful parsing data") - return samp_dict - - def convert_to_json(self, samp_dict): - j_list = [] - # Grab date from filename - result_regex = re.search( - "variants_long_table_(.*).csv", os.path.basename(self.file_path) - ) - if result_regex is None: - log.error("Analysis date not found in filename, aborting") - stderr.print( - "[red]Error: filename must include analysis date in format YYYYMMDD" - ) - stderr.print("[red]e.g. variants_long_table_20220830.csv") - sys.exit(1) - for key, values in samp_dict.items(): - j_dict = {"sample_name": key, "analysis_date": result_regex.group(1)} - j_dict["variants"] = values - j_list.append(j_dict) - return j_list - - def save_to_file(self, j_list): - """Transform the parsed data into a json file""" - date_now = datetime.now().strftime("%Y_%m_%d_%H_%M_%S") - file_name = "long_table_" + date_now + ".json" - file_path = os.path.join(self.output_directory, file_name) - - try: - with open(file_path, "w") as fh: - fh.write(json.dumps(j_list, indent=4)) - stderr.print("[green]\tParsed data successfully saved to file:", file_path) - except Exception as e: - stderr.print("[red]\tError saving parsed data to file:", str(e)) - - # FIXME: See fixme details in function parse_long_table relecov_tools.assets.pipeline_utils.viralrecon. - # def add_custom_longtable_data(self, j_data): - # """Auxiliary function to add custom fields likevariant-long-table #into j_data""" - # if len(self.file_path) == 0: - # long_table_path = "Not Provided [GENEPIO:0001668]" - # else: - # long_table_path = self.file_path - # for row in j_data: - # row["long_table_path"] = str(long_table_path) - # return j_data - - def parsing_csv(self): - """ - Function called when using the relecov-tools long-table-parse function. - """ - # Parsing longtable file - parsed_data = self.parse_file() - j_list = self.convert_to_json(parsed_data) - # Saving long table data into a file - self.save_to_file(j_list) - stderr.print("[green]\tProcess completed") - return From f2b152ce38a0bd621b8a65828cacb0c2dc941912 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Sun, 7 Apr 2024 19:47:33 +0200 Subject: [PATCH 1299/1454] Added method for appending bioinfo filepaths to readlab metadata, replacing old include_custom_data method --- .../assets/pipeline_utils/viralrecon.py | 25 ++---------------- relecov_tools/read_bioinfo_metadata.py | 26 ++++++++++++++++--- 2 files changed, 24 insertions(+), 27 deletions(-) diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py index e9257fd0..779784c7 100644 --- a/relecov_tools/assets/pipeline_utils/viralrecon.py +++ b/relecov_tools/assets/pipeline_utils/viralrecon.py @@ -33,7 +33,7 @@ class LongTableParse: """ - def __init__(self, file_path=None, output_directory=None, j_data=None): + def __init__(self, file_path=None, output_directory=None): if file_path is None: self.file_path = relecov_tools.utils.prompt_path( msg="Select the csv file which contains variant long table information" @@ -74,13 +74,6 @@ def __init__(self, file_path=None, output_directory=None, j_data=None): self.software_config = config_json.get_configuration("viralrecon") self.long_table_heading = self.software_config["variants_long_table"]["content"] - # FIXME: See fixme details in function parse_long_table relecov_tools.assets.pipeline_utils.viralrecon. - # if not j_data: - # stderr.print("[red]\tError: No read lab metadata file found. #Long-table-parsing aborted.") - # sys.exit(1) - # else: - # self.j_data = j_data - def validate_file(self, heading): """Check if long table file has all mandatory fields defined in configuration file @@ -171,17 +164,6 @@ def save_to_file(self, j_list): except Exception as e: stderr.print("[red]\tError saving parsed data to file:", str(e)) - # FIXME: See fixme details in function parse_long_table relecov_tools.assets.pipeline_utils.viralrecon. - # def add_custom_longtable_data(self, j_data): - # """Auxiliary function to add custom fields likevariant-long-table #into j_data""" - # if len(self.file_path) == 0: - # long_table_path = "Not Provided [GENEPIO:0001668]" - # else: - # long_table_path = self.file_path - # for row in j_data: - # row["long_table_path"] = str(long_table_path) - # return j_data - def parsing_csv(self): """ Function called when using the relecov-tools long-table-parse function. @@ -246,7 +228,7 @@ def parse_long_table(files_list): method_name = f"{parse_long_table.__name__}" method_log_report = BioinfoReportLog() - # Hanfling long table data + # Handling long table data if len(files_list) == 1: files_list_processed = files_list[0] if not os.path.isfile(files_list_processed): @@ -257,9 +239,6 @@ def parse_long_table(files_list): long_table = LongTableParse(files_list_processed) # Parsing long table data and saving it long_table.parsing_csv() - # FIXME: cannot write over j_data when this function is invoked from a differnt file. - # Adding custom long_table data to j_data - # self.j_data = long_table.add_custom_longtable_data(self.j_data) elif len(files_list) > 1: method_log_report.update_log_report( method_name, diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 93386e13..a382a90d 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -46,7 +46,6 @@ def print_log_report(self, name, sections): # TODO: Add method to validate bioinfo_config.json file requirements. # TODO: replace submitting_lab_id by sequencing_sample_id -# FIXME: Method include custom data. class BioinfoMetadata(BioinfoReportLog): def __init__( self, @@ -457,6 +456,24 @@ def add_fixed_values(self, j_data): self.log_report.print_log_report(method_name, ["valid", "waring"]) return j_data + def add_bioinfo_files_path(self, files_found_dict, j_data): + """Adds file paths (essential for handlers and mapping methods to process bioinformatics metadata) to the j_data. In instances where multiple files are identified per configuration item (e.g., viralrecon.mapping_consensus → *.consensus.fa), each sample in j_data receives its respective file path. If no file path is located, the function appends "Not Provided [GENEPIO:0001668]" to indicate missing data.g file. If no file path is found, then adds "Not Provided [GENEPIO:0001668]""" + for row in j_data: + sample_name = row["submitting_lab_sample_id"] + for key, value in files_found_dict.items(): + file_path = "Not Provided [GENEPIO:0001668]" + if value: # Check if value is not empty + if len(value) > 1: + for file in value: + if sample_name in file: + file_path = file + break # Exit loop if match found + else: + file_path = value[0] + path_key = f"{self.software_name}_filepath_{key}" + row[path_key] = file_path + return j_data + def collect_info_from_lab_json(self): """Create the list of dictionaries from the data that is on json lab metadata file. Return j_data that is used to add the rest of the fields @@ -485,10 +502,8 @@ def create_bioinfo_file(self): files_found_dict = self.scann_directory() stderr.print("[blue]Validating required files...") self.validate_software_mandatory_files(files_found_dict) - stderr.print( - f"[blue]Adding metadata from {self.input_folder} into read lab metadata..." - ) # Add bioinfo metadata to j_data + stderr.print("[blue]Adding bioinfo metadata to read lab metadata...") self.j_data = self.add_bioinfo_results_metadata(files_found_dict, self.j_data) stderr.print("[blue]Adding software versions to read lab metadata...") self.j_data = self.get_multiqc_software_versions( @@ -496,6 +511,9 @@ def create_bioinfo_file(self): ) stderr.print("[blue]Adding fixed values") self.j_data = self.add_fixed_values(self.j_data) + # Adding files path + stderr.print("[blue]Adding files path to read lab metadata") + self.j_data = self.add_bioinfo_files_path(files_found_dict, self.j_data) # Generate readlab + bioinfolab processed metadata. file_name = ( "bioinfo_" From 5a5bf1f9b8948daeea78b7d5e9a88252b16cd6aa Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Sun, 7 Apr 2024 20:04:54 +0200 Subject: [PATCH 1300/1454] fix missing mapping key in handle_consensus_fasta --- relecov_tools/assets/pipeline_utils/viralrecon.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py index 779784c7..07240c05 100644 --- a/relecov_tools/assets/pipeline_utils/viralrecon.py +++ b/relecov_tools/assets/pipeline_utils/viralrecon.py @@ -264,7 +264,7 @@ def handle_consensus_fasta(files_list): except FileNotFoundError as e: missing_consens.append(e.filename) continue - sample_key = os.path.splitext(os.path.basename(consensus_file))[0] + sample_key = os.path.basename(consensus_file).split(".")[0] # Update consensus data for the sample key consensus_data_processed[sample_key] = { @@ -285,5 +285,5 @@ def handle_consensus_fasta(files_list): "warning", f"{conserrs} samples missing in consensus file: {missing_consens}", ) - method_log_report.print_log_report(method_name, ["valid", "warning"]) + method_log_report.print_log_report(method_name, ["valid", "warning"]) return consensus_data_processed From f3563ef68e5a1e38a1d6492a1a7fc3888be3b32b Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Sun, 7 Apr 2024 20:16:59 +0200 Subject: [PATCH 1301/1454] replace sample mapping key according to #240 --- relecov_tools/read_bioinfo_metadata.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index a382a90d..b49a37d6 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -45,7 +45,6 @@ def print_log_report(self, name, sections): # TODO: Add method to validate bioinfo_config.json file requirements. -# TODO: replace submitting_lab_id by sequencing_sample_id class BioinfoMetadata(BioinfoReportLog): def __init__( self, @@ -318,7 +317,7 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): field_errors = {} field_vaild = {} for row in j_data: - sample_name = row["submitting_lab_sample_id"].replace("-", "_") + sample_name = row["sequencing_sample_id"].replace("-", "_") if sample_name in map_data.keys(): for field, value in mapping_fields.items(): try: @@ -412,7 +411,7 @@ def get_multiqc_software_versions(self, file_list, j_data): # Mapping multiqc sofware versions to j_data field_errors = {} for row in j_data: - sample_name = row["submitting_lab_sample_id"] + sample_name = row["sequencing_sample_id"] for field, values in ( self.software_config["workflow_summary"].get("content").items() ): @@ -459,7 +458,7 @@ def add_fixed_values(self, j_data): def add_bioinfo_files_path(self, files_found_dict, j_data): """Adds file paths (essential for handlers and mapping methods to process bioinformatics metadata) to the j_data. In instances where multiple files are identified per configuration item (e.g., viralrecon.mapping_consensus → *.consensus.fa), each sample in j_data receives its respective file path. If no file path is located, the function appends "Not Provided [GENEPIO:0001668]" to indicate missing data.g file. If no file path is found, then adds "Not Provided [GENEPIO:0001668]""" for row in j_data: - sample_name = row["submitting_lab_sample_id"] + sample_name = row["sequencing_sample_id"] for key, value in files_found_dict.items(): file_path = "Not Provided [GENEPIO:0001668]" if value: # Check if value is not empty From 83244828fb38a659eb7d8e1b0c5b1bd0ab3c58d2 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 8 Apr 2024 11:01:26 +0200 Subject: [PATCH 1302/1454] add image summarizing the process of read-bioinfo-metadata --- .../readBioinfoMetadata_processDiagram.png | Bin 0 -> 172817 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 relecov_tools/assets/images/readBioinfoMetadata_processDiagram.png diff --git a/relecov_tools/assets/images/readBioinfoMetadata_processDiagram.png b/relecov_tools/assets/images/readBioinfoMetadata_processDiagram.png new file mode 100644 index 0000000000000000000000000000000000000000..9c2837025e3adfe3f591976989365b70955bd778 GIT binary 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Date: Fri, 5 Apr 2024 14:31:40 +0200 Subject: [PATCH 1303/1454] Removed unused github token --- .github/workflows/test_modules.yml | 29 +++++++++++++---------------- 1 file changed, 13 insertions(+), 16 deletions(-) diff --git a/.github/workflows/test_modules.yml b/.github/workflows/test_modules.yml index 571ce7a1..3ec010a3 100755 --- a/.github/workflows/test_modules.yml +++ b/.github/workflows/test_modules.yml @@ -8,26 +8,23 @@ on: - opened branches: "**" -env: - GITHUB_TOKEN: ${{ secrets.TOKEN_ACTIONS }} - jobs: security_check: runs-on: ubuntu-latest steps: - - name: Get User Permission - id: checkAccess - uses: actions-cool/check-user-permission@v2 - with: - require: write - username: ${{ github.triggering_actor }} - - name: Check User Permission - if: steps.checkAccess.outputs.require-result == 'false' - run: | - echo "${{ github.triggering_actor }} does not have permissions on this repo." - echo "Current permission level is ${{ steps.checkAccess.outputs.user-permission }}" - echo "Job originally triggered by ${{ github.actor }}" - exit 1 + - name: Get User Permission + id: checkAccess + uses: actions-cool/check-user-permission@v2 + with: + require: write + username: ${{ github.triggering_actor }} + - name: Check User Permission + if: steps.checkAccess.outputs.require-result == 'false' + run: | + echo "${{ github.triggering_actor }} does not have permissions on this repo." + echo "Current permission level is ${{ steps.checkAccess.outputs.user-permission }}" + echo "Job originally triggered by ${{ github.actor }}" + exit 1 test_sftp_handle: runs-on: ubuntu-latest From 2a4fb3f5f2577ce60af7908111dbd1dca389380e Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 5 Apr 2024 14:32:11 +0200 Subject: [PATCH 1304/1454] Included blood as anatomical_material, where it should have been --- relecov_tools/conf/anatomical_material_collection_method.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/anatomical_material_collection_method.json b/relecov_tools/conf/anatomical_material_collection_method.json index 05e5c0cf..68e11b42 100755 --- a/relecov_tools/conf/anatomical_material_collection_method.json +++ b/relecov_tools/conf/anatomical_material_collection_method.json @@ -972,7 +972,7 @@ "anatomical_material": "Not Applicable" }, "Blood": { - "anatomical_part": "Not Applicable", + "anatomical_part": "Blood", "collection_method": "Not Applicable", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" From f698c34cd7c7529db34be73eb07d3ecbdac64008 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 5 Apr 2024 14:36:59 +0200 Subject: [PATCH 1305/1454] Fixed ontology for body_product --- relecov_tools/schema/relecov_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index ae7cd7e1..b6993c8b 100755 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -944,7 +944,7 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "SNOMED:364684009", + "ontology": "GENEPIO:0001216", "type": "string", "description": "", "examples": [ From ffd2a26b7e87a36b34421c7d8113d00ace0fb3e8 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 8 Apr 2024 09:25:22 +0200 Subject: [PATCH 1306/1454] Included address for a new laboratory --- relecov_tools/conf/laboratory_address.json | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index ef5119df..e6f39ed1 100755 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -1023,7 +1023,7 @@ "submitting_institution_address": "Av. Roma, s/n", "submitting_institution_email": "santiago.melon@sespa.es" }, - "Hospital de l'Esperansa": { + "Hospital de l'Esperança": { "collecting_institution_address": "Ptge. de Sant Josep la Muntanya, 12", "collecting_institution_email": "", "geo_loc_state": "Cataluña", @@ -1122,6 +1122,17 @@ "submitting_institution_address": "Carrer de la Selva, 10", "submitting_institution_email": "" }, + "Hospital del Mar": { + "collecting_institution_address": "Passeig Marítim, 25-29", + "collecting_institution_email": "", + "geo_loc_state": "Cataluña", + "geo_loc_region": "Barcelona", + "geo_loc_city": "Barcelona", + "geo_loc_country": "Spain", + "submitting_institution": "LABORATORI DE REFERENCIA DE CATALUNYA", + "submitting_institution_address": "Carrer de la Selva, 10", + "submitting_institution_email": "" + }, "Hospital de Jarrio": { "collecting_institution_address": "Lugar Jarrio, s/n", "collecting_institution_email": "", From b8899d37c3a52d05c81d359f85060d018f323ba9 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 8 Apr 2024 12:54:11 +0200 Subject: [PATCH 1307/1454] Added more possible status for pull requests in the tests --- .github/workflows/test_modules.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_modules.yml b/.github/workflows/test_modules.yml index 3ec010a3..6f1aa619 100755 --- a/.github/workflows/test_modules.yml +++ b/.github/workflows/test_modules.yml @@ -5,7 +5,7 @@ on: branches: "**" pull_request_target: types: - - opened + - [opened, reopened, synchronize, closed] branches: "**" jobs: From c539a7154fabdbd75c2dfb0f40d00a1fab29be9f Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 8 Apr 2024 12:55:56 +0200 Subject: [PATCH 1308/1454] Added more possible status for pull requests in the tests. Fixed --- .github/workflows/test_modules.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/test_modules.yml b/.github/workflows/test_modules.yml index 6f1aa619..dde617a0 100755 --- a/.github/workflows/test_modules.yml +++ b/.github/workflows/test_modules.yml @@ -4,8 +4,7 @@ on: push: branches: "**" pull_request_target: - types: - - [opened, reopened, synchronize, closed] + types: [opened, reopened, synchronize, closed] branches: "**" jobs: From 1f28585ba15c69fa34f87bbb6a1a584ad4523d41 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 9 Apr 2024 12:22:23 +0200 Subject: [PATCH 1309/1454] add reviewer sugestions #258 --- relecov_tools/__main__.py | 1 - .../assets/pipeline_utils/viralrecon.py | 75 +++++++-- relecov_tools/conf/bioinfo_config.json | 4 +- relecov_tools/read_bioinfo_metadata.py | 159 ++++++++++++++---- 4 files changed, 192 insertions(+), 47 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 75ded811..91c6c3ca 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -17,7 +17,6 @@ import relecov_tools.map_schema import relecov_tools.feed_database import relecov_tools.read_bioinfo_metadata -import relecov_tools.long_table_parse import relecov_tools.metadata_homogeneizer import relecov_tools.gisaid_upload import relecov_tools.upload_ena_protocol diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py index 07240c05..56552ea4 100644 --- a/relecov_tools/assets/pipeline_utils/viralrecon.py +++ b/relecov_tools/assets/pipeline_utils/viralrecon.py @@ -30,7 +30,6 @@ class LongTableParse: - saving_file(generated_JSON) - parsing_csv() : It manages all this proccess: - calling first to parse_a_list_of_dictionaries() and then calling to saving_file() - """ def __init__(self, file_path=None, output_directory=None): @@ -136,17 +135,32 @@ def convert_to_json(self, samp_dict): j_list = [] # Grab date from filename result_regex = re.search( - "variants_long_table_(.*).csv", os.path.basename(self.file_path) + "variants_long_table(?:_\d{8})?\.csv", os.path.basename(self.file_path) ) + stderr.print(result_regex.group(0)) if result_regex is None: - log.error("Analysis date not found in filename, aborting") stderr.print( - "[red]Error: filename must include analysis date in format YYYYMMDD" + "[red]\tWARN: Couldn't find variants long table file. Expected file name is:" + ) + stderr.print( + "[red]\t\t- variants_long_table.csv or variants_long_table_YYYYMMDD.csv. Aborting..." ) - stderr.print("[red]e.g. variants_long_table_20220830.csv") sys.exit(1) + else: + date_regex = re.search(r"(\d{8})", result_regex.group()) + if date_regex is not None: + analysis_date = date_regex + stderr.print( + f"[green]\tDate {analysis_date.group()} found in {self.file_path}" + ) + else: + analysis_date = "Not Provided [GENEPIO:0001668]" + stderr.print( + f"[yellow]\tWARN:No analysis date found in long table: {self.file_path}" + ) + for key, values in samp_dict.items(): - j_dict = {"sample_name": key, "analysis_date": result_regex.group(1)} + j_dict = {"sample_name": key, "analysis_date": analysis_date.group()} j_dict["variants"] = values j_list.append(j_dict) return j_list @@ -182,12 +196,20 @@ def parsing_csv(self): # START util functions def handle_pangolin_data(files_list): - """File handler to parse pangolin data (csv) into JSON structured format.""" + """File handler to parse pangolin data (csv) into JSON structured format. + + Args: + files_list (list): A list with paths to pangolin files. + + Returns: + pango_data_processed: A dictionary containing pangolin data handled. + """ method_name = f"{handle_pangolin_data.__name__}" method_log_report = BioinfoReportLog() # Handling pangolin data pango_data_processed = {} + valid_samples = [] try: files_list_processed = relecov_tools.utils.select_most_recent_files_per_sample( files_list @@ -208,23 +230,39 @@ def handle_pangolin_data(files_list): key.split()[0]: value for key, value in pango_data.items() } pango_data_processed.update(pango_data_updated) - method_log_report.update_log_report( - method_name, "valid", f"Successfully handled data in {pango_file}." - ) + valid_samples.append(pango_data_key.split()[0]) except (FileNotFoundError, IndexError) as e: method_log_report.update_log_report( - method_name, "error", f"Error processing file {pango_file}: {e}" + method_name, + "warning", + f"Error occurred while processing file {pango_file}: {e}", ) - sys.exit(method_log_report.print_log_report(method_name, ["error"])) + continue except Exception as e: method_log_report.update_log_report( - method_name, "error", f"Error occurred while processing files: {e}" + method_name, "warning", f"Error occurred while processing files: {e}" + ) + if len(valid_samples) > 0: + method_log_report.update_log_report( + method_name, + "valid", + f"Successfully handled data in samples: {', '.join(valid_samples)}", ) - sys.exit(method_log_report.print_log_report(method_name, ["error"])) + method_log_report.print_log_report(method_name, ["valid", "warning"]) return pango_data_processed def parse_long_table(files_list): + """File handler to retrieve data from long table files and convert it into a JSON structured format. + This function utilizes the LongTableParse class to parse the long table data. + Since this utility handles and maps data using a custom way, it returns None to be avoid being transferred to method read_bioinfo_metadata.BioinfoMetadata.mapping_over_table(). + + Args: + files_list (list): A list of paths to long table files. + + Returns: + None: Indicates that the function does not return any meaningful value. + """ method_name = f"{parse_long_table.__name__}" method_log_report = BioinfoReportLog() @@ -250,7 +288,14 @@ def parse_long_table(files_list): def handle_consensus_fasta(files_list): - """File handler to parse consensus fasta data (*.consensus.fa) into JSON structured format""" + """File handler to parse consensus data (fasta) into JSON structured format. + + Args: + files_list (list): A list with paths to condensus files. + + Returns: + consensus_data_processed: A dictionary containing consensus data handled. + """ method_name = f"{handle_consensus_fasta.__name__}" method_log_report = BioinfoReportLog() diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index 80a052b4..8789f387 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -1,7 +1,7 @@ { "viralrecon": { "mapping_stats": { - "fn": "mapping_illumina_stats.tab", + "fn": "mapping_illumina_stats(?:_\\d{8})?\\.tab", "sample_col_idx": 5, "header_row_idx": 1, "required": true, @@ -37,7 +37,7 @@ } }, "variants_long_table": { - "fn": "variants_long_table(?:_\\d{8})?\\.csv$", + "fn": "variants_long_table(?:_\\d{8})?\\.csv", "sample_col_idx": 1, "header_row_idx": 1, "required": true, diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index b49a37d6..cbfb7251 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -26,7 +26,19 @@ def __init__(self, log_report=None): self.report = log_report def update_log_report(self, method_name, status, message): - """Update progress log report""" + """Update the progress log report with the given method name, status, and message. + + Args: + method_name (str): The name of the method being logged. + status (str): The status of the log message, can be one of 'valid', 'error', or 'warning'. + message (str): The message to be logged. + + Returns: + dict: The updated progress log report. + + Raises: + ValueError: If an invalid status is provided. + """ if status == "valid": self.report["valid"].setdefault(method_name, []).append(message) return self.report @@ -40,7 +52,15 @@ def update_log_report(self, method_name, status, message): raise ValueError("Invalid status provided.") def print_log_report(self, name, sections): - """Calls log report printer.""" + """Prints the log report by calling util's function. + + Args: + name (str): The name of the log report. + sections (list of str): The sections of the log report to be printed. + + Returns: + None + """ relecov_tools.utils.print_log_report(self.report, name, sections) @@ -115,13 +135,24 @@ def __init__( ) def get_available_software(self, json): - """Get list of available software in configuration""" + """Get list of available software in configuration + + Args: + json (str): Path to bioinfo configuration json file. + + Returns: + available_software: List containing available software defined in json. + """ config = relecov_tools.utils.read_json_file(json) available_software = list(config.keys()) return available_software def scann_directory(self): - """Scanns bioinfo analysis directory and identifies files according to the file name patterns defined in the software configuration json.""" + """Scanns bioinfo analysis directory and identifies files according to the file name patterns defined in the software configuration json. + + Returns: + files_found: A dictionary containing file paths found based on the definitions provided in the bioinformatic JSON file within the software scope (self.software_config). + """ method_name = f"{self.scann_directory.__name__}" total_files = sum(len(files) for _, _, files in os.walk(self.input_folder)) files_found = {} @@ -159,7 +190,11 @@ def scann_directory(self): return files_found def validate_software_mandatory_files(self, files_dict): - """ "Validates the presence of all mandatory files as defined in the software configuration JSON.""" + """Validates the presence of all mandatory files as defined in the software configuration JSON. + + Args: + files_dict (dict{str:str}): A dictionary containing file paths found based on the definitions provided in the bioinformatic JSON file within the software scope (self.software_config). + """ method_name = f"{self.validate_software_mandatory_files.__name__}" missing_required = [] for key in self.software_config: @@ -182,14 +217,21 @@ def validate_software_mandatory_files(self, files_dict): self.log_report.update_log_report( method_name, "valid", "Successfull validation of mandatory files." ) - self.log_report.print_log_report(method_name, ["valid", "waring"]) + self.log_report.print_log_report(method_name, ["valid", "warning"]) return def add_bioinfo_results_metadata(self, files_dict, j_data): - """ - Adds metadata from bioinformatics results to j_data. - 1. Handles metadata in bioinformatic files found. - 2. Mapping handled bioinfo metadata into j_data. + """Adds metadata from bioinformatics results to j_data. + It first calls file_handlers and then maps the handled + data into j_data. + + Args: + files_dict (dict{str:str}): A dictionary containing file paths found based on the definitions provided in the bioinformatic JSON file within the software scope (self.software_config). + + j_data (list(dict{str:str}): A list of dictionaries containing metadata lab (list item per sample). + + Returns: + j_data_mapped: A list of dictionaries with bioinformatics metadata mapped into j_data. """ method_name = f"{self.add_bioinfo_results_metadata.__name__}" for key in self.software_config.keys(): @@ -225,13 +267,12 @@ def add_bioinfo_results_metadata(self, files_dict, j_data): f"No metadata found to perform standard mapping when processing '{self.software_name}.{key}'", ) continue - self.log_report.print_log_report(method_name, ["valid", "waring"]) + self.log_report.print_log_report(method_name, ["valid", "warning"]) return j_data_mapped def handling_files(self, file_list): - """ + """Handles different file formats to extract data regardless of their structure. The goal is to extract the data contained in files specified in ${file_list}, using either 'standard' handlers defined in this class or pipeline-specific file handlers. (inspired from ./metadata_homogenizer.py) - Handles different file formats to extract data regardless of their structure. The goal is to extract the data contained in files specified in ${file_list}, using either 'standard' handlers defined in this class or pipeline-specific file handlers. A file handler method must generate a data structure as follow: { @@ -249,11 +290,11 @@ def handling_files(self, file_list): } Note: ensure that 'field1','field2','field3' corresponds with the values especifies in the 'content' section of each software configuration scope (see: conf/bioinfo_config.json). - Input: + Args: file_list (list): A list of file path/s to be processed. Returns: - dict: A single dictionary containing extracted data for each sample. + data: A dictionary containing bioinfo metadata handled for each sample. """ method_name = f"{self.add_bioinfo_results_metadata.__name__}:{self.handling_files.__name__}" file_name = self.software_config[self.current_config_key].get("fn") @@ -309,20 +350,28 @@ def handling_files(self, file_list): return data def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): - """ - Function that maps structure data containing fields per sample into j_data. + """Maps bioinformatics metadata from map_data to j_data based on the mapping_fields. + + Args: + j_data (list(dict{str:str}): A list of dictionaries containing metadata lab (one item per sample). + map_data (dict(dict{str:str})): A dictionary containing bioinfo metadata handled by the method handling_files(). + mapping_fields (dict{str:str}): A dictionary of mapping fields defined in the 'content' definition under each software scope (see conf/bioinfo.config). + table_name (str): Path to the mapping file/table. + + Returns: + j_data: updated j_data with bioinformatic metadata mapped in it. """ method_name = f"{self.mapping_over_table.__name__}:{self.software_name}.{self.current_config_key}" errors = [] field_errors = {} - field_vaild = {} + field_valid = {} for row in j_data: - sample_name = row["sequencing_sample_id"].replace("-", "_") + sample_name = row["sequencing_sample_id"] if sample_name in map_data.keys(): for field, value in mapping_fields.items(): try: row[field] = map_data[sample_name][value] - field_vaild[sample_name] = {field: value} + field_valid[sample_name] = {field: value} except KeyError as e: field_errors[sample_name] = {field: e} row[field] = "Not Provided [GENEPIO:0001668]" @@ -357,13 +406,21 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): self.log_report.update_log_report( method_name, "valid", - f"Successfully mapped fields in {', '.join(field_vaild.keys())} - {table_name}.", + f"Successfully mapped fields in {', '.join(field_valid.keys())} - {table_name}.", ) self.log_report.print_log_report(method_name, ["valid", "warning"]) return j_data def get_multiqc_software_versions(self, file_list, j_data): - """Reads multiqc html file, finds table containing software version info, and map it to j_data""" + """Reads multiqc html file, finds table containing software version info, and map it to j_data + + Args: + file_list (list): A list containing the path to file multiqc_report.html. + j_data (list(dict{str:str}): A list of dictionaries containing metadata lab (one item per sample). + + Returns: + j_data: updated j_data with software version's info mapped in it. + """ method_name = f"{self.get_multiqc_software_versions.__name__}" # Handle multiqc_report.html f_path = file_list[0] @@ -437,7 +494,14 @@ def get_multiqc_software_versions(self, file_list, j_data): return j_data def add_fixed_values(self, j_data): - """include the fixed data defined in configuration or feed custom empty fields""" + """Add fixed values to j_data as defined in the bioinformatics configuration (definition: "fixed values") + + Args: + j_data (list(dict{str:str}): A list of dictionaries containing metadata lab (one item per sample). + + Returns: + j_data: updated j_data with fixxed values added in it. + """ method_name = f"{self.add_fixed_values.__name__}" try: f_values = self.software_config["fixed_values"] @@ -452,13 +516,37 @@ def add_fixed_values(self, j_data): method_name, "warning", f"Error found while adding fixed values: {e}" ) pass - self.log_report.print_log_report(method_name, ["valid", "waring"]) + self.log_report.print_log_report(method_name, ["valid", "warning"]) return j_data def add_bioinfo_files_path(self, files_found_dict, j_data): - """Adds file paths (essential for handlers and mapping methods to process bioinformatics metadata) to the j_data. In instances where multiple files are identified per configuration item (e.g., viralrecon.mapping_consensus → *.consensus.fa), each sample in j_data receives its respective file path. If no file path is located, the function appends "Not Provided [GENEPIO:0001668]" to indicate missing data.g file. If no file path is found, then adds "Not Provided [GENEPIO:0001668]""" + """Adds file paths essential for handling and mapping bioinformatics metadata to the j_data. + For each sample in j_data, the function assigns the corresponding file path based on the identified files in files_found_dict. + If multiple files are identified per configuration item (e.g., viralrecon.mapping_consensus → *.consensus.fa), each sample in j_data receives its respective file path. + If no file path is located, the function appends "Not Provided [GENEPIO:0001668]" to indicate missing data. + + Args: + files_found_dict (dict): A dictionary containing file paths identified for each configuration item. + j_data (list(dict{str:str}): A list of dictionaries containing metadata lab (one item per sample). + + Returns: + j_data: Updated j_data with file paths mapped for bioinformatic metadata. + """ + method_name = f"{self.add_bioinfo_files_path.__name__}" + sample_error = 0 for row in j_data: - sample_name = row["sequencing_sample_id"] + try: + sample_name = re.match( + r"^(.*?)_R1\.fastq\.gz", row["sequence_file_R1_fastq"] + ).group(1) + except AttributeError as e: + sample_error += 1 + self.log_report.update_log_report( + method_name, + "warning", + f" {row['sequence_file_R1_fastq']} doesn't match pattern '*_R1.fastq.gz'. Cannot add file paths (error: {e})", + ) + continue for key, value in files_found_dict.items(): file_path = "Not Provided [GENEPIO:0001668]" if value: # Check if value is not empty @@ -471,11 +559,21 @@ def add_bioinfo_files_path(self, files_found_dict, j_data): file_path = value[0] path_key = f"{self.software_name}_filepath_{key}" row[path_key] = file_path + self.log_report.print_log_report(method_name, ["warning"]) + if sample_error == 0: + self.log_report.update_log_report( + method_name, "valid", "File paths added successfully." + ) + self.log_report.print_log_report(method_name, ["valid"]) return j_data def collect_info_from_lab_json(self): - """Create the list of dictionaries from the data that is on json lab - metadata file. Return j_data that is used to add the rest of the fields + """Reads lab metadata from a JSON file and creates a list of dictionaries. + Reads lab metadata from the specified JSON file and converts it into a list of dictionaries. + This list is used to add the rest of the fields. + + Returns: + json_lab_data: A list of dictionaries containing lab metadata (aka j_data). """ method_name = f"{self.collect_info_from_lab_json.__name__}" try: @@ -494,7 +592,10 @@ def collect_info_from_lab_json(self): def create_bioinfo_file(self): """Create the bioinfodata json with collecting information from lab metadata json, mapping_stats, and more information from the files - inside input directory + inside input directory. + + Returns: + bool: True if the bioinfo file creation process was successful. """ # Find and validate bioinfo files stderr.print("[blue]Sanning input directory...") From 2de9f15bc9e0efc4ccf4584c4f193eada79a4302 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 15 Apr 2024 17:15:35 +0200 Subject: [PATCH 1310/1454] added fixed and remaining reviewer suggestions on #258 --- .../assets/pipeline_utils/viralrecon.py | 1 - relecov_tools/conf/bioinfo_config.json | 2 +- relecov_tools/read_bioinfo_metadata.py | 80 +++++++++++-------- 3 files changed, 48 insertions(+), 35 deletions(-) diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py index 56552ea4..be0648e5 100644 --- a/relecov_tools/assets/pipeline_utils/viralrecon.py +++ b/relecov_tools/assets/pipeline_utils/viralrecon.py @@ -137,7 +137,6 @@ def convert_to_json(self, samp_dict): result_regex = re.search( "variants_long_table(?:_\d{8})?\.csv", os.path.basename(self.file_path) ) - stderr.print(result_regex.group(0)) if result_regex is None: stderr.print( "[red]\tWARN: Couldn't find variants long table file. Expected file name is:" diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index 8789f387..9c626d71 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -33,7 +33,7 @@ "lineage_analysis_software_version": "pangolin_version", "lineage_analysis_scorpio_version": "scorpio_version", "lineage_analysis_constellation_version": "constellation_version", - "lineage_analysis_date":"Not Provided [GENEPIO:0001668]" + "lineage_analysis_date":"lineage_analysis_date" } }, "variants_long_table": { diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index cbfb7251..0bf7e336 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -274,7 +274,7 @@ def handling_files(self, file_list): """Handles different file formats to extract data regardless of their structure. The goal is to extract the data contained in files specified in ${file_list}, using either 'standard' handlers defined in this class or pipeline-specific file handlers. (inspired from ./metadata_homogenizer.py) - A file handler method must generate a data structure as follow: + A file handler method must generate a data structure as follow: { 'SAMPLE1': { 'field1': 'value1' @@ -288,7 +288,7 @@ def handling_files(self, file_list): }, ... } - Note: ensure that 'field1','field2','field3' corresponds with the values especifies in the 'content' section of each software configuration scope (see: conf/bioinfo_config.json). + Note: ensure that 'field1','field2','field3' corresponds with the values especifies in the 'content' section of each software configuration scope (see: conf/bioinfo_config.json). Args: file_list (list): A list of file path/s to be processed. @@ -366,7 +366,15 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): field_errors = {} field_valid = {} for row in j_data: - sample_name = row["sequencing_sample_id"] + # TODO: We should consider an independent module that verifies that sample's name matches this pattern. + # If we add warnings within this module, every time mapping_over_table is invoked it will print redundant warings + sample_match = re.match( + r"^(.*?)_R1\.fastq\.gz", row["sequence_file_R1_fastq"] + ) + if sample_match: + sample_name = sample_match.group(1) + else: + continue if sample_name in map_data.keys(): for field, value in mapping_fields.items(): try: @@ -380,13 +388,14 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): errors.append(sample_name) for field in mapping_fields.keys(): row[field] = "Not Provided [GENEPIO:0001668]" + # work around when map_data comes from several per-sample tables/files instead of single table + if len(table_name) > 2: + table_name = os.path.dirname(table_name[0]) + else: + table_name = table_name[0] + # Parse missing sample errors if errors: lenerrs = len(errors) - # work around when map_data comes from several per-sample tables/files instead of single table (from list to str) - if len(table_name) > 1: - table_name = os.path.dirname(table_name[0]) - else: - table_name = table_name[0] self.log_report.update_log_report( method_name, "warning", @@ -394,8 +403,12 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): ) else: self.log_report.update_log_report( - method_name, "valid", "Successfully mapped data." + method_name, + "valid", + f"All samples were successfully found in {table_name}.", ) + # Parse missing fields errors + # TODO: this stdout can be improved if len(field_errors) > 0: self.log_report.update_log_report( method_name, @@ -406,8 +419,9 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): self.log_report.update_log_report( method_name, "valid", - f"Successfully mapped fields in {', '.join(field_valid.keys())} - {table_name}.", + f"Successfully mapped fields in {', '.join(field_valid.keys())}.", ) + # Print report self.log_report.print_log_report(method_name, ["valid", "warning"]) return j_data @@ -468,7 +482,13 @@ def get_multiqc_software_versions(self, file_list, j_data): # Mapping multiqc sofware versions to j_data field_errors = {} for row in j_data: - sample_name = row["sequencing_sample_id"] + sample_match = re.match( + r"^(.*?)_R1\.fastq\.gz", row["sequence_file_R1_fastq"] + ) + if sample_match: + sample_name = sample_match.group(1) + else: + continue for field, values in ( self.software_config["workflow_summary"].get("content").items() ): @@ -488,7 +508,7 @@ def get_multiqc_software_versions(self, file_list, j_data): ) else: self.log_report.update_log_report( - method_name, "valid", "Successfully mapped data." + method_name, "valid", "Successfully field mapped data." ) self.log_report.print_log_report(method_name, ["valid", "warning"]) return j_data @@ -533,38 +553,32 @@ def add_bioinfo_files_path(self, files_found_dict, j_data): j_data: Updated j_data with file paths mapped for bioinformatic metadata. """ method_name = f"{self.add_bioinfo_files_path.__name__}" - sample_error = 0 + sample_name_error = 0 for row in j_data: - try: - sample_name = re.match( - r"^(.*?)_R1\.fastq\.gz", row["sequence_file_R1_fastq"] - ).group(1) - except AttributeError as e: - sample_error += 1 - self.log_report.update_log_report( - method_name, - "warning", - f" {row['sequence_file_R1_fastq']} doesn't match pattern '*_R1.fastq.gz'. Cannot add file paths (error: {e})", - ) + sample_match = re.match( + r"^(.*?)_R1\.fastq\.gz", row["sequence_file_R1_fastq"] + ) + if sample_match: + sample_name = sample_match.group(1) + else: continue for key, value in files_found_dict.items(): file_path = "Not Provided [GENEPIO:0001668]" if value: # Check if value is not empty - if len(value) > 1: - for file in value: - if sample_name in file: - file_path = file - break # Exit loop if match found - else: - file_path = value[0] + for file in value: + if sample_name in file: + file_path = file + break # Exit loop if match found + else: + file_path = value[0] path_key = f"{self.software_name}_filepath_{key}" row[path_key] = file_path self.log_report.print_log_report(method_name, ["warning"]) - if sample_error == 0: + if sample_name_error == 0: self.log_report.update_log_report( method_name, "valid", "File paths added successfully." ) - self.log_report.print_log_report(method_name, ["valid"]) + self.log_report.print_log_report(method_name, ["valid", "warning"]) return j_data def collect_info_from_lab_json(self): From 27db5f7f988b8413b2cf2cbef596e606ff9a99a1 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 16 Apr 2024 16:02:59 +0200 Subject: [PATCH 1311/1454] dummy change to fix rebarse-merge problem --- relecov_tools/read_bioinfo_metadata.py | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 0bf7e336..5c90ba79 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -478,7 +478,6 @@ def get_multiqc_software_versions(self, file_list, j_data): f"Failed to locate the required '{div_id}' div section in the '{f_path}' file.", ) sys.exit(self.log_report.print_log_report(method_name, ["error"])) - # Mapping multiqc sofware versions to j_data field_errors = {} for row in j_data: From 0bac7b6582868c6f34bc16b6b2929a2d0b18ecbb Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 22 Apr 2024 14:12:12 +0200 Subject: [PATCH 1312/1454] update read-bioinfo-metadata readme --- README.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ae99510c..075f3150 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,8 @@ relecov-tools is a set of helper tools for the assembly of the different element * [Installation](#installation) * [Usage](#usage) * [download](#download) - * [read-metadata](#read-metadata) + * [read-lab-metadata](#read-lab-metadata) + * [read-bioinfo-metadata](#read-bioinfo-metadata) * [validate](#validate) * [map](#map) * [upload-to-ena](#upload-to-ena) @@ -128,7 +129,7 @@ Usage: relecov-tools read-metadata [OPTIONS] An example for the metadata excel file can be found [here](./relecov_tools/example_data/METADATA_LAB_TEST.xlsx) #### read-bioinfo-metadata -`read-bioinfo-metadata` Include the results from the Bioinformatics analysis (default: viralrecon) into the Json previously created with read-lab-metadata module. +`read-bioinfo-metadata` Include the results from the Bioinformatics analysis into the Json previously created with read-lab-metadata module. ``` $ relecov-tools read-bioinfo-metadata --help @@ -139,8 +140,10 @@ Usage: relecov-tools read-bioinfo-metadata [OPTIONS] Options: -j, --json_file Json file containing lab metadata -i, --input_folder Path to folder containing analysis results + -s, --software_name Name of the software employed in the bioinformatics analysis (default: viralrecon). -o, --out_dir Path to save output file" ``` +- Note: Software-specific configurations are available in [bioinfo_config.json](./relecov_tools/conf/bioinfo_config.json). #### validate `validate` commands validate the data in json format outputted by `read-metadata` command against a json schema, in this case the relecov [schema specification](./relecov_tools/schema/relecov_schema.json). From 1e844685803911819b0a417de778e61e779f6bc1 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 16 May 2024 16:25:35 +0200 Subject: [PATCH 1313/1454] Restricted concurrency in sftp-handle tests --- .github/workflows/test_modules.yml | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test_modules.yml b/.github/workflows/test_modules.yml index dde617a0..4dc32263 100755 --- a/.github/workflows/test_modules.yml +++ b/.github/workflows/test_modules.yml @@ -1,6 +1,6 @@ name: Python Package using Conda -on: +on: push: branches: "**" pull_request_target: @@ -26,6 +26,10 @@ jobs: exit 1 test_sftp_handle: + needs: security_check + concurrency: + group: ${{ github.repository }}-test_sftp_handle + cancel-in-progress: false runs-on: ubuntu-latest strategy: max-parallel: 1 @@ -87,7 +91,7 @@ jobs: with: name: test-output path: output.txt - + test_all_modules: runs-on: ubuntu-latest strategy: @@ -95,18 +99,22 @@ jobs: matrix: modules: ["read-lab-metadata", "read-bioinfo-metadata", "validate"] steps: + - name: Set up Python 3.9.16 uses: actions/setup-python@v3 with: python-version: '3.9.16' + - name: Checkout code uses: actions/checkout@v3 with: path: . + - name: Install package and dependencies run: | pip install -r requirements.txt pip install . + - name: Run each module tests run: | if [ "${{ matrix.modules }}" == "read-lab-metadata" ]; then @@ -120,4 +128,4 @@ jobs: uses: actions/upload-artifact@v2 with: name: test-output - path: output.txt \ No newline at end of file + path: output.txt From 8f3e733903a438a05325cf571753c44547564a69 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 16 May 2024 16:30:49 +0200 Subject: [PATCH 1314/1454] Limit concurrency in sftp-handle tests. New workflow name --- .github/workflows/test_modules.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_modules.yml b/.github/workflows/test_modules.yml index 4dc32263..7519c5eb 100755 --- a/.github/workflows/test_modules.yml +++ b/.github/workflows/test_modules.yml @@ -1,4 +1,4 @@ -name: Python Package using Conda +name: test_modules on: push: From 0bc5a6a154bdc3dc3390abf96fa00fb4ce046eb9 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 16 May 2024 16:31:24 +0200 Subject: [PATCH 1315/1454] Utils read_excel_file() now uses header_flag instead of row --- relecov_tools/utils.py | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index c1edcc83..88493fef 100755 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -58,13 +58,16 @@ def read_json_file(j_file): return data -def read_excel_file(f_name, sheet_name, heading_row, leave_empty=True): +def read_excel_file(f_name, sheet_name, header_flag, leave_empty=True): """Read the input excel file and give the information in a list of dictionaries """ wb_file = openpyxl.load_workbook(f_name, data_only=True) ws_metadata_lab = wb_file[sheet_name] - heading = [i.value.strip() for i in ws_metadata_lab[heading_row] if i.value] + heading_row = [ + idx + 1 for idx, x in enumerate(ws_metadata_lab.values) if header_flag in x + ][0] + heading = [str(i.value).strip() for i in ws_metadata_lab[heading_row] if i.value] ws_data = [] for row in islice(ws_metadata_lab.values, heading_row, ws_metadata_lab.max_row): l_row = list(row) @@ -75,14 +78,14 @@ def read_excel_file(f_name, sheet_name, heading_row, leave_empty=True): for idx in range(0, len(heading)): if l_row[idx] is None: if leave_empty: - data_row[heading[idx]] = "" + data_row[heading[idx]] = None else: data_row[heading[idx]] = "Not Provided [GENEPIO:0001668]" else: data_row[heading[idx]] = l_row[idx] ws_data.append(data_row) - return ws_data + return ws_data, heading_row def read_csv_file_return_dict(file_name, sep, key_position=None): @@ -177,7 +180,7 @@ def read_md5_checksum(file_name, avoid_chars=list()): elif any("," in line for line in lines): lines = [line.strip().translate(translation).split(",") for line in lines] else: - lines = [line.strip().translate(translation).split(" ") for line in lines] + lines = [line.strip().translate(translation).split() for line in lines] clean_lines = [ x for x in lines if not any(ch in string for ch in avoid_chars for string in x) ] From 55a3df60a721a8dcecaee2aca62e0e97ccd0d83f Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 16 May 2024 16:32:02 +0200 Subject: [PATCH 1316/1454] Updated usage of utils.read_excel_file() --- relecov_tools/metadata_homogeneizer.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 9c05e7b0..2d8cc534 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -164,9 +164,9 @@ def handling_files(self, file_data, data_to_add): elif f_name.endswith(".csv"): data = relecov_tools.utils.read_csv_file_return_dict(f_name, ",") elif f_name.endswith(".xlsx"): - heading_row_number = 1 + header_flag = self.metadata_processing.get("header_flag") data = relecov_tools.utils.read_excel_file( - f_name, "Sheet", heading_row_number + f_name, "Sheet", header_flag, leave_empty=True ) else: log.error("Additional file extension %s is not supported ", f_name) From 651d7dd1a0f50c9035df55559297774f9b973e92 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 16 May 2024 16:44:32 +0200 Subject: [PATCH 1317/1454] Changed swabbing for swab so its closer to the ontology naming --- .../conf/anatomical_material_collection_method.json | 12 ++++++------ relecov_tools/schema/relecov_schema.json | 6 +++--- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/relecov_tools/conf/anatomical_material_collection_method.json b/relecov_tools/conf/anatomical_material_collection_method.json index 68e11b42..acb99584 100755 --- a/relecov_tools/conf/anatomical_material_collection_method.json +++ b/relecov_tools/conf/anatomical_material_collection_method.json @@ -809,21 +809,21 @@ "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, - "Pharynx Swabbing": { + "Pharynx Swab": { "anatomical_part": "Pharynx", - "collection_method": "Swabbing", + "collection_method": "Swab", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, - "Nasopharynx Swabbing": { + "Nasopharynx Swab": { "anatomical_part": "Nasopharynx", - "collection_method": "Swabbing", + "collection_method": "Swab", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, - "Oropharynx Swabbing": { + "Oropharynx Swab": { "anatomical_part": "Oropharynx", - "collection_method": "Swabbing", + "collection_method": "Swab", "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index b6993c8b..78e15a80 100755 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -771,9 +771,9 @@ "Middle Nasal Turbinate Scraping", "Nasopharynx Scraping", "Oropharynx Scraping", - "Nasopharynx Swabbing", - "Oropharynx Swabbing", - "Pharynx Swabbing", + "Nasopharynx Swab", + "Oropharynx Swa", + "Pharynx Swab", "Lower respiratory tract Wash", "Bronchus Wash", "Lung Wash", From a283e35e5c698696e7b5f77617d94a1c1fb4fd39 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 17 May 2024 09:05:46 +0200 Subject: [PATCH 1318/1454] Changed swabbing for swab. small fix --- relecov_tools/schema/relecov_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 78e15a80..d631537c 100755 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -772,7 +772,7 @@ "Nasopharynx Scraping", "Oropharynx Scraping", "Nasopharynx Swab", - "Oropharynx Swa", + "Oropharynx Swab", "Pharynx Swab", "Lower respiratory tract Wash", "Bronchus Wash", @@ -906,7 +906,7 @@ "Phlebotomy [NCIT:C28221]", "Rinsing [GENEPIO:0002116]", "Scraping [GENEPIO:0100035]", - "Swabbing [NCIT:C17627]", + "Swab [NCIT:C17627]", "Finger Pick [GENEPIO:0100036]", "Wash [NCIT:C65077]", "Washout Tear Collection [GENEPIO:0100038]", From ad6cfb0cc9113a9373cf27b3c503089d312987b4 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 23 May 2024 09:31:53 +0200 Subject: [PATCH 1319/1454] Separated sftp-handle from other tests, fixed pull-request checkout error --- .github/workflows/test_modules.yml | 60 ++---------------------- .github/workflows/test_sftp_handle.yml | 64 ++++++++++++++++++++++++++ 2 files changed, 67 insertions(+), 57 deletions(-) create mode 100644 .github/workflows/test_sftp_handle.yml diff --git a/.github/workflows/test_modules.yml b/.github/workflows/test_modules.yml index 7519c5eb..747c0845 100755 --- a/.github/workflows/test_modules.yml +++ b/.github/workflows/test_modules.yml @@ -3,65 +3,11 @@ name: test_modules on: push: branches: "**" - pull_request_target: + pull_request: types: [opened, reopened, synchronize, closed] branches: "**" jobs: - security_check: - runs-on: ubuntu-latest - steps: - - name: Get User Permission - id: checkAccess - uses: actions-cool/check-user-permission@v2 - with: - require: write - username: ${{ github.triggering_actor }} - - name: Check User Permission - if: steps.checkAccess.outputs.require-result == 'false' - run: | - echo "${{ github.triggering_actor }} does not have permissions on this repo." - echo "Current permission level is ${{ steps.checkAccess.outputs.user-permission }}" - echo "Job originally triggered by ${{ github.actor }}" - exit 1 - - test_sftp_handle: - needs: security_check - concurrency: - group: ${{ github.repository }}-test_sftp_handle - cancel-in-progress: false - runs-on: ubuntu-latest - strategy: - max-parallel: 1 - matrix: - download_options: ["download_only", "download_clean", "delete_only"] - target_folders: ["", "-t COD-test-1"] - - steps: - - name: Set up Python 3.9.16 - uses: actions/setup-python@v3 - with: - python-version: '3.9.16' - - - name: Checkout code - uses: actions/checkout@v3 - with: - path: . - - - name: Install package and dependencies - run: | - pip install -r requirements.txt - pip install . - - - name: Run sftp_handle tests - run: | - python3 tests/test_sftp_handle.py --download_option ${{ matrix.download_options }} ${{ matrix.target_folders }} - env: - TEST_USER: ${{ secrets.TEST_USER }} - TEST_PASSWORD: ${{ secrets.TEST_PASSWORD }} - TEST_PORT: ${{ secrets.TEST_PORT }} - OUTPUT_LOCATION: ${{ github.workspace }}/tests/ - test_map: runs-on: ubuntu-latest strategy: @@ -76,7 +22,7 @@ jobs: - name: Checkout code uses: actions/checkout@v3 with: - path: . + ref: ${{ github.event.pull_request.head.sha }} - name: Install package and dependencies run: | pip install -r requirements.txt @@ -108,7 +54,7 @@ jobs: - name: Checkout code uses: actions/checkout@v3 with: - path: . + ref: ${{ github.event.pull_request.head.sha }} - name: Install package and dependencies run: | diff --git a/.github/workflows/test_sftp_handle.yml b/.github/workflows/test_sftp_handle.yml new file mode 100644 index 00000000..f1bfc45e --- /dev/null +++ b/.github/workflows/test_sftp_handle.yml @@ -0,0 +1,64 @@ +name: test_sftp_handle + +on: + push: + branches: "**" + pull_request_target: + types: [opened, reopened, synchronize, closed] + branches: "**" + +jobs: + security_check: + runs-on: ubuntu-latest + steps: + - name: Get User Permission + id: checkAccess + uses: actions-cool/check-user-permission@v2 + with: + require: write + username: ${{ github.triggering_actor }} + - name: Check User Permission + if: steps.checkAccess.outputs.require-result == 'false' + run: | + echo "${{ github.triggering_actor }} does not have permissions on this repo." + echo "Current permission level is ${{ steps.checkAccess.outputs.user-permission }}" + echo "Job originally triggered by ${{ github.actor }}" + exit 1 + + test_sftp_handle: + needs: security_check + concurrency: + group: ${{ github.repository }}-test_sftp_handle + cancel-in-progress: false + runs-on: ubuntu-latest + strategy: + max-parallel: 1 + matrix: + download_options: ["download_only", "download_clean", "delete_only"] + target_folders: ["", "-t COD-test-1"] + + steps: + - name: Set up Python 3.9.16 + uses: actions/setup-python@v3 + with: + python-version: '3.9.16' + + - name: Checkout code + uses: actions/checkout@v3 + with: + ref: ${{ github.event.pull_request.head.sha }} + + - name: Install package and dependencies + run: | + pip install -r requirements.txt + pip install . + + - name: Run sftp_handle tests + run: | + python3 tests/test_sftp_handle.py --download_option ${{ matrix.download_options }} ${{ matrix.target_folders }} + env: + TEST_USER: ${{ secrets.TEST_USER }} + TEST_PASSWORD: ${{ secrets.TEST_PASSWORD }} + TEST_PORT: ${{ secrets.TEST_PORT }} + OUTPUT_LOCATION: ${{ github.workspace }}/tests/ + \ No newline at end of file From dcbf46f6a51a7d9fda39a74e46383a45399d51dc Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 23 May 2024 09:42:31 +0200 Subject: [PATCH 1320/1454] Splitted tests, fixed checkout error. Lint --- .github/workflows/test_sftp_handle.yml | 126 ++++++++++++------------- 1 file changed, 63 insertions(+), 63 deletions(-) diff --git a/.github/workflows/test_sftp_handle.yml b/.github/workflows/test_sftp_handle.yml index f1bfc45e..6bd72423 100644 --- a/.github/workflows/test_sftp_handle.yml +++ b/.github/workflows/test_sftp_handle.yml @@ -1,64 +1,64 @@ -name: test_sftp_handle - -on: - push: - branches: "**" - pull_request_target: - types: [opened, reopened, synchronize, closed] - branches: "**" - -jobs: - security_check: - runs-on: ubuntu-latest - steps: - - name: Get User Permission - id: checkAccess - uses: actions-cool/check-user-permission@v2 - with: - require: write - username: ${{ github.triggering_actor }} - - name: Check User Permission - if: steps.checkAccess.outputs.require-result == 'false' - run: | - echo "${{ github.triggering_actor }} does not have permissions on this repo." - echo "Current permission level is ${{ steps.checkAccess.outputs.user-permission }}" - echo "Job originally triggered by ${{ github.actor }}" - exit 1 - - test_sftp_handle: - needs: security_check - concurrency: - group: ${{ github.repository }}-test_sftp_handle - cancel-in-progress: false - runs-on: ubuntu-latest - strategy: - max-parallel: 1 - matrix: - download_options: ["download_only", "download_clean", "delete_only"] - target_folders: ["", "-t COD-test-1"] - - steps: - - name: Set up Python 3.9.16 - uses: actions/setup-python@v3 - with: - python-version: '3.9.16' - - - name: Checkout code - uses: actions/checkout@v3 - with: - ref: ${{ github.event.pull_request.head.sha }} - - - name: Install package and dependencies - run: | - pip install -r requirements.txt - pip install . - - - name: Run sftp_handle tests - run: | - python3 tests/test_sftp_handle.py --download_option ${{ matrix.download_options }} ${{ matrix.target_folders }} - env: - TEST_USER: ${{ secrets.TEST_USER }} - TEST_PASSWORD: ${{ secrets.TEST_PASSWORD }} - TEST_PORT: ${{ secrets.TEST_PORT }} - OUTPUT_LOCATION: ${{ github.workspace }}/tests/ +name: test_sftp_handle + +on: + push: + branches: "**" + pull_request_target: + types: [opened, reopened, synchronize, closed] + branches: "**" + +jobs: + security_check: + runs-on: ubuntu-latest + steps: + - name: Get User Permission + id: checkAccess + uses: actions-cool/check-user-permission@v2 + with: + require: write + username: ${{ github.triggering_actor }} + - name: Check User Permission + if: steps.checkAccess.outputs.require-result == 'false' + run: | + echo "${{ github.triggering_actor }} does not have permissions on this repo." + echo "Current permission level is ${{ steps.checkAccess.outputs.user-permission }}" + echo "Job originally triggered by ${{ github.actor }}" + exit 1 + + test_sftp_handle: + needs: security_check + concurrency: + group: ${{ github.repository }}-test_sftp_handle + cancel-in-progress: false + runs-on: ubuntu-latest + strategy: + max-parallel: 1 + matrix: + download_options: ["download_only", "download_clean", "delete_only"] + target_folders: ["", "-t COD-test-1"] + + steps: + - name: Set up Python 3.9.16 + uses: actions/setup-python@v3 + with: + python-version: '3.9.16' + + - name: Checkout code + uses: actions/checkout@v3 + with: + ref: ${{ github.event.pull_request.head.sha }} + + - name: Install package and dependencies + run: | + pip install -r requirements.txt + pip install . + + - name: Run sftp_handle tests + run: | + python3 tests/test_sftp_handle.py --download_option ${{ matrix.download_options }} ${{ matrix.target_folders }} + env: + TEST_USER: ${{ secrets.TEST_USER }} + TEST_PASSWORD: ${{ secrets.TEST_PASSWORD }} + TEST_PORT: ${{ secrets.TEST_PORT }} + OUTPUT_LOCATION: ${{ github.workspace }}/tests/ \ No newline at end of file From 40ebff71b93151e8844015e11920cd4b56a3dc41 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 23 May 2024 10:35:24 +0200 Subject: [PATCH 1321/1454] Fixed actions pull-requests error --- .github/workflows/test_modules.yml | 2 ++ .github/workflows/test_sftp_handle.yml | 1 + 2 files changed, 3 insertions(+) diff --git a/.github/workflows/test_modules.yml b/.github/workflows/test_modules.yml index 747c0845..35a96a01 100755 --- a/.github/workflows/test_modules.yml +++ b/.github/workflows/test_modules.yml @@ -23,6 +23,7 @@ jobs: uses: actions/checkout@v3 with: ref: ${{ github.event.pull_request.head.sha }} + fetch-depth: 0 - name: Install package and dependencies run: | pip install -r requirements.txt @@ -55,6 +56,7 @@ jobs: uses: actions/checkout@v3 with: ref: ${{ github.event.pull_request.head.sha }} + fetch-depth: 0 - name: Install package and dependencies run: | diff --git a/.github/workflows/test_sftp_handle.yml b/.github/workflows/test_sftp_handle.yml index 6bd72423..2d6e5ebd 100644 --- a/.github/workflows/test_sftp_handle.yml +++ b/.github/workflows/test_sftp_handle.yml @@ -47,6 +47,7 @@ jobs: uses: actions/checkout@v3 with: ref: ${{ github.event.pull_request.head.sha }} + fetch-depth: 0 - name: Install package and dependencies run: | From 7cb855318b8daf2771e879037ccce747a1812356 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 21 May 2024 10:26:39 +0200 Subject: [PATCH 1322/1454] Introduced new module for custom process logs --- relecov_tools/log_summary.py | 109 +++++++++++++++++++++++++++++++++++ 1 file changed, 109 insertions(+) create mode 100755 relecov_tools/log_summary.py diff --git a/relecov_tools/log_summary.py b/relecov_tools/log_summary.py new file mode 100755 index 00000000..5fc97ad7 --- /dev/null +++ b/relecov_tools/log_summary.py @@ -0,0 +1,109 @@ +#!/usr/bin/env python +import logging +import json +import os +from rich.console import Console +from datetime import datetime +from collections import OrderedDict +from relecov_tools.utils import rich_force_colors + + +# from relecov_tools.rest_api import RestApi + +log = logging.getLogger(__name__) +stderr = Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=rich_force_colors(), +) + + +class LogSum: + def __init__(self, output_location: str = None, only_samples: bool = False): + if not os.path.exists(output_location): + raise FileNotFoundError("Output location does not exist") + else: + self.output_location = output_location + # if only_samples is given, no "samples" key will be added to logs + if only_samples: + self.only_samples = True + else: + self.only_samples = False + self.logs = {} + return + + def feed_key(self, key, sample=None): + """Run update_summary() with no entry nor log_type. Add a new empty key""" + self.update_summary(log_type=None, key=key, entry=None, sample=sample) + + def add_error(self, key, entry, sample=None): + """Run update_summary() with log_type as errors""" + log.error(entry) + self.update_summary(log_type="errors", key=key, entry=entry, sample=sample) + return + + def add_warning(self, key, entry, sample=None): + """Run update_summary() with log_type as warnings""" + log.warning(entry) + self.update_summary(log_type="warnings", key=key, entry=entry, sample=sample) + return + + def update_summary(self, key, log_type, entry, sample=None): + """Create a dictionary with a defined structure for each new key. Add the + entry to the dictionary if it already exists. Add it to samples if its a sample + + Args: + key (str): Name of the key holding the logs. A folder or a sample. + log_type (str): Type of log being added. Either 'errors' or 'warnings' + entry (str): Content message of the log. + sample (str, optional): Name of a sample within key if the log is for it + one sample instead of the whole key/folder. Defaults to None. + """ + feed_dict = OrderedDict({"valid": True, "errors": [], "warnings": []}) + # Removing strange characters + current_key = str(key).replace("./", "") + if self.only_samples and sample != None: + log.warning( + f"No samples record can be added if only_samples is set to True. " + + f"Record will be added to {current_key}" + ) + sample = None + entry, sample = (str(entry), str(sample)) + if current_key not in self.logs.keys(): + self.logs[current_key] = feed_dict.copy() + if not self.only_samples: + self.logs[current_key]["samples"] = OrderedDict() + if log_type is None: + if sample != "None" and sample not in self.logs[current_key]["samples"]: + self.logs[current_key]["samples"][sample] = feed_dict.copy() + return + if sample == "None": + self.logs[current_key][log_type].append(entry) + else: + if sample not in self.logs[current_key]["samples"].keys(): + self.logs[current_key]["samples"][sample] = feed_dict.copy() + self.logs[current_key]["samples"][sample][log_type].append(entry) + return + + def create_error_summary(self, filename=None): + """Dump the log summary dictionary into a file with json format. If any of + the 'errors' key is not empty, the parent key value 'valid' is set to false. + + Args: + filename (str, optional): Name of the output file. Defaults to None. + """ + for key in self.logs.keys(): + if self.logs[key]["errors"]: + self.logs[key]["valid"] = False + if not self.only_samples: + for sample in self.logs[key]["samples"].keys(): + if self.logs[key]["samples"][sample]["errors"]: + self.logs[key]["samples"][sample]["valid"] = False + if not filename: + filename = datetime.today().strftime("%Y%m%d%-H%M%S") + "_log_summary.json" + summary_path = os.path.join(self.output_location, filename) + with open(summary_path, "w", encoding="utf-8") as f: + f.write(json.dumps(self.logs, indent=4, sort_keys=True, ensure_ascii=False)) + stderr.print(f"Process log summary printed in {summary_path}") + return From 89c437fcc29560881568ae6fa058ec9590fc0fc5 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 21 May 2024 10:31:00 +0200 Subject: [PATCH 1323/1454] Updated read_lab_metadata with new LogSum class. Now pre-filters by samples_data.json. Also some troubleshooting --- relecov_tools/read_lab_metadata.py | 189 +++++++++++++++++------------ 1 file changed, 111 insertions(+), 78 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 4c21bc0e..f82263f2 100755 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -5,10 +5,11 @@ import os import sys import re -from datetime import datetime +from datetime import datetime as dtime import relecov_tools.utils from relecov_tools.config_json import ConfigJson import relecov_tools.json_schema +from relecov_tools.log_summary import LogSum log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -17,7 +18,6 @@ highlight=False, force_terminal=relecov_tools.utils.rich_force_colors(), ) -# class RelecovMetadata: @@ -79,12 +79,42 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None "[orange]Property " + prop + " does not have 'label' attribute" ) continue - + self.logsum = LogSum(output_location=self.output_folder, only_samples=True) self.json_req_files = config_json.get_topic_data( "lab_metadata", "lab_metadata_req_json" ) self.schema_name = self.relecov_sch_json["title"] self.schema_version = self.relecov_sch_json["version"] + self.metadata_processing = config_json.get_topic_data( + "sftp_handle", "metadata_processing" + ) + self.samples_json_fields = config_json.get_topic_data( + "lab_metadata", "samples_json_fields" + ) + + def match_to_json(self, valid_metadata_rows): + """Keep only the rows from samples present in the input file samples.json + + Args: + valid_metadata_rows (list(dict)): List of rows from metadata_lab.xlsx file + + Returns: + clean_metadata_rows(list(dict)): _description_ + missing_samples(list(str)): + """ + samples_json = relecov_tools.utils.read_json_file(self.sample_list_file) + clean_metadata_rows = [] + missing_samples = [] + for row in valid_metadata_rows: + sample_id = str(row["sequencing_sample_id"]).strip() + self.logsum.feed_key(sample_id) + if sample_id in samples_json.keys(): + clean_metadata_rows.append(row) + else: + log_text = "Sample missing in samples data Json file" + self.logsum.add_error(key=sample_id, log_type="error", entry=log_text) + missing_samples.append(sample_id) + return clean_metadata_rows, missing_samples def adding_fixed_fields(self, m_data): """Include fixed data that are always the same for every sample""" @@ -148,6 +178,9 @@ def adding_ontology_to_enum(self, m_data): if m_data[idx][key] in e_values: m_data[idx][key] = e_values[m_data[idx][key]] else: + sample_id = m_data[idx]["sequencing_sample_id"] + log_text = f"No ontology found for {m_data[idx][key]} in {key}" + self.logsum.add_warning(sample_id, log_text) try: ontology_errors[key] += 1 except KeyError: @@ -165,32 +198,30 @@ def process_from_json(self, m_data, json_fields): map_field = json_fields["map_field"] json_data = json_fields["j_data"] for idx in range(len(m_data)): - try: - m_data[idx].update(json_data[m_data[idx][map_field]]) - except KeyError as error: - clean_error = re.sub("[\[].*?[\]]", "", str(error.args[0])) - if str(clean_error).lower().strip() == "not provided": - log.error("Label was not provided, auto-completing columns") - sample_id = m_data[idx]["collecting_lab_sample_id"] - stderr.print( - f"Label {map_field} was not provided in sample {sample_id}, " - + "auto-completing with Not Provided" - ) - else: - log.error( - f"Unknown map_field value {error} for json data: " - + f"{str(map_field)}. Aborting" - ) - stderr.print( - f"[red] Unknown value {error} for: {map_field} " - + f"in sample {idx}. Aborting" - ) - sys.exit(1) - fields_to_add = { - x: "Not Provided [GENEPIO:0001668]" - for x in json_fields["adding_fields"] - } - m_data[idx].update(fields_to_add) + sample_id = str(m_data[idx].get("sequencing_sample_id")) + if m_data[idx].get(map_field): + try: + m_data[idx].update(json_data[m_data[idx][map_field]]) + except KeyError as error: + clean_error = re.sub("[\[].*?[\]]", "", str(error.args[0])) + if str(clean_error).lower().strip() == "not provided": + log_text( + f"Label {map_field} was not provided in sample " + + f"{sample_id}, auto-completing with Not Provided" + ) + self.logsum.add_warning(key=sample_id, entry=log_text) + else: + log_text = ( + f"Unknown map_field value {error} for json data: " + + f"{str(map_field)} in sample {sample_id}. Skipped" + ) + self.logsum.add_warning(key=sample_id, entry=log_text) + continue + fields_to_add = { + x: "Not Provided [GENEPIO:0001668]" + for x in json_fields["adding_fields"] + } + m_data[idx].update(fields_to_add) return m_data def adding_fields(self, metadata): @@ -237,96 +268,98 @@ def read_configuration_json_files(self): return c_files def read_metadata_file(self): - """Reads the input metadata file from row 4, changes the metadata heading - with their property name values defined in schema. - Convert the date colunms value to the dd/mm/yyyy format. - Return list of dicts with data and errors + """Reads the input metadata file from header row, changes the metadata heading + with their property name values defined in schema. Convert the date columns + value to the yyyy/mm/dd format. Return list of dicts with data """ - heading_row_number = 4 - ws_metadata_lab = relecov_tools.utils.read_excel_file( - self.metadata_file, "METADATA_LAB", heading_row_number, leave_empty=False + meta_sheet = self.metadata_processing.get("excel_sheet") + header_flag = self.metadata_processing.get("header_flag") + ws_metadata_lab, heading_row_number = relecov_tools.utils.read_excel_file( + self.metadata_file, meta_sheet, header_flag, leave_empty=False ) valid_metadata_rows = [] - errors = {} row_number = heading_row_number for row in ws_metadata_lab: row_number += 1 property_row = {} try: - sample_number = row["Sample ID given for sequencing"] + sample_id = str(row["Sample ID given for sequencing"]).strip() except KeyError: - log.error( - "Sample ID given for sequencing not found in row %s", row_number - ) - stderr.print( - f"[red]Sample ID given for sequencing not found in row {row_number}" - ) + log_text = f"Sample ID given for sequencing empty in row {row_number}" + log.error(log_text) + stderr.print(f"[red]{log_text}") continue for key in row.keys(): # skip the first column of the Metadata lab file - if "campo" in key.lower(): + if header_flag in key: + continue + if row[key] is None or "not provided" in str(row[key]).lower(): + log_text = f"{key} not provided for sample {sample_id}" + self.logsum.add_warning(sample_id, log_text) continue if "date" in key.lower(): - if row[key] is None or str(row[key]).lower() == "not provided": - log.info("Date was not provided") - row[key] = "Not Provided [GENEPIO:0001668]" - elif isinstance(row[key], int) or isinstance(row[key], float): + # Check if date is a string. Format YYYY-MM-DD to YYYY/MM/DD + if re.match(r"^\d{4}[-/]\d{2}[-/]\d{2}$", str(row[key])): + row[key] = row[key].replace("/", "-") + if isinstance(row[key], int) or isinstance(row[key], float): log.info("Date given as an integer. Understood as a year") row[key] = str(int(row[key])) else: try: - row[key] = row[key].strftime("%Y-%m-%d") - except AttributeError: - # check if date is in string format - str_date = re.search(r"(\d{4}-\d{2}-\d{2}).*", row[key]) - if str_date: - row[key] = str_date.group(1) - else: - if sample_number not in errors: - errors[sample_number] = {} - errors[sample_number][key] = "Invalid date format" - log.error( - "Invalid date format in sample %s", row_number - ) - stderr.print( - f"[red]Invalid date format in sample {sample_number}, {key}" - ) + row[key] = str( + dtime.strptime(str(row[key]), "%Y-%m-%d").date() + ) + except ValueError: + log_text = f"Invalid date format in sample {str(key)}" + self.logsum.add_error(sample_id, log_text) + stderr.print(f"[red]{log_text}") + row[key] = None elif "sample id" in key.lower(): if isinstance(row[key], float) or isinstance(row[key], int): row[key] = str(int(row[key])) else: if isinstance(row[key], float) or isinstance(row[key], int): row[key] = str(row[key]) - try: - property_row[self.label_prop_dict[key]] = row[key] - except KeyError as e: - log.error("Error when mapping the label %s", e) - stderr.print(f"[red]Error when mapping the label {str(e)}") - continue + if row[key] is not None or "not provided" not in str(row[key]).lower(): + try: + property_row[self.label_prop_dict[key]] = row[key] + except KeyError as e: + log_text = f"Error when mapping the label {str(e)}" + self.logsum.add_error(sample_id, log_text) + stderr.print(f"[red]{log_text}") + continue valid_metadata_rows.append(property_row) - return valid_metadata_rows, errors + return valid_metadata_rows def create_metadata_json(self): stderr.print("[blue]Reading Lab Metadata Excel File") - valid_metadata_rows, errors = self.read_metadata_file() - if len(errors) > 0: - stderr.print("[red]Stopped executing because errors were found") - sys.exit(1) + valid_metadata_rows = self.read_metadata_file() + clean_metadata_rows, missing_samples = self.match_to_json(valid_metadata_rows) + if missing_samples: + num_miss = len(missing_samples) + log.warning( + "%s samples from metadata were not found: %s", num_miss, missing_samples + ) + stderr.print(f"[yellow]{num_miss} samples missing:\n{missing_samples}") # Continue by adding extra information stderr.print("[blue]Including additional information") - extended_metadata = self.adding_fields(valid_metadata_rows) + extended_metadata = self.adding_fields(clean_metadata_rows) stderr.print("[blue]Including post processing information") extended_metadata = self.adding_post_processing(extended_metadata) extended_metadata = self.adding_copy_from_other_field(extended_metadata) extended_metadata = self.adding_fixed_fields(extended_metadata) completed_metadata = self.adding_ontology_to_enum(extended_metadata) + if not completed_metadata: + stderr.print("Metadata was completely empty. No output file generated") + sys.exit(1) file_name = ( - "processed_metadata_lab_" + datetime.now().strftime("%Y_%m_%d") + ".json" + "processed_metadata_lab_" + dtime.now().strftime("%Y_%m_%d") + ".json" ) stderr.print("[blue]Writting output json file") os.makedirs(self.output_folder, exist_ok=True) + self.logsum.create_error_summary() file_path = os.path.join(self.output_folder, file_name) relecov_tools.utils.write_json_fo_file(completed_metadata, file_path) return True From f4855b7183a3719955fbe1c432a8a237ed0f3784 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 21 May 2024 10:31:49 +0200 Subject: [PATCH 1324/1454] Included adding_fields from config --- relecov_tools/read_lab_metadata.py | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index f82263f2..a9204a13 100755 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -143,7 +143,9 @@ def adding_post_processing(self, m_data): ) for idx in range(len(m_data)): for key, p_values in p_data.items(): - value = m_data[idx][key] + value = m_data[idx].get(key) + if not value: + continue if value in p_values: p_field, p_set = p_values[value].split("::") m_data[idx][p_field] = p_set @@ -236,20 +238,12 @@ def adding_fields(self, metadata): metadata = self.process_from_json(metadata, values) stderr.print(f"[green]Processed {key}") - # As sample data file is comming in an input parameter, it cannot - # be inside the configuration json file. # Include Sample information data from sample json file stderr.print("[blue]Processing sample data file") s_json = {} - s_json["map_field"] = "submitting_lab_sample_id" - s_json["adding_fields"] = [ - "fastq_r1_md5", - "fastq_r2_md5", - "sequence_file_R1_fastq", - "sequence_file_R2_fastq", - "r1_fastq_filepath", - "r2_fastq_filepath", - ] + # TODO: Change sequencing_sample_id for some unique ID used in RELECOV database + s_json["map_field"] = "sequencing_sample_id" + s_json["adding_fields"] = self.samples_json_fields s_json["j_data"] = relecov_tools.utils.read_json_file(self.sample_list_file) metadata = self.process_from_json(metadata, s_json) stderr.print("[green]Processed sample data file.") From 5bd7523799e47d3694f9fa5312cb58302690f04d Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 21 May 2024 10:35:05 +0200 Subject: [PATCH 1325/1454] Updated sftp_handle with new LogSum class --- relecov_tools/sftp_handle.py | 104 +++++++++++++++-------------------- 1 file changed, 43 insertions(+), 61 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 157f924f..f1585ea1 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -12,13 +12,13 @@ import relecov_tools.utils from datetime import datetime from itertools import islice -from collections import OrderedDict from secrets import token_hex from csv import writer as csv_writer, Error as CsvError from openpyxl import load_workbook as openpyxl_load_workbook from pandas import read_excel, ExcelWriter, concat from pandas.errors import ParserError, EmptyDataError from relecov_tools.config_json import ConfigJson +from relecov_tools.log_summary import LogSum # from relecov_tools.rest_api import RestApi @@ -113,7 +113,7 @@ def __init__( self.sftp_user = relecov_tools.utils.prompt_text(msg="Enter the user id") if isinstance(self.target_folders, str): self.target_folders = self.target_folders.split(",") - self.logs = {} + self.logsum = LogSum(output_location=self.platform_storage_folder) if self.sftp_passwd is None: self.sftp_passwd = relecov_tools.utils.prompt_password( msg="Enter your password" @@ -202,6 +202,7 @@ def recursive_list(folder_name): if recursive: directory_list = recursive_list(folder_name) + directory_list.append(folder_name) return directory_list try: directory_list = [ @@ -491,25 +492,28 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): return False sample_file_dict = {} metadata_ws, meta_header, header_row = self.read_metadata_file(meta_f_path) + # TODO Include these columns in config index_sampleID = meta_header.index("Sample ID given for sequencing") index_layout = meta_header.index("Library Layout") index_fastq_r1 = meta_header.index("Sequence file R1 fastq") index_fastq_r2 = meta_header.index("Sequence file R2 fastq") + counter = header_row for row in islice(metadata_ws.values, header_row, metadata_ws.max_row): + counter += 1 if row[index_sampleID] is not None: row_complete = True try: - s_name = str(row[index_sampleID]) + s_name = str(row[index_sampleID]).strip() except ValueError as e: stderr.print("[red]Unable to convert to string. ", e) continue if s_name not in sample_file_dict: sample_file_dict[s_name] = {} else: - stderr.print("Found duplicated sample name: ", s_name) - s_name = "_".join([s_name, str(token_hex(nbytes=8))]) - stderr.print("Duplicated sample renamed to ", s_name) - sample_file_dict[s_name] = {} + log_text = f"Found duplicated sample name: {s_name}. Skipped." + stderr.print(log_text) + self.include_warning(log_text, sample=s_name) + continue if row[index_layout] == "paired" and row[index_fastq_r2] is None: error_text = "Sample %s is paired-end, but no R2 given" log.error(str(error_text % str(row[index_sampleID]))) @@ -525,16 +529,18 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): # TODO: move these keys to configuration.json sample_file_dict[s_name]["sequence_file_R1_fastq"] = row[ index_fastq_r1 - ] + ].strip() if row[index_fastq_r2] is not None: sample_file_dict[s_name]["sequence_file_R2_fastq"] = row[ index_fastq_r2 - ] + ].strip() else: - error_text = "Fastq_R1 not defined in Metadata for sample %s" - log.error(str(error_text % s_name)) - stderr.print(f"[red]{str(error_text % s_name)}") - self.include_error(str(error_text % s_name), s_name) + log_text = "Fastq_R1 not defined in Metadata for sample %s" + log.error(str(log_text % s_name)) + stderr.print(f"[red]{str(log_text % s_name)}") + self.include_error(entry=str(log_text % s_name), sample=s_name) + else: + self.include_warning(entry=f"Row {counter} skipped. No sample ID given") # Remove duplicated files clean_sample_dict = self.remove_duplicated_values(sample_file_dict) return clean_sample_dict @@ -598,6 +604,9 @@ def validate_remote_files(self, remote_folder, local_folder): sample_files_dict = self.get_sample_fastq_file_names( out_folder, local_meta_file ) + # Include the samples in the process log summary + for sample in sample_files_dict.keys(): + self.include_new_key(sample=sample) metafiles_list = sorted( sum([list(fi.values()) for _, fi in sample_files_dict.items()], []) ) @@ -611,6 +620,7 @@ def validate_remote_files(self, remote_folder, local_folder): set_list = set(metafiles_list) mismatch_files = [fi for fi in filtered_files_list if fi not in set_list] mismatch_rev = [fi for fi in set_list if fi not in filtered_files_list] + error_text1 = "Files in folder missing in metadata %s" log.warning(error_text1 % str(mismatch_files)) self.include_warning(error_text1 % str(mismatch_files)) @@ -845,29 +855,27 @@ def upload_merged_df(merged_excel_path, last_main_folder, merged_df): pd_writer.close() dest = os.path.join(last_main_folder, os.path.basename(merged_excel_path)) self.client.put(merged_excel_path, dest) + os.remove(merged_excel_path) return def pre_validate_folder(folder, folder_files): """Check if remote folder has sequencing files and a valid metadata file""" if not any(file.endswith(tuple(exts)) for file in folder_files): error_text = "Remote folder %s skipped. No sequencing files found." - log.error(error_text % folder) self.include_error(error_text % folder) return try: downloaded_metadata = self.get_metadata_file(folder, output_location) except (FileNotFoundError, OSError, PermissionError, MetadataError) as err: error_text = "Remote folder %s skipped. Reason: %s" - log.error(error_text % (folder, err)) self.include_error(error_text % (folder, err)) return try: self.read_metadata_file(downloaded_metadata, return_data=False) - except MetadataError as header_error: - error_text = " Folder skipped: %s" + except (MetadataError, KeyError) as excel_error: + error_text = f"Folder {self.current_folder} skipped: %s" os.remove(downloaded_metadata) - log.error(str(folder, str(error_text % str(header_error)))) - self.include_error(error_text % header_error) + self.include_error(error_text % excel_error) return return downloaded_metadata @@ -877,6 +885,8 @@ def pre_validate_folder(folder, folder_files): stderr.print(f"[blue]Setting {len(target_folders.keys())} remote folders...") for folder in sorted(target_folders.keys()): self.current_folder = folder + # Include the folder in the final process log summary + self.include_new_key() downloaded_metadata = pre_validate_folder(folder, target_folders[folder]) if not downloaded_metadata: continue @@ -1043,9 +1053,9 @@ def process_filedict( for key, val in vals.items(): processed_dict[sample][key] = None if val in corrupted: - self.include_error(error_text % val, sample) + self.include_error(error_text % val, sample=sample) if val in md5miss: - self.include_warning(warning_text % val, sample) + self.include_warning(warning_text % val, sample=sample) for file in clean_fetchlist: if val in file: processed_dict[sample][key] = file @@ -1053,7 +1063,7 @@ def process_filedict( if not all(x in clean_fetchlist for x in processed_dict[sample].values()): if not corrupted: error_text = "Sample %s skipped: missing files in sftp" - self.include_error(str(error_text % sample), sample) + self.include_error(str(error_text % sample), sample=sample) log.error(str(error_text % sample)) del processed_dict[sample] return processed_dict @@ -1221,47 +1231,16 @@ def download(self, target_folders, option="download"): stderr.print(f"[green]Finished processing {folder}") return - def include_error(self, entry, sample=None): - self.update_summary(log_type="error", entry=entry, sample=sample) + def include_new_key(self, sample=None): + self.logsum.feed_key(key=self.current_folder, sample=sample) return - def include_warning(self, entry, sample=None): - self.update_summary(log_type="warning", entry=entry, sample=sample) - return - - def update_summary(self, log_type, entry, sample=None): - feed_dict = OrderedDict({"valid": False, "errors": [], "warnings": []}) - current_folder = str(self.current_folder).replace("./", "") - entry, sample = (str(entry), str(sample)) - if current_folder not in self.logs.keys(): - self.logs[current_folder] = feed_dict.copy() - self.logs[current_folder]["samples"] = OrderedDict() - if sample == "None": - if log_type == "error": - self.logs[current_folder]["errors"].append(entry) - elif log_type == "warning": - self.logs[current_folder]["warnings"].append(entry) - else: - if sample not in self.logs[current_folder]["samples"].keys(): - self.logs[current_folder]["samples"][sample] = feed_dict.copy() - if log_type == "error": - self.logs[current_folder]["samples"][sample]["errors"].append(entry) - elif log_type == "warning": - self.logs[current_folder]["samples"][sample]["warnings"].append(entry) + def include_error(self, entry, sample=None): + self.logsum.add_error(key=self.current_folder, entry=entry, sample=sample) return - def create_error_summary(self): - for folder in self.logs.keys(): - if not self.logs[folder]["errors"]: - self.logs[folder]["valid"] = True - for sample in self.logs[folder]["samples"].keys(): - if not self.logs[folder]["samples"][sample]["errors"]: - self.logs[folder]["samples"][sample]["valid"] = True - filename = datetime.today().strftime("%Y%m%d%-H%M%S") + "_log_summary.json" - summary_path = os.path.join(self.platform_storage_folder, filename) - with open(summary_path, "w", encoding="utf-8") as f: - f.write(json.dumps(self.logs, indent=4, sort_keys=True, ensure_ascii=False)) - stderr.print(f"Process summary printed in {summary_path}") + def include_warning(self, entry, sample=None): + self.logsum.add_warning(key=self.current_folder, entry=entry, sample=sample) return def execute_process(self): @@ -1282,7 +1261,10 @@ def execute_process(self): self.delete_remote_files(folder, files) stderr.print(f"Delete process finished in {folder}") self.close_connection() - if self.logs: + if self.logsum.logs: log.info("Printing process summary to %s", self.platform_storage_folder) - self.create_error_summary() + self.logsum.create_error_summary() + else: + log.info("Process log summary was empty. Not generated.") stderr.print("Finished execution") + return From 9700e0d743b34a96d14cb3a57f893f379e2fdf16 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 21 May 2024 10:36:25 +0200 Subject: [PATCH 1326/1454] New pre-merging of multiple metadata files in remote folder --- relecov_tools/sftp_handle.py | 72 ++++++++++++++++++++++++++++-------- 1 file changed, 57 insertions(+), 15 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index f1585ea1..c8e52d55 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -553,29 +553,71 @@ def get_metadata_file(self, remote_folder, local_folder): local_folder (str): path to the local folder Raises: - FileNotFoundError: If more than 1 metadata excel file or missing + FileNotFoundError: If missing metadata excel file or merging error. Returns: - local_meta_file: Path to downloaded metadata file. + local_meta_file: Path to downloaded metadata file / merged metadata file. """ remote_files_list = self.get_file_list(remote_folder) meta_files = [fi for fi in remote_files_list if fi.endswith(".xlsx")] + + def download_remote_metafile(target_meta_file): + local_meta_file = os.path.join( + local_folder, os.path.basename(target_meta_file) + ) + try: + self.get_from_sftp(target_meta_file, local_meta_file) + except (IOError, PermissionError) as e: + raise type(e)(f"[red]Unable to fetch metadata file {e}") + log.info( + "Obtained metadata file %s from %s", + local_meta_file, + remote_folder, + ) + return local_meta_file + if not meta_files: raise FileNotFoundError(f"Missing metadata file for {remote_folder}") - if len(meta_files) > 1: - raise MetadataError(f"[red]Too many metadata files in {remote_folder}") - target_meta_file = meta_files[0] os.makedirs(self.platform_storage_folder, exist_ok=True) - local_meta_file = os.path.join(local_folder, os.path.basename(target_meta_file)) - try: - self.get_from_sftp(target_meta_file, local_meta_file) - except (IOError, PermissionError) as e: - raise type(e)(f"[red]Unable to fetch metadata file {e}") - log.info( - "Obtained metadata file %s from %s", - local_meta_file, - remote_folder, - ) + if len(meta_files) > 1: + # Merging multiple excel files into a single one + log.warning(f"[yellow]Merging multiple metadata files in {remote_folder}") + metadata_ws = self.metadata_processing.get("excel_sheet") + header_flag = self.metadata_processing.get("header_flag") + local_meta_list = [] + for remote_metafile in meta_files: + local_meta_file = download_remote_metafile(remote_metafile) + local_meta_list.append(local_meta_file) + meta_df_list = [] + for loc_meta in local_meta_list: + try: + loc_meta_df = self.excel_to_df(loc_meta, metadata_ws, header_flag) + meta_df_list.append(loc_meta_df) + except (ParserError, EmptyDataError, MetadataError, KeyError) as e: + error_text = f"Could not process {os.path.basename(loc_meta)}: {e}" + log.error(error_text) + self.include_error(error_text) + os.remove(loc_meta) + if meta_df_list: + merged_df = meta_df_list[0] + else: + raise MetadataError("No single metadata file could be merged") + for meta_df in meta_df_list[1:]: + merged_df = self.merge_metadata(metadata_ws, merged_df, meta_df) + folder_name = os.path.dirname(local_meta_file) + excel_name = str(folder_name.split("/")[-1]) + "merged_metadata.xlsx" + merged_excel_path = os.path.join(folder_name, excel_name) + pd_writer = ExcelWriter(merged_excel_path, engine="xlsxwriter") + for sheet in merged_df.keys(): + format_sheet = merged_df[sheet].astype(str) + format_sheet.replace("nan", None, inplace=True) + format_sheet.to_excel(pd_writer, sheet_name=sheet, index=False) + pd_writer.close() + local_meta_file = merged_excel_path + return merged_excel_path + else: + target_meta_file = meta_files[0] + local_meta_file = download_remote_metafile(target_meta_file) return local_meta_file def validate_remote_files(self, remote_folder, local_folder): From f44c8adef73016912af13571847af18f3e7b419f Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 21 May 2024 10:37:11 +0200 Subject: [PATCH 1327/1454] Better empty folders and md5 handling in sftp_handle --- relecov_tools/sftp_handle.py | 23 ++++++++++++++++------- 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index c8e52d55..7ca37c52 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -688,6 +688,7 @@ def delete_remote_files(self, remote_folder, files): files (list(str)): list of file basenames in remote repository """ stderr.print(f"[blue]Deleting files in {remote_folder}...") + empty_folder = True for file in files: try: self.client.remove(os.path.join(remote_folder, os.path.basename(file))) @@ -695,7 +696,15 @@ def delete_remote_files(self, remote_folder, files): except (IOError, PermissionError) as e: log.error("Could not delete file %s.", str(e)) stderr.print(f"Could not delete file {file}. Error: {e}") + empty_folder = False continue + if empty_folder: + if len(remote_folder.replace("./", "").split("/")) >= 2: + try: + self.client.rmdir(remote_folder) + except (OSError, PermissionError) as e: + log.error("Could not delete folder %s.", str(e)) + stderr.print(f"Could not delete folder {remote_folder}. Error: {e}") return def move_processing_fastqs(self, folders_with_metadata): @@ -783,25 +792,24 @@ def md5_handler(md5sumlist, output_location): md5_dest = os.path.join(folder, os.path.basename(merged_md5_path)) self.client.put(localpath=merged_md5_path, remotepath=md5_dest) # Remove local files once merged and uploaded + os.remove(merged_md5_path) [os.remove(md5_file) for md5_file in downloaded_md5files] return md5_dest else: error_text = "No md5sum could be processed in remote folder" raise FileNotFoundError(error_text) - for folder in folders_with_metadata.keys(): + for folder, files in folders_with_metadata.items(): self.current_folder = folder.split("/")[0] - md5flag = "md5sum" - md5sumlist = [fi for fi in folders_with_metadata[folder] if md5flag in fi] + md5flags = [".md5", "md5sum", "md5checksum"] + md5sumlist = [fi for fi in files if any(flag in fi for flag in md5flags)] if not md5sumlist: error_text = "No md5sum could be found in remote folder" log.warning(error_text) stderr.print(f"[yellow]{error_text}") self.include_warning(error_text) continue - folders_with_metadata[folder] = [ - fi for fi in folders_with_metadata[folder] if fi not in md5sumlist - ] + folders_with_metadata[folder] = [fi for fi in files if fi not in md5sumlist] try: uploaded_md5 = md5_handler(md5sumlist, output_location) except (FileNotFoundError, OSError, PermissionError, CsvError) as e: @@ -1216,6 +1224,7 @@ def download(self, target_folders, option="download"): log.info("Finished md5 check for folder: %s", folder) stderr.print(f"[blue]Finished md5 verification for folder {folder}") else: + corrupted = [] error_text = "No single md5sum file could be found in %s" % folder log.warning(error_text) stderr.print(f"[red]{error_text}") @@ -1236,9 +1245,9 @@ def download(self, target_folders, option="download"): clean_fetchlist, files_to_compress, local_folder ) clean_pathlist = [os.path.join(local_folder, fi) for fi in clean_fetchlist] + not_md5sum = [] if remote_md5sum: # Get hashes from provided md5sum, create them for those not provided - not_md5sum = [] files_md5_dict = {} for path in clean_pathlist: f_name = os.path.basename(path) From b4f38a107fa0196c6a773d6d4b7ab8f0e70f8a83 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 21 May 2024 10:54:44 +0200 Subject: [PATCH 1328/1454] Introduced new log_summary module. Linting --- relecov_tools/log_summary.py | 4 ++-- relecov_tools/read_lab_metadata.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/relecov_tools/log_summary.py b/relecov_tools/log_summary.py index 5fc97ad7..e1ad1f07 100755 --- a/relecov_tools/log_summary.py +++ b/relecov_tools/log_summary.py @@ -63,9 +63,9 @@ def update_summary(self, key, log_type, entry, sample=None): feed_dict = OrderedDict({"valid": True, "errors": [], "warnings": []}) # Removing strange characters current_key = str(key).replace("./", "") - if self.only_samples and sample != None: + if self.only_samples and sample is not None: log.warning( - f"No samples record can be added if only_samples is set to True. " + "No samples record can be added if only_samples is set to True. " + f"Record will be added to {current_key}" ) sample = None diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index a9204a13..edba2cc9 100755 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -207,7 +207,7 @@ def process_from_json(self, m_data, json_fields): except KeyError as error: clean_error = re.sub("[\[].*?[\]]", "", str(error.args[0])) if str(clean_error).lower().strip() == "not provided": - log_text( + log_text = ( f"Label {map_field} was not provided in sample " + f"{sample_id}, auto-completing with Not Provided" ) From ba74f5f54f27427c8331df70598b3d81bcb67d99 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 23 May 2024 10:48:14 +0200 Subject: [PATCH 1329/1454] Fixed TypeError in read_lab_metadata --- relecov_tools/read_lab_metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index edba2cc9..63dd582d 100755 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -112,7 +112,7 @@ def match_to_json(self, valid_metadata_rows): clean_metadata_rows.append(row) else: log_text = "Sample missing in samples data Json file" - self.logsum.add_error(key=sample_id, log_type="error", entry=log_text) + self.logsum.add_error(sample_id, log_text) missing_samples.append(sample_id) return clean_metadata_rows, missing_samples From 311ba4488636ad307bd90036c962193ed1fab0cb Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 28 May 2024 16:24:56 +0200 Subject: [PATCH 1330/1454] Fixed tmp folder creation in /home --- relecov_tools/sftp_handle.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 7ca37c52..4423fbdb 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -202,7 +202,8 @@ def recursive_list(folder_name): if recursive: directory_list = recursive_list(folder_name) - directory_list.append(folder_name) + if "." != folder_name: + directory_list.append(folder_name) return directory_list try: directory_list = [ From bb0ae166da62cad3414fb5dfa7c9f35f8a8264b8 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 28 May 2024 16:25:09 +0200 Subject: [PATCH 1331/1454] Removed pdb imports --- relecov_tools/upload_ena_protocol.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/relecov_tools/upload_ena_protocol.py b/relecov_tools/upload_ena_protocol.py index f85efc21..f965712d 100755 --- a/relecov_tools/upload_ena_protocol.py +++ b/relecov_tools/upload_ena_protocol.py @@ -232,9 +232,6 @@ def update_json(self, updated_schemas_df, json_data): def xml_submission(self, json_data, schemas_dataframe, batch_index=None): """The metadata is submitted in an xml format""" - import pdb - - pdb.set_trace() schema_targets = extract_targets(self.action, schemas_dataframe) tool = self.config_json.get_configuration("ENA_fields")["tool"] @@ -266,9 +263,7 @@ def xml_submission(self, json_data, schemas_dataframe, batch_index=None): schema_xmls["submission"] = submission_xml stderr.print(f"\nProcessing submission to ENA server: {self.url}") - import pdb - pdb.set_trace() receipt = send_schemas(schema_xmls, self.url, self.user, self.passwd).text if not os.path.exists(self.output_path): os.mkdir(self.output_path) From 5eee5a1e3867894013781d12184b55a7d476af4a Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 28 May 2024 16:25:47 +0200 Subject: [PATCH 1332/1454] read-excel error handling when header flag is not found --- relecov_tools/utils.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 88493fef..8c3991d8 100755 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -64,9 +64,12 @@ def read_excel_file(f_name, sheet_name, header_flag, leave_empty=True): """ wb_file = openpyxl.load_workbook(f_name, data_only=True) ws_metadata_lab = wb_file[sheet_name] - heading_row = [ - idx + 1 for idx, x in enumerate(ws_metadata_lab.values) if header_flag in x - ][0] + try: + heading_row = [ + idx + 1 for idx, x in enumerate(ws_metadata_lab.values) if header_flag in x + ][0] + except IndexError: + raise KeyError(f"Header flag '{header_flag}' could not be found in {f_name}") heading = [str(i.value).strip() for i in ws_metadata_lab[heading_row] if i.value] ws_data = [] for row in islice(ws_metadata_lab.values, heading_row, ws_metadata_lab.max_row): From 31cc513f0b2f38f06810baaf465ee81724788bb2 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 28 May 2024 16:52:22 +0200 Subject: [PATCH 1333/1454] Fixed tmp folder creation in /home. lint --- relecov_tools/sftp_handle.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 4423fbdb..c485149e 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -202,7 +202,7 @@ def recursive_list(folder_name): if recursive: directory_list = recursive_list(folder_name) - if "." != folder_name: + if folder_name != ".": directory_list.append(folder_name) return directory_list try: From cb5965b2b6232b716232e6b8e898b68ad945267f Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 11 Jul 2024 10:59:52 +0200 Subject: [PATCH 1334/1454] fixed regex error while parsing date field in variants long table --- relecov_tools/assets/pipeline_utils/viralrecon.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py index be0648e5..25b026be 100644 --- a/relecov_tools/assets/pipeline_utils/viralrecon.py +++ b/relecov_tools/assets/pipeline_utils/viralrecon.py @@ -148,18 +148,17 @@ def convert_to_json(self, samp_dict): else: date_regex = re.search(r"(\d{8})", result_regex.group()) if date_regex is not None: - analysis_date = date_regex + analysis_date = date_regex.group() stderr.print( - f"[green]\tDate {analysis_date.group()} found in {self.file_path}" + f"[green]\tDate {analysis_date} found in {self.file_path}" ) else: analysis_date = "Not Provided [GENEPIO:0001668]" stderr.print( f"[yellow]\tWARN:No analysis date found in long table: {self.file_path}" ) - for key, values in samp_dict.items(): - j_dict = {"sample_name": key, "analysis_date": analysis_date.group()} + j_dict = {"sample_name": key, "analysis_date": analysis_date} j_dict["variants"] = values j_list.append(j_dict) return j_list From a6f9e39652b90b8023afd5bc23d35844d0af3c34 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 11 Jul 2024 11:44:00 +0200 Subject: [PATCH 1335/1454] fix regex to find file name --- relecov_tools/conf/bioinfo_config.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index 9c626d71..c3d3ed3a 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -1,7 +1,7 @@ { "viralrecon": { "mapping_stats": { - "fn": "mapping_illumina_stats(?:_\\d{8})?\\.tab", + "fn": "mapping_illumina(?:_\\d{8})?\\.tab", "sample_col_idx": 5, "header_row_idx": 1, "required": true, From ee6f8d98750ebb5618f1970d09007b72b8995443 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 11 Jul 2024 11:45:20 +0200 Subject: [PATCH 1336/1454] fixed assignment of fields 'software version' --- relecov_tools/conf/bioinfo_config.json | 13 ++++++++----- relecov_tools/read_bioinfo_metadata.py | 17 ++++++++++++----- 2 files changed, 20 insertions(+), 10 deletions(-) diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index c3d3ed3a..94d6e2ce 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -90,11 +90,14 @@ "required": true, "function": null, "content": { - "bioinformatics_protocol_software_version": "nf-core/viralrecon", - "consensus_sequence_software_version": "bcftools", - "dehosting_method_software_version": "kraken2", - "mapping_software_version":"bowtie2", - "preprocessing_software_version":"fastp","variant_calling_software_version":"ivar" + "software_version": { + "bioinformatics_protocol_software_version": "nf-core/viralrecon", + "consensus_sequence_software_version": "bcftools", + "dehosting_method_software_version": "kraken2", + "mapping_software_version":"bowtie2", + "preprocessing_software_version":"fastp", + "variant_calling_software_version":"ivar" + } } }, "fixed_values": { diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 5c90ba79..de47d74f 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -337,7 +337,6 @@ def handling_files(self, file_list): utils_name = f"relecov_tools.assets.pipeline_utils.{self.software_name}" import_statement = f"from {utils_name} import {func_name}" exec(import_statement) - # Get method name and execute it. data = eval(func_name + "(file_list)") except Exception as e: @@ -481,15 +480,23 @@ def get_multiqc_software_versions(self, file_list, j_data): # Mapping multiqc sofware versions to j_data field_errors = {} for row in j_data: + # Get sample name to track whether version assignment was successful or not. sample_match = re.match( - r"^(.*?)_R1\.fastq\.gz", row["sequence_file_R1_fastq"] + r"^[^_]+", row["sequence_file_R1_fastq"] ) if sample_match: - sample_name = sample_match.group(1) + sample_name = sample_match.group() else: + self.log_report.update_log_report( + method_name, + "warning", + f'Regex failed to find extract sample name from: {row["sequence_file_R1_fastq"]}. Skipping...', + ) continue - for field, values in ( - self.software_config["workflow_summary"].get("content").items() + + # Append software versions + software_version_config = self.software_config["workflow_summary"].get("content").get("software_version") + for field, values in (software_version_config.items() ): try: row[field] = program_versions[values] From 3589e60b231f87e91dfeeab166b651aa255c5c89 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 11 Jul 2024 12:24:50 +0200 Subject: [PATCH 1337/1454] allow adding software names to processed data --- relecov_tools/conf/bioinfo_config.json | 12 ++++++---- relecov_tools/read_bioinfo_metadata.py | 32 +++++++++++++++++--------- 2 files changed, 29 insertions(+), 15 deletions(-) diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index 94d6e2ce..523d7fde 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -97,6 +97,14 @@ "mapping_software_version":"bowtie2", "preprocessing_software_version":"fastp", "variant_calling_software_version":"ivar" + }, + "software_name": { + "bioinformatics_protocol_software_name": "nf-core/viralrecon", + "consensus_sequence_software_name": "bcftools", + "dehosting_method_software_name": "kraken2", + "mapping_software_name":"bowtie2", + "preprocessing_software_name":"fastp", + "variant_calling_software_name":"ivar" } } }, @@ -105,8 +113,6 @@ "assembly_params": "Not Provided [GENEPIO:0001668]", "commercial_open_source_both": "Open Source", "consensus_params": "-p vcf -f", - "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", - "dehosting_method_software_name": "KRAKEN2_KRAKEN2", "depth_of_coverage_threshold": ">10x", "if_assembly_other": "Not Provided [GENEPIO:0001668]", "if_bioinformatic_protocol_is_other_specify": "Not Provided [GENEPIO:0001668]", @@ -116,9 +122,7 @@ "if_preprocessing_other": "Not Provided [GENEPIO:0001668]", "lineage_analysis_software_name": "pangolin", "mapping_params": "--seed 1", - "mapping_software_name": "BOWTIE2_ALIGN", "preprocessing_params": "--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50", - "preprocessing_software_name": "FASTP", "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m10", "lineage_analysis_date": "Not Provided [GENEPIO:0001668]" } diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index de47d74f..1beb9040 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -432,7 +432,7 @@ def get_multiqc_software_versions(self, file_list, j_data): j_data (list(dict{str:str}): A list of dictionaries containing metadata lab (one item per sample). Returns: - j_data: updated j_data with software version's info mapped in it. + j_data: updated j_data with software details mapped in it. """ method_name = f"{self.get_multiqc_software_versions.__name__}" # Handle multiqc_report.html @@ -494,16 +494,26 @@ def get_multiqc_software_versions(self, file_list, j_data): ) continue - # Append software versions - software_version_config = self.software_config["workflow_summary"].get("content").get("software_version") - for field, values in (software_version_config.items() - ): - try: - row[field] = program_versions[values] - except KeyError as e: - field_errors[sample_name] = {field: e} - row[field] = "Not Provided [GENEPIO:0001668]" - continue + # Append software version and name + software_content_details = self.software_config["workflow_summary"].get("content") + for content_key, content_value in software_content_details.items(): + for key, value in content_value.items(): + # Add software versions + if "software_version" in content_key: + try: + row[key] = program_versions[value] + except KeyError as e: + field_errors[sample_name] = {value: e} + row[key] = "Not Provided [GENEPIO:0001668]" + continue + # Add software name + elif "software_name" in content_key: + try: + row[key] = value + except KeyError as e: + field_errors[sample_name] = {value: e} + row[key] = "Not Provided [GENEPIO:0001668]" + continue # update progress log if len(field_errors) > 0: From 7db5888b2a2a6145cd1b423ac1dc807165e51f5e Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 11 Jul 2024 13:11:27 +0200 Subject: [PATCH 1338/1454] fixed regex pattern that caused skippng of samples proessing --- relecov_tools/read_bioinfo_metadata.py | 22 +++++++++++++++++----- 1 file changed, 17 insertions(+), 5 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 1beb9040..7c04cc4e 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -368,16 +368,22 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): # TODO: We should consider an independent module that verifies that sample's name matches this pattern. # If we add warnings within this module, every time mapping_over_table is invoked it will print redundant warings sample_match = re.match( - r"^(.*?)_R1\.fastq\.gz", row["sequence_file_R1_fastq"] + r"^[^_]+", row["sequence_file_R1_fastq"] ) if sample_match: - sample_name = sample_match.group(1) + sample_name = sample_match.group() else: + self.log_report.update_log_report( + method_name, + "warning", + f'Regex failed to find extract sample name from: {row["sequence_file_R1_fastq"]}. Skipping...', + ) continue if sample_name in map_data.keys(): for field, value in mapping_fields.items(): try: - row[field] = map_data[sample_name][value] + # FIXME: we have to allow more than one data type to make json validation module work. + row[field] = str(map_data[sample_name][value]) field_valid[sample_name] = {field: value} except KeyError as e: field_errors[sample_name] = {field: e} @@ -558,6 +564,7 @@ def add_fixed_values(self, j_data): def add_bioinfo_files_path(self, files_found_dict, j_data): """Adds file paths essential for handling and mapping bioinformatics metadata to the j_data. For each sample in j_data, the function assigns the corresponding file path based on the identified files in files_found_dict. + If multiple files are identified per configuration item (e.g., viralrecon.mapping_consensus → *.consensus.fa), each sample in j_data receives its respective file path. If no file path is located, the function appends "Not Provided [GENEPIO:0001668]" to indicate missing data. @@ -572,11 +579,16 @@ def add_bioinfo_files_path(self, files_found_dict, j_data): sample_name_error = 0 for row in j_data: sample_match = re.match( - r"^(.*?)_R1\.fastq\.gz", row["sequence_file_R1_fastq"] + r"^[^_]+", row["sequence_file_R1_fastq"] ) if sample_match: - sample_name = sample_match.group(1) + sample_name = sample_match.group() else: + self.log_report.update_log_report( + method_name, + "warning", + f'Regex failed to find extract sample name from: {row["sequence_file_R1_fastq"]}. Skipping...', + ) continue for key, value in files_found_dict.items(): file_path = "Not Provided [GENEPIO:0001668]" From 45f921f8922823eef0647ffb64e8305288817092 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 11 Jul 2024 13:12:18 +0200 Subject: [PATCH 1339/1454] fixed black lining --- .../assets/pipeline_utils/viralrecon.py | 4 +--- relecov_tools/read_bioinfo_metadata.py | 16 ++++++---------- 2 files changed, 7 insertions(+), 13 deletions(-) diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py index 25b026be..38b2bb28 100644 --- a/relecov_tools/assets/pipeline_utils/viralrecon.py +++ b/relecov_tools/assets/pipeline_utils/viralrecon.py @@ -149,9 +149,7 @@ def convert_to_json(self, samp_dict): date_regex = re.search(r"(\d{8})", result_regex.group()) if date_regex is not None: analysis_date = date_regex.group() - stderr.print( - f"[green]\tDate {analysis_date} found in {self.file_path}" - ) + stderr.print(f"[green]\tDate {analysis_date} found in {self.file_path}") else: analysis_date = "Not Provided [GENEPIO:0001668]" stderr.print( diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 7c04cc4e..fbb1b1e9 100755 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -367,9 +367,7 @@ def mapping_over_table(self, j_data, map_data, mapping_fields, table_name): for row in j_data: # TODO: We should consider an independent module that verifies that sample's name matches this pattern. # If we add warnings within this module, every time mapping_over_table is invoked it will print redundant warings - sample_match = re.match( - r"^[^_]+", row["sequence_file_R1_fastq"] - ) + sample_match = re.match(r"^[^_]+", row["sequence_file_R1_fastq"]) if sample_match: sample_name = sample_match.group() else: @@ -487,9 +485,7 @@ def get_multiqc_software_versions(self, file_list, j_data): field_errors = {} for row in j_data: # Get sample name to track whether version assignment was successful or not. - sample_match = re.match( - r"^[^_]+", row["sequence_file_R1_fastq"] - ) + sample_match = re.match(r"^[^_]+", row["sequence_file_R1_fastq"]) if sample_match: sample_name = sample_match.group() else: @@ -501,7 +497,9 @@ def get_multiqc_software_versions(self, file_list, j_data): continue # Append software version and name - software_content_details = self.software_config["workflow_summary"].get("content") + software_content_details = self.software_config["workflow_summary"].get( + "content" + ) for content_key, content_value in software_content_details.items(): for key, value in content_value.items(): # Add software versions @@ -578,9 +576,7 @@ def add_bioinfo_files_path(self, files_found_dict, j_data): method_name = f"{self.add_bioinfo_files_path.__name__}" sample_name_error = 0 for row in j_data: - sample_match = re.match( - r"^[^_]+", row["sequence_file_R1_fastq"] - ) + sample_match = re.match(r"^[^_]+", row["sequence_file_R1_fastq"]) if sample_match: sample_name = sample_match.group() else: From ef9ec0d413cf52dc1f4a5710585e294f6c8b51ea Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 15 Jul 2024 14:09:33 +0200 Subject: [PATCH 1340/1454] Default filename includes module called --- relecov_tools/log_summary.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/relecov_tools/log_summary.py b/relecov_tools/log_summary.py index e1ad1f07..736a80d2 100755 --- a/relecov_tools/log_summary.py +++ b/relecov_tools/log_summary.py @@ -2,6 +2,7 @@ import logging import json import os +import inspect from rich.console import Console from datetime import datetime from collections import OrderedDict @@ -100,8 +101,12 @@ def create_error_summary(self, filename=None): for sample in self.logs[key]["samples"].keys(): if self.logs[key]["samples"][sample]["errors"]: self.logs[key]["samples"][sample]["valid"] = False + called_module = [ + fr.function for fr in inspect.stack() if "__main__.py" in fr.filename + ][0] if not filename: - filename = datetime.today().strftime("%Y%m%d%-H%M%S") + "_log_summary.json" + date = datetime.today().strftime("%Y%m%d%-H%M%S") + filename = "_".join([date, called_module, "log_summary.json"]) summary_path = os.path.join(self.output_location, filename) with open(summary_path, "w", encoding="utf-8") as f: f.write(json.dumps(self.logs, indent=4, sort_keys=True, ensure_ascii=False)) From e295507dccf5b5b4f67657bd172e7bdf066d783b Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 15 Jul 2024 14:09:58 +0200 Subject: [PATCH 1341/1454] Stop crashing when invalid date is met --- relecov_tools/read_lab_metadata.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 63dd582d..e4847f7d 100755 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -219,6 +219,7 @@ def process_from_json(self, m_data, json_fields): ) self.logsum.add_warning(key=sample_id, entry=log_text) continue + # TODO: Include Not Provided as a configuration field fields_to_add = { x: "Not Provided [GENEPIO:0001668]" for x in json_fields["adding_fields"] @@ -307,7 +308,7 @@ def read_metadata_file(self): log_text = f"Invalid date format in sample {str(key)}" self.logsum.add_error(sample_id, log_text) stderr.print(f"[red]{log_text}") - row[key] = None + continue elif "sample id" in key.lower(): if isinstance(row[key], float) or isinstance(row[key], int): row[key] = str(int(row[key])) @@ -321,8 +322,8 @@ def read_metadata_file(self): log_text = f"Error when mapping the label {str(e)}" self.logsum.add_error(sample_id, log_text) stderr.print(f"[red]{log_text}") - continue + valid_metadata_rows.append(property_row) return valid_metadata_rows From 5273751a90f37432387b036453c09e2234fdf1c2 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 15 Jul 2024 15:10:18 +0200 Subject: [PATCH 1342/1454] Fixed missing module --- relecov_tools/log_summary.py | 12 ++++++++---- relecov_tools/read_lab_metadata.py | 2 +- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/relecov_tools/log_summary.py b/relecov_tools/log_summary.py index 736a80d2..6b0f7a27 100755 --- a/relecov_tools/log_summary.py +++ b/relecov_tools/log_summary.py @@ -87,7 +87,7 @@ def update_summary(self, key, log_type, entry, sample=None): self.logs[current_key]["samples"][sample][log_type].append(entry) return - def create_error_summary(self, filename=None): + def create_error_summary(self, called_module, filename=None): """Dump the log summary dictionary into a file with json format. If any of the 'errors' key is not empty, the parent key value 'valid' is set to false. @@ -101,9 +101,13 @@ def create_error_summary(self, filename=None): for sample in self.logs[key]["samples"].keys(): if self.logs[key]["samples"][sample]["errors"]: self.logs[key]["samples"][sample]["valid"] = False - called_module = [ - fr.function for fr in inspect.stack() if "__main__.py" in fr.filename - ][0] + if not called_module: + try: + called_module = [ + f.function for f in inspect.stack() if "__main__.py" in f.filename + ][0] + except IndexError: + called_module = "" if not filename: date = datetime.today().strftime("%Y%m%d%-H%M%S") filename = "_".join([date, called_module, "log_summary.json"]) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index e4847f7d..fc555fed 100755 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -354,7 +354,7 @@ def create_metadata_json(self): ) stderr.print("[blue]Writting output json file") os.makedirs(self.output_folder, exist_ok=True) - self.logsum.create_error_summary() + self.logsum.create_error_summary(called_module="read-lab-metadata") file_path = os.path.join(self.output_folder, file_name) relecov_tools.utils.write_json_fo_file(completed_metadata, file_path) return True From fa1e044fbdb66683de3ff2611f89e1b18de25f66 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 15 Jul 2024 15:12:08 +0200 Subject: [PATCH 1343/1454] Set called_module default to None --- relecov_tools/log_summary.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/log_summary.py b/relecov_tools/log_summary.py index 6b0f7a27..13c89207 100755 --- a/relecov_tools/log_summary.py +++ b/relecov_tools/log_summary.py @@ -87,7 +87,7 @@ def update_summary(self, key, log_type, entry, sample=None): self.logs[current_key]["samples"][sample][log_type].append(entry) return - def create_error_summary(self, called_module, filename=None): + def create_error_summary(self, called_module=None, filename=None): """Dump the log summary dictionary into a file with json format. If any of the 'errors' key is not empty, the parent key value 'valid' is set to false. From c4af29fc73cee21520650de37f2d8b3070f9d860 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 16 Jul 2024 10:03:48 +0200 Subject: [PATCH 1344/1454] Invalid date error now outputs field --- relecov_tools/read_lab_metadata.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index fc555fed..445fc8c2 100755 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -305,9 +305,9 @@ def read_metadata_file(self): dtime.strptime(str(row[key]), "%Y-%m-%d").date() ) except ValueError: - log_text = f"Invalid date format in sample {str(key)}" + log_text = f"Invalid date format in {key}: {row[key]}" self.logsum.add_error(sample_id, log_text) - stderr.print(f"[red]{log_text}") + stderr.print(f"[red]{log_text} for sample {sample_id}") continue elif "sample id" in key.lower(): if isinstance(row[key], float) or isinstance(row[key], int): From e85093243a735e01e612bee1064bfe803b64e110 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 16 Jul 2024 10:42:01 +0200 Subject: [PATCH 1345/1454] Now creates a validated metadata json file --- relecov_tools/json_validation.py | 172 ++++++++++++++++++++----------- 1 file changed, 109 insertions(+), 63 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 94ccec00..c1162adf 100755 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -9,6 +9,7 @@ import relecov_tools.utils from relecov_tools.config_json import ConfigJson +from relecov_tools.log_summary import LogSum log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -50,11 +51,17 @@ def __init__( if not os.path.isfile(json_data_file): stderr.print("[red] Json file does not exists") sys.exit(1) + self.json_data_file = json_data_file + self.logsum = LogSum(output_location=self.out_folder, only_samples=True) stderr.print("[blue] Reading the json file") self.json_data = relecov_tools.utils.read_json_file(json_data_file) - self.metadata = metadata + try: + self.sample_id_field = self.get_sample_id_field() + except ValueError as e: + self.sample_id_field = None + self.SAMPLE_FIELD_ERROR = str(e) def validate_schema(self): """Validate json schema against draft""" @@ -64,6 +71,22 @@ def validate_schema(self): stderr.print("[red] Json schema does not fulfill Draft 202012 Validation") sys.exit(1) + def get_sample_id_field(self): + """Find the name of the field used to track the samples in the given schema""" + # TODO: Include this field in configuration.json + sample_id_ontology = "GENEPIO:0000079" + ontology_match = [ + x + for x, y in self.json_schema["properties"].items() + if y.get("ontology") == sample_id_ontology + ] + if ontology_match: + sample_id_field = ontology_match[0] + else: + error_text = f"No valid sample ID field ({sample_id_ontology}) in schema" + raise ValueError(error_text) + return sample_id_field + def validate_instances(self): """Validate data instances against a validated json schema""" @@ -74,11 +97,16 @@ def validate_instances(self): invalid_json = [] errors = {} error_keys = {} + if self.sample_id_field is None: + log_text = f"Logs keys set to None. Reason: {self.SAMPLE_FIELD_ERROR}" + self.logsum.add_warning(self.sample_id_field, log_text) stderr.print("[blue] Start processing the json file") for item_row in self.json_data: # validate(instance=item_row, schema=json_schema) + sample_id_value = item_row.get(self.sample_id_field) if validator.is_valid(item_row): validated_json_data.append(item_row) + self.logsum.feed_key(sample_id_value) else: # Count error types for error in validator.iter_errors(item_row): @@ -90,6 +118,7 @@ def validate_instances(self): errors[error.message] += 1 else: errors[error.message] = 1 + self.logsum.add_error(key=sample_id_value, entry=error.message) # append row with errors invalid_json.append(item_row) @@ -115,7 +144,7 @@ def validate_instances(self): ) stderr.print("[red] --------------------") - return invalid_json + return validated_json_data, invalid_json def create_invalid_metadata(self, invalid_json, metadata, out_folder): """Create a new sub excel file having only the samples that were invalid. @@ -124,70 +153,87 @@ def create_invalid_metadata(self, invalid_json, metadata, out_folder): The rows that match the value collected from json file on tag collecting_lab_sample_id are removed from excel """ - if len(invalid_json) == 0: + if self.sample_id_field is None: + log_text = f"Invalid excel file won't be created: {self.SAMPLE_FIELD_ERROR}" + self.logsum.add_error(key="000_VALIDATION_PROCESS_ERROR", entry=log_text) + return + log.error("Some of the samples in json metadata were not validated") + stderr.print("[red] Some of the Samples are not validate") + if metadata is None: + metadata = relecov_tools.utils.prompt_path( + msg="Select the metadata file to select those not-validated samples." + ) + if not os.path.isfile(metadata): + log.error("Metadata file %s does not exist", metadata) stderr.print( - "[green] Sucessful validation, no invalid file will be written!!" + "[red] Unable to create excel file for invalid samples. Metadata file ", + metadata, + " does not exist", ) - else: - log.error("Some of the samples in json metadata were not validated") - stderr.print("[red] Some of the Samples are not validate") - if metadata is None: - metadata = relecov_tools.utils.prompt_path( - msg="Select the metadata file to select those not-validated samples." - ) - if not os.path.isfile(metadata): - log.error("Metadata file %s does not exist", metadata) - stderr.print( - "[red] Unable to create excel file for invalid samples. Metadata file ", - metadata, - " does not exist", - ) - sys.exit(1) - - sample_list = [] - - stderr.print("Start preparation of invalid samples") - - for row in invalid_json: - sample_list.append(str(row["sequencing_sample_id"])) - - wb = openpyxl.load_workbook(metadata) - ws_sheet = wb["METADATA_LAB"] - row_to_del = [] - - for row in ws_sheet.iter_rows(min_row=5, max_row=ws_sheet.max_row): - # if not data on row 1 and 2 assume that no more data are in file - # then start deleting rows - if not row[2].value and not row[1].value: - break - if str(row[2].value) not in sample_list: - row_to_del.append(row[0].row) - - stderr.print("Collected rows to create the excel file") - if len(row_to_del) > 0: - row_to_del.sort(reverse=True) - for idx in row_to_del: - try: - ws_sheet.delete_rows(idx) - except TypeError as e: - log.error( - "Unable to delete row %s from metadata file because of", - idx, - e, - ) - stderr.print(f"[red] Unable to delete row {idx} becuase of {e}") - sys.exit(1) - - os.makedirs(out_folder, exist_ok=True) - new_name = "invalid_" + os.path.basename(metadata) - m_file = os.path.join(out_folder, new_name) - stderr.print("Saving excel file with the invalid samples") - wb.save(m_file) + sys.exit(1) + sample_list = [] + stderr.print("Start preparation of invalid samples") + for row in invalid_json: + sample_list.append(str(row[self.sample_id_field])) + wb = openpyxl.load_workbook(metadata) + # TODO: Include this as a key in configuration.json + ws_sheet = wb["METADATA_LAB"] + row_to_del = [] + for row in ws_sheet.iter_rows(min_row=5, max_row=ws_sheet.max_row): + # if not data on row 1 and 2 assume that no more data are in file + # then start deleting rows + if not row[2].value and not row[1].value: + break + if str(row[2].value) not in sample_list: + row_to_del.append(row[0].row) + stderr.print("Collected rows to create the excel file") + if len(row_to_del) > 0: + row_to_del.sort(reverse=True) + for idx in row_to_del: + try: + ws_sheet.delete_rows(idx) + except TypeError as e: + log.error( + "Unable to delete row %s from metadata file because of", + idx, + e, + ) + stderr.print(f"[red] Unable to delete row {idx} becuase of {e}") + sys.exit(1) + os.makedirs(out_folder, exist_ok=True) + new_name = "invalid_" + os.path.basename(metadata) + m_file = os.path.join(out_folder, new_name) + stderr.print("Saving excel file with the invalid samples") + wb.save(m_file) return - def validate(self): - """Write invalid samples from metadata to excel""" + def create_validated_json(self, valid_json_data, out_folder): + """Create a copy of the input json file, keeping only the validated samples + + Args: + valid_json_data (list(dict)): List of samples metadata as dictionaries + out_folder (str): path to folder where file will be created + """ + file_name = "_".join(["validated", self.json_data_file]) + file_path = os.path.join(out_folder, file_name) + log.info("Saving Json file with the validated samples as %s", file_name) + relecov_tools.utils.write_json_fo_file(valid_json_data, file_path) + return + def validate(self): + """Validate samples from metadata, create an excel with invalid samples, + and a json file with the validated ones + """ self.validate_schema() - invalid_json = self.validate_instances() - self.create_invalid_metadata(invalid_json, self.metadata, self.out_folder) + valid_json_data, invalid_json = self.validate_instances() + if not invalid_json: + stderr.print("[green]Sucessful validation, no invalid file created!!") + else: + self.create_invalid_metadata(invalid_json, self.metadata, self.out_folder) + if valid_json_data: + self.create_validated_json(valid_json_data, self.out_folder) + else: + log_text = "All the samples were invalid. No valid file created" + self.logsum.add_error(key="000_VALIDATION_PROCESS_ERROR", entry=log_text) + stderr.print(f"[red]{log_text}") + self.logsum.create_error_summary(called_module="validate") From 92acbb78275e20868408ea1fb7d86960eeccc088 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 16 Jul 2024 10:57:18 +0200 Subject: [PATCH 1346/1454] Updated json_validation. Fix --- relecov_tools/json_validation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index c1162adf..4b6f889e 100755 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -214,7 +214,7 @@ def create_validated_json(self, valid_json_data, out_folder): valid_json_data (list(dict)): List of samples metadata as dictionaries out_folder (str): path to folder where file will be created """ - file_name = "_".join(["validated", self.json_data_file]) + file_name = "_".join(["validated", os.path.basename(self.json_data_file)]) file_path = os.path.join(out_folder, file_name) log.info("Saving Json file with the validated samples as %s", file_name) relecov_tools.utils.write_json_fo_file(valid_json_data, file_path) From fe2e2e4a4d7378de488237a2e56c25a883df31f1 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 16 Jul 2024 11:32:33 +0200 Subject: [PATCH 1347/1454] Better sftp cleaning and download logging --- relecov_tools/sftp_handle.py | 145 +++++++++++++++++++++-------------- 1 file changed, 86 insertions(+), 59 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index c485149e..0160fb17 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -189,9 +189,6 @@ def recursive_list(folder_name): log.error("Invalid folder at remote sftp %s", e) raise for attribute in attribute_list: - # Messy workaround for corrupted folder - if "ion_torrent" in attribute.filename: - continue if stat.S_ISDIR(attribute.st_mode): abspath = os.path.join(folder_name, attribute.filename) directory_list.append(abspath) @@ -266,9 +263,9 @@ def create_local_folder(self, folder, date): log.info("Creating folder %s to download files", folder) platform_storage_folder = self.platform_storage_folder if platform_storage_folder == folder: - local_folder_path = os.path.join(platform_storage_folder, date) + local_folder_path = platform_storage_folder else: - local_folder_path = os.path.join(platform_storage_folder, folder, date) + local_folder_path = os.path.join(platform_storage_folder, folder) os.makedirs(local_folder_path, exist_ok=True) log.info("created the folder to download files %s", local_folder_path) return local_folder_path @@ -332,7 +329,6 @@ def verify_md5_checksum(self, local_folder, fetched_files, fetched_md5): hash_dict = relecov_tools.utils.read_md5_checksum(fetched_md5, avoid_chars) if not hash_dict: error_text = "md5sum file could not be read, md5 hashes won't be validated" - log.warning(error_text) self.include_warning(error_text) return fetched_files, False # check md5 checksum for each file @@ -362,7 +358,8 @@ def create_files_with_metadata_info( metadata_file (str): Name of the downloaded metadata file to rename it """ samples_to_delete = [] - prefix_file_name = "_".join(local_folder.split("/")[-3:-1]) + prefix_file_name = "_".join(local_folder.split("/")[-2:]) + prefix_file_name = prefix_file_name.replace("_tmp_processing", "") # TODO: Move these prefixes to configuration.json new_metadata_file = "metadata_lab_" + prefix_file_name + ".xlsx" sample_data_file = "samples_data_" + prefix_file_name + ".json" @@ -373,7 +370,6 @@ def create_files_with_metadata_info( data = copy.deepcopy(samples_dict) for sample, values in data.items(): if not all(val for val in values): - log.error(str(error_text % sample)) self.include_error(str(error_text % sample), sample) samples_to_delete.append(sample) continue @@ -416,7 +412,6 @@ def remove_duplicated_values(self, sample_file_dict): clean_sample_dict = {key: sample_file_dict[key] for key in non_duplicated_keys} if dup_samples_list: error_text = "Multiple samples in metadata pointing to the same file: %s" - log.warning(error_text % duplicated_dict) self.include_warning(error_text % duplicated_dict) stderr.print(f"[Orange]{error_text}") stderr.print("[Orange]These samples won't be processed: ", dup_samples_list) @@ -517,12 +512,10 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): continue if row[index_layout] == "paired" and row[index_fastq_r2] is None: error_text = "Sample %s is paired-end, but no R2 given" - log.error(str(error_text % str(row[index_sampleID]))) self.include_error(error_text % str(row[index_sampleID]), s_name) row_complete = False if row[index_layout] == "single" and row[index_fastq_r2] is not None: error_text = "Sample %s is single-end, but R1&R2 given" - log.error(str(error_text % str(row[index_sampleID]))) self.include_error(error_text % str(row[index_sampleID]), s_name) row_complete = False if row_complete: @@ -537,9 +530,9 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): ].strip() else: log_text = "Fastq_R1 not defined in Metadata for sample %s" - log.error(str(log_text % s_name)) stderr.print(f"[red]{str(log_text % s_name)}") self.include_error(entry=str(log_text % s_name), sample=s_name) + del sample_file_dict[s_name] else: self.include_warning(entry=f"Row {counter} skipped. No sample ID given") # Remove duplicated files @@ -596,7 +589,6 @@ def download_remote_metafile(target_meta_file): meta_df_list.append(loc_meta_df) except (ParserError, EmptyDataError, MetadataError, KeyError) as e: error_text = f"Could not process {os.path.basename(loc_meta)}: {e}" - log.error(error_text) self.include_error(error_text) os.remove(loc_meta) if meta_df_list: @@ -653,9 +645,8 @@ def validate_remote_files(self, remote_folder, local_folder): metafiles_list = sorted( sum([list(fi.values()) for _, fi in sample_files_dict.items()], []) ) - if all(file in filtered_files_list for file in metafiles_list): + if sorted(filtered_files_list) == sorted(metafiles_list): log.info("Files in %s match with metadata file", remote_folder) - stderr.print("Successfully validated files based on metadata") else: log_text = "Some files in %s do not match the ones described in metadata" log.warning(log_text % remote_folder) @@ -664,12 +655,12 @@ def validate_remote_files(self, remote_folder, local_folder): mismatch_files = [fi for fi in filtered_files_list if fi not in set_list] mismatch_rev = [fi for fi in set_list if fi not in filtered_files_list] - error_text1 = "Files in folder missing in metadata %s" - log.warning(error_text1 % str(mismatch_files)) - self.include_warning(error_text1 % str(mismatch_files)) - error_text2 = "Files in metadata missing in folder %s" - log.warning(error_text2 % str(mismatch_rev)) - self.include_warning(error_text2 % str(mismatch_rev)) + if mismatch_files: + error_text1 = "Files in folder missing in metadata %s" + self.include_warning(error_text1 % str(mismatch_files)) + if mismatch_rev: + error_text2 = "Files in metadata missing in folder %s" + self.include_warning(error_text2 % str(mismatch_rev)) # Try to check if the metadata filename lacks the proper extension log.info("Trying to match files without proper file extension") sample_files_dict = self.process_filedict( @@ -679,33 +670,63 @@ def validate_remote_files(self, remote_folder, local_folder): raise FileNotFoundError( "No files from metadata found in %s" % remote_folder ) + stderr.print("[blue]Finished validating files based on metadata") return sample_files_dict, local_meta_file - def delete_remote_files(self, remote_folder, files): + def delete_remote_files(self, remote_folder, files=None, skip_seqs=False): """Delete files from remote folder Args: remote_folder (str): path to folder in remote repository - files (list(str)): list of file basenames in remote repository + files (list(str), optional): list of target filenames in remote repository + skip_seqs (bool, optional): Skip sequencing files based on extension """ stderr.print(f"[blue]Deleting files in {remote_folder}...") - empty_folder = True - for file in files: + if files is None: + files_to_remove = self.get_file_list(remote_folder) + else: + files_to_remove = files + if any(file.endswith(tuple(self.allowed_file_ext)) for file in files_to_remove): + if skip_seqs is True: + log_text = f"Folder {remote_folder} has sequencing files. Not removed." + self.include_warning(log_text) + return + for file in files_to_remove: try: self.client.remove(os.path.join(remote_folder, os.path.basename(file))) log.info("%s Deleted from remote server", file) except (IOError, PermissionError) as e: - log.error("Could not delete file %s.", str(e)) - stderr.print(f"Could not delete file {file}. Error: {e}") - empty_folder = False - continue - if empty_folder: + self.include_warning(f"Could not delete remote file {file}: {e}") + stderr.print(f"Could not delete remote file {file}. Error: {e}") + return + + def delete_remote_folder(self, remote_folder): + """Delete a folder from remote sftp, check if it is empty or not first. + + Args: + remote_folder (str): path to folder in remote repository + """ + + def remove_client_dir(remote_folder): + # Never remove a folder in the top level if len(remote_folder.replace("./", "").split("/")) >= 2: + log.info("Trying to remove %s", remote_folder) try: self.client.rmdir(remote_folder) + log.info("Successfully removed %s", remote_folder) except (OSError, PermissionError) as e: - log.error("Could not delete folder %s.", str(e)) - stderr.print(f"Could not delete folder {remote_folder}. Error: {e}") + log_text = f"Could not delete remote {remote_folder}. Error: {e}" + self.include_warning(log_text) + stderr.print(log_text) + else: + log.info("%s is a top-level folder. Not removed", remote_folder) + + remote_folder_files = self.get_file_list(remote_folder) + if remote_folder_files: + log_text = f"Remote folder {remote_folder} not empty. Not removed" + self.include_warning(log_text) + else: + remove_client_dir(remote_folder) return def move_processing_fastqs(self, folders_with_metadata): @@ -733,11 +754,9 @@ def move_processing_fastqs(self, folders_with_metadata): except OSError: if file in folders_with_metadata[folder]: error_text = "File named %s already in %s. Skipped" - log.warning(error_text % (file, self.current_folder)) self.include_warning(error_text % (file, self.current_folder)) else: error_text = "Error while moving file %s" - log.error(error_text % file) self.include_error(error_text % file) folders_with_metadata[folder] = successful_files return folders_with_metadata @@ -757,8 +776,6 @@ def merge_md5sums(self, folders_with_metadata): folders_with_metadata: Same dict updated with the merged md5sum file """ output_location = self.platform_storage_folder - log.info("Merging md5sum files from remote folders...") - stderr.print("[blue]Merging md5sum files from remote folders...") # TODO: Include this function in relecov_tools.utils def md5_merger(md5_filelist, avoid_chars=None): @@ -802,12 +819,13 @@ def md5_handler(md5sumlist, output_location): for folder, files in folders_with_metadata.items(): self.current_folder = folder.split("/")[0] + log.info("Merging md5sum files from %s...", self.current_folder) + stderr.print(f"[blue]Merging md5sum files from {self.current_folder}...") md5flags = [".md5", "md5sum", "md5checksum"] md5sumlist = [fi for fi in files if any(flag in fi for flag in md5flags)] if not md5sumlist: - error_text = "No md5sum could be found in remote folder" - log.warning(error_text) - stderr.print(f"[yellow]{error_text}") + error_text = "No md5sum could be found in remote folder %s" + stderr.print(f"[yellow]{error_text % folder}") self.include_warning(error_text) continue folders_with_metadata[folder] = [fi for fi in files if fi not in md5sumlist] @@ -815,7 +833,6 @@ def md5_handler(md5sumlist, output_location): uploaded_md5 = md5_handler(md5sumlist, output_location) except (FileNotFoundError, OSError, PermissionError, CsvError) as e: error_text = "Could not merge md5files for %s. Reason: %s" - log.warning(error_text % (self.current_folder, str(e))) stderr.print(f"[yellow]{error_text % (self.current_folder, str(e))}") self.include_warning(error_text % (self.current_folder, str(e))) continue @@ -931,6 +948,7 @@ def pre_validate_folder(folder, folder_files): return downloaded_metadata folders_with_metadata = {} + processed_folders = [] merged_df = merged_excel_path = last_main_folder = excel_name = None log.info("Setting %s remote folders...", str(len(target_folders.keys()))) stderr.print(f"[blue]Setting {len(target_folders.keys())} remote folders...") @@ -964,7 +982,6 @@ def pre_validate_folder(folder, folder_files): folders_with_metadata[last_main_folder].append(excel_name) except OSError: error_text = "Error uploading merged metadata back to sftp: %s" - log.error(error_text % last_main_folder) self.include_error(error_text % last_main_folder) del folders_with_metadata[last_main_folder] try: @@ -972,8 +989,8 @@ def pre_validate_folder(folder, folder_files): except (ParserError, EmptyDataError, MetadataError, KeyError) as e: meta_name = os.path.basename(downloaded_metadata) error_text = "%s skipped. Error while processing excel %s: %s" - log.error(error_text % (main_folder, meta_name, str(e))) self.include_error(error_text % (main_folder, meta_name, str(e))) + os.remove(local_meta) continue folders_with_metadata[temp_folder] = [] folders_with_metadata[temp_folder].extend(filelist) @@ -988,6 +1005,8 @@ def pre_validate_folder(folder, folder_files): folders_with_metadata[temp_folder].extend(filelist) new_df = self.excel_to_df(local_meta, metadata_ws, header_flag) merged_df = self.merge_metadata(metadata_ws, merged_df, new_df) + os.remove(local_meta) + processed_folders.append(folder) # End of loop # Write last dataframe to file once loop is finished @@ -1003,7 +1022,7 @@ def pre_validate_folder(folder, folder_files): log_text = "Remote folders merged into %s folders. Proceed with processing" log.info(log_text % len(clean_target_folders.keys())) stderr.print(f"[green]{log_text % len(clean_target_folders.keys())}") - return clean_target_folders + return clean_target_folders, processed_folders def select_target_folders(self): """Find the selected folders in remote if given, else select every folder @@ -1068,7 +1087,6 @@ def compress_and_update(self, fetched_files, files_to_compress, local_folder): compressed = relecov_tools.utils.compress_file(f_path) if not compressed: error_text = "Could not compress file %s, file not found" % str(file) - log.error(error_text) self.include_error(error_text, f_path) continue # Remove file after compression is completed @@ -1168,7 +1186,6 @@ def download(self, target_folders, option="download"): ) if not fetched_files: error_text = "No files could be downloaded in folder %s" % str(folder) - log.warning(error_text) stderr.print(f"{error_text}") self.include_error(error_text) continue @@ -1197,9 +1214,8 @@ def download(self, target_folders, option="download"): corr_fold = os.path.join(local_folder, "corrupted") os.mkdir(corr_fold) error_text = "Found corrupted files: %s. Moved to: %s" - log.warning(error_text % (str(corrupted), corr_fold)) stderr.print(f"[red]{error_text % (str(corrupted), corr_fold)}") - self.include_warning(error_text % (str(corrupted), "/corrupt/")) + self.include_warning(error_text % (str(corrupted), corr_fold)) for corr_file in corrupted: path = os.path.join(local_folder, corr_file) try: @@ -1214,7 +1230,6 @@ def download(self, target_folders, option="download"): ) if self.abort_if_md5_mismatch: error_text = "Stop processing %s due to corrupted files." - log.error(error_text % folder) stderr.print(f"[red]{error_text % folder}") self.include_error(error_text % "folder") relecov_tools.utils.delete_local_folder(local_folder) @@ -1227,9 +1242,8 @@ def download(self, target_folders, option="download"): else: corrupted = [] error_text = "No single md5sum file could be found in %s" % folder - log.warning(error_text) stderr.print(f"[red]{error_text}") - self.include_error(error_text) + self.include_warning(error_text) clean_fetchlist = [ fi for fi in fetched_files if fi.endswith(tuple(self.allowed_file_ext)) @@ -1279,7 +1293,10 @@ def download(self, target_folders, option="download"): # If download_option is "download_clean", remove # sftp folder content after download is finished if option == "clean": - self.delete_remote_files(folder, files_to_download) + self.delete_remote_files(folder, files=files_to_download) + self.delete_remote_files(folder, skip_seqs=True) + self.delete_remote_folder(folder) + stderr.print(f"Delete process finished in {folder}") stderr.print(f"[green]Finished processing {folder}") return @@ -1302,20 +1319,30 @@ def execute_process(self): stderr.print("[red]Unable to establish sftp connection") sys.exit(1) target_folders = self.select_target_folders() - target_folders = self.merge_subfolders(target_folders) - if self.download_option == "download_only": - self.download(target_folders, option="download") - if self.download_option == "download_clean": - self.download(target_folders, option="clean") if self.download_option == "delete_only": log.info("Initiating delete_only process") - for folder, files in target_folders.items(): - self.delete_remote_files(folder, files) + for folder in target_folders.keys(): + self.current_folder = folder + self.delete_remote_files(folder) + self.delete_remote_folder(folder) stderr.print(f"Delete process finished in {folder}") + else: + target_folders, processed_folders = self.merge_subfolders(target_folders) + if self.download_option == "download_only": + self.download(target_folders, option="download") + if self.download_option == "download_clean": + self.download(target_folders, option="clean") + for folder in processed_folders: + self.current_folder = folder + self.delete_remote_files(folder, skip_seqs=True) + self.delete_remote_folder(folder) + stderr.print(f"Delete process finished in {folder}") + self.close_connection() + stderr.print(f"Processed {len(processed_folders)} folders: {processed_folders}") if self.logsum.logs: log.info("Printing process summary to %s", self.platform_storage_folder) - self.logsum.create_error_summary() + self.logsum.create_error_summary(called_module="download") else: log.info("Process log summary was empty. Not generated.") stderr.print("Finished execution") From 5162e83eaacaeed4aaf19576cf9b2a509386fe87 Mon Sep 17 00:00:00 2001 From: Shettland Date: Tue, 16 Jul 2024 11:58:16 +0200 Subject: [PATCH 1348/1454] Better remote cleaning. Fix1 --- relecov_tools/sftp_handle.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 0160fb17..db9a4b03 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -1321,7 +1321,8 @@ def execute_process(self): target_folders = self.select_target_folders() if self.download_option == "delete_only": log.info("Initiating delete_only process") - for folder in target_folders.keys(): + processed_folders = target_folders.keys() + for folder in processed_folders: self.current_folder = folder self.delete_remote_files(folder) self.delete_remote_folder(folder) From 31fb282abc9c21a205a4528d4d0d088a79eb5f57 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 18 Jul 2024 16:30:11 +0200 Subject: [PATCH 1349/1454] Removed tmp_processing from downloaded folder name --- relecov_tools/sftp_handle.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index db9a4b03..8911ae8a 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -250,12 +250,11 @@ def get_from_sftp(self, file, destination, exist_ok=False): log.error("Unable to fetch file %s ", e) return False - def create_local_folder(self, folder, date): + def create_local_folder(self, folder): """Create folder to download files in local path using date Args: folder (str): name of remote folder to be downloaded - date (datetime.datetime): datetime in YYYYMMDD format Returns: local_folder_path(str): path to the new created folder @@ -265,6 +264,7 @@ def create_local_folder(self, folder, date): if platform_storage_folder == folder: local_folder_path = platform_storage_folder else: + folder = folder.strip("_tmp_processing") local_folder_path = os.path.join(platform_storage_folder, folder) os.makedirs(local_folder_path, exist_ok=True) log.info("created the folder to download files %s", local_folder_path) @@ -681,7 +681,7 @@ def delete_remote_files(self, remote_folder, files=None, skip_seqs=False): files (list(str), optional): list of target filenames in remote repository skip_seqs (bool, optional): Skip sequencing files based on extension """ - stderr.print(f"[blue]Deleting files in {remote_folder}...") + stderr.print(f"[blue]Deleting files in remote {remote_folder}...") if files is None: files_to_remove = self.get_file_list(remote_folder) else: @@ -1167,7 +1167,7 @@ def download(self, target_folders, option="download"): stderr.print("[blue]Processing folder " + folder) # Validate that the files are the ones described in metadata. - local_folder = self.create_local_folder(folder, date) + local_folder = self.create_local_folder(folder) try: valid_filedict, meta_file = self.validate_remote_files( folder, local_folder @@ -1296,7 +1296,7 @@ def download(self, target_folders, option="download"): self.delete_remote_files(folder, files=files_to_download) self.delete_remote_files(folder, skip_seqs=True) self.delete_remote_folder(folder) - stderr.print(f"Delete process finished in {folder}") + stderr.print(f"Delete process finished in remote {folder}") stderr.print(f"[green]Finished processing {folder}") return From b2ca092685f0c01985a031ac8f2891898c364ff9 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 18 Jul 2024 16:32:05 +0200 Subject: [PATCH 1350/1454] updated sftp_handle. Linting --- relecov_tools/sftp_handle.py | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 8911ae8a..4437afbb 100755 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -1153,7 +1153,6 @@ def download(self, target_folders, option="download"): log.error("You do not have permissions to create folder %s", e) sys.exit(1) folders_to_download = target_folders - date = datetime.today().strftime("%Y%m%d") for folder in folders_to_download.keys(): self.current_folder = folder.split("/")[0] # Close previously open connection to avoid timeouts From 43a34ab7b4b9981505d43c028c834bb41023bd01 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 18 Jul 2024 16:45:19 +0200 Subject: [PATCH 1351/1454] Updated log_summary main keys and new path field --- relecov_tools/log_summary.py | 51 +++++++++++++++++++++++++++++------- 1 file changed, 41 insertions(+), 10 deletions(-) diff --git a/relecov_tools/log_summary.py b/relecov_tools/log_summary.py index 13c89207..09b3bdc8 100755 --- a/relecov_tools/log_summary.py +++ b/relecov_tools/log_summary.py @@ -3,6 +3,8 @@ import json import os import inspect +import sys +import copy from rich.console import Console from datetime import datetime from collections import OrderedDict @@ -21,36 +23,61 @@ class LogSum: - def __init__(self, output_location: str = None, only_samples: bool = False): + def __init__( + self, + output_location: str = None, + only_samples: bool = False, + unique_key: str = None, + path: str = None, + ): if not os.path.exists(output_location): raise FileNotFoundError("Output location does not exist") else: self.output_location = output_location + if only_samples and unique_key: + stderr.print("[red]LogSum only_samples and unique_key are incompatible") + sys.exit(1) # if only_samples is given, no "samples" key will be added to logs if only_samples: self.only_samples = True else: self.only_samples = False + # if unique_key is given, all entries will be saved inside that key by default + if unique_key: + self.unique_key = unique_key + else: + self.unique_key = None + # if path is given, all keys will include a field "path" with this value + if path: + self.path = path + else: + self.path = None self.logs = {} return - def feed_key(self, key, sample=None): + def feed_key(self, key=None, sample=None): """Run update_summary() with no entry nor log_type. Add a new empty key""" + if self.unique_key: + key = self.unique_key self.update_summary(log_type=None, key=key, entry=None, sample=sample) - def add_error(self, key, entry, sample=None): + def add_error(self, entry, key=None, sample=None): """Run update_summary() with log_type as errors""" + if self.unique_key: + key = self.unique_key log.error(entry) self.update_summary(log_type="errors", key=key, entry=entry, sample=sample) return - def add_warning(self, key, entry, sample=None): + def add_warning(self, entry, key=None, sample=None): """Run update_summary() with log_type as warnings""" + if self.unique_key: + key = self.unique_key log.warning(entry) self.update_summary(log_type="warnings", key=key, entry=entry, sample=sample) return - def update_summary(self, key, log_type, entry, sample=None): + def update_summary(self, log_type, key, entry, sample=None): """Create a dictionary with a defined structure for each new key. Add the entry to the dictionary if it already exists. Add it to samples if its a sample @@ -72,18 +99,20 @@ def update_summary(self, key, log_type, entry, sample=None): sample = None entry, sample = (str(entry), str(sample)) if current_key not in self.logs.keys(): - self.logs[current_key] = feed_dict.copy() + self.logs[current_key] = copy.deepcopy(feed_dict) + if self.path and "path" not in self.logs[current_key]: + self.logs[current_key].update({"path": self.path}) if not self.only_samples: self.logs[current_key]["samples"] = OrderedDict() if log_type is None: if sample != "None" and sample not in self.logs[current_key]["samples"]: - self.logs[current_key]["samples"][sample] = feed_dict.copy() + self.logs[current_key]["samples"][sample] = copy.deepcopy(feed_dict) return if sample == "None": self.logs[current_key][log_type].append(entry) else: if sample not in self.logs[current_key]["samples"].keys(): - self.logs[current_key]["samples"][sample] = feed_dict.copy() + self.logs[current_key]["samples"][sample] = copy.deepcopy(feed_dict) self.logs[current_key]["samples"][sample][log_type].append(entry) return @@ -113,6 +142,8 @@ def create_error_summary(self, called_module=None, filename=None): filename = "_".join([date, called_module, "log_summary.json"]) summary_path = os.path.join(self.output_location, filename) with open(summary_path, "w", encoding="utf-8") as f: - f.write(json.dumps(self.logs, indent=4, sort_keys=True, ensure_ascii=False)) - stderr.print(f"Process log summary printed in {summary_path}") + f.write( + json.dumps(self.logs, indent=4, sort_keys=False, ensure_ascii=False) + ) + stderr.print(f"Process log summary saved in {summary_path}") return From 98a5a88d6ea1440157494fd1a2ad552e6ff8b18d Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 18 Jul 2024 16:45:44 +0200 Subject: [PATCH 1352/1454] Updated logs in read-lab-metadata accordingly --- relecov_tools/read_lab_metadata.py | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 445fc8c2..49393bbd 100755 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -58,7 +58,11 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None ) else: self.output_folder = output_folder - + out_path = os.path.realpath(self.output_folder) + lab_code = out_path.split("/")[-2] + self.logsum = LogSum( + output_location=self.output_folder, unique_key=lab_code, path=out_path + ) config_json = ConfigJson() relecov_schema = config_json.get_topic_data("json_schemas", "relecov_schema") relecov_sch_path = os.path.join( @@ -79,7 +83,7 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None "[orange]Property " + prop + " does not have 'label' attribute" ) continue - self.logsum = LogSum(output_location=self.output_folder, only_samples=True) + self.json_req_files = config_json.get_topic_data( "lab_metadata", "lab_metadata_req_json" ) @@ -107,12 +111,12 @@ def match_to_json(self, valid_metadata_rows): missing_samples = [] for row in valid_metadata_rows: sample_id = str(row["sequencing_sample_id"]).strip() - self.logsum.feed_key(sample_id) + self.logsum.feed_key(sample=sample_id) if sample_id in samples_json.keys(): clean_metadata_rows.append(row) else: log_text = "Sample missing in samples data Json file" - self.logsum.add_error(sample_id, log_text) + self.logsum.add_error(sample=sample_id, entry=log_text) missing_samples.append(sample_id) return clean_metadata_rows, missing_samples @@ -182,7 +186,7 @@ def adding_ontology_to_enum(self, m_data): else: sample_id = m_data[idx]["sequencing_sample_id"] log_text = f"No ontology found for {m_data[idx][key]} in {key}" - self.logsum.add_warning(sample_id, log_text) + self.logsum.add_warning(sample=sample_id, entry=log_text) try: ontology_errors[key] += 1 except KeyError: @@ -211,13 +215,13 @@ def process_from_json(self, m_data, json_fields): f"Label {map_field} was not provided in sample " + f"{sample_id}, auto-completing with Not Provided" ) - self.logsum.add_warning(key=sample_id, entry=log_text) + self.logsum.add_warning(sample=sample_id, entry=log_text) else: log_text = ( f"Unknown map_field value {error} for json data: " + f"{str(map_field)} in sample {sample_id}. Skipped" ) - self.logsum.add_warning(key=sample_id, entry=log_text) + self.logsum.add_warning(sample=sample_id, entry=log_text) continue # TODO: Include Not Provided as a configuration field fields_to_add = { @@ -290,7 +294,7 @@ def read_metadata_file(self): continue if row[key] is None or "not provided" in str(row[key]).lower(): log_text = f"{key} not provided for sample {sample_id}" - self.logsum.add_warning(sample_id, log_text) + self.logsum.add_warning(sample=sample_id, entry=log_text) continue if "date" in key.lower(): # Check if date is a string. Format YYYY-MM-DD to YYYY/MM/DD @@ -306,7 +310,7 @@ def read_metadata_file(self): ) except ValueError: log_text = f"Invalid date format in {key}: {row[key]}" - self.logsum.add_error(sample_id, log_text) + self.logsum.add_error(sample=sample_id, entry=log_text) stderr.print(f"[red]{log_text} for sample {sample_id}") continue elif "sample id" in key.lower(): @@ -320,7 +324,7 @@ def read_metadata_file(self): property_row[self.label_prop_dict[key]] = row[key] except KeyError as e: log_text = f"Error when mapping the label {str(e)}" - self.logsum.add_error(sample_id, log_text) + self.logsum.add_error(sample=sample_id, entry=log_text) stderr.print(f"[red]{log_text}") continue From 120e01f10e532f47cfd67568373ef717af445d6b Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 18 Jul 2024 16:46:19 +0200 Subject: [PATCH 1353/1454] Updated logs in json_validation accordingly --- relecov_tools/json_validation.py | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 4b6f889e..d84b1742 100755 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -52,7 +52,11 @@ def __init__( stderr.print("[red] Json file does not exists") sys.exit(1) self.json_data_file = json_data_file - self.logsum = LogSum(output_location=self.out_folder, only_samples=True) + out_path = os.path.realpath(self.out_folder) + lab_code = out_path.split("/")[-2] + self.logsum = LogSum( + output_location=self.out_folder, unique_key=lab_code, path=out_path + ) stderr.print("[blue] Reading the json file") self.json_data = relecov_tools.utils.read_json_file(json_data_file) @@ -99,14 +103,14 @@ def validate_instances(self): error_keys = {} if self.sample_id_field is None: log_text = f"Logs keys set to None. Reason: {self.SAMPLE_FIELD_ERROR}" - self.logsum.add_warning(self.sample_id_field, log_text) + self.logsum.add_warning(sample=self.sample_id_field, entry=log_text) stderr.print("[blue] Start processing the json file") for item_row in self.json_data: # validate(instance=item_row, schema=json_schema) sample_id_value = item_row.get(self.sample_id_field) if validator.is_valid(item_row): validated_json_data.append(item_row) - self.logsum.feed_key(sample_id_value) + self.logsum.feed_key(sample=sample_id_value) else: # Count error types for error in validator.iter_errors(item_row): @@ -118,7 +122,7 @@ def validate_instances(self): errors[error.message] += 1 else: errors[error.message] = 1 - self.logsum.add_error(key=sample_id_value, entry=error.message) + self.logsum.add_error(sample=sample_id_value, entry=error.message) # append row with errors invalid_json.append(item_row) @@ -155,7 +159,7 @@ def create_invalid_metadata(self, invalid_json, metadata, out_folder): """ if self.sample_id_field is None: log_text = f"Invalid excel file won't be created: {self.SAMPLE_FIELD_ERROR}" - self.logsum.add_error(key="000_VALIDATION_PROCESS_ERROR", entry=log_text) + self.logsum.add_error(entry=log_text) return log.error("Some of the samples in json metadata were not validated") stderr.print("[red] Some of the Samples are not validate") @@ -229,11 +233,15 @@ def validate(self): if not invalid_json: stderr.print("[green]Sucessful validation, no invalid file created!!") else: + log_text = "Summary: %s valid and %s invalid samples" + self.logsum.add_warning( + entry=log_text % (len(valid_json_data), len(invalid_json)) + ) self.create_invalid_metadata(invalid_json, self.metadata, self.out_folder) if valid_json_data: self.create_validated_json(valid_json_data, self.out_folder) else: log_text = "All the samples were invalid. No valid file created" - self.logsum.add_error(key="000_VALIDATION_PROCESS_ERROR", entry=log_text) + self.logsum.add_error(entry=log_text) stderr.print(f"[red]{log_text}") self.logsum.create_error_summary(called_module="validate") From e26394f50b27da6e52b3323ecfe09afe9b042a62 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 24 Jul 2024 13:51:02 +0200 Subject: [PATCH 1354/1454] Updated custom logs in json_validation --- relecov_tools/json_validation.py | 25 ++++++++++--------------- 1 file changed, 10 insertions(+), 15 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index d84b1742..01802214 100755 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -122,7 +122,11 @@ def validate_instances(self): errors[error.message] += 1 else: errors[error.message] = 1 - self.logsum.add_error(sample=sample_id_value, entry=error.message) + if error_keys[error.message] == error.message: + error_text = error.message + else: + error_text = f"{error_keys[error.message]}:{error.message}" + self.logsum.add_error(sample=sample_id_value, entry=error_text) # append row with errors invalid_json.append(item_row) @@ -132,20 +136,11 @@ def validate_instances(self): stderr.print("[blue] --------------------") for error_type in errors.keys(): num_of_errors = str(errors[error_type]) - field_with_error = error_keys[error_type] - log.error( - "%s samples failed validation for %s:\n%s", - num_of_errors, - field_with_error, - error_type, - ) - stderr.print( - "[red]" - + num_of_errors - + " samples failed validation for " - + f"{field_with_error}:\n" - + error_type - ) + field_with_error = str(error_keys[error_type]) + error_text = "{} samples failed validation for {}:\n{}" + error_text = error_text.format(num_of_errors, field_with_error, error_type) + self.logsum.add_warning(entry=error_text) + stderr.print(f"[red]{error_text}") stderr.print("[red] --------------------") return validated_json_data, invalid_json From 2759456b0868aa628719f17ad968aa7ee2cbfd42 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 24 Jul 2024 16:32:16 +0200 Subject: [PATCH 1355/1454] Updated feed_databse with logs and full-update arg --- relecov_tools/__main__.py | 17 ++- relecov_tools/feed_database.py | 220 ++++++++++++++++++++------------- 2 files changed, 147 insertions(+), 90 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 91c6c3ca..3b6c0011 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -376,7 +376,7 @@ def launch(user): pass -# update_db +# update_db TODO: Include types of data and database servers in config file @relecov_tools_cli.command(help_priority=9) @click.option("-j", "--json", help="data in json format") @click.option( @@ -384,6 +384,7 @@ def launch(user): "--type", type=click.Choice(["sample", "bioinfodata", "variantdata"]), multiple=False, + default=None, help="Select the type of information to upload to database", ) @click.option( @@ -396,16 +397,24 @@ def launch(user): ] ), multiple=False, + default=None, help="name of the server which information is defined in config file", ) @click.option("-u", "--user", help="user name for login") @click.option("-p", "--password", help="password for the user to login") -def update_db(user, password, json, type, databaseServer): +@click.option( + "-f", + "--full_update", + is_flag=True, + default=False, + help="Sequentially run every update option", +) +def update_db(user, password, json, type, databaseServer, full_update): """feed database with json""" feed_database = relecov_tools.feed_database.FeedDatabase( - user, password, json, type, databaseServer + user, password, json, type, databaseServer, full_update ) - feed_database.store_data() + feed_database.update_db() # read metadata bioinformatics diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 2d1d7c33..076b827d 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -2,6 +2,7 @@ import sys import os import re +import glob import json import logging import rich.console @@ -10,6 +11,7 @@ import relecov_tools.utils from relecov_tools.config_json import ConfigJson from relecov_tools.rest_api import RestApi +from relecov_tools.log_summary import LogSum log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -28,6 +30,7 @@ def __init__( json_file=None, type_of_info=None, database_server=None, + full_update=None, ): if user is None: user = relecov_tools.utils.prompt_text( @@ -53,35 +56,30 @@ def __init__( "schema", self.config_json.get_topic_data("json_schemas", "relecov_schema"), ) - self.schema = relecov_tools.utils.read_json_file(schema) - - if type_of_info is None: - type_of_info = relecov_tools.utils.prompt_selection( - "Select:", - ["sample", "bioinfodata", "variantdata"], - ) + self.full_update = full_update + # TODO: Include types_of_data and database_servers as config fields + self.types_of_data = ["sample", "bioinfodata", "variantdata"] + self.db_servers_names = ["iskylims", "relecov"] + if not full_update: + if type_of_info is None: + type_of_info = relecov_tools.utils.prompt_selection( + "Select type of data to upload:", + self.types_of_data, + ) + if database_server is None: + database_server = relecov_tools.utils.prompt_selection( + "Select target database server:", + self.db_servers_names, + ) + self.server_name = database_server self.type_of_info = type_of_info - if database_server is None: - database_server = relecov_tools.utils.prompt_selection( - "Select:", - ["iskylims", "relecov"], - ) - self.server_type = database_server - # Get database settings - try: - self.database_settings = self.config_json.get_topic_data( - "external_url", database_server - ) - except KeyError: - log.error("Unable to get parameters for dataserver") - stderr.print(f"[red] Unable to fetch parameters data for {database_server}") - sys.exit(1) - self.database_server = self.database_settings["server"] - self.database_url = self.database_settings["url"] - - self.database_rest_api = RestApi(self.database_server, self.database_url) + json_dir = os.path.dirname(os.path.realpath(self.json_file)) + lab_code = json_dir.split("/")[-2] + self.logsum = LogSum( + output_location=json_dir, unique_key=lab_code, path=json_dir + ) def get_schema_ontology_values(self): """Read the schema and extract the values of ontology with the label""" @@ -136,20 +134,18 @@ def get_iskylims_fields_sample(self): try: sample_fields_raw = self.database_rest_api.get_request(sample_url, "", "") except AttributeError: - log.error("Unable to connect to server %s", self.database_server) - stderr.print(f"[red] Unable to connect to server {self.database_server}") - sys.exit(1) + logtxt = f"Unable to connect to {self.db_server} server" + self.logsum.add_error(entry=logtxt) + stderr.print(f"[red]{logtxt}") + return if "ERROR" in sample_fields_raw: - log.error( - "Unable to get parameters. Received error code %s", - sample_fields_raw["ERROR"], - ) - stderr.print( - f"[red] Unable to fetch data. Received error {sample_fields_raw['ERROR']}" - ) - sys.exit(1) + logtxt1 = f"Unable to fetch data from {self.db_server}." + logtxt2 = f" Received error {sample_fields_raw['ERROR']}" + self.logsum.add_error(entry=str(logtxt1 + logtxt2)) + stderr.print(f"[red]{logtxt1 + logtxt2}") + return - for key, values in sample_fields_raw["DATA"].items(): + for _, values in sample_fields_raw["DATA"].items(): if "ontology" in values: try: property = ontology_dict[values["ontology"]] @@ -157,11 +153,14 @@ def get_iskylims_fields_sample(self): # the field name for the sample sample_fields[property] = values["field_name"] except KeyError as e: - stderr.print(f"[red]Error in map ontology {e}") + self.logsum.add_warning(entry=f"Error mapping ontology {e}") + stderr.print(f"[red]Error mapping ontology {e}") else: # for the ones that do not have ontology label in the sample field # and have an empty value: sample_fields[key] = "" - log.info("not ontology for item %s", values["field_name"]) + logtxt = f"No ontology found for {values.get('field_name')}" + self.logsum.add_warning(entry=logtxt) + log.info(logtxt) # fetch label for sample Project s_project_url = self.database_settings["url_project_fields"] param = self.database_settings["param_sample_project"] @@ -170,14 +169,10 @@ def get_iskylims_fields_sample(self): s_project_url, param, p_name ) if "ERROR" in s_project_fields_raw: - log.error( - "Unable to get parameters. Received error code %s", - s_project_fields_raw["ERROR"], - ) - stderr.print( - f"[red] Unable to fetch data. Received error {s_project_fields_raw['ERROR']}" - ) - sys.exit(1) + logtxt1 = f"Unable to fetch data from {self.db_server}." + logtxt2 = f" Received error {s_project_fields_raw['ERROR']}" + self.logsum.add_error(entry=str(logtxt1 + logtxt2)) + return for field in s_project_fields_raw["DATA"]: s_project_fields.append(field["sampleProjectFieldName"]) return [sample_fields, s_project_fields] @@ -204,6 +199,7 @@ def update_database(self, field_values, post_url): for chunk in field_values: req_sample = "" request_count += 1 + # TODO: Include these fields in config file if "sample_name" in chunk: stderr.print( f"[blue] sending request for sample {chunk['sample_name']}" @@ -214,6 +210,7 @@ def update_database(self, field_values, post_url): f"[blue] sending request for sample {chunk['sequencing_sample_id']}" ) req_sample = chunk["sequencing_sample_id"] + self.logsum.feed_key(sample=req_sample) result = self.database_rest_api.post_request( json.dumps(chunk), {"user": self.user, "pass": self.passwd}, @@ -233,63 +230,61 @@ def update_database(self, field_values, post_url): if "ERROR" not in result: break if i == 9 and "ERROR" in result: - log.error("Unable to sent the request to remote server") - stderr.print( - "[red] Unable to sent the request to remote server" - ) - sys.exit(1) + logtxt = f"Unable to sent the request to {self.db_server}" + self.logsum.add_error(entry=logtxt, sample=req_sample) + stderr.print(f"[red]{logtxt}") + continue elif "is not defined" in result["ERROR_TEST"].lower(): - log.warning( - "Request to %s for %s was not accepted", - self.database_server, - req_sample, - ) - stderr.print(f"[yellow] Warning: {req_sample} is not defined") + logtxt = f"{req_sample} is not defined in {self.db_server}" + self.logsum.add_error(entry=logtxt, sample=req_sample) + stderr.print(f"[yellow]Warning: {logtxt}") continue elif "already defined" in result["ERROR_TEST"].lower(): - log.warning( - "Request to %s for %s was not accepted", - self.database_server, - req_sample, - ) - stderr.print( - f"[yellow] Warning request for {req_sample} already defined" - ) + logtxt = f"Request to {self.db_server} already defined" + self.logsum.add_warning(entry=logtxt, sample=req_sample) + stderr.print(f"[yellow]{logtxt} for sample {req_sample}") continue else: - log.error("Request to %s was not accepted", self.database_server) - stderr.print( - f"[red] Error {result['ERROR']} when sending request to {self.database_server}" - ) - sys.exit(1) + logtxt = f"Error {result['ERROR']} in request to {self.db_server}" + self.logsum.add_error(entry=logtxt, sample=req_sample) + stderr.print(f"[red]{logtxt}") + continue log.info( "stored data in %s iskylims for sample %s", - self.database_server, + self.db_server, req_sample, ) stderr.print(f"[green] Successful request for {req_sample}") suces_count += 1 if request_count == suces_count: stderr.print( - f"[gren] All information was sent sucessfuly to {self.server_type}" + f"All {self.type_of_info} data sent sucessfuly to {self.db_server}" ) else: + logtxt = "%s of the %s requests were sent to %s" + self.logsum.add_warning( + entry=logtxt % (suces_count, request_count, self.server_name) + ) stderr.print( - "[yellow] Some of your requests were not successful stored in database" + f"[yellow]{logtxt % (suces_count, request_count, self.server_name)}" ) - stderr.print(f"[yellow] {suces_count} of the {request_count} were done ok") return - def store_data(self): + def store_data(self, type_of_info, server_name): """Collect data from json file and split them to store data in iSkyLIMS and in Relecov Platform """ map_fields = {} # - if self.type_of_info == "sample": - if self.server_type == "iskylims": - stderr.print(f"[blue] Getting sample fields from {self.server_type}") + # TODO: Include all these hard-coded fields in config file + if type_of_info not in self.types_of_info: + self.logsum.add_error(entry=f"Invalid datatype {type_of_info} to upload") + stderr.print(f"[red]Invalid datatype {type_of_info} to upload") + return + if type_of_info == "sample": + if server_name == "iskylims": + stderr.print(f"[blue] Getting sample fields from {server_name}") sample_fields, s_project_fields = self.get_iskylims_fields_sample() stderr.print("[blue] Selecting sample fields") map_fields = self.map_iskylims_sample_fields_values( @@ -300,16 +295,69 @@ def store_data(self): map_fields = self.map_relecov_sample_data() post_url = "store_samples" - elif self.type_of_info == "bioinfodata": + elif type_of_info == "bioinfodata": post_url = "bioinfodata" map_fields = self.json_data - elif self.type_of_info == "variantdata": + elif type_of_info == "variantdata": post_url = "variantdata" map_fields = self.json_data - else: - stderr.print("[red] Invalid type to upload to database") - sys.exit(1) self.update_database(map_fields, post_url) - stderr.print(f"[green] Upload process to {self.server_type} completed") + stderr.print(f"[green]Upload process to {self.server_name} completed") + + def start_api(self, database_server): + """Open connection torwards database server API""" + # Get database settings + if database_server: + try: + self.database_settings = self.config_json.get_topic_data( + "external_url", database_server + ) + except KeyError: + logtxt = f"Unable to fetch parameters for {database_server}" + self.logsum.add_error(entry=logtxt) + stderr.print(f"[red]{logtxt}") + return + self.db_server = self.database_settings["server"] + self.db_url = self.database_settings["url"] + self.db_rest_api = RestApi(self.db_server, self.db_url) + else: + logtxt = f"No database server was selected for {self.type_of_info}. Skipped" + self.logsum.add_error(entry=logtxt) + stderr.print(f"[red]{logtxt}") + return + return + + def update_db(self): + """Run the update database process with the provided input""" + if self.full_update is True: + self.server_name = "iskylims" + self.type_of_info = "sample" + self.start_api(self.server_name) + self.store_data(self.type_of_info, self.server_name) + + self.server_name = "relecov" + self.start_api(self.server_name) + for datatype in self.types_of_data: + log_text = f"Sending {datatype} data to {self.server_name}" + log.info(log_text) + stderr.print(log_text) + self.type_of_info = datatype + # TODO: Handling for servers with different datatype needs + if datatype == "variantdata": + json_dir = os.path.dirname(os.path.realpath(self.json_file)) + long_tables = glob.glob(os.path.join(json_dir, "*long_table*.json")) + if not long_tables: + json_file = relecov_tools.utils.prompt_path( + msg="Select long_table json file for variant data" + ) + else: + json_file = long_tables[0] + log.info("Selected %s file for variant data", str(json_file)) + self.json_data = relecov_tools.utils.read_json_file(json_file) + self.store_data(datatype, self.server_name) + else: + self.start_api(self.server_name) + self.store_data(self.type_of_info, self.server_name) + self.logsum.create_error_summary(called_module="update-db") From 11b49fd18084f673965300a0b6d789e2bc4902c0 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 24 Jul 2024 16:34:21 +0200 Subject: [PATCH 1356/1454] Updated schema with new properties and fixed ontology values --- relecov_tools/schema/ena_schema.json | 17 +-- relecov_tools/schema/relecov_schema.json | 132 +++++++++++++++++------ 2 files changed, 103 insertions(+), 46 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 2d6ac920..997b7e05 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -602,7 +602,7 @@ "examples": [ "e.g. #131" ], - "ontology": "GENEPIO:0000079", + "ontology": "GENEPIO:0001398", "type": "string", "description": "a unique identifier by which each subject can be referred to, de-identified.", "clasification": "Host information", @@ -1172,7 +1172,7 @@ }, "sample_title": { "examples": [ - "" + "s_20201007_026" ], "ontology": "GENEPIO:0000079", "type": "string", @@ -1237,19 +1237,6 @@ "study" ] }, - "sample_name": { - "examples": [ - "s_20201007_026" - ], - "ontology": "GENEPIO:0000079", - "type": "string", - "description": "", - "clasification": "Submission ENA", - "label": "Sample name", - "table": [ - "sample" - ] - }, "study_alias": { "examples": [ "e.g Sweden" diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index d631537c..b01cebad 100755 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -587,6 +587,7 @@ "Research [GENEPIO:0100003]", "Protocol Testing [GENEPIO:0100024]", "Surveillance [GENEPIO:0100004]", + "Other [NCIT:C124261]", "Not Applicable [GENEPIO:0001619]", "Not Collected [GENEPIO:0001620]", "Not Provided [GENEPIO:0001668]", @@ -771,7 +772,7 @@ "Middle Nasal Turbinate Scraping", "Nasopharynx Scraping", "Oropharynx Scraping", - "Nasopharynx Swab", + "Nasopharynx swab", "Oropharynx Swab", "Pharynx Swab", "Lower respiratory tract Wash", @@ -874,6 +875,7 @@ "Sputum Collection Tube [GENEPIO:0002115]", "Suction Catheter [58253008]", "Swab [GENEPIO:0100027]", + "Other [NCIT:C17649]", "Not Applicable [GENEPIO:0001619]", "Not Collected [GENEPIO:0001620]", "Not Provided [GENEPIO:0001668]", @@ -1479,6 +1481,17 @@ "label": "If Enrichment panel/assay Is Other, Specify", "fill_mode": "batch" }, + "if_enrichment_panel_assay_version_other": { + "examples": [ + "" + ], + "ontology": "NCIT:C111093", + "type": "string", + "description": "", + "classification": "Sequencing", + "label": "If Enrichment panel/assay version Is Other, Specify", + "fill_mode": "batch" + }, "amplicon_pcr_primer_scheme": { "examples": [ "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv" @@ -1934,7 +1947,7 @@ "examples": [ "2.4.1" ], - "ontology": "0", + "ontology": "NCIT:C111093", "type": "string", "description": "The method version used to remove host reads from the pathogen sequence.", "classification": "Bioinformatic Analysis fields", @@ -1971,7 +1984,7 @@ "type": "string", "description": "The name of the bioinformatics protocol used.", "classification": "Bioinformatic Analysis fields", - "label": "If bioinformatic protocol Is Other, Specify", + "label": "If bioinformatics protocol Is Other, Specify", "fill_mode": "batch", "minLenght": "1" }, @@ -1983,7 +1996,7 @@ "type": "string", "description": "The version number of the bioinformatics protocol used.", "classification": "Bioinformatic Analysis fields", - "label": "bioinformatics protocol version", + "label": "Bioinformatics protocol version", "fill_mode": "batch", "minLenght": "1" }, @@ -2011,25 +2024,25 @@ "type": "string", "description": "Software used for preprocessing step.", "classification": "Bioinformatic Analysis fields", - "label": "Preprocessing", + "label": "Preprocessing software", "fill_mode": "batch" }, "preprocessing_software_version": { "examples": [ "v5.3.1" ], - "ontology": "0", + "ontology": "NCIT:C111093", "type": "string", "description": "Version of the preprocessing software used.", "classification": "Bioinformatic Analysis fields", - "label": "Preprocessing Version", + "label": "Preprocessing software version", "fill_mode": "batch" }, "if_preprocessing_other": { "examples": [ "" ], - "ontology": "0", + "ontology": "MS_1002386", "type": "string", "description": "Preprocessing software name other", "classification": "Bioinformatic Analysis fields", @@ -2055,18 +2068,18 @@ "type": "string", "description": "Software used for mapping step.", "classification": "Bioinformatic Analysis fields", - "label": "Mapping", + "label": "Mapping software", "fill_mode": "batch" }, "mapping_software_version": { "examples": [ "v7.0.1" ], - "ontology": "0", + "ontology": "NCIT:C111093", "type": "string", "description": "Version of the mapper used.", "classification": "Bioinformatic Analysis fields", - "label": "Mapping Version", + "label": "Mapping software version", "fill_mode": "batch" }, "if_mapping_other": { @@ -2099,7 +2112,18 @@ "type": "string", "description": "Software used for assembly of the pathogen genome.", "classification": "Bioinformatic Analysis fields", - "label": "Assembly", + "label": "Assembly software", + "fill_mode": "batch" + }, + "assembly_version": { + "examples": [ + "Spades" + ], + "ontology": "0", + "type": "string", + "description": "Software used for assembly of the pathogen genome.", + "classification": "Bioinformatic Analysis fields", + "label": "Assembly software version", "fill_mode": "batch" }, "if_assembly_other": { @@ -2121,7 +2145,18 @@ "type": "string", "description": "Params used for genome assembly.", "classification": "Bioinformatic Analysis fields", - "label": "Assambly params", + "label": "Assembly params", + "fill_mode": "batch" + }, + "vcf_filename": { + "examples": [ + "Ivar" + ], + "ontology": "0", + "type": "string", + "description": "Name of the vcf file.", + "classification": "Bioinformatic Variants", + "label": "VCF filename", "fill_mode": "batch" }, "variant_calling_software_name": { @@ -2132,18 +2167,18 @@ "type": "string", "description": "Software used for variant calling.", "classification": "Bioinformatic Variants", - "label": "Variant Calling", + "label": "Variant calling software", "fill_mode": "batch" }, "variant_calling_software_version": { "examples": [ "v4.1" ], - "ontology": "0", + "ontology": "NCIT:C111093", "type": "string", "description": "Variant calling software version", "classification": "Bioinformatic Variants", - "label": "Variant Calling Version", + "label": "Variant calling software version", "fill_mode": "batch" }, "if_variant_calling_other": { @@ -2165,7 +2200,7 @@ "type": "string", "description": "Params used for variant calling", "classification": "Bioinformatic Variants", - "label": "Variant Calling params", + "label": "Variant calling params", "fill_mode": "batch" }, "consensus_sequence_name": { @@ -2231,7 +2266,7 @@ "type": "string", "description": "The name of software used to generate the consensus sequence.", "classification": "Bioinformatic Analysis fields", - "label": "Consensus sequence software name", + "label": "Consensus software", "fill_mode": "batch" }, "if_consensus_other": { @@ -2240,7 +2275,7 @@ ], "ontology": "0", "type": "string", - "description": "The version of the software used to generate the consensus sequence.", + "description": "", "classification": "Bioinformatic Analysis fields", "label": "If consensus Is Other, Specify", "fill_mode": "batch" @@ -2249,11 +2284,11 @@ "examples": [ "1.3" ], - "ontology": "GENEPIO:0001469", + "ontology": "NCIT:C111093", "type": "string", "description": "The version of the software used to generate the consensus sequence.", "classification": "Bioinformatic Analysis fields", - "label": "Consensus sequence software version", + "label": "Consensus software version", "fill_mode": "batch" }, "consensus_params": { @@ -2264,7 +2299,7 @@ "type": "string", "description": "Parameters used for consensus generation", "classification": "Bioinformatic Analysis fields", - "label": "Consensus Params", + "label": "Consensus params", "fill_mode": "batch" }, "consensus_genome_length": { @@ -2414,11 +2449,44 @@ "examples": [ "B.1.1.7" ], - "ontology": "GENEPIO:0001500", + "ontology": "NCIT:C60792", + "type": "string", + "description": "The name of the lineage.", + "classification": "Lineage fields", + "label": "Lineage designation", + "fill_mode": "batch" + }, + "clade_name": { + "examples": [ + "B.1.1.7" + ], + "ontology": "NCIT:C179767", "type": "string", - "description": "The name of the lineage or clade.", + "description": "The name of the clade.", "classification": "Lineage fields", - "label": "Lineage/clade name", + "label": "Clade designation", + "fill_mode": "batch" + }, + "clade_type_software_name": { + "examples": [ + "Pangolin" + ], + "ontology": "GENEPIO:0001501", + "type": "string", + "description": "The name of the software used to determine the clade/type.", + "classification": "Lineage fields", + "label": "Clade/Type identification software", + "fill_mode": "batch" + }, + "if_clade_type_other": { + "examples": [ + "Pangolin" + ], + "ontology": "GENEPIO:0001501", + "type": "string", + "description": "The name of the software used to determine the clade/type.", + "classification": "Lineage fields", + "label": "If Clade/Type Is Other, Specify", "fill_mode": "batch" }, "lineage_analysis_software_name": { @@ -2429,7 +2497,7 @@ "type": "string", "description": "The name of the software used to determine the lineage/clade.", "classification": "Lineage fields", - "label": "lineage/clade analysis software name", + "label": "Lineage identification software", "fill_mode": "batch" }, "if_lineage_identification_other": { @@ -2438,7 +2506,7 @@ ], "ontology": "0", "type": "string", - "description": "The name of the software used to determine the lineage/clade.", + "description": "", "classification": "Lineage fields", "label": "If lineage identification Is Other, Specify", "fill_mode": "batch" @@ -2458,18 +2526,18 @@ "examples": [ "2.1.10" ], - "ontology": "GENEPIO:0001502", + "ontology": "NCIT:C111093", "type": "string", "description": "The version of the software used to determine the lineage/clade.", "classification": "Lineage fields", - "label": "Lineage/clade analysis software version", + "label": "Lineage software version", "fill_mode": "batch" }, "lineage_analysis_scorpio_version": { "examples": [ "2.1.10" ], - "ontology": "GENEPIO:0001502", + "ontology": "NCIT:C111093", "type": "string", "description": "The version of the scorpio data used to determine the lineage/clade.", "classification": "Lineage fields", @@ -2480,7 +2548,7 @@ "examples": [ "2.1.10" ], - "ontology": "GENEPIO:0001502", + "ontology": "NCIT:C111093", "type": "string", "description": "The version of the constellations databases used to determine the lineage/clade.", "classification": "Lineage fields", @@ -2561,6 +2629,7 @@ "orf10 [GENEPIO:0100181]", "orf14 [GENEPIO:0100182]", "SARS-COV-2 5' UTR [GENEPIO:0100183]", + "Other [NCIT:C124261]", "Not Applicable [GENEPIO:0001619]", "Not Collected [GENEPIO:0001620]", "Not Provided [GENEPIO:0001668]", @@ -2623,6 +2692,7 @@ "orf10 [GENEPIO:0100181]", "orf14 [GENEPIO:0100182]", "SARS-COV-2 5' UTR [GENEPIO:0100183]", + "Other [NCIT:C124261]", "Not Applicable [GENEPIO:0001619]", "Not Collected [GENEPIO:0001620]", "Not Provided [GENEPIO:0001668]", From 07c9ffbfaf5a95180e34c51d4e69372c6ff29059 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 24 Jul 2024 16:37:16 +0200 Subject: [PATCH 1357/1454] Included a new lab in addresses --- relecov_tools/conf/laboratory_address.json | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index e6f39ed1..3471f980 100755 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -1386,6 +1386,17 @@ "submitting_institution_address": "Ctra. Colmenar Viejo, km.9, 100", "submitting_institution_email": "" }, + "HU GREGORIO MARAÑÓN": { + "collecting_institution_address": "C. del Dr. Esquerdo, 46", + "collecting_institution_email": "", + "geo_loc_state": "Comunidad de Madrid", + "geo_loc_region": "Madrid", + "geo_loc_city": "Madrid", + "geo_loc_country": "Spain", + "submitting_institution": "HU GREGORIO MARAÑÓN", + "submitting_institution_address": "C. del Dr. Esquerdo, 46", + "submitting_institution_email": "" + }, "Hospital Universitario Cruces": { "collecting_institution_address": "Plaza Cruces, s/n", "collecting_institution_email": "", From 6813e2acabb33f5d22d3e97db58f93b49f0f6dbd Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 24 Jul 2024 16:37:45 +0200 Subject: [PATCH 1358/1454] Fixed variants_long_table regex pattern --- relecov_tools/conf/bioinfo_config.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json index 523d7fde..56fe98f0 100644 --- a/relecov_tools/conf/bioinfo_config.json +++ b/relecov_tools/conf/bioinfo_config.json @@ -37,7 +37,7 @@ } }, "variants_long_table": { - "fn": "variants_long_table(?:_\\d{8})?\\.csv", + "fn": "variants_long_table.csv", "sample_col_idx": 1, "header_row_idx": 1, "required": true, From 4180c1429efc79b719a67c15e7fa8e6a78a57e39 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 24 Jul 2024 16:38:13 +0200 Subject: [PATCH 1359/1454] Updated one field to match schema --- relecov_tools/conf/anatomical_material_collection_method.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/anatomical_material_collection_method.json b/relecov_tools/conf/anatomical_material_collection_method.json index acb99584..0ce2c125 100755 --- a/relecov_tools/conf/anatomical_material_collection_method.json +++ b/relecov_tools/conf/anatomical_material_collection_method.json @@ -815,7 +815,7 @@ "body_product": "Not Applicable", "anatomical_material": "Not Applicable" }, - "Nasopharynx Swab": { + "Nasopharynx swab": { "anatomical_part": "Nasopharynx", "collection_method": "Swab", "body_product": "Not Applicable", From 809521129a93be7fca8fc30863f68420deec3c99 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 24 Jul 2024 16:39:00 +0200 Subject: [PATCH 1360/1454] Included bioinfo_heading and new sequencing file extensions --- relecov_tools/conf/configuration.json | 41 ++++++++++++++++++++++++++- 1 file changed, 40 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 18ccb7b9..52598f4b 100755 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -56,6 +56,42 @@ "Sequence file R1 fastq", "Sequence file R2 fastq" ], + "bioinfo_heading": [ + "Consensus sequence filename", + "VCF filename", + "Variant designation table filename", + "Bioinformatics protocol", + "If bioinformatics protocol Is Other, Specify", + "Bioinformatics protocol version", + "Commercial/Open-source/both", + "Preprocessing software", + "Preprocessing software version", + "If preprocessing Is Other, Specify", + "Preprocessing params", + "Mapping software", + "Mapping software version", + "If mapping Is Other, Specify", + "Mapping params", + "Assembly software", + "Assembly software version", + "If assembly Is Other, Specify", + "Assembly params", + "Variant calling software", + "Variant calling software version", + "If variant calling Is Other, Specify", + "Variant calling params", + "Consensus software", + "Consensus software version", + "If consensus Is Other, Specify", + "Consensus params", + "Clade/Type identification software", + "Clade/Type software version", + "If Clade/Type Is Other, Specify", + "Lineage identification software", + "Lineage software version", + "If lineage identification Is Other, Specify", + "Quality control metrics (sample discard criteria)" + ], "lab_metadata_req_json": { "laboratory_data": { "file": "laboratory_address.json", @@ -215,7 +251,10 @@ ".fq", ".fq.gz", ".fasta", - ".fasta.gz" + ".fasta.gz", + ".fa", + ".fa.gz", + "bam" ], "allowed_download_options": [ "download_only", From 93c8c1edbdfda98f2f22a07e8189ed94e25ed4d5 Mon Sep 17 00:00:00 2001 From: Pablo Mata <76519482+Shettland@users.noreply.github.com> Date: Thu, 25 Jul 2024 12:15:59 +0200 Subject: [PATCH 1361/1454] Undo ontology change for host subject id --- relecov_tools/schema/ena_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 997b7e05..540cd553 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -602,7 +602,7 @@ "examples": [ "e.g. #131" ], - "ontology": "GENEPIO:0001398", + "ontology": "GENEPIO:0000079", "type": "string", "description": "a unique identifier by which each subject can be referred to, de-identified.", "clasification": "Host information", @@ -1348,4 +1348,4 @@ "fill_mode": "batch" } } -} \ No newline at end of file +} From 839c5ea2b696a5f770d245871880a6eec17a17e8 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 24 Jul 2024 17:44:20 +0200 Subject: [PATCH 1362/1454] starting the pipeline launch implementation --- relecov_tools/__main__.py | 33 ++++++ relecov_tools/conf/pipeline_config.json | 3 + relecov_tools/launch_pipeline.py | 139 ++++++++++++++++++++++++ 3 files changed, 175 insertions(+) create mode 100644 relecov_tools/conf/pipeline_config.json create mode 100644 relecov_tools/launch_pipeline.py diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 3b6c0011..ad03c75c 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -20,6 +20,7 @@ import relecov_tools.metadata_homogeneizer import relecov_tools.gisaid_upload import relecov_tools.upload_ena_protocol +import relecov_tools.launch_pipeline log = logging.getLogger() @@ -481,6 +482,38 @@ def metadata_homogeneizer(institution, directory, output): ) new_parse.converting_metadata() +# creating symbolic links +@relecov_tools_cli.command(help_priority=13) +@click.option( + "-i", + "--input", + type=click.Path(), + help="select input folder where are located the sample files", +) +@click.option( + "-v", + "--validate_file", + type=click.Path(), + help="select the json with the validate samples", +) +@click.option( + "-t", + "--template", + type=click.Path(), + help="select the template folder to be copied in the output folder", +) +@click.option( + "-c", + "--config", + type=click.Path(), + help="select the template config file", +) +@click.option("-o", "--output", type=click.Path(), help="select output folder") +def launch_pipeline(input, validate_file, template, output, config): + """ + Create the symbolic links for the samples which are validated. + """ + if __name__ == "__main__": run_relecov_tools() diff --git a/relecov_tools/conf/pipeline_config.json b/relecov_tools/conf/pipeline_config.json new file mode 100644 index 00000000..c8deeee0 --- /dev/null +++ b/relecov_tools/conf/pipeline_config.json @@ -0,0 +1,3 @@ +"pipeline" :{ + "analysis_name" = "RELECOV_icasas_C" +} \ No newline at end of file diff --git a/relecov_tools/launch_pipeline.py b/relecov_tools/launch_pipeline.py new file mode 100644 index 00000000..4580ffc2 --- /dev/null +++ b/relecov_tools/launch_pipeline.py @@ -0,0 +1,139 @@ +import json +import os +import sys +import shutil +import datetime +import logging +import rich.console + +import relecov_tools.utils + + +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + +class LaunchPipeline: + def __init__( + self, + input_folder=None, + validated_file=None, + template=None, + output_folder=None, + pipeline_conf_file = None + ): + current_date = datetime.date.today().strftime("%Y%m%d") + if input_folder is None: + self.input_folder = relecov_tools.utils.prompt_path( + msg="Select the folder which contains the fastq file of samples" + ) + else: + self.input_folder = input_folder + if not os.path.exists(self.input_folder): + log.error("Input folder %s does not exist ", self.input_folder) + stderr.print( + "[red] Input folder " + self.input_folder + " does not exist" + ) + sys.exit(1) + if template is None: + self.template = relecov_tools.utils.prompt_path( + msg="Select the path which contains the template structure" + ) + else: + self.template = template + if not os.path.exists(self.template): + log.error("Template folder %s does not exist ", self.template) + stderr.print( + "[red] Template folder " + self.template + " does not exist" + ) + sys.exit(1) + if validated_file is None: + self.validated_file = relecov_tools.utils.prompt_path( + msg="Select the json file which contains the validate samples" + ) + else: + self.validated_file = validated_file + if not os.path.exists(self.validated_file): + log.error("Json validate file %s does not exist ", self.validated_file) + stderr.print( + "[red] Json validate file " + self.validated_file + " does not exist" + ) + sys.exit(1) + if pipeline_conf_file is None: + self.pipeline_conf_file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), "conf", "pipeline_config.json" + ) + if not os.path.exists(self.pipeline_conf_file): + log.error("Pipeline config file %s does not exist ", self.pipeline_conf_file) + stderr.print( + "[red] Pipeline config file " + self.pipeline_conf_file + " does not exist" + ) + sys.exit(1) + data = relecov_tools.utils.read_json_file(self.pipeline_conf_file) + if not "analysis_name" in data: + log.error("Invalid pipeline config file %s ", self.pipeline_conf_file) + stderr.print( + "[red] Invalid pipeline config file " + self.pipeline_conf_file + ) + sys.exit(1) + else: + analysis_name = data["analysis_name"] + if output_folder is None: + output_folder = relecov_tools.utils.prompt_path( + msg="Select the output folder" + ) + self.output_folder = os.path.join(output_folder, current_date, analysis_name) + if os.path.exists(self.output_folder): + msg = "Analysis folder already exists and it will be deleted. Do you want to continue? Y/N" + confirmation = relecov_tools.utils.prompt_yn_question(msg) + if confirmation.lower() != "y": + sys.exit(1) + try: + os.makedirs(self.output_folder) + except OSError as e: + log.error("Unable to create output folder %s ", e) + stderr.print("[red] Unable to create output folder " + e) + sys.exit(1) + if not os.path.exists(self.output_folder): + log.error("Output folder %s does not exist ", self.output_folder) + stderr.print( + "[red] Output folder " + self.output_folder + " does not exist" + ) + sys.exit(1) + + self.sample_ids = [] + + def join_valid_items(self): + subfolders = [f.path for f in os.scandir(self.input_folder) if f.is_dir()] + latest_subfolders = [] + for subfolder in subfolders: + subfolder_date = os.path.basename(subfolder) + try: + subfolder_date = datetime.datetime.strptime(subfolder_date, "%Y%m%d").date() + latest_subfolders.append(subfolder) + except ValueError: + pass + # Now you have the latest subfolder for each date in latest_subfolders + # You can continue with your code logic here + + def pipeline_exc(self): + # copy template folder and subfolders in output folder + shutil.copytree(self.template, self.output_folder) + with open(self.validated_file) as fh: + data = json.load(fh) + # iterate over the list of the items + for item in data: + sequencing_sample_id = item["sequencing_sample_id"] + # join r1_fastq_file_path and sequencing_file_R1_fastq + r1_file_path = os.path.join(item["r1_fastq_file_path"], item["sequencing_file_R1_fastq"]) + if "sequencing_file_R2_fastq" in item: + r2_file_path = os.path.join(item["r2_fastq_file_path"], item["sequencing_file_R2_fastq"]) + else: + r2_file_path = None + + + \ No newline at end of file From 157e27e3297aa477172305e391406bc4cd9fd3db Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 30 Jul 2024 11:47:36 +0200 Subject: [PATCH 1363/1454] updated the first implementation, pending testing --- relecov_tools/__main__.py | 11 +- relecov_tools/conf/pipeline_config.json | 9 +- relecov_tools/launch_pipeline.py | 178 ++++++++++++++++-------- 3 files changed, 132 insertions(+), 66 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index ad03c75c..604d27f0 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -482,6 +482,7 @@ def metadata_homogeneizer(institution, directory, output): ) new_parse.converting_metadata() + # creating symbolic links @relecov_tools_cli.command(help_priority=13) @click.option( @@ -490,12 +491,6 @@ def metadata_homogeneizer(institution, directory, output): type=click.Path(), help="select input folder where are located the sample files", ) -@click.option( - "-v", - "--validate_file", - type=click.Path(), - help="select the json with the validate samples", -) @click.option( "-t", "--template", @@ -511,9 +506,9 @@ def metadata_homogeneizer(institution, directory, output): @click.option("-o", "--output", type=click.Path(), help="select output folder") def launch_pipeline(input, validate_file, template, output, config): """ - Create the symbolic links for the samples which are validated. + Create the symbolic links for the samples which are validated. """ - + if __name__ == "__main__": run_relecov_tools() diff --git a/relecov_tools/conf/pipeline_config.json b/relecov_tools/conf/pipeline_config.json index c8deeee0..17a05cd9 100644 --- a/relecov_tools/conf/pipeline_config.json +++ b/relecov_tools/conf/pipeline_config.json @@ -1,3 +1,6 @@ -"pipeline" :{ - "analysis_name" = "RELECOV_icasas_C" -} \ No newline at end of file +{ + "analysis_name" : "RELECOV_icasas_C", + "analysis_folder" : "ANALYSIS", + "sample_stored_folder" : "RAW", + "sample_link_folder" : "00_reads", +} diff --git a/relecov_tools/launch_pipeline.py b/relecov_tools/launch_pipeline.py index 4580ffc2..8a2250b8 100644 --- a/relecov_tools/launch_pipeline.py +++ b/relecov_tools/launch_pipeline.py @@ -1,4 +1,5 @@ import json +import re import os import sys import shutil @@ -17,14 +18,14 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) + class LaunchPipeline: def __init__( self, input_folder=None, - validated_file=None, template=None, output_folder=None, - pipeline_conf_file = None + pipeline_conf_file=None, ): current_date = datetime.date.today().strftime("%Y%m%d") if input_folder is None: @@ -35,9 +36,7 @@ def __init__( self.input_folder = input_folder if not os.path.exists(self.input_folder): log.error("Input folder %s does not exist ", self.input_folder) - stderr.print( - "[red] Input folder " + self.input_folder + " does not exist" - ) + stderr.print("[red] Input folder " + self.input_folder + " does not exist") sys.exit(1) if template is None: self.template = relecov_tools.utils.prompt_path( @@ -47,46 +46,43 @@ def __init__( self.template = template if not os.path.exists(self.template): log.error("Template folder %s does not exist ", self.template) - stderr.print( - "[red] Template folder " + self.template + " does not exist" - ) - sys.exit(1) - if validated_file is None: - self.validated_file = relecov_tools.utils.prompt_path( - msg="Select the json file which contains the validate samples" - ) - else: - self.validated_file = validated_file - if not os.path.exists(self.validated_file): - log.error("Json validate file %s does not exist ", self.validated_file) - stderr.print( - "[red] Json validate file " + self.validated_file + " does not exist" - ) + stderr.print("[red] Template folder " + self.template + " does not exist") sys.exit(1) if pipeline_conf_file is None: self.pipeline_conf_file = os.path.join( - os.path.dirname(os.path.realpath(__file__)), "conf", "pipeline_config.json" + os.path.dirname(os.path.realpath(__file__)), + "conf", + "pipeline_config.json", ) if not os.path.exists(self.pipeline_conf_file): - log.error("Pipeline config file %s does not exist ", self.pipeline_conf_file) + log.error( + "Pipeline config file %s does not exist ", self.pipeline_conf_file + ) stderr.print( - "[red] Pipeline config file " + self.pipeline_conf_file + " does not exist" + "[red] Pipeline config file " + + self.pipeline_conf_file + + " does not exist" ) sys.exit(1) data = relecov_tools.utils.read_json_file(self.pipeline_conf_file) - if not "analysis_name" in data: + if ( + not "analysis_name" in data + or not "sample_stored_folder" in data + or not "sample_link_folder" in data + ): log.error("Invalid pipeline config file %s ", self.pipeline_conf_file) stderr.print( "[red] Invalid pipeline config file " + self.pipeline_conf_file ) sys.exit(1) - else: - analysis_name = data["analysis_name"] + if output_folder is None: output_folder = relecov_tools.utils.prompt_path( msg="Select the output folder" ) - self.output_folder = os.path.join(output_folder, current_date, analysis_name) + self.output_folder = os.path.join( + output_folder, current_date + "_" + self.analysis_name + ) if os.path.exists(self.output_folder): msg = "Analysis folder already exists and it will be deleted. Do you want to continue? Y/N" confirmation = relecov_tools.utils.prompt_yn_question(msg) @@ -98,42 +94,114 @@ def __init__( log.error("Unable to create output folder %s ", e) stderr.print("[red] Unable to create output folder " + e) sys.exit(1) - if not os.path.exists(self.output_folder): - log.error("Output folder %s does not exist ", self.output_folder) - stderr.print( - "[red] Output folder " + self.output_folder + " does not exist" - ) - sys.exit(1) + self.analysis_name = os.path.join(self.output_folder, data["analysis_name"]) + self.analysis_folder = os.path.join(self.analysis_name, data["analysis_folder"]) + self.copied_sample_folder = os.path.join( + self.analysis_name, data["sample_stored_folder"] + ) + self.linked_sample_folder = os.path.join( + self.analysis_folder, data["sample_link_folder"] + ) self.sample_ids = [] def join_valid_items(self): - subfolders = [f.path for f in os.scandir(self.input_folder) if f.is_dir()] - latest_subfolders = [] - for subfolder in subfolders: - subfolder_date = os.path.basename(subfolder) - try: - subfolder_date = datetime.datetime.strptime(subfolder_date, "%Y%m%d").date() - latest_subfolders.append(subfolder) - except ValueError: - pass - # Now you have the latest subfolder for each date in latest_subfolders - # You can continue with your code logic here + def get_latest_lab_folder(self): + lab_folders = [f.path for f in os.scandir(self.input_folder) if f.is_dir()] + lab_latest_folders = {} + latest_date = datetime.datetime.strptime("20220101", "%Y%m%d").date() + for lab_folder in lab_folders: + existing_upload_folders = False + last_folder_date = datetime.datetime.strptime( + "20220101", "%Y%m%d" + ).date() + scan_folder = os.path.join(self.input_folder, lab_folder) + lab_sub_folders = [ + f.path for f in os.scandir(scan_folder) if f.is_dir() + ] + for lab_sub_folder in lab_sub_folders: + f_name = os.path.basename(lab_sub_folder) + f_date_match = re.match(r"(^\d{8}).*", f_name) + if not f_date_match: + continue + f_date = f_date_match.group(1) + try: + sub_f_date = datetime.datetime.strptime(f_date, "%Y%m%d").date() + except ValueError: + continue + if sub_f_date > last_folder_date: + last_folder_date = sub_f_date + latest_folder_name = os.path.join(lab_sub_folder, f_name) + existing_upload_folders = True + if existing_upload_folders: + lab_latest_folders[lab_folder] = { + "path": latest_folder_name, + "date": last_folder_date, + } + if last_folder_date > latest_date: + latest_date = last_folder_date + return lab_latest_folders, latest_date + + upload_lab_folders, latest_date = get_latest_lab_folder(self) + samples_data = [] + for lab, data_folder in upload_lab_folders.items(): + # check if laboratory folder is the latest date to process + if data_folder["date"] != latest_date: + continue + # fetch the validate file and get sample id and r1 and r2 file path + validate_files = [ + f + for f in os.listdir(data_folder["path"]) + if f.startswith("validated_") and f.endswith(".json") + ] + if not validate_files: + continue + for validate_file in validate_files: + validate_file_path = os.path.join(data_folder["path"], validate_file) + with open(validate_file_path) as fh: + data = json.load(fh) + for item in data: + sample = {} + sample["sample_ids"] = item["sequencing_sample_id"] + sample["r1_fastq_file_path"] = item["r1_fastq_file_path"] + if "r2_fastq_file_path" in item: + sample["r2_fastq_file_path"] = item["r2_fastq_file_path"] + samples_data.append(sample) + log.info("Collecting samples for %s", lab) + stderr.print("[blue] Collecting samples for " + lab) + return samples_data def pipeline_exc(self): # copy template folder and subfolders in output folder shutil.copytree(self.template, self.output_folder) - with open(self.validated_file) as fh: - data = json.load(fh) - # iterate over the list of the items - for item in data: - sequencing_sample_id = item["sequencing_sample_id"] + # collect json with all validated samples + samples_data = self.join_valid_items() + + # iterate over the sample_data to copy the fastq files in the output folder + for item in samples_data: + sequencing_r1_sample_id = item["sequencing_sample_id"] + "_R1" + ".fastq.gz" + sequencing_r2_sample_id = item["sequencing_sample_id"] + "_R2" + ".fastq.gz" # join r1_fastq_file_path and sequencing_file_R1_fastq - r1_file_path = os.path.join(item["r1_fastq_file_path"], item["sequencing_file_R1_fastq"]) - if "sequencing_file_R2_fastq" in item: - r2_file_path = os.path.join(item["r2_fastq_file_path"], item["sequencing_file_R2_fastq"]) + r1_file_path = os.path.join( + item["r1_fastq_file_path"], item["sequencing_file_R1_fastq"] + ) + # copy sequencing files into the output folder + raw_folder = os.path.join(self.output_folder, self.copied_sample_folder) + shutil.copy(r1_file_path, raw_folder) + # create simlink for the sample + sample_r1_link_path = os.path.join( + self.linked_sample_folder, sequencing_r1_sample_id + ) + os.symlink(r1_file_path, sample_r1_link_path) + if r2_file_path: + sample_r2_link_path = os.path.join( + self.linked_sample_folder, sequencing_r2_sample_id + ) + os.symlink(r2_file_path, sample_r2_link_path) + if "sequencing_file_R2_fastq" in item: + r2_file_path = os.path.join( + item["r2_fastq_file_path"], item["sequencing_file_R2_fastq"] + ) else: r2_file_path = None - - - \ No newline at end of file + # copy sequencing files into the output folder From eb70dbc7b9d97d672f3aee5604e8d2eb5018bdf8 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 1 Aug 2024 11:34:01 +0200 Subject: [PATCH 1364/1454] Changes done due to testing --- relecov_tools/__main__.py | 6 ++- relecov_tools/conf/pipeline_config.json | 2 +- relecov_tools/launch_pipeline.py | 52 +++++++++++++++++++------ 3 files changed, 46 insertions(+), 14 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 604d27f0..026cedf2 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -504,10 +504,14 @@ def metadata_homogeneizer(institution, directory, output): help="select the template config file", ) @click.option("-o", "--output", type=click.Path(), help="select output folder") -def launch_pipeline(input, validate_file, template, output, config): +def launch_pipeline(input, template, output, config): """ Create the symbolic links for the samples which are validated. """ + new_launch = relecov_tools.launch_pipeline.LaunchPipeline( + input, template, output, config + ) + new_launch.pipeline_exc() if __name__ == "__main__": diff --git a/relecov_tools/conf/pipeline_config.json b/relecov_tools/conf/pipeline_config.json index 17a05cd9..bef0b460 100644 --- a/relecov_tools/conf/pipeline_config.json +++ b/relecov_tools/conf/pipeline_config.json @@ -2,5 +2,5 @@ "analysis_name" : "RELECOV_icasas_C", "analysis_folder" : "ANALYSIS", "sample_stored_folder" : "RAW", - "sample_link_folder" : "00_reads", + "sample_link_folder" : "00_reads" } diff --git a/relecov_tools/launch_pipeline.py b/relecov_tools/launch_pipeline.py index 8a2250b8..29a4b685 100644 --- a/relecov_tools/launch_pipeline.py +++ b/relecov_tools/launch_pipeline.py @@ -80,20 +80,32 @@ def __init__( output_folder = relecov_tools.utils.prompt_path( msg="Select the output folder" ) + # Create the output folder if not exists + try: + os.makedirs(output_folder, exist_ok=True) + except OSError or FileExistsError as e: + log.error("Unable to create output folder %s ", e) + stderr.print("[red] Unable to create output folder ", e) + sys.exit(1) + # Update the output folder with the current date and analysis name self.output_folder = os.path.join( - output_folder, current_date + "_" + self.analysis_name + output_folder, current_date + "_" + data["analysis_name"] ) if os.path.exists(self.output_folder): msg = "Analysis folder already exists and it will be deleted. Do you want to continue? Y/N" confirmation = relecov_tools.utils.prompt_yn_question(msg) - if confirmation.lower() != "y": + if confirmation is False: sys.exit(1) + shutil.rmtree(self.output_folder) + """ try: - os.makedirs(self.output_folder) - except OSError as e: + os.makedirs(self.output_folder, exist_ok = True) + except OSError or FileExistsError as e: log.error("Unable to create output folder %s ", e) - stderr.print("[red] Unable to create output folder " + e) + import pdb; pdb.set_trace() + stderr.print("[red] Unable to create output folder ", e) sys.exit(1) + """ self.analysis_name = os.path.join(self.output_folder, data["analysis_name"]) self.analysis_folder = os.path.join(self.analysis_name, data["analysis_folder"]) self.copied_sample_folder = os.path.join( @@ -131,7 +143,8 @@ def get_latest_lab_folder(self): continue if sub_f_date > last_folder_date: last_folder_date = sub_f_date - latest_folder_name = os.path.join(lab_sub_folder, f_name) + # latest_folder_name = os.path.join(lab_sub_folder, f_name) + latest_folder_name = lab_sub_folder existing_upload_folders = True if existing_upload_folders: lab_latest_folders[lab_folder] = { @@ -140,6 +153,8 @@ def get_latest_lab_folder(self): } if last_folder_date > latest_date: latest_date = last_folder_date + log.info("Latest date to process is %s", latest_date) + stderr.print("[blue] Collecting samples from ", latest_date) return lab_latest_folders, latest_date upload_lab_folders, latest_date = get_latest_lab_folder(self) @@ -149,26 +164,39 @@ def get_latest_lab_folder(self): if data_folder["date"] != latest_date: continue # fetch the validate file and get sample id and r1 and r2 file path + validate_files = [ - f + os.path.join(data_folder["path"], f) for f in os.listdir(data_folder["path"]) - if f.startswith("validated_") and f.endswith(".json") + if f.startswith("validated_processed_metadata") and f.endswith(".json") ] if not validate_files: continue + # import pdb; pdb.set_trace() for validate_file in validate_files: + print("carpeta ", validate_file) + # import pdb; pdb.set_trace() + validate_file_path = os.path.join(data_folder["path"], validate_file) with open(validate_file_path) as fh: data = json.load(fh) for item in data: sample = {} + # import pdb; pdb.set_trace() sample["sample_ids"] = item["sequencing_sample_id"] - sample["r1_fastq_file_path"] = item["r1_fastq_file_path"] + sample["r1_fastq_file_path"] = os.path.join( + item["r1_fastq_file_path"], item["sequence_file_R1_fastq"] + ) if "r2_fastq_file_path" in item: - sample["r2_fastq_file_path"] = item["r2_fastq_file_path"] + sample["r2_fastq_file_path"] = os.path.join( + item["r2_fastq_file_path"], item["sequence_file_R2_fastq"] + ) samples_data.append(sample) - log.info("Collecting samples for %s", lab) - stderr.print("[blue] Collecting samples for " + lab) + # import pdb; pdb.set_trace() + lab_code = lab.split("/")[-1] + log.info("Collecting samples for %s", lab_code) + stderr.print("[blue] Collecting samples for ", lab_code) + # import pdb; pdb.set_trace() return samples_data def pipeline_exc(self): From 63d0a88fd8beb33804ebea23a829796c193c0886 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 1 Aug 2024 15:54:38 +0200 Subject: [PATCH 1365/1454] test completed --- relecov_tools/launch_pipeline.py | 114 ++++++++++++++++++------------- 1 file changed, 68 insertions(+), 46 deletions(-) diff --git a/relecov_tools/launch_pipeline.py b/relecov_tools/launch_pipeline.py index 29a4b685..a24cb339 100644 --- a/relecov_tools/launch_pipeline.py +++ b/relecov_tools/launch_pipeline.py @@ -49,12 +49,12 @@ def __init__( stderr.print("[red] Template folder " + self.template + " does not exist") sys.exit(1) if pipeline_conf_file is None: - self.pipeline_conf_file = os.path.join( + pipeline_conf_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "conf", "pipeline_config.json", ) - if not os.path.exists(self.pipeline_conf_file): + if not os.path.exists(pipeline_conf_file): log.error( "Pipeline config file %s does not exist ", self.pipeline_conf_file ) @@ -64,7 +64,7 @@ def __init__( + " does not exist" ) sys.exit(1) - data = relecov_tools.utils.read_json_file(self.pipeline_conf_file) + data = relecov_tools.utils.read_json_file(pipeline_conf_file) if ( not "analysis_name" in data or not "sample_stored_folder" in data @@ -88,6 +88,7 @@ def __init__( stderr.print("[red] Unable to create output folder ", e) sys.exit(1) # Update the output folder with the current date and analysis name + self.output_folder = os.path.join( output_folder, current_date + "_" + data["analysis_name"] ) @@ -97,26 +98,15 @@ def __init__( if confirmation is False: sys.exit(1) shutil.rmtree(self.output_folder) - """ - try: - os.makedirs(self.output_folder, exist_ok = True) - except OSError or FileExistsError as e: - log.error("Unable to create output folder %s ", e) - import pdb; pdb.set_trace() - stderr.print("[red] Unable to create output folder ", e) - sys.exit(1) - """ - self.analysis_name = os.path.join(self.output_folder, data["analysis_name"]) - self.analysis_folder = os.path.join(self.analysis_name, data["analysis_folder"]) + + self.analysis_folder = os.path.join(self.output_folder, data["analysis_folder"]) self.copied_sample_folder = os.path.join( - self.analysis_name, data["sample_stored_folder"] + self.output_folder, data["sample_stored_folder"] ) self.linked_sample_folder = os.path.join( self.analysis_folder, data["sample_link_folder"] ) - self.sample_ids = [] - def join_valid_items(self): def get_latest_lab_folder(self): lab_folders = [f.path for f in os.scandir(self.input_folder) if f.is_dir()] @@ -172,18 +162,14 @@ def get_latest_lab_folder(self): ] if not validate_files: continue - # import pdb; pdb.set_trace() for validate_file in validate_files: - print("carpeta ", validate_file) - # import pdb; pdb.set_trace() validate_file_path = os.path.join(data_folder["path"], validate_file) with open(validate_file_path) as fh: data = json.load(fh) for item in data: sample = {} - # import pdb; pdb.set_trace() - sample["sample_ids"] = item["sequencing_sample_id"] + sample["sequencing_sample_id"] = item["sequencing_sample_id"] sample["r1_fastq_file_path"] = os.path.join( item["r1_fastq_file_path"], item["sequence_file_R1_fastq"] ) @@ -192,44 +178,80 @@ def get_latest_lab_folder(self): item["r2_fastq_file_path"], item["sequence_file_R2_fastq"] ) samples_data.append(sample) - # import pdb; pdb.set_trace() lab_code = lab.split("/")[-1] log.info("Collecting samples for %s", lab_code) stderr.print("[blue] Collecting samples for ", lab_code) - # import pdb; pdb.set_trace() return samples_data def pipeline_exc(self): # copy template folder and subfolders in output folder shutil.copytree(self.template, self.output_folder) + # create the 00_reads folder + os.makedirs(self.linked_sample_folder, exist_ok=True) # collect json with all validated samples samples_data = self.join_valid_items() # iterate over the sample_data to copy the fastq files in the output folder + file_errors = [] + copied_samples = 0 + if len(samples_data) == 0: + stderr.print("[yellow] No samples were found. Deleting analysis folder") + shutil.rmtree(self.analysis_folder) + sys.exit(0) for item in samples_data: - sequencing_r1_sample_id = item["sequencing_sample_id"] + "_R1" + ".fastq.gz" - sequencing_r2_sample_id = item["sequencing_sample_id"] + "_R2" + ".fastq.gz" + + # import pdb; pdb.set_trace() + # fetch the file extension + ext_found = re.match(r".*(fastq.*|bam)", item["r1_fastq_file_path"]) + ext = ext_found.group(1) + sequencing_r1_sample_id = item["sequencing_sample_id"] + "_R1." + ext # join r1_fastq_file_path and sequencing_file_R1_fastq - r1_file_path = os.path.join( + """ r1_file_path = os.path.join( item["r1_fastq_file_path"], item["sequencing_file_R1_fastq"] - ) - # copy sequencing files into the output folder - raw_folder = os.path.join(self.output_folder, self.copied_sample_folder) - shutil.copy(r1_file_path, raw_folder) - # create simlink for the sample - sample_r1_link_path = os.path.join( - self.linked_sample_folder, sequencing_r1_sample_id - ) - os.symlink(r1_file_path, sample_r1_link_path) - if r2_file_path: - sample_r2_link_path = os.path.join( - self.linked_sample_folder, sequencing_r2_sample_id + ) """ + # copy r1 sequencing file into the output folder + # import pdb; pdb.set_trace() + raw_folder = os.path.join(self.analysis_folder, self.copied_sample_folder) + try: + shutil.copy(item["r1_fastq_file_path"], raw_folder) + # create simlink for the r1 + sample_r1_link_path = os.path.join( + self.linked_sample_folder, sequencing_r1_sample_id ) - os.symlink(r2_file_path, sample_r2_link_path) - if "sequencing_file_R2_fastq" in item: - r2_file_path = os.path.join( + os.symlink(item["r1_fastq_file_path"], sample_r1_link_path) + except FileNotFoundError as e: + log.error("File not found %s", e) + # stderr.print("[red] File not found ", e) + file_errors.append(item["r1_fastq_file_path"]) + continue + copied_samples += 1 + # check if there is a r2 file + if item["r2_fastq_file_path"] in item: + sequencing_r2_sample_id = item["sequencing_sample_id"] + "_R2." + ext + """ r2_file_path = os.path.join( item["r2_fastq_file_path"], item["sequencing_file_R2_fastq"] - ) - else: - r2_file_path = None - # copy sequencing files into the output folder + ) """ + try: + shutil.copy(item["r2_fastq_file_path"], raw_folder) + sample_r2_link_path = os.path.join( + self.linked_sample_folder, sequencing_r2_sample_id + ) + os.symlink(item["r2_fastq_file_path"], sample_r2_link_path) + except FileNotFoundError as e: + log.error("File not found %s", e) + # stderr.print("[red] File not found ", e) + file_errors.append(item["r2_fastq_file_path"]) + continue + if len(file_errors) > 0: + stderr.print( + "[red] Files do not found. Unable to copy", + "[red] " + str(len(file_errors)), + "[red]sample files", + ) + msg = "Do you want to delete analysis folder? Y/N" + confirmation = relecov_tools.utils.prompt_yn_question(msg) + if confirmation: + shutil.rmtree(self.output_folder) + sys.exit(1) + stderr.print("[green] Samples copied: ", copied_samples) + stderr.print("[blue] Pipeline launched successfully") From f76e2bb1d617f7e8d3535580053f92e2f4481d75 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 1 Aug 2024 16:01:19 +0200 Subject: [PATCH 1366/1454] Solving that R2 files were not copied --- relecov_tools/launch_pipeline.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/launch_pipeline.py b/relecov_tools/launch_pipeline.py index a24cb339..7489d38c 100644 --- a/relecov_tools/launch_pipeline.py +++ b/relecov_tools/launch_pipeline.py @@ -226,7 +226,7 @@ def pipeline_exc(self): continue copied_samples += 1 # check if there is a r2 file - if item["r2_fastq_file_path"] in item: + if "r2_fastq_file_path" in item: sequencing_r2_sample_id = item["sequencing_sample_id"] + "_R2." + ext """ r2_file_path = os.path.join( item["r2_fastq_file_path"], item["sequencing_file_R2_fastq"] From bfb6ddaf8320e59735866dc2f1d8835a9ace9767 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 1 Aug 2024 16:05:58 +0200 Subject: [PATCH 1367/1454] Correcting litin --- relecov_tools/launch_pipeline.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/relecov_tools/launch_pipeline.py b/relecov_tools/launch_pipeline.py index 7489d38c..812af6ab 100644 --- a/relecov_tools/launch_pipeline.py +++ b/relecov_tools/launch_pipeline.py @@ -66,9 +66,9 @@ def __init__( sys.exit(1) data = relecov_tools.utils.read_json_file(pipeline_conf_file) if ( - not "analysis_name" in data - or not "sample_stored_folder" in data - or not "sample_link_folder" in data + "analysis_name" not in data + or "sample_stored_folder" not in data + or "sample_link_folder" not in data ): log.error("Invalid pipeline config file %s ", self.pipeline_conf_file) stderr.print( From dcc6d54d7aed95337b501c142f1da2c9693ab3a2 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 8 Aug 2024 13:16:28 +0200 Subject: [PATCH 1368/1454] Update relecov_tools/conf/pipeline_config.json MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Sara Monzón --- relecov_tools/conf/pipeline_config.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/conf/pipeline_config.json b/relecov_tools/conf/pipeline_config.json index bef0b460..fb30f033 100644 --- a/relecov_tools/conf/pipeline_config.json +++ b/relecov_tools/conf/pipeline_config.json @@ -2,5 +2,5 @@ "analysis_name" : "RELECOV_icasas_C", "analysis_folder" : "ANALYSIS", "sample_stored_folder" : "RAW", - "sample_link_folder" : "00_reads" + "sample_link_folder" : "00-reads" } From 23fa2f756c247c8ca908e4ffd79698c66a632f6c Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 12 Aug 2024 16:27:31 +0200 Subject: [PATCH 1369/1454] pipeline config data are inclued in configuration.json file --- relecov_tools/conf/configuration.json | 6 ++++++ relecov_tools/conf/pipeline_config.json | 6 ------ relecov_tools/launch_pipeline.py | 5 +++-- 3 files changed, 9 insertions(+), 8 deletions(-) delete mode 100644 relecov_tools/conf/pipeline_config.json diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 52598f4b..84503966 100755 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -439,5 +439,11 @@ "fastq_r2_md5" ] } + }, + "launch_pipeline": { + "analysis_name": "RELECOV_icasas_C", + "analysis_folder": "ANALYSIS", + "sample_stored_folder": "RAW", + "sample_link_folder": "00-reads" } } diff --git a/relecov_tools/conf/pipeline_config.json b/relecov_tools/conf/pipeline_config.json deleted file mode 100644 index fb30f033..00000000 --- a/relecov_tools/conf/pipeline_config.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "analysis_name" : "RELECOV_icasas_C", - "analysis_folder" : "ANALYSIS", - "sample_stored_folder" : "RAW", - "sample_link_folder" : "00-reads" -} diff --git a/relecov_tools/launch_pipeline.py b/relecov_tools/launch_pipeline.py index 812af6ab..8b797c9e 100644 --- a/relecov_tools/launch_pipeline.py +++ b/relecov_tools/launch_pipeline.py @@ -52,7 +52,7 @@ def __init__( pipeline_conf_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), "conf", - "pipeline_config.json", + "configuration.json", ) if not os.path.exists(pipeline_conf_file): log.error( @@ -64,7 +64,8 @@ def __init__( + " does not exist" ) sys.exit(1) - data = relecov_tools.utils.read_json_file(pipeline_conf_file) + conf_settings = relecov_tools.utils.read_json_file(pipeline_conf_file) + data = conf_settings["pipeline_launch"] if ( "analysis_name" not in data or "sample_stored_folder" not in data From 4e987cf60168decf27f1afcb47880a82b47df08e Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 12 Aug 2024 16:36:52 +0200 Subject: [PATCH 1370/1454] remove unnecesary coments --- relecov_tools/launch_pipeline.py | 16 +--------------- 1 file changed, 1 insertion(+), 15 deletions(-) diff --git a/relecov_tools/launch_pipeline.py b/relecov_tools/launch_pipeline.py index 8b797c9e..1c7c06fb 100644 --- a/relecov_tools/launch_pipeline.py +++ b/relecov_tools/launch_pipeline.py @@ -134,7 +134,6 @@ def get_latest_lab_folder(self): continue if sub_f_date > last_folder_date: last_folder_date = sub_f_date - # latest_folder_name = os.path.join(lab_sub_folder, f_name) latest_folder_name = lab_sub_folder existing_upload_folders = True if existing_upload_folders: @@ -155,7 +154,6 @@ def get_latest_lab_folder(self): if data_folder["date"] != latest_date: continue # fetch the validate file and get sample id and r1 and r2 file path - validate_files = [ os.path.join(data_folder["path"], f) for f in os.listdir(data_folder["path"]) @@ -164,7 +162,6 @@ def get_latest_lab_folder(self): if not validate_files: continue for validate_file in validate_files: - validate_file_path = os.path.join(data_folder["path"], validate_file) with open(validate_file_path) as fh: data = json.load(fh) @@ -200,18 +197,11 @@ def pipeline_exc(self): shutil.rmtree(self.analysis_folder) sys.exit(0) for item in samples_data: - - # import pdb; pdb.set_trace() # fetch the file extension ext_found = re.match(r".*(fastq.*|bam)", item["r1_fastq_file_path"]) ext = ext_found.group(1) sequencing_r1_sample_id = item["sequencing_sample_id"] + "_R1." + ext - # join r1_fastq_file_path and sequencing_file_R1_fastq - """ r1_file_path = os.path.join( - item["r1_fastq_file_path"], item["sequencing_file_R1_fastq"] - ) """ # copy r1 sequencing file into the output folder - # import pdb; pdb.set_trace() raw_folder = os.path.join(self.analysis_folder, self.copied_sample_folder) try: shutil.copy(item["r1_fastq_file_path"], raw_folder) @@ -222,16 +212,12 @@ def pipeline_exc(self): os.symlink(item["r1_fastq_file_path"], sample_r1_link_path) except FileNotFoundError as e: log.error("File not found %s", e) - # stderr.print("[red] File not found ", e) file_errors.append(item["r1_fastq_file_path"]) continue copied_samples += 1 # check if there is a r2 file if "r2_fastq_file_path" in item: sequencing_r2_sample_id = item["sequencing_sample_id"] + "_R2." + ext - """ r2_file_path = os.path.join( - item["r2_fastq_file_path"], item["sequencing_file_R2_fastq"] - ) """ try: shutil.copy(item["r2_fastq_file_path"], raw_folder) sample_r2_link_path = os.path.join( @@ -240,7 +226,6 @@ def pipeline_exc(self): os.symlink(item["r2_fastq_file_path"], sample_r2_link_path) except FileNotFoundError as e: log.error("File not found %s", e) - # stderr.print("[red] File not found ", e) file_errors.append(item["r2_fastq_file_path"]) continue if len(file_errors) > 0: @@ -256,3 +241,4 @@ def pipeline_exc(self): sys.exit(1) stderr.print("[green] Samples copied: ", copied_samples) stderr.print("[blue] Pipeline launched successfully") + return From 43d636fc87661a4f8089e321494e6396279fd4ce Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 14 Aug 2024 17:32:24 +0200 Subject: [PATCH 1371/1454] Change name of pipeline manager --- relecov_tools/__main__.py | 2 +- relecov_tools/pipeline_manager.py | 288 ++++++++++++++++++++++++++++++ 2 files changed, 289 insertions(+), 1 deletion(-) create mode 100644 relecov_tools/pipeline_manager.py diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 026cedf2..11558983 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -20,7 +20,7 @@ import relecov_tools.metadata_homogeneizer import relecov_tools.gisaid_upload import relecov_tools.upload_ena_protocol -import relecov_tools.launch_pipeline +import relecov_tools.pipeline_manager log = logging.getLogger() diff --git a/relecov_tools/pipeline_manager.py b/relecov_tools/pipeline_manager.py new file mode 100644 index 00000000..7888407c --- /dev/null +++ b/relecov_tools/pipeline_manager.py @@ -0,0 +1,288 @@ +import json +import re +import os +import sys +import shutil +import datetime +import logging +import rich.console + +import relecov_tools.utils + + +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + + +class LaunchPipeline: + def __init__( + self, + input_folder=None, + template=None, + output_folder=None, + pipeline_conf_file=None, + ): + current_date = datetime.date.today().strftime("%Y%m%d") + if input_folder is None: + self.input_folder = relecov_tools.utils.prompt_path( + msg="Select the folder which contains the fastq file of samples" + ) + else: + self.input_folder = input_folder + if not os.path.exists(self.input_folder): + log.error("Input folder %s does not exist ", self.input_folder) + stderr.print("[red] Input folder " + self.input_folder + " does not exist") + sys.exit(1) + if template is None: + self.template = relecov_tools.utils.prompt_path( + msg="Select the path which contains the template structure" + ) + else: + self.template = template + if not os.path.exists(self.template): + log.error("Template folder %s does not exist ", self.template) + stderr.print("[red] Template folder " + self.template + " does not exist") + sys.exit(1) + if pipeline_conf_file is None: + pipeline_conf_file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), + "conf", + "configuration.json", + ) + if not os.path.exists(pipeline_conf_file): + log.error( + "Pipeline config file %s does not exist ", self.pipeline_conf_file + ) + stderr.print( + "[red] Pipeline config file " + + self.pipeline_conf_file + + " does not exist" + ) + sys.exit(1) + conf_settings = relecov_tools.utils.read_json_file(pipeline_conf_file) + try: + data = conf_settings["pipelines"]["relecov"] + except KeyError: + log.error("Invalid pipeline config file %s ", self.pipeline_conf_file) + stderr.print( + "[red] Invalid pipeline config file " + self.pipeline_conf_file + ) + if ( + "analysis_name" not in data + or "sample_stored_folder" not in data + or "sample_link_folder" not in data + ): + log.error("Invalid pipeline config file %s ", self.pipeline_conf_file) + stderr.print( + "[red] Invalid pipeline config file " + self.pipeline_conf_file + ) + sys.exit(1) + + if output_folder is None: + output_folder = relecov_tools.utils.prompt_path( + msg="Select the output folder" + ) + # Create the output folder if not exists + try: + os.makedirs(output_folder, exist_ok=True) + except OSError or FileExistsError as e: + log.error("Unable to create output folder %s ", e) + stderr.print("[red] Unable to create output folder ", e) + sys.exit(1) + # Update the output folder with the current date and analysis name + + self.output_folder = os.path.join( + output_folder, current_date + "_" + data["analysis_name"] + ) + if os.path.exists(self.output_folder): + msg = "Analysis folder already exists and it will be deleted. Do you want to continue? Y/N" + confirmation = relecov_tools.utils.prompt_yn_question(msg) + if confirmation is False: + sys.exit(1) + shutil.rmtree(self.output_folder) + + self.analysis_folder = os.path.join(self.output_folder, data["analysis_folder"]) + self.copied_sample_folder = os.path.join( + self.output_folder, data["sample_stored_folder"] + ) + self.linked_sample_folder = os.path.join( + self.analysis_folder, data["sample_link_folder"] + ) + + def join_valid_items(self): + def get_latest_lab_folder(self): + lab_folders = [f.path for f in os.scandir(self.input_folder) if f.is_dir()] + lab_latest_folders = {} + latest_date = datetime.datetime.strptime("20220101", "%Y%m%d").date() + for lab_folder in lab_folders: + existing_upload_folders = False + last_folder_date = datetime.datetime.strptime( + "20220101", "%Y%m%d" + ).date() + scan_folder = os.path.join(self.input_folder, lab_folder) + lab_sub_folders = [ + f.path for f in os.scandir(scan_folder) if f.is_dir() + ] + for lab_sub_folder in lab_sub_folders: + f_name = os.path.basename(lab_sub_folder) + f_date_match = re.match(r"(^\d{8}).*", f_name) + if not f_date_match: + continue + f_date = f_date_match.group(1) + try: + sub_f_date = datetime.datetime.strptime(f_date, "%Y%m%d").date() + except ValueError: + continue + if sub_f_date > last_folder_date: + last_folder_date = sub_f_date + latest_folder_name = lab_sub_folder + existing_upload_folders = True + if existing_upload_folders: + lab_latest_folders[lab_folder] = { + "path": latest_folder_name, + "date": last_folder_date, + } + if last_folder_date > latest_date: + latest_date = last_folder_date + log.info("Latest date to process is %s", latest_date) + stderr.print("[blue] Collecting samples from ", latest_date) + return lab_latest_folders, latest_date + + upload_lab_folders, latest_date = get_latest_lab_folder(self) + samples_data = [] + for lab, data_folder in upload_lab_folders.items(): + # check if laboratory folder is the latest date to process + if data_folder["date"] != latest_date: + continue + # fetch the validate file and get sample id and r1 and r2 file path + validate_files = [ + os.path.join(data_folder["path"], f) + for f in os.listdir(data_folder["path"]) + if f.startswith("validated_processed_metadata") and f.endswith(".json") + ] + if not validate_files: + continue + for validate_file in validate_files: + validate_file_path = os.path.join(data_folder["path"], validate_file) + with open(validate_file_path) as fh: + data = json.load(fh) + for item in data: + sample = {} + sample["sequencing_sample_id"] = item["sequencing_sample_id"] + sample["r1_fastq_file_path"] = os.path.join( + item["r1_fastq_file_path"], item["sequence_file_R1_fastq"] + ) + if "r2_fastq_file_path" in item: + sample["r2_fastq_file_path"] = os.path.join( + item["r2_fastq_file_path"], item["sequence_file_R2_fastq"] + ) + samples_data.append(sample) + lab_code = lab.split("/")[-1] + log.info("Collecting samples for %s", lab_code) + stderr.print("[blue] Collecting samples for ", lab_code) + return samples_data + + def pipeline_exc(self): + # copy template folder and subfolders in output folder + shutil.copytree(self.template, self.output_folder) + # create the 00_reads folder + os.makedirs(self.linked_sample_folder, exist_ok=True) + # collect json with all validated samples + samples_data = self.join_valid_items() + + # iterate over the sample_data to copy the fastq files in the output folder + file_errors = [] + copied_samples = 0 + if len(samples_data) == 0: + stderr.print("[yellow] No samples were found. Deleting analysis folder") + shutil.rmtree(self.analysis_folder) + sys.exit(0) + for item in samples_data: + # fetch the file extension + ext_found = re.match(r".*(fastq.*|bam)", item["r1_fastq_file_path"]) + ext = ext_found.group(1) + sequencing_r1_sample_id = item["sequencing_sample_id"] + "_R1." + ext + # copy r1 sequencing file into the output folder + raw_folder = os.path.join(self.analysis_folder, self.copied_sample_folder) + try: + shutil.copy(item["r1_fastq_file_path"], raw_folder) + # create simlink for the r1 + sample_r1_link_path = os.path.join( + self.linked_sample_folder, sequencing_r1_sample_id + ) + os.symlink(item["r1_fastq_file_path"], sample_r1_link_path) + except FileNotFoundError as e: + log.error("File not found %s", e) + file_errors.append(item["r1_fastq_file_path"]) + continue + copied_samples += 1 + # check if there is a r2 file + if "r2_fastq_file_path" in item: + sequencing_r2_sample_id = item["sequencing_sample_id"] + "_R2." + ext + try: + shutil.copy(item["r2_fastq_file_path"], raw_folder) + sample_r2_link_path = os.path.join( + self.linked_sample_folder, sequencing_r2_sample_id + ) + os.symlink(item["r2_fastq_file_path"], sample_r2_link_path) + except FileNotFoundError as e: + log.error("File not found %s", e) + file_errors.append(item["r2_fastq_file_path"]) + continue + if len(file_errors) > 0: + stderr.print( + "[red] Files do not found. Unable to copy", + "[red] " + str(len(file_errors)), + "[red]sample files", + ) + msg = "Do you want to delete analysis folder? Y/N" + confirmation = relecov_tools.utils.prompt_yn_question(msg) + if confirmation: + shutil.rmtree(self.output_folder) + sys.exit(1) + stderr.print("[green] Samples copied: ", copied_samples) + stderr.print("[blue] Pipeline launched successfully") + return + + +class ResultUpload: + def __init__(self, input_folder=None, conf_file=None): + if input_folder is None: + self.input_folder = relecov_tools.utils.prompt_path( + msg="Select the folder which contains the results" + ) + else: + self.input_folder = input_folder + if not os.path.exists(self.input_folder): + log.error("Input folder %s does not exist ", self.input_folder) + stderr.print("[red] Input folder " + self.input_folder + " does not exist") + sys.exit(1) + + conf_file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), + "conf", + "configuration.json", + ) + if not os.path.exists(conf_file): + log.error( + "Configuration file %s does not exist ", self.conf_file + ) + stderr.print( + "[red] Pipeline config file " + + self.pipeline_conf_file + + " does not exist" + ) + sys.exit(1) + conf_settings = relecov_tools.utils.read_json_file(conf_file) + try: + data = conf_settings["pipelines"]["relecov"] + except KeyError: + log.error("Invalid pipeline config file %s ", self.pipeline_conf_file) + stderr.print( + "[red] Invalid pipeline config file " + self.pipeline_conf_file + ) \ No newline at end of file From 8333114e0947430dccfc8a00256ff89b20ee0a1c Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 20 Aug 2024 13:44:52 +0200 Subject: [PATCH 1372/1454] update the main to rename module --- relecov_tools/__main__.py | 13 ++++--------- .../{sftp_handle.py => download_manager.py} | 0 2 files changed, 4 insertions(+), 9 deletions(-) rename relecov_tools/{sftp_handle.py => download_manager.py} (100%) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 11558983..226f4ad2 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -5,6 +5,7 @@ # from rich.prompt import Confirm import click +import relecov_tools.download_manager import rich.console import rich.logging import rich.traceback @@ -12,7 +13,7 @@ import relecov_tools.utils import relecov_tools.assets.pipeline_utils.viralrecon import relecov_tools.read_lab_metadata -import relecov_tools.sftp_handle +import relecov_tools.download_manager import relecov_tools.json_validation import relecov_tools.map_schema import relecov_tools.feed_database @@ -135,8 +136,6 @@ def relecov_tools_cli(verbose, log_file): @relecov_tools_cli.command(help_priority=2) @click.option("-u", "--user", help="User name for login to sftp server") @click.option("-p", "--password", help="password for the user to login") -@click.option("-r_u", "--user_relecov", help="User name for updating data to relecov") -@click.option("-p_r", "--password_relecov", help="password for relecov user") @click.option( "-f", "--conf_file", @@ -170,24 +169,20 @@ def download( user, password, conf_file, - user_relecov, - password_relecov, download_option, output_location, target_folders, ): """Download files located in sftp server.""" - sftp_connection = relecov_tools.sftp_handle.SftpHandle( + download_manager = relecov_tools.download_manager.DownloadManager( user, password, conf_file, - user_relecov, - password_relecov, download_option, output_location, target_folders, ) - sftp_connection.execute_process() + download_manager.execute_process() # metadata diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/download_manager.py similarity index 100% rename from relecov_tools/sftp_handle.py rename to relecov_tools/download_manager.py From 9853928766cf411756e5b760be08647dad368735 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 20 Aug 2024 16:40:35 +0200 Subject: [PATCH 1373/1454] create sftp class --- relecov_tools/download_manager.py | 46 ++++++++------ relecov_tools/sftp_client.py | 102 ++++++++++++++++++++++++++++++ 2 files changed, 128 insertions(+), 20 deletions(-) create mode 100644 relecov_tools/sftp_client.py diff --git a/relecov_tools/download_manager.py b/relecov_tools/download_manager.py index 4437afbb..4dfc3c1e 100755 --- a/relecov_tools/download_manager.py +++ b/relecov_tools/download_manager.py @@ -10,6 +10,7 @@ import rich.console import paramiko import relecov_tools.utils +import relecov_tools.sftp from datetime import datetime from itertools import islice from secrets import token_hex @@ -20,6 +21,7 @@ from relecov_tools.config_json import ConfigJson from relecov_tools.log_summary import LogSum + # from relecov_tools.rest_api import RestApi log = logging.getLogger(__name__) @@ -36,14 +38,12 @@ def __init__(self, message): super().__init__(message) -class SftpHandle: +class DownloadManager: def __init__( self, user=None, passwd=None, conf_file=None, - user_relecov=None, - password_relecov=None, download_option=None, output_location=None, target_folders=None, @@ -53,8 +53,8 @@ def __init__( self.allowed_file_ext = config_json.get_topic_data( "sftp_handle", "allowed_file_extensions" ) - self.sftp_user = user - self.sftp_passwd = passwd + sftp_user = user + sftp_passwd = passwd self.target_folders = target_folders self.allowed_download_options = config_json.get_topic_data( "sftp_handle", "allowed_download_options" @@ -66,8 +66,8 @@ def __init__( else: self.download_option = download_option if conf_file is None: - self.sftp_server = config_json.get_topic_data("sftp_handle", "sftp_server") - self.sftp_port = config_json.get_topic_data("sftp_handle", "sftp_port") + # self.sftp_server = config_json.get_topic_data("sftp_handle", "sftp_server") + # self.sftp_port = config_json.get_topic_data("sftp_handle", "sftp_port") self.platform_storage_folder = config_json.get_topic_data( "sftp_handle", "platform_storage_folder" ) @@ -87,8 +87,8 @@ def __init__( with open(conf_file, "r") as fh: config = yaml.load(fh, Loader=yaml.FullLoader) try: - self.sftp_server = config["sftp_server"] - self.sftp_port = config["sftp_port"] + # self.sftp_server = config["sftp_server"] + # self.sftp_port = config["sftp_port"] self.target_folders = config["target_folders"] try: self.platform_storage_folder = config["platform_storage_folder"] @@ -96,8 +96,8 @@ def __init__( self.platform_storage_folder = config_json.get_topic_data( "sftp_handle", "platform_storage_folder" ) - self.sftp_user = config["sftp_user"] - self.sftp_passwd = config["sftp_passwd"] + sftp_user = config["sftp_user"] + sftp_passwd = config["sftp_passwd"] except KeyError as e: log.error("Invalid configuration file %s", e) stderr.print(f"[red] Invalid configuration file {e} !") @@ -109,13 +109,13 @@ def __init__( log.error("Output location does not exist, aborting") stderr.print("[red] Output location does not exist, aborting") sys.exit(1) - if self.sftp_user is None: - self.sftp_user = relecov_tools.utils.prompt_text(msg="Enter the user id") + if sftp_user is None: + sftp_user = relecov_tools.utils.prompt_text(msg="Enter the user id") if isinstance(self.target_folders, str): self.target_folders = self.target_folders.split(",") self.logsum = LogSum(output_location=self.platform_storage_folder) - if self.sftp_passwd is None: - self.sftp_passwd = relecov_tools.utils.prompt_password( + if sftp_passwd is None: + sftp_passwd = relecov_tools.utils.prompt_password( msg="Enter your password" ) self.metadata_lab_heading = config_json.get_topic_data( @@ -130,9 +130,12 @@ def __init__( self.samples_json_fields = config_json.get_topic_data( "lab_metadata", "samples_json_fields" ) + # initialize the sftp client + self.my_sftp = relecov_tools.sftp.SftpRelecov(conf_file, sftp_user, sftp_passwd) + import pdb; pdb.set_trace() - def open_connection(self): - """Establishing sftp connection""" + """ def open_connection(self): + ""Establishing sftp connection"" log.info("Setting credentials for SFTP connection with remote server") self.client = paramiko.SSHClient() self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) @@ -153,13 +156,13 @@ def open_connection(self): return False def close_connection(self): - """Closes SFTP connection""" + ""Closes SFTP connection"" log.info("Closing SFTP connection") try: self.client.close() except NameError: return False - return True + return True """ def list_remote_folders(self, folder_name, recursive=False): """Creates a directories list from the given client remote path @@ -1313,7 +1316,10 @@ def include_warning(self, entry, sample=None): def execute_process(self): """Executes different processes depending on the download_option""" - if not self.open_connection(): + import pdb; pdb.set_trace() + # self.sftp_client.open_connection() + self.my_sftp.list_folders(".") + if not self.sftp_client.open_connection(): log.error("Unable to establish connection towards sftp server") stderr.print("[red]Unable to establish sftp connection") sys.exit(1) diff --git a/relecov_tools/sftp_client.py b/relecov_tools/sftp_client.py new file mode 100644 index 00000000..5fa1f375 --- /dev/null +++ b/relecov_tools/sftp_client.py @@ -0,0 +1,102 @@ +import logging +import os +import paramiko +import rich.console +import sys +from relecov_tools.config_json import ConfigJson +import relecov_tools.utils + +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + + +class SftpRelecov: + """Class to handle SFTP connection with remote server. It uses paramiko library to establish + the connection. The class can be used to upload and download files from the remote server. + The class can be initialized with a configuration file and with the username and password. + If the configuration file is not provided, the class will try to read the configuration from + the environment variables. If configuration file is provided, the class will read the + configuration from the file. The format of the configuration file should be a json file with + the following keys: + { + "sftp_server": "server_name", + "sftp_port": "port_number" + } + """ + def __init__(self, conf_file=None, username=None, password=None): + if conf_file is None: + config_json = ConfigJson() + self.sftp_server = config_json.get_topic_data("sftp_handle", "sftp_server") + self.sftp_port = config_json.get_topic_data("sftp_handle", "sftp_port") + else: + config_json = conf_file + if not os.path.isfile(conf_file): + log.error("Configuration file %s does not exists", conf_file) + stderr.print( + "[red] Configuration file does not exist. " + conf_file + "!" + ) + sys.exit(1) + j_data = relecov_tools.utils.read_json_file(conf_file) + try: + self.sftp_server = j_data["sftp_server"] + self.sftp_port = j_data["sftp_port"] + except KeyError as e: + log.error("Could not find the key %s in the config file", e) + stderr.print( + "[red] Could not find the key " + e + "in config file " + conf_file + ) + sys.exit(1) + self.user_name = username + self.password = password + self.client = paramiko.SSHClient() + self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) + + def open_connection(self): + """Establishing sftp connection""" + log.info("Setting credentials for SFTP connection with remote server") + self.client.connect( + hostname=self.sftp_server, + port=self.sftp_port, + username=self.user_name, + password=self.password, + allow_agent=False, + look_for_keys=False, + ) + try: + log.info("Trying to establish SFTP connection") + self.sftp = self.client.open_sftp() + except Exception as e: + log.error("Could not establish SFTP connection: %s", e) + stderr.print("[red]Could not establish SFTP connection") + return False + return True + + def list_folders(self, remote_path): + self.open_connection() + """List all the folders in the remote path""" + log.info("Listing folders in the remote path %s", remote_path) + try: + folders = self.sftp.listdir(remote_path) + except FileNotFoundError: + log.error("Remote path %s does not exist", remote_path) + stderr.print("[red]Remote path does not exist") + return None + return folders + + def pepe(self, pepe): + print(pepe) + + def close_connection(self): + log.info("Closing SFTP connection") + try: + self.sftp.close() + self.client.close() + except NameError: + return False + log.info("SFTP connection closed") + return True From 1ea2027ab1594df7fbc08f678732704efa265afe Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 20 Aug 2024 18:20:44 +0200 Subject: [PATCH 1374/1454] splited the sftp funtionalaity to another class --- relecov_tools/download_manager.py | 176 +++++------------------------- relecov_tools/sftp_client.py | 155 +++++++++++++++++++++++--- 2 files changed, 169 insertions(+), 162 deletions(-) diff --git a/relecov_tools/download_manager.py b/relecov_tools/download_manager.py index 4dfc3c1e..17c9d32e 100755 --- a/relecov_tools/download_manager.py +++ b/relecov_tools/download_manager.py @@ -10,7 +10,7 @@ import rich.console import paramiko import relecov_tools.utils -import relecov_tools.sftp +import relecov_tools.sftp_client from datetime import datetime from itertools import islice from secrets import token_hex @@ -131,127 +131,7 @@ def __init__( "lab_metadata", "samples_json_fields" ) # initialize the sftp client - self.my_sftp = relecov_tools.sftp.SftpRelecov(conf_file, sftp_user, sftp_passwd) - import pdb; pdb.set_trace() - - """ def open_connection(self): - ""Establishing sftp connection"" - log.info("Setting credentials for SFTP connection with remote server") - self.client = paramiko.SSHClient() - self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) - self.client.connect( - hostname=self.sftp_server, - port=self.sftp_port, - username=self.sftp_user, - password=self.sftp_passwd, - allow_agent=False, - look_for_keys=False, - ) - try: - log.info("Trying to establish SFTP connection") - self.client = self.client.open_sftp() - return True - except paramiko.SSHException as e: - log.error("Invalid Username/Password for %s:", e) - return False - - def close_connection(self): - ""Closes SFTP connection"" - log.info("Closing SFTP connection") - try: - self.client.close() - except NameError: - return False - return True """ - - def list_remote_folders(self, folder_name, recursive=False): - """Creates a directories list from the given client remote path - - Args: - folder_name (str): folder name in remote path - recursive (bool, optional): finds all subdirectories too. Defaults to False. - - Returns: - directory_list(list(str)): Names of all folders within remote folder - """ - log.info("Listing directories in %s", folder_name) - directory_list = [] - try: - content_list = self.client.listdir_attr(folder_name) - subfolders = any(stat.S_ISDIR(item.st_mode) for item in content_list) - except (FileNotFoundError, OSError) as e: - log.error("Invalid folder at remote sftp %s", e) - raise - if not subfolders: - return [folder_name] - - def recursive_list(folder_name): - try: - attribute_list = self.client.listdir_attr(folder_name) - except (FileNotFoundError, OSError) as e: - log.error("Invalid folder at remote sftp %s", e) - raise - for attribute in attribute_list: - if stat.S_ISDIR(attribute.st_mode): - abspath = os.path.join(folder_name, attribute.filename) - directory_list.append(abspath) - recursive_list(abspath) - else: - continue - return directory_list - - if recursive: - directory_list = recursive_list(folder_name) - if folder_name != ".": - directory_list.append(folder_name) - return directory_list - try: - directory_list = [ - item.filename for item in content_list if stat.S_ISDIR(item.st_mode) - ] - except AttributeError: - return False - return directory_list - - def get_file_list(self, folder_name): - """Return a tuple with file name and directory path from remote - - Args: - folder_name (str): name of folder in remote repository - - Returns: - file_list (list(str)): list of files in remote folder - """ - log.info("Listing files in %s", folder_name) - file_list = [] - content_list = self.client.listdir_attr(folder_name) - file_list = [ - os.path.join(folder_name, content.filename) - for content in content_list - if stat.S_ISREG(content.st_mode) - ] - return file_list - - def get_from_sftp(self, file, destination, exist_ok=False): - """Download a file from remote sftp - - Args: - file (str): path of the file in remote sftp - destination (str): local path of the file after download - exist_ok (bool): Skip download if file exists in local destination - - Returns: - bool: True if download was successful, False if it was not - """ - if os.path.exists(destination) and exist_ok: - return True - else: - try: - self.client.get(file, destination) - return True - except FileNotFoundError as e: - log.error("Unable to fetch file %s ", e) - return False + self.relecov_sftp = relecov_tools.sftp_client.SftpRelecov(conf_file, sftp_user, sftp_passwd) def create_local_folder(self, folder): """Create folder to download files in local path using date @@ -292,12 +172,12 @@ def get_remote_folder_files(self, folder, local_folder, file_list): for file in file_list: file_to_fetch = os.path.join(folder, os.path.basename(file)) output_file = os.path.join(local_folder, os.path.basename(file)) - if self.get_from_sftp(file_to_fetch, output_file, exist_ok=True): + if self.relecov_sftp.get_from_sftp(file_to_fetch, output_file, exist_ok=True): fetched_files.append(os.path.basename(file)) else: # Try to download again n times for _ in range(3): - if self.get_from_sftp(file_to_fetch, output_file): + if self.relecov_sftp.get_from_sftp(file_to_fetch, output_file): fetched_files.append(os.path.basename(file)) break else: @@ -314,7 +194,7 @@ def find_remote_md5sum(self, folder, pattern="md5sum"): Returns: md5_file(str): file basename if found. If not found returns False """ - all_files = self.get_file_list(folder) + all_files = self.relecov_sftp.get_file_list(folder) md5_file = [file for file in all_files if pattern in file] if len(md5_file) == 1: return md5_file[0] @@ -555,7 +435,7 @@ def get_metadata_file(self, remote_folder, local_folder): Returns: local_meta_file: Path to downloaded metadata file / merged metadata file. """ - remote_files_list = self.get_file_list(remote_folder) + remote_files_list = self.relecov_sftp.get_file_list(remote_folder) meta_files = [fi for fi in remote_files_list if fi.endswith(".xlsx")] def download_remote_metafile(target_meta_file): @@ -563,7 +443,7 @@ def download_remote_metafile(target_meta_file): local_folder, os.path.basename(target_meta_file) ) try: - self.get_from_sftp(target_meta_file, local_meta_file) + self.relecov_sftp.get_from_sftp(target_meta_file, local_meta_file) except (IOError, PermissionError) as e: raise type(e)(f"[red]Unable to fetch metadata file {e}") log.info( @@ -634,7 +514,7 @@ def validate_remote_files(self, remote_folder, local_folder): out_folder = os.path.dirname(local_meta_file) allowed_extensions = self.allowed_file_ext remote_files_list = [ - os.path.basename(file) for file in self.get_file_list(remote_folder) + os.path.basename(file) for file in self.relecov_sftp.get_file_list(remote_folder) ] filtered_files_list = sorted( [fi for fi in remote_files_list if fi.endswith(tuple(allowed_extensions))] @@ -686,7 +566,7 @@ def delete_remote_files(self, remote_folder, files=None, skip_seqs=False): """ stderr.print(f"[blue]Deleting files in remote {remote_folder}...") if files is None: - files_to_remove = self.get_file_list(remote_folder) + files_to_remove = self.relecov_sftp.get_file_list(remote_folder) else: files_to_remove = files if any(file.endswith(tuple(self.allowed_file_ext)) for file in files_to_remove): @@ -696,7 +576,7 @@ def delete_remote_files(self, remote_folder, files=None, skip_seqs=False): return for file in files_to_remove: try: - self.client.remove(os.path.join(remote_folder, os.path.basename(file))) + self.relecov_sftp.remove(os.path.join(remote_folder, os.path.basename(file))) log.info("%s Deleted from remote server", file) except (IOError, PermissionError) as e: self.include_warning(f"Could not delete remote file {file}: {e}") @@ -715,7 +595,7 @@ def remove_client_dir(remote_folder): if len(remote_folder.replace("./", "").split("/")) >= 2: log.info("Trying to remove %s", remote_folder) try: - self.client.rmdir(remote_folder) + self.relecov_sftp.rmdir(remote_folder) log.info("Successfully removed %s", remote_folder) except (OSError, PermissionError) as e: log_text = f"Could not delete remote {remote_folder}. Error: {e}" @@ -724,7 +604,7 @@ def remove_client_dir(remote_folder): else: log.info("%s is a top-level folder. Not removed", remote_folder) - remote_folder_files = self.get_file_list(remote_folder) + remote_folder_files = self.relecov_sftp.get_file_list(remote_folder) if remote_folder_files: log_text = f"Remote folder {remote_folder} not empty. Not removed" self.include_warning(log_text) @@ -752,7 +632,7 @@ def move_processing_fastqs(self, folders_with_metadata): file_dest = os.path.join(folder, os.path.basename(file)) try: # Paramiko.SSHClient.sftp_open does not have a method to copy files - self.client.rename(file, file_dest) + self.relecov_sftp.rename_file(file, file_dest) successful_files.append(file_dest) except OSError: if file in folders_with_metadata[folder]: @@ -801,7 +681,7 @@ def md5_handler(md5sumlist, output_location): for md5sum in md5sumlist: md5_name = "_".join([token_hex(nbytes=12), "md5_temp.md5"]) fetched_md5 = os.path.join(output_location, md5_name) - if self.get_from_sftp(file=md5sum, destination=fetched_md5): + if self.relecov_sftp.get_from_sftp(file=md5sum, destination=fetched_md5): downloaded_md5files.append(fetched_md5) merged_md5 = md5_merger(downloaded_md5files, self.avoidable_characters) if merged_md5: @@ -811,7 +691,7 @@ def md5_handler(md5sumlist, output_location): write_md5 = csv_writer(md5out, delimiter="\t") write_md5.writerows(merged_md5.items()) md5_dest = os.path.join(folder, os.path.basename(merged_md5_path)) - self.client.put(localpath=merged_md5_path, remotepath=md5_dest) + self.relecov_sftp.upload_file(merged_md5_path, md5_dest) # Remove local files once merged and uploaded os.remove(merged_md5_path) [os.remove(md5_file) for md5_file in downloaded_md5files] @@ -917,7 +797,7 @@ def merge_subfolders(self, target_folders): def upload_merged_df(merged_excel_path, last_main_folder, merged_df): """Upload metadata dataframe merged from all subfolders back to sftp""" - self.client.mkdir(last_main_folder) + self.relecov_sftp.make_dir(last_main_folder) pd_writer = ExcelWriter(merged_excel_path, engine="xlsxwriter") for sheet in merged_df.keys(): format_sheet = merged_df[sheet].astype(str) @@ -925,7 +805,7 @@ def upload_merged_df(merged_excel_path, last_main_folder, merged_df): format_sheet.to_excel(pd_writer, sheet_name=sheet, index=False) pd_writer.close() dest = os.path.join(last_main_folder, os.path.basename(merged_excel_path)) - self.client.put(merged_excel_path, dest) + self.relecov_sftp.upload_file(merged_excel_path, dest) os.remove(merged_excel_path) return @@ -1033,7 +913,7 @@ def select_target_folders(self): Returns: folders_to_process (dict(str:list)): Dictionary with folders and their files """ - root_directory_list = self.list_remote_folders(".", recursive=True) + root_directory_list = self.relecov_sftp.list_remote_folders(".", recursive=True) clean_root_list = [folder.replace("./", "") for folder in root_directory_list] if not root_directory_list: log.error("Error while listing folders in remote. Aborting") @@ -1056,12 +936,12 @@ def select_target_folders(self): folders_to_process = {} for targeted_folder in target_folders: try: - full_folders = self.list_remote_folders(targeted_folder, recursive=True) + full_folders = self.relecov_sftp.list_remote_folders(targeted_folder, recursive=True) except (FileNotFoundError, OSError) as e: log.error(f"Error during sftp listing. {targeted_folder} skipped:", e) continue for folder in full_folders: - list_files = self.get_file_list(folder) + list_files = self.relecov_sftp.get_file_list(folder) if list_files: folders_to_process[folder] = list_files else: @@ -1070,7 +950,7 @@ def select_target_folders(self): if len(folders_to_process) == 0: log.info("Exiting process, folders were empty.") log.error("There are no files in the selected folders.") - self.close_connection() + self.relecov_sftp.close_connection() sys.exit(0) return folders_to_process @@ -1160,11 +1040,11 @@ def download(self, target_folders, option="download"): self.current_folder = folder.split("/")[0] # Close previously open connection to avoid timeouts try: - self.close_connection() + self.relecov_sftp.close_connection() except paramiko.ssh_exception.NoValidConnectionsError: pass # Check if the connection has been closed due to time limit - self.open_connection() + self.relecov_sftp.open_connection() log.info("Processing folder %s", folder) stderr.print("[blue]Processing folder " + folder) # Validate that the files are the ones described in metadata. @@ -1199,7 +1079,7 @@ def download(self, target_folders, option="download"): fetched_md5 = os.path.join( local_folder, os.path.basename(remote_md5sum) ) - self.get_from_sftp(file=remote_md5sum, destination=fetched_md5) + self.relecov_sftp.get_from_sftp(file=remote_md5sum, destination=fetched_md5) successful_files, corrupted = self.verify_md5_checksum( local_folder, fetched_files, fetched_md5 ) @@ -1316,10 +1196,8 @@ def include_warning(self, entry, sample=None): def execute_process(self): """Executes different processes depending on the download_option""" - import pdb; pdb.set_trace() - # self.sftp_client.open_connection() - self.my_sftp.list_folders(".") - if not self.sftp_client.open_connection(): + import pdb + if not self.relecov_sftp.open_connection(): log.error("Unable to establish connection towards sftp server") stderr.print("[red]Unable to establish sftp connection") sys.exit(1) @@ -1344,7 +1222,7 @@ def execute_process(self): self.delete_remote_folder(folder) stderr.print(f"Delete process finished in {folder}") - self.close_connection() + self.relecov_sftp.close_connection() stderr.print(f"Processed {len(processed_folders)} folders: {processed_folders}") if self.logsum.logs: log.info("Printing process summary to %s", self.platform_storage_folder) diff --git a/relecov_tools/sftp_client.py b/relecov_tools/sftp_client.py index 5fa1f375..1f9be322 100644 --- a/relecov_tools/sftp_client.py +++ b/relecov_tools/sftp_client.py @@ -2,6 +2,7 @@ import os import paramiko import rich.console +import stat import sys from relecov_tools.config_json import ConfigJson import relecov_tools.utils @@ -76,26 +77,154 @@ def open_connection(self): return False return True - def list_folders(self, remote_path): + def list_remote_folders(self, folder_name, recursive=False): + """Creates a directories list from the given client remote path + + Args: + folder_name (str): folder name in remote path + recursive (bool, optional): finds all subdirectories too. Defaults to False. + + Returns: + directory_list(list(str)): Names of all folders within remote folder + """ + log.info("Listing directories in %s", folder_name) + directory_list = [] self.open_connection() - """List all the folders in the remote path""" - log.info("Listing folders in the remote path %s", remote_path) try: - folders = self.sftp.listdir(remote_path) + content_list = self.sftp.listdir_attr(folder_name) + subfolders = any(stat.S_ISDIR(item.st_mode) for item in content_list) + except (FileNotFoundError, OSError) as e: + log.error("Invalid folder at remote sftp %s", e) + raise + if not subfolders: + return [folder_name] + + def recursive_list(folder_name): + try: + attribute_list = self.sftp.listdir_attr(folder_name) + except (FileNotFoundError, OSError) as e: + log.error("Invalid folder at remote sftp %s", e) + raise + for attribute in attribute_list: + if stat.S_ISDIR(attribute.st_mode): + abspath = os.path.join(folder_name, attribute.filename) + directory_list.append(abspath) + recursive_list(abspath) + else: + continue + return directory_list + + if recursive: + directory_list = recursive_list(folder_name) + if folder_name != ".": + directory_list.append(folder_name) + return directory_list + try: + directory_list = [ + item.filename for item in content_list if stat.S_ISDIR(item.st_mode) + ] + except AttributeError: + return False + self.close_connection() + return directory_list + + def get_file_list(self, folder_name): + """Return a tuple with file name and directory path from remote + + Args: + folder_name (str): name of folder in remote repository + + Returns: + file_list (list(str)): list of files in remote folder + """ + log.info("Listing files in %s", folder_name) + file_list = [] + content_list = self.sftp.listdir_attr(folder_name) + file_list = [ + os.path.join(folder_name, content.filename) + for content in content_list + if stat.S_ISREG(content.st_mode) + ] + return file_list + + def get_from_sftp(self, file, destination, exist_ok=False): + """Download a file from remote sftp + + Args: + file (str): path of the file in remote sftp + destination (str): local path of the file after download + exist_ok (bool): Skip download if file exists in local destination + + Returns: + bool: True if download was successful, False if it was not + """ + if os.path.exists(destination) and exist_ok: + return True + else: + try: + self.sftp.get(file, destination) + return True + except FileNotFoundError as e: + log.error("Unable to fetch file %s ", e) + return False + + def make_dir(self, folder_name): + """Create a new directory in remote sftp + + Args: + folder_name (str): name of the directory to be created + + Returns: + bool: True if directory was created, False if it was not + """ + try: + self.sftp.mkdir(folder_name) + return True + except FileExistsError: + log.error("Directory %s already exists", folder_name) + stderr.print("[red]Directory already exists") + return False + + def rename_file(self, old_name, new_name): + """Rename a file in remote sftp + + Args: + old_name (str): current name of the file + new_name (str): new name of the file + + Returns: + bool: True if file was renamed, False if it was not + """ + try: + self.sftp.rename(old_name, new_name) + return True except FileNotFoundError: - log.error("Remote path %s does not exist", remote_path) - stderr.print("[red]Remote path does not exist") - return None - return folders - - def pepe(self, pepe): - print(pepe) - + log.error("File %s not found", old_name) + stderr.print("[red]File not found") + return False + + def upload_file(self, local_path, remote_file): + """Upload a file to remote sftp + + Args: + localpath (str): path of the file in local machine + remote_file (str): path of the file in remote sftp + + Returns: + bool: True if file was uploaded, False if it was not + """ + try: + self.sftp.put(local_path, remote_file) + return True + except FileNotFoundError as e: + log.error("File not found %s", e) + stderr.print("[red]File not found") + return False + def close_connection(self): log.info("Closing SFTP connection") try: self.sftp.close() - self.client.close() except NameError: return False log.info("SFTP connection closed") From d3d4e9dee5ecb3fd1eb0c0ae5a7f14cba73928b7 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 20 Aug 2024 22:47:47 +0200 Subject: [PATCH 1375/1454] litint --- relecov_tools/download_manager.py | 32 +++++++++++++++++++++---------- relecov_tools/sftp_client.py | 3 ++- 2 files changed, 24 insertions(+), 11 deletions(-) diff --git a/relecov_tools/download_manager.py b/relecov_tools/download_manager.py index 17c9d32e..39e22dd3 100755 --- a/relecov_tools/download_manager.py +++ b/relecov_tools/download_manager.py @@ -115,9 +115,7 @@ def __init__( self.target_folders = self.target_folders.split(",") self.logsum = LogSum(output_location=self.platform_storage_folder) if sftp_passwd is None: - sftp_passwd = relecov_tools.utils.prompt_password( - msg="Enter your password" - ) + sftp_passwd = relecov_tools.utils.prompt_password(msg="Enter your password") self.metadata_lab_heading = config_json.get_topic_data( "lab_metadata", "metadata_lab_heading" ) @@ -131,7 +129,9 @@ def __init__( "lab_metadata", "samples_json_fields" ) # initialize the sftp client - self.relecov_sftp = relecov_tools.sftp_client.SftpRelecov(conf_file, sftp_user, sftp_passwd) + self.relecov_sftp = relecov_tools.sftp_client.SftpRelecov( + conf_file, sftp_user, sftp_passwd + ) def create_local_folder(self, folder): """Create folder to download files in local path using date @@ -172,7 +172,9 @@ def get_remote_folder_files(self, folder, local_folder, file_list): for file in file_list: file_to_fetch = os.path.join(folder, os.path.basename(file)) output_file = os.path.join(local_folder, os.path.basename(file)) - if self.relecov_sftp.get_from_sftp(file_to_fetch, output_file, exist_ok=True): + if self.relecov_sftp.get_from_sftp( + file_to_fetch, output_file, exist_ok=True + ): fetched_files.append(os.path.basename(file)) else: # Try to download again n times @@ -514,7 +516,8 @@ def validate_remote_files(self, remote_folder, local_folder): out_folder = os.path.dirname(local_meta_file) allowed_extensions = self.allowed_file_ext remote_files_list = [ - os.path.basename(file) for file in self.relecov_sftp.get_file_list(remote_folder) + os.path.basename(file) + for file in self.relecov_sftp.get_file_list(remote_folder) ] filtered_files_list = sorted( [fi for fi in remote_files_list if fi.endswith(tuple(allowed_extensions))] @@ -576,7 +579,9 @@ def delete_remote_files(self, remote_folder, files=None, skip_seqs=False): return for file in files_to_remove: try: - self.relecov_sftp.remove(os.path.join(remote_folder, os.path.basename(file))) + self.relecov_sftp.remove( + os.path.join(remote_folder, os.path.basename(file)) + ) log.info("%s Deleted from remote server", file) except (IOError, PermissionError) as e: self.include_warning(f"Could not delete remote file {file}: {e}") @@ -681,7 +686,9 @@ def md5_handler(md5sumlist, output_location): for md5sum in md5sumlist: md5_name = "_".join([token_hex(nbytes=12), "md5_temp.md5"]) fetched_md5 = os.path.join(output_location, md5_name) - if self.relecov_sftp.get_from_sftp(file=md5sum, destination=fetched_md5): + if self.relecov_sftp.get_from_sftp( + file=md5sum, destination=fetched_md5 + ): downloaded_md5files.append(fetched_md5) merged_md5 = md5_merger(downloaded_md5files, self.avoidable_characters) if merged_md5: @@ -936,7 +943,9 @@ def select_target_folders(self): folders_to_process = {} for targeted_folder in target_folders: try: - full_folders = self.relecov_sftp.list_remote_folders(targeted_folder, recursive=True) + full_folders = self.relecov_sftp.list_remote_folders( + targeted_folder, recursive=True + ) except (FileNotFoundError, OSError) as e: log.error(f"Error during sftp listing. {targeted_folder} skipped:", e) continue @@ -1079,7 +1088,9 @@ def download(self, target_folders, option="download"): fetched_md5 = os.path.join( local_folder, os.path.basename(remote_md5sum) ) - self.relecov_sftp.get_from_sftp(file=remote_md5sum, destination=fetched_md5) + self.relecov_sftp.get_from_sftp( + file=remote_md5sum, destination=fetched_md5 + ) successful_files, corrupted = self.verify_md5_checksum( local_folder, fetched_files, fetched_md5 ) @@ -1197,6 +1208,7 @@ def include_warning(self, entry, sample=None): def execute_process(self): """Executes different processes depending on the download_option""" import pdb + if not self.relecov_sftp.open_connection(): log.error("Unable to establish connection towards sftp server") stderr.print("[red]Unable to establish sftp connection") diff --git a/relecov_tools/sftp_client.py b/relecov_tools/sftp_client.py index 1f9be322..5853af00 100644 --- a/relecov_tools/sftp_client.py +++ b/relecov_tools/sftp_client.py @@ -29,6 +29,7 @@ class SftpRelecov: "sftp_port": "port_number" } """ + def __init__(self, conf_file=None, username=None, password=None): if conf_file is None: config_json = ConfigJson() @@ -167,7 +168,7 @@ def get_from_sftp(self, file, destination, exist_ok=False): except FileNotFoundError as e: log.error("Unable to fetch file %s ", e) return False - + def make_dir(self, folder_name): """Create a new directory in remote sftp From 3a8dae7273f5a1e8673b0d67aa5974b780dcd818 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 20 Aug 2024 22:53:58 +0200 Subject: [PATCH 1376/1454] solving more errors of liting --- relecov_tools/download_manager.py | 3 --- relecov_tools/pipeline_manager.py | 13 +++++++------ 2 files changed, 7 insertions(+), 9 deletions(-) diff --git a/relecov_tools/download_manager.py b/relecov_tools/download_manager.py index 39e22dd3..fef918bc 100755 --- a/relecov_tools/download_manager.py +++ b/relecov_tools/download_manager.py @@ -4,7 +4,6 @@ import json import sys import os -import stat import yaml import warnings import rich.console @@ -1207,8 +1206,6 @@ def include_warning(self, entry, sample=None): def execute_process(self): """Executes different processes depending on the download_option""" - import pdb - if not self.relecov_sftp.open_connection(): log.error("Unable to establish connection towards sftp server") stderr.print("[red]Unable to establish sftp connection") diff --git a/relecov_tools/pipeline_manager.py b/relecov_tools/pipeline_manager.py index 7888407c..e13f61b6 100644 --- a/relecov_tools/pipeline_manager.py +++ b/relecov_tools/pipeline_manager.py @@ -262,12 +262,12 @@ def __init__(self, input_folder=None, conf_file=None): log.error("Input folder %s does not exist ", self.input_folder) stderr.print("[red] Input folder " + self.input_folder + " does not exist") sys.exit(1) - + conf_file = os.path.join( - os.path.dirname(os.path.realpath(__file__)), - "conf", - "configuration.json", - ) + os.path.dirname(os.path.realpath(__file__)), + "conf", + "configuration.json", + ) if not os.path.exists(conf_file): log.error( "Configuration file %s does not exist ", self.conf_file @@ -285,4 +285,5 @@ def __init__(self, input_folder=None, conf_file=None): log.error("Invalid pipeline config file %s ", self.pipeline_conf_file) stderr.print( "[red] Invalid pipeline config file " + self.pipeline_conf_file - ) \ No newline at end of file + ) + stderr.print(f"[blue] Configuration file loaded {data}") \ No newline at end of file From e392a3f81c59de3bd438a705b3b0b7afa0262c84 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 20 Aug 2024 22:55:28 +0200 Subject: [PATCH 1377/1454] adding new line end of file because of liting --- relecov_tools/pipeline_manager.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/pipeline_manager.py b/relecov_tools/pipeline_manager.py index e13f61b6..2a29dd22 100644 --- a/relecov_tools/pipeline_manager.py +++ b/relecov_tools/pipeline_manager.py @@ -286,4 +286,4 @@ def __init__(self, input_folder=None, conf_file=None): stderr.print( "[red] Invalid pipeline config file " + self.pipeline_conf_file ) - stderr.print(f"[blue] Configuration file loaded {data}") \ No newline at end of file + stderr.print(f"[blue] Configuration file loaded {data}") From dc631489b9e0e153730129aa409a922f5db04edc Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 20 Aug 2024 22:59:28 +0200 Subject: [PATCH 1378/1454] join log.error mesage in 1 line --- relecov_tools/pipeline_manager.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/relecov_tools/pipeline_manager.py b/relecov_tools/pipeline_manager.py index 2a29dd22..726d6355 100644 --- a/relecov_tools/pipeline_manager.py +++ b/relecov_tools/pipeline_manager.py @@ -269,9 +269,7 @@ def __init__(self, input_folder=None, conf_file=None): "configuration.json", ) if not os.path.exists(conf_file): - log.error( - "Configuration file %s does not exist ", self.conf_file - ) + log.error("Configuration file %s does not exist ", self.conf_file) stderr.print( "[red] Pipeline config file " + self.pipeline_conf_file From ee3cc40800e8e0544c8396b0a85323e6ba9ddd97 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 21 Aug 2024 10:13:29 +0200 Subject: [PATCH 1379/1454] update testing file --- tests/test_sftp_handle.py | 30 ++++++++++++++---------------- 1 file changed, 14 insertions(+), 16 deletions(-) diff --git a/tests/test_sftp_handle.py b/tests/test_sftp_handle.py index 1e09a70c..95e03580 100755 --- a/tests/test_sftp_handle.py +++ b/tests/test_sftp_handle.py @@ -2,7 +2,7 @@ import os import sys import argparse -from relecov_tools.sftp_handle import SftpHandle +from relecov_tools.download_manager import DownloadManager def main(): @@ -29,32 +29,30 @@ def main(): def prepare_remote_test(**kwargs): # First clean the repository. print("Initating sftp module") - sftp_connection = SftpHandle( + download_manager = DownloadManager( user=kwargs["user"], passwd=kwargs["password"], conf_file=None, - user_relecov=None, - password_relecov=None, download_option=kwargs["download_option"], output_location=kwargs["output_location"], target_folders=kwargs["target_folders"], ) print("Openning connection to sftp") - sftp_connection.sftp_port = os.environ["TEST_PORT"] - if not sftp_connection.open_connection(): + download_manager.relecov_sftp.sftp_port = os.environ["TEST_PORT"] + if not download_manager.relecov_sftp.open_connection(): print("Could not open connection to remote sftp") sys.exit(1) - remote_folders = sftp_connection.list_remote_folders(".", recursive=True) + remote_folders = download_manager.relecov_sftp.list_remote_folders(".", recursive=True) clean_folders = [folder.replace("./", "") for folder in remote_folders] print("Cleaning folders") for folder in clean_folders: if len(folder.split("/")) < 2: continue - filelist = sftp_connection.get_file_list(folder) + filelist = download_manager.relecov_sftp.get_file_list(folder) for file in filelist: - sftp_connection.client.remove(file) + download_manager.relecov_sftp.remove_file(file) print(f"Removing remote folder {folder}") - sftp_connection.client.rmdir(folder) + download_manager.relecov_sftp.remove_dir(folder) # Upload the test dataset to the sftp. data_loc = "tests/data/sftp_handle" @@ -68,20 +66,20 @@ def prepare_remote_test(**kwargs): else: continue base_folder = folder.split("/")[-1] - sftp_connection.client.mkdir(os.path.join(remote_dir, base_folder)) + download_manager.relecov_sftp.make_dir(os.path.join(remote_dir, base_folder)) print(f"Uploading files from {base_folder}") for file in files: remotepath = os.path.join(remote_dir, base_folder, file) local_path = os.path.join(os.path.abspath(folder), file) - sftp_connection.client.put(localpath=local_path, remotepath=remotepath) + download_manager.client.put(localpath=local_path, remotepath=remotepath) - sftp_connection.close_connection() + download_manager.relecov_sftp.close_connection() # Test download_module - def test_download(sftp_connection): - sftp_connection.execute_process() + def test_download(download_manager): + download_manager.execute_process() - test_download(sftp_connection) + test_download(download_manager) if __name__ == "__main__": From b0417cc5901ef25ceeac71c4cc05e3cc702a5287 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 21 Aug 2024 10:15:14 +0200 Subject: [PATCH 1380/1454] Moving delete folder and files to sftp class --- relecov_tools/download_manager.py | 4 ++-- relecov_tools/sftp_client.py | 34 +++++++++++++++++++++++++++++++ 2 files changed, 36 insertions(+), 2 deletions(-) diff --git a/relecov_tools/download_manager.py b/relecov_tools/download_manager.py index fef918bc..64df3a90 100755 --- a/relecov_tools/download_manager.py +++ b/relecov_tools/download_manager.py @@ -578,7 +578,7 @@ def delete_remote_files(self, remote_folder, files=None, skip_seqs=False): return for file in files_to_remove: try: - self.relecov_sftp.remove( + self.relecov_sftp.remove_file( os.path.join(remote_folder, os.path.basename(file)) ) log.info("%s Deleted from remote server", file) @@ -599,7 +599,7 @@ def remove_client_dir(remote_folder): if len(remote_folder.replace("./", "").split("/")) >= 2: log.info("Trying to remove %s", remote_folder) try: - self.relecov_sftp.rmdir(remote_folder) + self.relecov_sftp.remove_dir(remote_folder) log.info("Successfully removed %s", remote_folder) except (OSError, PermissionError) as e: log_text = f"Could not delete remote {remote_folder}. Error: {e}" diff --git a/relecov_tools/sftp_client.py b/relecov_tools/sftp_client.py index 5853af00..d9de82ca 100644 --- a/relecov_tools/sftp_client.py +++ b/relecov_tools/sftp_client.py @@ -204,6 +204,40 @@ def rename_file(self, old_name, new_name): stderr.print("[red]File not found") return False + def remove_file(self, file_name): + """Remove a file from remote sftp + + Args: + file_name (str): name of the file to be removed + + Returns: + bool: True if file was removed, False if it was not + """ + try: + self.sftp.remove(file_name) + return True + except FileNotFoundError: + log.error("File %s not found", file_name) + stderr.print("[red]File not found") + return False + + def remove_dir(self, folder_name): + """Remove a directory from remote sftp + + Args: + folder_name (str): name of the directory to be removed + + Returns: + bool: True if directory was removed, False if it was not + """ + try: + self.sftp.rmdir(folder_name) + return True + except FileNotFoundError: + log.error("Directory %s not found", folder_name) + stderr.print("[red]Directory not found") + return False + def upload_file(self, local_path, remote_file): """Upload a file to remote sftp From 5b671cda8b5874790286e345aae5409ab79075ea Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 21 Aug 2024 10:21:21 +0200 Subject: [PATCH 1381/1454] solving liting and solving fail --- tests/test_sftp_handle.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/tests/test_sftp_handle.py b/tests/test_sftp_handle.py index 95e03580..ee45aeb4 100755 --- a/tests/test_sftp_handle.py +++ b/tests/test_sftp_handle.py @@ -42,7 +42,9 @@ def prepare_remote_test(**kwargs): if not download_manager.relecov_sftp.open_connection(): print("Could not open connection to remote sftp") sys.exit(1) - remote_folders = download_manager.relecov_sftp.list_remote_folders(".", recursive=True) + remote_folders = download_manager.relecov_sftp.list_remote_folders( + ".", recursive=True + ) clean_folders = [folder.replace("./", "") for folder in remote_folders] print("Cleaning folders") for folder in clean_folders: @@ -71,7 +73,9 @@ def prepare_remote_test(**kwargs): for file in files: remotepath = os.path.join(remote_dir, base_folder, file) local_path = os.path.join(os.path.abspath(folder), file) - download_manager.client.put(localpath=local_path, remotepath=remotepath) + download_manager.relecov_sftp.upload_file( + localpath=local_path, remotepath=remotepath + ) download_manager.relecov_sftp.close_connection() From b5a62bbb9a78a443d688ca95276e90d5da53ab39 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 21 Aug 2024 10:24:25 +0200 Subject: [PATCH 1382/1454] solving fails at upload_file --- tests/test_sftp_handle.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/tests/test_sftp_handle.py b/tests/test_sftp_handle.py index ee45aeb4..ba738ddc 100755 --- a/tests/test_sftp_handle.py +++ b/tests/test_sftp_handle.py @@ -71,11 +71,9 @@ def prepare_remote_test(**kwargs): download_manager.relecov_sftp.make_dir(os.path.join(remote_dir, base_folder)) print(f"Uploading files from {base_folder}") for file in files: - remotepath = os.path.join(remote_dir, base_folder, file) + remote_path = os.path.join(remote_dir, base_folder, file) local_path = os.path.join(os.path.abspath(folder), file) - download_manager.relecov_sftp.upload_file( - localpath=local_path, remotepath=remotepath - ) + download_manager.relecov_sftp.upload_file(local_path, remote_path) download_manager.relecov_sftp.close_connection() From f71939eea7e1f95705c1297f9a1776b4592ef322 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 21 Aug 2024 16:24:45 +0200 Subject: [PATCH 1383/1454] Standardized date in long_table json --- relecov_tools/assets/pipeline_utils/viralrecon.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py index 38b2bb28..dcb1cc31 100644 --- a/relecov_tools/assets/pipeline_utils/viralrecon.py +++ b/relecov_tools/assets/pipeline_utils/viralrecon.py @@ -163,7 +163,7 @@ def convert_to_json(self, samp_dict): def save_to_file(self, j_list): """Transform the parsed data into a json file""" - date_now = datetime.now().strftime("%Y_%m_%d_%H_%M_%S") + date_now = datetime.now().strftime("%Y%m%d%H%M%S") file_name = "long_table_" + date_now + ".json" file_path = os.path.join(self.output_directory, file_name) From b09da00a7b15798cde74b0ec83bf354df8c348ad Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 21 Aug 2024 16:32:01 +0200 Subject: [PATCH 1384/1454] Standardized date in download xlsx --- relecov_tools/download_manager.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/download_manager.py b/relecov_tools/download_manager.py index 64df3a90..df770f3a 100755 --- a/relecov_tools/download_manager.py +++ b/relecov_tools/download_manager.py @@ -245,7 +245,7 @@ def create_files_with_metadata_info( prefix_file_name = "_".join(local_folder.split("/")[-2:]) prefix_file_name = prefix_file_name.replace("_tmp_processing", "") # TODO: Move these prefixes to configuration.json - new_metadata_file = "metadata_lab_" + prefix_file_name + ".xlsx" + new_metadata_file = "lab_metadata_" + prefix_file_name + ".xlsx" sample_data_file = "samples_data_" + prefix_file_name + ".json" sample_data_path = os.path.join(local_folder, sample_data_file) os.rename(metadata_file, os.path.join(local_folder, new_metadata_file)) From 61f17404bbd734913f97b7e9f2702b3a2970cb1e Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 21 Aug 2024 16:44:10 +0200 Subject: [PATCH 1385/1454] Standardize output filename --- relecov_tools/read_lab_metadata.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 49393bbd..7827ee47 100755 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -59,11 +59,12 @@ def __init__(self, metadata_file=None, sample_list_file=None, output_folder=None else: self.output_folder = output_folder out_path = os.path.realpath(self.output_folder) - lab_code = out_path.split("/")[-2] + self.lab_code = out_path.split("/")[-2] self.logsum = LogSum( - output_location=self.output_folder, unique_key=lab_code, path=out_path + output_location=self.output_folder, unique_key=self.lab_code, path=out_path ) config_json = ConfigJson() + # TODO: remove hardcoded schema selection relecov_schema = config_json.get_topic_data("json_schemas", "relecov_schema") relecov_sch_path = os.path.join( os.path.dirname(os.path.realpath(__file__)), "schema", relecov_schema @@ -128,6 +129,7 @@ def adding_fixed_fields(self, m_data): m_data[idx][key] = value m_data[idx]["schema_name"] = self.schema_name m_data[idx]["schema_version"] = self.schema_version + m_data[idx]["submitting_institution_id"] = self.lab_code return m_data def adding_copy_from_other_field(self, m_data): @@ -353,9 +355,8 @@ def create_metadata_json(self): if not completed_metadata: stderr.print("Metadata was completely empty. No output file generated") sys.exit(1) - file_name = ( - "processed_metadata_lab_" + dtime.now().strftime("%Y_%m_%d") + ".json" - ) + file_code = "lab_metadata_" + self.lab_code + "_" + file_name = file_code + dtime.now().strftime("%Y%m%d%H%M%S") + ".json" stderr.print("[blue]Writting output json file") os.makedirs(self.output_folder, exist_ok=True) self.logsum.create_error_summary(called_module="read-lab-metadata") From ca41463296fc03bd7238eef2af7e03e6e494ac10 Mon Sep 17 00:00:00 2001 From: Shettland Date: Wed, 21 Aug 2024 17:23:33 +0200 Subject: [PATCH 1386/1454] read-lab date error hotfix --- relecov_tools/read_lab_metadata.py | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 7827ee47..6ddb15f6 100755 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -299,12 +299,18 @@ def read_metadata_file(self): self.logsum.add_warning(sample=sample_id, entry=log_text) continue if "date" in key.lower(): - # Check if date is a string. Format YYYY-MM-DD to YYYY/MM/DD - if re.match(r"^\d{4}[-/]\d{2}[-/]\d{2}$", str(row[key])): - row[key] = row[key].replace("/", "-") - if isinstance(row[key], int) or isinstance(row[key], float): + # Check if date is a string. Format YYYY/MM/DD to YYYY-MM-DD + if isinstance(row[key], dtime): + row[key] = str(row[key].date()) + continue + try: + row[key] = str(int(float(row[key]))) log.info("Date given as an integer. Understood as a year") - row[key] = str(int(row[key])) + continue + except ValueError: + pass + if re.match(r"^\d{4}[-/]\d{2}[-/]\d{2}$", str(row[key])): + row[key] = row[key].replace("/", "-").replace(".", "-") else: try: row[key] = str( From 856d81873f191f5e207130c4c3895974ef2ade19 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 22 Aug 2024 09:06:39 +0200 Subject: [PATCH 1387/1454] hotfix read-lab date parse --- relecov_tools/read_lab_metadata.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 6ddb15f6..d299e80a 100755 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -300,16 +300,14 @@ def read_metadata_file(self): continue if "date" in key.lower(): # Check if date is a string. Format YYYY/MM/DD to YYYY-MM-DD - if isinstance(row[key], dtime): - row[key] = str(row[key].date()) - continue try: row[key] = str(int(float(row[key]))) log.info("Date given as an integer. Understood as a year") - continue except ValueError: pass - if re.match(r"^\d{4}[-/]\d{2}[-/]\d{2}$", str(row[key])): + if isinstance(row[key], dtime): + row[key] = str(row[key].date()) + elif re.match(r"^\d{4}[-/]\d{2}[-/]\d{2}$", str(row[key])): row[key] = row[key].replace("/", "-").replace(".", "-") else: try: From e2fd189cf0b6d2d4a3e0afc8e2404fbc6ebb64f7 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 22 Aug 2024 09:24:16 +0200 Subject: [PATCH 1388/1454] Hotfix for read-lab date --- relecov_tools/read_lab_metadata.py | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index d299e80a..faa1d653 100755 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -300,22 +300,19 @@ def read_metadata_file(self): continue if "date" in key.lower(): # Check if date is a string. Format YYYY/MM/DD to YYYY-MM-DD - try: - row[key] = str(int(float(row[key]))) - log.info("Date given as an integer. Understood as a year") - except ValueError: - pass + pattern = r"^\d{4}[-/.]\d{2}[-/.]\d{2}" if isinstance(row[key], dtime): row[key] = str(row[key].date()) - elif re.match(r"^\d{4}[-/]\d{2}[-/]\d{2}$", str(row[key])): + elif re.match(pattern, str(row[key])): row[key] = row[key].replace("/", "-").replace(".", "-") + row[key] = re.match(pattern, row[key]).group(0) else: try: - row[key] = str( - dtime.strptime(str(row[key]), "%Y-%m-%d").date() - ) - except ValueError: + row[key] = str(int(float(str(row[key])))) + log.info("Date given as an integer. Understood as a year") + except (ValueError, TypeError): log_text = f"Invalid date format in {key}: {row[key]}" + import pdb; pdb.set_trace() self.logsum.add_error(sample=sample_id, entry=log_text) stderr.print(f"[red]{log_text} for sample {sample_id}") continue From 12bb063352ef95b859612b9b3c094e15568e18b7 Mon Sep 17 00:00:00 2001 From: Shettland Date: Thu, 22 Aug 2024 09:25:13 +0200 Subject: [PATCH 1389/1454] read-lab parse date hotfix --- relecov_tools/read_lab_metadata.py | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index faa1d653..2d4efbda 100755 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -312,7 +312,6 @@ def read_metadata_file(self): log.info("Date given as an integer. Understood as a year") except (ValueError, TypeError): log_text = f"Invalid date format in {key}: {row[key]}" - import pdb; pdb.set_trace() self.logsum.add_error(sample=sample_id, entry=log_text) stderr.print(f"[red]{log_text} for sample {sample_id}") continue From 2fe9d03bb6fd584b6504016483ee317dd081bdb5 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 23 Aug 2024 15:38:48 +0200 Subject: [PATCH 1390/1454] fixing bugs --- relecov_tools/__main__.py | 2 +- relecov_tools/pipeline_manager.py | 24 ++++++++++-------------- 2 files changed, 11 insertions(+), 15 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 226f4ad2..7f6503cf 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -503,7 +503,7 @@ def launch_pipeline(input, template, output, config): """ Create the symbolic links for the samples which are validated. """ - new_launch = relecov_tools.launch_pipeline.LaunchPipeline( + new_launch = relecov_tools.pipeline_manager.LaunchPipeline( input, template, output, config ) new_launch.pipeline_exc() diff --git a/relecov_tools/pipeline_manager.py b/relecov_tools/pipeline_manager.py index 726d6355..c611934e 100644 --- a/relecov_tools/pipeline_manager.py +++ b/relecov_tools/pipeline_manager.py @@ -55,23 +55,18 @@ def __init__( "configuration.json", ) if not os.path.exists(pipeline_conf_file): - log.error( - "Pipeline config file %s does not exist ", self.pipeline_conf_file - ) + log.error("Pipeline config file %s does not exist ", pipeline_conf_file) stderr.print( - "[red] Pipeline config file " - + self.pipeline_conf_file - + " does not exist" + "[red] Pipeline config file " + pipeline_conf_file + " does not exist" ) sys.exit(1) conf_settings = relecov_tools.utils.read_json_file(pipeline_conf_file) try: - data = conf_settings["pipelines"]["relecov"] + data = conf_settings["launch_pipeline"] + # get_topic_data("launch_pipeline", "analysis_name") except KeyError: - log.error("Invalid pipeline config file %s ", self.pipeline_conf_file) - stderr.print( - "[red] Invalid pipeline config file " + self.pipeline_conf_file - ) + log.error("Invalid pipeline config file %s ", pipeline_conf_file) + stderr.print("[red] Invalid pipeline config file " + pipeline_conf_file) if ( "analysis_name" not in data or "sample_stored_folder" not in data @@ -163,7 +158,7 @@ def get_latest_lab_folder(self): validate_files = [ os.path.join(data_folder["path"], f) for f in os.listdir(data_folder["path"]) - if f.startswith("validated_processed_metadata") and f.endswith(".json") + if f.startswith("validated_lab_metadata") and f.endswith(".json") ] if not validate_files: continue @@ -175,11 +170,11 @@ def get_latest_lab_folder(self): sample = {} sample["sequencing_sample_id"] = item["sequencing_sample_id"] sample["r1_fastq_file_path"] = os.path.join( - item["r1_fastq_file_path"], item["sequence_file_R1_fastq"] + item["r1_fastq_filepath"], item["sequence_file_R1_fastq"] ) if "r2_fastq_file_path" in item: sample["r2_fastq_file_path"] = os.path.join( - item["r2_fastq_file_path"], item["sequence_file_R2_fastq"] + item["r1_fastq_filepath"], item["sequence_file_R2_fastq"] ) samples_data.append(sample) lab_code = lab.split("/")[-1] @@ -209,6 +204,7 @@ def pipeline_exc(self): sequencing_r1_sample_id = item["sequencing_sample_id"] + "_R1." + ext # copy r1 sequencing file into the output folder raw_folder = os.path.join(self.analysis_folder, self.copied_sample_folder) + try: shutil.copy(item["r1_fastq_file_path"], raw_folder) # create simlink for the r1 From a736f92adf56c35f7c476ae721e1f1070be0bea4 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 24 Aug 2024 09:14:03 +0200 Subject: [PATCH 1391/1454] Increase versio to create pip package --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 91770d8f..0448207a 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import setup, find_packages -version = "0.0.5" +version = "0.0.6" with open("README.md") as f: readme = f.read() From 91c524e2612fee1bf1a78411328807de32ead96d Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 19 Jun 2024 13:27:33 +0200 Subject: [PATCH 1392/1454] init skeleton for build_schema module --- relecov_tools/__main__.py | 31 +++++++++++++++++++ relecov_tools/build_schema.py | 58 +++++++++++++++++++++++++++++++++++ 2 files changed, 89 insertions(+) create mode 100644 relecov_tools/build_schema.py diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 7f6503cf..4ec80d52 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -21,7 +21,11 @@ import relecov_tools.metadata_homogeneizer import relecov_tools.gisaid_upload import relecov_tools.upload_ena_protocol +<<<<<<< HEAD import relecov_tools.pipeline_manager +======= +import relecov_tools.build_schema +>>>>>>> baa2c36 (init skeleton for build_schema module) log = logging.getLogger() @@ -508,6 +512,33 @@ def launch_pipeline(input, template, output, config): ) new_launch.pipeline_exc() +# schema builder +@relecov_tools_cli.command(help_priority=13) +@click.option( + "-i" + "--input_file", + type=click.Path(), + help="Path to the Excel document containing the database definition." +) +@click.option( + "-p", + "--print_diff", + type=click.BOOL, + help="Prints a changelog/diff between the current and incoming versions of the schema schema_relecov.json." +) +@click.option( + "-o", + "--out_dir", + type=click.Path(), + help="Path to save output file" +) +def build_schema(input_file, print_diff, out_dir): + """""" + schema_update = relecov_tools.build_schema.SchemaBuilder( + input_file, print_diff, out_dir + ) + #schema_update.() + if __name__ == "__main__": run_relecov_tools() diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py new file mode 100644 index 00000000..254e361e --- /dev/null +++ b/relecov_tools/build_schema.py @@ -0,0 +1,58 @@ +#!/usr/bin/env python +import logging +import rich.console + +import relecov_tools.utils + +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + + +class SchemaBuilder: + def __init__(self, excel_file_path=None, schema_file_path=None): + """ + Initialize the SchemaBuilder with paths to the Excel file containing the database definitions + and the schema_input.json file. + + Args: + excel_file_path (str): Path to the Excel file containing the database definitions. + schema_file_path (str): Path to the schema_input.json file. + """ + self.excel_file_path = excel_file_path + self.schema_file_path = schema_file_path + + def create_schema(self): + """ + Create schema_input.json when no schema is already present. + """ + # TODO: Read the Excel file and extract the database definitions. + + # TODO: Check if schema_input.json already exists. + + # TODO: If schema_input.json does not exist, create it and populate with the extracted definitions. + + def update_schema(self): + """ + Update the schema_input.json based on the definitions in the Excel file. + """ + # TODO: Read the Excel file and extract the database definitions. + + # TODO: Compare the extracted definitions with the current schema_input.json. + + # TODO: Update the schema_input.json with the new definitions. + + def print_schema_diff(self): + """ + Print the differences between the current version of schema_input.json + and the updated version after calling update_schema(). + """ + # TODO: Load the current schema_input.json. + + # TODO: Load the updated schema_input.json after calling update_schema(). + + # TODO: Compare the two versions and print/save the differences. From 53b2c9a1f4123812bce4efe8faf0f71707f8251a Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 20 Jun 2024 11:34:15 +0200 Subject: [PATCH 1393/1454] added constructor and method to read excel database --- relecov_tools/__main__.py | 19 ++++++++++------ relecov_tools/build_schema.py | 41 +++++++++++++++++++++++++++++++++-- 2 files changed, 51 insertions(+), 9 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 4ec80d52..07446ed5 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -515,14 +515,20 @@ def launch_pipeline(input, template, output, config): # schema builder @relecov_tools_cli.command(help_priority=13) @click.option( - "-i" + "-i", "--input_file", type=click.Path(), help="Path to the Excel document containing the database definition." ) @click.option( - "-p", - "--print_diff", + "-s", + "--schema_base", + type=click.Path(), + help="Path to the Excel document containing the database definition." +) +@click.option( + "-d", + "--diff", type=click.BOOL, help="Prints a changelog/diff between the current and incoming versions of the schema schema_relecov.json." ) @@ -532,13 +538,12 @@ def launch_pipeline(input, template, output, config): type=click.Path(), help="Path to save output file" ) -def build_schema(input_file, print_diff, out_dir): +def build_schema(input_file, schema_base, diff, out_dir): """""" schema_update = relecov_tools.build_schema.SchemaBuilder( - input_file, print_diff, out_dir + input_file, schema_base, diff, out_dir ) - #schema_update.() - + schema_update.handle_build_schema() if __name__ == "__main__": run_relecov_tools() diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 254e361e..35cd2ae7 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -1,6 +1,10 @@ #!/usr/bin/env python import logging import rich.console +import pandas as pd +import json +import os +import sys import relecov_tools.utils @@ -14,7 +18,13 @@ class SchemaBuilder: - def __init__(self, excel_file_path=None, schema_file_path=None): + def __init__( + self, + excel_file_path=None, + base_schema_path=None, + print_diff=False, + out_dir=None + ): """ Initialize the SchemaBuilder with paths to the Excel file containing the database definitions and the schema_input.json file. @@ -24,8 +34,33 @@ def __init__(self, excel_file_path=None, schema_file_path=None): schema_file_path (str): Path to the schema_input.json file. """ self.excel_file_path = excel_file_path - self.schema_file_path = schema_file_path + self.schema_file_path = base_schema_path + # Validate the Excel file path + if not self.excel_file_path or not os.path.isfile(self.excel_file_path): + raise ValueError("A valid Excel file path must be provided.") + if not self.excel_file_path.endswith('.xlsx'): + raise ValueError("The Excel file must have a .xlsx extension.") + + def read_database_definition(self): + """Reads the database definition and converts it into json format.""" + # Read excel file + df = pd.read_excel(self.excel_file_path) + + # Convert database to json format + json_data = {} + for _, row in df.iterrows(): + property_name = row[0] + values=row.drop(df.columns[0]).to_dict() + json_data[property_name] = values + + # Check json is not empty + if len(json_data) == 0: + stderr.print("[red]No data found in xlsx database") + sys.exit(1) + + + return(json_data) def create_schema(self): """ Create schema_input.json when no schema is already present. @@ -56,3 +91,5 @@ def print_schema_diff(self): # TODO: Load the updated schema_input.json after calling update_schema(). # TODO: Compare the two versions and print/save the differences. + def handle_build_schema(self): + self.read_database_definition() From f9b17acd5d5adede35848e068522bdc0b92077e5 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 20 Jun 2024 13:43:50 +0200 Subject: [PATCH 1394/1454] fixed access method to pandas object --- relecov_tools/build_schema.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 35cd2ae7..6ff38ef5 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -50,7 +50,7 @@ def read_database_definition(self): # Convert database to json format json_data = {} for _, row in df.iterrows(): - property_name = row[0] + property_name = row.iloc[0] values=row.drop(df.columns[0]).to_dict() json_data[property_name] = values @@ -58,6 +58,7 @@ def read_database_definition(self): if len(json_data) == 0: stderr.print("[red]No data found in xlsx database") sys.exit(1) + return(json_data) return(json_data) From e52f7d33e19d4f7862f0fd45a3b5f9d1bcf2ec20 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 20 Jun 2024 13:44:57 +0200 Subject: [PATCH 1395/1454] added method to create schema template based on draft version --- .../assets/schema_utils/jsonschema_draft.py | 49 +++++++++++++++++++ relecov_tools/build_schema.py | 17 +++++-- 2 files changed, 63 insertions(+), 3 deletions(-) create mode 100644 relecov_tools/assets/schema_utils/jsonschema_draft.py diff --git a/relecov_tools/assets/schema_utils/jsonschema_draft.py b/relecov_tools/assets/schema_utils/jsonschema_draft.py new file mode 100644 index 00000000..82817ee3 --- /dev/null +++ b/relecov_tools/assets/schema_utils/jsonschema_draft.py @@ -0,0 +1,49 @@ +import logging +import sys + +import rich.console + +import relecov_tools.utils +import pkg_resources + +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + +def create_draft(draft_version, required=None): + """Creates a JSON Schema Draft template with required fields.""" + available_schemas = ["2020-12"] + + if draft_version not in available_schemas: + stderr.print(f"[red] {draft_version} not found. Available schemas are: {', '.join(available_schemas)}") + sys.exit(1) + + url_str = f"https://json-schema.org/draft/{draft_version}/schema" + id_str = "https://github.com/BU-ISCIII/relecov-tools/blob/develop/relecov_tools/schema/relecov_schema.json" + description_str = "Json schema that specifies the structure, content, and validation rules for RELECOV metadata" + pakage_version_str = pkg_resources.get_distribution("relecov_tools").version + + # Construct the draft template + draft_template = { + "$schema": url_str, + "$id": id_str, + "title": "RELECOV schema", + "description": description_str, + "version": pakage_version_str, + "type": "object", + "properties": { + } + } + + # Include required fields if specified + if required: + draft_template["required"] = required + + return draft_template + + +# TODO: draft202012Validator should be implemented here diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 6ff38ef5..83342bae 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -7,6 +7,7 @@ import sys import relecov_tools.utils +import relecov_tools.assets.schema_utils.jsonschema_draft log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -60,9 +61,12 @@ def read_database_definition(self): sys.exit(1) return(json_data) + def create_schema_draft_template(self, draft_version): + "Loads JsonSchema template based on draft name: Available drafts: [2020-12]" + draft_template = relecov_tools.assets.schema_utils.jsonschema_draft.create_draft(draft_version) + return(draft_template) - return(json_data) - def create_schema(self): + def build_new_schema(self, template, json_data): """ Create schema_input.json when no schema is already present. """ @@ -93,4 +97,11 @@ def print_schema_diff(self): # TODO: Compare the two versions and print/save the differences. def handle_build_schema(self): - self.read_database_definition() + + # Load xlsx database and convert into json format + json_db = self.read_database_definition() + + # Create schema template based on version draft specification. + # TODO: this method should show a prompt to mannually select the desired draft version. + draft_template = self.create_schema_draft_template("2020-12") + From c41affe9c40e152a6d4b20fa3e724e028cc09721 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 20 Jun 2024 13:54:02 +0200 Subject: [PATCH 1396/1454] fix linting --- relecov_tools/__main__.py | 14 ++++------ .../assets/schema_utils/jsonschema_draft.py | 10 ++++--- relecov_tools/build_schema.py | 28 ++++++++++--------- 3 files changed, 26 insertions(+), 26 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 07446ed5..f4d17829 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -518,26 +518,21 @@ def launch_pipeline(input, template, output, config): "-i", "--input_file", type=click.Path(), - help="Path to the Excel document containing the database definition." + help="Path to the Excel document containing the database definition.", ) @click.option( "-s", "--schema_base", type=click.Path(), - help="Path to the Excel document containing the database definition." + help="Path to the Excel document containing the database definition.", ) @click.option( "-d", "--diff", type=click.BOOL, - help="Prints a changelog/diff between the current and incoming versions of the schema schema_relecov.json." -) -@click.option( - "-o", - "--out_dir", - type=click.Path(), - help="Path to save output file" + help="Prints a changelog/diff between the current and incoming versions of the schema schema_relecov.json.", ) +@click.option("-o", "--out_dir", type=click.Path(), help="Path to save output file") def build_schema(input_file, schema_base, diff, out_dir): """""" schema_update = relecov_tools.build_schema.SchemaBuilder( @@ -545,5 +540,6 @@ def build_schema(input_file, schema_base, diff, out_dir): ) schema_update.handle_build_schema() + if __name__ == "__main__": run_relecov_tools() diff --git a/relecov_tools/assets/schema_utils/jsonschema_draft.py b/relecov_tools/assets/schema_utils/jsonschema_draft.py index 82817ee3..53cae1c4 100644 --- a/relecov_tools/assets/schema_utils/jsonschema_draft.py +++ b/relecov_tools/assets/schema_utils/jsonschema_draft.py @@ -14,14 +14,17 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) + def create_draft(draft_version, required=None): """Creates a JSON Schema Draft template with required fields.""" available_schemas = ["2020-12"] if draft_version not in available_schemas: - stderr.print(f"[red] {draft_version} not found. Available schemas are: {', '.join(available_schemas)}") + stderr.print( + f"[red] {draft_version} not found. Available schemas are: {', '.join(available_schemas)}" + ) sys.exit(1) - + url_str = f"https://json-schema.org/draft/{draft_version}/schema" id_str = "https://github.com/BU-ISCIII/relecov-tools/blob/develop/relecov_tools/schema/relecov_schema.json" description_str = "Json schema that specifies the structure, content, and validation rules for RELECOV metadata" @@ -35,8 +38,7 @@ def create_draft(draft_version, required=None): "description": description_str, "version": pakage_version_str, "type": "object", - "properties": { - } + "properties": {}, } # Include required fields if specified diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 83342bae..67e598dd 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -2,7 +2,6 @@ import logging import rich.console import pandas as pd -import json import os import sys @@ -24,7 +23,7 @@ def __init__( excel_file_path=None, base_schema_path=None, print_diff=False, - out_dir=None + out_dir=None, ): """ Initialize the SchemaBuilder with paths to the Excel file containing the database definitions @@ -40,7 +39,7 @@ def __init__( # Validate the Excel file path if not self.excel_file_path or not os.path.isfile(self.excel_file_path): raise ValueError("A valid Excel file path must be provided.") - if not self.excel_file_path.endswith('.xlsx'): + if not self.excel_file_path.endswith(".xlsx"): raise ValueError("The Excel file must have a .xlsx extension.") def read_database_definition(self): @@ -52,19 +51,23 @@ def read_database_definition(self): json_data = {} for _, row in df.iterrows(): property_name = row.iloc[0] - values=row.drop(df.columns[0]).to_dict() + values = row.drop(df.columns[0]).to_dict() json_data[property_name] = values - + # Check json is not empty if len(json_data) == 0: stderr.print("[red]No data found in xlsx database") sys.exit(1) - return(json_data) + return json_data def create_schema_draft_template(self, draft_version): "Loads JsonSchema template based on draft name: Available drafts: [2020-12]" - draft_template = relecov_tools.assets.schema_utils.jsonschema_draft.create_draft(draft_version) - return(draft_template) + draft_template = ( + relecov_tools.assets.schema_utils.jsonschema_draft.create_draft( + draft_version + ) + ) + return draft_template def build_new_schema(self, template, json_data): """ @@ -96,12 +99,11 @@ def print_schema_diff(self): # TODO: Load the updated schema_input.json after calling update_schema(). # TODO: Compare the two versions and print/save the differences. + def handle_build_schema(self): - # Load xlsx database and convert into json format - json_db = self.read_database_definition() - + self.read_database_definition() + # Create schema template based on version draft specification. # TODO: this method should show a prompt to mannually select the desired draft version. - draft_template = self.create_schema_draft_template("2020-12") - + self.create_schema_draft_template("2020-12") From dfecb2f84dcdc1b56c4d94b4f6e46a7f99d360fc Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 21 Jun 2024 09:59:01 +0200 Subject: [PATCH 1397/1454] improve management of the out_dir param --- relecov_tools/__main__.py | 2 +- relecov_tools/build_schema.py | 19 +++++++++++++++++-- relecov_tools/utils.py | 35 +++++++++++++++++++++++++++++++++++ 3 files changed, 53 insertions(+), 3 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index f4d17829..d731189b 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -532,7 +532,7 @@ def launch_pipeline(input, template, output, config): type=click.BOOL, help="Prints a changelog/diff between the current and incoming versions of the schema schema_relecov.json.", ) -@click.option("-o", "--out_dir", type=click.Path(), help="Path to save output file") +@click.option("-o", "--out_dir", type=click.Path(), help="Path to save output file/s") def build_schema(input_file, schema_base, diff, out_dir): """""" schema_update = relecov_tools.build_schema.SchemaBuilder( diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 67e598dd..426a895a 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -22,7 +22,7 @@ def __init__( self, excel_file_path=None, base_schema_path=None, - print_diff=False, + show_diff=False, out_dir=None, ): """ @@ -35,12 +35,27 @@ def __init__( """ self.excel_file_path = excel_file_path self.schema_file_path = base_schema_path + self.show_diff = show_diff - # Validate the Excel file path + # Validate input variables if not self.excel_file_path or not os.path.isfile(self.excel_file_path): raise ValueError("A valid Excel file path must be provided.") if not self.excel_file_path.endswith(".xlsx"): raise ValueError("The Excel file must have a .xlsx extension.") + if not out_dir: + self.output_folder = relecov_tools.utils.prompt_path( + msg="Select the output folder:" + ) + else: + if not os.path.exists(out_dir): + stderr.print(f"[red]The directory {out_dir} does not exist. Please, try again. Bye") + sys.exit(1) + if not os.path.isdir(out_dir): + stderr.print("[red]The provided path is not a directory.") + sys.exit(1) + else: + self.out_dir = out_dir + def read_database_definition(self): """Reads the database definition and converts it into json format.""" diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 8c3991d8..9657fe67 100755 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -3,6 +3,7 @@ Common utility function used for relecov_tools package. """ import os +import sys import glob import hashlib import logging @@ -412,3 +413,37 @@ def print_log_report( tablefmt="fancy_grid", ) ) + +# TODO: not used so far but can help to handle output folder creation. +def prompt_create_outdir(path, folder_name=None, prompt_message="Define path to store the output:"): + """Ensure the directory exists or prompt the user to define and create it.""" + # Check path + if not path: + path = prompt_path("Define path to store the output:") + stderr.print(f"Chosen directory: {path}") + + # Check folder_name + if not folder_name: + default_folder = prompt_yn_question("Do you want to use default directory ('results') to store the results? (yes/no):") + if not default_folder: + folder_name = prompt_text("Write your output directory: ") + else: + folder_name = 'results' + + global_path = os.path.join(path, folder_name) + + if not os.path.exists(global_path): + create_folder = prompt_yn_question(f"The directory does not exist. Do you want to create '{folder_name}' folder in this path? (yes/no):") + if create_folder: + os.makedirs(global_path) + stderr.print(f"[green]Folder '{folder_name}' created at {path}") + else: + stderr.print("[red]Directory creation aborted.") + sys.exit(1) + elif os.path.isdir(global_path): + os.makedirs(global_path, exist_ok=True) + stderr.print(f"[green]Folder '{folder_name}' created at {path}") + else: + stderr.print("[red]The provided path is not a directory.") + sys.exit(1) + return (global_path) From 4d629c67bf686d86d363c5e2124cc122355a3bdc Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 21 Jun 2024 13:35:29 +0200 Subject: [PATCH 1398/1454] add method to get the 'in use' schema --- relecov_tools/build_schema.py | 45 +++++++++++++++++++++++++++++++---- 1 file changed, 41 insertions(+), 4 deletions(-) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 426a895a..58333e87 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -7,6 +7,7 @@ import relecov_tools.utils import relecov_tools.assets.schema_utils.jsonschema_draft +from relecov_tools.config_json import ConfigJson log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -83,8 +84,37 @@ def create_schema_draft_template(self, draft_version): ) ) return draft_template + + def get_current_schema(self): + """ + Check if the current RELECOV schema is available in the configuration file. + """ + try: + conf = ConfigJson() + schemas = conf.get_configuration("json_schemas") + + if "relecov_schema" in schemas: + current_schema = schemas["relecov_schema"] + stderr.print("[green]RELECOV schema found in the configuration.") + return current_schema + else: + stderr.print("[orange]RELECOV schema not found in the configuration.") + return None + + except FileNotFoundError as fnf_error: + stderr.print(f"[red]Configuration file not found: {fnf_error}") + return None - def build_new_schema(self, template, json_data): + except KeyError as key_error: + stderr.print(f"[orange]Configuration key error: {key_error}") + return None + + except Exception as e: + stderr.print(f"An unexpected error occurred: {e}") + return None + + + def build_new_schema(self, schema_draft, json_data): """ Create schema_input.json when no schema is already present. """ @@ -119,6 +149,13 @@ def handle_build_schema(self): # Load xlsx database and convert into json format self.read_database_definition() - # Create schema template based on version draft specification. - # TODO: this method should show a prompt to mannually select the desired draft version. - self.create_schema_draft_template("2020-12") + # Verify current schema used by relecov-tools: + current_schema = self.get_current_schema() + # TODO: if schema not found do something + #if not current_schema: + + # TODO: build new schema draft based on database definition. + # TODO: create_schema_draft_template should show a prompt to mannually select the desired draft version. + schema_draft_template = self.create_schema_draft_template() + + # TODO: Compare current vs new schema From 71c09001b14dc4bb22818593d5889e16090c147c Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 21 Jun 2024 13:49:22 +0200 Subject: [PATCH 1399/1454] added prompt to choose an available version of json shcema draft --- relecov_tools/assets/schema_utils/jsonschema_draft.py | 9 ++++----- relecov_tools/build_schema.py | 5 ++--- 2 files changed, 6 insertions(+), 8 deletions(-) diff --git a/relecov_tools/assets/schema_utils/jsonschema_draft.py b/relecov_tools/assets/schema_utils/jsonschema_draft.py index 53cae1c4..633a8264 100644 --- a/relecov_tools/assets/schema_utils/jsonschema_draft.py +++ b/relecov_tools/assets/schema_utils/jsonschema_draft.py @@ -19,11 +19,10 @@ def create_draft(draft_version, required=None): """Creates a JSON Schema Draft template with required fields.""" available_schemas = ["2020-12"] - if draft_version not in available_schemas: - stderr.print( - f"[red] {draft_version} not found. Available schemas are: {', '.join(available_schemas)}" - ) - sys.exit(1) + if not draft_version: + draft_version = relecov_tools.utils.prompt_checkbox("Choose a Json Schema valid version:", available_schemas) + elif draft_version not in available_schemas: + draft_version = relecov_tools.utils.prompt_checkbox(f"Draft version '{draft_version}' not found. Choose a valid Json Schema version:", available_schemas) url_str = f"https://json-schema.org/draft/{draft_version}/schema" id_str = "https://github.com/BU-ISCIII/relecov-tools/blob/develop/relecov_tools/schema/relecov_schema.json" diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 58333e87..ab6d59b1 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -76,7 +76,7 @@ def read_database_definition(self): sys.exit(1) return json_data - def create_schema_draft_template(self, draft_version): + def create_schema_draft_template(self, draft_version=None): "Loads JsonSchema template based on draft name: Available drafts: [2020-12]" draft_template = ( relecov_tools.assets.schema_utils.jsonschema_draft.create_draft( @@ -155,7 +155,6 @@ def handle_build_schema(self): #if not current_schema: # TODO: build new schema draft based on database definition. - # TODO: create_schema_draft_template should show a prompt to mannually select the desired draft version. - schema_draft_template = self.create_schema_draft_template() + schema_draft_template = self.create_schema_draft_template('2020-2') # TODO: Compare current vs new schema From fd7adb76ad94cb1edd60ac3e21c7aac1597e5720 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 21 Jun 2024 13:56:20 +0200 Subject: [PATCH 1400/1454] add remaning changes related to previous commit --- relecov_tools/assets/schema_utils/jsonschema_draft.py | 2 +- relecov_tools/build_schema.py | 5 +++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/relecov_tools/assets/schema_utils/jsonschema_draft.py b/relecov_tools/assets/schema_utils/jsonschema_draft.py index 633a8264..fe7d3ee9 100644 --- a/relecov_tools/assets/schema_utils/jsonschema_draft.py +++ b/relecov_tools/assets/schema_utils/jsonschema_draft.py @@ -15,7 +15,7 @@ ) -def create_draft(draft_version, required=None): +def create_draft(draft_version=None, required=None): """Creates a JSON Schema Draft template with required fields.""" available_schemas = ["2020-12"] diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index ab6d59b1..574088db 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -154,7 +154,8 @@ def handle_build_schema(self): # TODO: if schema not found do something #if not current_schema: - # TODO: build new schema draft based on database definition. - schema_draft_template = self.create_schema_draft_template('2020-2') + # Create schema draft template (leave empty to be prompted to list of available schema versions) + schema_draft_template = self.create_schema_draft_template("2020-2") + # build new schema draft based on database definition. # TODO: Compare current vs new schema From 060e75857e0a97760efc42465dd0b96dfa09b1f1 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 21 Jun 2024 13:57:57 +0200 Subject: [PATCH 1401/1454] fix black linting --- .../assets/schema_utils/jsonschema_draft.py | 10 +++++++--- relecov_tools/build_schema.py | 16 ++++++++-------- relecov_tools/utils.py | 19 +++++++++++++------ 3 files changed, 28 insertions(+), 17 deletions(-) diff --git a/relecov_tools/assets/schema_utils/jsonschema_draft.py b/relecov_tools/assets/schema_utils/jsonschema_draft.py index fe7d3ee9..54f015e9 100644 --- a/relecov_tools/assets/schema_utils/jsonschema_draft.py +++ b/relecov_tools/assets/schema_utils/jsonschema_draft.py @@ -1,5 +1,4 @@ import logging -import sys import rich.console @@ -20,9 +19,14 @@ def create_draft(draft_version=None, required=None): available_schemas = ["2020-12"] if not draft_version: - draft_version = relecov_tools.utils.prompt_checkbox("Choose a Json Schema valid version:", available_schemas) + draft_version = relecov_tools.utils.prompt_checkbox( + "Choose a Json Schema valid version:", available_schemas + ) elif draft_version not in available_schemas: - draft_version = relecov_tools.utils.prompt_checkbox(f"Draft version '{draft_version}' not found. Choose a valid Json Schema version:", available_schemas) + draft_version = relecov_tools.utils.prompt_checkbox( + f"Draft version '{draft_version}' not found. Choose a valid Json Schema version:", + available_schemas, + ) url_str = f"https://json-schema.org/draft/{draft_version}/schema" id_str = "https://github.com/BU-ISCIII/relecov-tools/blob/develop/relecov_tools/schema/relecov_schema.json" diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 574088db..e89f4f6b 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -49,7 +49,9 @@ def __init__( ) else: if not os.path.exists(out_dir): - stderr.print(f"[red]The directory {out_dir} does not exist. Please, try again. Bye") + stderr.print( + f"[red]The directory {out_dir} does not exist. Please, try again. Bye" + ) sys.exit(1) if not os.path.isdir(out_dir): stderr.print("[red]The provided path is not a directory.") @@ -57,7 +59,6 @@ def __init__( else: self.out_dir = out_dir - def read_database_definition(self): """Reads the database definition and converts it into json format.""" # Read excel file @@ -84,7 +85,7 @@ def create_schema_draft_template(self, draft_version=None): ) ) return draft_template - + def get_current_schema(self): """ Check if the current RELECOV schema is available in the configuration file. @@ -92,7 +93,7 @@ def get_current_schema(self): try: conf = ConfigJson() schemas = conf.get_configuration("json_schemas") - + if "relecov_schema" in schemas: current_schema = schemas["relecov_schema"] stderr.print("[green]RELECOV schema found in the configuration.") @@ -113,7 +114,6 @@ def get_current_schema(self): stderr.print(f"An unexpected error occurred: {e}") return None - def build_new_schema(self, schema_draft, json_data): """ Create schema_input.json when no schema is already present. @@ -152,10 +152,10 @@ def handle_build_schema(self): # Verify current schema used by relecov-tools: current_schema = self.get_current_schema() # TODO: if schema not found do something - #if not current_schema: - + # if not current_schema: + # Create schema draft template (leave empty to be prompted to list of available schema versions) schema_draft_template = self.create_schema_draft_template("2020-2") - # build new schema draft based on database definition. + # build new schema draft based on database definition. # TODO: Compare current vs new schema diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 9657fe67..e1d195c4 100755 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -414,8 +414,11 @@ def print_log_report( ) ) + # TODO: not used so far but can help to handle output folder creation. -def prompt_create_outdir(path, folder_name=None, prompt_message="Define path to store the output:"): +def prompt_create_outdir( + path, folder_name=None, prompt_message="Define path to store the output:" +): """Ensure the directory exists or prompt the user to define and create it.""" # Check path if not path: @@ -424,16 +427,20 @@ def prompt_create_outdir(path, folder_name=None, prompt_message="Define path to # Check folder_name if not folder_name: - default_folder = prompt_yn_question("Do you want to use default directory ('results') to store the results? (yes/no):") + default_folder = prompt_yn_question( + "Do you want to use default directory ('results') to store the results? (yes/no):" + ) if not default_folder: folder_name = prompt_text("Write your output directory: ") else: - folder_name = 'results' - + folder_name = "results" + global_path = os.path.join(path, folder_name) if not os.path.exists(global_path): - create_folder = prompt_yn_question(f"The directory does not exist. Do you want to create '{folder_name}' folder in this path? (yes/no):") + create_folder = prompt_yn_question( + f"The directory does not exist. Do you want to create '{folder_name}' folder in this path? (yes/no):" + ) if create_folder: os.makedirs(global_path) stderr.print(f"[green]Folder '{folder_name}' created at {path}") @@ -446,4 +453,4 @@ def prompt_create_outdir(path, folder_name=None, prompt_message="Define path to else: stderr.print("[red]The provided path is not a directory.") sys.exit(1) - return (global_path) + return global_path From 03ee97d695968cab01e4d51332a2b03f6e341581 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 24 Jun 2024 10:36:21 +0200 Subject: [PATCH 1402/1454] created new method to build schema based on database definition and template schema draft --- relecov_tools/build_schema.py | 55 +++++++++++++++++++++++++++++++---- 1 file changed, 50 insertions(+), 5 deletions(-) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index e89f4f6b..6c10e9e4 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -114,11 +114,52 @@ def get_current_schema(self): stderr.print(f"An unexpected error occurred: {e}") return None - def build_new_schema(self, schema_draft, json_data): + def build_new_schema(self, json_data, schema_draft): """ - Create schema_input.json when no schema is already present. + Create a json schema file based on input data and draf skeleton.. """ - # TODO: Read the Excel file and extract the database definitions. + try: + # List of properties to check in the features dictionary: + # key[database_key]: value[schema_key] + properties_to_check = { + 'which enums': 'enum', + 'examples': 'examples', + 'ontology_id': 'ontology', + 'Object type': 'type', # replace 'type' with 'Object type' + 'description': 'description', + 'classification': 'classification', + 'label_name': 'label', + 'fill_mode': 'fill_mode', + 'minLength': 'minLength' # replace 'minLenght' with 'minLength' + } + + for property_id, features in json_data.items(): + schema_property = {} + + for feature_key, schema_key in properties_to_check.items(): + if feature_key in features: + # For enum and examples, wrap the value in a list + if schema_key in ['enum', 'examples']: + value = str(features[feature_key]) + # if no value, json key wont be necessary, then avoid adding it + if len(value) > 0 and not value == 'nan': + schema_property[schema_key] = value + else: + schema_property[schema_key] = features[feature_key] + + # Set default values if not provided + if 'fill_mode' not in schema_property: + schema_property['fill_mode'] = None # FIXME: this does not appear in database definition + if 'minLength' not in schema_property: + schema_property['minLength'] = 1 # FIXME: this does not appear in database definition + + schema_draft['properties'][property_id] = schema_property + + return schema_draft + + except Exception as e: + stderr.print(f"[red]Error building schema: {str(e)}") + raise # TODO: Check if schema_input.json already exists. @@ -147,7 +188,7 @@ def print_schema_diff(self): def handle_build_schema(self): # Load xlsx database and convert into json format - self.read_database_definition() + database_dic = self.read_database_definition() # Verify current schema used by relecov-tools: current_schema = self.get_current_schema() @@ -155,7 +196,11 @@ def handle_build_schema(self): # if not current_schema: # Create schema draft template (leave empty to be prompted to list of available schema versions) - schema_draft_template = self.create_schema_draft_template("2020-2") + schema_draft_template = self.create_schema_draft_template("2020-12") # build new schema draft based on database definition. + res = self.build_new_schema(database_dic, schema_draft_template) + # TODO: Compare current vs new schema + + # TODO: add method to add new schema via input file instead of building new (encompases validation checks). From aee9899ca2cc9008d945d9e5ee47f1775bef3455 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 25 Jun 2024 12:00:43 +0200 Subject: [PATCH 1403/1454] update method to build new schema and add items to json draft --- .../assets/schema_utils/jsonschema_draft.py | 5 +++-- relecov_tools/build_schema.py | 20 ++++++++++++------- 2 files changed, 16 insertions(+), 9 deletions(-) diff --git a/relecov_tools/assets/schema_utils/jsonschema_draft.py b/relecov_tools/assets/schema_utils/jsonschema_draft.py index 54f015e9..f5c5cdaa 100644 --- a/relecov_tools/assets/schema_utils/jsonschema_draft.py +++ b/relecov_tools/assets/schema_utils/jsonschema_draft.py @@ -28,7 +28,7 @@ def create_draft(draft_version=None, required=None): available_schemas, ) - url_str = f"https://json-schema.org/draft/{draft_version}/schema" + url_str = Draft202012Validator.META_SCHEMA["$id"] id_str = "https://github.com/BU-ISCIII/relecov-tools/blob/develop/relecov_tools/schema/relecov_schema.json" description_str = "Json schema that specifies the structure, content, and validation rules for RELECOV metadata" pakage_version_str = pkg_resources.get_distribution("relecov_tools").version @@ -41,7 +41,8 @@ def create_draft(draft_version=None, required=None): "description": description_str, "version": pakage_version_str, "type": "object", - "properties": {}, + "required": [], + "properties": {} } # Include required fields if specified diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 6c10e9e4..b7c958e8 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -122,17 +122,19 @@ def build_new_schema(self, json_data, schema_draft): # List of properties to check in the features dictionary: # key[database_key]: value[schema_key] properties_to_check = { - 'which enums': 'enum', + 'enum': 'enum', 'examples': 'examples', 'ontology_id': 'ontology', - 'Object type': 'type', # replace 'type' with 'Object type' + 'type': 'type', 'description': 'description', 'classification': 'classification', 'label_name': 'label', 'fill_mode': 'fill_mode', - 'minLength': 'minLength' # replace 'minLenght' with 'minLength' + 'minLength': 'minLength', + 'required': 'required' } + # Filling properties for property_id, features in json_data.items(): schema_property = {} @@ -143,7 +145,11 @@ def build_new_schema(self, json_data, schema_draft): value = str(features[feature_key]) # if no value, json key wont be necessary, then avoid adding it if len(value) > 0 and not value == 'nan': - schema_property[schema_key] = value + # Enum is an array like object + if schema_key == 'enum': + schema_property[schema_key] = value.split(', ') + elif schema_key == 'examples': + schema_property[schema_key] = [value] else: schema_property[schema_key] = features[feature_key] @@ -160,10 +166,10 @@ def build_new_schema(self, json_data, schema_draft): except Exception as e: stderr.print(f"[red]Error building schema: {str(e)}") raise + # Once json schema is created, it requires validation - # TODO: Check if schema_input.json already exists. + # TODO: add validation chek - # TODO: If schema_input.json does not exist, create it and populate with the extracted definitions. def update_schema(self): """ @@ -199,7 +205,7 @@ def handle_build_schema(self): schema_draft_template = self.create_schema_draft_template("2020-12") # build new schema draft based on database definition. - res = self.build_new_schema(database_dic, schema_draft_template) + new_schema = self.build_new_schema(database_dic, schema_draft_template) # TODO: Compare current vs new schema From 27693370726452752ddcac157ac875e07381535f Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 25 Jun 2024 12:02:44 +0200 Subject: [PATCH 1404/1454] add method and utils to check new schema is valid --- relecov_tools/assets/schema_utils/jsonschema_draft.py | 11 +++++++++++ relecov_tools/build_schema.py | 8 +++++++- 2 files changed, 18 insertions(+), 1 deletion(-) diff --git a/relecov_tools/assets/schema_utils/jsonschema_draft.py b/relecov_tools/assets/schema_utils/jsonschema_draft.py index f5c5cdaa..293a42d6 100644 --- a/relecov_tools/assets/schema_utils/jsonschema_draft.py +++ b/relecov_tools/assets/schema_utils/jsonschema_draft.py @@ -4,6 +4,7 @@ import relecov_tools.utils import pkg_resources +from jsonschema import Draft202012Validator, ValidationError, exceptions log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -53,3 +54,13 @@ def create_draft(draft_version=None, required=None): # TODO: draft202012Validator should be implemented here +# TODO: this should be able to check_schema based on supported versions. +def check_schema_draft(schema_draft, version="2020-12"): + """Validates the schema_draft against the JSON Schema Draft 2020-12 meta-schema.""" + try: + Draft202012Validator.check_schema(schema_draft) + stderr.print("Schema is valid.") + except exceptions.SchemaError as e: + stderr.print(f"[red]Schema validation error: {e.message}") + except Exception as e: + stderr.print(f"An error occurred during schema validation: {str(e)}") \ No newline at end of file diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index b7c958e8..0b7bcf95 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -168,7 +168,11 @@ def build_new_schema(self, json_data, schema_draft): raise # Once json schema is created, it requires validation - # TODO: add validation chek + def verify_schema(self, schema): + """Verify the schema_draft follows the JSON Schema specification [XXXX] meta-schema.""" + relecov_tools.assets.schema_utils.jsonschema_draft.check_schema_draft(schema) + # TODO: specification version should be added to input params and self. + def update_schema(self): @@ -207,6 +211,8 @@ def handle_build_schema(self): # build new schema draft based on database definition. new_schema = self.build_new_schema(database_dic, schema_draft_template) + # Check new schema follows json schema specification rules. + self.verify_schema(new_schema) # TODO: Compare current vs new schema # TODO: add method to add new schema via input file instead of building new (encompases validation checks). From aa6ac462a8af70ed9d2c7a07d3737d072b586b0c Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 25 Jun 2024 12:43:33 +0200 Subject: [PATCH 1405/1454] implement json schema's required section --- .../assets/schema_utils/jsonschema_draft.py | 4 ++-- relecov_tools/build_schema.py | 21 +++++++++++++++++-- 2 files changed, 21 insertions(+), 4 deletions(-) diff --git a/relecov_tools/assets/schema_utils/jsonschema_draft.py b/relecov_tools/assets/schema_utils/jsonschema_draft.py index 293a42d6..66b36430 100644 --- a/relecov_tools/assets/schema_utils/jsonschema_draft.py +++ b/relecov_tools/assets/schema_utils/jsonschema_draft.py @@ -59,8 +59,8 @@ def check_schema_draft(schema_draft, version="2020-12"): """Validates the schema_draft against the JSON Schema Draft 2020-12 meta-schema.""" try: Draft202012Validator.check_schema(schema_draft) - stderr.print("Schema is valid.") + stderr.print("[green] New schema is valid based on JSON Specification rules.") except exceptions.SchemaError as e: stderr.print(f"[red]Schema validation error: {e.message}") except Exception as e: - stderr.print(f"An error occurred during schema validation: {str(e)}") \ No newline at end of file + stderr.print(f"An error occurred during schema validation: {str(e)}") diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 0b7bcf95..7dfeacbd 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -26,6 +26,7 @@ def __init__( show_diff=False, out_dir=None, ): + # TODO: Fix old description """ Initialize the SchemaBuilder with paths to the Excel file containing the database definitions and the schema_input.json file. @@ -131,12 +132,14 @@ def build_new_schema(self, json_data, schema_draft): 'label_name': 'label', 'fill_mode': 'fill_mode', 'minLength': 'minLength', - 'required': 'required' + 'required (Y/N )': 'required' } + schema_required_unique = [] # Filling properties for property_id, features in json_data.items(): schema_property = {} + schema_required = {} for feature_key, schema_key in properties_to_check.items(): if feature_key in features: @@ -150,6 +153,12 @@ def build_new_schema(self, json_data, schema_draft): schema_property[schema_key] = value.split(', ') elif schema_key == 'examples': schema_property[schema_key] = [value] + # Recover 'required' properties from database definition. + elif schema_key == 'required': + value = str(features[feature_key]) + if value != 'nan': + schema_required[property_id] = value + else: schema_property[schema_key] = features[feature_key] @@ -158,9 +167,17 @@ def build_new_schema(self, json_data, schema_draft): schema_property['fill_mode'] = None # FIXME: this does not appear in database definition if 'minLength' not in schema_property: schema_property['minLength'] = 1 # FIXME: this does not appear in database definition - + + # Finally, send schema_property object to new json schema. schema_draft['properties'][property_id] = schema_property + # Finally, send schema_required object to new json schema. + for key, values in schema_required.items(): + if value == 'Y': + schema_required_unique.append(key) + schema_draft['required'] = schema_required_unique + + # Return new schema return schema_draft except Exception as e: From 0e134c98f02a61225d5693d6381e20827e073043 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 25 Jun 2024 12:52:38 +0200 Subject: [PATCH 1406/1454] fix linting --- .../assets/schema_utils/jsonschema_draft.py | 4 +- relecov_tools/build_schema.py | 65 ++++++++++--------- 2 files changed, 36 insertions(+), 33 deletions(-) diff --git a/relecov_tools/assets/schema_utils/jsonschema_draft.py b/relecov_tools/assets/schema_utils/jsonschema_draft.py index 66b36430..8adec781 100644 --- a/relecov_tools/assets/schema_utils/jsonschema_draft.py +++ b/relecov_tools/assets/schema_utils/jsonschema_draft.py @@ -4,7 +4,7 @@ import relecov_tools.utils import pkg_resources -from jsonschema import Draft202012Validator, ValidationError, exceptions +from jsonschema import Draft202012Validator, exceptions log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -43,7 +43,7 @@ def create_draft(draft_version=None, required=None): "version": pakage_version_str, "type": "object", "required": [], - "properties": {} + "properties": {}, } # Include required fields if specified diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 7dfeacbd..87e467ef 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -123,16 +123,16 @@ def build_new_schema(self, json_data, schema_draft): # List of properties to check in the features dictionary: # key[database_key]: value[schema_key] properties_to_check = { - 'enum': 'enum', - 'examples': 'examples', - 'ontology_id': 'ontology', - 'type': 'type', - 'description': 'description', - 'classification': 'classification', - 'label_name': 'label', - 'fill_mode': 'fill_mode', - 'minLength': 'minLength', - 'required (Y/N )': 'required' + "enum": "enum", + "examples": "examples", + "ontology_id": "ontology", + "type": "type", + "description": "description", + "classification": "classification", + "label_name": "label", + "fill_mode": "fill_mode", + "minLength": "minLength", + "required (Y/N )": "required", } schema_required_unique = [] @@ -144,38 +144,42 @@ def build_new_schema(self, json_data, schema_draft): for feature_key, schema_key in properties_to_check.items(): if feature_key in features: # For enum and examples, wrap the value in a list - if schema_key in ['enum', 'examples']: + if schema_key in ["enum", "examples"]: value = str(features[feature_key]) # if no value, json key wont be necessary, then avoid adding it - if len(value) > 0 and not value == 'nan': + if len(value) > 0 and not value == "nan": # Enum is an array like object - if schema_key == 'enum': - schema_property[schema_key] = value.split(', ') - elif schema_key == 'examples': + if schema_key == "enum": + schema_property[schema_key] = value.split(", ") + elif schema_key == "examples": schema_property[schema_key] = [value] # Recover 'required' properties from database definition. - elif schema_key == 'required': + elif schema_key == "required": value = str(features[feature_key]) - if value != 'nan': + if value != "nan": schema_required[property_id] = value else: schema_property[schema_key] = features[feature_key] # Set default values if not provided - if 'fill_mode' not in schema_property: - schema_property['fill_mode'] = None # FIXME: this does not appear in database definition - if 'minLength' not in schema_property: - schema_property['minLength'] = 1 # FIXME: this does not appear in database definition - + if "fill_mode" not in schema_property: + schema_property["fill_mode"] = ( + None # FIXME: this does not appear in database definition + ) + if "minLength" not in schema_property: + schema_property["minLength"] = ( + 1 # FIXME: this does not appear in database definition + ) + # Finally, send schema_property object to new json schema. - schema_draft['properties'][property_id] = schema_property + schema_draft["properties"][property_id] = schema_property - # Finally, send schema_required object to new json schema. + # Finally, send schema_required object to new json schema. for key, values in schema_required.items(): - if value == 'Y': + if value == "Y": schema_required_unique.append(key) - schema_draft['required'] = schema_required_unique + schema_draft["required"] = schema_required_unique # Return new schema return schema_draft @@ -190,8 +194,6 @@ def verify_schema(self, schema): relecov_tools.assets.schema_utils.jsonschema_draft.check_schema_draft(schema) # TODO: specification version should be added to input params and self. - - def update_schema(self): """ Update the schema_input.json based on the definitions in the Excel file. @@ -218,7 +220,7 @@ def handle_build_schema(self): database_dic = self.read_database_definition() # Verify current schema used by relecov-tools: - current_schema = self.get_current_schema() + self.get_current_schema() # TODO: if schema not found do something # if not current_schema: @@ -228,8 +230,9 @@ def handle_build_schema(self): # build new schema draft based on database definition. new_schema = self.build_new_schema(database_dic, schema_draft_template) - # Check new schema follows json schema specification rules. + # Verify new schema follows json schema specification rules. self.verify_schema(new_schema) + # TODO: Compare current vs new schema - # TODO: add method to add new schema via input file instead of building new (encompases validation checks). + # TODO: add method to add new schema via input file instead of building new (encompases validation checks). From a3ec9f5b4aa817f6b616ba68b0460fd3c88e3255 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 25 Jun 2024 14:10:59 +0200 Subject: [PATCH 1407/1454] add draft version as module param and update utils to invoke functions based on draft version --- relecov_tools/__main__.py | 10 ++- .../assets/schema_utils/jsonschema_draft.py | 62 +++++++++++++------ relecov_tools/build_schema.py | 27 +++++--- 3 files changed, 70 insertions(+), 29 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index d731189b..9c16de67 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -526,6 +526,12 @@ def launch_pipeline(input, template, output, config): type=click.Path(), help="Path to the Excel document containing the database definition.", ) +@click.option( + "-v", + "--draft_version", + type=click.STRING, + help="Version of the JSON schema specification to be used. Example: '2020-12. See: https://json-schema.org/specification-links", +) @click.option( "-d", "--diff", @@ -533,10 +539,10 @@ def launch_pipeline(input, template, output, config): help="Prints a changelog/diff between the current and incoming versions of the schema schema_relecov.json.", ) @click.option("-o", "--out_dir", type=click.Path(), help="Path to save output file/s") -def build_schema(input_file, schema_base, diff, out_dir): +def build_schema(input_file, schema_base, draft_version, diff, out_dir): """""" schema_update = relecov_tools.build_schema.SchemaBuilder( - input_file, schema_base, diff, out_dir + input_file, schema_base, draft_version, diff, out_dir ) schema_update.handle_build_schema() diff --git a/relecov_tools/assets/schema_utils/jsonschema_draft.py b/relecov_tools/assets/schema_utils/jsonschema_draft.py index 8adec781..7f9995e0 100644 --- a/relecov_tools/assets/schema_utils/jsonschema_draft.py +++ b/relecov_tools/assets/schema_utils/jsonschema_draft.py @@ -1,5 +1,5 @@ import logging - +import sys import rich.console import relecov_tools.utils @@ -14,20 +14,39 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) +SCHEMA_VALIDATORS = { + "2020-12": Draft202012Validator, +} -def create_draft(draft_version=None, required=None): - """Creates a JSON Schema Draft template with required fields.""" - available_schemas = ["2020-12"] + +def check_valid_version(draft_version): + """Validate the provided draft version against available JSON Schema versions.""" + available_schemas = [version for version in SCHEMA_VALIDATORS.keys()] + try: + if not draft_version: + draft_version = relecov_tools.utils.prompt_selection( + "Choose a Json Schema valid version:", available_schemas + ) + elif draft_version not in available_schemas: + draft_version = relecov_tools.utils.prompt_selection( + f"Draft version '{draft_version}' not found. Choose a valid Json Schema version:", + available_schemas, + ) + except Exception as e: + stderr.print(f"[red]An error occurred while selecting the draft version: {e}") + sys.exit(1) if not draft_version: - draft_version = relecov_tools.utils.prompt_checkbox( - "Choose a Json Schema valid version:", available_schemas - ) - elif draft_version not in available_schemas: - draft_version = relecov_tools.utils.prompt_checkbox( - f"Draft version '{draft_version}' not found. Choose a valid Json Schema version:", - available_schemas, - ) + stderr.print("[red]No valid draft version selected. Exiting.") + sys.exit(1) + + stderr.print(f"[green]Using draft version: {draft_version}") + return draft_version + + +def create_draft(draft_version, required_items=None): + """Creates a JSON Schema Draft template with required fields.""" + # Check if required draft version is available url_str = Draft202012Validator.META_SCHEMA["$id"] id_str = "https://github.com/BU-ISCIII/relecov-tools/blob/develop/relecov_tools/schema/relecov_schema.json" @@ -42,24 +61,27 @@ def create_draft(draft_version=None, required=None): "description": description_str, "version": pakage_version_str, "type": "object", - "required": [], "properties": {}, } # Include required fields if specified - if required: - draft_template["required"] = required + if required_items: + draft_template["required"] = [] return draft_template -# TODO: draft202012Validator should be implemented here -# TODO: this should be able to check_schema based on supported versions. -def check_schema_draft(schema_draft, version="2020-12"): +def check_schema_draft(schema_draft, draft_version): """Validates the schema_draft against the JSON Schema Draft 2020-12 meta-schema.""" + if draft_version not in SCHEMA_VALIDATORS: + stderr.print(f"[red]Unsupported draft version: {draft_version}") + sys.exit(1) + + validator_class = SCHEMA_VALIDATORS[draft_version] + try: - Draft202012Validator.check_schema(schema_draft) - stderr.print("[green] New schema is valid based on JSON Specification rules.") + validator_class.check_schema(schema_draft) + stderr.print("[green]New schema is valid based on JSON Specification rules.") except exceptions.SchemaError as e: stderr.print(f"[red]Schema validation error: {e.message}") except Exception as e: diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 87e467ef..1f81ed52 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -18,11 +18,13 @@ ) +# TODO: user should be able to provide a custom schema as a file in order to replace the current one. class SchemaBuilder: def __init__( self, excel_file_path=None, base_schema_path=None, + draft_version=None, show_diff=False, out_dir=None, ): @@ -37,6 +39,7 @@ def __init__( """ self.excel_file_path = excel_file_path self.schema_file_path = base_schema_path + self.draft_version = draft_version self.show_diff = show_diff # Validate input variables @@ -60,6 +63,13 @@ def __init__( else: self.out_dir = out_dir + # Validate json schema draft version + self.draft_version = ( + relecov_tools.assets.schema_utils.jsonschema_draft.check_valid_version( + draft_version + ) + ) + def read_database_definition(self): """Reads the database definition and converts it into json format.""" # Read excel file @@ -78,11 +88,11 @@ def read_database_definition(self): sys.exit(1) return json_data - def create_schema_draft_template(self, draft_version=None): + def create_schema_draft_template(self): "Loads JsonSchema template based on draft name: Available drafts: [2020-12]" draft_template = ( relecov_tools.assets.schema_utils.jsonschema_draft.create_draft( - draft_version + self.draft_version, True ) ) return draft_template @@ -115,6 +125,7 @@ def get_current_schema(self): stderr.print(f"An unexpected error occurred: {e}") return None + # TODO: add strategy to deal with json schema objects, defs and refs def build_new_schema(self, json_data, schema_draft): """ Create a json schema file based on input data and draf skeleton.. @@ -172,12 +183,12 @@ def build_new_schema(self, json_data, schema_draft): 1 # FIXME: this does not appear in database definition ) - # Finally, send schema_property object to new json schema. + # Finally, send schema_property object to the new json schema. schema_draft["properties"][property_id] = schema_property - # Finally, send schema_required object to new json schema. + # Finally, send schema_required object to the new json schema. for key, values in schema_required.items(): - if value == "Y": + if values == "Y": schema_required_unique.append(key) schema_draft["required"] = schema_required_unique @@ -191,7 +202,9 @@ def build_new_schema(self, json_data, schema_draft): def verify_schema(self, schema): """Verify the schema_draft follows the JSON Schema specification [XXXX] meta-schema.""" - relecov_tools.assets.schema_utils.jsonschema_draft.check_schema_draft(schema) + relecov_tools.assets.schema_utils.jsonschema_draft.check_schema_draft( + schema, self.draft_version + ) # TODO: specification version should be added to input params and self. def update_schema(self): @@ -225,7 +238,7 @@ def handle_build_schema(self): # if not current_schema: # Create schema draft template (leave empty to be prompted to list of available schema versions) - schema_draft_template = self.create_schema_draft_template("2020-12") + schema_draft_template = self.create_schema_draft_template() # build new schema draft based on database definition. new_schema = self.build_new_schema(database_dic, schema_draft_template) From 7dbeeeee5ad1c4b86728cbbbb80bc6bca8541ccb Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 25 Jun 2024 14:19:02 +0200 Subject: [PATCH 1408/1454] rename the schema already in use as 'base schema' --- relecov_tools/__main__.py | 2 +- relecov_tools/build_schema.py | 21 +++++++++++---------- 2 files changed, 12 insertions(+), 11 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 9c16de67..2c4e591c 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -524,7 +524,7 @@ def launch_pipeline(input, template, output, config): "-s", "--schema_base", type=click.Path(), - help="Path to the Excel document containing the database definition.", + help="Path to in use json schema (optional).", ) @click.option( "-v", diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 1f81ed52..b85e7328 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -97,18 +97,18 @@ def create_schema_draft_template(self): ) return draft_template - def get_current_schema(self): + def get_base_schema(self): """ - Check if the current RELECOV schema is available in the configuration file. + Check if the current ('base') RELECOV schema is available in the configuration file. """ try: conf = ConfigJson() schemas = conf.get_configuration("json_schemas") if "relecov_schema" in schemas: - current_schema = schemas["relecov_schema"] + base_schema = schemas["relecov_schema"] stderr.print("[green]RELECOV schema found in the configuration.") - return current_schema + return base_schema else: stderr.print("[orange]RELECOV schema not found in the configuration.") return None @@ -213,16 +213,16 @@ def update_schema(self): """ # TODO: Read the Excel file and extract the database definitions. - # TODO: Compare the extracted definitions with the current schema_input.json. + # TODO: Compare the extracted definitions with the base schema_input.json. # TODO: Update the schema_input.json with the new definitions. def print_schema_diff(self): """ - Print the differences between the current version of schema_input.json + Print the differences between the base version of schema_input.json and the updated version after calling update_schema(). """ - # TODO: Load the current schema_input.json. + # TODO: Load the base schema_input.json. # TODO: Load the updated schema_input.json after calling update_schema(). @@ -233,9 +233,10 @@ def handle_build_schema(self): database_dic = self.read_database_definition() # Verify current schema used by relecov-tools: - self.get_current_schema() + self.get_base_schema() + # TODO: if schema not found do something - # if not current_schema: + # if not base_schema: # Create schema draft template (leave empty to be prompted to list of available schema versions) schema_draft_template = self.create_schema_draft_template() @@ -246,6 +247,6 @@ def handle_build_schema(self): # Verify new schema follows json schema specification rules. self.verify_schema(new_schema) - # TODO: Compare current vs new schema + # TODO: Compare base vs new schema # TODO: add method to add new schema via input file instead of building new (encompases validation checks). From 610efb367527218204d72bf88b7ca5ef2f1b5fad Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 25 Jun 2024 14:22:56 +0200 Subject: [PATCH 1409/1454] replace irerrows by itertuples --- relecov_tools/build_schema.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index b85e7328..389606bc 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -77,10 +77,10 @@ def read_database_definition(self): # Convert database to json format json_data = {} - for _, row in df.iterrows(): - property_name = row.iloc[0] - values = row.drop(df.columns[0]).to_dict() - json_data[property_name] = values + for row in df.itertuples(index=False): + property_name = row[0] + values = row[1:] + json_data[property_name] = dict(zip(df.columns[1:], values)) # Check json is not empty if len(json_data) == 0: From 4f01e076e0dd47618faf1c49b81d8bcf7ee6fdb2 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 28 Jun 2024 18:01:33 +0200 Subject: [PATCH 1410/1454] fix get_base_schema and implement method to get diff between base and new schema --- relecov_tools/build_schema.py | 100 ++++++++++++++++++++++++++-------- requirements.txt | 3 +- 2 files changed, 78 insertions(+), 25 deletions(-) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 389606bc..e48661ba 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -4,6 +4,8 @@ import pandas as pd import os import sys +import json +import difflib import relecov_tools.utils import relecov_tools.assets.schema_utils.jsonschema_draft @@ -103,20 +105,27 @@ def get_base_schema(self): """ try: conf = ConfigJson() - schemas = conf.get_configuration("json_schemas") - - if "relecov_schema" in schemas: - base_schema = schemas["relecov_schema"] - stderr.print("[green]RELECOV schema found in the configuration.") - return base_schema + relecov_schema_conf = conf.get_topic_data("json_schemas", "relecov_schema") + + if relecov_schema_conf: + try: + base_schema_path = os.path.join( + os.path.dirname(os.path.realpath(__file__)), + "schema", + relecov_schema_conf, + ) + os.path.isfile(base_schema_path) + stderr.print("[green]RELECOV schema found in the configuration.") + base_schema_json = relecov_tools.utils.read_json_file( + base_schema_path + ) + return base_schema_json + except FileNotFoundError as fnf_error: + stderr.print(f"[red]Configuration file not found: {fnf_error}") + return None else: stderr.print("[orange]RELECOV schema not found in the configuration.") return None - - except FileNotFoundError as fnf_error: - stderr.print(f"[red]Configuration file not found: {fnf_error}") - return None - except KeyError as key_error: stderr.print(f"[orange]Configuration key error: {key_error}") return None @@ -207,6 +216,53 @@ def verify_schema(self, schema): ) # TODO: specification version should be added to input params and self. + def print_schema_diff(self, base_schema, new_schema): + """ + Print the differences between the base version of schema_input.json + and the updated version. + """ + # Set diff input + base_schema_lines = json.dumps(base_schema, indent=4).splitlines() + new_schema_lines = json.dumps(new_schema, indent=4).splitlines() + + # Get diff lines + diff_lines = list( + difflib.unified_diff( + base_schema_lines, + new_schema_lines, + fromfile="base_schema.json", + tofile="new_schema.json", + ) + ) + + if not diff_lines: + stderr.print( + "[orange]No differencess were found between already installed and new generated schema. Exiting. No changes made" + ) + return None + else: + stderr.print( + "Differences found between the existing schema and the newly generated schema." + ) + # Set user's choices + choices = ["Print to sandard output (stdout)", "Save to file", "Both"] + diff_output_choice = relecov_tools.utils.prompt_selection( + "How would you like to print the diff between schemes?:", choices + ) + if diff_output_choice in ["Print to sandard output (stdout)", "Both"]: + for line in diff_lines: + print(line) + return True + if diff_output_choice in ["Save to file", "Both"]: + stderr.print(self.out_dir) + diff_filepath = os.path.join( + os.path.realpath(self.out_dir) + "/build_schema_diff.txt" + ) + with open(diff_filepath, "w") as diff_file: + diff_file.write("\n".join(diff_lines)) + stderr.print(f"[green]Schema differences saved to {diff_filepath}") + return True + def update_schema(self): """ Update the schema_input.json based on the definitions in the Excel file. @@ -217,24 +273,16 @@ def update_schema(self): # TODO: Update the schema_input.json with the new definitions. - def print_schema_diff(self): - """ - Print the differences between the base version of schema_input.json - and the updated version after calling update_schema(). - """ - # TODO: Load the base schema_input.json. - - # TODO: Load the updated schema_input.json after calling update_schema(). - - # TODO: Compare the two versions and print/save the differences. - def handle_build_schema(self): # Load xlsx database and convert into json format database_dic = self.read_database_definition() # Verify current schema used by relecov-tools: - self.get_base_schema() - + base_schema = self.get_base_schema() + if not base_schema: + stderr.print("[red]Couldn't find relecov base schema. Exiting...)") + sys.exit() + # TODO: if schema not found do something # if not base_schema: @@ -248,5 +296,9 @@ def handle_build_schema(self): self.verify_schema(new_schema) # TODO: Compare base vs new schema + schema_diff = self.print_schema_diff(base_schema, new_schema) + if schema_diff: + # TODO: If diff ask user to update schema (allow a preview). Else exit. ¿bump version? + self.update_schema() # TODO: add method to add new schema via input file instead of building new (encompases validation checks). diff --git a/requirements.txt b/requirements.txt index 53959139..1792bce4 100644 --- a/requirements.txt +++ b/requirements.txt @@ -12,4 +12,5 @@ ena-upload-cli bio==1.4.0 xlsxwriter bs4==0.0.2 -tabulate \ No newline at end of file +tabulate +cdifflib==1.2.6 \ No newline at end of file From 6467ce4d25e607ba18aec2ecef1e046ef0fbcbf0 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 1 Jul 2024 09:01:01 +0200 Subject: [PATCH 1411/1454] add missing library, update descritpion and add todos --- relecov_tools/__main__.py | 8 +++++--- relecov_tools/build_schema.py | 15 +++++++-------- requirements.txt | 2 +- 3 files changed, 13 insertions(+), 12 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 2c4e591c..85d1b5b1 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -518,13 +518,15 @@ def launch_pipeline(input, template, output, config): "-i", "--input_file", type=click.Path(), - help="Path to the Excel document containing the database definition.", + help="Path to the Excel document containing the database definition. This file must have a .xlsx extension.", + required=True, ) @click.option( "-s", "--schema_base", type=click.Path(), - help="Path to in use json schema (optional).", + help="Path to the base schema file. This file is used as a reference to compare it with the schema generated using this module.", + required=False, ) @click.option( "-v", @@ -536,7 +538,7 @@ def launch_pipeline(input, template, output, config): "-d", "--diff", type=click.BOOL, - help="Prints a changelog/diff between the current and incoming versions of the schema schema_relecov.json.", + help="Prints a changelog/diff between the base and incoming versions of the schema.", ) @click.option("-o", "--out_dir", type=click.Path(), help="Path to save output file/s") def build_schema(input_file, schema_base, draft_version, diff, out_dir): diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index e48661ba..01d2af84 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -32,12 +32,8 @@ def __init__( ): # TODO: Fix old description """ - Initialize the SchemaBuilder with paths to the Excel file containing the database definitions - and the schema_input.json file. - - Args: - excel_file_path (str): Path to the Excel file containing the database definitions. - schema_file_path (str): Path to the schema_input.json file. + Initialize the SchemaBuilder class. This class generates a JSON Schema file based on the provided draft version. + It reads the database definition from an Excel file and allows customization of the schema generation process. """ self.excel_file_path = excel_file_path self.schema_file_path = base_schema_path @@ -185,11 +181,11 @@ def build_new_schema(self, json_data, schema_draft): # Set default values if not provided if "fill_mode" not in schema_property: schema_property["fill_mode"] = ( - None # FIXME: this does not appear in database definition + None ) if "minLength" not in schema_property: schema_property["minLength"] = ( - 1 # FIXME: this does not appear in database definition + 1 ) # Finally, send schema_property object to the new json schema. @@ -302,3 +298,6 @@ def handle_build_schema(self): self.update_schema() # TODO: add method to add new schema via input file instead of building new (encompases validation checks). + # TODO: Add versioning of schema when it is updated. + # TODO: Add method to register logs any time schema is updated + # TODO: After updating schema, generate the excell template. diff --git a/requirements.txt b/requirements.txt index 1792bce4..b2c64107 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,4 +13,4 @@ bio==1.4.0 xlsxwriter bs4==0.0.2 tabulate -cdifflib==1.2.6 \ No newline at end of file +difflib \ No newline at end of file From 4205d498135424764f68308529743bc25b46156d Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 1 Jul 2024 09:09:58 +0200 Subject: [PATCH 1412/1454] removed conflicting library --- requirements.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index b2c64107..e54911f2 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,4 +13,3 @@ bio==1.4.0 xlsxwriter bs4==0.0.2 tabulate -difflib \ No newline at end of file From 71cfaf22c1913fd759e7b853494e0ad5595deb34 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 1 Jul 2024 10:20:02 +0200 Subject: [PATCH 1413/1454] update path to validate the base schema --- relecov_tools/build_schema.py | 88 +++++++++++++++-------------------- 1 file changed, 37 insertions(+), 51 deletions(-) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 01d2af84..e229dc23 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -30,14 +30,11 @@ def __init__( show_diff=False, out_dir=None, ): - # TODO: Fix old description """ Initialize the SchemaBuilder class. This class generates a JSON Schema file based on the provided draft version. It reads the database definition from an Excel file and allows customization of the schema generation process. """ self.excel_file_path = excel_file_path - self.schema_file_path = base_schema_path - self.draft_version = draft_version self.show_diff = show_diff # Validate input variables @@ -68,6 +65,26 @@ def __init__( ) ) + # Validate base schema + if not base_schema_path: + try: + config_json = ConfigJson() + relecov_schema = config_json.get_topic_data("json_schemas", "relecov_schema") + try: + self.base_schema_path = os.path.join( + os.path.dirname(os.path.realpath(__file__)), + "schema", + relecov_schema, + ) + os.path.isfile(self.base_schema_path) + stderr.print("[green]RELECOV schema found in the configuration.") + except FileNotFoundError as fnf_error: + stderr.print(f"[red]Configuration file not found: {fnf_error}") + sys.exit(1) + except KeyError as key_error: + stderr.print(f"[orange]Configuration key error: {key_error}") + sys.exit(1) + def read_database_definition(self): """Reads the database definition and converts it into json format.""" # Read excel file @@ -95,41 +112,6 @@ def create_schema_draft_template(self): ) return draft_template - def get_base_schema(self): - """ - Check if the current ('base') RELECOV schema is available in the configuration file. - """ - try: - conf = ConfigJson() - relecov_schema_conf = conf.get_topic_data("json_schemas", "relecov_schema") - - if relecov_schema_conf: - try: - base_schema_path = os.path.join( - os.path.dirname(os.path.realpath(__file__)), - "schema", - relecov_schema_conf, - ) - os.path.isfile(base_schema_path) - stderr.print("[green]RELECOV schema found in the configuration.") - base_schema_json = relecov_tools.utils.read_json_file( - base_schema_path - ) - return base_schema_json - except FileNotFoundError as fnf_error: - stderr.print(f"[red]Configuration file not found: {fnf_error}") - return None - else: - stderr.print("[orange]RELECOV schema not found in the configuration.") - return None - except KeyError as key_error: - stderr.print(f"[orange]Configuration key error: {key_error}") - return None - - except Exception as e: - stderr.print(f"An unexpected error occurred: {e}") - return None - # TODO: add strategy to deal with json schema objects, defs and refs def build_new_schema(self, json_data, schema_draft): """ @@ -210,7 +192,6 @@ def verify_schema(self, schema): relecov_tools.assets.schema_utils.jsonschema_draft.check_schema_draft( schema, self.draft_version ) - # TODO: specification version should be added to input params and self. def print_schema_diff(self, base_schema, new_schema): """ @@ -259,7 +240,7 @@ def print_schema_diff(self, base_schema, new_schema): stderr.print(f"[green]Schema differences saved to {diff_filepath}") return True - def update_schema(self): + def update_schema(self, ): """ Update the schema_input.json based on the definitions in the Excel file. """ @@ -274,28 +255,33 @@ def handle_build_schema(self): database_dic = self.read_database_definition() # Verify current schema used by relecov-tools: - base_schema = self.get_base_schema() - if not base_schema: + base_schema_json = relecov_tools.utils.read_json_file( + self.base_schema_path + ) + if not base_schema_json: stderr.print("[red]Couldn't find relecov base schema. Exiting...)") - sys.exit() - - # TODO: if schema not found do something - # if not base_schema: + sys.exit(1) # Create schema draft template (leave empty to be prompted to list of available schema versions) schema_draft_template = self.create_schema_draft_template() # build new schema draft based on database definition. - new_schema = self.build_new_schema(database_dic, schema_draft_template) + new_schema_json = self.build_new_schema(database_dic, schema_draft_template) # Verify new schema follows json schema specification rules. - self.verify_schema(new_schema) + self.verify_schema(new_schema_json) - # TODO: Compare base vs new schema - schema_diff = self.print_schema_diff(base_schema, new_schema) + # Compare base vs new schema + schema_diff = self.print_schema_diff(base_schema_json, new_schema_json) if schema_diff: # TODO: If diff ask user to update schema (allow a preview). Else exit. ¿bump version? - self.update_schema() + # TODO: Register / update version + call_update_schema = relecov_tools.utils.prompt_yn_question("Do you want to update the schema?: ") + if call_update_schema: + self.update_schema(new_schema_json) + else: + stderr.print("[green]No changes made. Exiting...") + sys.exit(1) # TODO: add method to add new schema via input file instead of building new (encompases validation checks). # TODO: Add versioning of schema when it is updated. From 2e1fb6148cbf96cd74e06eb9305199075135b05f Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 1 Jul 2024 11:02:50 +0200 Subject: [PATCH 1414/1454] update output folder validation --- relecov_tools/build_schema.py | 23 ++++++----------------- 1 file changed, 6 insertions(+), 17 deletions(-) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index e229dc23..da7aaa16 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -42,21 +42,10 @@ def __init__( raise ValueError("A valid Excel file path must be provided.") if not self.excel_file_path.endswith(".xlsx"): raise ValueError("The Excel file must have a .xlsx extension.") - if not out_dir: - self.output_folder = relecov_tools.utils.prompt_path( - msg="Select the output folder:" - ) - else: - if not os.path.exists(out_dir): - stderr.print( - f"[red]The directory {out_dir} does not exist. Please, try again. Bye" - ) - sys.exit(1) - if not os.path.isdir(out_dir): - stderr.print("[red]The provided path is not a directory.") - sys.exit(1) - else: - self.out_dir = out_dir + + # Validate output folder + relecov_tools.utils.prompt_create_outdir(os.getcwd(), out_dir) + self.output_folder = os.path.join(os.getcwd(), out_dir) # Validate json schema draft version self.draft_version = ( @@ -231,9 +220,9 @@ def print_schema_diff(self, base_schema, new_schema): print(line) return True if diff_output_choice in ["Save to file", "Both"]: - stderr.print(self.out_dir) + stderr.print(self.output_folder) diff_filepath = os.path.join( - os.path.realpath(self.out_dir) + "/build_schema_diff.txt" + os.path.realpath(self.output_folder) + "/build_schema_diff.txt" ) with open(diff_filepath, "w") as diff_file: diff_file.write("\n".join(diff_lines)) From 2012b9b630f1551878d646b82f6be2cb3a53e791 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 1 Jul 2024 11:16:33 +0200 Subject: [PATCH 1415/1454] added method to save the schema generated by SchemaBuilder --- relecov_tools/build_schema.py | 61 ++++++++++++++++++----------------- 1 file changed, 32 insertions(+), 29 deletions(-) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index da7aaa16..d783ea54 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -58,7 +58,9 @@ def __init__( if not base_schema_path: try: config_json = ConfigJson() - relecov_schema = config_json.get_topic_data("json_schemas", "relecov_schema") + relecov_schema = config_json.get_topic_data( + "json_schemas", "relecov_schema" + ) try: self.base_schema_path = os.path.join( os.path.dirname(os.path.realpath(__file__)), @@ -66,7 +68,9 @@ def __init__( relecov_schema, ) os.path.isfile(self.base_schema_path) - stderr.print("[green]RELECOV schema found in the configuration.") + stderr.print( + "[green]RELECOV schema successfully found in the configuration." + ) except FileNotFoundError as fnf_error: stderr.print(f"[red]Configuration file not found: {fnf_error}") sys.exit(1) @@ -151,13 +155,9 @@ def build_new_schema(self, json_data, schema_draft): # Set default values if not provided if "fill_mode" not in schema_property: - schema_property["fill_mode"] = ( - None - ) + schema_property["fill_mode"] = None if "minLength" not in schema_property: - schema_property["minLength"] = ( - 1 - ) + schema_property["minLength"] = 1 # Finally, send schema_property object to the new json schema. schema_draft["properties"][property_id] = schema_property @@ -220,33 +220,38 @@ def print_schema_diff(self, base_schema, new_schema): print(line) return True if diff_output_choice in ["Save to file", "Both"]: - stderr.print(self.output_folder) diff_filepath = os.path.join( os.path.realpath(self.output_folder) + "/build_schema_diff.txt" ) with open(diff_filepath, "w") as diff_file: diff_file.write("\n".join(diff_lines)) - stderr.print(f"[green]Schema differences saved to {diff_filepath}") + stderr.print(f"[green]Schema diff file saved to {diff_filepath}") return True - def update_schema(self, ): + def save_new_schema(self, json_data): """ - Update the schema_input.json based on the definitions in the Excel file. + Saves the schema generated by SchemaBuilder class into output folder. """ - # TODO: Read the Excel file and extract the database definitions. - - # TODO: Compare the extracted definitions with the base schema_input.json. - - # TODO: Update the schema_input.json with the new definitions. + try: + path_to_save = self.output_folder + "/relecov_schema.json" + with open(path_to_save, "w") as schema_file: + json.dump(json_data, schema_file, ensure_ascii=False, indent=4) + stderr.print(f"[green]New JSON schema saved to: {path_to_save} ") + return True + except PermissionError as perm_error: + stderr.print(f"[red]Permission error: {perm_error}") + except IOError as io_error: + stderr.print(f"[red]I/O error: {io_error}") + except Exception as e: + stderr.print(f"[red]An unexpected error occurred: {str(e)}") + return False def handle_build_schema(self): # Load xlsx database and convert into json format database_dic = self.read_database_definition() # Verify current schema used by relecov-tools: - base_schema_json = relecov_tools.utils.read_json_file( - self.base_schema_path - ) + base_schema_json = relecov_tools.utils.read_json_file(self.base_schema_path) if not base_schema_json: stderr.print("[red]Couldn't find relecov base schema. Exiting...)") sys.exit(1) @@ -260,17 +265,15 @@ def handle_build_schema(self): # Verify new schema follows json schema specification rules. self.verify_schema(new_schema_json) - # Compare base vs new schema + # Compare base vs new schema and saves new JSON schema schema_diff = self.print_schema_diff(base_schema_json, new_schema_json) if schema_diff: - # TODO: If diff ask user to update schema (allow a preview). Else exit. ¿bump version? - # TODO: Register / update version - call_update_schema = relecov_tools.utils.prompt_yn_question("Do you want to update the schema?: ") - if call_update_schema: - self.update_schema(new_schema_json) - else: - stderr.print("[green]No changes made. Exiting...") - sys.exit(1) + self.save_new_schema(new_schema_json) + else: + stderr.print( + f"[green]No changes found against base schema ({self.base_schema_path}). Exiting..." + ) + sys.exit(1) # TODO: add method to add new schema via input file instead of building new (encompases validation checks). # TODO: Add versioning of schema when it is updated. From f015ceab1656aab209a94545c727a2114881e259 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 8 Jul 2024 13:26:50 +0200 Subject: [PATCH 1416/1454] add method to validate input database required fields --- relecov_tools/build_schema.py | 47 +++++++++++++++++++++++++++++++++-- 1 file changed, 45 insertions(+), 2 deletions(-) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index d783ea54..ac164961 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -78,6 +78,38 @@ def __init__( stderr.print(f"[orange]Configuration key error: {key_error}") sys.exit(1) + def validate_database_definition(self, json_data): + """Validate the mandatory features of each property in json_data.""" + # Check mandatory key features to build a json schema + notvalid_properties = {} + mandatory_features = [ + "enum", + "examples", + "ontology_id", + "type", + "description", + "classification", + "label_name", + "fill_mode", + "minLength", + "required (Y/N)", + ] + # Iterate over each property in json_data + for j_key, j_value in json_data.items(): + missing_features = [] + for feature in mandatory_features: + if feature not in j_value: + missing_features.append(feature) + + if missing_features: + notvalid_properties[j_key] = missing_features + + # Summarize validation + if notvalid_properties: + return notvalid_properties + else: + return None + def read_database_definition(self): """Reads the database definition and converts it into json format.""" # Read excel file @@ -94,7 +126,18 @@ def read_database_definition(self): if len(json_data) == 0: stderr.print("[red]No data found in xlsx database") sys.exit(1) - return json_data + + # Perform validation of database content + validation_out = self.validate_database_definition(json_data) + + if validation_out: + stderr.print( + f"[red]Validation of database content falied. Missing mandatory features in: {validation_out}" + ) + sys.exit(1) + else: + stderr.print("[green]Validation of database content passed.") + return json_data def create_schema_draft_template(self): "Loads JsonSchema template based on draft name: Available drafts: [2020-12]" @@ -123,7 +166,7 @@ def build_new_schema(self, json_data, schema_draft): "label_name": "label", "fill_mode": "fill_mode", "minLength": "minLength", - "required (Y/N )": "required", + "required (Y/N)": "required", } schema_required_unique = [] From 642e198313e9acc4e66fc837350528368a3e091f Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 11 Jul 2024 09:39:08 +0200 Subject: [PATCH 1417/1454] added tmp comments --- relecov_tools/build_schema.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index ac164961..0037527f 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -319,6 +319,11 @@ def handle_build_schema(self): sys.exit(1) # TODO: add method to add new schema via input file instead of building new (encompases validation checks). + # - if user adds its own schema dile + # --> check it follows json schema specification rules + # --> check diff + # --> if diff --> save diffs + # --> generae excell? # TODO: Add versioning of schema when it is updated. # TODO: Add method to register logs any time schema is updated # TODO: After updating schema, generate the excell template. From 7c8d40cc6841b4191b7e1344bab6b9d96d1f1a4b Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 16 Jul 2024 15:49:58 +0200 Subject: [PATCH 1418/1454] update todos --- relecov_tools/build_schema.py | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 0037527f..fca20128 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -271,6 +271,7 @@ def print_schema_diff(self, base_schema, new_schema): stderr.print(f"[green]Schema diff file saved to {diff_filepath}") return True + # FIXME: Add version tag to file name def save_new_schema(self, json_data): """ Saves the schema generated by SchemaBuilder class into output folder. @@ -317,13 +318,14 @@ def handle_build_schema(self): f"[green]No changes found against base schema ({self.base_schema_path}). Exiting..." ) sys.exit(1) + + # Build EXCEL template + # TODO: Three tabs in file + # - Overview + # - METADATA_LAB + # - DATA_VALIDATION + # - Add versinon tag to filename + + # TODO: Bump json schema version when it gets updated? + # TODO: Publish a log file that register modification in json schema? - # TODO: add method to add new schema via input file instead of building new (encompases validation checks). - # - if user adds its own schema dile - # --> check it follows json schema specification rules - # --> check diff - # --> if diff --> save diffs - # --> generae excell? - # TODO: Add versioning of schema when it is updated. - # TODO: Add method to register logs any time schema is updated - # TODO: After updating schema, generate the excell template. From dc624bc5a3984349a80f7bc808c2ad91b3c1294c Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 16 Jul 2024 17:13:41 +0200 Subject: [PATCH 1419/1454] Add initial implementation of method to create metadata lab template file --- relecov_tools/build_schema.py | 84 ++++++++++++++++++++++++++++++++--- 1 file changed, 77 insertions(+), 7 deletions(-) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index fca20128..56b9a691 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -6,6 +6,7 @@ import sys import json import difflib +import xlsxwriter import relecov_tools.utils import relecov_tools.assets.schema_utils.jsonschema_draft @@ -290,6 +291,73 @@ def save_new_schema(self, json_data): stderr.print(f"[red]An unexpected error occurred: {str(e)}") return False + def create_metadatalab_excel(self, json_data): + """ + Generate the metadatalab templet file in xlsx format. It contains: + - Overview tab: + - Metadata LAB tab: + - Validation Tab: + """ + # Create a new workbook and add the 'overview' worksheet + excel_file_path = os.path.join( + os.path.realpath(self.output_folder) + "/metadatalab_template.xlsx" + ) + workbook = xlsxwriter.Workbook(excel_file_path) + # Define a bold format for headers + bold = workbook.add_format({"bold": True}) + + # + # Overview Tab + # + overview_sheet = workbook.add_worksheet("Overview") + overview_tab_headers = [ + "", + "Label name", + "Description", + "Group", + "Mandatory (Y/N)", + "Example", + "METADATA_LAB COLUMN", + ] + + # Write the headers to the worksheet + for col_num, header in enumerate(overview_tab_headers): + overview_sheet.write(0, col_num, header, bold) + + # Set Starting column + column_index = ord("A") + + row_num = 1 + for property_id, details in json_data.items(): + label_name = details.get("label_name", "") + description = details.get("description", "") + group = details.get("classification", "") + mandatory = details.get("required (Y/N)", "") + example = details.get("examples", [""]) + metadata_column = chr(column_index) + + # Fill the overview tab with processed data + # FIXME: Got few errors while filling table + try: + overview_sheet.write(row_num, 0, group) + overview_sheet.write(row_num, 1, label_name) + overview_sheet.write(row_num, 2, description) + overview_sheet.write(row_num, 3, group) + overview_sheet.write(row_num, 4, mandatory) + overview_sheet.write(row_num, 5, example) + overview_sheet.write(row_num, 6, metadata_column) + except TypeError as e: + stderr.print( + f"[red] Error when filling excell in property '{property_id}': {e}" + ) + pass + column_index += 1 + row_num += 1 + + # Close the workbook + workbook.close() + print(f"Excel file saved to {excel_file_path}") + def handle_build_schema(self): # Load xlsx database and convert into json format database_dic = self.read_database_definition() @@ -318,14 +386,16 @@ def handle_build_schema(self): f"[green]No changes found against base schema ({self.base_schema_path}). Exiting..." ) sys.exit(1) - + + if schema_diff: + self.create_metadatalab_excel(database_dic) + # Build EXCEL template - # TODO: Three tabs in file - # - Overview - # - METADATA_LAB - # - DATA_VALIDATION - # - Add versinon tag to filename + # TODO: Three tabs in file + # - Overview + # - METADATA_LAB + # - DATA_VALIDATION + # - Add versinon tag to filename # TODO: Bump json schema version when it gets updated? # TODO: Publish a log file that register modification in json schema? - From e4b2ca13add53dd774bc9ee379554f7101c4fcca Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 30 Jul 2024 10:30:50 +0200 Subject: [PATCH 1420/1454] improve readability, and update method to build schema draft --- relecov_tools/build_schema.py | 58 +++++++++++++++++++---------------- 1 file changed, 32 insertions(+), 26 deletions(-) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 56b9a691..4f53ef78 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -92,8 +92,8 @@ def validate_database_definition(self, json_data): "classification", "label_name", "fill_mode", - "minLength", "required (Y/N)", + "complex_field (Y/N)", ] # Iterate over each property in json_data for j_key, j_value in json_data.items(): @@ -114,8 +114,8 @@ def validate_database_definition(self, json_data): def read_database_definition(self): """Reads the database definition and converts it into json format.""" # Read excel file - df = pd.read_excel(self.excel_file_path) - + # FIXME: I think reading first tab by defining the tab name might be too harcoded. + df = pd.read_excel(self.excel_file_path, sheet_name='main') # Convert database to json format json_data = {} for row in df.itertuples(index=False): @@ -157,7 +157,7 @@ def build_new_schema(self, json_data, schema_draft): try: # List of properties to check in the features dictionary: # key[database_key]: value[schema_key] - properties_to_check = { + features_to_check = { "enum": "enum", "examples": "examples", "ontology_id": "ontology", @@ -166,51 +166,57 @@ def build_new_schema(self, json_data, schema_draft): "classification": "classification", "label_name": "label", "fill_mode": "fill_mode", - "minLength": "minLength", "required (Y/N)": "required", } - schema_required_unique = [] + required_property_unique = [] - # Filling properties - for property_id, features in json_data.items(): + # Read property_ids in the database. + # Perform checks and create (for each property) feature object like: + # {'example':'A', 'ontology': 'B'...}. + # Finally this objet will be written to the draft schema. + for property_id, features_dic in json_data.items(): schema_property = {} - schema_required = {} - - for feature_key, schema_key in properties_to_check.items(): - if feature_key in features: + required_property = {} + schema_property_complex = [] + + # Record property_ids that have complex objects.q + if json_data[property_id].get('complex_field (Y/N)') == 'Y': + schema_property_complex.append(property_id) + # Iterate over all property's features to check. + for database_key, schema_key in features_to_check.items(): + # Verifiy that database_key is present in the database (processed excel (aka json_data)) + if database_key not in features_dic: + stderr.print(f"[INFO] Feature {database_key} is not present in database ({self.excel_file_path})") + else: # For enum and examples, wrap the value in a list if schema_key in ["enum", "examples"]: - value = str(features[feature_key]) + value = str(features_dic[database_key]) # if no value, json key wont be necessary, then avoid adding it if len(value) > 0 and not value == "nan": - # Enum is an array like object if schema_key == "enum": schema_property[schema_key] = value.split(", ") elif schema_key == "examples": schema_property[schema_key] = [value] # Recover 'required' properties from database definition. elif schema_key == "required": - value = str(features[feature_key]) + value = str(features_dic[database_key]) if value != "nan": - schema_required[property_id] = value - + required_property[property_id] = value else: - schema_property[schema_key] = features[feature_key] - + schema_property[schema_key] = features_dic[database_key] + # Set default values if not provided if "fill_mode" not in schema_property: schema_property["fill_mode"] = None - if "minLength" not in schema_property: - schema_property["minLength"] = 1 - # Finally, send schema_property object to the new json schema. + # Finally, send schema_property object to the new json schema draft. schema_draft["properties"][property_id] = schema_property - # Finally, send schema_required object to the new json schema. - for key, values in schema_required.items(): + # Add to schema draft the recorded porperty_ids. + for key, values in required_property.items(): if values == "Y": - schema_required_unique.append(key) - schema_draft["required"] = schema_required_unique + required_property_unique.append(key) + schema_draft["required"] = required_property_unique # Return new schema return schema_draft From fe807ac9a07794068759b5fa69e2a2b8b7e42b30 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 30 Jul 2024 12:31:52 +0200 Subject: [PATCH 1421/1454] refactor method to build schema separating standard objects from complex --- relecov_tools/build_schema.py | 118 +++++++++++++++++++++++----------- 1 file changed, 81 insertions(+), 37 deletions(-) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 4f53ef78..72425001 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -149,19 +149,70 @@ def create_schema_draft_template(self): ) return draft_template + # TODO: in progress + def create_complex_schema_object(self, property_id): + # Read the tab specific to the complex field + complex_df = pd.read_excel(self.excel_file_path, sheet_name=property_id) + properties = {} + required = [] + for _, complex_row in complex_df.iterrows(): + field_name = complex_row['property_id'] + field_type = complex_row['type'] + field_schema = {"type": field_type} + # FIXME: enums not working + #if complex_row['enum'] and complex_row['enum'] != 'nan': + # field_enum = complex_row['enum'] + # stderr.print(field_enum["enum"]) +# + #if field_enum: + # field_schema["enum"] = field_enum.split(', ') +# + properties[field_name] = field_schema + required.append(field_name) # Assuming all fields are required + + # Set schema for complex fields + dict_out = { + "type": "object", + "properties": properties, + "required": required, + "additionalProperties": False + } + return False + + def standar_jsonschema_object(self, data_dict, target_key): + """"Create standar json schema object""" + # For enum and examples, wrap the value in a list + json_dict = {} + + if target_key in ["enum", "examples"]: + value = str(data_dict[target_key]) + # if no value, json key wont be necessary, then avoid adding it + if len(value) > 0 and not value == "nan": + if target_key == "enum": + json_dict[target_key] = value.split(", ") + elif target_key == "examples": + json_dict[target_key] = [value] + else: + json_dict[target_key] = data_dict[target_key] + return json_dict + + def complex_json_schema_object(self): + """"Create complex/nested json schema object""" + # TODO: add strategy to deal with json schema objects, defs and refs + # TODO: Reorder porperty's features returned. def build_new_schema(self, json_data, schema_draft): """ Create a json schema file based on input data and draf skeleton.. """ try: - # List of properties to check in the features dictionary: - # key[database_key]: value[schema_key] + # List of properties to check in the features dictionary (it maps values between database features and json schema features): + # key[db_feature_key]: value[schema_feature_key] features_to_check = { + "type": "type", "enum": "enum", "examples": "examples", "ontology_id": "ontology", - "type": "type", "description": "description", "classification": "classification", "label_name": "label", @@ -169,46 +220,39 @@ def build_new_schema(self, json_data, schema_draft): "required (Y/N)": "required", } required_property_unique = [] + complex_property = [] # Read property_ids in the database. - # Perform checks and create (for each property) feature object like: - # {'example':'A', 'ontology': 'B'...}. - # Finally this objet will be written to the draft schema. - for property_id, features_dic in json_data.items(): + # Perform checks and create (for each property) feature object like: + # {'example':'A', 'ontology': 'B'...}. + # Finally this objet will be written to the draft schema. + for property_id, db_features_dic in json_data.items(): schema_property = {} required_property = {} - schema_property_complex = [] - # Record property_ids that have complex objects.q + # Record property_ids that have complex objects. + # TODO: This might be a bit harcoded. if json_data[property_id].get('complex_field (Y/N)') == 'Y': - schema_property_complex.append(property_id) - # Iterate over all property's features to check. - for database_key, schema_key in features_to_check.items(): - # Verifiy that database_key is present in the database (processed excel (aka json_data)) - if database_key not in features_dic: - stderr.print(f"[INFO] Feature {database_key} is not present in database ({self.excel_file_path})") - else: - # For enum and examples, wrap the value in a list - if schema_key in ["enum", "examples"]: - value = str(features_dic[database_key]) - # if no value, json key wont be necessary, then avoid adding it - if len(value) > 0 and not value == "nan": - if schema_key == "enum": - schema_property[schema_key] = value.split(", ") - elif schema_key == "examples": - schema_property[schema_key] = [value] - # Recover 'required' properties from database definition. - elif schema_key == "required": - value = str(features_dic[database_key]) - if value != "nan": - required_property[property_id] = value + complex_property.append(property_id) + continue + # Iterate over all property's features that follows standard format. + else: + for db_feature_key, schema_feature_key in features_to_check.items(): + # Verifiy that db_feature_key is present in the database (processed excel (aka 'json_data')) + if db_feature_key not in db_features_dic: + stderr.print(f"[INFO] Feature {db_feature_key} is not present in database ({self.excel_file_path})") + continue + # Record the required value for each property + if 'required' in db_feature_key or "required" == schema_feature_key: + is_required = str(db_features_dic[db_feature_key]) + if is_required != 'nan': + required_property[property_id] = is_required else: - schema_property[schema_key] = features_dic[database_key] - - # Set default values if not provided - if "fill_mode" not in schema_property: - schema_property["fill_mode"] = None - + std_json_feature = self.standar_jsonschema_object(db_features_dic, db_feature_key) + if std_json_feature: + schema_property[schema_feature_key] = std_json_feature[db_feature_key] + else: + continue # Finally, send schema_property object to the new json schema draft. schema_draft["properties"][property_id] = schema_property @@ -217,7 +261,7 @@ def build_new_schema(self, json_data, schema_draft): if values == "Y": required_property_unique.append(key) schema_draft["required"] = required_property_unique - + # Return new schema return schema_draft From ecbe87db633fec9f95f7963ef7faa18cc46990f7 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 30 Jul 2024 15:26:50 +0200 Subject: [PATCH 1422/1454] added method to deal with complex fields to be included in json schema --- relecov_tools/build_schema.py | 104 +++++++++++++++++++--------------- 1 file changed, 57 insertions(+), 47 deletions(-) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 72425001..90cf275f 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -4,6 +4,7 @@ import pandas as pd import os import sys +import re import json import difflib import xlsxwriter @@ -22,6 +23,7 @@ # TODO: user should be able to provide a custom schema as a file in order to replace the current one. +# TODO: still need to work in logs class SchemaBuilder: def __init__( self, @@ -111,11 +113,11 @@ def validate_database_definition(self, json_data): else: return None - def read_database_definition(self): + def read_database_definition(self, sheet_id='main'): """Reads the database definition and converts it into json format.""" # Read excel file # FIXME: I think reading first tab by defining the tab name might be too harcoded. - df = pd.read_excel(self.excel_file_path, sheet_name='main') + df = pd.read_excel(self.excel_file_path, sheet_name=sheet_id, na_values=['nan', 'N/A', 'NA', '']) # Convert database to json format json_data = {} for row in df.itertuples(index=False): @@ -149,55 +151,61 @@ def create_schema_draft_template(self): ) return draft_template - # TODO: in progress - def create_complex_schema_object(self, property_id): - # Read the tab specific to the complex field - complex_df = pd.read_excel(self.excel_file_path, sheet_name=property_id) - properties = {} - required = [] - for _, complex_row in complex_df.iterrows(): - field_name = complex_row['property_id'] - field_type = complex_row['type'] - field_schema = {"type": field_type} - # FIXME: enums not working - #if complex_row['enum'] and complex_row['enum'] != 'nan': - # field_enum = complex_row['enum'] - # stderr.print(field_enum["enum"]) -# - #if field_enum: - # field_schema["enum"] = field_enum.split(', ') -# - properties[field_name] = field_schema - required.append(field_name) # Assuming all fields are required - - # Set schema for complex fields - dict_out = { - "type": "object", - "properties": properties, - "required": required, - "additionalProperties": False - } - return False - - def standar_jsonschema_object(self, data_dict, target_key): + # TODO: we have to discuss wether NaN (empty) values need to be handled + def standard_jsonschema_object(self, data_dict, target_key): """"Create standar json schema object""" # For enum and examples, wrap the value in a list json_dict = {} + + # Function to handle NaN values + def handle_nan(value): + if pd.isna(value) or value in ['nan', 'NaN', 'None', 'none']: + return "" + return str(value) if target_key in ["enum", "examples"]: - value = str(data_dict[target_key]) - # if no value, json key wont be necessary, then avoid adding it - if len(value) > 0 and not value == "nan": + value = handle_nan(data_dict.get(target_key, "")) + # if no value, json key won't be necessary, then avoid adding it + if len(value) > 0: if target_key == "enum": json_dict[target_key] = value.split(", ") - elif target_key == "examples": - json_dict[target_key] = [value] + elif target_key == "examples": + json_dict[target_key] = [value] + elif target_key == "description": + json_dict[target_key] = handle_nan(data_dict.get(target_key, "")) else: - json_dict[target_key] = data_dict[target_key] + json_dict[target_key] = handle_nan(data_dict.get(target_key, "")) return json_dict - def complex_json_schema_object(self): + def complex_jsonschema_object(self, property_id, features_dict): """"Create complex/nested json schema object""" + json_dict = {"type": "object", "properties":{}} + + # Read tab-dedicated sheet in excell database + try: + complex_json_data = self.read_database_definition(sheet_id=property_id) + except ValueError as e: + stderr.print(f"[red]{e}") + return None + + # Add sub property items + # TODO: add try_excepts + #try: + for sub_property_id, _ in complex_json_data.items(): + json_dict["properties"][sub_property_id] = {} + complex_json_feature = {} + for db_feature_key, json_key in features_dict.items(): + if json_key == 'required': + continue + feature_schema = self.standard_jsonschema_object(complex_json_data[sub_property_id], db_feature_key) + if feature_schema: + complex_json_feature[json_key] = feature_schema[db_feature_key] + json_dict["properties"][sub_property_id] = complex_json_feature + + return json_dict + #except: + # stderr.print(f"[red]Error while generating comples json object for {property_id}") + # return None # TODO: add strategy to deal with json schema objects, defs and refs # TODO: Reorder porperty's features returned. @@ -220,7 +228,6 @@ def build_new_schema(self, json_data, schema_draft): "required (Y/N)": "required", } required_property_unique = [] - complex_property = [] # Read property_ids in the database. # Perform checks and create (for each property) feature object like: @@ -230,12 +237,15 @@ def build_new_schema(self, json_data, schema_draft): schema_property = {} required_property = {} - # Record property_ids that have complex objects. - # TODO: This might be a bit harcoded. + # Parse property_ids that needs to be incorporated as complex fields in json_schema if json_data[property_id].get('complex_field (Y/N)') == 'Y': - complex_property.append(property_id) - continue - # Iterate over all property's features that follows standard format. + complex_json_feature = self.complex_jsonschema_object(property_id, features_to_check) + if complex_json_feature: + schema_property["type"] = "array" + schema_property["items"] = complex_json_feature + schema_property["additionalProperties"]= "false" + schema_property["required"] = [ key for key in complex_json_feature["properties"].keys()] + # For those that follows standard format, add them to json schema as well. else: for db_feature_key, schema_feature_key in features_to_check.items(): # Verifiy that db_feature_key is present in the database (processed excel (aka 'json_data')) @@ -248,7 +258,7 @@ def build_new_schema(self, json_data, schema_draft): if is_required != 'nan': required_property[property_id] = is_required else: - std_json_feature = self.standar_jsonschema_object(db_features_dic, db_feature_key) + std_json_feature = self.standard_jsonschema_object(db_features_dic, db_feature_key) if std_json_feature: schema_property[schema_feature_key] = std_json_feature[db_feature_key] else: From 0f2511536bd633e5dc40e7d4f1f753297055b13e Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 1 Aug 2024 12:21:24 +0200 Subject: [PATCH 1423/1454] refactored strategy to generate metadata lab template --- .../schema_utils/metadatalab_template.py | 75 +++++++++++++++++++ relecov_tools/build_schema.py | 67 ++++------------- 2 files changed, 90 insertions(+), 52 deletions(-) create mode 100644 relecov_tools/assets/schema_utils/metadatalab_template.py diff --git a/relecov_tools/assets/schema_utils/metadatalab_template.py b/relecov_tools/assets/schema_utils/metadatalab_template.py new file mode 100644 index 00000000..06643fc4 --- /dev/null +++ b/relecov_tools/assets/schema_utils/metadatalab_template.py @@ -0,0 +1,75 @@ +#!/usr/bin/env python +import logging +import rich.console +import json +import xlsxwriter + +import relecov_tools.utils + + +log = logging.getLogger(__name__) +stderr = rich.console.Console( + stderr=True, + style="dim", + highlight=False, + force_terminal=relecov_tools.utils.rich_force_colors(), +) + + +def overview_tab(json_schema, excel_file, header, start_col="A", start_row=1, tab_name="Overview"): + """""" + errors_record = {} + # Create workbook object + workbook = xlsxwriter.Workbook(excel_file) + sheet = workbook.add_worksheet(tab_name) + bold = workbook.add_format({"bold": True}) + + # Write the headers to the worksheet and setup dimentions + for col_num, col_name in enumerate(header): + sheet.write(0, col_num, col_name, bold) + col_index = ord(start_col) + row_index = start_row + + # Get schema property ID and its features + # TODO: try except + required_list = json_schema.get('required') + properties_dict = json_schema.get('properties') + + for property_id, features in properties_dict.items(): + label_name = features.get("label", "") + description = features.get("description", "") + group = features.get("classification", "") + mandatory = "Y" if property_id in required_list else "N" + example = features.get("examples", [""])[0] + metadata_column = chr(col_index) + # Fill the overview tab with processed data + try: + sheet.write(row_index, 0, group) + sheet.write(row_index, 1, label_name) + sheet.write(row_index, 2, description) + sheet.write(row_index, 3, group) + sheet.write(row_index, 4, mandatory) + sheet.write(row_index, 5, example) + sheet.write(row_index, 6, metadata_column) + except TypeError as e: + stderr.print( + f"[red] Error when filling excell in property '{property_id}': {e}" + ) + pass + col_index += 1 + row_index += 1 + + if len(errors_record)>0: + stderr.print(f"[red]Errors encountered while generating the {tab_name} sheet. See errors {errors_record}") + return False + else: + # Close the workbook + workbook.close() + return True + +def metadatalab_tab(): + """""" + return True +def datavalidation_tab(): + """""" + return True diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 90cf275f..2c9a268a 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -11,6 +11,7 @@ import relecov_tools.utils import relecov_tools.assets.schema_utils.jsonschema_draft +import relecov_tools.assets.schema_utils.metadatalab_template from relecov_tools.config_json import ConfigJson log = logging.getLogger(__name__) @@ -116,7 +117,6 @@ def validate_database_definition(self, json_data): def read_database_definition(self, sheet_id='main'): """Reads the database definition and converts it into json format.""" # Read excel file - # FIXME: I think reading first tab by defining the tab name might be too harcoded. df = pd.read_excel(self.excel_file_path, sheet_name=sheet_id, na_values=['nan', 'N/A', 'NA', '']) # Convert database to json format json_data = {} @@ -208,7 +208,6 @@ def complex_jsonschema_object(self, property_id, features_dict): # return None # TODO: add strategy to deal with json schema objects, defs and refs - # TODO: Reorder porperty's features returned. def build_new_schema(self, json_data, schema_draft): """ Create a json schema file based on input data and draf skeleton.. @@ -216,6 +215,7 @@ def build_new_schema(self, json_data, schema_draft): try: # List of properties to check in the features dictionary (it maps values between database features and json schema features): # key[db_feature_key]: value[schema_feature_key] + # TODO: This should be a config variable available for all elements in this class features_to_check = { "type": "type", "enum": "enum", @@ -278,7 +278,7 @@ def build_new_schema(self, json_data, schema_draft): except Exception as e: stderr.print(f"[red]Error building schema: {str(e)}") raise - # Once json schema is created, it requires validation + # TODO: Once json schema is created, it requires validation def verify_schema(self, schema): """Verify the schema_draft follows the JSON Schema specification [XXXX] meta-schema.""" @@ -351,26 +351,23 @@ def save_new_schema(self, json_data): stderr.print(f"[red]An unexpected error occurred: {str(e)}") return False - def create_metadatalab_excel(self, json_data): + # TODO: rename json_data to json_schema + def create_metadatalab_excel(self, json_schema): """ - Generate the metadatalab templet file in xlsx format. It contains: + Generate the metadatalab template file in xlsx format. It contains: - Overview tab: - Metadata LAB tab: - Validation Tab: """ - # Create a new workbook and add the 'overview' worksheet - excel_file_path = os.path.join( + # Create a new workbook + out_file = os.path.join( os.path.realpath(self.output_folder) + "/metadatalab_template.xlsx" ) - workbook = xlsxwriter.Workbook(excel_file_path) - # Define a bold format for headers - bold = workbook.add_format({"bold": True}) - + # - # Overview Tab + # Overview sheet # - overview_sheet = workbook.add_worksheet("Overview") - overview_tab_headers = [ + overview_header = [ "", "Label name", "Description", @@ -379,44 +376,10 @@ def create_metadatalab_excel(self, json_data): "Example", "METADATA_LAB COLUMN", ] + write_overview = relecov_tools.assets.schema_utils.metadatalab_template.overview_tab(json_schema, out_file, overview_header) + if write_overview: + stderr.print(f"[green]Excel file saved to {out_file}") - # Write the headers to the worksheet - for col_num, header in enumerate(overview_tab_headers): - overview_sheet.write(0, col_num, header, bold) - - # Set Starting column - column_index = ord("A") - - row_num = 1 - for property_id, details in json_data.items(): - label_name = details.get("label_name", "") - description = details.get("description", "") - group = details.get("classification", "") - mandatory = details.get("required (Y/N)", "") - example = details.get("examples", [""]) - metadata_column = chr(column_index) - - # Fill the overview tab with processed data - # FIXME: Got few errors while filling table - try: - overview_sheet.write(row_num, 0, group) - overview_sheet.write(row_num, 1, label_name) - overview_sheet.write(row_num, 2, description) - overview_sheet.write(row_num, 3, group) - overview_sheet.write(row_num, 4, mandatory) - overview_sheet.write(row_num, 5, example) - overview_sheet.write(row_num, 6, metadata_column) - except TypeError as e: - stderr.print( - f"[red] Error when filling excell in property '{property_id}': {e}" - ) - pass - column_index += 1 - row_num += 1 - - # Close the workbook - workbook.close() - print(f"Excel file saved to {excel_file_path}") def handle_build_schema(self): # Load xlsx database and convert into json format @@ -448,7 +411,7 @@ def handle_build_schema(self): sys.exit(1) if schema_diff: - self.create_metadatalab_excel(database_dic) + self.create_metadatalab_excel(new_schema_json) # Build EXCEL template # TODO: Three tabs in file From 9c82efb3f7de0c715c400afc2eb1c92b755616dc Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 5 Aug 2024 10:35:37 +0200 Subject: [PATCH 1424/1454] refactor v2 of method that creates excel template --- .../schema_utils/metadatalab_template.py | 89 ++++------ relecov_tools/build_schema.py | 164 +++++++++++++++--- 2 files changed, 170 insertions(+), 83 deletions(-) diff --git a/relecov_tools/assets/schema_utils/metadatalab_template.py b/relecov_tools/assets/schema_utils/metadatalab_template.py index 06643fc4..3b0e4292 100644 --- a/relecov_tools/assets/schema_utils/metadatalab_template.py +++ b/relecov_tools/assets/schema_utils/metadatalab_template.py @@ -1,8 +1,10 @@ #!/usr/bin/env python import logging import rich.console +import os import json import xlsxwriter +import pandas as pd import relecov_tools.utils @@ -15,61 +17,34 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) - -def overview_tab(json_schema, excel_file, header, start_col="A", start_row=1, tab_name="Overview"): - """""" - errors_record = {} - # Create workbook object - workbook = xlsxwriter.Workbook(excel_file) - sheet = workbook.add_worksheet(tab_name) - bold = workbook.add_format({"bold": True}) - - # Write the headers to the worksheet and setup dimentions - for col_num, col_name in enumerate(header): - sheet.write(0, col_num, col_name, bold) - col_index = ord(start_col) - row_index = start_row +def schema_to_flatten_json(json_data): + """This function flattens schema when nested items are found""" + flatten_json = {} + for property_id, features in json_data.items(): + # TODO: might be another way to identify a nested dict property + if features.get('type') == 'array': + complex_properties= json_data[property_id]["items"].get('properties') + for complex_property_id, complex_feature in complex_properties.items(): + flatten_json.update({complex_property_id : complex_feature}) + else: + flatten_json.update({property_id : features} ) + return flatten_json + +def schema_properties_to_df(json_data): + # Initialize an empty list to store the rows of the DataFrame + rows = [] + + # Iterate over each property in the JSON data + for property_id, property_features in json_data.items(): + # Create a dictionary to hold the property features + row = {'property_id': property_id} + row.update(property_features) + + # Append the row to the list of rows + rows.append(row) - # Get schema property ID and its features - # TODO: try except - required_list = json_schema.get('required') - properties_dict = json_schema.get('properties') - - for property_id, features in properties_dict.items(): - label_name = features.get("label", "") - description = features.get("description", "") - group = features.get("classification", "") - mandatory = "Y" if property_id in required_list else "N" - example = features.get("examples", [""])[0] - metadata_column = chr(col_index) - # Fill the overview tab with processed data - try: - sheet.write(row_index, 0, group) - sheet.write(row_index, 1, label_name) - sheet.write(row_index, 2, description) - sheet.write(row_index, 3, group) - sheet.write(row_index, 4, mandatory) - sheet.write(row_index, 5, example) - sheet.write(row_index, 6, metadata_column) - except TypeError as e: - stderr.print( - f"[red] Error when filling excell in property '{property_id}': {e}" - ) - pass - col_index += 1 - row_index += 1 - - if len(errors_record)>0: - stderr.print(f"[red]Errors encountered while generating the {tab_name} sheet. See errors {errors_record}") - return False - else: - # Close the workbook - workbook.close() - return True - -def metadatalab_tab(): - """""" - return True -def datavalidation_tab(): - """""" - return True + # Create a DataFrame from the list of rows + df = pd.DataFrame(rows) + + # Return the DataFrame + return df diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 2c9a268a..8201e7bd 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -351,7 +351,6 @@ def save_new_schema(self, json_data): stderr.print(f"[red]An unexpected error occurred: {str(e)}") return False - # TODO: rename json_data to json_schema def create_metadatalab_excel(self, json_schema): """ Generate the metadatalab template file in xlsx format. It contains: @@ -359,27 +358,144 @@ def create_metadatalab_excel(self, json_schema): - Metadata LAB tab: - Validation Tab: """ - # Create a new workbook - out_file = os.path.join( - os.path.realpath(self.output_folder) + "/metadatalab_template.xlsx" - ) - - # - # Overview sheet - # - overview_header = [ - "", - "Label name", - "Description", - "Group", - "Mandatory (Y/N)", - "Example", - "METADATA_LAB COLUMN", - ] - write_overview = relecov_tools.assets.schema_utils.metadatalab_template.overview_tab(json_schema, out_file, overview_header) - if write_overview: - stderr.print(f"[green]Excel file saved to {out_file}") + try: + # Set up metadatalab configuration + out_file = os.path.join( + self.excel_file_path, + os.path.join(self.output_folder, "metadatalab_template" + ".xlsx") + ) + required_classification = [ + "Database Identifiers", + "Sample collection and processing", + "Host information", + "Sequencing", + "Pathogen Diagnostic testing", + "Contributor Acknowledgement" + ] + required_properties = json_schema.get('required') + schema_properties = json_schema.get('properties') + + # Read json schema properties and convert it into pandas df + try: + schema_properties_flatten = relecov_tools.assets.schema_utils.metadatalab_template.schema_to_flatten_json( + schema_properties + ) + df = relecov_tools.assets.schema_utils.metadatalab_template.schema_properties_to_df (schema_properties_flatten) + df = df[df['classification'].isin(required_classification)] + df['required'] = df['property_id'].apply(lambda x: 'Y' if x in required_properties else 'N') + except Exception as e: + stderr.print(f"Error processing schema properties: {e}") + return + + # Overview sheet + try: + overview_header = [ + "", + "Label name", + "Description", + "Group", + "Mandatory (Y/N)", + "Example", + "METADATA_LAB COLUMN", + ] + df_overview = pd.DataFrame(columns=[col_name for col_name in overview_header]) + df_overview[''] = df['classification'] + df_overview['Label name'] = df['label'] + df_overview['Description'] = df['description'] + df_overview['Group'] = df['classification'] + df_overview['Example'] = df['examples'].apply(lambda x: x[0] if isinstance(x, list) else x) + except Exception as e: + stderr.print(f"Error creating overview sheet: {e}") + return + + # MetadataLab sheet + try: + metadatalab_header = [ + "", + "EJEMPLOS", + "DESCRIPCIÓN", + "CAMPO" + ] + df_metadata = pd.DataFrame(columns=[col_name for col_name in metadatalab_header]) + df_metadata[''] = df['label'].apply(lambda _: '') + df_metadata['EJEMPLOS'] = df['examples'].apply(lambda x: x[0] if isinstance(x, list) else x) + df_metadata['DESCRIPCIÓN'] = df['description'] + df_metadata['CAMPO'] = df['label'] + df_metadata = df_metadata.transpose() + except Exception as e: + stderr.print(f"[red]Error creating MetadataLab sheet: {e}") + return + + # DataValidation sheet + try: + datavalidation_header = [ + "", + "EJEMPLOS", + "DESCRIPCIÓN", + "CAMPO", + "" + ] + df_hasenum = df[(pd.notnull(df.enum))] + df_validation = pd.DataFrame(columns=[col_name for col_name in datavalidation_header]) + df_validation['tmp_property'] = df_hasenum['property_id'] + df_validation[''] = df_hasenum['label'].apply(lambda _: '') + df_validation['EJEMPLOS'] = df_hasenum['examples'].apply(lambda x: x[0] if isinstance(x, list) else x) + df_validation['DESCRIPCIÓN'] = df_hasenum['description'] + df_validation['CAMPO'] = df_hasenum['label'] + except Exception as e: + stderr.print(f"[red]Error creating DataValidation sheet: {e}") + return + try: + # Since enums have different lengths we need further processing. + # Convert df into dict to perform data manipulation. + enum_dict = {property: [] for property in df_hasenum['property_id']} + enum_maxitems = 0 + # Populate the dictionary with flattened lists + for key in enum_dict.keys(): + enum_values = df_hasenum[df_hasenum['property_id'] == key]['enum'].values + if enum_values.size > 0: + enum_list = enum_values[0] # Extract the list + enum_dict[key] = enum_list # Assign the list to the dictionary + if enum_maxitems < len(enum_list): + enum_maxitems = len(enum_list) + else: + enum_dict[key] = [] + + # Reshape list dimensions based on enum length. + for key in enum_dict.keys(): + if len(enum_dict[key]) < enum_maxitems: + num_nas = enum_maxitems - len(enum_dict[key]) + for _ in range(num_nas): + enum_dict[key].append('NaN') + + new_df = pd.DataFrame(enum_dict) + new_index = range(len(new_df.columns)) + new_df.reindex(columns=new_index) + + valid_index = df_validation['tmp_property'].values + valid_transposed = df_validation.transpose() + valid_transposed.columns = valid_index + + frames = [valid_transposed, new_df] + df_validation = pd.concat(frames) + except Exception as e: + stderr.print(f"[red]Error processing enums and combining data: {e}") + return None + + # WRITE EXCEL + try: + with pd.ExcelWriter(out_file) as writer: + df_overview.to_excel(writer, sheet_name='OVERVIEW') + df_metadata.to_excel(writer, sheet_name='METADATA_LAB') + df_validation.to_excel(writer, sheet_name='DATA VALIDATION') + stderr.print(f"[green]Excel template successfuly created in: {out_file}") + except Exception as e: + stderr.print(f"[red]Error writing to Excel: {e}") + return None + except Exception as e: + stderr.print(f"[red]Error in create_metadatalab_excel: {e}") + return None def handle_build_schema(self): # Load xlsx database and convert into json format @@ -414,11 +530,7 @@ def handle_build_schema(self): self.create_metadatalab_excel(new_schema_json) # Build EXCEL template - # TODO: Three tabs in file - # - Overview - # - METADATA_LAB - # - DATA_VALIDATION # - Add versinon tag to filename - # TODO: Bump json schema version when it gets updated? + # TODO: metod to ask whether to bump version when json schema is generated? # TODO: Publish a log file that register modification in json schema? From bc50894a2f1b5802ec117a0494de5f323d7716f1 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 5 Aug 2024 14:07:05 +0200 Subject: [PATCH 1425/1454] added utils to perform excel formatting --- .../schema_utils/metadatalab_template.py | 128 ++++++++++++++---- relecov_tools/build_schema.py | 18 ++- 2 files changed, 113 insertions(+), 33 deletions(-) diff --git a/relecov_tools/assets/schema_utils/metadatalab_template.py b/relecov_tools/assets/schema_utils/metadatalab_template.py index 3b0e4292..0d701066 100644 --- a/relecov_tools/assets/schema_utils/metadatalab_template.py +++ b/relecov_tools/assets/schema_utils/metadatalab_template.py @@ -5,6 +5,8 @@ import json import xlsxwriter import pandas as pd +import xlsxwriter + import relecov_tools.utils @@ -19,32 +21,106 @@ def schema_to_flatten_json(json_data): """This function flattens schema when nested items are found""" - flatten_json = {} - for property_id, features in json_data.items(): - # TODO: might be another way to identify a nested dict property - if features.get('type') == 'array': - complex_properties= json_data[property_id]["items"].get('properties') - for complex_property_id, complex_feature in complex_properties.items(): - flatten_json.update({complex_property_id : complex_feature}) - else: - flatten_json.update({property_id : features} ) - return flatten_json + try: + flatten_json = {} + for property_id, features in json_data.items(): + try: + if features.get('type') == 'array': + complex_properties = json_data[property_id]["items"].get('properties') + for complex_property_id, complex_feature in complex_properties.items(): + flatten_json.update({complex_property_id: complex_feature}) + else: + flatten_json.update({property_id: features}) + except Exception as e: + stderr.print(f"[red]Error processing property {property_id}: {e}") + return flatten_json + except Exception as e: + stderr.print(f"[red]Error in schema_to_flatten_json: {e}") + return None def schema_properties_to_df(json_data): - # Initialize an empty list to store the rows of the DataFrame - rows = [] - - # Iterate over each property in the JSON data - for property_id, property_features in json_data.items(): - # Create a dictionary to hold the property features - row = {'property_id': property_id} - row.update(property_features) + try: + # Initialize an empty list to store the rows of the DataFrame + rows = [] + + # Iterate over each property in the JSON data + for property_id, property_features in json_data.items(): + try: + # Create a dictionary to hold the property features + row = {'property_id': property_id} + row.update(property_features) + + # Append the row to the list of rows + rows.append(row) + except Exception as e: + stderr.print(f"[red]Error processing property {property_id}: {e}") + + # Create a DataFrame from the list of rows + df = pd.DataFrame(rows) + + # Return the DataFrame + return df + except Exception as e: + stderr.print(f"[red]Error in schema_properties_to_df: {e}") + return None + + +def excel_formater(df, writer, sheet, out_file, have_index=True, have_header=True): + try: + + # Write the DataFrame to the specified sheet + df.to_excel(writer, sheet_name=sheet, startrow=1, index=have_index, header=have_header) + + # Get the xlsxwriter workbook and worksheet objects. + workbook = writer.book + worksheet = writer.sheets[sheet] + + # setup excel formaters + worksheet.set_column(0, len(df.columns), 30) + header_formater = workbook.add_format({ + 'bold': True, + 'text_wrap': False, + 'valign': 'top', + 'fg_color': '#ADD8E6', + 'border': 1 + }) + first_col_formater = workbook.add_format({ + 'bold': True, + 'text_wrap': False, + 'valign': 'center', + 'fg_color': '#ADD8E6', + 'border': 1 + }) + if sheet == 'OVERVIEW': + # Write the column headers with the defined format. + for col_num, value in enumerate(df.columns.values): + try: + worksheet.write(0, col_num + 1, value, header_formater) + except Exception as e: + stderr.print(f"Error writing header at column {col_num + 1}: {e}") + + # Write the first column with the defined format. + for row_num in range(1, len(df) + 1): + try: + worksheet.write(row_num, 0, df.iloc[row_num - 1, 0], first_col_formater) + except Exception as e: + stderr.print(f"Error writing first column at row {row_num}: {e}") + + if sheet == 'METADATA_LAB': + # Write the column headers with the defined format. + for col_num, value in enumerate(df.columns.values): + for row_num in range(0, len(df)): + try: + worksheet.write(row_num + 1, col_num + 1, df.iloc[row_num-1, col_num], header_formater) + except Exception as e: + stderr.print(f"Error writing header at column {col_num + 1}: {e}") + + # Write the first column with the defined format. + for row_num in range(1, len(df)+1): + try: + worksheet.write(row_num, 0, df.index[row_num-1], first_col_formater) + except Exception as e: + stderr.print(f"Error writing first column at row {row_num}: {e}") - # Append the row to the list of rows - rows.append(row) - - # Create a DataFrame from the list of rows - df = pd.DataFrame(rows) - - # Return the DataFrame - return df + except Exception as e: + stderr.print(f"Error in excel_formater: {e}") diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 8201e7bd..5c55365f 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -351,6 +351,8 @@ def save_new_schema(self, json_data): stderr.print(f"[red]An unexpected error occurred: {str(e)}") return False + #TODO: overview-tab - add mapping column to overview tab + #TODO: overview-tab - FIX first column values def create_metadatalab_excel(self, json_schema): """ Generate the metadatalab template file in xlsx format. It contains: @@ -403,6 +405,7 @@ def create_metadatalab_excel(self, json_schema): df_overview['Label name'] = df['label'] df_overview['Description'] = df['description'] df_overview['Group'] = df['classification'] + df_overview['Mandatory (Y/N)'] = df['required'] df_overview['Example'] = df['examples'].apply(lambda x: x[0] if isinstance(x, list) else x) except Exception as e: stderr.print(f"Error creating overview sheet: {e}") @@ -411,13 +414,11 @@ def create_metadatalab_excel(self, json_schema): # MetadataLab sheet try: metadatalab_header = [ - "", "EJEMPLOS", "DESCRIPCIÓN", "CAMPO" ] df_metadata = pd.DataFrame(columns=[col_name for col_name in metadatalab_header]) - df_metadata[''] = df['label'].apply(lambda _: '') df_metadata['EJEMPLOS'] = df['examples'].apply(lambda x: x[0] if isinstance(x, list) else x) df_metadata['DESCRIPCIÓN'] = df['description'] df_metadata['CAMPO'] = df['label'] @@ -467,7 +468,7 @@ def create_metadatalab_excel(self, json_schema): if len(enum_dict[key]) < enum_maxitems: num_nas = enum_maxitems - len(enum_dict[key]) for _ in range(num_nas): - enum_dict[key].append('NaN') + enum_dict[key].append('') new_df = pd.DataFrame(enum_dict) new_index = range(len(new_df.columns)) @@ -485,11 +486,14 @@ def create_metadatalab_excel(self, json_schema): # WRITE EXCEL try: - with pd.ExcelWriter(out_file) as writer: - df_overview.to_excel(writer, sheet_name='OVERVIEW') - df_metadata.to_excel(writer, sheet_name='METADATA_LAB') - df_validation.to_excel(writer, sheet_name='DATA VALIDATION') + + writer = pd.ExcelWriter(out_file, engine="xlsxwriter") + relecov_tools.assets.schema_utils.metadatalab_template.excel_formater(df_overview, writer, 'OVERVIEW', out_file, have_index=False, have_header=False) + relecov_tools.assets.schema_utils.metadatalab_template.excel_formater(df_metadata, writer, 'METADATA_LAB', out_file, have_index=True, have_header=False) + writer.close() + #TODO: add formater to last sheet stderr.print(f"[green]Excel template successfuly created in: {out_file}") + except Exception as e: stderr.print(f"[red]Error writing to Excel: {e}") return None From 6f45b549972ab3d18e0a28fc6391cbbf792bb6a3 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 8 Aug 2024 11:22:56 +0200 Subject: [PATCH 1426/1454] fix row and column indexing while formating and add data_validation sheet --- .../schema_utils/metadatalab_template.py | 24 ++++++++++--------- relecov_tools/build_schema.py | 12 +++------- 2 files changed, 16 insertions(+), 20 deletions(-) diff --git a/relecov_tools/assets/schema_utils/metadatalab_template.py b/relecov_tools/assets/schema_utils/metadatalab_template.py index 0d701066..ea0efbe3 100644 --- a/relecov_tools/assets/schema_utils/metadatalab_template.py +++ b/relecov_tools/assets/schema_utils/metadatalab_template.py @@ -75,7 +75,7 @@ def excel_formater(df, writer, sheet, out_file, have_index=True, have_header=Tru workbook = writer.book worksheet = writer.sheets[sheet] - # setup excel formaters + # setup excel format worksheet.set_column(0, len(df.columns), 30) header_formater = workbook.add_format({ 'bold': True, @@ -91,6 +91,7 @@ def excel_formater(df, writer, sheet, out_file, have_index=True, have_header=Tru 'fg_color': '#ADD8E6', 'border': 1 }) + if sheet == 'OVERVIEW': # Write the column headers with the defined format. for col_num, value in enumerate(df.columns.values): @@ -105,22 +106,23 @@ def excel_formater(df, writer, sheet, out_file, have_index=True, have_header=Tru worksheet.write(row_num, 0, df.iloc[row_num - 1, 0], first_col_formater) except Exception as e: stderr.print(f"Error writing first column at row {row_num}: {e}") - - if sheet == 'METADATA_LAB': + + if sheet == 'METADATA_LAB' or sheet == 'DATA_VALIDATION': # Write the column headers with the defined format. - for col_num, value in enumerate(df.columns.values): + for col_num in range(0, len(df.columns)): for row_num in range(0, len(df)): - try: - worksheet.write(row_num + 1, col_num + 1, df.iloc[row_num-1, col_num], header_formater) - except Exception as e: - stderr.print(f"Error writing header at column {col_num + 1}: {e}") + if row_num < 3: + stderr.print(f"{df.iloc[row_num, col_num]} for col {col_num} and row {row_num}") + try: + worksheet.write(row_num + 1, col_num + 1, df.iloc[row_num, col_num], header_formater) + except Exception as e: + stderr.print(f"Error writing first column at row {row_num}: {e}") # Write the first column with the defined format. - for row_num in range(1, len(df)+1): + for index_num, index_val in enumerate(df.index): try: - worksheet.write(row_num, 0, df.index[row_num-1], first_col_formater) + worksheet.write(index_num + 1, 0, index_val, first_col_formater) except Exception as e: stderr.print(f"Error writing first column at row {row_num}: {e}") - except Exception as e: stderr.print(f"Error in excel_formater: {e}") diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 5c55365f..b35ab209 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -392,7 +392,6 @@ def create_metadatalab_excel(self, json_schema): # Overview sheet try: overview_header = [ - "", "Label name", "Description", "Group", @@ -401,7 +400,6 @@ def create_metadatalab_excel(self, json_schema): "METADATA_LAB COLUMN", ] df_overview = pd.DataFrame(columns=[col_name for col_name in overview_header]) - df_overview[''] = df['classification'] df_overview['Label name'] = df['label'] df_overview['Description'] = df['description'] df_overview['Group'] = df['classification'] @@ -430,16 +428,13 @@ def create_metadatalab_excel(self, json_schema): # DataValidation sheet try: datavalidation_header = [ - "", "EJEMPLOS", "DESCRIPCIÓN", - "CAMPO", - "" + "CAMPO" ] df_hasenum = df[(pd.notnull(df.enum))] df_validation = pd.DataFrame(columns=[col_name for col_name in datavalidation_header]) df_validation['tmp_property'] = df_hasenum['property_id'] - df_validation[''] = df_hasenum['label'].apply(lambda _: '') df_validation['EJEMPLOS'] = df_hasenum['examples'].apply(lambda x: x[0] if isinstance(x, list) else x) df_validation['DESCRIPCIÓN'] = df_hasenum['description'] df_validation['CAMPO'] = df_hasenum['label'] @@ -480,20 +475,19 @@ def create_metadatalab_excel(self, json_schema): frames = [valid_transposed, new_df] df_validation = pd.concat(frames) + df_validation = df_validation.drop(index=['tmp_property']) except Exception as e: stderr.print(f"[red]Error processing enums and combining data: {e}") return None # WRITE EXCEL try: - writer = pd.ExcelWriter(out_file, engine="xlsxwriter") relecov_tools.assets.schema_utils.metadatalab_template.excel_formater(df_overview, writer, 'OVERVIEW', out_file, have_index=False, have_header=False) relecov_tools.assets.schema_utils.metadatalab_template.excel_formater(df_metadata, writer, 'METADATA_LAB', out_file, have_index=True, have_header=False) + relecov_tools.assets.schema_utils.metadatalab_template.excel_formater(df_validation, writer, 'DATA_VALIDATION', out_file, have_index=True, have_header=False) writer.close() - #TODO: add formater to last sheet stderr.print(f"[green]Excel template successfuly created in: {out_file}") - except Exception as e: stderr.print(f"[red]Error writing to Excel: {e}") return None From a53e0d70474d2f1f9826d24cc02e0fa190a24b81 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 8 Aug 2024 13:24:29 +0200 Subject: [PATCH 1427/1454] improve logs, prompts and error handling --- relecov_tools/__main__.py | 2 +- .../assets/schema_utils/jsonschema_draft.py | 11 ++++- .../schema_utils/metadatalab_template.py | 1 - relecov_tools/build_schema.py | 46 +++++++++++-------- 4 files changed, 38 insertions(+), 22 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 85d1b5b1..e02ea777 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -525,7 +525,7 @@ def launch_pipeline(input, template, output, config): "-s", "--schema_base", type=click.Path(), - help="Path to the base schema file. This file is used as a reference to compare it with the schema generated using this module.", + help="Path to the base schema file. This file is used as a reference to compare it with the schema generated using this module. (Default: installed schema in 'relecov-tools/relecov_tools/schema/relecov_schema.json')", required=False, ) @click.option( diff --git a/relecov_tools/assets/schema_utils/jsonschema_draft.py b/relecov_tools/assets/schema_utils/jsonschema_draft.py index 7f9995e0..2da2ba62 100644 --- a/relecov_tools/assets/schema_utils/jsonschema_draft.py +++ b/relecov_tools/assets/schema_utils/jsonschema_draft.py @@ -83,6 +83,13 @@ def check_schema_draft(schema_draft, draft_version): validator_class.check_schema(schema_draft) stderr.print("[green]New schema is valid based on JSON Specification rules.") except exceptions.SchemaError as e: - stderr.print(f"[red]Schema validation error: {e.message}") + stderr.print(f"[yellow]Schema validation error: {e.message}") + promp_answ = relecov_tools.utils.prompt_yn_question('Errors found during schema validation, proceed?:') + if not promp_answ: + sys.exit(1) except Exception as e: - stderr.print(f"An error occurred during schema validation: {str(e)}") + stderr.print(f"[yellow]Error occurred during schema validation: {e}") + relecov_tools.utils.prompt_yn_question('Errors found during schema validation, proceed?:') + promp_answ = relecov_tools.utils.prompt_yn_question('Errors found during schema validation, proceed?:') + if not promp_answ: + sys.exit(1) \ No newline at end of file diff --git a/relecov_tools/assets/schema_utils/metadatalab_template.py b/relecov_tools/assets/schema_utils/metadatalab_template.py index ea0efbe3..972e686a 100644 --- a/relecov_tools/assets/schema_utils/metadatalab_template.py +++ b/relecov_tools/assets/schema_utils/metadatalab_template.py @@ -112,7 +112,6 @@ def excel_formater(df, writer, sheet, out_file, have_index=True, have_header=Tru for col_num in range(0, len(df.columns)): for row_num in range(0, len(df)): if row_num < 3: - stderr.print(f"{df.iloc[row_num, col_num]} for col {col_num} and row {row_num}") try: worksheet.write(row_num + 1, col_num + 1, df.iloc[row_num, col_num], header_formater) except Exception as e: diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index b35ab209..c98c465d 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -1,4 +1,5 @@ #!/usr/bin/env python +# TODO: add utils to requirements import logging import rich.console import pandas as pd @@ -8,6 +9,7 @@ import json import difflib import xlsxwriter +import inspect import relecov_tools.utils import relecov_tools.assets.schema_utils.jsonschema_draft @@ -24,7 +26,6 @@ # TODO: user should be able to provide a custom schema as a file in order to replace the current one. -# TODO: still need to work in logs class SchemaBuilder: def __init__( self, @@ -47,9 +48,9 @@ def __init__( if not self.excel_file_path.endswith(".xlsx"): raise ValueError("The Excel file must have a .xlsx extension.") - # Validate output folder - relecov_tools.utils.prompt_create_outdir(os.getcwd(), out_dir) - self.output_folder = os.path.join(os.getcwd(), out_dir) + # Validate output folder creation + self.output_folder = relecov_tools.utils.prompt_create_outdir(None, out_dir) + stderr.print(self.output_folder) # Validate json schema draft version self.draft_version = ( @@ -59,7 +60,13 @@ def __init__( ) # Validate base schema - if not base_schema_path: + if base_schema_path is not None: + if relecov_tools.utils.file_exists(base_schema_path): + self.base_schema_path = base_schema_path + else: + stderr.print(f"[Error]Defined base schema file not found: {base_schema_path}. Exiting...") + sys.exit(1) + else: try: config_json = ConfigJson() relecov_schema = config_json.get_topic_data( @@ -71,7 +78,9 @@ def __init__( "schema", relecov_schema, ) - os.path.isfile(self.base_schema_path) + if not relecov_tools.utils.file_exists(self.base_schema_path): + stderr.print("[Error]Fatal error. Relecov schema were not found in current relecov-tools installation. Make sure relecov-tools command is functioning. Exiting...") + sys.exit(1) stderr.print( "[green]RELECOV schema successfully found in the configuration." ) @@ -116,6 +125,7 @@ def validate_database_definition(self, json_data): def read_database_definition(self, sheet_id='main'): """Reads the database definition and converts it into json format.""" + caller_method = inspect.stack()[1][3] # Read excel file df = pd.read_excel(self.excel_file_path, sheet_name=sheet_id, na_values=['nan', 'N/A', 'NA', '']) # Convert database to json format @@ -127,7 +137,7 @@ def read_database_definition(self, sheet_id='main'): # Check json is not empty if len(json_data) == 0: - stderr.print("[red]No data found in xlsx database") + stderr.print(f"{caller_method}{sheet_id}) [red]No data found in xlsx database") sys.exit(1) # Perform validation of database content @@ -135,11 +145,11 @@ def read_database_definition(self, sheet_id='main'): if validation_out: stderr.print( - f"[red]Validation of database content falied. Missing mandatory features in: {validation_out}" + f"({caller_method}:{sheet_id}) [red]Validation of database content falied. Missing mandatory features in: {validation_out}" ) sys.exit(1) else: - stderr.print("[green]Validation of database content passed.") + stderr.print(f"({caller_method}:{sheet_id}) [green]Validation of database content passed.") return json_data def create_schema_draft_template(self): @@ -185,7 +195,7 @@ def complex_jsonschema_object(self, property_id, features_dict): try: complex_json_data = self.read_database_definition(sheet_id=property_id) except ValueError as e: - stderr.print(f"[red]{e}") + stderr.print(f"[yellow]{e}") return None # Add sub property items @@ -307,12 +317,12 @@ def print_schema_diff(self, base_schema, new_schema): if not diff_lines: stderr.print( - "[orange]No differencess were found between already installed and new generated schema. Exiting. No changes made" + "[yellow]No differencess were found between already installed and new generated schema. Exiting. No changes made" ) return None else: stderr.print( - "Differences found between the existing schema and the newly generated schema." + "[yellow]Differences found between the existing schema and the newly generated schema." ) # Set user's choices choices = ["Print to sandard output (stdout)", "Save to file", "Both"] @@ -362,10 +372,7 @@ def create_metadatalab_excel(self, json_schema): """ try: # Set up metadatalab configuration - out_file = os.path.join( - self.excel_file_path, - os.path.join(self.output_folder, "metadatalab_template" + ".xlsx") - ) + out_file = os.path.join(self.output_folder, "metadatalab_template" + ".xlsx") required_classification = [ "Database Identifiers", "Sample collection and processing", @@ -487,7 +494,7 @@ def create_metadatalab_excel(self, json_schema): relecov_tools.assets.schema_utils.metadatalab_template.excel_formater(df_metadata, writer, 'METADATA_LAB', out_file, have_index=True, have_header=False) relecov_tools.assets.schema_utils.metadatalab_template.excel_formater(df_validation, writer, 'DATA_VALIDATION', out_file, have_index=True, have_header=False) writer.close() - stderr.print(f"[green]Excel template successfuly created in: {out_file}") + stderr.print(f"[green]Metadata lab template successfuly created in: {out_file}") except Exception as e: stderr.print(f"[red]Error writing to Excel: {e}") return None @@ -497,6 +504,7 @@ def create_metadatalab_excel(self, json_schema): def handle_build_schema(self): # Load xlsx database and convert into json format + stderr.print("[white]Start reading xlsx database") database_dic = self.read_database_definition() # Verify current schema used by relecov-tools: @@ -525,7 +533,9 @@ def handle_build_schema(self): sys.exit(1) if schema_diff: - self.create_metadatalab_excel(new_schema_json) + promp_answ = relecov_tools.utils.prompt_yn_question('Do you want to create a metadata lab file?:') + if promp_answ: + self.create_metadatalab_excel(new_schema_json) # Build EXCEL template # - Add versinon tag to filename From d0d999501bb01aa8d026c6589837565c8676bcc0 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 8 Aug 2024 13:28:40 +0200 Subject: [PATCH 1428/1454] fix linting --- .../assets/schema_utils/jsonschema_draft.py | 14 +- .../schema_utils/metadatalab_template.py | 84 ++++--- relecov_tools/build_schema.py | 220 +++++++++++------- 3 files changed, 201 insertions(+), 117 deletions(-) diff --git a/relecov_tools/assets/schema_utils/jsonschema_draft.py b/relecov_tools/assets/schema_utils/jsonschema_draft.py index 2da2ba62..929edbc4 100644 --- a/relecov_tools/assets/schema_utils/jsonschema_draft.py +++ b/relecov_tools/assets/schema_utils/jsonschema_draft.py @@ -84,12 +84,18 @@ def check_schema_draft(schema_draft, draft_version): stderr.print("[green]New schema is valid based on JSON Specification rules.") except exceptions.SchemaError as e: stderr.print(f"[yellow]Schema validation error: {e.message}") - promp_answ = relecov_tools.utils.prompt_yn_question('Errors found during schema validation, proceed?:') + promp_answ = relecov_tools.utils.prompt_yn_question( + "Errors found during schema validation, proceed?:" + ) if not promp_answ: sys.exit(1) except Exception as e: stderr.print(f"[yellow]Error occurred during schema validation: {e}") - relecov_tools.utils.prompt_yn_question('Errors found during schema validation, proceed?:') - promp_answ = relecov_tools.utils.prompt_yn_question('Errors found during schema validation, proceed?:') + relecov_tools.utils.prompt_yn_question( + "Errors found during schema validation, proceed?:" + ) + promp_answ = relecov_tools.utils.prompt_yn_question( + "Errors found during schema validation, proceed?:" + ) if not promp_answ: - sys.exit(1) \ No newline at end of file + sys.exit(1) diff --git a/relecov_tools/assets/schema_utils/metadatalab_template.py b/relecov_tools/assets/schema_utils/metadatalab_template.py index 972e686a..0e3bab19 100644 --- a/relecov_tools/assets/schema_utils/metadatalab_template.py +++ b/relecov_tools/assets/schema_utils/metadatalab_template.py @@ -1,11 +1,7 @@ #!/usr/bin/env python import logging import rich.console -import os -import json -import xlsxwriter import pandas as pd -import xlsxwriter import relecov_tools.utils @@ -19,15 +15,21 @@ force_terminal=relecov_tools.utils.rich_force_colors(), ) + def schema_to_flatten_json(json_data): """This function flattens schema when nested items are found""" try: flatten_json = {} for property_id, features in json_data.items(): try: - if features.get('type') == 'array': - complex_properties = json_data[property_id]["items"].get('properties') - for complex_property_id, complex_feature in complex_properties.items(): + if features.get("type") == "array": + complex_properties = json_data[property_id]["items"].get( + "properties" + ) + for ( + complex_property_id, + complex_feature, + ) in complex_properties.items(): flatten_json.update({complex_property_id: complex_feature}) else: flatten_json.update({property_id: features}) @@ -38,6 +40,7 @@ def schema_to_flatten_json(json_data): stderr.print(f"[red]Error in schema_to_flatten_json: {e}") return None + def schema_properties_to_df(json_data): try: # Initialize an empty list to store the rows of the DataFrame @@ -47,7 +50,7 @@ def schema_properties_to_df(json_data): for property_id, property_features in json_data.items(): try: # Create a dictionary to hold the property features - row = {'property_id': property_id} + row = {"property_id": property_id} row.update(property_features) # Append the row to the list of rows @@ -67,55 +70,70 @@ def schema_properties_to_df(json_data): def excel_formater(df, writer, sheet, out_file, have_index=True, have_header=True): try: - + # Write the DataFrame to the specified sheet - df.to_excel(writer, sheet_name=sheet, startrow=1, index=have_index, header=have_header) - + df.to_excel( + writer, sheet_name=sheet, startrow=1, index=have_index, header=have_header + ) + # Get the xlsxwriter workbook and worksheet objects. workbook = writer.book worksheet = writer.sheets[sheet] - + # setup excel format worksheet.set_column(0, len(df.columns), 30) - header_formater = workbook.add_format({ - 'bold': True, - 'text_wrap': False, - 'valign': 'top', - 'fg_color': '#ADD8E6', - 'border': 1 - }) - first_col_formater = workbook.add_format({ - 'bold': True, - 'text_wrap': False, - 'valign': 'center', - 'fg_color': '#ADD8E6', - 'border': 1 - }) - - if sheet == 'OVERVIEW': + header_formater = workbook.add_format( + { + "bold": True, + "text_wrap": False, + "valign": "top", + "fg_color": "#ADD8E6", + "border": 1, + } + ) + first_col_formater = workbook.add_format( + { + "bold": True, + "text_wrap": False, + "valign": "center", + "fg_color": "#ADD8E6", + "border": 1, + } + ) + + if sheet == "OVERVIEW": # Write the column headers with the defined format. for col_num, value in enumerate(df.columns.values): try: worksheet.write(0, col_num + 1, value, header_formater) except Exception as e: stderr.print(f"Error writing header at column {col_num + 1}: {e}") - + # Write the first column with the defined format. for row_num in range(1, len(df) + 1): try: - worksheet.write(row_num, 0, df.iloc[row_num - 1, 0], first_col_formater) + worksheet.write( + row_num, 0, df.iloc[row_num - 1, 0], first_col_formater + ) except Exception as e: stderr.print(f"Error writing first column at row {row_num}: {e}") - if sheet == 'METADATA_LAB' or sheet == 'DATA_VALIDATION': + if sheet == "METADATA_LAB" or sheet == "DATA_VALIDATION": # Write the column headers with the defined format. for col_num in range(0, len(df.columns)): for row_num in range(0, len(df)): if row_num < 3: try: - worksheet.write(row_num + 1, col_num + 1, df.iloc[row_num, col_num], header_formater) + worksheet.write( + row_num + 1, + col_num + 1, + df.iloc[row_num, col_num], + header_formater, + ) except Exception as e: - stderr.print(f"Error writing first column at row {row_num}: {e}") + stderr.print( + f"Error writing first column at row {row_num}: {e}" + ) # Write the first column with the defined format. for index_num, index_val in enumerate(df.index): diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index c98c465d..7ee290a6 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -5,10 +5,8 @@ import pandas as pd import os import sys -import re import json import difflib -import xlsxwriter import inspect import relecov_tools.utils @@ -64,7 +62,9 @@ def __init__( if relecov_tools.utils.file_exists(base_schema_path): self.base_schema_path = base_schema_path else: - stderr.print(f"[Error]Defined base schema file not found: {base_schema_path}. Exiting...") + stderr.print( + f"[Error]Defined base schema file not found: {base_schema_path}. Exiting..." + ) sys.exit(1) else: try: @@ -79,7 +79,9 @@ def __init__( relecov_schema, ) if not relecov_tools.utils.file_exists(self.base_schema_path): - stderr.print("[Error]Fatal error. Relecov schema were not found in current relecov-tools installation. Make sure relecov-tools command is functioning. Exiting...") + stderr.print( + "[Error]Fatal error. Relecov schema were not found in current relecov-tools installation. Make sure relecov-tools command is functioning. Exiting..." + ) sys.exit(1) stderr.print( "[green]RELECOV schema successfully found in the configuration." @@ -123,11 +125,15 @@ def validate_database_definition(self, json_data): else: return None - def read_database_definition(self, sheet_id='main'): + def read_database_definition(self, sheet_id="main"): """Reads the database definition and converts it into json format.""" caller_method = inspect.stack()[1][3] # Read excel file - df = pd.read_excel(self.excel_file_path, sheet_name=sheet_id, na_values=['nan', 'N/A', 'NA', '']) + df = pd.read_excel( + self.excel_file_path, + sheet_name=sheet_id, + na_values=["nan", "N/A", "NA", ""], + ) # Convert database to json format json_data = {} for row in df.itertuples(index=False): @@ -137,7 +143,9 @@ def read_database_definition(self, sheet_id='main'): # Check json is not empty if len(json_data) == 0: - stderr.print(f"{caller_method}{sheet_id}) [red]No data found in xlsx database") + stderr.print( + f"{caller_method}{sheet_id}) [red]No data found in xlsx database" + ) sys.exit(1) # Perform validation of database content @@ -149,7 +157,9 @@ def read_database_definition(self, sheet_id='main'): ) sys.exit(1) else: - stderr.print(f"({caller_method}:{sheet_id}) [green]Validation of database content passed.") + stderr.print( + f"({caller_method}:{sheet_id}) [green]Validation of database content passed." + ) return json_data def create_schema_draft_template(self): @@ -163,13 +173,13 @@ def create_schema_draft_template(self): # TODO: we have to discuss wether NaN (empty) values need to be handled def standard_jsonschema_object(self, data_dict, target_key): - """"Create standar json schema object""" + """ "Create standar json schema object""" # For enum and examples, wrap the value in a list json_dict = {} - + # Function to handle NaN values def handle_nan(value): - if pd.isna(value) or value in ['nan', 'NaN', 'None', 'none']: + if pd.isna(value) or value in ["nan", "NaN", "None", "none"]: return "" return str(value) @@ -188,32 +198,34 @@ def handle_nan(value): return json_dict def complex_jsonschema_object(self, property_id, features_dict): - """"Create complex/nested json schema object""" - json_dict = {"type": "object", "properties":{}} - + """ "Create complex/nested json schema object""" + json_dict = {"type": "object", "properties": {}} + # Read tab-dedicated sheet in excell database try: complex_json_data = self.read_database_definition(sheet_id=property_id) except ValueError as e: stderr.print(f"[yellow]{e}") return None - + # Add sub property items - # TODO: add try_excepts - #try: - for sub_property_id, _ in complex_json_data.items(): + # TODO: add try_excepts + # try: + for sub_property_id, _ in complex_json_data.items(): json_dict["properties"][sub_property_id] = {} complex_json_feature = {} for db_feature_key, json_key in features_dict.items(): - if json_key == 'required': + if json_key == "required": continue - feature_schema = self.standard_jsonschema_object(complex_json_data[sub_property_id], db_feature_key) + feature_schema = self.standard_jsonschema_object( + complex_json_data[sub_property_id], db_feature_key + ) if feature_schema: complex_json_feature[json_key] = feature_schema[db_feature_key] json_dict["properties"][sub_property_id] = complex_json_feature return json_dict - #except: + # except: # stderr.print(f"[red]Error while generating comples json object for {property_id}") # return None @@ -240,37 +252,50 @@ def build_new_schema(self, json_data, schema_draft): required_property_unique = [] # Read property_ids in the database. - # Perform checks and create (for each property) feature object like: + # Perform checks and create (for each property) feature object like: # {'example':'A', 'ontology': 'B'...}. # Finally this objet will be written to the draft schema. for property_id, db_features_dic in json_data.items(): schema_property = {} required_property = {} - + # Parse property_ids that needs to be incorporated as complex fields in json_schema - if json_data[property_id].get('complex_field (Y/N)') == 'Y': - complex_json_feature = self.complex_jsonschema_object(property_id, features_to_check) + if json_data[property_id].get("complex_field (Y/N)") == "Y": + complex_json_feature = self.complex_jsonschema_object( + property_id, features_to_check + ) if complex_json_feature: schema_property["type"] = "array" schema_property["items"] = complex_json_feature - schema_property["additionalProperties"]= "false" - schema_property["required"] = [ key for key in complex_json_feature["properties"].keys()] - # For those that follows standard format, add them to json schema as well. + schema_property["additionalProperties"] = "false" + schema_property["required"] = [ + key for key in complex_json_feature["properties"].keys() + ] + # For those that follows standard format, add them to json schema as well. else: for db_feature_key, schema_feature_key in features_to_check.items(): # Verifiy that db_feature_key is present in the database (processed excel (aka 'json_data')) if db_feature_key not in db_features_dic: - stderr.print(f"[INFO] Feature {db_feature_key} is not present in database ({self.excel_file_path})") + stderr.print( + f"[INFO] Feature {db_feature_key} is not present in database ({self.excel_file_path})" + ) continue # Record the required value for each property - if 'required' in db_feature_key or "required" == schema_feature_key: + if ( + "required" in db_feature_key + or "required" == schema_feature_key + ): is_required = str(db_features_dic[db_feature_key]) - if is_required != 'nan': + if is_required != "nan": required_property[property_id] = is_required else: - std_json_feature = self.standard_jsonschema_object(db_features_dic, db_feature_key) + std_json_feature = self.standard_jsonschema_object( + db_features_dic, db_feature_key + ) if std_json_feature: - schema_property[schema_feature_key] = std_json_feature[db_feature_key] + schema_property[schema_feature_key] = std_json_feature[ + db_feature_key + ] else: continue # Finally, send schema_property object to the new json schema draft. @@ -281,14 +306,13 @@ def build_new_schema(self, json_data, schema_draft): if values == "Y": required_property_unique.append(key) schema_draft["required"] = required_property_unique - + # Return new schema return schema_draft except Exception as e: stderr.print(f"[red]Error building schema: {str(e)}") raise - # TODO: Once json schema is created, it requires validation def verify_schema(self, schema): """Verify the schema_draft follows the JSON Schema specification [XXXX] meta-schema.""" @@ -361,8 +385,8 @@ def save_new_schema(self, json_data): stderr.print(f"[red]An unexpected error occurred: {str(e)}") return False - #TODO: overview-tab - add mapping column to overview tab - #TODO: overview-tab - FIX first column values + # TODO: overview-tab - add mapping column to overview tab + # TODO: overview-tab - FIX first column values def create_metadatalab_excel(self, json_schema): """ Generate the metadatalab template file in xlsx format. It contains: @@ -372,26 +396,32 @@ def create_metadatalab_excel(self, json_schema): """ try: # Set up metadatalab configuration - out_file = os.path.join(self.output_folder, "metadatalab_template" + ".xlsx") + out_file = os.path.join( + self.output_folder, "metadatalab_template" + ".xlsx" + ) required_classification = [ "Database Identifiers", "Sample collection and processing", "Host information", "Sequencing", "Pathogen Diagnostic testing", - "Contributor Acknowledgement" + "Contributor Acknowledgement", ] - required_properties = json_schema.get('required') - schema_properties = json_schema.get('properties') + required_properties = json_schema.get("required") + schema_properties = json_schema.get("properties") # Read json schema properties and convert it into pandas df try: schema_properties_flatten = relecov_tools.assets.schema_utils.metadatalab_template.schema_to_flatten_json( schema_properties ) - df = relecov_tools.assets.schema_utils.metadatalab_template.schema_properties_to_df (schema_properties_flatten) - df = df[df['classification'].isin(required_classification)] - df['required'] = df['property_id'].apply(lambda x: 'Y' if x in required_properties else 'N') + df = relecov_tools.assets.schema_utils.metadatalab_template.schema_properties_to_df( + schema_properties_flatten + ) + df = df[df["classification"].isin(required_classification)] + df["required"] = df["property_id"].apply( + lambda x: "Y" if x in required_properties else "N" + ) except Exception as e: stderr.print(f"Error processing schema properties: {e}") return @@ -406,27 +436,31 @@ def create_metadatalab_excel(self, json_schema): "Example", "METADATA_LAB COLUMN", ] - df_overview = pd.DataFrame(columns=[col_name for col_name in overview_header]) - df_overview['Label name'] = df['label'] - df_overview['Description'] = df['description'] - df_overview['Group'] = df['classification'] - df_overview['Mandatory (Y/N)'] = df['required'] - df_overview['Example'] = df['examples'].apply(lambda x: x[0] if isinstance(x, list) else x) + df_overview = pd.DataFrame( + columns=[col_name for col_name in overview_header] + ) + df_overview["Label name"] = df["label"] + df_overview["Description"] = df["description"] + df_overview["Group"] = df["classification"] + df_overview["Mandatory (Y/N)"] = df["required"] + df_overview["Example"] = df["examples"].apply( + lambda x: x[0] if isinstance(x, list) else x + ) except Exception as e: stderr.print(f"Error creating overview sheet: {e}") return # MetadataLab sheet try: - metadatalab_header = [ - "EJEMPLOS", - "DESCRIPCIÓN", - "CAMPO" - ] - df_metadata = pd.DataFrame(columns=[col_name for col_name in metadatalab_header]) - df_metadata['EJEMPLOS'] = df['examples'].apply(lambda x: x[0] if isinstance(x, list) else x) - df_metadata['DESCRIPCIÓN'] = df['description'] - df_metadata['CAMPO'] = df['label'] + metadatalab_header = ["EJEMPLOS", "DESCRIPCIÓN", "CAMPO"] + df_metadata = pd.DataFrame( + columns=[col_name for col_name in metadatalab_header] + ) + df_metadata["EJEMPLOS"] = df["examples"].apply( + lambda x: x[0] if isinstance(x, list) else x + ) + df_metadata["DESCRIPCIÓN"] = df["description"] + df_metadata["CAMPO"] = df["label"] df_metadata = df_metadata.transpose() except Exception as e: stderr.print(f"[red]Error creating MetadataLab sheet: {e}") @@ -434,17 +468,17 @@ def create_metadatalab_excel(self, json_schema): # DataValidation sheet try: - datavalidation_header = [ - "EJEMPLOS", - "DESCRIPCIÓN", - "CAMPO" - ] + datavalidation_header = ["EJEMPLOS", "DESCRIPCIÓN", "CAMPO"] df_hasenum = df[(pd.notnull(df.enum))] - df_validation = pd.DataFrame(columns=[col_name for col_name in datavalidation_header]) - df_validation['tmp_property'] = df_hasenum['property_id'] - df_validation['EJEMPLOS'] = df_hasenum['examples'].apply(lambda x: x[0] if isinstance(x, list) else x) - df_validation['DESCRIPCIÓN'] = df_hasenum['description'] - df_validation['CAMPO'] = df_hasenum['label'] + df_validation = pd.DataFrame( + columns=[col_name for col_name in datavalidation_header] + ) + df_validation["tmp_property"] = df_hasenum["property_id"] + df_validation["EJEMPLOS"] = df_hasenum["examples"].apply( + lambda x: x[0] if isinstance(x, list) else x + ) + df_validation["DESCRIPCIÓN"] = df_hasenum["description"] + df_validation["CAMPO"] = df_hasenum["label"] except Exception as e: stderr.print(f"[red]Error creating DataValidation sheet: {e}") return @@ -452,11 +486,13 @@ def create_metadatalab_excel(self, json_schema): try: # Since enums have different lengths we need further processing. # Convert df into dict to perform data manipulation. - enum_dict = {property: [] for property in df_hasenum['property_id']} + enum_dict = {property: [] for property in df_hasenum["property_id"]} enum_maxitems = 0 # Populate the dictionary with flattened lists for key in enum_dict.keys(): - enum_values = df_hasenum[df_hasenum['property_id'] == key]['enum'].values + enum_values = df_hasenum[df_hasenum["property_id"] == key][ + "enum" + ].values if enum_values.size > 0: enum_list = enum_values[0] # Extract the list enum_dict[key] = enum_list # Assign the list to the dictionary @@ -470,19 +506,19 @@ def create_metadatalab_excel(self, json_schema): if len(enum_dict[key]) < enum_maxitems: num_nas = enum_maxitems - len(enum_dict[key]) for _ in range(num_nas): - enum_dict[key].append('') + enum_dict[key].append("") new_df = pd.DataFrame(enum_dict) new_index = range(len(new_df.columns)) new_df.reindex(columns=new_index) - valid_index = df_validation['tmp_property'].values + valid_index = df_validation["tmp_property"].values valid_transposed = df_validation.transpose() valid_transposed.columns = valid_index frames = [valid_transposed, new_df] df_validation = pd.concat(frames) - df_validation = df_validation.drop(index=['tmp_property']) + df_validation = df_validation.drop(index=["tmp_property"]) except Exception as e: stderr.print(f"[red]Error processing enums and combining data: {e}") return None @@ -490,11 +526,34 @@ def create_metadatalab_excel(self, json_schema): # WRITE EXCEL try: writer = pd.ExcelWriter(out_file, engine="xlsxwriter") - relecov_tools.assets.schema_utils.metadatalab_template.excel_formater(df_overview, writer, 'OVERVIEW', out_file, have_index=False, have_header=False) - relecov_tools.assets.schema_utils.metadatalab_template.excel_formater(df_metadata, writer, 'METADATA_LAB', out_file, have_index=True, have_header=False) - relecov_tools.assets.schema_utils.metadatalab_template.excel_formater(df_validation, writer, 'DATA_VALIDATION', out_file, have_index=True, have_header=False) + relecov_tools.assets.schema_utils.metadatalab_template.excel_formater( + df_overview, + writer, + "OVERVIEW", + out_file, + have_index=False, + have_header=False, + ) + relecov_tools.assets.schema_utils.metadatalab_template.excel_formater( + df_metadata, + writer, + "METADATA_LAB", + out_file, + have_index=True, + have_header=False, + ) + relecov_tools.assets.schema_utils.metadatalab_template.excel_formater( + df_validation, + writer, + "DATA_VALIDATION", + out_file, + have_index=True, + have_header=False, + ) writer.close() - stderr.print(f"[green]Metadata lab template successfuly created in: {out_file}") + stderr.print( + f"[green]Metadata lab template successfuly created in: {out_file}" + ) except Exception as e: stderr.print(f"[red]Error writing to Excel: {e}") return None @@ -533,7 +592,9 @@ def handle_build_schema(self): sys.exit(1) if schema_diff: - promp_answ = relecov_tools.utils.prompt_yn_question('Do you want to create a metadata lab file?:') + promp_answ = relecov_tools.utils.prompt_yn_question( + "Do you want to create a metadata lab file?:" + ) if promp_answ: self.create_metadatalab_excel(new_schema_json) @@ -541,4 +602,3 @@ def handle_build_schema(self): # - Add versinon tag to filename # TODO: metod to ask whether to bump version when json schema is generated? - # TODO: Publish a log file that register modification in json schema? From 8b3b04628bc6f4a142f38b9596014664043209f7 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 8 Aug 2024 13:36:12 +0200 Subject: [PATCH 1429/1454] fix package requirements --- requirements.txt | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index e54911f2..52e31080 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,6 +10,8 @@ pyyaml openpyxl>=3.1.2 ena-upload-cli bio==1.4.0 -xlsxwriter +xlsxwriter==3.2.0 bs4==0.0.2 tabulate +difflib==1.2.6 +pandas==2.2.2 From 555dce2b559fe1c155066e084edb9e4e3e36fba6 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 8 Aug 2024 13:41:32 +0200 Subject: [PATCH 1430/1454] fix conflicting package --- requirements.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index 52e31080..2f779018 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,5 +13,5 @@ bio==1.4.0 xlsxwriter==3.2.0 bs4==0.0.2 tabulate -difflib==1.2.6 -pandas==2.2.2 +cdifflib==1.2.6 +pandas From 78fea171aa2a608c0079904135f0fa4ef8ae3cee Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 8 Aug 2024 14:26:01 +0200 Subject: [PATCH 1431/1454] fix todos and allow to bump version --- .../assets/schema_utils/jsonschema_draft.py | 26 ++++++++++++++++--- relecov_tools/build_schema.py | 19 ++------------ 2 files changed, 25 insertions(+), 20 deletions(-) diff --git a/relecov_tools/assets/schema_utils/jsonschema_draft.py b/relecov_tools/assets/schema_utils/jsonschema_draft.py index 929edbc4..cb522539 100644 --- a/relecov_tools/assets/schema_utils/jsonschema_draft.py +++ b/relecov_tools/assets/schema_utils/jsonschema_draft.py @@ -46,12 +46,32 @@ def check_valid_version(draft_version): def create_draft(draft_version, required_items=None): """Creates a JSON Schema Draft template with required fields.""" - # Check if required draft version is available - url_str = Draft202012Validator.META_SCHEMA["$id"] + def bump_version(version): + """Increment the patch version by 1.""" + major, minor, patch = map(int, version.split(".")) + return f"{major}.{minor}.{patch + 1}" + + # Check if the user wants to bump the version + current_version = pkg_resources.get_distribution("relecov_tools").version + version_sel_choice = relecov_tools.utils.prompt_selection( + "Use default or custom/bumped version?", + ["Use default", "Bump version", "Custom"], + ) + stderr.print(version_sel_choice) + if version_sel_choice == "Bump version": + pakage_version_str = bump_version(current_version) + if version_sel_choice == "Custom": + pakage_version_str = relecov_tools.utils.prompt_text( + "Write the desired version using semantic versioning:" + ) + if version_sel_choice == "Use default": + pakage_version_str = current_version + + # Get parameters to set create the schema + url_str = SCHEMA_VALIDATORS[draft_version].META_SCHEMA["$id"] id_str = "https://github.com/BU-ISCIII/relecov-tools/blob/develop/relecov_tools/schema/relecov_schema.json" description_str = "Json schema that specifies the structure, content, and validation rules for RELECOV metadata" - pakage_version_str = pkg_resources.get_distribution("relecov_tools").version # Construct the draft template draft_template = { diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 7ee290a6..fa019a76 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# TODO: add utils to requirements import logging import rich.console import pandas as pd @@ -23,7 +22,6 @@ ) -# TODO: user should be able to provide a custom schema as a file in order to replace the current one. class SchemaBuilder: def __init__( self, @@ -171,7 +169,6 @@ def create_schema_draft_template(self): ) return draft_template - # TODO: we have to discuss wether NaN (empty) values need to be handled def standard_jsonschema_object(self, data_dict, target_key): """ "Create standar json schema object""" # For enum and examples, wrap the value in a list @@ -209,8 +206,6 @@ def complex_jsonschema_object(self, property_id, features_dict): return None # Add sub property items - # TODO: add try_excepts - # try: for sub_property_id, _ in complex_json_data.items(): json_dict["properties"][sub_property_id] = {} complex_json_feature = {} @@ -225,11 +220,7 @@ def complex_jsonschema_object(self, property_id, features_dict): json_dict["properties"][sub_property_id] = complex_json_feature return json_dict - # except: - # stderr.print(f"[red]Error while generating comples json object for {property_id}") - # return None - # TODO: add strategy to deal with json schema objects, defs and refs def build_new_schema(self, json_data, schema_draft): """ Create a json schema file based on input data and draf skeleton.. @@ -237,7 +228,6 @@ def build_new_schema(self, json_data, schema_draft): try: # List of properties to check in the features dictionary (it maps values between database features and json schema features): # key[db_feature_key]: value[schema_feature_key] - # TODO: This should be a config variable available for all elements in this class features_to_check = { "type": "type", "enum": "enum", @@ -385,8 +375,8 @@ def save_new_schema(self, json_data): stderr.print(f"[red]An unexpected error occurred: {str(e)}") return False - # TODO: overview-tab - add mapping column to overview tab - # TODO: overview-tab - FIX first column values + # FIXME: overview-tab - FIX first column values + # FIXME: overview-tab - Still need to add the column that maps to tab metadatalab def create_metadatalab_excel(self, json_schema): """ Generate the metadatalab template file in xlsx format. It contains: @@ -597,8 +587,3 @@ def handle_build_schema(self): ) if promp_answ: self.create_metadatalab_excel(new_schema_json) - - # Build EXCEL template - # - Add versinon tag to filename - - # TODO: metod to ask whether to bump version when json schema is generated? From 4b2cfab7e6dff903a3390f3c004b779b046df324 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 26 Aug 2024 15:21:56 +0200 Subject: [PATCH 1432/1454] added reviewer1 suggestions in #273 --- README.md | 45 ++++++++ relecov_tools/__main__.py | 4 +- .../schema_utils/metadatalab_template.py | 2 + relecov_tools/build_schema.py | 108 +++++++++++++++--- requirements.txt | 1 - 5 files changed, 138 insertions(+), 22 deletions(-) diff --git a/README.md b/README.md index 075f3150..04888914 100644 --- a/README.md +++ b/README.md @@ -19,6 +19,7 @@ relecov-tools is a set of helper tools for the assembly of the different element * [upload-to-gisaid](#upload-to-gisaid) * [launch](#launch) * [update-db](#update-db) + * [build-schema](#build-schema) * [Aknowledgements](#aknowledgements) ## Installation @@ -68,6 +69,7 @@ Commands: upload-to-gisaid parsed data to create files to upload to gisaid update-db feed database with metadata jsons launch launch viralrecon in hpc + build-schema Generates and updates JSON Schema files from... ``` #### download The command `download` connects to a transfer protocol (currently sftp) and downloads all files in the different available folders in the passed credentials. In addition, it checks if the files in the current folder match the files in the metadata file and also checks if there are md5sum for each file. Else, it creates one before storing in the final repository. @@ -232,6 +234,49 @@ Usage: relecov-tools upload-to-gisaid [OPTIONS] -t, --type Select the type of information to upload to database [sample,bioinfodata,variantdata] -d, --databaseServer Name of the database server receiving the data [iskylims,relecov] +### build-schema +The `build-schema` module provides functionality to generate and manage JSON Schema files based on database definitions from Excel spreadsheets. It automates the creation of JSON Schemas, including validation, drafting, and comparison with existing schemas. + +``` +Usage: relecov-tools build-schema [OPTIONS] + + Generates and updates JSON Schema files from Excel-based database + definitions. + +Options: + -i, --input_file PATH Path to the Excel document containing the database + definition. This file must have a .xlsx extension. + [required] + -s, --schema_base PATH Path to the base schema file. This file is used as + a reference to compare it with the schema + generated using this module. (Default: installed + schema in 'relecov- + tools/relecov_tools/schema/relecov_schema.json') + -v, --draft_version TEXT Version of the JSON schema specification to be + used. Example: '2020-12'. See: https://json- + schema.org/specification-links + -d, --diff BOOLEAN Prints a changelog/diff between the base and + incoming versions of the schema. + -o, --out_dir PATH Path to save output file/s + --help Show this message and exit. +``` + +#### Mandatory Fields +Ensure that the fields below are properly defined as headers in your Excel sheet (dataase definition): + +``` +enum: List of possible values for enumeration. +examples: Example values for the property. +ontology_id: Identifier for ontology. +type: Data type of the property (e.g., string, integer). +description: Description of the property. +classification: Classification or category of the property. +label_name: Label or name for the property. +fill_mode: Mode for filling in the property (e.g., required, optional). +required (Y/N): Indicates if the property is required (Y) or optional (N). +complex_field (Y/N): Indicates if the property is a complex (nested) field (Y) or a standard field (N). +``` + #### launch SOON diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index e02ea777..9b2f6d15 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -532,7 +532,7 @@ def launch_pipeline(input, template, output, config): "-v", "--draft_version", type=click.STRING, - help="Version of the JSON schema specification to be used. Example: '2020-12. See: https://json-schema.org/specification-links", + help="Version of the JSON schema specification to be used. Example: '2020-12'. See: https://json-schema.org/specification-links", ) @click.option( "-d", @@ -542,7 +542,7 @@ def launch_pipeline(input, template, output, config): ) @click.option("-o", "--out_dir", type=click.Path(), help="Path to save output file/s") def build_schema(input_file, schema_base, draft_version, diff, out_dir): - """""" + """Generates and updates JSON Schema files from Excel-based database definitions.""" schema_update = relecov_tools.build_schema.SchemaBuilder( input_file, schema_base, draft_version, diff, out_dir ) diff --git a/relecov_tools/assets/schema_utils/metadatalab_template.py b/relecov_tools/assets/schema_utils/metadatalab_template.py index 0e3bab19..db4d4a1d 100644 --- a/relecov_tools/assets/schema_utils/metadatalab_template.py +++ b/relecov_tools/assets/schema_utils/metadatalab_template.py @@ -89,6 +89,7 @@ def excel_formater(df, writer, sheet, out_file, have_index=True, have_header=Tru "valign": "top", "fg_color": "#ADD8E6", "border": 1, + "locked": True, } ) first_col_formater = workbook.add_format( @@ -98,6 +99,7 @@ def excel_formater(df, writer, sheet, out_file, have_index=True, have_header=Tru "valign": "center", "fg_color": "#ADD8E6", "border": 1, + "locked": True, } ) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index fa019a76..780494bb 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -92,7 +92,16 @@ def __init__( sys.exit(1) def validate_database_definition(self, json_data): - """Validate the mandatory features of each property in json_data.""" + """Validate the mandatory features of each property in json_data. + Validate the mandatory features of each property in json_data. + + Args: + json_data (dict): The JSON data representing the database definition. + + Returns: + dict or None: A dictionary with properties that are missing mandatory/invalid features, + or None if all mandatory features are present + """ # Check mandatory key features to build a json schema notvalid_properties = {} mandatory_features = [ @@ -124,7 +133,14 @@ def validate_database_definition(self, json_data): return None def read_database_definition(self, sheet_id="main"): - """Reads the database definition and converts it into json format.""" + """Reads the database definition from an Excel sheet and converts it into JSON format. + + Args: + sheet_id (str): The sheet name or ID in the Excel file to read from. Defaults to "main". + + Returns: + json_data (dict): The JSON data representing the database definition. + """ caller_method = inspect.stack()[1][3] # Read excel file df = pd.read_excel( @@ -161,7 +177,13 @@ def read_database_definition(self, sheet_id="main"): return json_data def create_schema_draft_template(self): - "Loads JsonSchema template based on draft name: Available drafts: [2020-12]" + """ + Create a JSON Schema draft template based on the draft version. + Available drafts: [2020-12] + + Returns: + draft_template(dict): The JSON Schema draft template. + """ draft_template = ( relecov_tools.assets.schema_utils.jsonschema_draft.create_draft( self.draft_version, True @@ -169,8 +191,17 @@ def create_schema_draft_template(self): ) return draft_template - def standard_jsonschema_object(self, data_dict, target_key): - """ "Create standar json schema object""" + def standard_jsonschema_object(seschemalf, data_dict, target_key): + """ + Create a standard JSON Schema object for a given key in the data dictionary. + + Args: + data_dict (dict): The data dictionary containing the properties. + target_key (str): The key for which to create the JSON Schema object. + + Returns: + json_dict (dict): The JSON Schema object for the target key. + """ # For enum and examples, wrap the value in a list json_dict = {} @@ -195,7 +226,16 @@ def handle_nan(value): return json_dict def complex_jsonschema_object(self, property_id, features_dict): - """ "Create complex/nested json schema object""" + """ + Create a complex (nested) JSON Schema object for a given property ID. + + Args: + property_id (str): The ID of the property for which to create the JSON Schema object. + features_dict (dict): A dictionary mapping database features to JSON Schema features. + + Returns: + json_dict (dict): The complex JSON Schema object. + """ json_dict = {"type": "object", "properties": {}} # Read tab-dedicated sheet in excell database @@ -223,7 +263,14 @@ def complex_jsonschema_object(self, property_id, features_dict): def build_new_schema(self, json_data, schema_draft): """ - Create a json schema file based on input data and draf skeleton.. + Build a new JSON Schema based on the provided JSON data and draft template. + + Parameters: + json_data (dict): The JSON data representing the database definition. + schema_template (dict): The JSON Schema draft template. + + Returns: + schema_draft (dict): The newly created JSON Schema. """ try: # List of properties to check in the features dictionary (it maps values between database features and json schema features): @@ -305,15 +352,29 @@ def build_new_schema(self, json_data, schema_draft): raise def verify_schema(self, schema): - """Verify the schema_draft follows the JSON Schema specification [XXXX] meta-schema.""" + """ + Verify that the given schema adheres to the JSON Schema specification for the specified draft version. + + Args: + schema (dict): The JSON Schema to be verified. + + Raises: + ValueError: If the schema does not conform to the JSON Schema specification. + """ relecov_tools.assets.schema_utils.jsonschema_draft.check_schema_draft( schema, self.draft_version ) def print_schema_diff(self, base_schema, new_schema): """ - Print the differences between the base version of schema_input.json - and the updated version. + Print the differences between the base schema and the newly generated schema. + + Args: + base_schema (dict): The base JSON Schema to compare against. + new_schema (dict): The newly generated JSON Schema to compare. + + Returns: + bool: True if differences are found, False otherwise. """ # Set diff input base_schema_lines = json.dumps(base_schema, indent=4).splitlines() @@ -359,7 +420,13 @@ def print_schema_diff(self, base_schema, new_schema): # FIXME: Add version tag to file name def save_new_schema(self, json_data): """ - Saves the schema generated by SchemaBuilder class into output folder. + Save the generated JSON Schema to the output folder. + + Args: + json_data (dict): The JSON Schema to be saved. + + Returns: + bool: True if the schema was successfully saved, False otherwise. """ try: path_to_save = self.output_folder + "/relecov_schema.json" @@ -379,10 +446,13 @@ def save_new_schema(self, json_data): # FIXME: overview-tab - Still need to add the column that maps to tab metadatalab def create_metadatalab_excel(self, json_schema): """ - Generate the metadatalab template file in xlsx format. It contains: - - Overview tab: - - Metadata LAB tab: - - Validation Tab: + Generate an Excel template file for Metadata LAB with three tabs: Overview, Metadata LAB, and Data Validation. + + Args: + json_schema (dict): The JSON Schema from which the Excel template is generated. It should include properties and required fields. + + Returns: + None: if any error occurs during the process. """ try: # Set up metadatalab configuration @@ -414,7 +484,7 @@ def create_metadatalab_excel(self, json_schema): ) except Exception as e: stderr.print(f"Error processing schema properties: {e}") - return + return None # Overview sheet try: @@ -438,7 +508,7 @@ def create_metadatalab_excel(self, json_schema): ) except Exception as e: stderr.print(f"Error creating overview sheet: {e}") - return + return None # MetadataLab sheet try: @@ -454,7 +524,7 @@ def create_metadatalab_excel(self, json_schema): df_metadata = df_metadata.transpose() except Exception as e: stderr.print(f"[red]Error creating MetadataLab sheet: {e}") - return + return None # DataValidation sheet try: @@ -471,7 +541,7 @@ def create_metadatalab_excel(self, json_schema): df_validation["CAMPO"] = df_hasenum["label"] except Exception as e: stderr.print(f"[red]Error creating DataValidation sheet: {e}") - return + return None try: # Since enums have different lengths we need further processing. diff --git a/requirements.txt b/requirements.txt index 2f779018..372438f1 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,5 +13,4 @@ bio==1.4.0 xlsxwriter==3.2.0 bs4==0.0.2 tabulate -cdifflib==1.2.6 pandas From ae10664e85ae42d680fc355241fc72706503b322 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 27 Aug 2024 13:53:43 +0200 Subject: [PATCH 1433/1454] added reviewer2 suggestions in #273 --- relecov_tools/__main__.py | 2 +- .../assets/schema_utils/jsonschema_draft.py | 8 +- relecov_tools/build_schema.py | 78 +++++++++++-------- relecov_tools/json_validation.py | 7 +- relecov_tools/utils.py | 14 ++-- 5 files changed, 61 insertions(+), 48 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 9b2f6d15..dc165665 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -537,7 +537,7 @@ def launch_pipeline(input, template, output, config): @click.option( "-d", "--diff", - type=click.BOOL, + is_flag=True, help="Prints a changelog/diff between the base and incoming versions of the schema.", ) @click.option("-o", "--out_dir", type=click.Path(), help="Path to save output file/s") diff --git a/relecov_tools/assets/schema_utils/jsonschema_draft.py b/relecov_tools/assets/schema_utils/jsonschema_draft.py index cb522539..6539b873 100644 --- a/relecov_tools/assets/schema_utils/jsonschema_draft.py +++ b/relecov_tools/assets/schema_utils/jsonschema_draft.py @@ -4,6 +4,7 @@ import relecov_tools.utils import pkg_resources +import jsonschema from jsonschema import Draft202012Validator, exceptions log = logging.getLogger(__name__) @@ -102,8 +103,8 @@ def check_schema_draft(schema_draft, draft_version): try: validator_class.check_schema(schema_draft) stderr.print("[green]New schema is valid based on JSON Specification rules.") - except exceptions.SchemaError as e: - stderr.print(f"[yellow]Schema validation error: {e.message}") + except jsonschema.ValidationError: + stderr.print(f"[red] Json schema does not fulfill ${draft_version} Validation") promp_answ = relecov_tools.utils.prompt_yn_question( "Errors found during schema validation, proceed?:" ) @@ -111,9 +112,6 @@ def check_schema_draft(schema_draft, draft_version): sys.exit(1) except Exception as e: stderr.print(f"[yellow]Error occurred during schema validation: {e}") - relecov_tools.utils.prompt_yn_question( - "Errors found during schema validation, proceed?:" - ) promp_answ = relecov_tools.utils.prompt_yn_question( "Errors found during schema validation, proceed?:" ) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 780494bb..7cb6a894 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -1,5 +1,6 @@ #!/usr/bin/env python import logging +import relecov_tools.json_validation import rich.console import pandas as pd import os @@ -28,7 +29,7 @@ def __init__( excel_file_path=None, base_schema_path=None, draft_version=None, - show_diff=False, + show_diff=None, out_dir=None, ): """ @@ -36,8 +37,6 @@ def __init__( It reads the database definition from an Excel file and allows customization of the schema generation process. """ self.excel_file_path = excel_file_path - self.show_diff = show_diff - # Validate input variables if not self.excel_file_path or not os.path.isfile(self.excel_file_path): raise ValueError("A valid Excel file path must be provided.") @@ -45,9 +44,17 @@ def __init__( raise ValueError("The Excel file must have a .xlsx extension.") # Validate output folder creation - self.output_folder = relecov_tools.utils.prompt_create_outdir(None, out_dir) - stderr.print(self.output_folder) + if not out_dir or not os.path.isfile(out_dir): + self.output_folder = relecov_tools.utils.prompt_create_outdir(None, out_dir) + else: + self.output_folder = out_dir + # Validate show diff option + if not show_diff: + self.show_diff = None + else: + self.show_diff = True + # Validate json schema draft version self.draft_version = ( relecov_tools.assets.schema_utils.jsonschema_draft.check_valid_version( @@ -304,7 +311,7 @@ def build_new_schema(self, json_data, schema_draft): if complex_json_feature: schema_property["type"] = "array" schema_property["items"] = complex_json_feature - schema_property["additionalProperties"] = "false" + schema_property["additionalProperties"] = False schema_property["required"] = [ key for key in complex_json_feature["properties"].keys() ] @@ -365,7 +372,7 @@ def verify_schema(self, schema): schema, self.draft_version ) - def print_schema_diff(self, base_schema, new_schema): + def get_schema_diff(self, base_schema, new_schema): """ Print the differences between the base schema and the newly generated schema. @@ -399,23 +406,26 @@ def print_schema_diff(self, base_schema, new_schema): stderr.print( "[yellow]Differences found between the existing schema and the newly generated schema." ) - # Set user's choices - choices = ["Print to sandard output (stdout)", "Save to file", "Both"] - diff_output_choice = relecov_tools.utils.prompt_selection( - "How would you like to print the diff between schemes?:", choices + return self.print_save_schema_diff(diff_lines) + + def print_save_schema_diff(self, diff_lines=None): + # Set user's choices + choices = ["Print to sandard output (stdout)", "Save to file", "Both"] + diff_output_choice = relecov_tools.utils.prompt_selection( + "How would you like to print the diff between schemes?:", choices + ) + if diff_output_choice in ["Print to sandard output (stdout)", "Both"]: + for line in diff_lines: + print(line) + return True + if diff_output_choice in ["Save to file", "Both"]: + diff_filepath = os.path.join( + os.path.realpath(self.output_folder) + "/build_schema_diff.txt" ) - if diff_output_choice in ["Print to sandard output (stdout)", "Both"]: - for line in diff_lines: - print(line) - return True - if diff_output_choice in ["Save to file", "Both"]: - diff_filepath = os.path.join( - os.path.realpath(self.output_folder) + "/build_schema_diff.txt" - ) - with open(diff_filepath, "w") as diff_file: - diff_file.write("\n".join(diff_lines)) - stderr.print(f"[green]Schema diff file saved to {diff_filepath}") - return True + with open(diff_filepath, "w") as diff_file: + diff_file.write("\n".join(diff_lines)) + stderr.print(f"[green]Schema diff file saved to {diff_filepath}") + return True # FIXME: Add version tag to file name def save_new_schema(self, json_data): @@ -642,18 +652,22 @@ def handle_build_schema(self): self.verify_schema(new_schema_json) # Compare base vs new schema and saves new JSON schema - schema_diff = self.print_schema_diff(base_schema_json, new_schema_json) + stderr.print(self.show_diff) + if self.show_diff: + schema_diff = self.get_schema_diff(base_schema_json, new_schema_json) + else: + schema_diff = None + if schema_diff: self.save_new_schema(new_schema_json) else: stderr.print( - f"[green]No changes found against base schema ({self.base_schema_path}). Exiting..." + f"[green]No changes found against base schema ({self.base_schema_path})." ) - sys.exit(1) - if schema_diff: - promp_answ = relecov_tools.utils.prompt_yn_question( - "Do you want to create a metadata lab file?:" - ) - if promp_answ: - self.create_metadatalab_excel(new_schema_json) + # Create metadata lab template + promp_answ = relecov_tools.utils.prompt_yn_question( + "Do you want to create a metadata lab file?:" + ) + if promp_answ: + self.create_metadatalab_excel(new_schema_json) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 01802214..22fef7a3 100755 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -8,6 +8,7 @@ import openpyxl import relecov_tools.utils +import relecov_tools.assets.schema_utils.jsonschema_draft from relecov_tools.config_json import ConfigJson from relecov_tools.log_summary import LogSum @@ -69,11 +70,7 @@ def __init__( def validate_schema(self): """Validate json schema against draft""" - try: - Draft202012Validator.check_schema(self.json_schema) - except jsonschema.ValidationError: - stderr.print("[red] Json schema does not fulfill Draft 202012 Validation") - sys.exit(1) + relecov_tools.assets.schema_utils.jsonschema_draft.check_schema_draft(self.json_schema, "2020-12") def get_sample_id_field(self): """Find the name of the field used to track the samples in the given schema""" diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index e1d195c4..925ac467 100755 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -415,27 +415,30 @@ def print_log_report( ) -# TODO: not used so far but can help to handle output folder creation. def prompt_create_outdir( path, folder_name=None, prompt_message="Define path to store the output:" ): """Ensure the directory exists or prompt the user to define and create it.""" # Check path if not path: - path = prompt_path("Define path to store the output:") + path = prompt_path(prompt_message) stderr.print(f"Chosen directory: {path}") # Check folder_name if not folder_name: default_folder = prompt_yn_question( - "Do you want to use default directory ('results') to store the results? (yes/no):" + "Do you want to use the default directory ('results') to store the results? (yes/no):" ) if not default_folder: folder_name = prompt_text("Write your output directory: ") else: folder_name = "results" - global_path = os.path.join(path, folder_name) + # Prevent duplicate folder names in the path + if os.path.basename(path) == folder_name: + global_path = path + else: + global_path = os.path.join(path, folder_name) if not os.path.exists(global_path): create_folder = prompt_yn_question( @@ -449,8 +452,9 @@ def prompt_create_outdir( sys.exit(1) elif os.path.isdir(global_path): os.makedirs(global_path, exist_ok=True) - stderr.print(f"[green]Folder '{folder_name}' created at {path}") + stderr.print(f"[green]Defining '{folder_name}' as output folder") else: stderr.print("[red]The provided path is not a directory.") sys.exit(1) + return global_path From 8b2a9bb476247b03adfdb193d39d5ed510c989bf Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 27 Aug 2024 13:57:00 +0200 Subject: [PATCH 1434/1454] fix linting --- relecov_tools/build_schema.py | 4 ++-- relecov_tools/json_validation.py | 5 +++-- relecov_tools/utils.py | 2 +- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/relecov_tools/build_schema.py b/relecov_tools/build_schema.py index 7cb6a894..175ecac7 100644 --- a/relecov_tools/build_schema.py +++ b/relecov_tools/build_schema.py @@ -54,7 +54,7 @@ def __init__( self.show_diff = None else: self.show_diff = True - + # Validate json schema draft version self.draft_version = ( relecov_tools.assets.schema_utils.jsonschema_draft.check_valid_version( @@ -407,7 +407,7 @@ def get_schema_diff(self, base_schema, new_schema): "[yellow]Differences found between the existing schema and the newly generated schema." ) return self.print_save_schema_diff(diff_lines) - + def print_save_schema_diff(self, diff_lines=None): # Set user's choices choices = ["Print to sandard output (stdout)", "Save to file", "Both"] diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index 22fef7a3..a6724231 100755 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -1,7 +1,6 @@ #!/usr/bin/env python import logging import rich.console -import jsonschema from jsonschema import Draft202012Validator import sys import os @@ -70,7 +69,9 @@ def __init__( def validate_schema(self): """Validate json schema against draft""" - relecov_tools.assets.schema_utils.jsonschema_draft.check_schema_draft(self.json_schema, "2020-12") + relecov_tools.assets.schema_utils.jsonschema_draft.check_schema_draft( + self.json_schema, "2020-12" + ) def get_sample_id_field(self): """Find the name of the field used to track the samples in the given schema""" diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index 925ac467..e048d276 100755 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -456,5 +456,5 @@ def prompt_create_outdir( else: stderr.print("[red]The provided path is not a directory.") sys.exit(1) - + return global_path From 2265586150e7c0a67699050e9bed865258c6df04 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 27 Aug 2024 14:12:06 +0200 Subject: [PATCH 1435/1454] fixed missing conflict --- relecov_tools/__main__.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index dc165665..60561e85 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -21,11 +21,8 @@ import relecov_tools.metadata_homogeneizer import relecov_tools.gisaid_upload import relecov_tools.upload_ena_protocol -<<<<<<< HEAD import relecov_tools.pipeline_manager -======= import relecov_tools.build_schema ->>>>>>> baa2c36 (init skeleton for build_schema module) log = logging.getLogger() From 9791f9b7332947d4a4897140dba60400906df55d Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 27 Aug 2024 14:15:35 +0200 Subject: [PATCH 1436/1454] fixed linting after conflict update --- relecov_tools/__main__.py | 1 + relecov_tools/assets/schema_utils/jsonschema_draft.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 60561e85..a03ca9b0 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -509,6 +509,7 @@ def launch_pipeline(input, template, output, config): ) new_launch.pipeline_exc() + # schema builder @relecov_tools_cli.command(help_priority=13) @click.option( diff --git a/relecov_tools/assets/schema_utils/jsonschema_draft.py b/relecov_tools/assets/schema_utils/jsonschema_draft.py index 6539b873..96f2c750 100644 --- a/relecov_tools/assets/schema_utils/jsonschema_draft.py +++ b/relecov_tools/assets/schema_utils/jsonschema_draft.py @@ -5,7 +5,7 @@ import relecov_tools.utils import pkg_resources import jsonschema -from jsonschema import Draft202012Validator, exceptions +from jsonschema import Draft202012Validator log = logging.getLogger(__name__) stderr = rich.console.Console( From 6278593fdce052d78abc053aeb52ccb8756c5c45 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 28 Aug 2024 13:54:59 +0200 Subject: [PATCH 1437/1454] Fixing errors and update to allow to upload to skylims --- relecov_tools/__main__.py | 22 +-- relecov_tools/conf/configuration.json | 86 ++++----- .../{feed_database.py => upload_database.py} | 167 ++++++++++-------- 3 files changed, 151 insertions(+), 124 deletions(-) rename relecov_tools/{feed_database.py => upload_database.py} (74%) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index a03ca9b0..4aa1b2ba 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -16,7 +16,7 @@ import relecov_tools.download_manager import relecov_tools.json_validation import relecov_tools.map_schema -import relecov_tools.feed_database +import relecov_tools.upload_database import relecov_tools.read_bioinfo_metadata import relecov_tools.metadata_homogeneizer import relecov_tools.gisaid_upload @@ -60,7 +60,7 @@ def run_relecov_tools(): ) # stderr.print("[green] `._,._,'\n", highlight=False) - __version__ = "0.0.5" + __version__ = "0.0.6" stderr.print( "\n" "[grey39] RELECOV-tools version {}".format(__version__), highlight=False ) @@ -373,7 +373,6 @@ def launch(user): pass -# update_db TODO: Include types of data and database servers in config file @relecov_tools_cli.command(help_priority=9) @click.option("-j", "--json", help="data in json format") @click.option( @@ -385,8 +384,8 @@ def launch(user): help="Select the type of information to upload to database", ) @click.option( - "-d", - "databaseServer", + "-plat", + "--platform", type=click.Choice( [ "iskylims", @@ -395,10 +394,11 @@ def launch(user): ), multiple=False, default=None, - help="name of the server which information is defined in config file", + help="name of the platform where data is uploaded", ) @click.option("-u", "--user", help="user name for login") @click.option("-p", "--password", help="password for the user to login") +@click.option("-s", "--server_url", help="url of the platform server") @click.option( "-f", "--full_update", @@ -406,12 +406,12 @@ def launch(user): default=False, help="Sequentially run every update option", ) -def update_db(user, password, json, type, databaseServer, full_update): - """feed database with json""" - feed_database = relecov_tools.feed_database.FeedDatabase( - user, password, json, type, databaseServer, full_update +def update_db(user, password, json, type, platform, server_url, full_update): + """upload the information included in json file to the database""" + update_database_obj = relecov_tools.upload_database.UpdateDatabase( + user, password, json, type, platform, server_url, full_update ) - feed_database.update_db() + update_database_obj.update_db() # read metadata bioinformatics diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 84503966..2c4c20f7 100755 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -270,54 +270,56 @@ "GISAID_configuration": { "submitter": "GISAID_ID" }, - "external_url": { - "iskylims": { - "server": "http://relecov-iskylims.isciiides.es", - "url": "/wetlab/api/", - "store_samples": "createSampleData", - "url_project_fields": "sampleProjectFields", - "url_sample_fields": "sampleFields", - "param_sample_project": "project", - "project_name": "relecov", - "token": "" - }, - "relecov": { - "server": "http://relecov-platform.isciiides.es", - "url": "/api/", + "upload_database": { + "platform":{ + "iskylims": { + "server_url": "http://relecov-iskylims.isciiides.es", + "api_url": "/wetlab/api/", + "store_samples": "create-sample", + "url_project_fields": "projects-fields", + "url_sample_fields": "sample-fields", + "param_sample_project": "project", + "project_name": "relecov", + "token": "" + }, + "relecov": { + "server_url": "http://relecov-platform.isciiides.es", + "api_url": "/api/", "store_samples": "createSampleData", "bioinfodata": "createBioinfoData", "variantdata": "createVariantData", "sftp_info": "sftpInfo", "token": "" - } - }, - "iskylims_fixed_values": { - "patientCore": "", - "sampleProject": "Relecov", - "onlyRecorded": "Yes", - "sampleLocation": "Not defined" + } + }, + "iskylims_fixed_values": { + "patient_core": "", + "sample_project": "Relecov", + "only_recorded": "Yes", + "sample_location": "Not defined" + }, + "relecov_sample_metadata": [ + "authors", + "collecting_institution", + "collecting_lab_sample_id", + "ena_broker_name", + "ena_sample_accession", + "gisaid_accession_id", + "gisaid_virus_name", + "microbiology_lab_sample_id", + "r1_fastq_filepath", + "r2_fastq_filepath", + "schema_name", + "schema_version", + "sequencing_date", + "sequence_file_R1_md5", + "sequence_file_R2_md5", + "sequence_file_R1_fastq", + "sequence_file_R2_fastq", + "sequencing_sample_id", + "submitting_lab_sample_id" + ] }, - "relecov_sample_metadata": [ - "authors", - "collecting_institution", - "collecting_lab_sample_id", - "ena_broker_name", - "ena_sample_accession", - "gisaid_accession_id", - "gisaid_virus_name", - "microbiology_lab_sample_id", - "r1_fastq_filepath", - "r2_fastq_filepath", - "schema_name", - "schema_version", - "sequencing_date", - "sequence_file_R1_md5", - "sequence_file_R2_md5", - "sequence_file_R1_fastq", - "sequence_file_R2_fastq", - "sequencing_sample_id", - "submitting_lab_sample_id" - ], "ENA_fields": { "ENA_configuration": { "study_alias": "RELECOV", diff --git a/relecov_tools/feed_database.py b/relecov_tools/upload_database.py similarity index 74% rename from relecov_tools/feed_database.py rename to relecov_tools/upload_database.py index 076b827d..cf54715f 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/upload_database.py @@ -22,16 +22,18 @@ ) -class FeedDatabase: +class UpdateDatabase: def __init__( self, user=None, passwd=None, json_file=None, type_of_info=None, - database_server=None, - full_update=None, + platform=None, + server_url=None, + full_update=False, ): + # Get the user and password for the database if user is None: user = relecov_tools.utils.prompt_text( msg="Enter username for upload data to server" @@ -40,6 +42,7 @@ def __init__( if passwd is None: passwd = relecov_tools.utils.prompt_text(msg="Enter credential password") self.passwd = passwd + # get the default coonfiguration used the instance self.config_json = ConfigJson() if json_file is None: json_file = relecov_tools.utils.prompt_path( @@ -57,23 +60,36 @@ def __init__( self.config_json.get_topic_data("json_schemas", "relecov_schema"), ) self.schema = relecov_tools.utils.read_json_file(schema) - self.full_update = full_update - # TODO: Include types_of_data and database_servers as config fields - self.types_of_data = ["sample", "bioinfodata", "variantdata"] - self.db_servers_names = ["iskylims", "relecov"] - if not full_update: + if full_update is True: + self.full_update = True + self.server_url = None + else: + self.full_update = False if type_of_info is None: type_of_info = relecov_tools.utils.prompt_selection( - "Select type of data to upload:", - self.types_of_data, + "Select:", + ["sample", "bioinfodata", "variantdata"], ) - if database_server is None: - database_server = relecov_tools.utils.prompt_selection( - "Select target database server:", - self.db_servers_names, + self.type_of_info = type_of_info + # collect data for plarform to upload data + if platform is None: + platform = relecov_tools.utils.prompt_selection( + "Select:", + ["iskylims", "relecov"], ) - self.server_name = database_server - self.type_of_info = type_of_info + self.platform = platform + if server_url is None: + self.server_url = server_url + # Get configuration settings for upload database + try: + self.platform_settings = self.config_json.get_topic_data( + "upload_database", "platform" + ) + except KeyError as e: + logtxt = f"Unable to fetch parameters for {platform} {e}" + stderr.print(f"[red]{logtxt}") + log.error(logtxt) + sys.exit(1) json_dir = os.path.dirname(os.path.realpath(self.json_file)) lab_code = json_dir.split("/")[-2] @@ -111,12 +127,26 @@ def map_iskylims_sample_fields_values(self, sample_fields, s_project_fields): # be included in iSkyLIMS request log.info("not key %s in iSkyLIMS", key) # include the fixed value - fixed_value = self.config_json.get_configuration("iskylims_fixed_values") + fixed_value = self.config_json.get_topic_data( + "upload_database", "iskylims_fixed_values" + ) for prop, val in fixed_value.items(): s_dict[prop] = val - # Adding tha specimen_source field to set sampleType - s_dict["sampleType"] = row["specimen_source"] + # Adding tha specimen_source field to set sample_type + try: + s_dict["sample_type"] = row["specimen_source"] + except KeyError as e: + logtxt = f"Unable to fetch specimen_source from json file {e}" + self.logsum.add_warning(entry=logtxt) + s_dict["sample_type"] = "Other" sample_list.append(s_dict) + # if sample_entry_date is not set then, add the current date + if "sample_entry_date" not in row: + logtxt = "sample_entry_date is not in the sample fields" + self.logsum.add_warning(entry=logtxt) + stderr.print(f"[yellow]{logtxt}") + s_dict["sample_entry_date"] = time.strftime("%Y-%m-%d") + return sample_list def get_iskylims_fields_sample(self): @@ -130,20 +160,15 @@ def get_iskylims_fields_sample(self): s_project_fields = [] # get the ontology values for mapping values in sample fields ontology_dict = self.get_schema_ontology_values() - sample_url = self.database_settings["url_sample_fields"] - try: - sample_fields_raw = self.database_rest_api.get_request(sample_url, "", "") - except AttributeError: - logtxt = f"Unable to connect to {self.db_server} server" - self.logsum.add_error(entry=logtxt) - stderr.print(f"[red]{logtxt}") - return + sample_url = self.platform_settings["iskylims"]["url_sample_fields"] + sample_fields_raw = self.platform_rest_api.get_request(sample_url, "", "") + if "ERROR" in sample_fields_raw: - logtxt1 = f"Unable to fetch data from {self.db_server}." + logtxt1 = f"Unable to fetch data from {self.platform}." logtxt2 = f" Received error {sample_fields_raw['ERROR']}" self.logsum.add_error(entry=str(logtxt1 + logtxt2)) stderr.print(f"[red]{logtxt1 + logtxt2}") - return + sys.exit(1) for _, values in sample_fields_raw["DATA"].items(): if "ontology" in values: @@ -162,19 +187,22 @@ def get_iskylims_fields_sample(self): self.logsum.add_warning(entry=logtxt) log.info(logtxt) # fetch label for sample Project - s_project_url = self.database_settings["url_project_fields"] - param = self.database_settings["param_sample_project"] - p_name = self.database_settings["project_name"] - s_project_fields_raw = self.database_rest_api.get_request( + s_project_url = self.platform_settings["iskylims"]["url_project_fields"] + param = self.platform_settings["iskylims"]["param_sample_project"] + p_name = self.platform_settings["iskylims"]["project_name"] + s_project_fields_raw = self.platform_rest_api.get_request( s_project_url, param, p_name ) if "ERROR" in s_project_fields_raw: - logtxt1 = f"Unable to fetch data from {self.db_server}." + logtxt1 = f"Unable to fetch data from {self.platform}." logtxt2 = f" Received error {s_project_fields_raw['ERROR']}" self.logsum.add_error(entry=str(logtxt1 + logtxt2)) return + else: + log.info("Fetched sample project fields from iSkyLIMS") + stderr.print("[blue] Fetched sample project fields from iSkyLIMS") for field in s_project_fields_raw["DATA"]: - s_project_fields.append(field["sampleProjectFieldName"]) + s_project_fields.append(field["sample_project_field_name"]) return [sample_fields, s_project_fields] def map_relecov_sample_data(self): @@ -194,12 +222,12 @@ def map_relecov_sample_data(self): def update_database(self, field_values, post_url): """Send the request to update database""" + post_url = self.platform_settings[self.platform][post_url] suces_count = 0 request_count = 0 for chunk in field_values: req_sample = "" request_count += 1 - # TODO: Include these fields in config file if "sample_name" in chunk: stderr.print( f"[blue] sending request for sample {chunk['sample_name']}" @@ -211,10 +239,10 @@ def update_database(self, field_values, post_url): ) req_sample = chunk["sequencing_sample_id"] self.logsum.feed_key(sample=req_sample) - result = self.database_rest_api.post_request( + result = self.platform_rest_api.post_request( json.dumps(chunk), {"user": self.user, "pass": self.passwd}, - self.database_settings[post_url], + post_url, ) if "ERROR" in result: if result["ERROR"] == "Server not available": @@ -222,44 +250,45 @@ def update_database(self, field_values, post_url): for i in range(10): # wait 5 sec before resending the request time.sleep(5) - result = self.database_rest_api.post_request( + result = self.platform_rest_api.post_request( json.dumps(chunk), {"user": self.user, "pass": self.passwd}, - self.database_settings[post_url], + self.platform_settings[post_url], ) if "ERROR" not in result: break if i == 9 and "ERROR" in result: - logtxt = f"Unable to sent the request to {self.db_server}" + logtxt = f"Unable to sent the request to {self.platform}" self.logsum.add_error(entry=logtxt, sample=req_sample) stderr.print(f"[red]{logtxt}") continue elif "is not defined" in result["ERROR_TEST"].lower(): - logtxt = f"{req_sample} is not defined in {self.db_server}" + error_txt = result["ERROR_TEST"] + logtxt = f"Sample {req_sample}: {error_txt}" self.logsum.add_error(entry=logtxt, sample=req_sample) stderr.print(f"[yellow]Warning: {logtxt}") continue elif "already defined" in result["ERROR_TEST"].lower(): - logtxt = f"Request to {self.db_server} already defined" + logtxt = f"Request to {self.platform} already defined" self.logsum.add_warning(entry=logtxt, sample=req_sample) stderr.print(f"[yellow]{logtxt} for sample {req_sample}") continue else: - logtxt = f"Error {result['ERROR']} in request to {self.db_server}" + logtxt = f"Error {result['ERROR']} in request to {self.platform}" self.logsum.add_error(entry=logtxt, sample=req_sample) stderr.print(f"[red]{logtxt}") continue log.info( "stored data in %s iskylims for sample %s", - self.db_server, + self.platform, req_sample, ) stderr.print(f"[green] Successful request for {req_sample}") suces_count += 1 if request_count == suces_count: stderr.print( - f"All {self.type_of_info} data sent sucessfuly to {self.db_server}" + f"All {self.type_of_info} data sent sucessfuly to {self.platform}" ) else: logtxt = "%s of the %s requests were sent to %s" @@ -275,16 +304,16 @@ def store_data(self, type_of_info, server_name): """Collect data from json file and split them to store data in iSkyLIMS and in Relecov Platform """ + map_fields = {} - map_fields = {} # - # TODO: Include all these hard-coded fields in config file - if type_of_info not in self.types_of_info: + """ if type_of_info not in self.types_of_info: self.logsum.add_error(entry=f"Invalid datatype {type_of_info} to upload") stderr.print(f"[red]Invalid datatype {type_of_info} to upload") - return + return """ if type_of_info == "sample": if server_name == "iskylims": stderr.print(f"[blue] Getting sample fields from {server_name}") + sample_fields, s_project_fields = self.get_iskylims_fields_sample() stderr.print("[blue] Selecting sample fields") map_fields = self.map_iskylims_sample_fields_values( @@ -304,29 +333,25 @@ def store_data(self, type_of_info, server_name): map_fields = self.json_data self.update_database(map_fields, post_url) - stderr.print(f"[green]Upload process to {self.server_name} completed") + stderr.print(f"[green]Upload process to {self.platform} completed") - def start_api(self, database_server): + def start_api(self, platform): """Open connection torwards database server API""" # Get database settings - if database_server: - try: - self.database_settings = self.config_json.get_topic_data( - "external_url", database_server - ) - except KeyError: - logtxt = f"Unable to fetch parameters for {database_server}" - self.logsum.add_error(entry=logtxt) - stderr.print(f"[red]{logtxt}") - return - self.db_server = self.database_settings["server"] - self.db_url = self.database_settings["url"] - self.db_rest_api = RestApi(self.db_server, self.db_url) - else: - logtxt = f"No database server was selected for {self.type_of_info}. Skipped" - self.logsum.add_error(entry=logtxt) + try: + p_settings = self.platform_settings[platform] + except KeyError as e: + logtxt = f"Unable to fetch parameters for {platform} {e}" stderr.print(f"[red]{logtxt}") - return + log.error(logtxt) + sys.exit(1) + if self.server_url is None: + server_url = p_settings["server_url"] + else: + server_url = self.server_url + self.platform = platform + self.api_url = p_settings["api_url"] + self.platform_rest_api = RestApi(server_url, self.api_url) return def update_db(self): @@ -358,6 +383,6 @@ def update_db(self): self.json_data = relecov_tools.utils.read_json_file(json_file) self.store_data(datatype, self.server_name) else: - self.start_api(self.server_name) - self.store_data(self.type_of_info, self.server_name) + self.start_api(self.platform) + self.store_data(self.type_of_info, self.platform) self.logsum.create_error_summary(called_module="update-db") From 350eaffe10ec524e5404b8b1c49de7ad9668e447 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 29 Aug 2024 11:02:24 +0200 Subject: [PATCH 1438/1454] fixing errors --- relecov_tools/upload_database.py | 52 +++++++++++++++----------------- 1 file changed, 25 insertions(+), 27 deletions(-) diff --git a/relecov_tools/upload_database.py b/relecov_tools/upload_database.py index cf54715f..25b168d0 100644 --- a/relecov_tools/upload_database.py +++ b/relecov_tools/upload_database.py @@ -11,7 +11,6 @@ import relecov_tools.utils from relecov_tools.config_json import ConfigJson from relecov_tools.rest_api import RestApi -from relecov_tools.log_summary import LogSum log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -93,9 +92,6 @@ def __init__( json_dir = os.path.dirname(os.path.realpath(self.json_file)) lab_code = json_dir.split("/")[-2] - self.logsum = LogSum( - output_location=json_dir, unique_key=lab_code, path=json_dir - ) def get_schema_ontology_values(self): """Read the schema and extract the values of ontology with the label""" @@ -137,13 +133,13 @@ def map_iskylims_sample_fields_values(self, sample_fields, s_project_fields): s_dict["sample_type"] = row["specimen_source"] except KeyError as e: logtxt = f"Unable to fetch specimen_source from json file {e}" - self.logsum.add_warning(entry=logtxt) + log.warning(logtxt) s_dict["sample_type"] = "Other" sample_list.append(s_dict) # if sample_entry_date is not set then, add the current date if "sample_entry_date" not in row: logtxt = "sample_entry_date is not in the sample fields" - self.logsum.add_warning(entry=logtxt) + log.warning(logtxt) stderr.print(f"[yellow]{logtxt}") s_dict["sample_entry_date"] = time.strftime("%Y-%m-%d") @@ -166,7 +162,7 @@ def get_iskylims_fields_sample(self): if "ERROR" in sample_fields_raw: logtxt1 = f"Unable to fetch data from {self.platform}." logtxt2 = f" Received error {sample_fields_raw['ERROR']}" - self.logsum.add_error(entry=str(logtxt1 + logtxt2)) + log.error(str(logtxt1 + logtxt2)) stderr.print(f"[red]{logtxt1 + logtxt2}") sys.exit(1) @@ -178,13 +174,12 @@ def get_iskylims_fields_sample(self): # the field name for the sample sample_fields[property] = values["field_name"] except KeyError as e: - self.logsum.add_warning(entry=f"Error mapping ontology {e}") - stderr.print(f"[red]Error mapping ontology {e}") + log.info(f"Error mapping ontology {e}") + # stderr.print(f"[red]Error mapping ontology {e}") else: # for the ones that do not have ontology label in the sample field # and have an empty value: sample_fields[key] = "" logtxt = f"No ontology found for {values.get('field_name')}" - self.logsum.add_warning(entry=logtxt) log.info(logtxt) # fetch label for sample Project s_project_url = self.platform_settings["iskylims"]["url_project_fields"] @@ -196,7 +191,7 @@ def get_iskylims_fields_sample(self): if "ERROR" in s_project_fields_raw: logtxt1 = f"Unable to fetch data from {self.platform}." logtxt2 = f" Received error {s_project_fields_raw['ERROR']}" - self.logsum.add_error(entry=str(logtxt1 + logtxt2)) + log.error(str(logtxt1 + logtxt2)) return else: log.info("Fetched sample project fields from iSkyLIMS") @@ -208,7 +203,12 @@ def get_iskylims_fields_sample(self): def map_relecov_sample_data(self): """Select the values from self.json_data""" field_values = [] - r_fields = self.config_json.get_configuration("relecov_sample_metadata") + import pdb + + pdb.set_trace() + r_fields = self.config_json.get_topic_data( + "upload_database", "relecov_sample_metadata" + ) for row in self.json_data: s_dict = {} @@ -238,7 +238,6 @@ def update_database(self, field_values, post_url): f"[blue] sending request for sample {chunk['sequencing_sample_id']}" ) req_sample = chunk["sequencing_sample_id"] - self.logsum.feed_key(sample=req_sample) result = self.platform_rest_api.post_request( json.dumps(chunk), {"user": self.user, "pass": self.passwd}, @@ -259,24 +258,24 @@ def update_database(self, field_values, post_url): break if i == 9 and "ERROR" in result: logtxt = f"Unable to sent the request to {self.platform}" - self.logsum.add_error(entry=logtxt, sample=req_sample) + log.error(logtxt) stderr.print(f"[red]{logtxt}") continue elif "is not defined" in result["ERROR_TEST"].lower(): error_txt = result["ERROR_TEST"] logtxt = f"Sample {req_sample}: {error_txt}" - self.logsum.add_error(entry=logtxt, sample=req_sample) + log.error(logtxt) stderr.print(f"[yellow]Warning: {logtxt}") continue elif "already defined" in result["ERROR_TEST"].lower(): logtxt = f"Request to {self.platform} already defined" - self.logsum.add_warning(entry=logtxt, sample=req_sample) + log.warning(logtxt) stderr.print(f"[yellow]{logtxt} for sample {req_sample}") continue else: logtxt = f"Error {result['ERROR']} in request to {self.platform}" - self.logsum.add_error(entry=logtxt, sample=req_sample) + log.error(logtxt) stderr.print(f"[red]{logtxt}") continue log.info( @@ -291,12 +290,14 @@ def update_database(self, field_values, post_url): f"All {self.type_of_info} data sent sucessfuly to {self.platform}" ) else: - logtxt = "%s of the %s requests were sent to %s" - self.logsum.add_warning( - entry=logtxt % (suces_count, request_count, self.server_name) + log.warning( + "%s of the %s requests were sent to %s", + suces_count, + request_count, + self.platform, ) stderr.print( - f"[yellow]{logtxt % (suces_count, request_count, self.server_name)}" + f"[yellow]logtxt % {suces_count} {request_count} {self.platform})" ) return @@ -306,15 +307,12 @@ def store_data(self, type_of_info, server_name): """ map_fields = {} - """ if type_of_info not in self.types_of_info: - self.logsum.add_error(entry=f"Invalid datatype {type_of_info} to upload") - stderr.print(f"[red]Invalid datatype {type_of_info} to upload") - return """ if type_of_info == "sample": if server_name == "iskylims": + log.info("Getting sample fields from %s", server_name) stderr.print(f"[blue] Getting sample fields from {server_name}") - sample_fields, s_project_fields = self.get_iskylims_fields_sample() + log.info("Selecting sample fields") stderr.print("[blue] Selecting sample fields") map_fields = self.map_iskylims_sample_fields_values( sample_fields, s_project_fields @@ -385,4 +383,4 @@ def update_db(self): else: self.start_api(self.platform) self.store_data(self.type_of_info, self.platform) - self.logsum.create_error_summary(called_module="update-db") + return From 33091ccd1d786d8e9736bd412e89e1ba6b6b870d Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 29 Aug 2024 11:04:48 +0200 Subject: [PATCH 1439/1454] fixing litin --- relecov_tools/upload_database.py | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/upload_database.py b/relecov_tools/upload_database.py index 25b168d0..e7b76039 100644 --- a/relecov_tools/upload_database.py +++ b/relecov_tools/upload_database.py @@ -91,7 +91,6 @@ def __init__( sys.exit(1) json_dir = os.path.dirname(os.path.realpath(self.json_file)) - lab_code = json_dir.split("/")[-2] def get_schema_ontology_values(self): """Read the schema and extract the values of ontology with the label""" From 4c92fe1906e49809160bc7b46e5872309088a6be Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 29 Aug 2024 11:07:26 +0200 Subject: [PATCH 1440/1454] remove variable does not used --- relecov_tools/upload_database.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/relecov_tools/upload_database.py b/relecov_tools/upload_database.py index e7b76039..26f61f8f 100644 --- a/relecov_tools/upload_database.py +++ b/relecov_tools/upload_database.py @@ -90,8 +90,6 @@ def __init__( log.error(logtxt) sys.exit(1) - json_dir = os.path.dirname(os.path.realpath(self.json_file)) - def get_schema_ontology_values(self): """Read the schema and extract the values of ontology with the label""" ontology_dict = {} From d9642d5f604b2837e176b283c6c14b5720694c02 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 29 Aug 2024 16:08:24 +0200 Subject: [PATCH 1441/1454] defined back the log summary file --- relecov_tools/upload_database.py | 39 +++++++++++++++++--------------- 1 file changed, 21 insertions(+), 18 deletions(-) diff --git a/relecov_tools/upload_database.py b/relecov_tools/upload_database.py index 26f61f8f..29145a5c 100644 --- a/relecov_tools/upload_database.py +++ b/relecov_tools/upload_database.py @@ -11,6 +11,7 @@ import relecov_tools.utils from relecov_tools.config_json import ConfigJson from relecov_tools.rest_api import RestApi +from relecov_tools.log_summary import LogSum log = logging.getLogger(__name__) stderr = rich.console.Console( @@ -89,6 +90,12 @@ def __init__( stderr.print(f"[red]{logtxt}") log.error(logtxt) sys.exit(1) + # create the instance for logging the summary information + json_dir = os.path.dirname(os.path.realpath(self.json_file)) + lab_code = json_dir.split("/")[-2] + self.logsum = LogSum( + output_location=json_dir, unique_key=lab_code, path=json_dir + ) def get_schema_ontology_values(self): """Read the schema and extract the values of ontology with the label""" @@ -118,7 +125,7 @@ def map_iskylims_sample_fields_values(self, sample_fields, s_project_fields): if key not in s_project_fields and key not in s_fields: # just for debugging, write the fields that will not # be included in iSkyLIMS request - log.info("not key %s in iSkyLIMS", key) + log.debug("not key %s in iSkyLIMS", key) # include the fixed value fixed_value = self.config_json.get_topic_data( "upload_database", "iskylims_fixed_values" @@ -130,13 +137,13 @@ def map_iskylims_sample_fields_values(self, sample_fields, s_project_fields): s_dict["sample_type"] = row["specimen_source"] except KeyError as e: logtxt = f"Unable to fetch specimen_source from json file {e}" - log.warning(logtxt) + self.logsum.add_warning(entry=logtxt) s_dict["sample_type"] = "Other" sample_list.append(s_dict) # if sample_entry_date is not set then, add the current date if "sample_entry_date" not in row: logtxt = "sample_entry_date is not in the sample fields" - log.warning(logtxt) + self.logsum.add_warning(entry=logtxt) stderr.print(f"[yellow]{logtxt}") s_dict["sample_entry_date"] = time.strftime("%Y-%m-%d") @@ -159,7 +166,7 @@ def get_iskylims_fields_sample(self): if "ERROR" in sample_fields_raw: logtxt1 = f"Unable to fetch data from {self.platform}." logtxt2 = f" Received error {sample_fields_raw['ERROR']}" - log.error(str(logtxt1 + logtxt2)) + self.logsum.add_error(entry=str(logtxt1 + logtxt2)) stderr.print(f"[red]{logtxt1 + logtxt2}") sys.exit(1) @@ -188,7 +195,7 @@ def get_iskylims_fields_sample(self): if "ERROR" in s_project_fields_raw: logtxt1 = f"Unable to fetch data from {self.platform}." logtxt2 = f" Received error {s_project_fields_raw['ERROR']}" - log.error(str(logtxt1 + logtxt2)) + self.logsum.add_error(entry=str(logtxt1 + logtxt2)) return else: log.info("Fetched sample project fields from iSkyLIMS") @@ -200,9 +207,6 @@ def get_iskylims_fields_sample(self): def map_relecov_sample_data(self): """Select the values from self.json_data""" field_values = [] - import pdb - - pdb.set_trace() r_fields = self.config_json.get_topic_data( "upload_database", "relecov_sample_metadata" ) @@ -255,24 +259,24 @@ def update_database(self, field_values, post_url): break if i == 9 and "ERROR" in result: logtxt = f"Unable to sent the request to {self.platform}" - log.error(logtxt) + self.logsum.add_error(entry=logtxt) stderr.print(f"[red]{logtxt}") continue elif "is not defined" in result["ERROR_TEST"].lower(): error_txt = result["ERROR_TEST"] logtxt = f"Sample {req_sample}: {error_txt}" - log.error(logtxt) + self.logsum.add_error(entry=logtxt) stderr.print(f"[yellow]Warning: {logtxt}") continue elif "already defined" in result["ERROR_TEST"].lower(): logtxt = f"Request to {self.platform} already defined" - log.warning(logtxt) + self.logsum.add_warning(entry=logtxt) stderr.print(f"[yellow]{logtxt} for sample {req_sample}") continue else: logtxt = f"Error {result['ERROR']} in request to {self.platform}" - log.error(logtxt) + self.logsum.add_error(entry=logtxt) stderr.print(f"[red]{logtxt}") continue log.info( @@ -287,11 +291,9 @@ def update_database(self, field_values, post_url): f"All {self.type_of_info} data sent sucessfuly to {self.platform}" ) else: - log.warning( - "%s of the %s requests were sent to %s", - suces_count, - request_count, - self.platform, + logtxt = "%s of the %s requests were sent to %s" + self.logsum.add_warning( + entry=logtxt % (suces_count, request_count, self.platform) ) stderr.print( f"[yellow]logtxt % {suces_count} {request_count} {self.platform})" @@ -338,7 +340,7 @@ def start_api(self, platform): except KeyError as e: logtxt = f"Unable to fetch parameters for {platform} {e}" stderr.print(f"[red]{logtxt}") - log.error(logtxt) + self.logsum.add_error(entry=logtxt) sys.exit(1) if self.server_url is None: server_url = p_settings["server_url"] @@ -380,4 +382,5 @@ def update_db(self): else: self.start_api(self.platform) self.store_data(self.type_of_info, self.platform) + self.logsum.create_error_summary(called_module="update-db") return From 3ce530bb98d8953a068ec8f34dac816e2602e05e Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 30 Aug 2024 10:02:12 +0200 Subject: [PATCH 1442/1454] updated log summary comments from the PR review --- relecov_tools/upload_database.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/relecov_tools/upload_database.py b/relecov_tools/upload_database.py index 29145a5c..4c41681b 100644 --- a/relecov_tools/upload_database.py +++ b/relecov_tools/upload_database.py @@ -239,6 +239,7 @@ def update_database(self, field_values, post_url): f"[blue] sending request for sample {chunk['sequencing_sample_id']}" ) req_sample = chunk["sequencing_sample_id"] + self.logsum.feed_key(sample=req_sample) result = self.platform_rest_api.post_request( json.dumps(chunk), {"user": self.user, "pass": self.passwd}, @@ -259,24 +260,24 @@ def update_database(self, field_values, post_url): break if i == 9 and "ERROR" in result: logtxt = f"Unable to sent the request to {self.platform}" - self.logsum.add_error(entry=logtxt) + self.logsum.add_error(entry=logtxt, sample=req_sample) stderr.print(f"[red]{logtxt}") continue elif "is not defined" in result["ERROR_TEST"].lower(): error_txt = result["ERROR_TEST"] logtxt = f"Sample {req_sample}: {error_txt}" - self.logsum.add_error(entry=logtxt) + self.logsum.add_error(entry=logtxt, sample=req_sample) stderr.print(f"[yellow]Warning: {logtxt}") continue elif "already defined" in result["ERROR_TEST"].lower(): logtxt = f"Request to {self.platform} already defined" - self.logsum.add_warning(entry=logtxt) + self.logsum.add_warning(entry=logtxt, sample=req_sample) stderr.print(f"[yellow]{logtxt} for sample {req_sample}") continue else: logtxt = f"Error {result['ERROR']} in request to {self.platform}" - self.logsum.add_error(entry=logtxt) + self.logsum.add_error(entry=logtxt, sample=req_sample) stderr.print(f"[red]{logtxt}") continue log.info( @@ -293,7 +294,8 @@ def update_database(self, field_values, post_url): else: logtxt = "%s of the %s requests were sent to %s" self.logsum.add_warning( - entry=logtxt % (suces_count, request_count, self.platform) + entry=logtxt % (suces_count, request_count, self.platform), + sample=req_sample, ) stderr.print( f"[yellow]logtxt % {suces_count} {request_count} {self.platform})" From d74f6981bfefb53ea2795b66169503ee518648a5 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 30 Aug 2024 14:00:57 +0200 Subject: [PATCH 1443/1454] Updated ena and relecov schemas to v2.0.0 --- relecov_tools/schema/ena_schema.json | 1 + relecov_tools/schema/relecov_schema.json | 7 +++++-- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 540cd553..048d8d05 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -1,5 +1,6 @@ { "schema": "ENA", + "version": "2.0.0", "required": [ "sample_title", "collecting institution", diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index b01cebad..27b9bbe8 100755 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -3,7 +3,7 @@ "id": "https://github.com/BU-ISCIII/relecov-tools/blob/develop/relecov_tools/schema/relecov_schema.json", "title": "RELECOV schema", "description":"Json schema that specifies the structure, content, and validation rules for RELECOV metadata", - "version": "1.0.0", + "version": "2.0.0", "required": [ "collecting_lab_sample_id", "sequencing_sample_id", @@ -17,6 +17,8 @@ "host_scientific_name", "sequencing_instrument_model", "sequencing_instrument_platform", + "library_source", + "library_layout", "enrichment_panel", "enrichment_panel_version" ], @@ -560,7 +562,7 @@ "Exome Sequencing [OBI:0002118]", "Pooled Clone Sequencing [OBI:2100402]", "Transcriptome Sequencing [NCIT:C124261]", - "Other [NCIT:C124261]" + "Other [NCIT:C17649]" ], "ontology": "GENEPIO:0000156", "type": "string", @@ -995,6 +997,7 @@ "Not Collected [GENEPIO:0001620]", "Not Provided [GENEPIO:0001668]", "Missing [GENEPIO:0001618]", + "Other [NCIT:C17649]", "Restricted Access [GENEPIO:0001810]" ], "ontology": "GENEPIO:0001223", From da16b0bd82c3ba2007876b67174615168051dbb3 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 30 Aug 2024 14:03:33 +0200 Subject: [PATCH 1444/1454] Handled relative paths for json_validation lab_code var --- relecov_tools/json_validation.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index a6724231..cb0cd05a 100755 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -52,10 +52,10 @@ def __init__( stderr.print("[red] Json file does not exists") sys.exit(1) self.json_data_file = json_data_file - out_path = os.path.realpath(self.out_folder) - lab_code = out_path.split("/")[-2] + out_path = os.path.dirname(os.path.realpath(self.json_data_file)) + self.lab_code = out_path.split("/")[-2] self.logsum = LogSum( - output_location=self.out_folder, unique_key=lab_code, path=out_path + output_location=self.out_folder, unique_key=self.lab_code, path=out_path ) stderr.print("[blue] Reading the json file") From 04864a340123861de3b929bf335ae10b10b3e973 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 30 Aug 2024 14:04:03 +0200 Subject: [PATCH 1445/1454] Updated pyyaml required version to 6.0.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 372438f1..adef8f84 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,7 +6,7 @@ prompt_toolkit>=3.0.3 rich>=10.0.0 requests==2.27.1 paramiko>=2.10.1 -pyyaml +pyyaml==6.0.1 openpyxl>=3.1.2 ena-upload-cli bio==1.4.0 From 0ac87eff60cf60b31a4bd34522ca3de79669370b Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 30 Aug 2024 14:06:27 +0200 Subject: [PATCH 1446/1454] Updated README.md for release 1.0.0 --- README.md | 68 +++++++++++++++++++++++++++++++++++++++---------------- 1 file changed, 48 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index 04888914..e3524bc8 100644 --- a/README.md +++ b/README.md @@ -8,19 +8,28 @@ relecov-tools is a set of helper tools for the assembly of the different element ## Table of contents -* [Installation](#installation) -* [Usage](#usage) - * [download](#download) - * [read-lab-metadata](#read-lab-metadata) - * [read-bioinfo-metadata](#read-bioinfo-metadata) - * [validate](#validate) - * [map](#map) - * [upload-to-ena](#upload-to-ena) - * [upload-to-gisaid](#upload-to-gisaid) - * [launch](#launch) - * [update-db](#update-db) - * [build-schema](#build-schema) -* [Aknowledgements](#aknowledgements) +- [relecov-tools](#relecov-tools) + - [Table of contents](#table-of-contents) + - [Installation](#installation) + - [Bioconda](#bioconda) + - [Pip](#pip) + - [Development version](#development-version) + - [Usage](#usage) + - [Command-line](#command-line) + - [download](#download) + - [read-lab-metadata](#read-lab-metadata) + - [read-bioinfo-metadata](#read-bioinfo-metadata) + - [validate](#validate) + - [map](#map) + - [upload-to-ena](#upload-to-ena) + - [upload-to-gisaid](#upload-to-gisaid) + - [update-db](#update-db) + - [build-schema](#build-schema) + - [Mandatory Fields](#mandatory-fields) + - [launch-pipeline](#launch-pipeline) + - [custom logs](#custom-logs) + - [Python package mode](#python-package-mode) + - [Acknowledgements](#acknowledgements) ## Installation @@ -28,7 +37,10 @@ relecov-tools is a set of helper tools for the assembly of the different element Soon ### Pip -Soon +relecov-tools is available in Pypi and can be installed via pip: +``` +pip install relecov-tools +``` ### Development version If you want to install the latest code in the repository: @@ -50,7 +62,7 @@ $ relecov-tools --help \ \ / |__ / |__ | |___ | | | \ / / / \ | \ | | | | | | \ / / |--| | \ |___ |___ |___ |___ |___| \/ -RELECOV-tools version 0.0.1 +RELECOV-tools version 1.0.0 Usage: relecov-tools [OPTIONS] COMMAND [ARGS]... Options: @@ -68,8 +80,8 @@ Commands: upload-to-ena parsed data to create xml files to upload to ena upload-to-gisaid parsed data to create files to upload to gisaid update-db feed database with metadata jsons - launch launch viralrecon in hpc build-schema Generates and updates JSON Schema files from... + launch-pipeline Create the symbolic links for the samples which... ``` #### download The command `download` connects to a transfer protocol (currently sftp) and downloads all files in the different available folders in the passed credentials. In addition, it checks if the files in the current folder match the files in the metadata file and also checks if there are md5sum for each file. Else, it creates one before storing in the final repository. @@ -158,7 +170,7 @@ Usage: relecov-tools validate [OPTIONS] Options: -j, --json_file TEXT Json file to validate - -s, --json_schema TEXT Json schema + -s, --json_schema TEXT Json schema (default: relecov-schema) -m, --metadata PATH Origin file containing metadata -o, --out_folder TEXT Path to save validate json file --help Show this message and exit. @@ -262,7 +274,7 @@ Options: ``` #### Mandatory Fields -Ensure that the fields below are properly defined as headers in your Excel sheet (dataase definition): +Ensure that the fields below are properly defined as headers in your Excel sheet (database definition): ``` enum: List of possible values for enumeration. @@ -277,8 +289,24 @@ required (Y/N): Indicates if the property is required (Y) or optional (N). complex_field (Y/N): Indicates if the property is a complex (nested) field (Y) or a standard field (N). ``` -#### launch -SOON +#### launch-pipeline +Create the folder structure to execute the given pipeline for the latest sample batches after executing download, read-lab-metadata and validate modules. This module will create symbolic links for each sample and generate the necessary files for pipeline execution using the information from validated_BATCH-NAME_DATE.json. +``` +Usage: relecov-tools launch-pipeline [OPTIONS] + + Create the symbolic links for the samples which are validated to prepare for + bioinformatics pipeline execution. + +Options: + -i, --input PATH Path to the input folder where sample files are located + -t, --template PATH Path to the pipeline template folder to be copied in the output folder + -c, --config PATH Path to the the template config file + -o, --out_dir PATH Path to output folder + --help Show this message and exit. +``` + +#### custom logs +After executing each of these modules, you may find a custom log report in json format named "DATE_EXECUTED-MODULE_log_summary.json. These custom log summaries can be useful to detect errors in metadata in order to fix them and/or notify the users. ### Python package mode relecov-tools is designed in a way that you can use import the different modules and use them in your own scripts, for example: From 35b91f7ec99119202e2837b90132bce16a968682 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 30 Aug 2024 14:06:52 +0200 Subject: [PATCH 1447/1454] Updated __main__.py for release 1.0.0 --- relecov_tools/__main__.py | 32 ++++---------------------------- 1 file changed, 4 insertions(+), 28 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 4aa1b2ba..710066bb 100755 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -60,7 +60,7 @@ def run_relecov_tools(): ) # stderr.print("[green] `._,._,'\n", highlight=False) - __version__ = "0.0.6" + __version__ = "1.0.0" stderr.print( "\n" "[grey39] RELECOV-tools version {}".format(__version__), highlight=False ) @@ -365,14 +365,6 @@ def upload_to_gisaid( upload_gisaid.gisaid_upload() -# launch -@relecov_tools_cli.command(help_priority=8) -@click.option("-u", "--user", help="user name for connecting to the server") -def launch(user): - """launch viralrecon in hpc""" - pass - - @relecov_tools_cli.command(help_priority=9) @click.option("-j", "--json", help="data in json format") @click.option( @@ -439,23 +431,6 @@ def read_bioinfo_metadata(json_file, input_folder, out_dir, software_name): new_bioinfo_metadata.create_bioinfo_file() -# read metadata bioinformatics -@relecov_tools_cli.command(help_priority=11) -@click.option( - "-l", - "--longtable_file", - type=click.Path(), - help="file containing variant long table ", -) -@click.option("-o", "--output", type=click.Path(), help="Path to save json output") -def long_table_parse(longtable_file, output): - new_json_parse = relecov_tools.assets.pipeline_utils.viralrecon.LongTableParse( - longtable_file, output - ) - """Create Json file from long table""" - new_json_parse.parsing_csv() - - # read metadata bioinformatics @relecov_tools_cli.command(help_priority=12) @click.option( @@ -491,7 +466,7 @@ def metadata_homogeneizer(institution, directory, output): "-t", "--template", type=click.Path(), - help="select the template folder to be copied in the output folder", + help="select the pipeline template folder to be copied in the output folder", ) @click.option( "-c", @@ -502,7 +477,8 @@ def metadata_homogeneizer(institution, directory, output): @click.option("-o", "--output", type=click.Path(), help="select output folder") def launch_pipeline(input, template, output, config): """ - Create the symbolic links for the samples which are validated. + Create the symbolic links for the samples which are validated to prepare for + bioinformatics pipeline execution. """ new_launch = relecov_tools.pipeline_manager.LaunchPipeline( input, template, output, config From 84710fc288924308abff1fa04148671d29a7f123 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 30 Aug 2024 14:08:02 +0200 Subject: [PATCH 1448/1454] Included CONTRIBUTING.md doc --- .github/CONTRIBUTING.md | 72 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100755 .github/CONTRIBUTING.md diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md new file mode 100755 index 00000000..4a13da18 --- /dev/null +++ b/.github/CONTRIBUTING.md @@ -0,0 +1,72 @@ +# relecov-tools: Contributing Guidelines + +## Contribution workflow + +If you'd like to write or modify some code for relecov-tools, the standard workflow is as follows: + +1. Check that there isn't already an issue about your idea in the [relecov-tools issues](https://github.com/BU-ISCIII/relecov-tools/issues) to avoid duplicating work. **If there isn't one already, please create one so that others know you're working on this**. +2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [relecov-tools repository](https://github.com/BU-ISCIII/relecov-tools/) to your GitHub account. +3. Make the necessary changes / additions within your forked repository following the [code style guidelines](#code-style-guidelines). +4. Modify the [`CHANGELOG`](../CHANGELOG.md) file according to your changes in the appropiate section ([X.X.Xdev]), you should register your changes regarding: + 1. Added enhancements + 2. New modules + 3. Fixes + 4. Removed stuff + 5. Requirements added or version update +5. Update any documentation as needed. +6. [Submit a Pull Request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request) against the `develop` branch and send the url to the #pipelines-dev channel in slack (if you are not in the slack channel just wait fot the PR to be reviewed and rebased). + +If you're not used to this workflow with git, you can start with: + +- Some [docs in the bu-isciii wiki](https://github.com/BU-ISCIII/BU-ISCIII/wiki/Github--gitflow). +- [some slides](https://docs.google.com/presentation/d/1PruqGxPQVxtNcuEbOd86mylXorgYIU5a/edit?pli=1#slide=id.p1) (in spanish). +- some github generic docs [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests). +- even their [excellent `git` resources](https://try.github.io/). + +### relecov-tools repo branches + +relecov-tools repo works with a two branching scheme: `main` and `develop`. + +- `main`: stable code only for releases. +- `develop`: new code development for the different modules. + +You need to submit your PR always against `develop`. Once approbed, this changes must be **`rebased`** so we do not create empty unwanted merges. + +## Tests + +When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. +Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. + +There are typically two types of tests that run: + +### Lint tests + +We use black and flake8 linting based on PEP8 guidelines for python coding. You can check more information [here](https://github.com/BU-ISCIII/BU-ISCIII/wiki/Python#linting). + +### Code tests + +Download, read-lab-metadata, map and validate modules are executed using a test dataset. + +Anyhow you should always submit locally tested code!! + +### New version bumping and release + +In order to create a new release you need to follow the next steps: + +1. Set the new version according to [semantic versioning](https://semver.org/), in our particular case, changes in the `hotfix` branch will change the PATCH version (third one), and changes in develop will typicaly change the MINOR version, unless the developing team decides otherwise. +2. Create a PR bumping the new version against `develop`. For bumping a new version just change [this line](https://github.com/BU-ISCIII/relecov-tools/blob/09c00c1ddd11f7489de7757841aff506ef4b7e1d/setup.py#L5) with the new version. +3. Once that PR is merged, create via web another PR against `main` (origin `develop`). This PR would need 2 approvals. +4. [Create a new release](https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository) copying the appropiate notes from the `CHANGELOG`. +5. Once the release is approved and merged, you're all set! + +PRs from one branch to another, like in a release should be **`merged`** not rebased, so we avoid conflicts and the branch merge is correctly visualize in the commits history. + +### Code style guidelines + +We follow PEP8 conventions as code style guidelines, please check [here](https://github.com/BU-ISCIII/BU-ISCIII/wiki/Python#pep-8-guidelines-read-the-full-pep-8-documentation) for more detail. + +When developing new code, we strongly recommend to implement LogSum() functions from log_summary.py instead of the classic python logging in order to keep track of all the warnings and errors that may appear during any of the processes. + +## Getting help + +For further information/help, please ask on the `#pipelines-dev` slack channel or write us an email! 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R1C1FZ4@?^p&wx1&^k1bpIyL|R literal 0 HcmV?d00001 From 4b5e7c93885e16eec720a81ace2880031c356ba6 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 30 Aug 2024 14:09:18 +0200 Subject: [PATCH 1450/1454] Included a new laboratory --- relecov_tools/conf/laboratory_address.json | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/laboratory_address.json b/relecov_tools/conf/laboratory_address.json index 3471f980..4acbf284 100755 --- a/relecov_tools/conf/laboratory_address.json +++ b/relecov_tools/conf/laboratory_address.json @@ -1440,6 +1440,16 @@ "submitting_institution": "Hospital Universitario Cruces", "submitting_institution_address": "Plaza Cruces, s/n", "submitting_institution_email": "" + }, + "Hospital Virgen Macarena": { + "collecting_institution_address": "Av. Dr. Fedriani, 3", + "collecting_institution_email": "", + "geo_loc_state": "Andalucia", + "geo_loc_region": "Sevilla", + "geo_loc_city": "Sevilla", + "geo_loc_country": "Spain", + "submitting_institution": "Plataforma de Medicina Computacional, Fundación Progreso y Salud", + "submitting_institution_address": "Avda. Américo Vespucio, 15, Sevilla", + "submitting_institution_email": "joaquin.dopazo@juntadeandalucia.es" } - } From dac9d4ee4e1f30fd793a27feac29394df6e5e74d Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 30 Aug 2024 14:10:15 +0200 Subject: [PATCH 1451/1454] Introduced a new action to publish releases on pypi --- .github/workflows/pypi_publish.yml | 88 ++++++++++++++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 .github/workflows/pypi_publish.yml diff --git a/.github/workflows/pypi_publish.yml b/.github/workflows/pypi_publish.yml new file mode 100644 index 00000000..350681b6 --- /dev/null +++ b/.github/workflows/pypi_publish.yml @@ -0,0 +1,88 @@ +name: Publish package python distribution to Pypi + +on: + push: + branches: "main" + +jobs: + build: + name: Build distribution + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: "3.9.16" + - name: Install pypi/build + run: >- + python3 -m + pip install + build + --user + - name: Build a binary wheel and a source tarball + run: python3 -m build + - name: Store the distribution packages + uses: actions/upload-artifact@v3 + with: + name: python-package-distributions + path: dist/ + + publish-to-pypi: + name: Publish dist to PyPI + if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes + needs: + - build + runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/relecov-tools + permissions: + id-token: write + steps: + - name: Download all the dists + uses: actions/download-artifact@v3 + with: + name: python-package-distributions + path: dist/ + - name: Publish to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + + github-release: + name: Sign dist with Sigstore and upload to GitHub Release + needs: + - publish-to-pypi + runs-on: ubuntu-latest + permissions: + contents: write + id-token: write + steps: + - name: Download all the dists + uses: actions/download-artifact@v3 + with: + name: python-package-distributions + path: dist/ + - name: Sign the dists with Sigstore + uses: sigstore/gh-action-sigstore-python@v2.1.1 + with: + inputs: >- + ./dist/*.tar.gz + ./dist/*.whl + - name: Create GitHub Release + env: + GITHUB_TOKEN: ${{ github.token }} + run: >- + gh release create + '${{ github.ref_name }}' + --repo '${{ github.repository }}' + --notes "" + - name: Upload artifact signatures to GitHub Release + env: + GITHUB_TOKEN: ${{ github.token }} + # Upload to GitHub Release using the `gh` CLI. + # `dist/` contains the built packages, and the + # sigstore-produced signatures and certificates. + run: >- + gh release upload + '${{ github.ref_name }}' dist/** + --repo '${{ github.repository }}' \ No newline at end of file From 2fb3f87e820b372bd6092740fd560b41e7821247 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 30 Aug 2024 14:10:41 +0200 Subject: [PATCH 1452/1454] Updated version to 1.0.0 in setup.py --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 0448207a..eca2a714 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import setup, find_packages -version = "0.0.6" +version = "1.0.0" with open("README.md") as f: readme = f.read() From 59b23c9270b42c425a29ec4d8aba898657ddb4a1 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 30 Aug 2024 14:10:56 +0200 Subject: [PATCH 1453/1454] Introduced CHANGELOG.md for 1.0.0 release --- CHANGELOG.md | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100755 CHANGELOG.md diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100755 index 00000000..8913ab80 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,38 @@ +# relecov-tools Changelog + +All notable changes to this project will be documented in this file. + +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +## [1.1.0dev] - 2024-0X-0X : https://github.com/BU-ISCIII/relecov-tools/releases/tag/1.1.X + +### Credits + +Code contributions to the hotfix: + +### Modules + +#### Added enhancements + +#### Fixes + +#### Changed + +#### Removed + +### Requirements + +## [1.0.0] - 2024-0X-0X : https://github.com/BU-ISCIII/relecov-tools/releases/tag/1.0.0 + +### Credits + +Code contributions to the inital release: + +- [Sara Monzón](https://github.com/saramonzon) +- [Sarai Varona](https://github.com/svarona) +- [Guillermo Gorines](https://github.com/GuilleGorines) +- [Pablo Mata](https://github.com/Shettland) +- [Luis Chapado](https://github.com/luissian) +- [Erika Kvalem](https://github.com/ErikaKvalem) +- [Alberto Lema](https://github.com/Alema91) +- [Daniel Valle](https://github.com/Daniel-VM) From 3324f398b878a85c8738179e196aab024b4d9064 Mon Sep 17 00:00:00 2001 From: Shettland Date: Mon, 2 Sep 2024 09:20:25 +0200 Subject: [PATCH 1454/1454] Latest changes pre-release 1.0.0 --- relecov_tools/upload_database.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/upload_database.py b/relecov_tools/upload_database.py index 4c41681b..eb5d5c4f 100644 --- a/relecov_tools/upload_database.py +++ b/relecov_tools/upload_database.py @@ -178,13 +178,13 @@ def get_iskylims_fields_sample(self): # the field name for the sample sample_fields[property] = values["field_name"] except KeyError as e: - log.info(f"Error mapping ontology {e}") + self.logsum.add_warning(entry=f"Error mapping ontology {e}") # stderr.print(f"[red]Error mapping ontology {e}") else: # for the ones that do not have ontology label in the sample field # and have an empty value: sample_fields[key] = "" logtxt = f"No ontology found for {values.get('field_name')}" - log.info(logtxt) + self.logsum.add_warning(entry=(logtxt)) # fetch label for sample Project s_project_url = self.platform_settings["iskylims"]["url_project_fields"] param = self.platform_settings["iskylims"]["param_sample_project"]

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+220684,378006,327920,90.79470602585997,89.28,292768,292274,63,93.0,75.0,33,3,25,25046.84,NA,NA +220685,319610,276336,86.64379595854322,84.52,233558,233170,56,91.0,75.0,39,3,29,25488.49,NA,NA From 07edcfaff172ddc2e37b59874770de4423602cc9 Mon Sep 17 00:00:00 2001 From: Alema91 Date: Tue, 7 Jun 2022 12:06:28 +0200 Subject: [PATCH 0515/1454] Pangolin version talbe load --- relecov_tools/read_bioinfo_metadata.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 7600cc10..ab968214 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -85,6 +85,9 @@ def bioinfo_parse(self, file_name): software_versions_path = os.path.join( self.input_folder, "software_versions.yml" ) + pangolin_versions_path = os.path.join( + self.input_folder, "pangolin_version.csv" + ) self.md5_file_name = config_json.get_configuration("md5_file_name") md5_info_path = os.path.join( self.input_folder, From a0245613ab2983ed253fe117b5e6e35f1956b8c0 Mon Sep 17 00:00:00 2001 From: Alema91 Date: Tue, 7 Jun 2022 12:08:53 +0200 Subject: [PATCH 0516/1454] Pangolin load table: 2 --- relecov_tools/read_bioinfo_metadata.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index ab968214..62c85b90 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -101,6 +101,7 @@ def bioinfo_parse(self, file_name): consensus_genome_length_path, header=None, sep="," ) md5_info = pd.read_csv(md5_info_path, header=None, sep=",") + pangolin_version_software = pd.read_csv(pangolin_versions_path, header=None, sep="\t") with open(software_versions_path) as file: software_versions = yaml.load(file, Loader=yaml.FullLoader) From f94dc33ce32bb2c6d1c4a162662531782de8edf1 Mon Sep 17 00:00:00 2001 From: Alema91 Date: Tue, 7 Jun 2022 12:37:02 +0200 Subject: [PATCH 0517/1454] Select only one column from pangolin version --- relecov_tools/read_bioinfo_metadata.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 62c85b90..eb21b175 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -101,7 +101,8 @@ def bioinfo_parse(self, file_name): consensus_genome_length_path, header=None, sep="," ) md5_info = pd.read_csv(md5_info_path, header=None, sep=",") - pangolin_version_software = pd.read_csv(pangolin_versions_path, header=None, sep="\t") + pangolin_version_table = pd.read_csv(pangolin_versions_path, header=None, sep="\t") + pangolin_version_software = pangolin_version_table[1] with open(software_versions_path) as file: software_versions = yaml.load(file, Loader=yaml.FullLoader) From a5132e4b7d0dce52e40d7de7328d1cf1435fc8f8 Mon Sep 17 00:00:00 2001 From: Alema91 Date: Tue, 7 Jun 2022 12:39:29 +0200 Subject: [PATCH 0518/1454] Add pangolin version to json --- relecov_tools/read_bioinfo_metadata.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index eb21b175..55f9af90 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -182,6 +182,9 @@ def bioinfo_parse(self, file_name): bioinfo_dict["mapping_software_version"] = str( list(software_versions["BOWTIE2_ALIGN"].values())[0] ) + bioinfo_dict["pangolin_software_version"] = str( + list(pangolin_version_software["lineage_analysis_software_version"].values())[0] + ) bioinfo_list[str(sample_name)] = bioinfo_dict c = c + 1 From 0e1e9549792f145f7c9779a44f93404b9b2c0da1 Mon Sep 17 00:00:00 2001 From: Alema91 Date: Tue, 7 Jun 2022 12:46:25 +0200 Subject: [PATCH 0519/1454] Add pangolin version to json: 2 --- relecov_tools/read_bioinfo_metadata.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 55f9af90..c650e379 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -182,8 +182,8 @@ def bioinfo_parse(self, file_name): bioinfo_dict["mapping_software_version"] = str( list(software_versions["BOWTIE2_ALIGN"].values())[0] ) - bioinfo_dict["pangolin_software_version"] = str( - list(pangolin_version_software["lineage_analysis_software_version"].values())[0] + bioinfo_dict["lineage_analysis_software_version"] = str( + pangolin_version_software.iloc[c, 0] ) bioinfo_list[str(sample_name)] = bioinfo_dict From 4d2c8f5310b516444cef90311fb2802735791548 Mon Sep 17 00:00:00 2001 From: Alema91 Date: Tue, 7 Jun 2022 12:53:24 +0200 Subject: [PATCH 0520/1454] Remove pangolin version from configuration.json --- relecov_tools/conf/configuration.json | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index b921f142..5cf49208 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -83,7 +83,6 @@ "if_mapping_other": "None", "mapping_params": "--seed 1", "lineage_analysis_software_name": "pangolin", - "lineage_analysis_software_version": "4.0.6", "if_lineage_identification_other": "None" }, "mapping_illumina_tab_field_list": { From f9bd9322affcf8d778966e9a4e6aa01d37a06d24 Mon Sep 17 00:00:00 2001 From: Alema91 Date: Tue, 7 Jun 2022 12:59:45 +0200 Subject: [PATCH 0521/1454] Black --- relecov_tools/read_bioinfo_metadata.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index c650e379..f8d7744b 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -85,9 +85,7 @@ def bioinfo_parse(self, file_name): software_versions_path = os.path.join( self.input_folder, "software_versions.yml" ) - pangolin_versions_path = os.path.join( - self.input_folder, "pangolin_version.csv" - ) + pangolin_versions_path = os.path.join(self.input_folder, "pangolin_version.csv") self.md5_file_name = config_json.get_configuration("md5_file_name") md5_info_path = os.path.join( self.input_folder, @@ -101,7 +99,9 @@ def bioinfo_parse(self, file_name): consensus_genome_length_path, header=None, sep="," ) md5_info = pd.read_csv(md5_info_path, header=None, sep=",") - pangolin_version_table = pd.read_csv(pangolin_versions_path, header=None, sep="\t") + pangolin_version_table = pd.read_csv( + pangolin_versions_path, header=None, sep="\t" + ) pangolin_version_software = pangolin_version_table[1] with open(software_versions_path) as file: From e434b68d5de31ba2cdeec847cbcaf6f8fb7e14dd Mon Sep 17 00:00:00 2001 From: Alema91 Date: Tue, 7 Jun 2022 13:03:57 +0200 Subject: [PATCH 0522/1454] Remove metrics mqc table --- .../summary_variants_metrics_mqc.csv | 97 ------------------- 1 file changed, 97 deletions(-) delete mode 100755 relecov_tools/example_data/summary_variants_metrics_mqc.csv diff --git a/relecov_tools/example_data/summary_variants_metrics_mqc.csv b/relecov_tools/example_data/summary_variants_metrics_mqc.csv deleted file mode 100755 index 2edeb8d9..00000000 --- a/relecov_tools/example_data/summary_variants_metrics_mqc.csv +++ /dev/null @@ -1,97 +0,0 @@ -Sample,# Input reads,# Trimmed reads (fastp),% Non-host reads (Kraken 2),% Mapped reads,# Mapped reads,# Trimmed reads (iVar),Coverage median,% Coverage > 1x,% Coverage > 10x,# SNPs,# INDELs,# Missense variants,# Ns per 100kb consensus,Pangolin lineage,Nextclade clade -214821,316942,285604,98.9180823797986,98.54,281428,281038,287,98.0,92.0,20,1,12,8442.32,NA,NA -214822,382722,306868,36.6652762751411,20.09,61642,61447,6,67.0,41.0,16,2,12,58831.99,NA,NA -214823,298848,196898,41.969953986327944,0.1,204,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA -214824,364,248,66.93548387096774,55.65,138,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA 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-220684,378006,327920,90.79470602585997,89.28,292768,292274,63,93.0,75.0,33,3,25,25046.84,NA,NA -220685,319610,276336,86.64379595854322,84.52,233558,233170,56,91.0,75.0,39,3,29,25488.49,NA,NA From 2c4b08726ab7906f653b7997f6a37bdcd4655061 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 8 Jun 2022 20:29:55 +0200 Subject: [PATCH 0523/1454] Fixed bugs to upload sample to relecov --- relecov_tools/conf/configuration.json | 2 +- relecov_tools/feed_database.py | 11 +++++++++-- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 1a71ca74..cd3b0c46 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -44,7 +44,7 @@ "relecov": { "server": "http://relecov-platform.isciiides.es", "url": "/api/", - "store_samples": "storeData", + "store_samples": "createSampleData", "token": "" } }, diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index 317ba98d..e49fef0e 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -242,8 +242,15 @@ def update_database(self, field_values): f"[red] Error {result['ERROR']} when sending request to iSkyLIMS " ) sys.exit(1) - - log.info("stored data in iskylims for sample %s", chunk["sampleName"]) + if "sampleName" in chunk: + log.info("stored data in iskylims for sample %s", chunk["sampleName"]) + elif "sequencing_sample_id" in chunk: + log.info( + "stored data in relecov for sample %s", + chunk["sequencing_sample_id"], + ) + else: + log.info("stored data in relecov") return def store_data(self): From b5c72c12481bbc6f0c8e45ef24c9b689a9c3acec Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 9 Jun 2022 10:47:43 +0200 Subject: [PATCH 0524/1454] changes in relecov and trying to fix login ena --- relecov_tools/conf/configuration.json | 21 +++++++---- relecov_tools/ena_upload.py | 30 ++++++++-------- relecov_tools/map_schema.py | 3 +- relecov_tools/schema/relecov_schema.json | 45 ++++++++++++++++++++---- 4 files changed, 70 insertions(+), 29 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 1a71ca74..e4756a24 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -55,11 +55,18 @@ "sampleLocation": "Not defined" }, "relecov_sample_metadata": [ - "bioproject_accession_ENA" , "bioproject_umbrella_accession_ENA", - "biosample_accession_ENA", "GenBank_ENA_DDBJ_accession", - "GISAID_accession", "gisaid_id", "host_specimen_voucher", - "isolate_sample_id", "microbiology_lab_sample_id", - "sequencing_sample_id", "SRA_accession", "submitting_lab_sample_id", + "bioproject_accession_ENA", + "bioproject_umbrella_accession_ENA", + "biosample_accession_ENA", + "GenBank_ENA_DDBJ_accession", + "GISAID_accession", + "gisaid_id", + "host_specimen_voucher", + "isolate_sample_id", + "microbiology_lab_sample_id", + "sequencing_sample_id", + "SRA_accession", + "submitting_lab_sample_id", "virus_name" ], "relecov_bioinfo_metadata": { @@ -70,7 +77,7 @@ "variant_calling_software_name": "IVAR_VARIANTS", "variant_calling_params": "--ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0';-t 0.25 -q 20 -m 10", "consensus_sequence_software_name": "BCFTOOLS_CONSENSUS", - "if_consensur_other": "None", + "if_consensus_other": "None", "consensus_params": "-p vcf -f", "depth_of_coverage_threshold": ">10x", "bioinformatics_protocol_software_name": "nf-core/viralrecon", @@ -129,4 +136,4 @@ "CALLER", "LINEAGE" ] -} +} \ No newline at end of file diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index b56dbb57..025338c1 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,4 +1,5 @@ import logging +import pdb import rich.console import json @@ -108,8 +109,10 @@ def create_structure_to_ena(self): esquema_json = json.load(fh_esquema) fh_esquema.close() - df_schemas = pd.DataFrame.from_dict(esquema_json, orient="index") - df_transposed = df_schemas.T + df_schemas = pd.DataFrame(esquema_json) + + # df_transposed = df_schemas.T + df_transposed = df_schemas df_study = df_transposed[ ["study_alias", "study_title", "study_type", "study_abstract"] ] @@ -124,17 +127,14 @@ def create_structure_to_ena(self): "sample_name", "sample_title", "taxon_id", - "sample_description", - "collection date", - "geographic location (country and/or sea)", - "host common name", - "host scientific name", - "host subject id", - "host health state", - "host sex", + "collection_date", + "geographic_location_(country_and/or_sea)", + "host_common_name", + "host_scientific_name", + "host_sex", "scientific_name", - "collector name", - "collecting institution", + "collector_name", + "collecting_institution", "isolate", ] ] @@ -156,7 +156,8 @@ def create_structure_to_ena(self): "r1_fastq_filepath", "r2_fastq_filepath", "file_type", - "file_checksum", + "fastq_r1_md5", + "fastq_r2_md5", ] ] df_run.insert(3, "status", self.action) @@ -168,14 +169,12 @@ def create_structure_to_ena(self): "experiment_alias", "study_title", "study_alias", - "design_description", "sample_name", "library_name", "library_strategy", "library_source", "library_selection", "library_layout", - "platform", "instrument_model", ] ] @@ -205,6 +204,7 @@ def create_structure_to_ena(self): file_paths[os.path.basename(path)] = os.path.abspath(path) # submit data to webin ftp server + chec = submit_data(file_paths, self.passwd, self.user) print(chec) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index f96de788..a03fd140 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -153,7 +153,6 @@ def additional_formating(self, mapped_json_data): """ if self.destination_schema == "ENA": for idx in range(len(self.json_data)): - mapped_json_data[idx]["fastq_r1_md5"] = self.json_data[idx][ "fastq_r1_md5" ] @@ -162,10 +161,12 @@ def additional_formating(self, mapped_json_data): ] mapped_json_data[idx]["r1_fastq_filepath"] = ( self.json_data[idx]["r1_fastq_filepath"] + + "/" + self.json_data[idx]["sequence_file_R1_fastq"] ) mapped_json_data[idx]["r2_fastq_filepath"] = ( self.json_data[idx]["r2_fastq_filepath"] + + "/" + self.json_data[idx]["sequence_file_R2_fastq"] ) mapped_json_data[idx]["collecting_institution"] = self.json_data[idx][ diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 2679e30b..4ff14734 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1189,7 +1189,7 @@ "label": "Library Layout", "fill_mode": "batch" }, - "dehosting_software_name": { + "dehosting_method_software_name": { "examples": [ "Nanostripper" ], @@ -1200,7 +1200,7 @@ "label": "Dehosting Method", "fill_mode": "batch" }, - "dehosting_software_version": { + "dehosting_method_software_version": { "examples": [ "2.4.1" ], @@ -1288,7 +1288,18 @@ "label": "Variant Calling params", "fill_mode": "batch" }, - "consensus_sequence_name": { + "consensus_sequence_R1_name": { + "ontology": "GENEPIO:0001461", + "type": "string", + "description": "The name of the consensus sequence.", + "examples": [ + "ncov123assembly3" + ], + "classification": "Bioinformatic Analysis fields", + "label": "Consensus sequence name", + "fill_mode": "batch" + }, + "consensus_sequence_R2_name": { "ontology": "GENEPIO:0001460", "type": "string", "description": "The name of the consensus sequence.", @@ -1299,7 +1310,7 @@ "label": "Consensus sequence name", "fill_mode": "batch" }, - "consensus_sequence_name_md5": { + "consensus_sequence_R1_md5": { "ontology": "NMR:1000568", "type": "string", "description": "The name of the consensus sequence.", @@ -1310,6 +1321,17 @@ "label": "Consensus sequence name md5", "fill_mode": "batch" }, + "consensus_sequence_R2_md5": { + "ontology": "NMR:1000569", + "type": "string", + "description": "The name of the consensus sequence.", + "examples": [ + "ncov123assembly3" + ], + "classification": "Bioinformatic Analysis fields", + "label": "Consensus sequence name md5", + "fill_mode": "batch" + }, "consensus_sequence_filepath": { "examples": [ "/User/Documents/RespLab/Data/ncov123assembly.fasta" @@ -1321,6 +1343,17 @@ "label": "Consensus sequence filepath", "fill_mode": "batch" }, + "long_table_path": { + "examples": [ + "1.3" + ], + "ontology": "0", + "type": "string", + "description": "The path where the long table is ", + "classification": "Bioinformatic Analysis fields", + "label": "Long table path", + "fill_mode": "batch" + }, "consensus_sequence_software_name": { "examples": [ "Ivar" @@ -1817,7 +1850,7 @@ "label": "% genome greater 10x", "fill_mode": "batch" }, - "mean_depth_of_coverage_value": { + "median_depth_of_coverage_value": { "examples": [ "" ], @@ -2494,4 +2527,4 @@ "fill_mode": "batch" } } -} +} \ No newline at end of file From 982c250fdbb69ee4a9bbe4e453e5368b4b67aac0 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Thu, 9 Jun 2022 10:53:32 +0200 Subject: [PATCH 0525/1454] lintin --- relecov_tools/ena_upload.py | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 025338c1..9455450a 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,5 +1,4 @@ import logging -import pdb import rich.console import json From c1f554fd4d9356cc86dfb7831a9717795b13793d Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 10 Jun 2022 11:06:30 +0200 Subject: [PATCH 0526/1454] modified schema --- relecov_tools/ena_upload.py | 44 ++++++++++++++++++++++-- relecov_tools/read_bioinfo_metadata.py | 2 +- relecov_tools/schema/relecov_schema.json | 15 ++++++-- 3 files changed, 55 insertions(+), 6 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 9455450a..879693f6 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,7 +1,7 @@ import logging import rich.console import json - +import paramiko import pandas as pd import sys import os @@ -204,8 +204,46 @@ def create_structure_to_ena(self): # submit data to webin ftp server - chec = submit_data(file_paths, self.passwd, self.user) - print(chec) + # chec = submit_data(file_paths, self.passwd, self.user) + sftp_server = "webin2.ebi.ac.uk" + sftp_port = 21 + + def open_connection(self, file_paths): + """Establish sftp connection""" + self.client = paramiko.SSHClient() + self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) + self.client.connect( + hostname=sftp_server, + port=sftp_port, + username=self.user, + password=self.passwd, + allow_agent=False, + look_for_keys=False, + ) + try: + self.client = self.client.open_sftp() + + return True + except paramiko.SSHException as e: + log.error("Invalid Username/Password for %s:", e) + return False + + for filename, path in file_paths.items(): + print(f"uploading {path}") + try: + filename = "/" + filename + self.client.put(path, filename) + except BaseException as err: + print(f"ERROR: {err}") + print( + "ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000." + ) + raise + + def close_connection(self): + """Closes SFTP connection""" + self.client.close() + return True # when ADD/MODIFY, # requires source XMLs for 'run', 'experiment', 'sample', 'experiment' diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index f8d7744b..faad1187 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -158,7 +158,7 @@ def bioinfo_parse(self, file_name): bioinfo_dict["consensus_sequence_R1_md5"] = str( md5_info.iloc[c * 2, 0][0:32] ) - bioinfo_dict["consensus_sequence__R2_md5"] = str( + bioinfo_dict["consensus_sequence_R2_md5"] = str( md5_info.iloc[c * 2 + 1, 0][0:32] ) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 4ff14734..47aa600d 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1420,6 +1420,17 @@ "label": "Depth of coverage value ", "fill_mode": "batch" }, + "sample_name": { + "examples": [ + "234546" + ], + "ontology": "0", + "type": "string", + "description": "", + "classification": "Files info", + "label": "Sample Name", + "fill_mode": "batch" + }, "depth_of_coverage_threshold": { "examples": [ "100x" @@ -1431,7 +1442,7 @@ "label": "Depth of coverage threshold", "fill_mode": "batch" }, - "sequence_file_R1_fastq": { + "fastq_r1": { "examples": [ "ABC123_S1_L001_R1_001.fastq.gz" ], @@ -1442,7 +1453,7 @@ "label": "Sequence file R1 fastq", "fill_mode": "sample" }, - "sequence_file_R2_fastq": { + "fastq_r2": { "examples": [ "ABC123_S1_L001_R2_002.fastq.gz" ], From f62bc34954bf529a6f2f5abdef00d4604aab137b Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 10 Jun 2022 11:08:37 +0200 Subject: [PATCH 0527/1454] lintin --- relecov_tools/ena_upload.py | 41 +------------------------------------ 1 file changed, 1 insertion(+), 40 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 879693f6..d8cf4ab4 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -204,46 +204,7 @@ def create_structure_to_ena(self): # submit data to webin ftp server - # chec = submit_data(file_paths, self.passwd, self.user) - sftp_server = "webin2.ebi.ac.uk" - sftp_port = 21 - - def open_connection(self, file_paths): - """Establish sftp connection""" - self.client = paramiko.SSHClient() - self.client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) - self.client.connect( - hostname=sftp_server, - port=sftp_port, - username=self.user, - password=self.passwd, - allow_agent=False, - look_for_keys=False, - ) - try: - self.client = self.client.open_sftp() - - return True - except paramiko.SSHException as e: - log.error("Invalid Username/Password for %s:", e) - return False - - for filename, path in file_paths.items(): - print(f"uploading {path}") - try: - filename = "/" + filename - self.client.put(path, filename) - except BaseException as err: - print(f"ERROR: {err}") - print( - "ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000." - ) - raise - - def close_connection(self): - """Closes SFTP connection""" - self.client.close() - return True + chec = submit_data(file_paths, self.passwd, self.user) # when ADD/MODIFY, # requires source XMLs for 'run', 'experiment', 'sample', 'experiment' From ba7789ecc97fba3b3cf91c5bc4740e3ba5e614a8 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 10 Jun 2022 11:31:11 +0200 Subject: [PATCH 0528/1454] lintin --- relecov_tools/ena_upload.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index d8cf4ab4..83ef6044 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,7 +1,8 @@ import logging import rich.console import json -import paramiko + +# import paramiko import pandas as pd import sys import os @@ -205,6 +206,7 @@ def create_structure_to_ena(self): # submit data to webin ftp server chec = submit_data(file_paths, self.passwd, self.user) + print(chec) # when ADD/MODIFY, # requires source XMLs for 'run', 'experiment', 'sample', 'experiment' From fc51711b9fc5fc5873893acf4de5c9336001c6ef Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 13 Jun 2022 10:30:25 +0200 Subject: [PATCH 0529/1454] latest changes friday --- relecov_tools/ena_upload.py | 34 +++++++++++++++++++++----- relecov_tools/read_bioinfo_metadata.py | 3 ++- 2 files changed, 30 insertions(+), 7 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 83ef6044..289f9d92 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -6,6 +6,7 @@ import pandas as pd import sys import os +import ftplib import relecov_tools.utils from relecov_tools.config_json import ConfigJson @@ -113,6 +114,7 @@ def create_structure_to_ena(self): # df_transposed = df_schemas.T df_transposed = df_schemas + df_study = df_transposed[ ["study_alias", "study_title", "study_type", "study_abstract"] ] @@ -151,8 +153,6 @@ def create_structure_to_ena(self): df_run = df_transposed[ [ "experiment_alias", - "sequence_file_R1_fastq", - "sequence_file_R2_fastq", "r1_fastq_filepath", "r2_fastq_filepath", "file_type", @@ -160,9 +160,15 @@ def create_structure_to_ena(self): "fastq_r2_md5", ] ] + df_run.insert( + 1, "sequence_file_R1_fastq", df_transposed["r1_fastq_filepath"][0][31:57] + ) + df_run.insert( + 2, "sequence_file_R2_fastq", df_transposed["r2_fastq_filepath"][0][31:57] + ) df_run.insert(3, "status", self.action) df_run.insert(4, "alias", df_run["experiment_alias"]) - df_run.insert(4, "file_name", df_run["sequence_file_R1_fastq"]) + df_run.insert(5, "file_name", df_run["sequence_file_R1_fastq"]) df_experiments = df_transposed[ [ @@ -205,8 +211,25 @@ def create_structure_to_ena(self): # submit data to webin ftp server - chec = submit_data(file_paths, self.passwd, self.user) - print(chec) + session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) + for filename, path in file_paths.items(): + print("Uploading" + path) + try: + + file = open(file_paths, "rb") # file to send + g = session.storbinary(f"STOR {file_paths.name}", file) + print(g) # send the file + file.close() # close file and FTP + g2 = session.quit() + print(g2) + except BaseException as err: + print(f"ERROR: {err}") + print( + "ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000." + ) + + # chec = submit_data(file_paths, self.passwd, self.user) + # print(chec) # when ADD/MODIFY, # requires source XMLs for 'run', 'experiment', 'sample', 'experiment' @@ -214,7 +237,6 @@ def create_structure_to_ena(self): tool = config_json.get_configuration("tool") - print(checklist) schema_xmls = run_construct( template_path, schema_targets, self.center, checklist, tool ) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index faad1187..2af45670 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -182,8 +182,9 @@ def bioinfo_parse(self, file_name): bioinfo_dict["mapping_software_version"] = str( list(software_versions["BOWTIE2_ALIGN"].values())[0] ) + bioinfo_dict["lineage_analysis_software_version"] = str( - pangolin_version_software.iloc[c, 0] + pangolin_version_software.iloc[c] ) bioinfo_list[str(sample_name)] = bioinfo_dict From aa2b31d018d9c5b446800dd44c4bff8ddb72acde Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 13 Jun 2022 10:37:21 +0200 Subject: [PATCH 0530/1454] ftp function --- relecov_tools/ena_upload.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 289f9d92..abf9393e 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -210,7 +210,7 @@ def create_structure_to_ena(self): file_paths[os.path.basename(path)] = os.path.abspath(path) # submit data to webin ftp server - + # def ftp_connect(self): session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) for filename, path in file_paths.items(): print("Uploading" + path) @@ -227,6 +227,8 @@ def create_structure_to_ena(self): print( "ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000." ) + # l = ftp_connect(self) + # print(l) # chec = submit_data(file_paths, self.passwd, self.user) # print(chec) From 86179598d7efd2d16e288d8f1d21e30750c75924 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 13 Jun 2022 10:38:40 +0200 Subject: [PATCH 0531/1454] latest change --- relecov_tools/ena_upload.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index abf9393e..9bc6086d 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -227,6 +227,7 @@ def create_structure_to_ena(self): print( "ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000." ) + # l = ftp_connect(self) # print(l) From 75f7cf3a7c8abc2c5fb50dbeaa77eddd9ba878d2 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 13 Jun 2022 10:40:20 +0200 Subject: [PATCH 0532/1454] lintin --- relecov_tools/ena_upload.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 9bc6086d..8bdbce4d 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -11,7 +11,8 @@ from relecov_tools.config_json import ConfigJson from ena_upload.ena_upload import extract_targets -from ena_upload.ena_upload import submit_data + +# from ena_upload.ena_upload import submit_data from ena_upload.ena_upload import run_construct from ena_upload.ena_upload import construct_submission from ena_upload.ena_upload import send_schemas From 7a11c41aa8629e7d956d6f72a01dfddc97735a22 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 13 Jun 2022 22:38:10 +0200 Subject: [PATCH 0533/1454] Reformating the long table parse for joining all variants per sample --- relecov_tools/__main__.py | 4 +- relecov_tools/long_table_parse.py | 211 +++++++++++++----------------- 2 files changed, 91 insertions(+), 124 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index 203a80cc..d7364aa5 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -323,7 +323,7 @@ def read_bioinfo_metadata(metadata_file, input_folder, metadata_out): metadata_file, input_folder, metadata_out ) - new_bioinfo_metadata.bioinfo_parse(metadata_file) + new_bioinfo_metadata.bioinfo_parse() # read metadata bioinformatics @@ -332,7 +332,7 @@ def read_bioinfo_metadata(metadata_file, input_folder, metadata_out): "-l", "--longtable_file", type=click.Path(), - help="file containing long table ", + help="file containing variant long table ", ) @click.option("-o", "--output", type=click.Path(), help="Path to save json output") def long_table_parse(longtable_file, output): diff --git a/relecov_tools/long_table_parse.py b/relecov_tools/long_table_parse.py index b14128f6..ca3652a7 100644 --- a/relecov_tools/long_table_parse.py +++ b/relecov_tools/long_table_parse.py @@ -1,28 +1,3 @@ -""" -============================================================= -HEADER -============================================================= -INSTITUTION: BU-ISCIII -AUTHOR: Luis D. Aranda Lillo -MAIL: laranda@isciii.es -VERSION: 0 -CREATED: 31-5-2022 -REVISED: 31-5-2022 -REVISED BY: Luis Chapado -DESCRIPTION: - - Parse a csv file and save the results in a file - -REQUIREMENTS: - -Python - -TO DO: - -================================================================ -END_OF_HEADER -================================================================ -""" - from datetime import datetime import json import logging @@ -58,20 +33,22 @@ class LongTableParse: def __init__(self, file_path=None, output_directory=None): if file_path is None: self.file_path = relecov_tools.utils.prompt_path( - msg="Select the csv file which contains metadata" + msg="Select the csv file which contains variant long table information" ) else: self.file_path = file_path if not os.path.exists(self.file_path): - log.error("Metadata file %s does not exist ", self.file_path) - stderr.print("[red] Metadata file " + self.file_path + " does not exist") + log.error("Variant long table file %s does not exist ", self.file_path) + stderr.print( + f"[red] Variant long table file {self.file_path} does not exist" + ) sys.exit(1) if not self.file_path.endswith(".csv"): - log.error("Metadata file %s is not a csv file ", self.file_path) + log.error("Variant long table file %s is not a csv file ", self.file_path) stderr.print( - "[red] Metadata file " + self.file_path + " must be a csv file" + f"[red] Variant long table file {self.file_path} must be a csv file" ) sys.exit(1) @@ -86,110 +63,100 @@ def __init__(self, file_path=None, output_directory=None): config_json = ConfigJson() self.long_table_heading = config_json.get_configuration("long_table_heading") - def saving_file(self, generated_JSON): + def valid_file(self, heading): + """Check if long table file has all mandatory fields defined in + configuration file """ - Save the list of dictionaries, generated by the parse_a_list_of_dictionaries() function , - to a json file, naming as "long_table_JSON_" + "current date" + ".json" + for field in self.long_table_heading: + if field not in heading: + return False + return True - Args: - generated_JSON (a list of dictionaries) - """ - date_now = datetime.now() - file_name = "long_table_JSON_" + str(date_now) + ".json" - complete_path = os.path.join(self.output_directory, file_name) - with open(complete_path, "w") as fh: - fh.write(generated_JSON) - - def parse_a_list_of_dictionaries(self): + def parse_file(self): """_summary_ - This function generates a json file from the csv file entered by the user (long_table.csv). - - It checks if the headers of both files are the same - - It checks if both files contain the same number of fields + This function generates a json file from the csv file entered by the user + (long_table.csv). + - Checks if expected headers match with file headers Returns: - A list of dictionaries in json format. + dictionary with key as sample and value the list of variants """ + with open(self.file_path) as fh: + lines = fh.readlines() - try: - with open(self.file_path) as fh: - lines = fh.readlines() - - except FileNotFoundError: - stderr.print("[red]The file we're looking for... doesn't exist") + if not self.valid_file(lines[0].strip().split(",")): + stderr.print("[red]Incorrect Format, fields don't match") sys.exit(1) - list_of_dictionaries = [] + heading_index = {} headings_from_csv = lines[0].strip().split(",") - dict_index_of_heading = {} - for heading in self.long_table_heading: - dict_index_of_heading[heading] = self.long_table_heading.index(heading) - - # check if the headers of both files are the same - for heading_csv in headings_from_csv: - if heading_csv not in dict_index_of_heading: - stderr.print("[red]Incorrect Format, fields don't match") - sys.exit(1) - - # check if both files contain the same number of fields - if len(self.long_table_heading) is len(headings_from_csv): - - for line in lines[1:]: - data_dict_from_long_table = {} - data_list = line.strip().split(",") - - data_dict_from_long_table["Chromosome"] = { - "chromosome": data_list[dict_index_of_heading["CHROM"]] - } - - data_dict_from_long_table["Position"] = { - "pos": data_list[dict_index_of_heading["POS"]], - "nucleotide": data_list[dict_index_of_heading["ALT"]], - } - - data_dict_from_long_table["Filter"] = { - "filter": data_list[dict_index_of_heading["FILTER"]] - } - - data_dict_from_long_table["VariantInSample"] = { - "dp": data_list[dict_index_of_heading["DP"]], - "ref_dp": data_list[dict_index_of_heading["REF_DP"]], - "alt_dp": data_list[dict_index_of_heading["ALT_DP"]], - "af": data_list[dict_index_of_heading["AF"]], - } - - data_dict_from_long_table["Gene"] = { - "gene": data_list[dict_index_of_heading["GENE"]] - } - - data_dict_from_long_table["Effect"] = { - "effect": data_list[dict_index_of_heading["EFFECT"]], - "hgvs_c": data_list[dict_index_of_heading["HGVS_C"]], - "hgvs_p": data_list[dict_index_of_heading["HGVS_P"]], - "hgvs_p_1_letter": data_list[ - dict_index_of_heading["HGVS_P_1LETTER"] - ], - } - - data_dict_from_long_table["Variant"] = { - "ref": data_list[dict_index_of_heading["REF"]] - } - - data_dict_from_long_table["Sample"] = { - "sample": data_list[dict_index_of_heading["SAMPLE"]] - } - - list_of_dictionaries.append(data_dict_from_long_table) - - return json.dumps(list_of_dictionaries, indent=4) - else: - print( - "[red]Incorrect format, the headers do not have the same number of fields" - ) - sys.exit(1) + heading_index[heading] = headings_from_csv.index(heading) + + samp_dict = {} + for line in lines[1:]: + line_s = line.strip().split(",") + + sample = line_s[heading_index["SAMPLE"]] + if sample not in samp_dict: + samp_dict[sample] = [] + variant_dict = {} + variant_dict["Chromosome"] = {"chromosome": line_s[heading_index["CHROM"]]} + + variant_dict["Position"] = { + "pos": line_s[heading_index["POS"]], + "nucleotide": line_s[heading_index["ALT"]], + } + + variant_dict["Filter"] = {"filter": line_s[heading_index["FILTER"]]} + + variant_dict["VariantInSample"] = { + "dp": line_s[heading_index["DP"]], + "ref_dp": line_s[heading_index["REF_DP"]], + "alt_dp": line_s[heading_index["ALT_DP"]], + "af": line_s[heading_index["AF"]], + } + + variant_dict["Gene"] = {"gene": line_s[heading_index["GENE"]]} + + variant_dict["Effect"] = { + "effect": line_s[heading_index["EFFECT"]], + "hgvs_c": line_s[heading_index["HGVS_C"]], + "hgvs_p": line_s[heading_index["HGVS_P"]], + "hgvs_p_1_letter": line_s[heading_index["HGVS_P_1LETTER"]], + } + + variant_dict["Variant"] = {"ref": line_s[heading_index["REF"]]} + + samp_dict[sample].append(variant_dict) + + return samp_dict + + def convert_to_json(self, samp_dict): + """ """ + j_list = [] + for key, values in samp_dict.items(): + j_dict = {"sample": key} + j_dict["variants"] = values + j_list.append(j_dict) + return j_list + + def saving_file(self, j_list): + """ + Transform the p0arsed data into a jsonf file, naming as + "long_table_" + "current date" + ".json" + """ + date_now = datetime.now().strftime("%Y_%m_%d_%H_%M_%S") + file_name = "long_table_" + date_now + ".json" + file_path = os.path.join(self.output_directory, file_name) + + with open(file_path, "w") as fh: + fh.write(json.dumps(j_list, indent=4)) + return def parsing_csv(self): """ function called when using the relecov-tools long-table-parse function. """ - generated_json = self.parse_a_list_of_dictionaries() - self.saving_file(generated_JSON=generated_json) + parsed_data = self.parse_file() + j_list = self.convert_to_json(parsed_data) + self.saving_file(j_list) From 39e6841cd4716af4903b624f1d67b75d1f51a10b Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 13 Jun 2022 22:48:16 +0200 Subject: [PATCH 0534/1454] added long_table json for testing --- .../long_table_2022_06_13_22_34_59.json | 100657 +++++++++++++++ 1 file changed, 100657 insertions(+) create mode 100644 relecov_tools/example_data/long_table_2022_06_13_22_34_59.json diff --git a/relecov_tools/example_data/long_table_2022_06_13_22_34_59.json b/relecov_tools/example_data/long_table_2022_06_13_22_34_59.json new file mode 100644 index 00000000..d9fce212 --- /dev/null +++ b/relecov_tools/example_data/long_table_2022_06_13_22_34_59.json @@ -0,0 +1,100657 @@ +[ + { + "sample": "214821", + "variants": [ + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "11132", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "366", + "ref_dp": "0", + "alt_dp": "363", + "af": "0.99" + }, + "Gene": { + "gene": "orf1ab" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.10867G>T", + "hgvs_p": "p.Ala3623Ser", + "hgvs_p_1_letter": "p.A3623S" + }, + "Variant": { + "ref": "G" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "14408", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "333", + "ref_dp": "2", + "alt_dp": "331", + "af": "0.99" + }, + "Gene": { + "gene": "orf1ab" + }, + "Effect": { + "effect": "synonymous_variant", + "hgvs_c": "c.14143C>T", + "hgvs_p": "p.Leu4715Leu", + "hgvs_p_1_letter": "p.L4715L" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "16726", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "697", + "ref_dp": "1", + "alt_dp": "695", + "af": "1.0" + }, + "Gene": { + "gene": "orf1ab" + }, + "Effect": { + "effect": "synonymous_variant", + "hgvs_c": "c.16461C>T", + "hgvs_p": "p.Tyr5487Tyr", + "hgvs_p_1_letter": "p.Y5487Y" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "17658", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "3710", + "ref_dp": "6", + "alt_dp": "3690", + "af": "0.99" + }, + "Gene": { + "gene": "orf1ab" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.17393G>T", + "hgvs_p": "p.Cys5798Phe", + "hgvs_p_1_letter": "p.C5798F" + }, + "Variant": { + "ref": "G" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "20132", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "83", + "ref_dp": "0", + "alt_dp": "83", + "af": "1.0" + }, + "Gene": { + "gene": "orf1ab" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.19867C>T", + "hgvs_p": "p.Pro6623Ser", + "hgvs_p_1_letter": "p.P6623S" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "21255", + "nucleotide": "C" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "78", + "ref_dp": "0", + "alt_dp": "78", + "af": "1.0" + }, + "Gene": { + "gene": "orf1ab" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.20990G>C", + "hgvs_p": "p.Arg6997Pro", + "hgvs_p_1_letter": "p.R6997P" + }, + "Variant": { + "ref": "G" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "21786", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "276", + "ref_dp": "0", + "alt_dp": "275", + "af": "1.0" + }, + "Gene": { + "gene": "S" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.224G>T", + "hgvs_p": "p.Gly75Val", + "hgvs_p_1_letter": "p.G75V" + }, + "Variant": { + "ref": "G" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "23403", + "nucleotide": "G" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "2590", + "ref_dp": "2", + "alt_dp": "2588", + "af": "1.0" + }, + "Gene": { + "gene": "S" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.1841A>G", + "hgvs_p": "p.Asp614Gly", + "hgvs_p_1_letter": "p.D614G" + }, + "Variant": { + "ref": "A" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "24138", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "1594", + "ref_dp": "913", + "alt_dp": "679", + "af": "0.43" + }, + "Gene": { + "gene": "S" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.2576C>T", + "hgvs_p": "p.Thr859Ile", + "hgvs_p_1_letter": "p.T859I" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "26801", + "nucleotide": "G" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "896", + "ref_dp": "0", + "alt_dp": "892", + "af": "1.0" + }, + "Gene": { + "gene": "M" + }, + "Effect": { + "effect": "synonymous_variant", + "hgvs_c": "c.279C>G", + "hgvs_p": "p.Leu93Leu", + "hgvs_p_1_letter": "p.L93L" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "28932", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "242", + "ref_dp": "5", + "alt_dp": "236", + "af": "0.98" + }, + "Gene": { + "gene": "N" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.659C>T", + "hgvs_p": "p.Ala220Val", + "hgvs_p_1_letter": "p.A220V" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "29645", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "84", + "ref_dp": "0", + "alt_dp": "82", + "af": "0.98" + }, + "Gene": { + "gene": "ORF10" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.88G>T", + "hgvs_p": "p.Val30Leu", + "hgvs_p_1_letter": "p.V30L" + }, + "Variant": { + "ref": "G" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "3037", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "330", + "ref_dp": "0", + "alt_dp": "330", + "af": "1.0" + }, + "Gene": { + "gene": "orf1ab" + }, + "Effect": { + "effect": "synonymous_variant", + "hgvs_c": "c.2772C>T", + "hgvs_p": "p.Phe924Phe", + "hgvs_p_1_letter": "p.F924F" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "4230", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "57", + "ref_dp": "0", + "alt_dp": "57", + "af": "1.0" + }, + "Gene": { + "gene": "orf1ab" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.3965C>T", + "hgvs_p": "p.Thr1322Ile", + "hgvs_p_1_letter": "p.T1322I" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "445", + "nucleotide": "C" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "8440", + "ref_dp": "24", + "alt_dp": "8415", + "af": "1.0" + }, + "Gene": { + "gene": "orf1ab" + }, + "Effect": { + "effect": "synonymous_variant", + "hgvs_c": "c.180T>C", + "hgvs_p": "p.Val60Val", + "hgvs_p_1_letter": "p.V60V" + }, + "Variant": { + "ref": "T" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "504", + "nucleotide": "C" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "7769", + "ref_dp": "7715", + "alt_dp": "6191", + "af": "0.8" + 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"Position": { + "pos": "24130", + "nucleotide": "A" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "171", + "ref_dp": "0", + "alt_dp": "171", + "af": "1.0" + }, + "Gene": { + "gene": "S" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.2568C>A", + "hgvs_p": "p.Asn856Lys", + "hgvs_p_1_letter": "p.N856K" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "24424", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "101", + "ref_dp": "3", + "alt_dp": "98", + "af": "0.97" + }, + "Gene": { + "gene": "S" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.2862A>T", + "hgvs_p": "p.Gln954His", + "hgvs_p_1_letter": "p.Q954H" + }, + "Variant": { + "ref": "A" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "24469", + "nucleotide": "A" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "402", + "ref_dp": "1", + "alt_dp": "400", + "af": "1.0" + }, + "Gene": { + "gene": "S" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.2907T>A", + "hgvs_p": "p.Asn969Lys", + "hgvs_p_1_letter": "p.N969K" + }, + "Variant": { + "ref": "T" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "24503", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "469", + "ref_dp": "11", + "alt_dp": "458", + "af": "0.98" + }, + "Gene": { + "gene": "S" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.2941C>T", + "hgvs_p": "p.Leu981Phe", + "hgvs_p_1_letter": "p.L981F" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "25000", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "19", + "ref_dp": "0", + "alt_dp": "19", + "af": "1.0" + }, + "Gene": { + "gene": "S" + }, + "Effect": { + "effect": "synonymous_variant", + "hgvs_c": "c.3438C>T", + "hgvs_p": "p.Asp1146Asp", + "hgvs_p_1_letter": "p.D1146D" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "25584", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "50", + "ref_dp": "0", + "alt_dp": "50", + "af": "1.0" + }, + "Gene": { + "gene": "ORF3a" + }, + "Effect": { + "effect": "synonymous_variant", + "hgvs_c": "c.192C>T", + "hgvs_p": "p.Thr64Thr", + "hgvs_p_1_letter": "p.T64T" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "26270", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "114", + "ref_dp": "0", + "alt_dp": "114", + "af": "1.0" + }, + "Gene": { + "gene": "E" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.26C>T", + "hgvs_p": "p.Thr9Ile", + "hgvs_p_1_letter": "p.T9I" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "26530", + "nucleotide": "G" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "48", + "ref_dp": "0", + "alt_dp": "48", + "af": "1.0" + }, + "Gene": { + "gene": "M" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.8A>G", + "hgvs_p": "p.Asp3Gly", + "hgvs_p_1_letter": "p.D3G" + }, + "Variant": { + "ref": "A" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "26577", + "nucleotide": "G" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "36", + "ref_dp": "0", + "alt_dp": "36", + "af": "1.0" + }, + "Gene": { + "gene": "M" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.55C>G", + "hgvs_p": "p.Gln19Glu", + "hgvs_p_1_letter": "p.Q19E" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "26709", + "nucleotide": "A" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "37", + "ref_dp": "0", + "alt_dp": "37", + "af": "1.0" + }, + "Gene": { + "gene": "M" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.187G>A", + "hgvs_p": "p.Ala63Thr", + "hgvs_p_1_letter": "p.A63T" + }, + "Variant": { + "ref": "G" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "27259", + "nucleotide": "C" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "82", + "ref_dp": "0", + "alt_dp": "82", + "af": "1.0" + }, + "Gene": { + "gene": "ORF6" + }, + "Effect": { + "effect": "synonymous_variant", + "hgvs_c": "c.58A>C", + "hgvs_p": "p.Arg20Arg", + "hgvs_p_1_letter": "p.R20R" + }, + "Variant": { + "ref": "A" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "27807", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "23", + "ref_dp": "0", + "alt_dp": "23", + "af": "1.0" + }, + "Gene": { + "gene": "ORF7b" + }, + "Effect": { + "effect": "synonymous_variant", + "hgvs_c": "c.52C>T", + "hgvs_p": "p.Leu18Leu", + "hgvs_p_1_letter": "p.L18L" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "28271", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "315", + "ref_dp": "0", + "alt_dp": "313", + "af": "0.99" + }, + "Gene": { + "gene": "N" + }, + "Effect": { + "effect": "upstream_gene_variant", + "hgvs_c": "c.-3A>T", + "hgvs_p": ".", + "hgvs_p_1_letter": "." + }, + "Variant": { + "ref": "A" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "28311", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "318", + "ref_dp": "8", + "alt_dp": "308", + "af": "0.97" + }, + "Gene": { + "gene": "N" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.38C>T", + "hgvs_p": "p.Pro13Leu", + "hgvs_p_1_letter": "p.P13L" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "2832", + "nucleotide": "G" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "19", + "ref_dp": "0", + "alt_dp": "19", + "af": "1.0" + }, + "Gene": { + "gene": "orf1ab" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.2567A>G", + "hgvs_p": "p.Lys856Arg", + "hgvs_p_1_letter": "p.K856R" + }, + "Variant": { + "ref": "A" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "28333", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "307", + "ref_dp": "4", + "alt_dp": "303", + "af": "0.99" + }, + "Gene": { + "gene": "N" + }, + "Effect": { + "effect": "synonymous_variant", + "hgvs_c": "c.60C>T", + "hgvs_p": "p.Pro20Pro", + "hgvs_p_1_letter": "p.P20P" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "28361", + "nucleotide": "G" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "258", + "ref_dp": "256", + "alt_dp": "188", + "af": "0.73" + }, + "Gene": { + "gene": "N" + }, + "Effect": { + "effect": "disruptive_inframe_deletion", + "hgvs_c": "c.90_98delAGAACGCAG", + "hgvs_p": "p.Glu31_Ser33del", + "hgvs_p_1_letter": "p.E31_S33del" + }, + "Variant": { + "ref": "GGAGAACGCA" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "28512", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "186", + "ref_dp": "124", + "alt_dp": "56", + "af": "0.3" + }, + "Gene": { + "gene": "N" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.239C>T", + "hgvs_p": "p.Pro80Leu", + "hgvs_p_1_letter": "p.P80L" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "28881", + "nucleotide": "AA" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "3917", + "ref_dp": "51", + "alt_dp": "3864", + "af": "0.99" + }, + "Gene": { + "gene": "N" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.608_609delGGinsAA", + "hgvs_p": "p.Arg203Lys", + "hgvs_p_1_letter": "p.R203K" + }, + "Variant": { + "ref": "GG" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "28883", + "nucleotide": "C" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "3900", + "ref_dp": "4", + "alt_dp": "3892", + "af": "1.0" + }, + "Gene": { + "gene": "N" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.610G>C", + "hgvs_p": "p.Gly204Arg", + "hgvs_p_1_letter": "p.G204R" + }, + "Variant": { + "ref": "G" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "3037", + "nucleotide": "T" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "13", + "ref_dp": "0", + "alt_dp": "13", + "af": "1.0" + }, + "Gene": { + "gene": "orf1ab" + }, + "Effect": { + "effect": "synonymous_variant", + "hgvs_c": "c.2772C>T", + "hgvs_p": "p.Phe924Phe", + "hgvs_p_1_letter": "p.F924F" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "4710", + "nucleotide": "A" + }, + "Filter": { + "filter": "ft" + }, + "VariantInSample": { + "dp": "12", + "ref_dp": "7", + "alt_dp": "5", + "af": "0.42" + }, + "Gene": { + "gene": "orf1ab" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.4445C>A", + "hgvs_p": "p.Ala1482Asp", + "hgvs_p_1_letter": "p.A1482D" + }, + "Variant": { + "ref": "C" + } + }, + { + "Chromosome": { + "chromosome": "NC_045512.2" + }, + "Position": { + "pos": "8393", + "nucleotide": "A" + }, + "Filter": { + "filter": "PASS" + }, + "VariantInSample": { + "dp": "2105", + "ref_dp": "5", + "alt_dp": "2100", + "af": "1.0" + }, + "Gene": { + "gene": "orf1ab" + }, + "Effect": { + "effect": "missense_variant", + "hgvs_c": "c.8128G>A", + "hgvs_p": "p.Ala2710Thr", + "hgvs_p_1_letter": "p.A2710T" + }, + "Variant": { + "ref": "G" + } + } + ] + } +] \ No newline at end of file From 84bfe74d5e9435c17ac3c0c6ff5ddd2ca12b67d8 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 14 Jun 2022 10:38:10 +0200 Subject: [PATCH 0535/1454] changes in shcema and ena upload --- relecov_tools/ena_upload.py | 62 +++++++++++++++----------- relecov_tools/map_schema.py | 3 ++ relecov_tools/schema/ena_schema.json | 66 ++++++++++++++-------------- 3 files changed, 73 insertions(+), 58 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 8bdbce4d..36363d1c 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,4 +1,5 @@ import logging +from pyparsing import col import rich.console import json @@ -113,19 +114,14 @@ def create_structure_to_ena(self): df_schemas = pd.DataFrame(esquema_json) - # df_transposed = df_schemas.T - df_transposed = df_schemas - - df_study = df_transposed[ + df_study = df_schemas[ ["study_alias", "study_title", "study_type", "study_abstract"] ] - # df_study.columns.values[0] = "alias" - # df_study.columns.values[1] = "title" df_study = df_study.rename(columns={"study_alias": "alias"}) df_study = df_study.rename(columns={"study_title": "title"}) df_study.insert(3, "status", self.action) - df_samples = df_transposed[ + df_samples = df_schemas[ [ "sample_name", "sample_title", @@ -141,17 +137,34 @@ def create_structure_to_ena(self): "isolate", ] ] - # df_samples.columns.values[0] = "alias" - # df_samples.columns.values[1] = "title" df_samples = df_samples.rename(columns={"sample_name": "alias"}) df_samples = df_samples.rename(columns={"sample_title": "title"}) + df_samples = df_samples.rename( + columns={ + "geographic_location_(country_and/or_sea)": "geographic location (country and/or sea)" + } + ) + df_samples = df_samples.rename(columns={"collection_date": "collection date"}) + df_samples = df_samples.rename(columns={"host_common_name": "host common name"}) + df_samples = df_samples.rename(columns={"host_common_name": "host common name"}) + df_samples = df_samples.rename(columns={"host_sex": "host sex"}) + df_samples = df_samples.rename( + columns={"host_scientific_name": "host scientific name"} + ) + df_samples = df_samples.rename(columns={"collector_name": "collector name"}) + df_samples = df_samples.rename( + columns={"collecting_institution": "collecting institution"} + ) df_samples.insert(3, "status", self.action) + df_samples.insert(3, "host subject id", "") + df_samples.insert(3, "host health state", "") config_json = ConfigJson() checklist = config_json.get_configuration("checklist") df_samples.insert(4, "ENA_CHECKLIST", checklist) + df_samples.insert(5, "sample_description", "") - df_run = df_transposed[ + df_run = df_schemas[ [ "experiment_alias", "r1_fastq_filepath", @@ -162,16 +175,17 @@ def create_structure_to_ena(self): ] ] df_run.insert( - 1, "sequence_file_R1_fastq", df_transposed["r1_fastq_filepath"][0][31:57] + 1, "sequence_file_R1_fastq", df_schemas["r1_fastq_filepath"][0][31:57] ) df_run.insert( - 2, "sequence_file_R2_fastq", df_transposed["r2_fastq_filepath"][0][31:57] + 2, "sequence_file_R2_fastq", df_schemas["r2_fastq_filepath"][0][31:57] ) df_run.insert(3, "status", self.action) + df_run = df_run.rename(columns={"fastq_r1_md5": "file_checksum"}) df_run.insert(4, "alias", df_run["experiment_alias"]) df_run.insert(5, "file_name", df_run["sequence_file_R1_fastq"]) - df_experiments = df_transposed[ + df_experiments = df_schemas[ [ "experiment_alias", "study_title", @@ -188,9 +202,6 @@ def create_structure_to_ena(self): df_experiments.insert(3, "status", self.action) df_experiments.insert(4, "alias", df_experiments["experiment_alias"]) - # df_experiments.columns.values[0] = "title" - # df_experiments.columns.values[1] = "sample_alias" - df_experiments = df_experiments.rename(columns={"study_title": "title"}) df_experiments = df_experiments.rename(columns={"sample_name": "sample_alias"}) @@ -212,23 +223,24 @@ def create_structure_to_ena(self): # submit data to webin ftp server # def ftp_connect(self): + session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) for filename, path in file_paths.items(): - print("Uploading" + path) - try: - file = open(file_paths, "rb") # file to send - g = session.storbinary(f"STOR {file_paths.name}", file) + print("Uploading path " + path + " and filename: " + filename) + + try: + file = open(path, "rb") # file to send + g = session.storbinary(f"STOR {filename}", file) print(g) # send the file file.close() # close file and FTP - g2 = session.quit() - print(g2) except BaseException as err: + print(f"ERROR: {err}") - print( - "ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000." - ) + # print("ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000.") + g2 = session.quit() + # print(g2) # l = ftp_connect(self) # print(l) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index a03fd140..3a54cac6 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -197,6 +197,9 @@ def additional_formating(self, mapped_json_data): mapped_json_data[idx]["study_abstract"] = self.json_data[idx][ "study_title" ] + mapped_json_data[idx]["sample_description"] = self.json_data[idx][ + "sequence_file_R1_fastq" + ] return mapped_json_data diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index aca6249e..24407f52 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -745,44 +745,44 @@ ] }, "sequence_file_R1_fastq": { - "examples": [ - "ABC123_S1_L001_R1_001.fastq.gz" - ], - "ontology": "GENEPIO:0001476", - "type": "string", - "description": "The user-specified filename of the r1 FASTQ file.", - "clasification": "Bioinformatics and QC metrics", - "label": "Sequence file R1 fastq" + "examples": [ + "ABC123_S1_L001_R1_001.fastq.gz" + ], + "ontology": "GENEPIO:0001476", + "type": "string", + "description": "The user-specified filename of the r1 FASTQ file.", + "clasification": "Bioinformatics and QC metrics", + "label": "Sequence file R1 fastq" }, "sequence_file_R2_fastq": { - "examples": [ - "ABC123_S1_L001_R2_001.fastq.gz" - ], - "ontology": "GENEPIO:0001477", - "type": "string", - "description": "The user-specified filename of the r2 FASTQ file.", - "clasification": "Bioinformatics and QC metrics", - "label": "Sequence file R2 fastq" + "examples": [ + "ABC123_S1_L001_R2_001.fastq.gz" + ], + "ontology": "GENEPIO:0001477", + "type": "string", + "description": "The user-specified filename of the r2 FASTQ file.", + "clasification": "Bioinformatics and QC metrics", + "label": "Sequence file R2 fastq" }, "r1_fastq_filepath": { - "examples": [ - "/User/Documents/RespLab/Data/" - ], - "ontology": "GENEPIO:0001478", - "type": "string", - "description": "The filepath of the r1 FASTQ file.", - "clasification": "Bioinformatics and QC metrics", - "label": "Filepath R1 fastq" + "examples": [ + "/User/Documents/RespLab/Data/" + ], + "ontology": "GENEPIO:0001478", + "type": "string", + "description": "The filepath of the r1 FASTQ file.", + "clasification": "Bioinformatics and QC metrics", + "label": "Filepath R1 fastq" }, "r2_fastq_filepath": { - "examples": [ - "/User/Documents/RespLab/Data/" - ], - "ontology": "GENEPIO:0001479", - "type": "string", - "description": "The filepath of the r2 FASTQ file.", - "clasification": "Bioinformatics and QC metrics", - "label": "Filepath R2 fastq" + "examples": [ + "/User/Documents/RespLab/Data/" + ], + "ontology": "GENEPIO:0001479", + "type": "string", + "description": "The filepath of the r2 FASTQ file.", + "clasification": "Bioinformatics and QC metrics", + "label": "Filepath R2 fastq" }, "file_type": { "examples": [ @@ -1495,4 +1495,4 @@ "label": "First created date" } } -} +} \ No newline at end of file From 0f4b9ae6c51e8f7d0d5a8d00ecbc4ae518ac5f02 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 14 Jun 2022 13:38:45 +0200 Subject: [PATCH 0536/1454] update with new changes in selecting opitons --- relecov_tools/feed_database.py | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/relecov_tools/feed_database.py b/relecov_tools/feed_database.py index e49fef0e..fcce8bdf 100644 --- a/relecov_tools/feed_database.py +++ b/relecov_tools/feed_database.py @@ -75,7 +75,7 @@ def __init__( if type_of_info is None: type_of_info = relecov_tools.utils.prompt_selection( "Select:", - ["sample", "analysis"], + ["sample", "analysis", "longtable"], ) self.type_of_info = type_of_info @@ -211,13 +211,13 @@ def map_relecov_sample_data(self): field_values.append(s_dict) return field_values - def update_database(self, field_values): + def update_database(self, field_values, post_url): """Send the request to update database""" for chunk in field_values: result = self.database_rest_api.post_request( json.dumps(chunk), {"user": self.user, "pass": self.passwd}, - self.database_settings["store_samples"], + self.database_settings[post_url], ) if "ERROR" in result: if result["ERROR"] == "Server not available": @@ -228,7 +228,7 @@ def update_database(self, field_values): result = self.iskylims_rest_api.post_request( json.dumps(chunk), {"user": self.user, "pass": self.passwd}, - self.iskylims_settings["store_samples"], + self.iskylims_settings[post_url], ) if "ERROR" not in result: break @@ -265,6 +265,12 @@ def store_data(self): ) else: map_fields = self.map_relecov_sample_data() + post_url = "store_samples" + elif self.type_of_info == "analysis": + post_url = "analysis" + elif self.type_of_info == "longtable": + post_url = "long_table" else: - pass - self.update_database(map_fields) + stderr.print("[red] Invalid type to upload to database") + sys.exit(1) + self.update_database(map_fields, post_url) From 1aedac8311f6cd58e439d63c7ee9d69808d2733c Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 14 Jun 2022 13:45:08 +0200 Subject: [PATCH 0537/1454] added url for analysis and longtable --- relecov_tools/conf/configuration.json | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index 541b3a8c..b81afa14 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -45,6 +45,8 @@ "server": "http://relecov-platform.isciiides.es", "url": "/api/", "store_samples": "createSampleData", + "analysis": "bioinfoData", + "long_table": "longtableData", "token": "" } }, @@ -136,4 +138,4 @@ "CALLER", "LINEAGE" ] -} \ No newline at end of file +} From 27fb7be5167c9628a3171502985bf968c6980673 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 14 Jun 2022 14:18:11 +0200 Subject: [PATCH 0538/1454] changes in read lab metadata --- relecov_tools/ena_upload.py | 7 +++++-- relecov_tools/read_lab_metadata.py | 2 +- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 36363d1c..ac08e1c7 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -201,7 +201,9 @@ def create_structure_to_ena(self): ] df_experiments.insert(3, "status", self.action) df_experiments.insert(4, "alias", df_experiments["experiment_alias"]) - + df_experiments.insert(5, "design_description", "") + df_experiments.insert(5, "insert_size", 150) + df_experiments.insert(5, "platform", "ILLUMINA") df_experiments = df_experiments.rename(columns={"study_title": "title"}) df_experiments = df_experiments.rename(columns={"sample_name": "sample_alias"}) @@ -223,7 +225,7 @@ def create_structure_to_ena(self): # submit data to webin ftp server # def ftp_connect(self): - + """ session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) for filename, path in file_paths.items(): @@ -240,6 +242,7 @@ def create_structure_to_ena(self): # print("ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000.") g2 = session.quit() + """ # print(g2) # l = ftp_connect(self) # print(l) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index dece7455..d8029c34 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -115,7 +115,7 @@ def include_fixed_data(self): "type": "betacoronavirus", "tax_id": "2697049", "organism": "Severe acute respiratory syndrome coronavirus 2", - "common_name": "PEPITO", + "common_name": "Severe acute respiratory syndrome", "sample_description": "Sample for surveillance", } fixed_data.update(self.configuration.get_configuration("ENA_configuration")) From 189196ce8f191d51edbde5c807f4e68c8b3407b1 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Tue, 14 Jun 2022 14:21:32 +0200 Subject: [PATCH 0539/1454] changes in ena upload --- relecov_tools/ena_upload.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index ac08e1c7..e75b71d1 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,5 +1,6 @@ import logging -from pyparsing import col + +# from pyparsing import col import rich.console import json @@ -7,7 +8,8 @@ import pandas as pd import sys import os -import ftplib + +# import ftplib import relecov_tools.utils from relecov_tools.config_json import ConfigJson From 7faaf493ec4eb34f28ea1e4992597d89cd04ae6a Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 14 Jun 2022 21:10:34 +0200 Subject: [PATCH 0540/1454] replace empty values for experiment_alias and run_alias by the first fastq sequence --- relecov_tools/conf/configuration.json | 2 -- relecov_tools/read_lab_metadata.py | 23 +++++++++++++++++++++-- 2 files changed, 21 insertions(+), 4 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index b81afa14..c8c4e0cf 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -20,8 +20,6 @@ "ENA_configuration": { "study_alias": "RELECOV", "design_description": "Design Description", - "experiment_alias": "", - "run_alias": "", "experiment_title": "Example project for ENA submission RELECOV", "study_title": "RELECOV Spanish Network for genomics surveillance", "study_type": "", diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index d8029c34..0967285b 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -8,6 +8,7 @@ import openpyxl import os import sys +import re import relecov_tools.utils from relecov_tools.config_json import ConfigJson import relecov_tools.json_schema @@ -82,6 +83,16 @@ def read_json_file(self, j_file): data = json.load(fh) return data + def get_experiment_run_alias(self, row_data): + exp_alias = "NOT_FOUND" + run_alias = "NOT_FOUND.fastq.gz" + if "fastq_r1" in row_data: + match = re.search(r"(.+)_R1_.*", row_data["fastq_r1"]) + if match: + exp_alias = match.group(1) + run_alias = match.group(1) + ".fastq.gz" + return exp_alias, run_alias + def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): """Fetch the laboratory location and return a dictionary""" data = {} @@ -159,8 +170,12 @@ def include_processed_data(self, metadata): if metadata["sequencing_instrument_model"] in values: new_data["sequencing_instrument_platform"] = key break - return new_data + return new_data + """ + "experiment_alias": "", + "run_alias": "", + """ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): """Add the additional information that must be included in final metadata metadata Origin metadata @@ -173,7 +188,7 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): lab_json = self.read_json_file(lab_json_file) geo_loc_json = self.read_json_file(geo_loc_file) samples_json = self.read_json_file(self.sample_list_file) - + exp_alias, run_alias = self.get_experiment_run_alias(metadata[0]) for row_sample in metadata: """Include sample data from sample json""" try: @@ -218,7 +233,11 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): ] row["sequencing_instrument_platform"] = "To change" """ + # Add experiment_alias and run_alias + row_sample["experiment_alias"] = exp_alias + row_sample["run_alias"] = run_alias additional_metadata.append(row_sample) + return additional_metadata def request_information(external_url, request): From 8940aa428a8b3154233291427be706191bbd437a Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 14 Jun 2022 21:13:49 +0200 Subject: [PATCH 0541/1454] code included in behalf of Erika --- relecov_tools/map_schema.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 3a54cac6..a92c4fb1 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -200,6 +200,9 @@ def additional_formating(self, mapped_json_data): mapped_json_data[idx]["sample_description"] = self.json_data[idx][ "sequence_file_R1_fastq" ] + mapped_json_data[idx][ + "sequencing_instrument_platform" + ] = self.json_data[idx]["sequencing_instrument_platform"] return mapped_json_data From d8ac9141063f4ecdd74583e5ec16630bd9c88e66 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 14 Jun 2022 21:15:22 +0200 Subject: [PATCH 0542/1454] litin --- relecov_tools/read_lab_metadata.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 0967285b..73fd4707 100644 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -172,10 +172,7 @@ def include_processed_data(self, metadata): break return new_data - """ - "experiment_alias": "", - "run_alias": "", - """ + def add_additional_data(self, metadata, lab_json_file, geo_loc_file): """Add the additional information that must be included in final metadata metadata Origin metadata From 35b418e2443fef299faf0d2b6408f2625c19840f Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 15 Jun 2022 11:08:21 +0200 Subject: [PATCH 0543/1454] latest change in ena upload --- relecov_tools/ena_upload.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index e75b71d1..ff040dd7 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -204,7 +204,7 @@ def create_structure_to_ena(self): df_experiments.insert(3, "status", self.action) df_experiments.insert(4, "alias", df_experiments["experiment_alias"]) df_experiments.insert(5, "design_description", "") - df_experiments.insert(5, "insert_size", 150) + df_experiments.insert(5, "insert_size", 0) df_experiments.insert(5, "platform", "ILLUMINA") df_experiments = df_experiments.rename(columns={"study_title": "title"}) df_experiments = df_experiments.rename(columns={"sample_name": "sample_alias"}) From 0723d9463c4297fe4063db2b7e0c9881a992ab1f Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 15 Jun 2022 15:35:37 +0200 Subject: [PATCH 0544/1454] latest cahgnes in upload --- relecov_tools/ena_upload.py | 37 +++++++++++++++++++++++++------------ 1 file changed, 25 insertions(+), 12 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index ff040dd7..a0f4ffd9 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,15 +1,15 @@ import logging -# from pyparsing import col +from pyparsing import col import rich.console import json -# import paramiko + import pandas as pd import sys import os -# import ftplib +import ftplib import relecov_tools.utils from relecov_tools.config_json import ConfigJson @@ -176,12 +176,18 @@ def create_structure_to_ena(self): "fastq_r2_md5", ] ] - df_run.insert( - 1, "sequence_file_R1_fastq", df_schemas["r1_fastq_filepath"][0][31:57] - ) - df_run.insert( - 2, "sequence_file_R2_fastq", df_schemas["r2_fastq_filepath"][0][31:57] - ) + + df_run.insert(1, "sequence_file_R1_fastq", "None") + df_run.insert(2, "sequence_file_R2_fastq", "None") + for i in range(len(df_schemas)): + df_run.loc[i, "sequence_file_R1_fastq"] = df_schemas.loc[ + i, "sequence_file_R1_fastq" + ] + + df_run.loc[i, "sequence_file_R2_fastq"] = df_schemas.loc[ + i, "sequence_file_R2_fastq" + ] + df_run.insert(3, "status", self.action) df_run = df_run.rename(columns={"fastq_r1_md5": "file_checksum"}) df_run.insert(4, "alias", df_run["experiment_alias"]) @@ -201,8 +207,15 @@ def create_structure_to_ena(self): "instrument_model", ] ] + df_experiments.insert(3, "status", self.action) - df_experiments.insert(4, "alias", df_experiments["experiment_alias"]) + + for i in range(len(df_experiments)): + df_experiments.loc[i, "alias"] = ( + str(df_run.loc[i, "sequence_file_R1_fastq"]) + + "_" + + str(df_run.loc[i, "sequence_file_R2_fastq"]) + ) df_experiments.insert(5, "design_description", "") df_experiments.insert(5, "insert_size", 0) df_experiments.insert(5, "platform", "ILLUMINA") @@ -227,7 +240,7 @@ def create_structure_to_ena(self): # submit data to webin ftp server # def ftp_connect(self): - """ + session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) for filename, path in file_paths.items(): @@ -244,7 +257,7 @@ def create_structure_to_ena(self): # print("ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000.") g2 = session.quit() - """ + # print(g2) # l = ftp_connect(self) # print(l) From 1625b11dc8fd51d47b6ab398e6993e9147a7c233 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 15 Jun 2022 16:51:16 +0200 Subject: [PATCH 0545/1454] last modifications ena upload --- relecov_tools/ena_upload.py | 61 ++++++++++++++++++++++++++++--------- 1 file changed, 46 insertions(+), 15 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index a0f4ffd9..e6b9b62c 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -109,13 +109,20 @@ def convert_input_json_to_ena(self): def create_structure_to_ena(self): """Convert json to dataframe required by ena-upload-cli package""" - esquema = self.source_json_file - fh_esquema = open(esquema) - esquema_json = json.load(fh_esquema) - fh_esquema.close() + squema = self.source_json_file + fh_squema = open(squema) + squema_json = json.load(fh_squema) + fh_squema.close() - df_schemas = pd.DataFrame(esquema_json) + df_schemas = pd.DataFrame(squema_json) + # df_schema + """ + collecting_institution collection_date collector_name ... study_title study_type taxon_id +0 Hospital Clínic de Barcelona 2021-05-10 Inmaculada Casas ... RELECOV Spanish Network for genomics surveillance Surveillance 2697049 +1 Hospital Clínic de Barcelona 2021-05-07 Inmaculada Casas ... RELECOV Spanish Network for genomics surveillance Surveillance 2697049 + + """ df_study = df_schemas[ ["study_alias", "study_title", "study_type", "study_abstract"] ] @@ -123,6 +130,13 @@ def create_structure_to_ena(self): df_study = df_study.rename(columns={"study_alias": "alias"}) df_study = df_study.rename(columns={"study_title": "title"}) df_study.insert(3, "status", self.action) + + # df_study + """ + alias title study_type status study_abstract +0 RELECOV RELECOV Spanish Network for genomics surveillance Surveillance ADD RELECOV Spanish Network for genomics surveillance +1 RELECOV RELECOV Spanish Network for genomics surveillance Surveillance ADD RELECOV Spanish Network for genomics surveillance + """ df_samples = df_schemas[ [ "sample_name", @@ -166,6 +180,14 @@ def create_structure_to_ena(self): df_samples.insert(4, "ENA_CHECKLIST", checklist) df_samples.insert(5, "sample_description", "") + # df_samples + """ + alias title taxon_id host health state ... scientific_name collector name collecting institution isolate +0 212164375 212164375 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212164375 +1 212163777 212163777 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212163777 +2 212153091 212153091 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212153091 + """ + df_run = df_schemas[ [ "experiment_alias", @@ -193,6 +215,14 @@ def create_structure_to_ena(self): df_run.insert(4, "alias", df_run["experiment_alias"]) df_run.insert(5, "file_name", df_run["sequence_file_R1_fastq"]) + # df_run + """ + experiment_alias sequence_file_R1_fastq sequence_file_R2_fastq ... file_type file_checksum fastq_r2_md5 +0 214821_S12 214821_S12_R1_001.fastq.gz 214821_S12_R2_001.fastq.gz ... fastq 372ca8b10a8eeb7a04107634baf340ab 7f5081eec1b64b171402b66f37fe640d +1 214821_S12 214822_S13_R1_001.fastq.gz 214822_S13_R2_001.fastq.gz ... fastq b268d7be80e80455bec0807b5961d23c a15be39feaf73eec9b2c026717878bba +2 214821_S12 214823_S1_R1_001.fastq.gz 214823_S1_R2_001.fastq.gz ... fastq c16bdbfc03c354496fcfb2c107e3cbf6 4d9b80b977a75bf7e2a4282ca910d94a + + """ df_experiments = df_schemas[ [ "experiment_alias", @@ -222,6 +252,14 @@ def create_structure_to_ena(self): df_experiments = df_experiments.rename(columns={"study_title": "title"}) df_experiments = df_experiments.rename(columns={"sample_name": "sample_alias"}) + # df_experiments example + """ + experiment_alias title study_alias ... library_layout instrument_model alias +0 214821_S12 RELECOV Spanish Network for genomics surveillance RELECOV ... PAIRED Illumina MiSeq 214821_S12_R1_001.fastq.gz_214821_S12_R2_001.f... +1 214821_S12 RELECOV Spanish Network for genomics surveillance RELECOV ... PAIRED Illumina MiSeq 214822_S13_R1_001.fastq.gz_214822_S13_R2_001.f... +2 214821_S12 RELECOV Spanish Network for genomics surveillance RELECOV ... PAIRED Illumina MiSeq 214823_S1_R1_001.fastq.gz_214823_S1_R2_001.fas... + + """ ena_config = config_json.get_configuration("ENA_configuration") schema_dataframe = {} schema_dataframe["sample"] = df_samples @@ -239,8 +277,7 @@ def create_structure_to_ena(self): file_paths[os.path.basename(path)] = os.path.abspath(path) # submit data to webin ftp server - # def ftp_connect(self): - + """ session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) for filename, path in file_paths.items(): @@ -257,11 +294,8 @@ def create_structure_to_ena(self): # print("ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000.") g2 = session.quit() - - # print(g2) - # l = ftp_connect(self) - # print(l) - + """ + # THE ENA_UPLOAD_CLI METHOD DOES NOT WORK (below) # chec = submit_data(file_paths, self.passwd, self.user) # print(chec) @@ -303,9 +337,6 @@ def create_structure_to_ena(self): schema_dataframe, schema_targets, schema_update ) - # save updates in new tables - # save_update(schema_tables, schema_dataframe) - def upload(self): """Create the required files and upload to ENA""" self.convert_input_json_to_ena() From 45f7c9c37992e6f2ca9611e35dfbeab36c0b91c9 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 15 Jun 2022 16:53:48 +0200 Subject: [PATCH 0546/1454] lintin --- relecov_tools/ena_upload.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index e6b9b62c..e98b9ce0 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -1,6 +1,6 @@ import logging -from pyparsing import col +# from pyparsing import col import rich.console import json @@ -277,7 +277,7 @@ def create_structure_to_ena(self): file_paths[os.path.basename(path)] = os.path.abspath(path) # submit data to webin ftp server - """ + session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) for filename, path in file_paths.items(): @@ -294,7 +294,7 @@ def create_structure_to_ena(self): # print("ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000.") g2 = session.quit() - """ + # THE ENA_UPLOAD_CLI METHOD DOES NOT WORK (below) # chec = submit_data(file_paths, self.passwd, self.user) # print(chec) From 6225ee518ae26276bd87c59e1fb87978330f24d7 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 15 Jun 2022 16:54:57 +0200 Subject: [PATCH 0547/1454] lintin2 --- relecov_tools/ena_upload.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index e98b9ce0..7fdd69d5 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -294,6 +294,7 @@ def create_structure_to_ena(self): # print("ERROR: If your connection times out at this stage, it propably is because of a firewall that is in place. FTP is used in passive mode and connection will be opened to one of the ports: 40000 and 50000.") g2 = session.quit() + print(g2) # THE ENA_UPLOAD_CLI METHOD DOES NOT WORK (below) # chec = submit_data(file_paths, self.passwd, self.user) From 992b73ea3fbe53a249379a4225961ab1ffdf84db Mon Sep 17 00:00:00 2001 From: luisiJavo Date: Fri, 17 Jun 2022 12:54:20 +0200 Subject: [PATCH 0548/1454] modified relecov_schema.json --- relecov_tools/__main__.py | 2 +- relecov_tools/read_bioinfo_metadata.py | 3 +++ relecov_tools/schema/relecov_schema.json | 8 ++++---- 3 files changed, 8 insertions(+), 5 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index d7364aa5..3f4656b2 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -323,7 +323,7 @@ def read_bioinfo_metadata(metadata_file, input_folder, metadata_out): metadata_file, input_folder, metadata_out ) - new_bioinfo_metadata.bioinfo_parse() + new_bioinfo_metadata.bioinfo_parse(metadata_file) # read metadata bioinformatics diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 2af45670..8419d5eb 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -18,6 +18,7 @@ from relecov_tools.config_json import ConfigJson import relecov_tools.json_schema + log = logging.getLogger(__name__) stderr = rich.console.Console( stderr=True, @@ -122,11 +123,13 @@ def bioinfo_parse(self, file_name): bioinfo_dict["sample_name"] = str(sample_name) bioinfo_dict["fastq_r1"] = fastq_r1 bioinfo_dict["fastq_r2"] = fastq_r2 + # inserting all keys from configuration.json relecov_bioinfo_metadata into bioinfo_dict for key in relecov_bioinfo_metadata.keys(): bioinfo_dict[key] = relecov_bioinfo_metadata[key] bioinfo_dict["consensus_sequence_filepath"] = self.input_folder bioinfo_dict["long_table_path"] = self.input_folder + # fields from mapping_illumina.tab for key in self.mapping_illumina_tab_field_list.keys(): diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 47aa600d..586a9f5c 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1427,7 +1427,7 @@ "ontology": "0", "type": "string", "description": "", - "classification": "Files info", + "classification": "Bioinformatics and QC metrics fields", "label": "Sample Name", "fill_mode": "batch" }, @@ -1449,7 +1449,7 @@ "ontology": "GENEPIO:0001476", "type": "string", "description": "The user-specified filename of the r1 FASTQ file.", - "classification": "Files info", + "classification": "Bioinformatics and QC metrics fields", "label": "Sequence file R1 fastq", "fill_mode": "sample" }, @@ -1460,7 +1460,7 @@ "ontology": "GENEPIO:0001477", "type": "string", "description": "The user-specified filename of the r2 FASTQ file.", - "classification": "Files info", + "classification": "Bioinformatics and QC metrics fields", "label": "Sequence file R2 fastq", "fill_mode": "sample" }, @@ -1802,7 +1802,7 @@ "examples": [ "E gene (orf4) [GENEPIO:0100151]" ], - "classification": "Bioinformatics and QC metrics fields", + "classification": "Pathogen diagnostic testing", "label": "Gene Name 1", "fill_mode": "batch" }, From 5bd2fc9603b6d95338bd9550a76c14be499941d7 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Fri, 17 Jun 2022 14:24:00 +0200 Subject: [PATCH 0549/1454] changes in ena upload that made it work --- relecov_tools/ena_upload.py | 34 +++++++++++++++++++++++++++------- 1 file changed, 27 insertions(+), 7 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 7fdd69d5..505f5f79 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -130,7 +130,6 @@ def create_structure_to_ena(self): df_study = df_study.rename(columns={"study_alias": "alias"}) df_study = df_study.rename(columns={"study_title": "title"}) df_study.insert(3, "status", self.action) - # df_study """ alias title study_type status study_abstract @@ -179,7 +178,6 @@ def create_structure_to_ena(self): checklist = config_json.get_configuration("checklist") df_samples.insert(4, "ENA_CHECKLIST", checklist) df_samples.insert(5, "sample_description", "") - # df_samples """ alias title taxon_id host health state ... scientific_name collector name collecting institution isolate @@ -187,7 +185,6 @@ def create_structure_to_ena(self): 1 212163777 212163777 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212163777 2 212153091 212153091 2697049 ... Severe acute respiratory syndrome coronavirus 2 Inmaculada Casas Hospital Clínic de Barcelona 212153091 """ - df_run = df_schemas[ [ "experiment_alias", @@ -212,8 +209,24 @@ def create_structure_to_ena(self): df_run.insert(3, "status", self.action) df_run = df_run.rename(columns={"fastq_r1_md5": "file_checksum"}) - df_run.insert(4, "alias", df_run["experiment_alias"]) + + for i in range(len(df_run)): + df_run.loc[i, "alias"] = ( + str(df_run.loc[i, "sequence_file_R1_fastq"]) + + "_" + + str(df_run.loc[i, "sequence_file_R2_fastq"]) + ) + df_run.loc[i, "experiment_alias"] = ( + str(df_run.loc[i, "sequence_file_R1_fastq"]) + + "_" + + str(df_run.loc[i, "sequence_file_R2_fastq"]) + ) + df_run.insert(5, "file_name", df_run["sequence_file_R1_fastq"]) + df_run2 = df_run.copy() + df_run2["file_name"] = df_run["sequence_file_R2_fastq"] + df_run_final = pd.concat([df_run, df_run2]) + df_run_final.reset_index() # df_run """ @@ -223,6 +236,7 @@ def create_structure_to_ena(self): 2 214821_S12 214823_S1_R1_001.fastq.gz 214823_S1_R2_001.fastq.gz ... fastq c16bdbfc03c354496fcfb2c107e3cbf6 4d9b80b977a75bf7e2a4282ca910d94a """ + df_experiments = df_schemas[ [ "experiment_alias", @@ -263,7 +277,7 @@ def create_structure_to_ena(self): ena_config = config_json.get_configuration("ENA_configuration") schema_dataframe = {} schema_dataframe["sample"] = df_samples - schema_dataframe["run"] = df_run + schema_dataframe["run"] = df_run_final schema_dataframe["experiment"] = df_experiments schema_targets = extract_targets(self.action, schema_dataframe) @@ -272,13 +286,19 @@ def create_structure_to_ena(self): if self.action == "ADD" or self.action == "add": file_paths = {} + file_paths_r2 = {} - for path in df_run["r1_fastq_filepath"]: + for path in df_schemas["r1_fastq_filepath"]: file_paths[os.path.basename(path)] = os.path.abspath(path) - # submit data to webin ftp server + for path in df_schemas["r2_fastq_filepath"]: + file_paths_r2[os.path.basename(path)] = os.path.abspath(path) + + file_paths.update(file_paths_r2) + # submit data to webin ftp server session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) + for filename, path in file_paths.items(): print("Uploading path " + path + " and filename: " + filename) From b8523ff876e07597e6fc5019b46bd1948a9ddf8c Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 20 Jun 2022 11:31:01 +0200 Subject: [PATCH 0550/1454] changes in schema --- relecov_tools/conf/configuration.json | 6 +++--- relecov_tools/read_bioinfo_metadata.py | 10 ++++++++++ relecov_tools/schema/relecov_schema.json | 13 +------------ 3 files changed, 14 insertions(+), 15 deletions(-) diff --git a/relecov_tools/conf/configuration.json b/relecov_tools/conf/configuration.json index c8c4e0cf..2d7e5741 100644 --- a/relecov_tools/conf/configuration.json +++ b/relecov_tools/conf/configuration.json @@ -95,12 +95,12 @@ "mapping_illumina_tab_field_list": { "lineage_name": "Lineage", "variant_designation": "Variantsinconsensusx10", - "per_qc_filtered": "Coverage>10x(%)", + "per_genome_greater_10x": "Coverage>10x(%)", "per_reads_host": "%readshost", "per_reads_virus": "%readsvirus", "per_unmapped": "%unmapedreads", "per_Ns": "%Ns10x", - "median_depth_of_coverage_value": "medianDPcoveragevirus", + "depth_of_coverage_value": "medianDPcoveragevirus", "number_of_variants_AF_greater_75percent": "Variantsinconsensusx10", "number_of_variants_with_effect": "MissenseVariants" }, @@ -136,4 +136,4 @@ "CALLER", "LINEAGE" ] -} +} \ No newline at end of file diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 2af45670..7a19eaeb 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -3,6 +3,8 @@ import logging import json +import datetime +import os import rich.console @@ -142,6 +144,10 @@ def bioinfo_parse(self, file_name): bioinfo_dict["ns_per_100_kbp"] = str( summary_variants_metrics["# Ns per 100kb consensus"][c] ) + bioinfo_dict["qc_filtered"] = str( + summary_variants_metrics["# Trimmed reads (fastp)"][c] + ) + # fields from variants_long_table.csv bioinfo_dict["reference_genome_accession"] = str( variants_long_table["CHROM"][c] @@ -187,6 +193,10 @@ def bioinfo_parse(self, file_name): pangolin_version_software.iloc[c] ) + c_time = os.path.getctime(variants_long_table_path) + dt_c = datetime.datetime.fromtimestamp(c_time) + bioinfo_dict["analysis_date"] = str(dt_c) + bioinfo_list[str(sample_name)] = bioinfo_dict c = c + 1 diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 47aa600d..cfc25b86 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -1398,17 +1398,6 @@ "label": "Consensus Params", "fill_mode": "batch" }, - "quality_control_metrics": { - "examples": [ - "" - ], - "ontology": "data_3914", - "type": "string", - "description": "", - "classification": "Bioinformatics and QC metrics fields", - "label": "Quality control metrics ", - "fill_mode": "batch" - }, "depth_of_coverage_value": { "examples": [ "400x" @@ -1806,7 +1795,7 @@ "label": "Gene Name 1", "fill_mode": "batch" }, - "per_qc_filtered": { + "qc_filtered": { "examples": [ "" ], From 20bb1ff5bff2bdf7a95e7b2e2bde06d44b84f353 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 20 Jun 2022 16:58:16 +0200 Subject: [PATCH 0551/1454] latest changes to upload to ena + 01 --- relecov_tools/__main__.py | 5 +++-- relecov_tools/ena_upload.py | 4 +++- relecov_tools/read_bioinfo_metadata.py | 8 ++++++++ 3 files changed, 14 insertions(+), 3 deletions(-) diff --git a/relecov_tools/__main__.py b/relecov_tools/__main__.py index d7364aa5..59171f9c 100644 --- a/relecov_tools/__main__.py +++ b/relecov_tools/__main__.py @@ -241,10 +241,11 @@ def map(origin_schema, json_data, destination_schema, schema_file, output): type=click.Choice(["add", "modify", "cancel", "release"], case_sensitive=False), help="select one of the available options", ) -@click.option("--dev/--production", default=True) +@click.option("--dev", is_flag=True, default=False) @click.option("-o", "--output_path", help="output folder for the xml generated files") def upload_to_ena(user, password, center, ena_json, dev, study, action, output_path): """parsed data to create xml files to upload to ena""" + upload_ena = relecov_tools.ena_upload.EnaUpload( user, password, center, ena_json, dev, study, action, output_path ) @@ -323,7 +324,7 @@ def read_bioinfo_metadata(metadata_file, input_folder, metadata_out): metadata_file, input_folder, metadata_out ) - new_bioinfo_metadata.bioinfo_parse() + new_bioinfo_metadata.bioinfo_parse(metadata_file) # read metadata bioinformatics diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 505f5f79..181dba0a 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -77,6 +77,7 @@ def __init__( ) else: self.dev = dev + if customized_project is None: self.customized_project = None else: @@ -153,7 +154,7 @@ def create_structure_to_ena(self): ] ] - df_samples = df_samples.rename(columns={"sample_name": "alias"}) + df_samples = df_samples.rename(columns={"sample_name": "01" + "alias"}) df_samples = df_samples.rename(columns={"sample_title": "title"}) df_samples = df_samples.rename( columns={ @@ -297,6 +298,7 @@ def create_structure_to_ena(self): file_paths.update(file_paths_r2) # submit data to webin ftp server + session = ftplib.FTP("webin2.ebi.ac.uk", self.user, self.passwd) for filename, path in file_paths.items(): diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 7a19eaeb..44476b85 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -196,7 +196,15 @@ def bioinfo_parse(self, file_name): c_time = os.path.getctime(variants_long_table_path) dt_c = datetime.datetime.fromtimestamp(c_time) bioinfo_dict["analysis_date"] = str(dt_c) + bioinfo_dict["lineage_identification_date"] = str(dt_c) + """ + IDEA + pango_time = os.path.getctime( + self.input_folder + "/" + str(sample_name) + ".pangolin.csv" + ) + dt_pango = datetime.datetime.fromtimestamp(pango_time) + """ bioinfo_list[str(sample_name)] = bioinfo_dict c = c + 1 From 261264319ce974440a948fe7689f2d1dba151ce0 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 20 Jun 2022 17:08:29 +0200 Subject: [PATCH 0552/1454] latest changes to upload to ena - 01 --- relecov_tools/ena_upload.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 181dba0a..0ffd86b1 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -154,7 +154,7 @@ def create_structure_to_ena(self): ] ] - df_samples = df_samples.rename(columns={"sample_name": "01" + "alias"}) + df_samples = df_samples.rename(columns={"sample_name": "alias"}) df_samples = df_samples.rename(columns={"sample_title": "title"}) df_samples = df_samples.rename( columns={ From 53dd78199039f849affe55ca55bfc3d63ef6dfd8 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 22 Jun 2022 10:27:47 +0200 Subject: [PATCH 0553/1454] lintin --- relecov_tools/read_bioinfo_metadata.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py index 44476b85..a12702e1 100644 --- a/relecov_tools/read_bioinfo_metadata.py +++ b/relecov_tools/read_bioinfo_metadata.py @@ -4,7 +4,8 @@ import logging import json import datetime -import os + +# import os import rich.console @@ -199,7 +200,7 @@ def bioinfo_parse(self, file_name): bioinfo_dict["lineage_identification_date"] = str(dt_c) """ - IDEA + IDEA pango_time = os.path.getctime( self.input_folder + "/" + str(sample_name) + ".pangolin.csv" ) From 34b9d2f4cf92faed650b0950daca92a398cec83a Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Mon, 27 Jun 2022 14:06:36 +0200 Subject: [PATCH 0554/1454] corrected different md5 generation --- relecov_tools/utils.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/relecov_tools/utils.py b/relecov_tools/utils.py index e6fd447b..76344bbd 100644 --- a/relecov_tools/utils.py +++ b/relecov_tools/utils.py @@ -53,8 +53,7 @@ def get_md5_from_local_folder(local_folder): def calculate_md5(file_name): """Calculate the md5 value for the file name""" - block_size = 2**20 - return hashlib.md5(open(file_name, "rb").read(block_size)).hexdigest() + return hashlib.md5(open(file_name, "rb").read()).hexdigest() def write_md5_file(file_name, md5_value): From e3c3717a6cf37601d7b9bf774d70e0479a2b8f99 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 29 Jun 2022 11:52:32 +0200 Subject: [PATCH 0555/1454] create new module: metadata homogeneizer --- relecov_tools/metadata_homogeneizer.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 relecov_tools/metadata_homogeneizer.py diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py new file mode 100644 index 00000000..e69de29b From 32408abf4e1748310b0cd8a3d8907f6b04c1cf50 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 29 Jun 2022 11:59:59 +0200 Subject: [PATCH 0556/1454] testing update --- relecov_tools/metadata_homogeneizer.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index e69de29b..4265cc3e 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -0,0 +1 @@ +#!/usr/bin/env python From ddef259ab496d508fe5e6eeb809693bf7c9e5a4a Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 29 Jun 2022 12:05:49 +0200 Subject: [PATCH 0557/1454] update to testing --- relecov_tools/metadata_homogeneizer.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 4265cc3e..cda98065 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -1 +1,7 @@ #!/usr/bin/env python + +# Imports +import pandas as pd + +# Homogeneizer object + From b61aec1b2a5a9cd24c3bf0e577d7f6c94b97f16f Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 29 Jun 2022 12:24:26 +0200 Subject: [PATCH 0558/1454] first serious commit --- relecov_tools/metadata_homogeneizer.py | 41 ++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index cda98065..c5ee640d 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -1,7 +1,48 @@ #!/usr/bin/env python # Imports +import json import pandas as pd # Homogeneizer object +class Homogeneizer: + def __init__(filename, self): + self.filename = filename + self.centre = None + self.dataframe = None + self.translated_dataframe = None + pass + return + + def detect_centre(self): + """Detect the origin centre of the metadata""" + # Check name of the file attribute of the object + # Check schema with all centres and find their json + # associate centre and json with object + pass + return + + def load_dataframe(self): + """Read the metadata file""" + # check possible extensions + # load with pandas + + pass + return + + def load_dictionary(self): + """Load the corresponding dictionary""" + pass + return + + def translate_dataframe(self): + """Use the corresponding dictionary to translate the df""" + pass + return + + def verify_translated_dataframe(self): + """Checks if the dataframe holds all the needed values for the relecov tools suite""" + + pass + return \ No newline at end of file From 7897a7fae2237196e91942ebefcf942539130795 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 29 Jun 2022 12:37:54 +0200 Subject: [PATCH 0559/1454] updated --- relecov_tools/metadata_homogeneizer.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index c5ee640d..51365d53 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -20,6 +20,8 @@ def detect_centre(self): # Check name of the file attribute of the object # Check schema with all centres and find their json # associate centre and json with object + # raise error when in doubt + # must check on schema/institution_schemas pass return @@ -27,7 +29,6 @@ def load_dataframe(self): """Read the metadata file""" # check possible extensions # load with pandas - pass return From 8ebdcb1049b74b25cd61f085d3bdaba9cfaf1530 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 29 Jun 2022 12:38:26 +0200 Subject: [PATCH 0560/1454] json for institution --- relecov_tools/schema/institution_to_schema.json | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 relecov_tools/schema/institution_to_schema.json diff --git a/relecov_tools/schema/institution_to_schema.json b/relecov_tools/schema/institution_to_schema.json new file mode 100644 index 00000000..39a5590a --- /dev/null +++ b/relecov_tools/schema/institution_to_schema.json @@ -0,0 +1,4 @@ +{ + "ITER" : "1.json", + "0001" : "1.json" +} \ No newline at end of file From 8afe9b8eefdafccea26907a0d7daf63d3048d68b Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 29 Jun 2022 12:38:37 +0200 Subject: [PATCH 0561/1454] primer on ISCIII schema --- .../schema/institution_schemas/ISCIII.json | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 relecov_tools/schema/institution_schemas/ISCIII.json diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json new file mode 100644 index 00000000..f369a462 --- /dev/null +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -0,0 +1,20 @@ +{ + "equivalence": + {"Public Health sample id": "Código SiViEs", + "Sample ID given by originating laboratory": "Ref Hospital", + "Sample ID given by the submitting laboratory": "ID CNM", + "Sample ID given in the microbiology lab": "ID VI-VRP", + "Sample ID given if multiple rna-extraction or passages": "ID VI-VRP", + "Sample ID given for sequencing": "ID VI-VRP", + "GISAID id": "ID GISAID", + "Originating Laboratory": "Hospital", + "Sample Collection Date": "Fecha de toma ", + "Sample Received Date": "Fecha recepción", + "Host Age": "Grupo edad", + "Diagnostic Pcr Ct Value 1": "PCR genE", + "Sequencing Date": "Fecha de secuenciación", + "Rna Extraction Protocol": ""}, + "constants": {}, + "empty": [], + "outer": {} +} \ No newline at end of file From 3e211b0ad928556dd4e256c318949451514c3f2d Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 29 Jun 2022 13:02:33 +0200 Subject: [PATCH 0562/1454] updated institution_to_schema file --- relecov_tools/schema/institution_to_schema.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/relecov_tools/schema/institution_to_schema.json b/relecov_tools/schema/institution_to_schema.json index 39a5590a..43535fd5 100644 --- a/relecov_tools/schema/institution_to_schema.json +++ b/relecov_tools/schema/institution_to_schema.json @@ -1,4 +1,5 @@ { "ITER" : "1.json", - "0001" : "1.json" + "0001" : "1.json", + "ISCIII" : "ISCIII.json" } \ No newline at end of file From 30252c607e6d53c4de8a9f32e08085e1f7e3de0b Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 29 Jun 2022 13:02:57 +0200 Subject: [PATCH 0563/1454] added detect_centre method --- relecov_tools/metadata_homogeneizer.py | 29 +++++++++++++++++++++++--- 1 file changed, 26 insertions(+), 3 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 51365d53..7ab1e71f 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -1,6 +1,7 @@ #!/usr/bin/env python # Imports +import sys import json import pandas as pd @@ -8,6 +9,7 @@ class Homogeneizer: def __init__(filename, self): self.filename = filename + self.dictionary = None self.centre = None self.dataframe = None self.translated_dataframe = None @@ -16,15 +18,35 @@ def __init__(filename, self): return def detect_centre(self): - """Detect the origin centre of the metadata""" + """Detect the origin centre of the metadata, and finds the corresponding json file to use""" + + # Check name of the file attribute of the object # Check schema with all centres and find their json # associate centre and json with object # raise error when in doubt # must check on schema/institution_schemas - pass + + path_to_institution_json = "" + detected = [] + institution_dict = json.load(path_to_json) + + for key in institution_dict.keys(): + if key in self.filename: + detected.append(institution_dict[key]) + + if len(set(detected)) != 1: + print("some problems arised!!!") # change this to an elegant form + sys.exit() # maybe check which ones are being mixed or when none is being found + else: + print("works fine") # delete this after testing + self.dictionary = detected[0] # first item, they are all equal + return + + + def load_dataframe(self): """Read the metadata file""" # check possible extensions @@ -46,4 +68,5 @@ def verify_translated_dataframe(self): """Checks if the dataframe holds all the needed values for the relecov tools suite""" pass - return \ No newline at end of file + return + From 4444130483b2c294f92191a1b946d46129493767 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 29 Jun 2022 13:10:15 +0200 Subject: [PATCH 0564/1454] latest change ena --- relecov_tools/ena_upload.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index 0ffd86b1..c7bc326d 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -207,7 +207,9 @@ def create_structure_to_ena(self): df_run.loc[i, "sequence_file_R2_fastq"] = df_schemas.loc[ i, "sequence_file_R2_fastq" ] + import pdb + pdb.set_trace() df_run.insert(3, "status", self.action) df_run = df_run.rename(columns={"fastq_r1_md5": "file_checksum"}) From 59226d6049c3ec3653828ab627bc47a350841206 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 29 Jun 2022 13:34:05 +0200 Subject: [PATCH 0565/1454] removed "empty" --- relecov_tools/schema/institution_schemas/ISCIII.json | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/schema/institution_schemas/ISCIII.json b/relecov_tools/schema/institution_schemas/ISCIII.json index f369a462..33d6dbc2 100644 --- a/relecov_tools/schema/institution_schemas/ISCIII.json +++ b/relecov_tools/schema/institution_schemas/ISCIII.json @@ -15,6 +15,5 @@ "Sequencing Date": "Fecha de secuenciación", "Rna Extraction Protocol": ""}, "constants": {}, - "empty": [], "outer": {} } \ No newline at end of file From 4f7a8e73e195c287aa1bd587a6ca968fd667b648 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 29 Jun 2022 13:35:45 +0200 Subject: [PATCH 0566/1454] updated load dataframe (almost done?) and load dictionary --- relecov_tools/metadata_homogeneizer.py | 38 +++++++++++++++++++++----- 1 file changed, 31 insertions(+), 7 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index 7ab1e71f..f6db14a9 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -3,8 +3,17 @@ # Imports import sys import json +from tkinter.ttk import Separator import pandas as pd +# functions + +def check_extension(instring, extensions): + for extension in extensions: + if instring.endswith(extension): + return True + + # Homogeneizer object class Homogeneizer: def __init__(filename, self): @@ -17,10 +26,9 @@ def __init__(filename, self): pass return - def detect_centre(self): + def associate_dict(self): """Detect the origin centre of the metadata, and finds the corresponding json file to use""" - # Check name of the file attribute of the object # Check schema with all centres and find their json # associate centre and json with object @@ -28,6 +36,7 @@ def detect_centre(self): # must check on schema/institution_schemas path_to_institution_json = "" + detected = [] institution_dict = json.load(path_to_json) @@ -44,19 +53,34 @@ def detect_centre(self): return - - - def load_dataframe(self): """Read the metadata file""" # check possible extensions # load with pandas - pass + + excel_extensions = [".xlsx", ".xls", ".xlsm", ".xlsb"] + odf_extension = [".odf"] + csv_extensions = [".csv"] + tsv_extensions = [".tsv"] + + if check_extension(self.filename, excel_extensions): + self.dataframe = pd.read_excel(self.filename, header=0) + elif check_extension(self.filename, odf_extension): + # Needs a special package + self.dataframe = pd.read_excel(self.filename, engine="odf", header=0) + elif check_extension(self.filename, csv_extensions): + self.dataframe = pd.read_csv(self.filename, sep=",", header=0) + elif check_extension(self.filename, tsv_extensions): + self.dataframe = pd.read_csv(self.filename, sep="\t", header=0) + return def load_dictionary(self): """Load the corresponding dictionary""" - pass + + path_to_tools = "" + dict_path = path_to_tools + "/schema/institution_schemas" + self.filename + self.dictionary = json.load(dict_path) return def translate_dataframe(self): From b7359712be341ff2b9fd3a0816243a3e4db7974d Mon Sep 17 00:00:00 2001 From: mlarjim Date: Wed, 29 Jun 2022 13:43:34 +0200 Subject: [PATCH 0567/1454] Modified gisaid_schema.json --- relecov_tools/schema/gisaid_schema.json | 69 ++++++++++++++----------- 1 file changed, 40 insertions(+), 29 deletions(-) diff --git a/relecov_tools/schema/gisaid_schema.json b/relecov_tools/schema/gisaid_schema.json index cb2a2cf9..797eb590 100644 --- a/relecov_tools/schema/gisaid_schema.json +++ b/relecov_tools/schema/gisaid_schema.json @@ -1,22 +1,24 @@ { "schema": "GISAID#", "required": [ - "type", - "virus_name", + "covv_type", + "covv_virus_name", "submitter", - "originating_lab", - "collecting_address", - "collection_date", - "location", - "host", - "patient_age", - "gender", - "sequencing_technology", - "fasta_filename" + "covv_passage", + "covv_orig_lab", + "covv_orig_lab_addr", + "covv_collection_date", + "covv_location", + "covv_host", + "covv_patient_age", + "covv_gender", + "covv_seq_technology", + "covv_subm_lab", + "covv_subm_lab_addr" ], "type": "object", "properties": { - "type": { + "covv_type": { "examples": [ "betacoronavirus" ], @@ -35,7 +37,7 @@ "clasification": "Database Identifiers", "label": "Collecting Sample id" }, - "virus_name": { + "covv_virus_name": { "examples": [ "hCoV-19/Canada/prov_rona_99/2020" ], @@ -55,7 +57,7 @@ "clasification": "enter your GISAID-Username", "label": "GISAID Id" }, - "originating_lab": { + "covv_orig_lab": { "examples": [ "Public Health Agency of Canada" ], @@ -64,7 +66,7 @@ "description": "The name of the agency that collected the original sample.", "label": "Originating Laboratory" }, - "collecting_address": { + "covv_orig_lab_addr": { "examples": [ "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" ], @@ -74,7 +76,7 @@ "clasification": "Sample collection and processing", "label": "Originating Laboratory Address" }, - "submitting_address": { + "covv_subm_lab_addr": { "examples": [ "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" ], @@ -84,7 +86,7 @@ "clasification": "Sample collection and processing", "label": "Submitting Institution Address" }, - "collection_date": { + "covv_collection_date": { "examples": [ "3/19/2020" ], @@ -95,7 +97,7 @@ "classification": "Sample collection and processing", "label": "Sample Collection Date" }, - "location": { + "covv_location": { "examples": [ "e.g. Europe / Germany / Bavaria / Munich" ], @@ -105,7 +107,7 @@ "clasification": "Sample collection and processing", "label": "Geo Loc Autonomic Country" }, - "host": { + "covv_host": { "examples": [ "e.g. Human, Environment, Canine, Manis javanica, Rhinolophus affinis, etc" ], @@ -115,7 +117,7 @@ "clasification": "Host information", "label": "Host Scientific Name" }, - "patient_age": { + "covv_patient_age": { "ontology": "GENEPIO:0001392", "anyOf": [ { @@ -158,7 +160,7 @@ "classification": "Sample collection and processing", "label": "Organism Substance" }, - "Assembly method": { + "covv_assembly_method": { "examples": [ "Ivar" ], @@ -168,7 +170,7 @@ "clasification": "Bioinformatics and QC metrics", "label": "Consensus sequence software name" }, - "gender": { + "covv_gender": { "Enums": [ "Female [NCIT:C46110]", "Male [NCIT:C46109]", @@ -190,7 +192,7 @@ "description": "The gender of the host at the time of sample collection.", "clasification": "Host information" }, - "sequencing_technology": { + "covv_seq_technology": { "examples": [ "e.g. Illumina Miseq, Sanger, Nanopore MinION, Ion Torrent, etc." ], @@ -200,7 +202,7 @@ "classification": "Sequencing", "label": "Sequencing Instrument Model" }, - "authors": { + "covv_authors": { "examples": [ "" ], @@ -210,7 +212,7 @@ "clasification": "Contributor Acknowledgement", "label": "Authors" }, - "coverage": { + "covv_coverage": { "examples": [ "400x" ], @@ -239,7 +241,7 @@ "clasification": "Host information", "label": "Additional Host Information" }, - "Last vaccinated": { + "covv_last_vaccinated": { "examples": [ "e.g. 04/09/2021" ], @@ -249,7 +251,7 @@ "format": "date", "clasification": "Host information" }, - "outbreak": { + "covv_outbreak": { "examples": [ "Date, Location e.g. type of gathering, Family cluster, etc." ], @@ -259,7 +261,7 @@ "clasification": "Host information", "label": "Outbreak Exposure Event Location" }, - "Sampling Strategy": { + "covv_sampling_strategy": { "examples": [ "e.g. Sentinel surveillance (ILI), Sentinel surveillance (ARI), Sentinel surveillance (SARI), Non-sentinel-surveillance (hospital), Non-sentinel-surveillance (GP network), Longitudinal sampling on same patient(s), S gene dropout" ], @@ -278,7 +280,7 @@ "description": "Sample ID given by the submitting laboratory", "clasification": "Database Identifiers" }, - "submitting_lab": { + "covv_subm_lab": { "examples": [ "Centers for Disease Control and Prevention" ], @@ -286,6 +288,15 @@ "type": "string", "description": "The name of the agency that generated the sequence.", "label": "Submitting Institution" + }, + "covv_passage": { + "examples": [ + "Original", "Vero" + ], + "ontology": "GENEPIO:0100039", + "type": "string", + "description": "The process of growing a virus in serial iterations(original/vero)", + "label": "Virus passage" } } } From 07798680e32b4410c1f1a6be1e34b336c3bb9083 Mon Sep 17 00:00:00 2001 From: GuilleGorines Date: Wed, 29 Jun 2022 13:49:09 +0200 Subject: [PATCH 0568/1454] removed weird crap --- relecov_tools/metadata_homogeneizer.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/relecov_tools/metadata_homogeneizer.py b/relecov_tools/metadata_homogeneizer.py index f6db14a9..3b389da0 100644 --- a/relecov_tools/metadata_homogeneizer.py +++ b/relecov_tools/metadata_homogeneizer.py @@ -3,7 +3,6 @@ # Imports import sys import json -from tkinter.ttk import Separator import pandas as pd # functions @@ -38,7 +37,7 @@ def associate_dict(self): path_to_institution_json = "" detected = [] - institution_dict = json.load(path_to_json) + institution_dict = json.load(path_to_institution_json) for key in institution_dict.keys(): if key in self.filename: From ea76c4d76b8da9e3025b04bfbbfbf07e8cef8c40 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Wed, 29 Jun 2022 14:01:13 +0200 Subject: [PATCH 0569/1454] cleaning example data relecov_tools Biohack day1-morning --- .../download_module/ENA_TEST1_V1.R1.fastq.gz | Bin 0 -> 4221 bytes .../example_data/download_module/README | 3 + .../validate_module/METADATA_LAB_TEST.xlsx | Bin 0 -> 493368 bytes .../example_data/validate_module/README | 6 + .../processed_METADATA_LAB_TEST.json | 782 ++++++++++++++++++ 5 files changed, 791 insertions(+) create mode 100644 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z5B6_I-|Y>kfdT(xmCetDAE&JD?+g95DcF7|{P$g=pAY?U#^8QV>$mNT%YTRSZ!=s! zAN=D*?){{~Z(FcC_~7pq@IR&)e&+mmb$EXb_}hl-3HRd#^3MnUc)juW2U2>01^n$& p^5+A89JKy@r6K#k{p#XGUK-|ZOa%Z?-~F4s8;byZ?*>PJ{|EcIS6Ki6 diff --git a/relecov_tools/example_data/processed_METADATA_LAB_TEST.json b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json index fda2fd6c..f62143ad 100644 --- a/relecov_tools/example_data/processed_METADATA_LAB_TEST.json +++ b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json @@ -10,6 +10,7 @@ "collecting_institution": "Hospital Universitario Miguel Servet", "collecting_lab_sample_id": "1197860", "collection_device": "Swab", + "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "45", "diagnostic_pcr_Ct_value_2": "34", "enrichment_protocol": "Amplicon", @@ -77,6 +78,7 @@ "collecting_institution": "Hospital Universitario Miguel Servet", "collecting_lab_sample_id": "1197824", "collection_device": "Swab", + "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "12", "diagnostic_pcr_Ct_value_2": "16", "enrichment_protocol": "Amplicon", @@ -144,6 +146,7 @@ "collecting_institution": "Hospital Universitario Miguel Servet", "collecting_lab_sample_id": "1197767", "collection_device": "Swab", + "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "45", "diagnostic_pcr_Ct_value_2": "41", "enrichment_protocol": "Amplicon", @@ -211,6 +214,7 @@ "collecting_institution": "Hospital Universitario Miguel Servet", "collecting_lab_sample_id": "8328199", "collection_device": "Swab", + "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "23", "diagnostic_pcr_Ct_value_2": "23", "enrichment_protocol": "Amplicon", @@ -278,6 +282,7 @@ "collecting_institution": "Hospital Universitario Miguel Servet", "collecting_lab_sample_id": "1197677", "collection_device": "Swab", + "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "12", "diagnostic_pcr_Ct_value_2": "10", "enrichment_protocol": "Amplicon", @@ -345,6 +350,7 @@ "collecting_institution": "Hospital Universitario Miguel Servet", "collecting_lab_sample_id": "1197678", "collection_device": "Swab", + "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "56", "diagnostic_pcr_Ct_value_2": "19", "enrichment_protocol": "Amplicon", @@ -412,6 +418,7 @@ "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", "collecting_lab_sample_id": "1197737", "collection_device": "Swab", + "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "11", "diagnostic_pcr_Ct_value_2": "11", "enrichment_protocol": "Amplicon", @@ -479,6 +486,7 @@ "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", "collecting_lab_sample_id": "1197663", "collection_device": "Swab", + "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "34", "diagnostic_pcr_Ct_value_2": "36", "enrichment_protocol": "Amplicon", @@ -546,6 +554,7 @@ "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", "collecting_lab_sample_id": "1197689", "collection_device": "Swab", + "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "23", "diagnostic_pcr_Ct_value_2": "20", "enrichment_protocol": "Amplicon", @@ -613,6 +622,7 @@ "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", "collecting_lab_sample_id": "1197685", "collection_device": "Swab", + "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "32", "diagnostic_pcr_Ct_value_2": "32", "enrichment_protocol": "Amplicon", From f9a927fbecd44681fa7c6d3c18be362491c2b5c9 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 6 Apr 2022 23:09:10 +0200 Subject: [PATCH 0298/1454] litin changes --- relecov_tools/map_schema.py | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 6a7b7d86..a5ca98d8 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -132,7 +132,9 @@ def maping_schemas_based_on_geontology(self): # There is no exact match on ontology. Search for the parent # to be implemented later stderr.print(f"[red] Ontology value {e} not in phage plus schema") - import pdb; pdb.set_trace() + import pdb + + pdb.set_trace() return mapped_dict def mapping_json_data(self, mapping_schema_dict): @@ -155,10 +157,16 @@ def write_json_fo_file(self, mapped_json_data): os.makedirs(self.output_folder, exist_ok=True) time = datetime.now().strftime("%Y_%m_%d_%H_%M") f_sub_name = os.path.basename(self.json_file).split(".")[0] - file_name = f_sub_name + "_" + time + "_" + self.destination_schema + "_mapped.json" + file_name = ( + f_sub_name + "_" + time + "_" + self.destination_schema + "_mapped.json" + ) json_file = os.path.join(self.output_folder, file_name) with open(json_file, "w", encoding="utf-8") as fh: - fh.write(json.dumps(mapped_json_data, indent=4, sort_keys=True, ensure_ascii=False)) + fh.write( + json.dumps( + mapped_json_data, indent=4, sort_keys=True, ensure_ascii=False + ) + ) return True def map_to_data_to_new_schema(self): From 69d575c77fd9e6fc06717dac57624a1240216802 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 6 Apr 2022 23:44:32 +0200 Subject: [PATCH 0299/1454] Removed extra spaces in GENEPIO:0001181 --- relecov_tools/schema/ena_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 679c91fb..b2938425 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -406,7 +406,7 @@ "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], - "ontology": "GENEPIO:0001181 ", + "ontology": "GENEPIO:0001181", "type": "string", "description": "The country of origin of the sample.", "examples": [ From 74457bd3bd6d852f6f4cb1237707536e85b59f6a Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 6 Apr 2022 23:45:32 +0200 Subject: [PATCH 0300/1454] Add geo_loc_country for laboratory --- relecov_tools/read_metadata.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 1b201fc8..e24e61e0 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -96,6 +96,7 @@ def get_laboratory_data(self, lab_json, geo_loc_json, lab_name): if city["geo_loc_city"] == data["geo_loc_city"]: data["geo_loc_latitude"] = city["geo_loc_latitude"] data["geo_loc_longitude"] = city["geo_loc_longitude"] + data["geo_loc_country"] = data["geo_loc_country"] break return data From 039daf704cb88ac7514f6ad374045d2798aad324 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 6 Apr 2022 23:48:32 +0200 Subject: [PATCH 0301/1454] update test cases --- relecov_tools/test/test_cases.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/test/test_cases.txt b/relecov_tools/test/test_cases.txt index 804e7e61..dc985041 100644 --- a/relecov_tools/test/test_cases.txt +++ b/relecov_tools/test/test_cases.txt @@ -1,4 +1,4 @@ relecov-tools read-metadata -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -s relecov_tools/example_data/samples_data_COD_test_01_20220330.json -o /tmp -relecov-tools validate -j relecov_tools/example_data/invalid_METADATA_LAB_TEST.json -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx +relecov-tools validate -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -o /tmp relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -o /tmp From 1a0d4be275432c12be97a04641077109fa5f625c Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 7 Apr 2022 00:13:15 +0200 Subject: [PATCH 0302/1454] Changed attribute last update from format to label --- relecov_tools/schema/ena_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index b2938425..cb039d67 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -1142,7 +1142,7 @@ "clasification": "Submission ENA", "label": "First Public date" }, - "last_updated_date": { + "last_updated": { "examples": [ "e.g 2020-07-29" ], @@ -1150,7 +1150,7 @@ "type": "string", "description": "", "clasification": "Submission ENA", - "format": "Last Updated" + "label": "Last Updated" }, "experiment_title": { "examples": [ From bc23dde4a059e2ebcb591571afb04a0d75d9ac99 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 7 Apr 2022 00:13:49 +0200 Subject: [PATCH 0303/1454] fixing bugs in mapping to ENA --- relecov_tools/map_schema.py | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index a5ca98d8..599ec933 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -122,19 +122,17 @@ def __init__( def maping_schemas_based_on_geontology(self): """Return a dictionnary with the properties of the mapped_to_schema as key and - properties of phagePlusSchema as value + properties of Relecov Schema as value """ mapped_dict = OrderedDict() for key, values in self.mapped_to_schema["properties"].items(): + if values['ontology'] == "0": + continue try: mapped_dict[key] = self.ontology[values["ontology"]] except KeyError as e: - # There is no exact match on ontology. Search for the parent - # to be implemented later - stderr.print(f"[red] Ontology value {e} not in phage plus schema") - import pdb - - pdb.set_trace() + log.error("Invalid ontology for %s", key) + stderr.print(f"[red] Ontology value {e} not in relecov schema") return mapped_dict def mapping_json_data(self, mapping_schema_dict): @@ -148,7 +146,6 @@ def mapping_json_data(self, mapping_schema_dict): map_sample_dict[item] = data[value] except KeyError as e: log.warning("Property %s not set in the source data", e) - print(e) mapped_data.append(map_sample_dict) return mapped_data From 893ca0e34f37dca3155381a513f221abb76b04d7 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 7 Apr 2022 00:14:14 +0200 Subject: [PATCH 0304/1454] fixing bugs in mapping to ENA --- relecov_tools/map_schema.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 599ec933..cba0b079 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -126,7 +126,7 @@ def maping_schemas_based_on_geontology(self): """ mapped_dict = OrderedDict() for key, values in self.mapped_to_schema["properties"].items(): - if values['ontology'] == "0": + if values["ontology"] == "0": continue try: mapped_dict[key] = self.ontology[values["ontology"]] From 7b614dd074427c171346085f246766ab597358ba Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 8 Apr 2022 00:36:24 +0200 Subject: [PATCH 0305/1454] md5 tags changes becaues they were not as the same in the relecov schema --- relecov_tools/sftp_handle.py | 31 +++++++++++++++++++++---------- 1 file changed, 21 insertions(+), 10 deletions(-) diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index a922563b..6dca44ef 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -34,8 +34,8 @@ def __init__(self, user=None, passwd=None, conf_file=None): self.sftp_user = user self.sftp_passwd = passwd if conf_file is None: - self.server = config_json.get_topic_data("sftp_connection", "sftp_server") - self.port = config_json.get_topic_data("sftp_connection", "sftp_port") + self.sftp_server = config_json.get_topic_data("sftp_connection", "sftp_server") + self.sftp_port = config_json.get_topic_data("sftp_connection", "sftp_port") self.storage_local_folder = config_json.get_configuration( "storage_local_folder" ) @@ -243,8 +243,15 @@ def create_tmp_files_with_metadata_info( for f_type, f_name in values.items(): if not f_name.endswith(tuple(self.allowed_sample_ext)): stderr.print("[red] " + f_name + " has a not valid extension") - data[s_name]["local_folder"] = md5_data[f_name][0] - data[s_name][f_type + "_md5"] = md5_data[f_name][1] + if "_R1_" in f_name: + data[s_name]["r1_fastq_filepath"] = md5_data[f_name][0] + data[s_name]["fastq_r1_md5"] = md5_data[f_name][1] + elif "_R2_" in f_name: + data[s_name]["r2_fastq_filepath"] = md5_data[f_name][0] + data[s_name]["fastq_r2_md5"] = md5_data[f_name][1] + else: + # reserved for future develoment + pass with open(sample_data_path, "w", encoding="utf-8") as fh: fh.write(json.dumps(data, indent=4, sort_keys=True, ensure_ascii=False)) @@ -288,18 +295,22 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): index_fastq_r2 = col.column - 1 for row in islice(ws_metadata_lab.values, 4, ws_metadata_lab.max_row): if row[2] is not None: - if row[2] not in sample_file_list: - sample_file_list[row[2]] = {} + try: + s_name = str(int(row[2])) + except ValueError: + s_name = str(row[2]) + if s_name not in sample_file_list: + sample_file_list[s_name] = {} if row[index_fastq_r1] is not None: - sample_file_list[row[2]]["fastq_r1"] = row[index_fastq_r1] + sample_file_list[s_name]["sequence_file_R1_fastq"] = row[index_fastq_r1] else: log.error( - "Fastq_R1 not defined in Metadata file for sample %s", row[2] + "Fastq_R1 not defined in Metadata file for sample %s", s_name ) - stderr.print("[red] No fastq R1 file for sample " + row[2]) + stderr.print("[red] No fastq R1 file for sample " + s_name) return False if row[index_fastq_r2] is not None: - sample_file_list[row[2]]["fastq_r2"] = row[index_fastq_r2] + sample_file_list[s_name]["sequence_file_R2_fastq"] = row[index_fastq_r2] return sample_file_list def validate_download_files(self, sample_file_list, local_folder): From 1c6d3b7868b25d85ffd15ffd0b7b4d2d7d77e1f7 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 8 Apr 2022 00:37:31 +0200 Subject: [PATCH 0306/1454] Collecting the MD5 values and the path for fastq files --- relecov_tools/read_metadata.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index e24e61e0..9ee7e490 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -160,11 +160,11 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): for row_sample in metadata: """Include sample data from sample json""" - for row_sample_data in samples_json: - if row_sample_data == row_sample: - for key, value in row_sample_data.items(): - row_sample[key] = value - + try: + for key, value in samples_json[row_sample["collecting_lab_sample_id"]].items(): + row_sample[key] = value + except KeyError: + pass """ Fetch the information related to the laboratory. Info is stored in lab_data, to prevent to call get_laboratory_data each time for each sample that belongs to the same lab From 5e688de0e7d4679dd880d9855e8a6a3e114ee0cc Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 8 Apr 2022 00:39:19 +0200 Subject: [PATCH 0307/1454] adding download test case. --- relecov_tools/test/test_cases.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/relecov_tools/test/test_cases.txt b/relecov_tools/test/test_cases.txt index dc985041..a58d3d94 100644 --- a/relecov_tools/test/test_cases.txt +++ b/relecov_tools/test/test_cases.txt @@ -1,4 +1,4 @@ - -relecov-tools read-metadata -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -s relecov_tools/example_data/samples_data_COD_test_01_20220330.json -o /tmp +relecov-tools -l /tmp/logs.log download -u usuario_test -p U[9[Gpyu3. +relecov-tools read-metadata -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -s relecov_tools/example_data/samples_data_COD_test_01_20220408.json -o /tmp relecov-tools validate -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -o /tmp relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -o /tmp From d4309d1721bfa274845de2d3ca96f2d4d6ba31e8 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 8 Apr 2022 00:41:57 +0200 Subject: [PATCH 0308/1454] including MD5 into the mapping --- relecov_tools/map_schema.py | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index cba0b079..7a9cd2c5 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -149,6 +149,18 @@ def mapping_json_data(self, mapping_schema_dict): mapped_data.append(map_sample_dict) return mapped_data + def additional_formating(self, mapped_json_data): + """Update data like MD5 to split in two fields, one for R1 file and + second for R2 + """ + if self.destination_schema == "ENA": + for idx in range(len(self.json_data)): + import pdb; pdb.set_trace() + mapped_json_data[idx]["fastq_md5_r1"] = self.json_data[idx]["fastq_md5_r1"] + mapped_json_data[idx]["fastq_md5_r2"] = self.json_data[idx]["fastq_md5_r2"] + + return mapped_json_data + def write_json_fo_file(self, mapped_json_data): """Write metadata to json file""" os.makedirs(self.output_folder, exist_ok=True) @@ -170,5 +182,6 @@ def map_to_data_to_new_schema(self): """Mapping the json data from phage plus schema to the requested one""" mapping_schema_dict = self.maping_schemas_based_on_geontology() mapped_json_data = self.mapping_json_data(mapping_schema_dict) - self.write_json_fo_file(mapped_json_data) + updated_json_data = self.additional_formating(mapped_json_data) + self.write_json_fo_file(updated_json_data) return From 388c4e652c8493d7d87b850b35c8f6714c8c8e33 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 8 Apr 2022 00:43:29 +0200 Subject: [PATCH 0309/1454] adding example for processed metadata --- .../processed_METADATA_LAB_TEST.json | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/relecov_tools/example_data/processed_METADATA_LAB_TEST.json b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json index f62143ad..a8ff18e9 100644 --- a/relecov_tools/example_data/processed_METADATA_LAB_TEST.json +++ b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json @@ -18,6 +18,8 @@ "environmental_site": "Earth surface", "experiment_alias": "", "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "f2facbd1d6c7e0972074ced31ccbfd8e", + "fastq_r2_md5": "fd9948be8da7a38b0f80659dfc21aeea", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -47,6 +49,8 @@ "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU01394", "purpose_of_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -86,6 +90,8 @@ "environmental_site": "Earth surface", "experiment_alias": "", "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "9a460a812086516536c1a1023ab5f7fe", + "fastq_r2_md5": "41cd79b8a167d85eb06309207fd120cf", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -115,6 +121,8 @@ "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU01469", "purpose_of_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -154,6 +162,8 @@ "environmental_site": "Earth surface", "experiment_alias": "", "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "c78fcb585a0f44734ce8c2aebf3eff33", + "fastq_r2_md5": "8361d5a6b50279fbc8c93226ecc3568a", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -183,6 +193,8 @@ "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU03926", "purpose_of_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -222,6 +234,8 @@ "environmental_site": "Earth surface", "experiment_alias": "", "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "aa557fc40d3a9e16f470ac595fb5eb3e", + "fastq_r2_md5": "a2dd5e08b75815dab892e392cb8468fc", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -251,6 +265,8 @@ "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU06554", "purpose_of_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -290,6 +306,8 @@ "environmental_site": "Earth surface", "experiment_alias": "", "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "b0a13671031ef5aa7e0e6559a925a688", + "fastq_r2_md5": "8c420a603c81823e68436003825b1e1f", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -319,6 +337,8 @@ "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU03790", "purpose_of_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -358,6 +378,8 @@ "environmental_site": "Earth surface", "experiment_alias": "", "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "13e01498a0526303f5e32f3eef077b5a", + "fastq_r2_md5": "61d1f52e84237320d97fd7fc2da56116", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -387,6 +409,8 @@ "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU03901", "purpose_of_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -426,6 +450,8 @@ "environmental_site": "Earth surface", "experiment_alias": "", "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "f5b60a93b39a0b98781efb434d577a57", + "fastq_r2_md5": "e19f883b4e05045895f990c2296009a8", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -455,6 +481,8 @@ "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU03862", "purpose_of_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -494,6 +522,8 @@ "environmental_site": "Earth surface", "experiment_alias": "", "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "83043c429b0ab94375236cf7f51860f0", + "fastq_r2_md5": "c00859a1f83e2364cca953fb25da3cf2", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -523,6 +553,8 @@ "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU03614", "purpose_of_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -562,6 +594,8 @@ "environmental_site": "Earth surface", "experiment_alias": "", "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "bc720a024263a518f6a6cd9301b308ac", + "fastq_r2_md5": "6bf6d95b59c950691effcaf8a0e83068", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -591,6 +625,8 @@ "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU04252", "purpose_of_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", @@ -630,6 +666,8 @@ "environmental_site": "Earth surface", "experiment_alias": "", "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "a86f4fa0c92d76df34fd000a29d1cdd3", + "fastq_r2_md5": "8c4309dc00d725496c48bee6da0e4bbf", "flowcell_kit": "HiSeq 3000/4000 PE Cluster Kit", "gene_name_1": "ORF 1ab", "gene_name_2": "S", @@ -659,6 +697,8 @@ "organism": "Severe acute respiratory syndrome coronavirus 2", "public_health_sample_id_sivies": "2022CEU04223", "purpose_of_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", "rna_extraction_protocol": "In-house method for Opetrons robots", "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", From df95d00fa6a00dc67bac5d18d1856c93cd0f5e54 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 8 Apr 2022 00:45:23 +0200 Subject: [PATCH 0310/1454] Adding sample file for testing after including MD5 changes --- .../samples_data_COD_test_01_20220330.json | 72 ------------------- 1 file changed, 72 deletions(-) delete mode 100644 relecov_tools/example_data/samples_data_COD_test_01_20220330.json diff --git a/relecov_tools/example_data/samples_data_COD_test_01_20220330.json b/relecov_tools/example_data/samples_data_COD_test_01_20220330.json deleted file mode 100644 index ab634772..00000000 --- a/relecov_tools/example_data/samples_data_COD_test_01_20220330.json +++ /dev/null @@ -1,72 +0,0 @@ -{ - "1197663.0": { - "fastq_r1": "ABC123_S1_L001_R1_008.fastq.gz", - "fastq_r1_md5": "83043c429b0ab94375236cf7f51860f0", - "fastq_r2": "ABC123_S1_L001_R2_008.fastq.gz", - "fastq_r2_md5": "c00859a1f83e2364cca953fb25da3cf2", - "local_folder": "/tmp/relecov/COD_test_01/20220330" - }, - "1197677.0": { - "fastq_r1": "ABC123_S1_L001_R1_005.fastq.gz", - "fastq_r1_md5": "b0a13671031ef5aa7e0e6559a925a688", - "fastq_r2": "ABC123_S1_L001_R2_005.fastq.gz", - "fastq_r2_md5": "8c420a603c81823e68436003825b1e1f", - "local_folder": "/tmp/relecov/COD_test_01/20220330" - }, - "1197678.0": { - "fastq_r1": "ABC123_S1_L001_R1_006.fastq.gz", - "fastq_r1_md5": "13e01498a0526303f5e32f3eef077b5a", - "fastq_r2": "ABC123_S1_L001_R2_006.fastq.gz", - "fastq_r2_md5": "61d1f52e84237320d97fd7fc2da56116", - "local_folder": "/tmp/relecov/COD_test_01/20220330" - }, - "1197685.0": { - "fastq_r1": "ABC123_S1_L001_R1_0010.fastq.gz", - "fastq_r1_md5": "a86f4fa0c92d76df34fd000a29d1cdd3", - "fastq_r2": "ABC123_S1_L001_R2_0010.fastq.gz", - "fastq_r2_md5": "8c4309dc00d725496c48bee6da0e4bbf", - "local_folder": "/tmp/relecov/COD_test_01/20220330" - }, - "1197689.0": { - "fastq_r1": "ABC123_S1_L001_R1_009.fastq.gz", - "fastq_r1_md5": "bc720a024263a518f6a6cd9301b308ac", - "fastq_r2": "ABC123_S1_L001_R2_009.fastq.gz", - "fastq_r2_md5": "6bf6d95b59c950691effcaf8a0e83068", - "local_folder": "/tmp/relecov/COD_test_01/20220330" - }, - "1197737.0": { - "fastq_r1": "ABC123_S1_L001_R1_007.fastq.gz", - "fastq_r1_md5": "f5b60a93b39a0b98781efb434d577a57", - "fastq_r2": "ABC123_S1_L001_R2_007.fastq.gz", - "fastq_r2_md5": "e19f883b4e05045895f990c2296009a8", - "local_folder": "/tmp/relecov/COD_test_01/20220330" - }, - "1197767.0": { - "fastq_r1": "ABC123_S1_L001_R1_003.fastq.gz", - "fastq_r1_md5": "c78fcb585a0f44734ce8c2aebf3eff33", - "fastq_r2": "ABC123_S1_L001_R2_003.fastq.gz", - "fastq_r2_md5": "8361d5a6b50279fbc8c93226ecc3568a", - "local_folder": "/tmp/relecov/COD_test_01/20220330" - }, - "1197824.0": { - "fastq_r1": "ABC123_S1_L001_R1_002.fastq.gz", - "fastq_r1_md5": "9a460a812086516536c1a1023ab5f7fe", - "fastq_r2": "ABC123_S1_L001_R2_002.fastq.gz", - "fastq_r2_md5": "41cd79b8a167d85eb06309207fd120cf", - "local_folder": "/tmp/relecov/COD_test_01/20220330" - }, - "1197860.0": { - "fastq_r1": "ABC123_S1_L001_R1_001.fastq.gz", - "fastq_r1_md5": "f2facbd1d6c7e0972074ced31ccbfd8e", - "fastq_r2": "ABC123_S1_L001_R2_001.fastq.gz", - "fastq_r2_md5": "fd9948be8da7a38b0f80659dfc21aeea", - "local_folder": "/tmp/relecov/COD_test_01/20220330" - }, - "8328199.0": { - "fastq_r1": "ABC123_S1_L001_R1_004.fastq.gz", - "fastq_r1_md5": "aa557fc40d3a9e16f470ac595fb5eb3e", - "fastq_r2": "ABC123_S1_L001_R2_004.fastq.gz", - "fastq_r2_md5": "a2dd5e08b75815dab892e392cb8468fc", - "local_folder": "/tmp/relecov/COD_test_01/20220330" - } -} \ No newline at end of file From d4b7a24ad8643fce1d2688854b1236f5281c5f83 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 8 Apr 2022 00:46:04 +0200 Subject: [PATCH 0311/1454] Adding sample file for testing after including MD5 changes --- .../samples_data_COD_test_01_20220408.json | 82 +++++++++++++++++++ 1 file changed, 82 insertions(+) create mode 100644 relecov_tools/example_data/samples_data_COD_test_01_20220408.json diff --git a/relecov_tools/example_data/samples_data_COD_test_01_20220408.json b/relecov_tools/example_data/samples_data_COD_test_01_20220408.json new file mode 100644 index 00000000..5403a0e1 --- /dev/null +++ b/relecov_tools/example_data/samples_data_COD_test_01_20220408.json @@ -0,0 +1,82 @@ +{ + "1197663": { + "fastq_r1_md5": "83043c429b0ab94375236cf7f51860f0", + "fastq_r2_md5": "c00859a1f83e2364cca953fb25da3cf2", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_008.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_008.fastq.gz" + }, + "1197677": { + "fastq_r1_md5": "b0a13671031ef5aa7e0e6559a925a688", + "fastq_r2_md5": "8c420a603c81823e68436003825b1e1f", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_005.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_005.fastq.gz" + }, + "1197678": { + "fastq_r1_md5": "13e01498a0526303f5e32f3eef077b5a", + "fastq_r2_md5": "61d1f52e84237320d97fd7fc2da56116", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_006.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_006.fastq.gz" + }, + "1197685": { + "fastq_r1_md5": "a86f4fa0c92d76df34fd000a29d1cdd3", + "fastq_r2_md5": "8c4309dc00d725496c48bee6da0e4bbf", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_0010.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_0010.fastq.gz" + }, + "1197689": { + "fastq_r1_md5": "bc720a024263a518f6a6cd9301b308ac", + "fastq_r2_md5": "6bf6d95b59c950691effcaf8a0e83068", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_009.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_009.fastq.gz" + }, + "1197737": { + "fastq_r1_md5": "f5b60a93b39a0b98781efb434d577a57", + "fastq_r2_md5": "e19f883b4e05045895f990c2296009a8", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_007.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_007.fastq.gz" + }, + "1197767": { + "fastq_r1_md5": "c78fcb585a0f44734ce8c2aebf3eff33", + "fastq_r2_md5": "8361d5a6b50279fbc8c93226ecc3568a", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_003.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_003.fastq.gz" + }, + "1197824": { + "fastq_r1_md5": "9a460a812086516536c1a1023ab5f7fe", + "fastq_r2_md5": "41cd79b8a167d85eb06309207fd120cf", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_002.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_002.fastq.gz" + }, + "1197860": { + "fastq_r1_md5": "f2facbd1d6c7e0972074ced31ccbfd8e", + "fastq_r2_md5": "fd9948be8da7a38b0f80659dfc21aeea", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_001.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_001.fastq.gz" + }, + "8328199": { + "fastq_r1_md5": "aa557fc40d3a9e16f470ac595fb5eb3e", + "fastq_r2_md5": "a2dd5e08b75815dab892e392cb8468fc", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_004.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_004.fastq.gz" + } +} \ No newline at end of file From 70f288af664413efc066d20efa4d8bead2989ca1 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 8 Apr 2022 00:47:50 +0200 Subject: [PATCH 0312/1454] litin before upload to repo --- relecov_tools/map_schema.py | 14 ++++++++++---- relecov_tools/read_metadata.py | 4 +++- relecov_tools/sftp_handle.py | 12 +++++++++--- 3 files changed, 22 insertions(+), 8 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index 7a9cd2c5..afbc8dae 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -151,13 +151,19 @@ def mapping_json_data(self, mapping_schema_dict): def additional_formating(self, mapped_json_data): """Update data like MD5 to split in two fields, one for R1 file and - second for R2 + second for R2 """ if self.destination_schema == "ENA": for idx in range(len(self.json_data)): - import pdb; pdb.set_trace() - mapped_json_data[idx]["fastq_md5_r1"] = self.json_data[idx]["fastq_md5_r1"] - mapped_json_data[idx]["fastq_md5_r2"] = self.json_data[idx]["fastq_md5_r2"] + import pdb + + pdb.set_trace() + mapped_json_data[idx]["fastq_md5_r1"] = self.json_data[idx][ + "fastq_md5_r1" + ] + mapped_json_data[idx]["fastq_md5_r2"] = self.json_data[idx][ + "fastq_md5_r2" + ] return mapped_json_data diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 9ee7e490..476b086d 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -161,7 +161,9 @@ def add_additional_data(self, metadata, lab_json_file, geo_loc_file): for row_sample in metadata: """Include sample data from sample json""" try: - for key, value in samples_json[row_sample["collecting_lab_sample_id"]].items(): + for key, value in samples_json[ + row_sample["collecting_lab_sample_id"] + ].items(): row_sample[key] = value except KeyError: pass diff --git a/relecov_tools/sftp_handle.py b/relecov_tools/sftp_handle.py index 6dca44ef..e3b8b90f 100644 --- a/relecov_tools/sftp_handle.py +++ b/relecov_tools/sftp_handle.py @@ -34,7 +34,9 @@ def __init__(self, user=None, passwd=None, conf_file=None): self.sftp_user = user self.sftp_passwd = passwd if conf_file is None: - self.sftp_server = config_json.get_topic_data("sftp_connection", "sftp_server") + self.sftp_server = config_json.get_topic_data( + "sftp_connection", "sftp_server" + ) self.sftp_port = config_json.get_topic_data("sftp_connection", "sftp_port") self.storage_local_folder = config_json.get_configuration( "storage_local_folder" @@ -302,7 +304,9 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): if s_name not in sample_file_list: sample_file_list[s_name] = {} if row[index_fastq_r1] is not None: - sample_file_list[s_name]["sequence_file_R1_fastq"] = row[index_fastq_r1] + sample_file_list[s_name]["sequence_file_R1_fastq"] = row[ + index_fastq_r1 + ] else: log.error( "Fastq_R1 not defined in Metadata file for sample %s", s_name @@ -310,7 +314,9 @@ def get_sample_fastq_file_names(self, local_folder, meta_f_path): stderr.print("[red] No fastq R1 file for sample " + s_name) return False if row[index_fastq_r2] is not None: - sample_file_list[s_name]["sequence_file_R2_fastq"] = row[index_fastq_r2] + sample_file_list[s_name]["sequence_file_R2_fastq"] = row[ + index_fastq_r2 + ] return sample_file_list def validate_download_files(self, sample_file_list, local_folder): From 31a0e2f04038ec307c0d7895dfaf9035980abdeb Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 8 Apr 2022 09:47:14 +0200 Subject: [PATCH 0313/1454] Change for deleting samples to create the metadata for having data in only one sheet --- relecov_tools/json_validation.py | 33 ++++++++++++++------------------ 1 file changed, 14 insertions(+), 19 deletions(-) diff --git a/relecov_tools/json_validation.py b/relecov_tools/json_validation.py index a6eb28be..b096886e 100644 --- a/relecov_tools/json_validation.py +++ b/relecov_tools/json_validation.py @@ -72,26 +72,21 @@ def create_invalid_metadata(metadata_file, invalid_json, out_folder): for row in json_data: sample_list.append(row["collecting_lab_sample_id"]) wb = openpyxl.load_workbook(metadata_file) - exclude_sheet = ["Overview", "METADATA_LAB", "DATA VALIDATION"] - for sheet in wb.sheetnames: - if sheet in exclude_sheet: - continue - ws_sheet = wb[sheet] - row_to_del = [] - # Findout where the sample index is - idx_sample = 2 if ws_sheet.title == "1.Database Identifiers" else 1 + ws_sheet = wb["METADATA_LAB"] + row_to_del = [] - for row in ws_sheet.iter_rows(min_row=4, max_row=ws_sheet.max_row): - if not row[2].value and not row[1].value: - if len(row_to_del) > 0: - row_to_del.sort(reverse=True) - for idx in row_to_del: - ws_sheet.delete_rows(idx) - break - if row[0].value == "CAMPO": - continue - if str(row[idx_sample].value) not in sample_list: - row_to_del.append(row[0].row) + for row in ws_sheet.iter_rows(min_row=5, max_row=ws_sheet.max_row): + # if not data on row 1 and 2 assume that no more data are in file + # then start deleting rows + if not row[2].value and not row[1].value: + if len(row_to_del) > 0: + row_to_del.sort(reverse=True) + for idx in row_to_del: + ws_sheet.delete_rows(idx) + break + + if str(row[2].value) not in sample_list: + row_to_del.append(row[0].row) new_name = "invalid_" + os.path.basename(metadata_file) m_file = os.path.join(out_folder, new_name) From e7b78e2d066651078295678a17246d398d664a24 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 8 Apr 2022 09:56:05 +0200 Subject: [PATCH 0314/1454] add test for download when using config file --- relecov_tools/test/test_cases.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/test/test_cases.txt b/relecov_tools/test/test_cases.txt index a58d3d94..0e810fa9 100644 --- a/relecov_tools/test/test_cases.txt +++ b/relecov_tools/test/test_cases.txt @@ -1,4 +1,5 @@ relecov-tools -l /tmp/logs.log download -u usuario_test -p U[9[Gpyu3. +relecov-tools -l /tmp/logs.log download -f relecov_tools/test/sftp_config.yaml relecov-tools read-metadata -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -s relecov_tools/example_data/samples_data_COD_test_01_20220408.json -o /tmp relecov-tools validate -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -m relecov_tools/example_data/METADATA_LAB_TEST.xlsx -o /tmp relecov-tools map -j relecov_tools/example_data/processed_METADATA_LAB_TEST.json -o /tmp From cbe76f8a1689709fcd76dad600d3668e4519f30b Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 8 Apr 2022 10:33:13 +0200 Subject: [PATCH 0315/1454] added fastq_r1 and r2 for file and filepath --- relecov_tools/schema/ena_schema.json | 51 +++++++++++++++++++++------- 1 file changed, 39 insertions(+), 12 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index cb039d67..4a4b3fe5 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -746,18 +746,45 @@ "experiments" ] }, - "file_name": { - "examples": [ - "ABC123_S1_L001_R1_001.fastq.gz" - ], - "ontology": "GENEPIO:0001476", - "type": "string", - "description": "The user-specified filename of the r1 FASTQ file.", - "clasification": "Bioinformatics and QC metrics", - "label": "Sequence file R1 fastq", - "table": [ - "runs" - ] + "sequence_file_R1_fastq": { + "examples": [ + "ABC123_S1_L001_R1_001.fastq.gz" + ], + "ontology": "GENEPIO:0001476", + "type": "string", + "description": "The user-specified filename of the r1 FASTQ file.", + "clasification": "Bioinformatics and QC metrics", + "label": "Sequence file R1 fastq" + }, + "sequence_file_R2_fastq": { + "examples": [ + "ABC123_S1_L001_R2_001.fastq.gz" + ], + "ontology": "GENEPIO:0001477", + "type": "string", + "description": "The user-specified filename of the r2 FASTQ file.", + "clasification": "Bioinformatics and QC metrics", + "label": "Sequence file R2 fastq" + }, + "r1_fastq_filepath": { + "examples": [ + "/User/Documents/RespLab/Data/" + ], + "ontology": "GENEPIO:0001478", + "type": "string", + "description": "The filepath of the r1 FASTQ file.", + "clasification": "Bioinformatics and QC metrics", + "label": "Filepath R1 fastq" + }, + "r2_fastq_filepath": { + "examples": [ + "/User/Documents/RespLab/Data/" + ], + "ontology": "GENEPIO:0001479", + "type": "string", + "description": "The filepath of the r2 FASTQ file.", + "clasification": "Bioinformatics and QC metrics", + "label": "Filepath R2 fastq" }, "file_type": { "examples": [ From 1a1bda8cfadd09ba2cc4f16115cddf92e15a24c4 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 8 Apr 2022 10:45:38 +0200 Subject: [PATCH 0316/1454] added common_name in the fixed data. Needs to change because I wrote a dummy value --- relecov_tools/read_metadata.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 476b086d..8f51d2ae 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -107,6 +107,7 @@ def include_fixed_data(self): "type": "betacoronavirus", "tax_id": "2697049", "organism": "Severe acute respiratory syndrome coronavirus 2", + "common_name": "PEPITO", } fixed_data.update(self.configuration.get_configuration("ENA_configuration")) return fixed_data From 6817f74b1f7457905eeeeaf9d6005d114f3e0d65 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 8 Apr 2022 10:52:33 +0200 Subject: [PATCH 0317/1454] Added sample_description. with a suggested value --- relecov_tools/read_metadata.py | 1 + 1 file changed, 1 insertion(+) diff --git a/relecov_tools/read_metadata.py b/relecov_tools/read_metadata.py index 8f51d2ae..d3ef2aa7 100644 --- a/relecov_tools/read_metadata.py +++ b/relecov_tools/read_metadata.py @@ -108,6 +108,7 @@ def include_fixed_data(self): "tax_id": "2697049", "organism": "Severe acute respiratory syndrome coronavirus 2", "common_name": "PEPITO", + "sample_description" : "Sample for surveillance", } fixed_data.update(self.configuration.get_configuration("ENA_configuration")) return fixed_data From a9c0e969dd0f5a6bdcd33f39314de9b5e8d8ee41 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 8 Apr 2022 10:55:22 +0200 Subject: [PATCH 0318/1454] remove host_subject_id from the list of mandatory fields --- relecov_tools/schema/ena_schema.json | 1 - 1 file changed, 1 deletion(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 4a4b3fe5..21b8ec1a 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -7,7 +7,6 @@ "isolate", "host_scientific_name", "host_common_name", - "host_subject_id", "instrument_model", "file_name", "tax_id", From 38a2eaea00210448173bce0cc6773f732b782208 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 8 Apr 2022 10:56:06 +0200 Subject: [PATCH 0319/1454] rename the field for md5 field --- relecov_tools/map_schema.py | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/relecov_tools/map_schema.py b/relecov_tools/map_schema.py index afbc8dae..fb227f4a 100644 --- a/relecov_tools/map_schema.py +++ b/relecov_tools/map_schema.py @@ -155,14 +155,11 @@ def additional_formating(self, mapped_json_data): """ if self.destination_schema == "ENA": for idx in range(len(self.json_data)): - import pdb - - pdb.set_trace() - mapped_json_data[idx]["fastq_md5_r1"] = self.json_data[idx][ - "fastq_md5_r1" + mapped_json_data[idx]["fastq_r1_md5"] = self.json_data[idx][ + "fastq_r1_md5" ] - mapped_json_data[idx]["fastq_md5_r2"] = self.json_data[idx][ - "fastq_md5_r2" + mapped_json_data[idx]["fastq_r2_md5"] = self.json_data[idx][ + "fastq_r2_md5" ] return mapped_json_data From 65dfc5b710dab7befa9cd6b5845fe2583f2a6659 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 8 Apr 2022 11:20:09 +0200 Subject: [PATCH 0320/1454] updated wrong ontology value for Collector name --- relecov_tools/schema/ena_schema.json | 2 +- relecov_tools/schema/relecov_schema.json | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 21b8ec1a..88bf377e 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -53,7 +53,7 @@ "examples": [ "John Smith" ], - "ontology": "NCIT:C164471", + "ontology": "GENEPIO:0001153", "type": "string", "description": "Name of the person who collected the specimen", "clasification": "Sample collection and processing", diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 4122ca7f..7232b4cd 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2784,7 +2784,7 @@ "examples": [ "John Smith" ], - "ontology": "NCIT:C164471", + "ontology": "GENEPIO:0001153", "type": "string", "description": "Name of the person who collected the specimen", "clasification": "Sample collection and processing", @@ -3219,4 +3219,4 @@ "clasification": "Database Identifiers" } } -} \ No newline at end of file +} From a7b9ebbd6450efd6ffa99fe3882da73dfc2916a1 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 11 Apr 2022 10:21:39 +0200 Subject: [PATCH 0321/1454] changes in schema ena and relecov --- example_data_ena/.DS_Store | Bin 0 -> 6148 bytes example_data_ena/._.DS_Store | Bin 0 -> 120 bytes example_data_ena/._runs | Bin 0 -> 212 bytes example_data_ena/._samples | Bin 0 -> 212 bytes example_data_ena/._sequences | Bin 0 -> 212 bytes ...er_tool_metadata_v5_genome_assemblies.xlsx | Bin 0 -> 278 bytes ...er_tool_metadata_v5_genome_assemblies.xlsx | Bin 0 -> 32639 bytes example_data_ena/runs/.DS_Store | Bin 0 -> 6148 bytes example_data_ena/runs/._.DS_Store | Bin 0 -> 120 bytes example_data_ena/runs/._interactive | Bin 0 -> 212 bytes example_data_ena/runs/._programmatic | Bin 0 -> 212 bytes example_data_ena/runs/._webin-cli | Bin 0 -> 212 bytes .../runs/SARS-CoV-2-Sample1_1.fastq.gz | Bin 0 -> 568 bytes .../runs/SARS-CoV-2-Sample1_2.fastq.gz | Bin 0 -> 636 bytes .../runs/SARS-CoV-2-Sample2_1.fastq.gz | Bin 0 -> 597 bytes .../runs/SARS-CoV-2-Sample2_2.fastq.gz | Bin 0 -> 638 bytes .../runs/SARS-CoV-2-Sample3_1.fastq.gz | Bin 0 -> 609 bytes .../runs/SARS-CoV-2-Sample3_2.fastq.gz | Bin 0 -> 685 bytes .../runs/interactive/._pairedfastq.tsv | Bin 0 -> 212 bytes .../runs/interactive/pairedfastq.tsv | 5 + .../runs/programmatic/._experiments.xml | Bin 0 -> 212 bytes example_data_ena/runs/programmatic/._runs.xml | Bin 0 -> 212 bytes .../runs/programmatic/._submission.xml | Bin 0 -> 212 bytes .../runs/programmatic/experiments.xml | 66 ++++ example_data_ena/runs/programmatic/runs.xml | 33 ++ .../runs/programmatic/submission.xml | 10 + .../paired_fastq_manifest_sample1.txt | 13 + .../paired_fastq_manifest_sample2.txt | 13 + .../paired_fastq_manifest_sample3.txt | 13 + example_data_ena/samples/.DS_Store | Bin 0 -> 6148 bytes example_data_ena/samples/._.DS_Store | Bin 0 -> 120 bytes example_data_ena/samples/._interactive | Bin 0 -> 212 bytes example_data_ena/samples/._programmatic | Bin 0 -> 212 bytes .../interactive/._sample_spreadsheet.tsv | Bin 0 -> 268 bytes .../interactive/._sample_spreadsheet.xlsx | Bin 0 -> 244 bytes .../interactive/sample_spreadsheet.tsv | 7 + .../interactive/sample_spreadsheet.xlsx | Bin 0 -> 12010 bytes .../samples/programmatic/._samples.xml | Bin 0 -> 212 bytes .../samples/programmatic/._submission.xml | Bin 0 -> 212 bytes .../programmatic/._submission_modify.xml | Bin 0 -> 212 bytes .../samples/programmatic/samples.xml | 318 ++++++++++++++++++ .../samples/programmatic/submission.xml | 10 + .../samples/programmatic/submission_add.xml | 10 + .../programmatic/submission_modify.xml | 10 + example_data_ena/sequences/._webin-cli | Bin 0 -> 212 bytes example_data_ena/sequences/._webin-cli-rest | Bin 0 -> 212 bytes .../webin-cli-rest/hCoV-19_isolate_1.json | 13 + .../webin-cli-rest/hCoV-19_isolate_2.json | 13 + .../webin-cli-rest/hCoV-19_isolate_3.json | 15 + .../._hCoV-19_isolate_1_manifest.txt | Bin 0 -> 212 bytes .../._hCoV-19_isolate_2_manifest.txt | Bin 0 -> 212 bytes .../._hCoV-19_isolate_3_manifest.txt | Bin 0 -> 212 bytes .../webin-cli/hCoV-19_isolate_1.fasta.gz | Bin 0 -> 337 bytes .../hCoV-19_isolate_1_chrm_list.txt.gz | Bin 0 -> 84 bytes .../webin-cli/hCoV-19_isolate_1_manifest.txt | 13 + .../webin-cli/hCoV-19_isolate_2.fasta.gz | Bin 0 -> 272 bytes .../hCoV-19_isolate_2_chrm_list.txt.gz | Bin 0 -> 84 bytes .../webin-cli/hCoV-19_isolate_2_manifest.txt | 13 + .../webin-cli/hCoV-19_isolate_3.fasta.gz | Bin 0 -> 268 bytes .../hCoV-19_isolate_3_chrm_list.txt.gz | Bin 0 -> 84 bytes .../webin-cli/hCoV-19_isolate_3_manifest.txt | 15 + .../study/programmatic/project.xml | 9 + .../study/programmatic/receipt.xml | 13 + .../study/programmatic/submission.xml | 10 + relecov_tools/example_data/to_ena.json | 2 - relecov_tools/schema/relecov_schema.json | 65 ++-- 66 files changed, 663 insertions(+), 26 deletions(-) create mode 100644 example_data_ena/.DS_Store create mode 100644 example_data_ena/._.DS_Store create mode 100755 example_data_ena/._runs create mode 100755 example_data_ena/._samples create mode 100755 example_data_ena/._sequences create mode 100644 example_data_ena/drag_and_drop/._uploader_tool_metadata_v5_genome_assemblies.xlsx create mode 100644 example_data_ena/drag_and_drop/uploader_tool_metadata_v5_genome_assemblies.xlsx create mode 100644 example_data_ena/runs/.DS_Store create mode 100644 example_data_ena/runs/._.DS_Store create mode 100755 example_data_ena/runs/._interactive create mode 100755 example_data_ena/runs/._programmatic create mode 100755 example_data_ena/runs/._webin-cli create mode 100644 example_data_ena/runs/SARS-CoV-2-Sample1_1.fastq.gz create mode 100644 example_data_ena/runs/SARS-CoV-2-Sample1_2.fastq.gz create mode 100644 example_data_ena/runs/SARS-CoV-2-Sample2_1.fastq.gz create mode 100644 example_data_ena/runs/SARS-CoV-2-Sample2_2.fastq.gz create mode 100644 example_data_ena/runs/SARS-CoV-2-Sample3_1.fastq.gz create mode 100644 example_data_ena/runs/SARS-CoV-2-Sample3_2.fastq.gz create mode 100644 example_data_ena/runs/interactive/._pairedfastq.tsv create mode 100644 example_data_ena/runs/interactive/pairedfastq.tsv create mode 100644 example_data_ena/runs/programmatic/._experiments.xml create mode 100644 example_data_ena/runs/programmatic/._runs.xml create mode 100644 example_data_ena/runs/programmatic/._submission.xml create mode 100644 example_data_ena/runs/programmatic/experiments.xml create mode 100644 example_data_ena/runs/programmatic/runs.xml create mode 100644 example_data_ena/runs/programmatic/submission.xml create mode 100644 example_data_ena/runs/webin-cli/paired_fastq_manifest_sample1.txt create mode 100644 example_data_ena/runs/webin-cli/paired_fastq_manifest_sample2.txt create mode 100644 example_data_ena/runs/webin-cli/paired_fastq_manifest_sample3.txt create mode 100644 example_data_ena/samples/.DS_Store create mode 100644 example_data_ena/samples/._.DS_Store create mode 100755 example_data_ena/samples/._interactive create mode 100755 example_data_ena/samples/._programmatic create mode 100644 example_data_ena/samples/interactive/._sample_spreadsheet.tsv create mode 100644 example_data_ena/samples/interactive/._sample_spreadsheet.xlsx create mode 100644 example_data_ena/samples/interactive/sample_spreadsheet.tsv create mode 100644 example_data_ena/samples/interactive/sample_spreadsheet.xlsx create mode 100644 example_data_ena/samples/programmatic/._samples.xml create mode 100644 example_data_ena/samples/programmatic/._submission.xml 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forward_file_unencrypted_md5 reverse_file_unencrypted_md5 +ERS####### PRJEB##### Illumina NovaSeq 6000 SARS-CoV-2 library 1 VIRAL RNA RT-PCR AMPLICON PAIRED SARS-CoV-2-Sample1_1.fastq.gz 79fd9a51e0a56882ad33bcc8c1ab9cde SARS-CoV-2-Sample1_2.fastq.gz 31b0061cb66950132e4cac8e559c8851 Amplicons were cleaned-up with AMPure XP beads (Beckman Coulter) with a 1:1 ratio and amplicon concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) 100 +ERS####### PRJEB##### Illumina NovaSeq 6000 SARS-CoV-2 library 2 VIRAL RNA RT-PCR AMPLICON PAIRED SARS-CoV-2-Sample2_1.fastq.gz 79fd9a51e0a56882ad33bcc8c1ab9cde SARS-CoV-2-Sample2_2.fastq.gz 31b0061cb66950132e4cac8e559c8851 Amplicons were cleaned-up with AMPure XP beads (Beckman Coulter) with a 1:1 ratio and amplicon concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) 100 +ERS####### PRJEB##### Illumina NovaSeq 6000 SARS-CoV-2 library 3 VIRAL RNA RT-PCR AMPLICON PAIRED SARS-CoV-2-Sample3_1.fastq.gz 79fd9a51e0a56882ad33bcc8c1ab9cde SARS-CoV-2-Sample3_2.fastq.gz 31b0061cb66950132e4cac8e559c8851 Amplicons were cleaned-up with AMPure XP beads (Beckman Coulter) with a 1:1 ratio and amplicon concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) 100 diff --git a/example_data_ena/runs/programmatic/._experiments.xml b/example_data_ena/runs/programmatic/._experiments.xml new file mode 100644 index 0000000000000000000000000000000000000000..89f04770778303036c554a736916c5e4d908917a GIT binary patch literal 212 zcmZQz6=P>$Vqox1Ojhs@R)|o50+1L3ClDI}@gg7w@vi_e5x_AdBnYYuq+J^qI7A5ADWagzZ6zUroSQuKH8Jeb;r&(B7J7*N-=cZblxHwxn lS(;hux*3|A>6#cA8tXbbn!4&58kv|myO@}mx|kU=004fSA2a{} literal 0 HcmV?d00001 diff --git a/example_data_ena/runs/programmatic/._runs.xml b/example_data_ena/runs/programmatic/._runs.xml new file mode 100644 index 0000000000000000000000000000000000000000..89f04770778303036c554a736916c5e4d908917a GIT binary 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1:1 ratio and amplicon concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) + + + AMPLICON + VIRAL RNA + RT-PCR + + + + + + + + Illumina NovaSeq 6000 + + + + + SARS-CoV-2 UNIBS-AP66-0320 experiment 1 + + + Amplicons were cleaned-up with AMPure XP beads (Beckman Coulter) with a 1:1 ratio and amplicon concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) + + + AMPLICON + VIRAL RNA + RT-PCR + + + + + + + + Illumina NovaSeq 6000 + + + + + SARS-CoV-2 UNIBS-AP66-0320 experiment 1 + + + Amplicons were cleaned-up with AMPure XP beads (Beckman Coulter) with a 1:1 ratio and amplicon concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) + + + AMPLICON + VIRAL RNA + RT-PCR + + + + + + + + Illumina NovaSeq 6000 + + + + diff --git a/example_data_ena/runs/programmatic/runs.xml b/example_data_ena/runs/programmatic/runs.xml new file mode 100644 index 00000000..5180cad5 --- /dev/null +++ b/example_data_ena/runs/programmatic/runs.xml @@ -0,0 +1,33 @@ + + + + SARS-CoV-2 paired fastqs for sample 1 + + + + + + + + + + SARS-CoV-2 paired fastqs for sample 2 + + + + + + + + + + SARS-CoV-2 paired fastqs for sample 3 + + + + + + + + + diff --git a/example_data_ena/runs/programmatic/submission.xml b/example_data_ena/runs/programmatic/submission.xml new file mode 100644 index 00000000..8edfc2ad --- /dev/null +++ b/example_data_ena/runs/programmatic/submission.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/example_data_ena/runs/webin-cli/paired_fastq_manifest_sample1.txt b/example_data_ena/runs/webin-cli/paired_fastq_manifest_sample1.txt new file mode 100644 index 00000000..19f219dc --- /dev/null +++ b/example_data_ena/runs/webin-cli/paired_fastq_manifest_sample1.txt @@ -0,0 +1,13 @@ +STUDY PRJEB### or ERP### +SAMPLE SAMEA#### or ERS#### +NAME SARS-CoV-2 sample 1 reads +PLATFORM ILLUMINA +INSTRUMENT Illumina NovaSeq 6000 +INSERT_SIZE 100 +LIBRARY_NAME SARS-CoV-2 library 1 +LIBRARY_SOURCE VIRAL RNA +LIBRARY_SELECTION RT-PCR +LIBRARY_STRATEGY AMPLICON +DESCRIPTION Amplicons were cleaned-up with AMPure XP beads (Beckman Coulter) with a 1:1 ratio and amplicon concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) +FASTQ SARS-CoV-2-Sample1_1.fastq.gz +FASTQ SARS-CoV-2-Sample1_2.fastq.gz diff --git a/example_data_ena/runs/webin-cli/paired_fastq_manifest_sample2.txt b/example_data_ena/runs/webin-cli/paired_fastq_manifest_sample2.txt new file mode 100644 index 00000000..31a9da8f --- /dev/null +++ b/example_data_ena/runs/webin-cli/paired_fastq_manifest_sample2.txt @@ -0,0 +1,13 @@ +STUDY PRJEB### or ERP### +SAMPLE SAMEA#### or ERS#### +NAME SARS-CoV-2 sample 2 reads +PLATFORM ILLUMINA +INSTRUMENT Illumina NovaSeq 6000 +INSERT_SIZE 100 +LIBRARY_NAME SARS-CoV-2 library 2 +LIBRARY_SOURCE VIRAL RNA +LIBRARY_SELECTION RT-PCR +LIBRARY_STRATEGY AMPLICON +DESCRIPTION Amplicons were cleaned-up with AMPure 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collector name + Michael C + + + collecting institution + Institute for Infectious Diseases, University of Bern + + + isolate + hCoV-19/isolate/2 + + + receipt date + 2020-09-22 + + + sample capture status + active surveillance in response to outbreak + + + geographic location (latitude) + 46.8182 + DD + + + geographic location (longitude) + 8.2275 + DD + + + geographic location (region and locality) + Bern + + + host disease outcome + recovered + + + host age + 25 + years + + + virus identifier + SS1 + + + definition for seropositive sample + 80 + + + host habitat + other + + + isolation source host-associated + Nasopharyngeal exudate + + + host behaviour + domestic + + + ENA-CHECKLIST + ERC000033 + + + + + SARS Sample 3 + + 2697049 + Severe acute respiratory syndrome coronavirus 2 + + SARS-CoV-2 Sample #3 + + + collection date + 2020-09-20 + + + geographic location (country and/or sea) + Switzerland + + + host common name + Homo Sapiens + + + host subject id + 3 + + + host health state + diseased + + + host sex + female + + + host scientific name + homo sapiens + + + collector name + Michael C + + + collecting institution + Institute for Infectious Diseases, University of Bern + + + isolate + hCoV-19/isolate/3 + + + receipt date + 2020-09-22 + + + sample capture status + active surveillance in response to outbreak + + + geographic location (latitude) + 46.8182 + DD + + + geographic location (longitude) + 8.2275 + DD + + + geographic location (region and locality) + Bern + + + host disease outcome + recovered + + + host age + 40 + years + + + virus identifier + SS1 + + + definition for seropositive sample + 80 + + + host habitat + other + + + isolation source host-associated + Nasopharyngeal exudate + + + host behaviour + domestic + + + ENA-CHECKLIST + ERC000033 + + + + diff --git a/example_data_ena/samples/programmatic/submission.xml b/example_data_ena/samples/programmatic/submission.xml new file mode 100644 index 00000000..8edfc2ad --- /dev/null +++ b/example_data_ena/samples/programmatic/submission.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/example_data_ena/samples/programmatic/submission_add.xml b/example_data_ena/samples/programmatic/submission_add.xml new file mode 100644 index 00000000..8edfc2ad --- /dev/null +++ b/example_data_ena/samples/programmatic/submission_add.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/example_data_ena/samples/programmatic/submission_modify.xml b/example_data_ena/samples/programmatic/submission_modify.xml new file mode 100644 index 00000000..d9bc1a3a --- /dev/null +++ b/example_data_ena/samples/programmatic/submission_modify.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/example_data_ena/sequences/._webin-cli b/example_data_ena/sequences/._webin-cli new file mode 100755 index 0000000000000000000000000000000000000000..89f04770778303036c554a736916c5e4d908917a GIT binary patch literal 212 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"hCov-19_isolate_1", + "coverage": 100, + "program": "ARTIC fieldbioinformatics (minimap2/nanopolish) 1.1.3 (nanopolish 0.13.2)", + "platform": "ILLUMINA", + "minGapLength": 3, + "moleculeType": "genomic RNA", + "description": "example sequence #1 for workshop", + "sequence": "NNNNNNNNNTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGG" +} diff --git a/example_data_ena/sequences/webin-cli-rest/hCoV-19_isolate_2.json b/example_data_ena/sequences/webin-cli-rest/hCoV-19_isolate_2.json new file mode 100644 index 00000000..40f4d346 --- /dev/null +++ b/example_data_ena/sequences/webin-cli-rest/hCoV-19_isolate_2.json @@ -0,0 +1,13 @@ +{ + "study": "PRJEB#####", + "sample": "ERS#######", + "runRef": "ERR#######", + "name": "hCov-19_isolate_2", + "coverage": 1000, + "program": "ARTIC fieldbioinformatics (minimap2/nanopolish) 1.1.3 (nanopolish 0.13.2)", + "platform": "ILLUMINA", + "minGapLength": 3, + "moleculeType": "genomic RNA", + "description": "example sequence #2 for workshop", + "sequence": "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACT" +} diff --git a/example_data_ena/sequences/webin-cli-rest/hCoV-19_isolate_3.json b/example_data_ena/sequences/webin-cli-rest/hCoV-19_isolate_3.json new file mode 100644 index 00000000..98462bf7 --- /dev/null +++ b/example_data_ena/sequences/webin-cli-rest/hCoV-19_isolate_3.json @@ -0,0 +1,15 @@ +{ + "study": "PRJEB#####", + "sample": "ERS#######", + "runRef": "ERR#######", + "name": "hCov-19_isolate_3", + "coverage": 95.1, + "program": "MPileup", + "platform": "ILLUMINA", + "minGapLength": 1, + "moleculeType": "genomic RNA", + "description": "example sequence #3 for workshop", + "sequence": "AAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCATCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGT", + "authors": "ZW", + "address": "EBI" +} diff --git a/example_data_ena/sequences/webin-cli/._hCoV-19_isolate_1_manifest.txt b/example_data_ena/sequences/webin-cli/._hCoV-19_isolate_1_manifest.txt new file mode 100644 index 0000000000000000000000000000000000000000..89f04770778303036c554a736916c5e4d908917a GIT binary patch literal 212 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b/example_data_ena/sequences/webin-cli/hCoV-19_isolate_1_chrm_list.txt.gz new file mode 100644 index 0000000000000000000000000000000000000000..c83f637b5c64aa12422007c48c9ed5b441788303 GIT binary patch literal 84 zcmV-a0IUBWiwFp+AYfqt1875URxL3(Uuko1Y+-a|Uol@}XmV{|Y-w|JE_8Tw0LyUB q57RZY)Xyx=&q*vv)i>lcf4kDrh8*Xj0r+<#wxr_cI+>(Xd@ zYu2$>QjgzVQYyneeA~yJwB^@`A$7BZlUccm#)Tni`pi9YonZD!*{8;A7lY{zF)d?! z%FXQ5oEpl*Kx8SX+Q23v1xggeQXV&SZZIYfZT17EuE=pMazq(8-;G>U7>$hRO@>Ct zGD#m2M|l?U@UTjVbx6g@=)tSFS%-P(h&PJt&SWG+5$9PQo8m+aP{GZQ&>;&f)U>fA W5hWAq$>P`+VEqG@cw*)_0ssK;`hhP1 literal 0 HcmV?d00001 diff --git a/example_data_ena/sequences/webin-cli/hCoV-19_isolate_2_chrm_list.txt.gz b/example_data_ena/sequences/webin-cli/hCoV-19_isolate_2_chrm_list.txt.gz new file mode 100644 index 0000000000000000000000000000000000000000..2e9631278d9dce92599d1815e6e35b12470433fc GIT binary patch literal 84 zcmV-a0IUBWiwFo|Az)zu1875URxL3(Uuko1Y+-a|Uou}~XmV{|Y-w|JE_8Tw0LyUB q57RZY)Xyx=&q*vv)i>faJ zE)YH;RhocM;R~4bDFQzb_(gJm;wLXV!+6KCEot8GetbN?yxqQkA3vXeU$@t%BUN>` zT6VW>{v~U+uRVE}+Vk}!6HbxOoZxCP6K-a{;`CfQp*4FDMQ9RrW)fpXArm)D-83)3 zL?9JHQ^YtpxKEMwHgyzCkTre + + Example project for ENA submission workshop + This study was created as part of an ENA submissions workshop + + + + + diff --git a/example_data_ena/study/programmatic/receipt.xml b/example_data_ena/study/programmatic/receipt.xml new file mode 100644 index 00000000..4b43c31b --- /dev/null +++ b/example_data_ena/study/programmatic/receipt.xml @@ -0,0 +1,13 @@ + + curl -u Webin-60330:W2b3nENA%2021 -F "SUBMISSION=@submission.xml" -F "PROJECT=@project.xml" "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/" + + + + + + + + + This submission is a TEST submission and will be discarded within 24 hours + + ADD diff --git a/example_data_ena/study/programmatic/submission.xml b/example_data_ena/study/programmatic/submission.xml new file mode 100644 index 00000000..8edfc2ad --- /dev/null +++ b/example_data_ena/study/programmatic/submission.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/relecov_tools/example_data/to_ena.json b/relecov_tools/example_data/to_ena.json index fa46d819..e9d06f17 100644 --- a/relecov_tools/example_data/to_ena.json +++ b/relecov_tools/example_data/to_ena.json @@ -25,8 +25,6 @@ "study_alias": "study_alias_1", "study_title": "study_title", "study_type": "RNASeq", - "study_abstract": "study_abstract_1", - "pubmed_id": "pubmed_id_2", "run_alias": "run_alias_1a", "experiment_alias": "experiment_alias_7a", "file_type": "fastq", diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 5846f4ce..0aa7fa36 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -846,16 +846,6 @@ "classification": "Sample collection and processing", "label": "Public Health sample id (SIVIES)" }, - "isolate_sample_id": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "", - "label": "Sample ID given if multiple rna-extraction or passages" - }, "geo_loc_region": { "examples": [ "Derbyshire" @@ -2207,6 +2197,16 @@ "classification": "Bioinformatics and QC metrics", "label": "Depth of coverage threshold" }, + "file_type": { + "examples": [ + "" + ], + "ontology": "", + "type": "string", + "description": "", + "classification": "", + "label": "" + }, "sequence_file_R1_fastq": { "examples": [ "ABC123_S1_L001_R1_001.fastq.gz" @@ -2416,7 +2416,7 @@ "classification": "Lineage and Variant information", "label": "Mapping params" }, - "lineage/clade_name": { + "lineage_name": { "examples": [ "B.1.1.7" ], @@ -2426,7 +2426,7 @@ "classification": "Lineage and Variant information", "label": "Lineage/clade name" }, - "lineage/clade_analysis_software_name": { + "lineage_analysis_software_name": { "examples": [ "Pangolin" ], @@ -2446,7 +2446,7 @@ "classification": "Lineage and Variant information", "label": "If lineage identification Is Other, Specify" }, - "lineage/clade_analysis_software_version": { + "lineage_analysis_software_version": { "examples": [ "2.1.10" ], @@ -2456,6 +2456,26 @@ "classification": "Lineage and Variant information", "label": "Lineage/clade analysis software version" }, + "design_description": { + "examples": [ + "" + ], + "ontology": "NCIT:C147139", + "type": "string", + "description": "", + "classification": "", + "label": "" + }, + "isolate_sample_id": { + "examples": [ + "" + ], + "ontology": "NCIT:C53471", + "type": "string", + "description": "", + "classification": "", + "label": "" + }, "variant_designation": { "Enums": [ "Variant of Interest (VOI) [GENEPIO:0100082]", @@ -2531,7 +2551,7 @@ "classification": "Pathogen diagnostic testing", "label": "Gene Name 1" }, - "Protocol_SARS-CoV-2_detection": { + "protocol_SARS-CoV-2_detection": { "examples": [ "" ], @@ -2541,7 +2561,7 @@ "classification": "Pathogen diagnostic testing", "label": "Protocol SARS-CoV-2 detection" }, - "%qc_filtered": { + "per_qc_filtered": { "examples": [ "" ], @@ -2551,7 +2571,7 @@ "classification": "Pathogen diagnostic testing", "label": "%qc filtered" }, - "%reads_host": { + "per_reads_host": { "examples": [ "" ], @@ -2561,7 +2581,7 @@ "classification": "Pathogen diagnostic testing", "label": "%reads host" }, - "%reads_virus": { + "per_reads_virus": { "examples": [ "" ], @@ -2571,7 +2591,7 @@ "classification": "Pathogen diagnostic testing", "label": "%reads virus" }, - "%unmapped": { + "per_unmapped": { "examples": [ "" ], @@ -2581,7 +2601,7 @@ "classification": "Pathogen diagnostic testing", "label": "%unmapped" }, - "%genome _greater_10x": { + "per_genome _greater_10x": { "examples": [ "" ], @@ -2601,7 +2621,7 @@ "classification": "Pathogen diagnostic testing", "label": "mean depth of coverage value" }, - "%Ns": { + "per_Ns": { "examples": [ "" ], @@ -2611,7 +2631,7 @@ "classification": "Pathogen diagnostic testing", "label": "%Ns" }, - "Number_of_variants_(AF_greater_75%)": { + "Number_of_variants_AF_greater_75percent": { "examples": [ "" ], @@ -2839,7 +2859,6 @@ "classification": "Sequencing", "label": "Source material" }, -<<<<<<< HEAD "nominal_length": { "examples": [ "" @@ -2849,8 +2868,6 @@ "description": "", "classification": "Sequencing" }, -======= ->>>>>>> 9c936c3849ca0ab49bfbae14d04d81d56726156c "analysis_accession": { "examples": [ "" From ab0ac5b5f9ee4f826ec803bc6a55064c095c524b Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 11 Apr 2022 16:34:00 +0200 Subject: [PATCH 0322/1454] adding example data after latest changes --- .../processed_METADATA_LAB_TEST.json | 20 +++++++++++++++++++ relecov_tools/schema/ena_schema.json | 1 - 2 files changed, 20 insertions(+), 1 deletion(-) diff --git a/relecov_tools/example_data/processed_METADATA_LAB_TEST.json b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json index a8ff18e9..cdb3cbc7 100644 --- a/relecov_tools/example_data/processed_METADATA_LAB_TEST.json +++ b/relecov_tools/example_data/processed_METADATA_LAB_TEST.json @@ -10,6 +10,7 @@ "collecting_institution": "Hospital Universitario Miguel Servet", "collecting_lab_sample_id": "1197860", "collection_device": "Swab", + "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "45", "diagnostic_pcr_Ct_value_2": "34", @@ -55,6 +56,7 @@ "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", "sample_collection_date": "2021/04/13", + "sample_description": "Sample for surveillance", "sample_received_date": "2021/05/13", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_001.fastq.gz", @@ -82,6 +84,7 @@ "collecting_institution": "Hospital Universitario Miguel Servet", "collecting_lab_sample_id": "1197824", "collection_device": "Swab", + "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "12", "diagnostic_pcr_Ct_value_2": "16", @@ -127,6 +130,7 @@ "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", "sample_collection_date": "2021/03/31", + "sample_description": "Sample for surveillance", "sample_received_date": "2021/05/13", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_002.fastq.gz", @@ -154,6 +158,7 @@ "collecting_institution": "Hospital Universitario Miguel Servet", "collecting_lab_sample_id": "1197767", "collection_device": "Swab", + "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "45", "diagnostic_pcr_Ct_value_2": "41", @@ -199,6 +204,7 @@ "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", "sample_collection_date": "2022/01/13", + "sample_description": "Sample for surveillance", "sample_received_date": "2022/01/18", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_003.fastq.gz", @@ -226,6 +232,7 @@ "collecting_institution": "Hospital Universitario Miguel Servet", "collecting_lab_sample_id": "8328199", "collection_device": "Swab", + "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "23", "diagnostic_pcr_Ct_value_2": "23", @@ -271,6 +278,7 @@ "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", "sample_collection_date": "2022/01/11", + "sample_description": "Sample for surveillance", "sample_received_date": "2022/01/20", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_004.fastq.gz", @@ -298,6 +306,7 @@ "collecting_institution": "Hospital Universitario Miguel Servet", "collecting_lab_sample_id": "1197677", "collection_device": "Swab", + "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "12", "diagnostic_pcr_Ct_value_2": "10", @@ -343,6 +352,7 @@ "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", "sample_collection_date": "2022/01/10", + "sample_description": "Sample for surveillance", "sample_received_date": "2022/01/20", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_005.fastq.gz", @@ -370,6 +380,7 @@ "collecting_institution": "Hospital Universitario Miguel Servet", "collecting_lab_sample_id": "1197678", "collection_device": "Swab", + "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "56", "diagnostic_pcr_Ct_value_2": "19", @@ -415,6 +426,7 @@ "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", "sample_collection_date": "2022/01/12", + "sample_description": "Sample for surveillance", "sample_received_date": "2022/01/20", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_006.fastq.gz", @@ -442,6 +454,7 @@ "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", "collecting_lab_sample_id": "1197737", "collection_device": "Swab", + "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "11", "diagnostic_pcr_Ct_value_2": "11", @@ -487,6 +500,7 @@ "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", "sample_collection_date": "2022/01/02", + "sample_description": "Sample for surveillance", "sample_received_date": "2022/01/20", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_007.fastq.gz", @@ -514,6 +528,7 @@ "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", "collecting_lab_sample_id": "1197663", "collection_device": "Swab", + "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "34", "diagnostic_pcr_Ct_value_2": "36", @@ -559,6 +574,7 @@ "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", "sample_collection_date": "2022/01/23", + "sample_description": "Sample for surveillance", "sample_received_date": "2022/01/25", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_008.fastq.gz", @@ -586,6 +602,7 @@ "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", "collecting_lab_sample_id": "1197689", "collection_device": "Swab", + "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "23", "diagnostic_pcr_Ct_value_2": "20", @@ -631,6 +648,7 @@ "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", "sample_collection_date": "2022/01/18", + "sample_description": "Sample for surveillance", "sample_received_date": "2022/01/26", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_009.fastq.gz", @@ -658,6 +676,7 @@ "collecting_institution": "Hospital Clínico Universitario Lozano Blesa", "collecting_lab_sample_id": "1197685", "collection_device": "Swab", + "common_name": "PEPITO", "design_description": "Design Description", "diagnostic_pcr_Ct_value_1": "32", "diagnostic_pcr_Ct_value_2": "32", @@ -703,6 +722,7 @@ "runID": "MiSeq_GEN_267_20220208_ICasas", "run_alias": "", "sample_collection_date": "2022/01/19", + "sample_description": "Sample for surveillance", "sample_received_date": "2022/01/26", "sample_storage_conditions": " -80ºC", "sequence_file_R1_fastq": "ABC123_S1_L001_R1_0010.fastq.gz", diff --git a/relecov_tools/schema/ena_schema.json b/relecov_tools/schema/ena_schema.json index 88bf377e..40327552 100644 --- a/relecov_tools/schema/ena_schema.json +++ b/relecov_tools/schema/ena_schema.json @@ -8,7 +8,6 @@ "host_scientific_name", "host_common_name", "instrument_model", - "file_name", "tax_id", "scientific_name", "common_name", From 13c49088c7884acf9dd60cc8398bf8f179206e51 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 11 Apr 2022 17:11:13 +0200 Subject: [PATCH 0323/1454] fixing merging conflict --- relecov_tools/schema/relecov_schema.json | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 81e21c55..5bd8aa5b 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2839,18 +2839,6 @@ "classification": "Sequencing", "label": "Source material" }, -<<<<<<< HEAD - "nominal_length": { - "examples": [ - "" - ], - "ontology": "0", - "type": "string", - "description": "", - "classification": "Sequencing" - }, -======= ->>>>>>> 9c936c3849ca0ab49bfbae14d04d81d56726156c "analysis_accession": { "examples": [ "" From 0908caed0befdb6aea6e90a2196e078e01bd5093 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 11 Apr 2022 17:15:50 +0200 Subject: [PATCH 0324/1454] Fixing validation error in schema for analysis_date and lineage_identification_date --- relecov_tools/schema/relecov_schema.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/relecov_tools/schema/relecov_schema.json b/relecov_tools/schema/relecov_schema.json index 5bd8aa5b..e53582bb 100644 --- a/relecov_tools/schema/relecov_schema.json +++ b/relecov_tools/schema/relecov_schema.json @@ -2713,10 +2713,10 @@ }, "analysis_date": { "examples": [ - "" + "e.g 2020-08-07" ], "ontology": "0", - "type": "date", + "type": "string", "format": "date", "description": "", "classification": "Bioinformatics and QC metrics", @@ -2727,7 +2727,7 @@ "" ], "ontology": "0", - "type": "date", + "type": "string", "format": "date", "description": "", "classification": "Bioinformatics and QC metrics", From 155a8e79e9b465203396218be34ffe6dc245ed35 Mon Sep 17 00:00:00 2001 From: "erika.kvalem" Date: Mon, 11 Apr 2022 17:40:05 +0200 Subject: [PATCH 0325/1454] added creation of dataframes --- relecov_tools/ena_upload.py | 70 +++++++++++++++++++++---------------- 1 file changed, 40 insertions(+), 30 deletions(-) diff --git a/relecov_tools/ena_upload.py b/relecov_tools/ena_upload.py index fac92f33..d482396d 100644 --- a/relecov_tools/ena_upload.py +++ b/relecov_tools/ena_upload.py @@ -3,7 +3,7 @@ import rich.console import json -# import pandas as pd +import pandas as pd import sys import relecov_tools.utils from relecov_tools.config_json import ConfigJson @@ -95,40 +95,50 @@ def create_structure_to_ena(self): fh = open(map_file) map_structure_json = json.load(fh) fh.close() + + esquema = self.source_json_file + fh_esquema = open(esquema) + esquema_json = json.load(fh_esquema) + fh_esquema.close() # lista = ["study", "runs", "samples", "experiments"] + + llaves = esquema_json.keys() import pdb pdb.set_trace() - for i in map_structure_json["properties"].keys(): - - if "table" in i.keys() and "study" in i["table"]: - - print(i["table"]) - - """ - for xml_file in lista: - if self.project is not None and xml_file in self.project: - pass - elif config_json.get_configuration(xml_file): - df = pd.DataFrame.from_dict( - config_json.get_configuration(xml_file), orient="index" - ) - - else: - data = [] - for chunk in self.json_data: - xml_dict = {} - for key, value in chunk.items(): - if key in map_structure_json[xml_file]: - xml_dict[map_structure_json[xml_file][key]] = value - data.append(xml_dict) - if xml_file in map_structure_json["one_loop_in_mapping"]: - break - df = ena_upload.check_columns(df, xml_file, self.action, self.dev, False) - schema_dataframe[xml_file] = df - return schema_dataframe - """ + df = pd.DataFrame.from_dict(esquema_json, orient="index") + df_transposed = df.T + df_study = df_transposed[["study_alias", "study_title", "study_type"]] + df_samples = df_transposed[ + [ + "sample_name", + "tax_id", + "sample_description", + "collection_date", + "geographic_location_(country_and/or_sea)", + "host_common_name", + "host_gender", + "host_scientific_name", + "isolate", + ] + ] + df_runs = df_transposed[ + ["experiment_alias", "sequence_file_R1_fastq", "sequence_file_R2_fastq"] + ] + df_experiments = df_transposed[ + [ + "experiment_alias", + "study_title", + "sample_name", + "library_strategy", + "library_source", + "library_selection", + "library_layout", + "instrument_platform", + "instrument_model", + ] + ] def upload(self): """Create the required files and upload to ENA""" From 38b030e6864b9652399fc6e2fb12b8e099bb1139 Mon Sep 17 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a/example_data_ena/runs/interactive/pairedfastq.tsv b/example_data_ena/runs/interactive/pairedfastq.tsv deleted file mode 100644 index 0335cc2f..00000000 --- a/example_data_ena/runs/interactive/pairedfastq.tsv +++ /dev/null @@ -1,5 +0,0 @@ -FileType fastq Read submission file type -sample study instrument_model library_name library_source library_selection library_strategy library_layout forward_file_name forward_file_md5 reverse_file_name reverse_file_md5 library_design library_construction_protocol design_description insert_size forward_file_unencrypted_md5 reverse_file_unencrypted_md5 -ERS####### PRJEB##### Illumina NovaSeq 6000 SARS-CoV-2 library 1 VIRAL RNA RT-PCR AMPLICON PAIRED SARS-CoV-2-Sample1_1.fastq.gz 79fd9a51e0a56882ad33bcc8c1ab9cde SARS-CoV-2-Sample1_2.fastq.gz 31b0061cb66950132e4cac8e559c8851 Amplicons were cleaned-up with AMPure XP beads (Beckman Coulter) with a 1:1 ratio and amplicon concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) 100 -ERS####### PRJEB##### Illumina NovaSeq 6000 SARS-CoV-2 library 2 VIRAL RNA RT-PCR AMPLICON PAIRED SARS-CoV-2-Sample2_1.fastq.gz 79fd9a51e0a56882ad33bcc8c1ab9cde SARS-CoV-2-Sample2_2.fastq.gz 31b0061cb66950132e4cac8e559c8851 Amplicons were cleaned-up with AMPure XP beads (Beckman Coulter) with a 1:1 ratio and amplicon concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) 100 -ERS####### PRJEB##### Illumina NovaSeq 6000 SARS-CoV-2 library 3 VIRAL RNA RT-PCR AMPLICON PAIRED SARS-CoV-2-Sample3_1.fastq.gz 79fd9a51e0a56882ad33bcc8c1ab9cde SARS-CoV-2-Sample3_2.fastq.gz 31b0061cb66950132e4cac8e559c8851 Amplicons were cleaned-up with AMPure XP beads (Beckman Coulter) with a 1:1 ratio and amplicon concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) 100 diff --git a/example_data_ena/runs/programmatic/._experiments.xml b/example_data_ena/runs/programmatic/._experiments.xml deleted file mode 100644 index 89f04770778303036c554a736916c5e4d908917a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 212 zcmZQz6=P>$Vqox1Ojhs@R)|o50+1L3ClDI}@gg7w@vi_e5x_AdBnYYuq+J^qI7A5ADWagzZ6zUroSQuKH8Jeb;r&(B7J7*N-=cZblxHwxn lS(;hux*3|A>6#cA8tXbbn!4&58kv|myO@}mx|kU=004fSA2a{} diff --git a/example_data_ena/runs/programmatic/._runs.xml b/example_data_ena/runs/programmatic/._runs.xml deleted file mode 100644 index 89f04770778303036c554a736916c5e4d908917a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 212 zcmZQz6=P>$Vqox1Ojhs@R)|o50+1L3ClDI}@gg7w@vi_e5x_AdBnYYuq+J^qI7A5ADWagzZ6zUroSQuKH8Jeb;r&(B7J7*N-=cZblxHwxn lS(;hux*3|A>6#cA8tXbbn!4&58kv|myO@}mx|kU=004fSA2a{} diff --git a/example_data_ena/runs/programmatic/._submission.xml b/example_data_ena/runs/programmatic/._submission.xml deleted file mode 100644 index 89f04770778303036c554a736916c5e4d908917a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 212 zcmZQz6=P>$Vqox1Ojhs@R)|o50+1L3ClDI}@gg7w@vi_e5x_AdBnYYuq+J^qI7A5ADWagzZ6zUroSQuKH8Jeb;r&(B7J7*N-=cZblxHwxn lS(;hux*3|A>6#cA8tXbbn!4&58kv|myO@}mx|kU=004fSA2a{} diff --git a/example_data_ena/runs/programmatic/experiments.xml b/example_data_ena/runs/programmatic/experiments.xml deleted file mode 100644 index 031917be..00000000 --- a/example_data_ena/runs/programmatic/experiments.xml +++ /dev/null @@ -1,66 +0,0 @@ - - - - SARS-CoV-2 experiment 1 - - - Amplicons were cleaned-up with AMPure XP beads (Beckman Coulter) with a 1:1 ratio and amplicon concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) - - - AMPLICON - VIRAL RNA - RT-PCR - - - - - - - - Illumina NovaSeq 6000 - - - - - SARS-CoV-2 UNIBS-AP66-0320 experiment 1 - - - Amplicons were cleaned-up with AMPure XP beads (Beckman Coulter) with a 1:1 ratio and amplicon concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) - - - AMPLICON - VIRAL RNA - RT-PCR - - - - - - - - Illumina NovaSeq 6000 - - - - - SARS-CoV-2 UNIBS-AP66-0320 experiment 1 - - - Amplicons were cleaned-up with AMPure XP beads (Beckman Coulter) with a 1:1 ratio and amplicon concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) - - - AMPLICON - VIRAL RNA - RT-PCR - - - - - - - - Illumina NovaSeq 6000 - - - - diff --git a/example_data_ena/runs/programmatic/runs.xml b/example_data_ena/runs/programmatic/runs.xml deleted file mode 100644 index 5180cad5..00000000 --- a/example_data_ena/runs/programmatic/runs.xml +++ /dev/null @@ -1,33 +0,0 @@ - - - - SARS-CoV-2 paired fastqs for sample 1 - - - - - - - - - - SARS-CoV-2 paired fastqs for sample 2 - - - - - - - - - - SARS-CoV-2 paired fastqs for sample 3 - - - - - - - - - diff --git a/example_data_ena/runs/programmatic/submission.xml b/example_data_ena/runs/programmatic/submission.xml deleted file mode 100644 index 8edfc2ad..00000000 --- a/example_data_ena/runs/programmatic/submission.xml +++ /dev/null @@ -1,10 +0,0 @@ - - - - - - - - - - diff --git a/example_data_ena/runs/webin-cli/paired_fastq_manifest_sample1.txt b/example_data_ena/runs/webin-cli/paired_fastq_manifest_sample1.txt deleted file mode 100644 index 19f219dc..00000000 --- a/example_data_ena/runs/webin-cli/paired_fastq_manifest_sample1.txt +++ /dev/null @@ -1,13 +0,0 @@ -STUDY PRJEB### or ERP### -SAMPLE SAMEA#### or ERS#### -NAME SARS-CoV-2 sample 1 reads -PLATFORM ILLUMINA -INSTRUMENT Illumina NovaSeq 6000 -INSERT_SIZE 100 -LIBRARY_NAME SARS-CoV-2 library 1 -LIBRARY_SOURCE VIRAL RNA -LIBRARY_SELECTION RT-PCR -LIBRARY_STRATEGY AMPLICON -DESCRIPTION Amplicons were cleaned-up with AMPure XP beads (Beckman Coulter) with a 1:1 ratio and amplicon concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) -FASTQ SARS-CoV-2-Sample1_1.fastq.gz -FASTQ SARS-CoV-2-Sample1_2.fastq.gz diff --git a/example_data_ena/runs/webin-cli/paired_fastq_manifest_sample2.txt b/example_data_ena/runs/webin-cli/paired_fastq_manifest_sample2.txt deleted file mode 100644 index 31a9da8f..00000000 --- a/example_data_ena/runs/webin-cli/paired_fastq_manifest_sample2.txt +++ /dev/null @@ -1,13 +0,0 @@ -STUDY PRJEB### or ERP### -SAMPLE SAMEA#### or ERS#### -NAME SARS-CoV-2 sample 2 reads -PLATFORM ILLUMINA -INSTRUMENT Illumina NovaSeq 6000 -INSERT_SIZE 100 -LIBRARY_NAME SARS-CoV-2 library 2 -LIBRARY_SOURCE VIRAL RNA -LIBRARY_SELECTION RT-PCR -LIBRARY_STRATEGY AMPLICON -DESCRIPTION Amplicons were cleaned-up with AMPure XP beads (Beckman Coulter) with a 1:1 ratio and amplicon concentrations were quantified with the Qubit Fluorometric Quantitation system (Life Technologies) -FASTQ SARS-CoV-2-Sample2_1.fastq.gz -FASTQ SARS-CoV-2-Sample2_2.fastq.gz diff --git a/example_data_ena/runs/webin-cli/paired_fastq_manifest_sample3.txt b/example_data_ena/runs/webin-cli/paired_fastq_manifest_sample3.txt deleted file 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location (region and locality) sample capture status host disease outcome host common name host subject id host age host health state host sex host scientific name virus identifier collector name collecting institution receipt date definition for seropositive sample serotype (required for a seropositive sample) isolate host habitat isolation source host-associated host behaviour isolation source non-host-associated GISAID Accesion ID max_cycle_threshold -#units DD DD years -2697049 Severe acute respiratory syndrome coronavirus 2 SARS Sample 1 SARS Sample 1 SARS-CoV-2 Sample #1 2020-09-20 Switzerland 46.8182 8.2275 Bern active surveillance in response to outbreak recovered Homo Sapiens 1 30 not collected female homo sapiens SS1 Michael C "Institute for Infectious Diseases, University of Bern" 2020-09-22 80 hCoV-19/isolate/1 other Nasopharyngeal exudate domestic EPI_ISL_1234 1150 -2697049 Severe acute respiratory syndrome coronavirus 2 SARS Sample 2 SARS Sample 2 SARS-CoV-2 Sample #2 2020-09-20 Switzerland 46.8182 8.2275 Bern active surveillance in response to outbreak recovered Homo Sapiens 2 25 diseased male homo sapiens SS1 Michael C "Institute for Infectious Diseases, University of Bern" 2020-09-22 80 hCoV-19/isolate/2 other Nasopharyngeal exudate domestic EPI_ISL_1235 1150 -2697049 Severe acute respiratory syndrome coronavirus 2 SARS Sample 3 SARS Sample 3 SARS-CoV-2 Sample #3 2020-09-20 Switzerland 46.8182 8.2275 Bern active surveillance in response to outbreak recovered Homo Sapiens 3 40 diseased female homo sapiens SS1 Michael C "Institute for Infectious Diseases, University of Bern" 2020-09-22 80 hCoV-19/isolate/3 other Nasopharyngeal exudate domestic EPI_ISL_1236 1150 - diff --git a/example_data_ena/samples/interactive/sample_spreadsheet.xlsx b/example_data_ena/samples/interactive/sample_spreadsheet.xlsx deleted file mode 100644 index 07f57879e95506dcd787c13b9e75468ec5aa4e49..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 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a/example_data_ena/samples/programmatic/._submission.xml b/example_data_ena/samples/programmatic/._submission.xml deleted file mode 100644 index 89f04770778303036c554a736916c5e4d908917a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 212 zcmZQz6=P>$Vqox1Ojhs@R)|o50+1L3ClDI}@gg7w@vi_e5x_AdBnYYuq+J^qI7A5ADWagzZ6zUroSQuKH8Jeb;r&(B7J7*N-=cZblxHwxn lS(;hux*3|A>6#cA8tXbbn!4&58kv|myO@}mx|kU=004fSA2a{} diff --git a/example_data_ena/samples/programmatic/._submission_modify.xml b/example_data_ena/samples/programmatic/._submission_modify.xml deleted file mode 100644 index 89f04770778303036c554a736916c5e4d908917a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 212 zcmZQz6=P>$Vqox1Ojhs@R)|o50+1L3ClDI}@gg7w@vi_e5x_AdBnYYuq+J^qI7A5ADWagzZ6zUroSQuKH8Jeb;r&(B7J7*N-=cZblxHwxn lS(;hux*3|A>6#cA8tXbbn!4&58kv|myO@}mx|kU=004fSA2a{} diff --git a/example_data_ena/samples/programmatic/samples.xml b/example_data_ena/samples/programmatic/samples.xml deleted file mode 100644 index 596409a4..00000000 --- a/example_data_ena/samples/programmatic/samples.xml +++ /dev/null @@ -1,318 +0,0 @@ - - - - SARS Sample 1 - - 2697049 - Severe acute respiratory syndrome coronavirus 2 - - SARS-CoV-2 Sample #1 - - - collection date - 2020-09-20 - - - geographic location (country and/or sea) - Switzerland - - - host common name - Homo Sapiens - - - host subject id - 1 - - - host health state - diseased - - - host sex - male - - - host scientific name - homo sapiens - - - collector name - Michael C - - - collecting institution - Institute for Infectious Diseases, University of Bern - - - isolate - hCoV-19/isolate/1 - - - receipt date - 2020-09-22 - - - sample capture status - active surveillance in response to outbreak - - - geographic location (latitude) - 46.8182 - DD - - - geographic location (longitude) - 8.2275 - DD - - - geographic location (region and locality) - Bern - - - host disease outcome - recovered - - - host age - 25 - years - - - virus identifier - SS1 - - - definition for seropositive sample - 80 - - - host habitat - other - - - isolation source host-associated - Nasopharyngeal exudate - - - host behaviour - domestic - - - ENA-CHECKLIST - ERC000033 - - - - - SARS Sample 2 - - 2697049 - Severe acute respiratory syndrome coronavirus 2 - - SARS-CoV-2 Sample #2 - - - collection date - 2020-09-20 - - - geographic location (country and/or sea) - Switzerland - - - host common name - Homo Sapiens - - - host subject id - 2 - - - host health state - diseased - - - host sex - male - - - host scientific name - homo sapiens - - - collector name - Michael C - - - collecting institution - Institute for Infectious Diseases, University of Bern - - - isolate - hCoV-19/isolate/2 - - - receipt date - 2020-09-22 - - - sample capture status - active surveillance in response to outbreak - - - geographic location (latitude) - 46.8182 - DD - - - geographic location (longitude) - 8.2275 - DD - - - geographic location (region and locality) - Bern - - - host disease outcome - recovered - - - host age - 25 - years - - - virus identifier - SS1 - - - definition for seropositive sample - 80 - - - host habitat - other - - - isolation source host-associated - Nasopharyngeal exudate - - - host behaviour - domestic - - - ENA-CHECKLIST - ERC000033 - - - - - SARS Sample 3 - - 2697049 - Severe acute respiratory syndrome coronavirus 2 - - SARS-CoV-2 Sample #3 - - - collection date - 2020-09-20 - - - geographic location (country and/or sea) - Switzerland - - - host common name - Homo Sapiens - - - host subject id - 3 - - - host health state - diseased - - - host sex - female - - - host scientific name - homo sapiens - - - collector name - Michael C - - - collecting institution - Institute for Infectious Diseases, University of Bern - - - isolate - hCoV-19/isolate/3 - - - receipt date - 2020-09-22 - - - sample capture status - active surveillance in response to outbreak - - - geographic location (latitude) - 46.8182 - DD - - - geographic location (longitude) - 8.2275 - DD - - - geographic location (region and locality) - Bern - - - host disease outcome - recovered - - - host age - 40 - years - - - virus identifier - SS1 - - - definition for seropositive sample - 80 - - - host habitat - other - - - isolation source host-associated - Nasopharyngeal exudate - - - host behaviour - domestic - - - ENA-CHECKLIST - ERC000033 - - - - diff --git a/example_data_ena/samples/programmatic/submission.xml b/example_data_ena/samples/programmatic/submission.xml deleted file mode 100644 index 8edfc2ad..00000000 --- a/example_data_ena/samples/programmatic/submission.xml +++ /dev/null @@ -1,10 +0,0 @@ - - - - - - - - - - diff --git a/example_data_ena/samples/programmatic/submission_add.xml b/example_data_ena/samples/programmatic/submission_add.xml deleted file mode 100644 index 8edfc2ad..00000000 --- a/example_data_ena/samples/programmatic/submission_add.xml +++ /dev/null @@ -1,10 +0,0 @@ - - - - - - - - - - diff --git a/example_data_ena/samples/programmatic/submission_modify.xml b/example_data_ena/samples/programmatic/submission_modify.xml deleted file mode 100644 index d9bc1a3a..00000000 --- a/example_data_ena/samples/programmatic/submission_modify.xml +++ /dev/null @@ -1,10 +0,0 @@ - - - - - - - - - - diff --git a/example_data_ena/sequences/._webin-cli b/example_data_ena/sequences/._webin-cli deleted file mode 100755 index 89f04770778303036c554a736916c5e4d908917a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 212 zcmZQz6=P>$Vqox1Ojhs@R)|o50+1L3ClDI}@gg7w@vi_e5x_AdBnYYuq+J^qI7A5ADWagzZ6zUroSQuKH8Jeb;r&(B7J7*N-=cZblxHwxn lS(;hux*3|A>6#cA8tXbbn!4&58kv|myO@}mx|kU=004fSA2a{} diff --git a/example_data_ena/sequences/._webin-cli-rest b/example_data_ena/sequences/._webin-cli-rest deleted file mode 100755 index 89f04770778303036c554a736916c5e4d908917a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 212 zcmZQz6=P>$Vqox1Ojhs@R)|o50+1L3ClDI}@gg7w@vi_e5x_AdBnYYuq+J^qI7A5ADWagzZ6zUroSQuKH8Jeb;r&(B7J7*N-=cZblxHwxn lS(;hux*3|A>6#cA8tXbbn!4&58kv|myO@}mx|kU=004fSA2a{} diff --git a/example_data_ena/sequences/webin-cli-rest/hCoV-19_isolate_1.json b/example_data_ena/sequences/webin-cli-rest/hCoV-19_isolate_1.json deleted file mode 100644 index 53737790..00000000 --- a/example_data_ena/sequences/webin-cli-rest/hCoV-19_isolate_1.json +++ /dev/null @@ -1,13 +0,0 @@ -{ - "study": "PRJEB#####", - "sample": "ERS#######", - "runRef": "ERR#######", - "name": "hCov-19_isolate_1", - "coverage": 100, - "program": "ARTIC fieldbioinformatics (minimap2/nanopolish) 1.1.3 (nanopolish 0.13.2)", - "platform": "ILLUMINA", - "minGapLength": 3, - "moleculeType": "genomic RNA", - "description": "example sequence #1 for workshop", - "sequence": "NNNNNNNNNTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGG" -} diff --git a/example_data_ena/sequences/webin-cli-rest/hCoV-19_isolate_2.json b/example_data_ena/sequences/webin-cli-rest/hCoV-19_isolate_2.json deleted file mode 100644 index 40f4d346..00000000 --- a/example_data_ena/sequences/webin-cli-rest/hCoV-19_isolate_2.json +++ /dev/null @@ -1,13 +0,0 @@ -{ - "study": "PRJEB#####", - "sample": "ERS#######", - "runRef": "ERR#######", - "name": "hCov-19_isolate_2", - "coverage": 1000, - "program": "ARTIC fieldbioinformatics (minimap2/nanopolish) 1.1.3 (nanopolish 0.13.2)", - "platform": "ILLUMINA", - "minGapLength": 3, - "moleculeType": "genomic RNA", - "description": "example sequence #2 for workshop", - "sequence": "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACT" -} diff --git a/example_data_ena/sequences/webin-cli-rest/hCoV-19_isolate_3.json b/example_data_ena/sequences/webin-cli-rest/hCoV-19_isolate_3.json deleted file mode 100644 index 98462bf7..00000000 --- a/example_data_ena/sequences/webin-cli-rest/hCoV-19_isolate_3.json +++ /dev/null @@ -1,15 +0,0 @@ -{ - "study": "PRJEB#####", - "sample": "ERS#######", - "runRef": "ERR#######", - "name": "hCov-19_isolate_3", - "coverage": 95.1, - "program": "MPileup", - "platform": "ILLUMINA", - "minGapLength": 1, - "moleculeType": "genomic RNA", - "description": "example sequence #3 for workshop", - "sequence": "AAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCATCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGT", - "authors": "ZW", - "address": "EBI" -} diff --git a/example_data_ena/sequences/webin-cli/._hCoV-19_isolate_1_manifest.txt b/example_data_ena/sequences/webin-cli/._hCoV-19_isolate_1_manifest.txt deleted file mode 100644 index 89f04770778303036c554a736916c5e4d908917a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 212 zcmZQz6=P>$Vqox1Ojhs@R)|o50+1L3ClDI}@gg7w@vi_e5x_AdBnYYuq+J^qI7A5ADWagzZ6zUroSQuKH8Jeb;r&(B7J7*N-=cZblxHwxn lS(;hux*3|A>6#cA8tXbbn!4&58kv|myO@}mx|kU=004fSA2a{} diff --git a/example_data_ena/sequences/webin-cli/._hCoV-19_isolate_2_manifest.txt b/example_data_ena/sequences/webin-cli/._hCoV-19_isolate_2_manifest.txt deleted file mode 100644 index 89f04770778303036c554a736916c5e4d908917a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 212 zcmZQz6=P>$Vqox1Ojhs@R)|o50+1L3ClDI}@gg7w@vi_e5x_AdBnYYuq+J^qI7A5ADWagzZ6zUroSQuKH8Jeb;r&(B7J7*N-=cZblxHwxn lS(;hux*3|A>6#cA8tXbbn!4&58kv|myO@}mx|kU=004fSA2a{} diff --git a/example_data_ena/sequences/webin-cli/._hCoV-19_isolate_3_manifest.txt b/example_data_ena/sequences/webin-cli/._hCoV-19_isolate_3_manifest.txt deleted file mode 100644 index 89f04770778303036c554a736916c5e4d908917a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 212 zcmZQz6=P>$Vqox1Ojhs@R)|o50+1L3ClDI}@gg7w@vi_e5x_AdBnYYuq+J^qI7A5ADWagzZ6zUroSQuKH8Jeb;r&(B7J7*N-=cZblxHwxn 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patch literal 0 HcmV?d00001 literal 84 zcmV-a0IUBWiwFp+AYfqt1875URxL3(Uuko1Y+-a|Uol@}XmV{|Y-w|JE_8Tw0LyUB q57RZY)Xyx=&q*vv)i>lcf4kDrh8*Xj0r+<#wxr_cI+>(Xd@ zYu2$>QjgzVQYyneeA~yJwB^@`A$7BZlUccm#)Tni`pi9YonZD!*{8;A7lY{zF)d?! z%FXQ5oEpl*Kx8SX+Q23v1xggeQXV&SZZIYfZT17EuE=pMazq(8-;G>U7>$hRO@>Ct zGD#m2M|l?U@UTjVbx6g@=)tSFS%-P(h&PJt&SWG+5$9PQo8m+aP{GZQ&>;&f)U>fA W5hWAq$>P`+VEqG@cw*)_0ssK;`hhP1 diff --git a/example_data_ena/sequences/webin-cli/hCoV-19_isolate_2_chrm_list.txt.gz b/example_data_ena/sequences/webin-cli/hCoV-19_isolate_2_chrm_list.txt.gz deleted file mode 100644 index 2e9631278d9dce92599d1815e6e35b12470433fc..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 84 zcmV-a0IUBWiwFo|Az)zu1875URxL3(Uuko1Y+-a|Uou}~XmV{|Y-w|JE_8Tw0LyUB q57RZY)Xyx=&q*vv)i>faJ zE)YH;RhocM;R~4bDFQzb_(gJm;wLXV!+6KCEot8GetbN?yxqQkA3vXeU$@t%BUN>` zT6VW>{v~U+uRVE}+Vk}!6HbxOoZxCP6K-a{;`CfQp*4FDMQ9RrW)fpXArm)D-83)3 zL?9JHQ^YtpxKEMwHgyzCkTre - - Example project for ENA submission workshop - This study was created as part of an ENA submissions workshop - - - - - diff --git a/example_data_ena/study/programmatic/receipt.xml b/example_data_ena/study/programmatic/receipt.xml deleted file mode 100644 index 4b43c31b..00000000 --- a/example_data_ena/study/programmatic/receipt.xml +++ /dev/null @@ -1,13 +0,0 @@ - - curl -u Webin-60330:W2b3nENA%2021 -F "SUBMISSION=@submission.xml" -F "PROJECT=@project.xml" "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/" - - - - - - - - - This submission is a TEST submission and will be discarded within 24 hours - - ADD diff --git a/example_data_ena/study/programmatic/submission.xml b/example_data_ena/study/programmatic/submission.xml deleted file mode 100644 index 8edfc2ad..00000000 --- a/example_data_ena/study/programmatic/submission.xml +++ /dev/null @@ -1,10 +0,0 @@ - - - - - - - - - - diff --git a/relecov_tools/example_data/to_ena_2.json b/relecov_tools/example_data/to_ena_2.json new file mode 100644 index 00000000..951803d8 --- /dev/null +++ b/relecov_tools/example_data/to_ena_2.json @@ -0,0 +1,38 @@ +{ + "collection_date": "2021/04/13", + "common_name": "PEPITO", + "experiment_alias": "", + "experiment_title": "Example project for ENA submission RELECOV", + "fastq_r1_md5": "f2facbd1d6c7e0972074ced31ccbfd8e", + "fastq_r2_md5": "fd9948be8da7a38b0f80659dfc21aeea", + "geographic location (latitude)": "41.6483", + "geographic location (longitude)": "-0.8830", + "geographic_location_(country_and/or_sea)": "Spain", + "host_common_name": "Human", + "host_gender": "Mujer", + "host_scientific_name": "Homo Sapiens", + "instrument_model": "Illumina MiSeq", + "instrument_platform": "Illumina", + "isolate": "1197860", + "isolation source host-associated": "Nasopharynx aspirate", + "isolation source non-host-associated": "Other", + "library_layout": "Single End", + "library_selection": "RT-PCR", + "library_source": "RNA", + "library_strategy": "WGS strategy", + "purpose_sampling": "Surveillance", + "r1_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "r2_fastq_filepath": "/tmp/relecov/COD_test_01/20220408", + "receipt_date": "2021/05/13", + "run_alias": "", + "sample_description": "Sample for surveillance", + "sample_name": "1197860", + "sample_storage_conditions": " -80ºC", + "scientific_name": "Severe acute respiratory syndrome coronavirus 2", + "sequence_file_R1_fastq": "ABC123_S1_L001_R1_001.fastq.gz", + "sequence_file_R2_fastq": "ABC123_S1_L001_R2_001.fastq.gz", + "study_alias": "RELECOV", + "study_title": "RELECOV Spanish Network for genomics surveillance", + "study_type": "RELECOV Spanish Network for genomics surveillance", + "tax_id": "2697049" +} \ No newline at end of file diff --git a/relecov_tools/test/pruebas.ipynb b/relecov_tools/test/pruebas.ipynb index 1f1fb881..f3727b96 100644 --- a/relecov_tools/test/pruebas.ipynb +++ b/relecov_tools/test/pruebas.ipynb @@ -2,622 +2,556 @@ "cells": [ { "cell_type": "code", - "execution_count": 3, - "id": "a99df8ae", - "metadata": {}, - "outputs": [], - "source": [ - "import json\n", - "import openpyxl" - ] - }, - { - "cell_type": "code", - "execution_count": 220, - "id": "dd64f661", - "metadata": {}, - "outputs": [], - "source": [ - "f = open(\"schema/small_schema.json\")\n", - "json_phage_plus_schema = json.load(f)" - ] - }, - { - "cell_type": "code", - "execution_count": 221, - "id": "9057ba90", - "metadata": {}, - "outputs": [], - "source": [ - "json_phage_plus_schema;" - ] - }, - { - "cell_type": "code", - "execution_count": 222, - "id": "97b35c6a", - "metadata": {}, - "outputs": [], - "source": [ - " wb_file = openpyxl.load_workbook(\"example_data/dummy_data_small.xlsx\", data_only=True)\n", - "ws_metadata_lab = wb_file[\"METADATA_LAB\"]\n", - "heading = []\n", - "for cell in ws_metadata_lab[1]:\n", - " heading.append(cell.value)\n" - ] - }, - { - "cell_type": "code", - "execution_count": 223, - "id": "986c372a", - "metadata": {}, - "outputs": [], - "source": [ - "heading;" - ] - }, - { - "cell_type": "code", - "execution_count": 224, - "id": "895b82c2", - "metadata": {}, - "outputs": [], - "source": [ - "for row in islice(ws_metadata_lab.values, 1, ws_metadata_lab.max_row):\n", - " sample_data_row = {}\n", - " for idx in range(len(heading)):\n", - " if \"date\" in heading[idx]:\n", - " sample_data_row[heading[idx]] = row[idx].strftime(\"%d/%m/%Y\")\n", - " else:\n", - " sample_data_row[heading[idx]] = row[idx]\n", - " \n", - "fila = sample_data_row" - ] - }, - { - "cell_type": "code", - "execution_count": 225, - "id": "c441ba9d", - "metadata": {}, - "outputs": [], - "source": [ - "list(fila.keys());" - ] - }, - { - "cell_type": "code", - "execution_count": 226, - "id": "a2f1610b", - "metadata": {}, - "outputs": [], - "source": [ - "json_phage_plus_schema['properties'];" - ] - }, - { - "cell_type": "code", - "execution_count": 227, - "id": "2b3da23d", - "metadata": {}, - "outputs": [], - "source": [ - "instance = [{}, 3, \"foo\"]" - ] - }, - { - "cell_type": "code", - "execution_count": 228, - "id": "2b30fc71", + "execution_count": 1, + "id": "ca2ef1c4", "metadata": {}, "outputs": [], "source": [ - "validate(instance = list(fila.keys()), schema =json_phage_plus_schema['properties']) " + "esquema_json = {'collection_date': '2021/04/13', 'common_name': 'PEPITO', 'experiment_alias': '', 'experiment_title': 'Example project for ENA submission RELECOV', 'fastq_r1_md5': 'f2facbd1d6c7e0972074ced31ccbfd8e', 'fastq_r2_md5': 'fd9948be8da7a38b0f80659dfc21aeea', 'geographic location (latitude)': '41.6483', 'geographic location (longitude)': '-0.8830', 'geographic_location_(country_and/or_sea)': 'Spain', 'host_common_name': 'Human', 'host_gender': 'Mujer', 'host_scientific_name': 'Homo Sapiens', 'instrument_model': 'Illumina MiSeq', 'instrument_platform': 'Illumina', 'isolate': '1197860', 'isolation source host-associated': 'Nasopharynx aspirate', 'isolation source non-host-associated': 'Other', 'library_layout': 'Single End', 'library_selection': 'RT-PCR', 'library_source': 'RNA', 'library_strategy': 'WGS strategy', 'purpose_sampling': 'Surveillance', 'r1_fastq_filepath': '/tmp/relecov/COD_test_01/20220408', 'r2_fastq_filepath': '/tmp/relecov/COD_test_01/20220408', 'receipt_date': '2021/05/13', 'run_alias': '', 'sample_description': 'Sample for surveillance', 'sample_name': '1197860', 'sample_storage_conditions': ' -80ºC', 'scientific_name': 'Severe acute respiratory syndrome coronavirus 2', 'sequence_file_R1_fastq': 'ABC123_S1_L001_R1_001.fastq.gz', 'sequence_file_R2_fastq': 'ABC123_S1_L001_R2_001.fastq.gz', 'study_alias': 'RELECOV', 'study_title': 'RELECOV Spanish Network for genomics surveillance', 'study_type': 'RELECOV Spanish Network for genomics surveillance', 'tax_id': '2697049'}\n" ] }, { "cell_type": "code", - "execution_count": 229, - "id": "cc3c4bac", + "execution_count": 2, + "id": "226a90e0", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "'prov_rona_99'" + "{'collection_date': '2021/04/13',\n", + " 'common_name': 'PEPITO',\n", + " 'experiment_alias': '',\n", + " 'experiment_title': 'Example project for ENA submission RELECOV',\n", + " 'fastq_r1_md5': 'f2facbd1d6c7e0972074ced31ccbfd8e',\n", + " 'fastq_r2_md5': 'fd9948be8da7a38b0f80659dfc21aeea',\n", + " 'geographic location (latitude)': '41.6483',\n", + " 'geographic location (longitude)': '-0.8830',\n", + " 'geographic_location_(country_and/or_sea)': 'Spain',\n", + " 'host_common_name': 'Human',\n", + " 'host_gender': 'Mujer',\n", + " 'host_scientific_name': 'Homo Sapiens',\n", + " 'instrument_model': 'Illumina MiSeq',\n", + " 'instrument_platform': 'Illumina',\n", + " 'isolate': '1197860',\n", + " 'isolation source host-associated': 'Nasopharynx aspirate',\n", + " 'isolation source non-host-associated': 'Other',\n", + " 'library_layout': 'Single End',\n", + " 'library_selection': 'RT-PCR',\n", + " 'library_source': 'RNA',\n", + " 'library_strategy': 'WGS strategy',\n", + " 'purpose_sampling': 'Surveillance',\n", + " 'r1_fastq_filepath': '/tmp/relecov/COD_test_01/20220408',\n", + " 'r2_fastq_filepath': '/tmp/relecov/COD_test_01/20220408',\n", + " 'receipt_date': '2021/05/13',\n", + " 'run_alias': '',\n", + " 'sample_description': 'Sample for surveillance',\n", + " 'sample_name': '1197860',\n", + " 'sample_storage_conditions': ' -80ºC',\n", + " 'scientific_name': 'Severe acute respiratory syndrome coronavirus 2',\n", + " 'sequence_file_R1_fastq': 'ABC123_S1_L001_R1_001.fastq.gz',\n", + " 'sequence_file_R2_fastq': 'ABC123_S1_L001_R2_001.fastq.gz',\n", + " 'study_alias': 'RELECOV',\n", + " 'study_title': 'RELECOV Spanish Network for genomics surveillance',\n", + " 'study_type': 'RELECOV Spanish Network for genomics surveillance',\n", + " 'tax_id': '2697049'}" ] }, - "execution_count": 229, + "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "sample_data_row[\"Collecting Sample id\"]" - ] - }, - { - "cell_type": "code", - "execution_count": 63, - "id": "72587d32", - "metadata": {}, - "outputs": [], - "source": [ - "heading =['Collecting Sample id', 'Originating Laboratory', 'Submitting Institution', 'Sample Collection Date', 'geo_loc_country', 'geo_loc_state', 'organism', 'isolate', 'host_scientific_name', 'Host Common Name', 'host_disease', 'Sequencing Instrument Model', 'Sequencing Platforms', 'consensus_sequence_software_name', 'consensus_sequence_software_version', 'file_name', 'tax_id', 'sample_description', 'Library Source', 'Library Selection', 'Library Strategy', 'Library Layout', 'type', 'GISAID Virus Name', 'GISAID Id', 'Originating Laboratory Address']\n" + "esquema_json" ] }, { "cell_type": "code", - "execution_count": 71, - "id": "7ea69469", + "execution_count": 3, + "id": "be0cb85c", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "26" + "dict_keys(['collection_date', 'common_name', 'experiment_alias', 'experiment_title', 'fastq_r1_md5', 'fastq_r2_md5', 'geographic location (latitude)', 'geographic location (longitude)', 'geographic_location_(country_and/or_sea)', 'host_common_name', 'host_gender', 'host_scientific_name', 'instrument_model', 'instrument_platform', 'isolate', 'isolation source host-associated', 'isolation source non-host-associated', 'library_layout', 'library_selection', 'library_source', 'library_strategy', 'purpose_sampling', 'r1_fastq_filepath', 'r2_fastq_filepath', 'receipt_date', 'run_alias', 'sample_description', 'sample_name', 'sample_storage_conditions', 'scientific_name', 'sequence_file_R1_fastq', 'sequence_file_R2_fastq', 'study_alias', 'study_title', 'study_type', 'tax_id'])" ] }, - "execution_count": 71, + "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "len(heading)" + "esquema_json.keys()" ] }, { "cell_type": "code", - "execution_count": 64, - "id": "54afd367", + "execution_count": 4, + "id": "8d390edf", "metadata": {}, "outputs": [], "source": [ - "map_file = open(\"schema/mapping_file.json\")\n", - "mapping_file = json.load(map_file)" + "llaves = list(esquema_json.keys())" ] }, { "cell_type": "code", - "execution_count": 65, - "id": "3d1e0f63", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'Collecting Sample id': 'sample_name',\n", - " 'Originating Laboratory': 'collecting_institution',\n", - " 'Submitting Institution': 'submitting_institution',\n", - " 'Sample Collection Date': 'sample_collection_date',\n", - " 'geo_loc_country': 'geo_loc_country',\n", - " 'geo_loc_state': 'geo_loc_state',\n", - " 'organism': 'organism',\n", - " 'isolate': 'isolate',\n", - " 'host_scientific_name': 'host_scientific_name',\n", - " 'Host Common Name': 'host_common_name',\n", - " 'host_disease': 'host_disease',\n", - " 'Sequencing Instrument Model': 'sequencing_instrument_model',\n", - " 'Sequencing Platforms': 'sequencing_instrument_platform',\n", - " 'consensus_sequence_software_name': 'consensus_sequence_software_name',\n", - " 'consensus_sequence_software_version': 'consensus_sequence_software_version',\n", - " 'file_name': 'file_name',\n", - " 'tax_id': 'tax_id',\n", - " 'sample_description': 'sample_description',\n", - " 'Library Source': 'library_source',\n", - " 'Library Selection': 'library_selection',\n", - " 'Library Strategy': 'library_strategy',\n", - " 'Library Layout': 'library_layout',\n", - " 'type': 'type',\n", - " 'GISAID Virus Name': 'virus_name',\n", - " 'GISAID Id': 'submitter',\n", - " 'Originating Laboratory Address': 'collecting_address'}" - ] - }, - "execution_count": 65, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "mapping_file" - ] - }, - { - "cell_type": "code", - "execution_count": 54, - "id": "def77932", + "execution_count": 5, + "id": "ec640155", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "'sample_name'" + "['collection_date',\n", + " 'common_name',\n", + " 'experiment_alias',\n", + " 'experiment_title',\n", + " 'fastq_r1_md5',\n", + " 'fastq_r2_md5',\n", + " 'geographic location (latitude)',\n", + " 'geographic location (longitude)',\n", + " 'geographic_location_(country_and/or_sea)',\n", + " 'host_common_name',\n", + " 'host_gender',\n", + " 'host_scientific_name',\n", + " 'instrument_model',\n", + " 'instrument_platform',\n", + " 'isolate',\n", + " 'isolation source host-associated',\n", + " 'isolation source non-host-associated',\n", + " 'library_layout',\n", + " 'library_selection',\n", + " 'library_source',\n", + " 'library_strategy',\n", + " 'purpose_sampling',\n", + " 'r1_fastq_filepath',\n", + " 'r2_fastq_filepath',\n", + " 'receipt_date',\n", + " 'run_alias',\n", + " 'sample_description',\n", + " 'sample_name',\n", + " 'sample_storage_conditions',\n", + " 'scientific_name',\n", + " 'sequence_file_R1_fastq',\n", + " 'sequence_file_R2_fastq',\n", + " 'study_alias',\n", + " 'study_title',\n", + " 'study_type',\n", + " 'tax_id']" ] }, - "execution_count": 54, + "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "list(mapping_file.values())[0]" + "llaves" ] }, { "cell_type": "code", - "execution_count": 70, - "id": "34b84069", + "execution_count": 15, + "id": "85d6577f", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "0\n", - "1\n", - "2\n", - "3\n", - "4\n", - "5\n", - "6\n", - "7\n", - "8\n", - "9\n", - "10\n", - "11\n", - "12\n", - "13\n", - "14\n", - "15\n", - "16\n", - "17\n", - "18\n", - "19\n", - "20\n", - "21\n", - "22\n", - "23\n", - "24\n", - "25\n" + "collection_date\n", + "common_name\n", + "experiment_alias\n", + "experiment_title\n", + "fastq_r1_md5\n", + "fastq_r2_md5\n", + "geographic location (latitude)\n", + "geographic location (longitude)\n", + "geographic_location_(country_and/or_sea)\n", + "host_common_name\n", + "host_gender\n", + "host_scientific_name\n", + "instrument_model\n", + "instrument_platform\n", + "isolate\n", + "isolation source host-associated\n", + "isolation source non-host-associated\n", + "library_layout\n", + "library_selection\n", + "library_source\n", + "library_strategy\n", + "purpose_sampling\n", + "r1_fastq_filepath\n", + "r2_fastq_filepath\n", + "receipt_date\n", + "run_alias\n", + "sample_description\n", + "sample_name\n", + "sample_storage_conditions\n", + "scientific_name\n", + "sequence_file_R1_fastq\n", + "sequence_file_R2_fastq\n", + "study_alias\n", + "study_title\n", + "study_type\n", + "tax_id\n" ] } ], "source": [ - "for i in range(len(heading)):\n", - " print(i)" + "for key, value in esquema_json.items():\n", + " print (key)" ] }, { "cell_type": "code", - "execution_count": 72, - "id": "1caa1045", + "execution_count": 11, + "id": "961f966c", "metadata": {}, "outputs": [], "source": [ - "for i in range(len(heading)):\n", - " if heading[i] in list(mapping_file.keys()):\n", - " index = list(mapping_file).index(heading[i])\n", - " heading[index] = list(mapping_file.values())[index]\n", - " \n", - " \n" + "import pandas as pd" ] }, { "cell_type": "code", - "execution_count": 73, - "id": "8ab4a0c2", + "execution_count": 18, + "id": "04bb5f74", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['sample_name',\n", - " 'collecting_institution',\n", - " 'submitting_institution',\n", - " 'sample_collection_date',\n", - " 'geo_loc_country',\n", - " 'geo_loc_state',\n", - " 'organism',\n", - " 'isolate',\n", - " 'host_scientific_name',\n", + "['collection_date',\n", + " 'common_name',\n", + " 'experiment_alias',\n", + " 'experiment_title',\n", + " 'fastq_r1_md5',\n", + " 'fastq_r2_md5',\n", + " 'geographic location (latitude)',\n", + " 'geographic location (longitude)',\n", + " 'geographic_location_(country_and/or_sea)',\n", " 'host_common_name',\n", - " 'host_disease',\n", - " 'sequencing_instrument_model',\n", - " 'sequencing_instrument_platform',\n", - " 'consensus_sequence_software_name',\n", - " 'consensus_sequence_software_version',\n", - " 'file_name',\n", - " 'tax_id',\n", - " 'sample_description',\n", - " 'library_source',\n", + " 'host_gender',\n", + " 'host_scientific_name',\n", + " 'instrument_model',\n", + " 'instrument_platform',\n", + " 'isolate',\n", + " 'isolation source host-associated',\n", + " 'isolation source non-host-associated',\n", + " 'library_layout',\n", " 'library_selection',\n", + " 'library_source',\n", " 'library_strategy',\n", - " 'library_layout',\n", - " 'type',\n", - " 'virus_name',\n", - " 'submitter',\n", - " 'collecting_address']" + " 'purpose_sampling',\n", + " 'r1_fastq_filepath',\n", + " 'r2_fastq_filepath',\n", + " 'receipt_date',\n", + " 'run_alias',\n", + " 'sample_description',\n", + " 'sample_name',\n", + " 'sample_storage_conditions',\n", + " 'scientific_name',\n", + " 'sequence_file_R1_fastq',\n", + " 'sequence_file_R2_fastq',\n", + " 'study_alias',\n", + " 'study_title',\n", + " 'study_type',\n", + " 'tax_id']" ] }, - "execution_count": 73, + "execution_count": 18, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "heading" + "columnas = list(esquema_json.keys())\n" ] }, { "cell_type": "code", - "execution_count": null, - "id": "4689d46e", + "execution_count": 23, + "id": "036986a0", "metadata": {}, "outputs": [], "source": [ - "dictionary = {'test':{1,3}, 'test2':{2}, 'test3':{2,3}}\n", - "\n", - "if 'test' in dictionary:\n", - " print(list(dictionary).index('test'))" + "df = pd.DataFrame.from_dict(esquema_json, orient=\"index\")" ] }, { "cell_type": "code", - "execution_count": 27, - "id": "5ae4de88", + "execution_count": 25, + "id": "a6b4f961", "metadata": {}, "outputs": [ { "data": { + "text/html": [ + "